--- /srv/rebuilderd/tmp/rebuilderdnNHCuH/inputs/libball1.5-doc_1.5.0+git20180813.37fc53c-11.1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdnNHCuH/out/libball1.5-doc_1.5.0+git20180813.37fc53c-11.1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2025-08-18 23:10:41.000000 debian-binary │ --rw-r--r-- 0 0 0 126760 2025-08-18 23:10:41.000000 control.tar.xz │ --rw-r--r-- 0 0 0 9222344 2025-08-18 23:10:41.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 126768 2025-08-18 23:10:41.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 9239412 2025-08-18 23:10:41.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./control │ │ │ @@ -1,13 +1,13 @@ │ │ │ Package: libball1.5-doc │ │ │ Source: ball │ │ │ Version: 1.5.0+git20180813.37fc53c-11.1 │ │ │ Architecture: all │ │ │ Maintainer: Debian Med Packaging Team │ │ │ -Installed-Size: 131258 │ │ │ +Installed-Size: 131259 │ │ │ Depends: libjs-jquery │ │ │ Suggests: libball1.5 │ │ │ Conflicts: libball1.3-doc, libball1.4-doc │ │ │ Section: doc │ │ │ Priority: optional │ │ │ Multi-Arch: foreign │ │ │ Homepage: http://www.ball-project.org/ │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -507,14 +507,15 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d8d/a07602.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d8e/a04879.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d8f/a04202.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d90/a02127.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d90/a05159.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d90/a06171.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d93/a00875.html │ │ │ │ +usr/share/doc/libball1.5/html/BALL/d1/d93/a00875_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d95/a06703.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d96/a05654.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d96/a05654.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d96/a06787.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d96/a06918.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d96/a06918.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d98/a00407.html │ │ │ │ @@ -532,15 +533,14 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d9f/a05714.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/d9f/a05714.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da2/a04991.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da3/a03835.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da4/a03766.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da4/a04242.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da7/a01709.html │ │ │ │ -usr/share/doc/libball1.5/html/BALL/d1/da7/a01709_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da8/a00230.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da8/a00230_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da9/a04807.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da9/a07530.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/da9/a07530.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/daa/a00638.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/daa/a00638_source.html │ │ │ │ @@ -599,21 +599,21 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dd6/a07282.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dd6/a07534.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dd6/a07534.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dd7/a06039.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dd7/a07498.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dd7/a07498.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dd8/a01022.html │ │ │ │ -usr/share/doc/libball1.5/html/BALL/d1/dd8/a01022_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dd8/a03743.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/ddb/a05106.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/ddb/a05106.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/ddc/a07238.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/ddc/a08535.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dde/a01496.html │ │ │ │ +usr/share/doc/libball1.5/html/BALL/d1/dde/a01496_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dde/a04187.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dde/a04223.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/ddf/a06955.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/ddf/a07743.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/de1/a05950.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/de1/a05950.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/de1/a08011.html │ │ │ │ @@ -635,14 +635,15 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/df7/a06002.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/df7/a06002.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/df7/a06894.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/df7/a06894.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/df9/a03555.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/df9/a06550.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dfa/a01097.html │ │ │ │ +usr/share/doc/libball1.5/html/BALL/d1/dfa/a01097_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dfb/a03775.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dfe/a08586.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d1/dfe/a08586.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d04/a00281.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d04/a00281_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d04/a04815.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d08/a02148.html │ │ │ │ @@ -719,26 +720,25 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d41/a01037_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d41/a01493.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d41/a01493_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d44/a05675.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d44/a06130.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d44/a06130.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d45/a01826.html │ │ │ │ +usr/share/doc/libball1.5/html/BALL/d2/d45/a01826_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d48/a01472.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d48/a01472_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d49/a01067.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d49/a01067_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d4a/a00758.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d4a/a00758_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d4c/a01307.html │ │ │ │ -usr/share/doc/libball1.5/html/BALL/d2/d4c/a01307_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d4c/a08211.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d4c/a08539.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d4d/a01079.html │ │ │ │ -usr/share/doc/libball1.5/html/BALL/d2/d4d/a01079_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d4d/a04263.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d4e/a06998.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d4f/a04347.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d50/a02081.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d50/a02081_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d54/a08578.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d2/d57/a07027.html │ │ │ │ @@ -1002,15 +1002,14 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1a/a00251_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1a/a04798.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1a/a04798.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1b/a03227.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1c/a03551.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1d/a07143.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1e/a02093.html │ │ │ │ -usr/share/doc/libball1.5/html/BALL/d3/d1e/a02093_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1e/a04766.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1e/a05462.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1e/a05462.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d1f/a05983.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d20/a05927.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d21/a08015.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d23/a02120.html │ │ │ │ @@ -1075,16 +1074,14 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d4c/a01724_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d4c/a05943.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d4c/a08174.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d4c/a08174.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d4e/a01991.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d4e/a01991_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d4e/a05623.html │ │ │ │ -usr/share/doc/libball1.5/html/BALL/d3/d4f/a00761.html │ │ │ │ -usr/share/doc/libball1.5/html/BALL/d3/d4f/a00761_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d4f/a06898.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d4f/a06898.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d50/a07731.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d52/a00023.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d52/a00023_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d52/a03535.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d53/a01262.html │ │ │ │ @@ -1150,14 +1147,15 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d87/a00539.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d87/a00539_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d87/a03490.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d89/a06454.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8a/a00899.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8a/a00899_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8b/a00059.html │ │ │ │ +usr/share/doc/libball1.5/html/BALL/d3/d8b/a00059_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8c/a04318.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8d/a02178.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8d/a07878.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8d/a07878.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8e/a00647.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8e/a00647_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d8f/a05099.html │ │ │ │ @@ -1174,14 +1172,16 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d97/a03603.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d97/a05375.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d99/a08246.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d9a/a04075.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d9a/a08387.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d9c/a06419.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/d9f/a05854.html │ │ │ │ +usr/share/doc/libball1.5/html/BALL/d3/da1/a01613.html │ │ │ │ +usr/share/doc/libball1.5/html/BALL/d3/da1/a01613_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/da1/a06278.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/da1/a06278.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/da3/a07239.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/da4/a01343.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/da4/a01343_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/da4/a03571.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/da4/a07871.html │ │ │ │ @@ -1263,16 +1263,14 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/de5/a00209_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/de5/a00956.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/de5/a00956_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/de5/a07315.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/de9/a07014.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/de9/a07014.png │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/dea/a05363.html │ │ │ │ -usr/share/doc/libball1.5/html/BALL/d3/deb/a01619.html │ │ │ │ -usr/share/doc/libball1.5/html/BALL/d3/deb/a01619_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/deb/a06543.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/def/a00446.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/def/a00446_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/def/a01985.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/def/a01985_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/df0/a05067.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d3/df2/a03614.html │ │ │ │ @@ -1330,14 +1328,15 @@ │ │ │ │ usr/share/doc/libball1.5/html/BALL/d4/d1f/a00506_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d4/d20/a01421.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d4/d20/a01421_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d4/d20/a05586.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/d4/d20/a05586.png │ │ │ │ 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usr/share/doc/libball1.5/html/BALL/df/d88/a00962.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d88/a00962_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d88/a04358.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d8c/a08351.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d8f/a07379.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d90/a06587.html │ │ │ │ +usr/share/doc/libball1.5/html/BALL/df/d91/a00335.html │ │ │ │ +usr/share/doc/libball1.5/html/BALL/df/d91/a00335_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d91/a07819.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d92/a04962.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d93/a06099.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d93/a07346.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d95/a00299.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d95/a00299_source.html │ │ │ │ usr/share/doc/libball1.5/html/BALL/df/d96/a03402.html ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ 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23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d0/dce/a03971.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d0/dcf/ │ │ │ -rw-r--r-- 0 root (0) root (0) 12330 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d0/dcf/a05131.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d0/dd0/ │ │ │ -rw-r--r-- 0 root (0) root (0) 6527 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d0/dd0/a04159.html │ │ │ -rw-r--r-- 0 root (0) root (0) 10153 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d0/dd0/a07195.html │ │ │ -rw-r--r-- 0 root (0) root (0) 15552 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d0/dd0/a07451.html │ │ │ @@ -412,42 +412,42 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d0/dd4/ │ │ │ -rw-r--r-- 0 root (0) root (0) 5226 2025-08-18 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2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d46/a04047.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d48/ │ │ │ -rw-r--r-- 0 root (0) root (0) 63986 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d48/a03218.html │ │ │ -rw-r--r-- 0 root (0) root (0) 7421 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d48/a03218.png │ │ │ -rw-r--r-- 0 root (0) root (0) 5008 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d48/a04575.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d4a/ │ │ │ @@ -639,32 +639,32 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d54/ │ │ │ -rw-r--r-- 0 root (0) root (0) 25646 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d54/a06426.html │ │ │ -rw-r--r-- 0 root (0) root (0) 538 2025-08-18 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./usr/share/doc/libball1.5/html/BALL/d1/d5d/a00311_source.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 5376 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d5d/a00311.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 11772 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d5d/a00311_source.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d5e/ │ │ │ -rw-r--r-- 0 root (0) root (0) 73860 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d5e/a03502.html │ │ │ -rw-r--r-- 0 root (0) root (0) 15548 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d5e/a05403.html │ │ │ -rw-r--r-- 0 root (0) root (0) 27889 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d5e/a08051.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d5f/ │ │ │ -rw-r--r-- 0 root (0) root (0) 32034 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d5f/a03706.html │ │ │ -rw-r--r-- 0 root (0) root (0) 593 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d5f/a03706.png │ │ │ @@ -680,27 +680,27 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d67/ │ │ │ -rw-r--r-- 0 root (0) root (0) 32410 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d67/a06846.html │ │ │ -rw-r--r-- 0 root (0) root (0) 1922 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d67/a06846.png │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d69/ │ │ │ -rw-r--r-- 0 root (0) root (0) 96011 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d69/a03834.html │ │ │ -rw-r--r-- 0 root (0) root (0) 4338 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d69/a03834.png │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 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./usr/share/doc/libball1.5/html/BALL/d1/d72/a01319.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 71615 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d72/a01319_source.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d76/ │ │ │ -rw-r--r-- 0 root (0) root (0) 23471 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d76/a08067.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d77/ │ │ │ -rw-r--r-- 0 root (0) root (0) 174116 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d77/a04806.html │ │ │ -rw-r--r-- 0 root (0) root (0) 1234 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d77/a04806.png │ │ │ -rw-r--r-- 0 root (0) root (0) 14618 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d77/a05915.html │ │ │ -rw-r--r-- 0 root (0) root (0) 6369 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d77/a07154.html │ │ │ @@ -708,16 +708,16 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 25480 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d78/a03714.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7a/ │ │ │ -rw-r--r-- 0 root (0) root (0) 5449 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7a/a03679.html │ │ │ -rw-r--r-- 0 root (0) root (0) 11609 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7a/a04262.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7b/ │ │ │ -rw-r--r-- 0 root (0) root (0) 10586 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7b/a03639.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7e/ │ │ │ --rw-r--r-- 0 root (0) root (0) 6201 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7e/a00434.html │ │ │ --rw-r--r-- 0 root (0) root (0) 35345 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7e/a00434_source.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 5673 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7e/a00434.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 23329 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7e/a00434_source.html │ │ │ -rw-r--r-- 0 root (0) root (0) 18258 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7e/a04206.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7f/ │ │ │ -rw-r--r-- 0 root (0) root (0) 12373 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d7f/a06591.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d80/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3941 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d80/a07383.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d82/ │ │ │ -rw-r--r-- 0 root (0) root (0) 17784 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d82/a03450.html │ │ │ @@ -726,19 +726,19 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d84/ │ │ │ -rw-r--r-- 0 root (0) root (0) 9528 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d84/a07063.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d86/ │ │ │ -rw-r--r-- 0 root (0) root (0) 14331 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d86/a04746.html │ │ │ -rw-r--r-- 0 root (0) root (0) 1550 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d86/a04746.png │ │ │ -rw-r--r-- 0 root (0) root (0) 98403 2025-08-18 23:10:41.000000 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./usr/share/doc/libball1.5/html/BALL/d1/d88/a00128_source.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 6351 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d88/a00128.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 47678 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d88/a00128_source.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d89/ │ │ │ -rw-r--r-- 0 root (0) root (0) 10966 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d89/a04875.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d8b/ │ │ │ -rw-r--r-- 0 root (0) root (0) 31937 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d8b/a08454.html │ │ │ -rw-r--r-- 0 root (0) root (0) 4645 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d1/d8b/a08454.png │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 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./usr/share/doc/libball1.5/html/BALL/d5/d60/a05279.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d5/d61/ │ │ │ -rw-r--r-- 0 root (0) root (0) 31112 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d5/d61/a05982.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2409 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d5/d61/a05982.png │ │ │ @@ -2580,46 +2576,46 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d5/d63/ │ │ │ -rw-r--r-- 0 root (0) root (0) 4103 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d5/d63/a02123.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d5/d64/ │ │ │ -rw-r--r-- 0 root (0) root (0) 8193 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d5/d64/a04719.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 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2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d7/db6/a01556_source.html │ │ │ -rw-r--r-- 0 root (0) root (0) 8805 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d7/db6/a06930.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d7/db7/ │ │ │ -rw-r--r-- 0 root (0) root (0) 6208 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d7/db7/a02198.html │ │ │ -rw-r--r-- 0 root (0) root (0) 47531 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d7/db7/a05762.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2901 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d7/db7/a05762.png │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d7/db8/ │ │ │ -rw-r--r-- 0 root (0) root (0) 6350 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/d7/db8/a06794.html │ │ │ @@ -3728,16 +3725,16 @@ │ │ │ drwxr-xr-x 0 root (0) root 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23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de5/a04426.png │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de7/ │ │ │ -rw-r--r-- 0 root (0) root (0) 4475 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de7/a02142.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de8/ │ │ │ --rw-r--r-- 0 root (0) root (0) 5195 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de8/a00839.html │ │ │ --rw-r--r-- 0 root (0) root (0) 40204 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de8/a00839_source.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 4622 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de8/a00839.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 11915 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de8/a00839_source.html │ │ │ -rw-r--r-- 0 root (0) root (0) 8031 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de8/a06334.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/ │ │ │ --rw-r--r-- 0 root (0) root (0) 4874 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a00923.html │ │ │ --rw-r--r-- 0 root (0) root (0) 11531 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a00923_source.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 4873 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a00923.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 14528 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a00923_source.html │ │ │ -rw-r--r-- 0 root (0) root (0) 77325 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a02153.html │ │ │ -rw-r--r-- 0 root (0) root (0) 61291 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a04534.html │ │ │ -rw-r--r-- 0 root (0) root (0) 5738 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a04534.png │ │ │ -rw-r--r-- 0 root (0) root (0) 43828 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a05538.html │ │ │ -rw-r--r-- 0 root (0) root (0) 9474 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a05538.png │ │ │ -rw-r--r-- 0 root (0) root (0) 16444 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a05682.html │ │ │ -rw-r--r-- 0 root (0) root (0) 1140 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a05682.png │ │ │ @@ -7487,29 +7488,29 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 53422 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a08114.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2661 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/de9/a08114.png │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dea/ │ │ │ -rw-r--r-- 0 root (0) root (0) 8088 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dea/a03391.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/ded/ │ │ │ -rw-r--r-- 0 root (0) root (0) 11723 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/ded/a07111.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dee/ │ │ │ --rw-r--r-- 0 root (0) root (0) 4748 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dee/a01646.html │ │ │ --rw-r--r-- 0 root (0) root (0) 20844 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dee/a01646_source.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 4768 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dee/a01646.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 17638 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dee/a01646_source.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df1/ │ │ │ -rw-r--r-- 0 root (0) root (0) 107475 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df1/a07118.html │ │ │ -rw-r--r-- 0 root (0) root (0) 960 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df1/a07118.png │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df2/ │ │ │ -rw-r--r-- 0 root (0) root (0) 36849 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df2/a03638.html │ │ │ -rw-r--r-- 0 root (0) root (0) 602 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df2/a03638.png │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df6/ │ │ │ -rw-r--r-- 0 root (0) root (0) 106178 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df6/a04914.html │ │ │ -rw-r--r-- 0 root (0) root (0) 1108 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df6/a04914.png │ │ │ -rw-r--r-- 0 root (0) root (0) 14357 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df6/a06087.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df7/ │ │ │ --rw-r--r-- 0 root (0) root (0) 5065 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df7/a00731.html │ │ │ --rw-r--r-- 0 root (0) root (0) 28357 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df7/a00731_source.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 5285 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df7/a00731.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 18994 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df7/a00731_source.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df8/ │ │ │ -rw-r--r-- 0 root (0) root (0) 14656 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df8/a05883.html │ │ │ -rw-r--r-- 0 root (0) root (0) 21308 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/df8/a07267.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dfb/ │ │ │ -rw-r--r-- 0 root (0) root (0) 109857 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dfb/a03946.html │ │ │ -rw-r--r-- 0 root (0) root (0) 4272 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/df/dfb/a03946.png │ │ │ -rw-r--r-- 0 root (0) root (0) 9422 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/dir_005ed1ee88b92ac0a0364846f1678e90.html │ │ │ @@ -8032,23 +8033,23 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 200330 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_10.js │ │ │ -rw-r--r-- 0 root (0) root (0) 141821 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_11.js │ │ │ -rw-r--r-- 0 root (0) root (0) 9515 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_12.js │ │ │ -rw-r--r-- 0 root (0) root (0) 214902 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_13.js │ │ │ -rw-r--r-- 0 root (0) root (0) 405207 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_14.js │ │ │ -rw-r--r-- 0 root (0) root (0) 109640 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_15.js │ │ │ -rw-r--r-- 0 root (0) root (0) 49469 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_16.js │ │ │ --rw-r--r-- 0 root (0) root (0) 44454 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_17.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 44464 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_17.js │ │ │ -rw-r--r-- 0 root (0) root (0) 32075 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_18.js │ │ │ -rw-r--r-- 0 root (0) root (0) 5518 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_19.js │ │ │ -rw-r--r-- 0 root (0) root (0) 3384 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_1a.js │ │ │ -rw-r--r-- 0 root (0) root (0) 3699 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_1b.js │ │ │ -rw-r--r-- 0 root (0) root (0) 99657 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_1c.js │ │ │ -rw-r--r-- 0 root (0) root (0) 142726 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_2.js │ │ │ -rw-r--r-- 0 root (0) root (0) 119037 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_3.js │ │ │ --rw-r--r-- 0 root (0) root (0) 278596 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_4.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 278582 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_4.js │ │ │ -rw-r--r-- 0 root (0) root (0) 101654 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_5.js │ │ │ -rw-r--r-- 0 root (0) root (0) 85047 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_6.js │ │ │ -rw-r--r-- 0 root (0) root (0) 91042 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_7.js │ │ │ -rw-r--r-- 0 root (0) root (0) 351492 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_8.js │ │ │ -rw-r--r-- 0 root (0) root (0) 78970 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_9.js │ │ │ -rw-r--r-- 0 root (0) root (0) 154688 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_a.js │ │ │ -rw-r--r-- 0 root (0) root (0) 2670 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/search/all_b.js │ │ │ @@ -8305,15 +8306,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 173 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/tab_bd.png │ │ │ -rw-r--r-- 0 root (0) root (0) 177 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/tab_h.png │ │ │ -rw-r--r-- 0 root (0) root (0) 180 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/tab_hd.png │ │ │ -rw-r--r-- 0 root (0) root (0) 184 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/tab_s.png │ │ │ -rw-r--r-- 0 root (0) root (0) 188 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/tab_sd.png │ │ │ -rw-r--r-- 0 root (0) root (0) 10560 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/tabs.css │ │ │ -rw-r--r-- 0 root (0) root (0) 27010 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/html/BALL/topics.html │ │ │ --rw-r--r-- 0 root (0) root (0) 370518 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/tutorial.pdf.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 370516 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5/tutorial.pdf.gz │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5-doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1535 2025-08-18 23:10:41.000000 ./usr/share/doc/libball1.5-doc/changelog.Debian.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 227 2018-08-13 10:41:31.000000 ./usr/share/doc/libball1.5-doc/changelog.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2225 2022-12-21 15:06:35.000000 ./usr/share/doc/libball1.5-doc/copyright │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-08-18 23:10:41.000000 ./usr/share/doc-base/ │ │ │ -rw-r--r-- 0 root (0) root (0) 598 2022-12-21 15:06:35.000000 ./usr/share/doc-base/libball1.5-doc.ball-manual │ │ │ -rw-r--r-- 0 root (0) root (0) 473 2022-12-21 15:06:35.000000 ./usr/share/doc-base/libball1.5-doc.ball-tutorial │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d00/a01286.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: haighMallionShiftProcessor.h File Reference │ │ │ +BALL: antechamberFile.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,35 +65,31 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │
│ │ │ Classes | │ │ │ Namespaces
│ │ │ -
haighMallionShiftProcessor.h File Reference
│ │ │ +
antechamberFile.h File Reference
│ │ │
│ │ │
│ │ │ -
#include <BALL/common.h>
│ │ │ -#include <BALL/CONCEPT/processor.h>
│ │ │ -#include <BALL/NMR/shiftModule.h>
│ │ │ -#include <BALL/DATATYPE/stringHashMap.h>
│ │ │ -#include <list>
│ │ │ +
#include <BALL/FORMAT/genericMolFile.h>
│ │ │
│ │ │

Go to the source code of this file.

│ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

│ │ │ Classes

class  BALL::HaighMallionShiftProcessor
class  BALL::AntechamberFile
 
│ │ │ │ │ │ │ │ │ │ │ │

│ │ │ Namespaces

namespace  BALL
 
│ │ │ ├── html2text {} │ │ │ │ @@ -1,23 +1,19 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _N_M_R │ │ │ │ + * _F_O_R_M_A_T │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -haighMallionShiftProcessor.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ -#include <_B_A_L_L_/_N_M_R_/_s_h_i_f_t_M_o_d_u_l_e_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_H_a_s_h_M_a_p_._h> │ │ │ │ -#include │ │ │ │ +antechamberFile.h File Reference │ │ │ │ +#include <_B_A_L_L_/_F_O_R_M_A_T_/_g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_H_a_i_g_h_M_a_l_l_i_o_n_S_h_i_f_t_P_r_o_c_e_s_s_o_r │ │ │ │ +class   _B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d00/a01286_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: haighMallionShiftProcessor.h Source File │ │ │ +BALL: antechamberFile.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,207 +70,89 @@ │ │ │
│ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ -
haighMallionShiftProcessor.h
│ │ │ +
antechamberFile.h
│ │ │
│ │ │
│ │ │ Go to the documentation of this file.
1// -*- Mode: C++; tab-width: 2; -*-
│ │ │
2// vi: set ts=2:
│ │ │
3//
│ │ │ -
4// $Id: haighMallionShiftProcessor.h,v 1.16.10.6 2007-04-12 13:53:54 anne Exp $
│ │ │ -
5//
│ │ │ -
6
│ │ │ -
7#ifndef BALL_COMMON_H
│ │ │ -
8# include <BALL/common.h>
│ │ │ -
9#endif
│ │ │ -
10
│ │ │ -
11#ifndef BALL_CONCEPT_PROCESSOR_H
│ │ │ -
12# include <BALL/CONCEPT/processor.h>
│ │ │ -
13#endif
│ │ │ -
14
│ │ │ -
15#ifndef BALL_NMR_SHIFTMODULE_H
│ │ │ -
16# include<BALL/NMR/shiftModule.h>
│ │ │ -
17#endif
│ │ │ -
18
│ │ │ -
19#ifndef BALL_DATATYPE_STRINGHASHMAP_H
│ │ │ -
20# include <BALL/DATATYPE/stringHashMap.h>
│ │ │ -
21#endif
│ │ │ -
22
│ │ │ -
23#include <list>
│ │ │ -
24
│ │ │ -
25namespace BALL
│ │ │ -
26{
│ │ │ -
│ │ │ -
30 class BALL_EXPORT HaighMallionShiftProcessor
│ │ │ -
31 : public ShiftModule
│ │ │ -
32 {
│ │ │ -
33 public:
│ │ │ -
34
│ │ │ -
35 BALL_CREATE(HaighMallionShiftProcessor)
│ │ │ -
36
│ │ │ -
37
│ │ │ -
40
│ │ │ -
41
│ │ │ -
44 static const char* PROPERTY__RING_CURRENT_SHIFT;
│ │ │ -
45
│ │ │ -
47
│ │ │ +
4
│ │ │ +
5#ifndef BALL_FORMAT_ANTECHAMBERFILE_H
│ │ │ +
6#define BALL_FORMAT_ANTECHAMBERFILE_H
│ │ │ +
7
│ │ │ +
8#ifndef BALL_FORMAT_GENERICMOLFILE_H
│ │ │ +
9# include <BALL/FORMAT/genericMolFile.h>
│ │ │ +
10#endif
│ │ │ +
11
│ │ │ +
12namespace BALL
│ │ │ +
13{
│ │ │ +
14 class Atom;
│ │ │ +
15 class AtomContainer;
│ │ │ +
16 class System;
│ │ │ +
17
│ │ │ +
│ │ │ +
25 class BALL_EXPORT AntechamberFile
│ │ │ +
26 : public GenericMolFile
│ │ │ +
27 {
│ │ │ +
28 public:
│ │ │ +
29
│ │ │ +
33
│ │ │ +
36 AntechamberFile();
│ │ │ +
37
│ │ │ +
41 AntechamberFile(const String& filename, File::OpenMode open_mode = std::ios::in);
│ │ │ +
42
│ │ │ +
44 virtual ~AntechamberFile();
│ │ │ +
46
│ │ │
50
│ │ │ -
53 HaighMallionShiftProcessor();
│ │ │ -
54
│ │ │ -
57 HaighMallionShiftProcessor(const HaighMallionShiftProcessor& processor);
│ │ │ -
58
│ │ │ -
61 virtual ~HaighMallionShiftProcessor();
│ │ │ -
62
│ │ │ -
63
│ │ │ +
54 virtual bool write(const AtomContainer& ac);
│ │ │ +
55
│ │ │ +
59 virtual bool write(const System& system);
│ │ │ +
60
│ │ │ +
64 virtual bool read(System& system);
│ │ │
65
│ │ │ -
68
│ │ │ -
85 virtual void init();
│ │ │ -
86
│ │ │ -
88
│ │ │ -
89
│ │ │ -
91
│ │ │ -
94
│ │ │ -
100 virtual bool start();
│ │ │ -
101
│ │ │ -
102
│ │ │ -
108 virtual Processor::Result operator () (Composite& atom);
│ │ │ -
109
│ │ │ -
110
│ │ │ -
123 virtual bool finish();
│ │ │ -
124
│ │ │ -
125
│ │ │ -
127
│ │ │ -
128
│ │ │ -
129 protected:
│ │ │ -
130
│ │ │ -
131 /*_ A flag indicating whether Hydrogens are effected by all effectors or
│ │ │ -
132 just by effectors of the same residue.
│ │ │ -
133 Set this flag by specifying the option {\tt H_influenced_by_all_effectors = true} in
│ │ │ -
134 the HaighMallionRingCurrent section of the parameter file.
│ │ │ -
135 Default is false.
│ │ │ -
136 */
│ │ │ -
137 bool H_influenced_by_all_effectors_;
│ │ │ -
138
│ │ │ -
139 /*_ A flag indicating whether HA Hydrogens are effected by all effectors or
│ │ │ -
140 just by effectors of the same residue.
│ │ │ -
141 Set this flag by specifying the option {\tt HA_influenced_by_all_effectors = true} in
│ │ │ -
142 the HaighMallionRingCurrent section of the parameter file.
│ │ │ -
143 Default is false.
│ │ │ -
144 */
│ │ │ -
145 bool HA_influenced_by_all_effectors_;
│ │ │ -
146
│ │ │ -
147 /*_ A flag indicating whether a cutoff for the ring current effect is used.
│ │ │ -
148 Set this flag by specifying the option {\tt use_cut_off = true} in
│ │ │ -
149 the HaighMallionRingCurrent section of the parameter file.
│ │ │ -
150 Default is false.
│ │ │ -
151 */
│ │ │ -
152 bool use_cut_off_;
│ │ │ -
153
│ │ │ -
154
│ │ │ -
155 /*_ A cut off value for the ring current effect computation via Haigh Mallion.
│ │ │ -
156 Set this flag by specifying the option {\tt cut_off = 15.} in
│ │ │ -
157 the HaighMallionRingCurrent section of the parameter file.
│ │ │ -
158 Default is 15.*15.
│ │ │ -
159 */
│ │ │ -
160 float cut_off2_;
│ │ │ -
161
│ │ │ -
162 /*_ A flag indicating whether all hydrogens are targets.
│ │ │ -
163 Set this flag by specifying the option {\tt all_hydrogen_are_targets = true} in
│ │ │ -
164 the HaighMallionRingCurrent section of the parameter file.
│ │ │ -
165 Default is false.
│ │ │ -
166 */
│ │ │ -
167 bool all_hydrogen_are_targets_;
│ │ │ -
168
│ │ │ -
173 bool correct_CA_shifts_;
│ │ │ -
174
│ │ │ -
175 /*_ A flag indicating whether for the computation of the ring current effect
│ │ │ -
176 the target has to be projected onto the effector ring plane or not.
│ │ │ -
177 Set this flag by specifying the option {\tt project_target_to_ring_plane = true} in
│ │ │ -
178 the HaighMallionRingCurrent section of the parameter file.
│ │ │ -
179 Default is false.
│ │ │ -
180 */
│ │ │ -
181 bool project_target_to_ring_plane_;
│ │ │ -
182
│ │ │ -
183 /*_ The values of the target nucleus factors F.
│ │ │ -
184 */
│ │ │ -
185 StringHashMap<float> target_nucleus_factors_;
│ │ │ -
186
│ │ │ -
187 /*_ The default value of the target nucleus factors F for hydrogen atoms.
│ │ │ -
188 */
│ │ │ -
189 float default_hydrogen_target_nucleus_factor_;
│ │ │ -
190
│ │ │ -
191 /*_ The default factor of negative ring current factors
│ │ │ -
192 */
│ │ │ -
193 float negative_ringcurrent_factor_ ;
│ │ │ -
194
│ │ │ -
195 /*_ The effector residues stored as a vector of atoms the collected by {\tt operator ()}.
│ │ │ -
196 */
│ │ │ -
197 std::vector< std::vector<Atom*> > effectors_;
│ │ │ -
198
│ │ │ -
199 /*_ The effector residue types stored as a vector of strings collected by {\tt operator ()}.
│ │ │ -
200 This is necessary to allow, e.g., TRP1 and TRP2 as two different kinds of rings.
│ │ │ -
201 */
│ │ │ -
202 std::vector<String> effector_types_;
│ │ │ -
203
│ │ │ -
204 /*_ The effector names collected from the ini-file by {\tt init ()}.
│ │ │ -
205 */
│ │ │ -
206 std::vector<BALL::String> effector_names_;
│ │ │ -
207
│ │ │ -
208 /*_ The intensities of the effecting residues collected from the ini-file by {\tt init ()}.
│ │ │ -
209 */
│ │ │ -
210 StringHashMap<float> intensity_factors_;
│ │ │ -
211
│ │ │ -
212 /*_ The ring atom names of the effecting residues collected from the ini-file by {\tt init ()}.
│ │ │ -
213 */
│ │ │ -
214 std::vector< std::vector<BALL::String> > ring_atoms_;
│ │ │ -
215
│ │ │ -
216 /*_ The targeted atom names collected by {\tt init ()}.
│ │ │ -
217 */
│ │ │ -
218 std::vector< BALL::String> target_names_;
│ │ │ -
219
│ │ │ -
220 /*_ The targeted atoms collected by {\tt operator ()}.
│ │ │ -
221 */
│ │ │ -
222 std::vector<Atom* > targets_;
│ │ │ -
223
│ │ │ -
224 private:
│ │ │ -
225
│ │ │ -
226 void printParameters_();
│ │ │ -
227 void printEffectors_();
│ │ │ -
228 void printTargets_();
│ │ │ -
229 void postprocessing_();
│ │ │ -
230
│ │ │ -
231 };
│ │ │ -
│ │ │ -
232
│ │ │ -
233} // namespace BALL
│ │ │ -
234
│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
BALL_CREATE
#define BALL_CREATE(name)
Definition create.h:62
│ │ │ -
std
STL namespace.
│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
│ │ │ +
69 virtual Molecule* read();
│ │ │ +
70
│ │ │ +
74 virtual bool write(const Molecule& molecule);
│ │ │ +
75
│ │ │ +
77
│ │ │ +
78 protected:
│ │ │ +
79 void ac_split_(const String& line, std::vector<String>& split);
│ │ │ +
80 };
│ │ │ +
│ │ │ +
81}
│ │ │ +
82#endif
│ │ │ + │ │ │ + │ │ │ +
BALL::PDB::Atom
char Atom[5]
Definition PDBdefs.h:257
│ │ │ + │ │ │ + │ │ │ +
BALL::AntechamberFile::AntechamberFile
AntechamberFile(const String &filename, File::OpenMode open_mode=std::ios::in)
│ │ │ +
BALL::AntechamberFile::~AntechamberFile
virtual ~AntechamberFile()
Destructor.
│ │ │ +
BALL::AntechamberFile::read
virtual Molecule * read()
│ │ │ +
BALL::AntechamberFile::write
virtual bool write(const AtomContainer &ac)
│ │ │ +
BALL::AntechamberFile::read
virtual bool read(System &system)
│ │ │ +
BALL::AntechamberFile::ac_split_
void ac_split_(const String &line, std::vector< String > &split)
│ │ │ + │ │ │ +
BALL::AntechamberFile::write
virtual bool write(const System &system)
│ │ │ +
BALL::AntechamberFile::write
virtual bool write(const Molecule &molecule)
│ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
BALL::File::OpenMode
std::ios::openmode OpenMode
Definition file.h:165
│ │ │ +
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ │
│ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,221 +1,101 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _N_M_R │ │ │ │ -haighMallionShiftProcessor.h │ │ │ │ + * _F_O_R_M_A_T │ │ │ │ +antechamberFile.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: haighMallionShiftProcessor.h,v 1.16.10.6 2007-04-12 13:53:54 anne Exp │ │ │ │ -$ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_COMMON_H │ │ │ │ -8# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -9#endif │ │ │ │ -10 │ │ │ │ -11#ifndef BALL_CONCEPT_PROCESSOR_H │ │ │ │ -12# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ -13#endif │ │ │ │ -14 │ │ │ │ -15#ifndef BALL_NMR_SHIFTMODULE_H │ │ │ │ -16# include<_B_A_L_L_/_N_M_R_/_s_h_i_f_t_M_o_d_u_l_e_._h> │ │ │ │ -17#endif │ │ │ │ -18 │ │ │ │ -19#ifndef BALL_DATATYPE_STRINGHASHMAP_H │ │ │ │ -20# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_H_a_s_h_M_a_p_._h> │ │ │ │ -21#endif │ │ │ │ -22 │ │ │ │ -23#include │ │ │ │ -24 │ │ │ │ -25namespace _B_A_L_L │ │ │ │ -26{ │ │ │ │ -_3_0 class _B_A_L_L___E_X_P_O_R_T _H_a_i_g_h_M_a_l_l_i_o_n_S_h_i_f_t_P_r_o_c_e_s_s_o_r │ │ │ │ -31 : public _S_h_i_f_t_M_o_d_u_l_e │ │ │ │ -32 { │ │ │ │ -33 public: │ │ │ │ -34 │ │ │ │ -35 _B_A_L_L___C_R_E_A_T_E(_H_a_i_g_h_M_a_l_l_i_o_n_S_h_i_f_t_P_r_o_c_e_s_s_o_r) │ │ │ │ -36 │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_FORMAT_ANTECHAMBERFILE_H │ │ │ │ +6#define BALL_FORMAT_ANTECHAMBERFILE_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_FORMAT_GENERICMOLFILE_H │ │ │ │ +9# include <_B_A_L_L_/_F_O_R_M_A_T_/_g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12namespace _B_A_L_L │ │ │ │ +13{ │ │ │ │ +14 class _A_t_o_m; │ │ │ │ +15 class AtomContainer; │ │ │ │ +16 class System; │ │ │ │ +17 │ │ │ │ +_2_5 class _B_A_L_L___E_X_P_O_R_T _A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ +26 : public _G_e_n_e_r_i_c_M_o_l_F_i_l_e │ │ │ │ +27 { │ │ │ │ +28 public: │ │ │ │ +29 │ │ │ │ +33 │ │ │ │ +_3_6 _A_n_t_e_c_h_a_m_b_e_r_F_i_l_e(); │ │ │ │ 37 │ │ │ │ -40 │ │ │ │ -41 │ │ │ │ -_4_4 static const char* PROPERTY__RING_CURRENT_SHIFT; │ │ │ │ -45 │ │ │ │ -47 │ │ │ │ +_4_1 _A_n_t_e_c_h_a_m_b_e_r_F_i_l_e(const _S_t_r_i_n_g& filename, _F_i_l_e_:_:_O_p_e_n_M_o_d_e open_mode = std:: │ │ │ │ +ios::in); │ │ │ │ +42 │ │ │ │ +_4_4 virtual _~_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e(); │ │ │ │ +46 │ │ │ │ 50 │ │ │ │ -_5_3 _H_a_i_g_h_M_a_l_l_i_o_n_S_h_i_f_t_P_r_o_c_e_s_s_o_r(); │ │ │ │ -54 │ │ │ │ -_5_7 _H_a_i_g_h_M_a_l_l_i_o_n_S_h_i_f_t_P_r_o_c_e_s_s_o_r(const _H_a_i_g_h_M_a_l_l_i_o_n_S_h_i_f_t_P_r_o_c_e_s_s_o_r& processor); │ │ │ │ -58 │ │ │ │ -_6_1 virtual ~_H_a_i_g_h_M_a_l_l_i_o_n_S_h_i_f_t_P_r_o_c_e_s_s_o_r(); │ │ │ │ -62 │ │ │ │ -63 │ │ │ │ +_5_4 virtual bool _w_r_i_t_e(const _A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ +55 │ │ │ │ +_5_9 virtual bool _w_r_i_t_e(const _S_y_s_t_e_m& system); │ │ │ │ +60 │ │ │ │ +_6_4 virtual bool _r_e_a_d(_S_y_s_t_e_m& system); │ │ │ │ 65 │ │ │ │ -68 │ │ │ │ -_8_5 virtual void init(); │ │ │ │ -86 │ │ │ │ -88 │ │ │ │ -89 │ │ │ │ -91 │ │ │ │ -94 │ │ │ │ -_1_0_0 virtual bool start(); │ │ │ │ -101 │ │ │ │ -102 │ │ │ │ -_1_0_8 virtual _P_r_o_c_e_s_s_o_r::_R_e_s_u_l_t operator () (_C_o_m_p_o_s_i_t_e& atom); │ │ │ │ -109 │ │ │ │ -110 │ │ │ │ -_1_2_3 virtual bool finish(); │ │ │ │ -124 │ │ │ │ -125 │ │ │ │ -127 │ │ │ │ -128 │ │ │ │ -129 protected: │ │ │ │ -130 │ │ │ │ -131 /*_ A flag indicating whether Hydrogens are effected by all effectors or │ │ │ │ -132 just by effectors of the same residue. │ │ │ │ -133 Set this flag by specifying the option {\tt H_influenced_by_all_effectors = │ │ │ │ -true} in │ │ │ │ -134 the HaighMallionRingCurrent section of the parameter file. │ │ │ │ -135 Default is false. │ │ │ │ -136 */ │ │ │ │ -_1_3_7 bool H_influenced_by_all_effectors_; │ │ │ │ -138 │ │ │ │ -139 /*_ A flag indicating whether HA Hydrogens are effected by all effectors or │ │ │ │ -140 just by effectors of the same residue. │ │ │ │ -141 Set this flag by specifying the option {\tt HA_influenced_by_all_effectors │ │ │ │ -= true} in │ │ │ │ -142 the HaighMallionRingCurrent section of the parameter file. │ │ │ │ -143 Default is false. │ │ │ │ -144 */ │ │ │ │ -_1_4_5 bool HA_influenced_by_all_effectors_; │ │ │ │ -146 │ │ │ │ -147 /*_ A flag indicating whether a cutoff for the ring current effect is used. │ │ │ │ -148 Set this flag by specifying the option {\tt use_cut_off = true} in │ │ │ │ -149 the HaighMallionRingCurrent section of the parameter file. │ │ │ │ -150 Default is false. │ │ │ │ -151 */ │ │ │ │ -_1_5_2 bool use_cut_off_; │ │ │ │ -153 │ │ │ │ -154 │ │ │ │ -155 /*_ A cut off value for the ring current effect computation via Haigh │ │ │ │ -Mallion. │ │ │ │ -156 Set this flag by specifying the option {\tt cut_off = 15.} in │ │ │ │ -157 the HaighMallionRingCurrent section of the parameter file. │ │ │ │ -158 Default is 15.*15. │ │ │ │ -159 */ │ │ │ │ -_1_6_0 float cut_off2_; │ │ │ │ -161 │ │ │ │ -162 /*_ A flag indicating whether all hydrogens are targets. │ │ │ │ -163 Set this flag by specifying the option {\tt all_hydrogen_are_targets = │ │ │ │ -true} in │ │ │ │ -164 the HaighMallionRingCurrent section of the parameter file. │ │ │ │ -165 Default is false. │ │ │ │ -166 */ │ │ │ │ -_1_6_7 bool all_hydrogen_are_targets_; │ │ │ │ -168 │ │ │ │ -_1_7_3 bool correct_CA_shifts_; │ │ │ │ -174 │ │ │ │ -175 /*_ A flag indicating whether for the computation of the ring current │ │ │ │ -effect │ │ │ │ -176 the target has to be projected onto the effector ring plane or not. │ │ │ │ -177 Set this flag by specifying the option {\tt project_target_to_ring_plane = │ │ │ │ -true} in │ │ │ │ -178 the HaighMallionRingCurrent section of the parameter file. │ │ │ │ -179 Default is false. │ │ │ │ -180 */ │ │ │ │ -_1_8_1 bool project_target_to_ring_plane_; │ │ │ │ -182 │ │ │ │ -183 /*_ The values of the target nucleus factors F. │ │ │ │ -184 */ │ │ │ │ -_1_8_5 _S_t_r_i_n_g_H_a_s_h_M_a_p target_nucleus_factors_; │ │ │ │ -186 │ │ │ │ -187 /*_ The default value of the target nucleus factors F for hydrogen atoms. │ │ │ │ -188 */ │ │ │ │ -_1_8_9 float default_hydrogen_target_nucleus_factor_; │ │ │ │ -190 │ │ │ │ -191 /*_ The default factor of negative ring current factors │ │ │ │ -192 */ │ │ │ │ -_1_9_3 float negative_ringcurrent_factor_ ; │ │ │ │ -194 │ │ │ │ -195 /*_ The effector residues stored as a vector of atoms the collected by {\tt │ │ │ │ -operator ()}. │ │ │ │ -196 */ │ │ │ │ -_1_9_7 _s_t_d::vector< _s_t_d::vector<_A_t_o_m*> > effectors_; │ │ │ │ -198 │ │ │ │ -199 /*_ The effector residue types stored as a vector of strings collected by │ │ │ │ -{\tt operator ()}. │ │ │ │ -200 This is necessary to allow, e.g., TRP1 and TRP2 as two different kinds of │ │ │ │ -rings. │ │ │ │ -201 */ │ │ │ │ -_2_0_2 _s_t_d::vector<_S_t_r_i_n_g> effector_types_; │ │ │ │ -203 │ │ │ │ -204 /*_ The effector names collected from the ini-file by {\tt init ()}. │ │ │ │ -205 */ │ │ │ │ -_2_0_6 _s_t_d::vector<_B_A_L_L::_S_t_r_i_n_g> effector_names_; │ │ │ │ -207 │ │ │ │ -208 /*_ The intensities of the effecting residues collected from the ini-file │ │ │ │ -by {\tt init ()}. │ │ │ │ -209 */ │ │ │ │ -_2_1_0 _S_t_r_i_n_g_H_a_s_h_M_a_p intensity_factors_; │ │ │ │ -211 │ │ │ │ -212 /*_ The ring atom names of the effecting residues collected from the ini- │ │ │ │ -file by {\tt init ()}. │ │ │ │ -213 */ │ │ │ │ -_2_1_4 _s_t_d::vector< _s_t_d::vector<_B_A_L_L::_S_t_r_i_n_g> > ring_atoms_; │ │ │ │ -215 │ │ │ │ -216 /*_ The targeted atom names collected by {\tt init ()}. │ │ │ │ -217 */ │ │ │ │ -_2_1_8 _s_t_d::vector< _B_A_L_L::_S_t_r_i_n_g> target_names_; │ │ │ │ -219 │ │ │ │ -220 /*_ The targeted atoms collected by {\tt operator ()}. │ │ │ │ -221 */ │ │ │ │ -_2_2_2 _s_t_d::vector<_A_t_o_m* > targets_; │ │ │ │ -223 │ │ │ │ -224 private: │ │ │ │ -225 │ │ │ │ -226 void printParameters_(); │ │ │ │ -227 void printEffectors_(); │ │ │ │ -228 void printTargets_(); │ │ │ │ -229 void postprocessing_(); │ │ │ │ -230 │ │ │ │ -231 }; │ │ │ │ -232 │ │ │ │ -233} // namespace BALL │ │ │ │ -234 │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_s_h_i_f_t_M_o_d_u_l_e_._h │ │ │ │ -_s_t_r_i_n_g_H_a_s_h_M_a_p_._h │ │ │ │ -_p_r_o_c_e_s_s_o_r_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ -_s_t_d │ │ │ │ -STL namespace. │ │ │ │ +_6_9 virtual _M_o_l_e_c_u_l_e* _r_e_a_d(); │ │ │ │ +70 │ │ │ │ +_7_4 virtual bool _w_r_i_t_e(const _M_o_l_e_c_u_l_e& molecule); │ │ │ │ +75 │ │ │ │ +77 │ │ │ │ +78 protected: │ │ │ │ +_7_9 void _a_c___s_p_l_i_t__(const _S_t_r_i_n_g& line, std::vector& split); │ │ │ │ +80 }; │ │ │ │ +81} │ │ │ │ +82#endif │ │ │ │ +_g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ -DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_P_D_B_:_:_A_t_o_m │ │ │ │ +char Atom[5] │ │ │ │ +DDeeffiinniittiioonn _P_D_B_d_e_f_s_._h_:_2_5_7 │ │ │ │ _B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g_H_a_s_h_M_a_p │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_H_a_s_h_M_a_p_._h_:_4_2 │ │ │ │ -_B_A_L_L_:_:_R_e_s_u_l_t │ │ │ │ -DDeeffiinniittiioonn _r_e_s_u_l_t_._h_:_2_2 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_H_a_i_g_h_M_a_l_l_i_o_n_S_h_i_f_t_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _h_a_i_g_h_M_a_l_l_i_o_n_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_M_o_d_u_l_e │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_M_o_d_u_l_e_._h_:_4_3 │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ +DDeeffiinniittiioonn _a_n_t_e_c_h_a_m_b_e_r_F_i_l_e_._h_:_2_7 │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ +AntechamberFile(const String &filename, File::OpenMode open_mode=std::ios::in) │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_~_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ +virtual ~AntechamberFile() │ │ │ │ +Destructor. │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_r_e_a_d │ │ │ │ +virtual Molecule * read() │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_w_r_i_t_e │ │ │ │ +virtual bool write(const AtomContainer &ac) │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_r_e_a_d │ │ │ │ +virtual bool read(System &system) │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_a_c___s_p_l_i_t__ │ │ │ │ +void ac_split_(const String &line, std::vector< String > &split) │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ +AntechamberFile() │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_w_r_i_t_e │ │ │ │ +virtual bool write(const System &system) │ │ │ │ +_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_w_r_i_t_e │ │ │ │ +virtual bool write(const Molecule &molecule) │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_r_i_c_M_o_l_F_i_l_e │ │ │ │ +DDeeffiinniittiioonn _g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h_:_5_8 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e │ │ │ │ +DDeeffiinniittiioonn _m_o_l_e_c_u_l_e_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ +DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ +_B_A_L_L_:_:_F_i_l_e_:_:_O_p_e_n_M_o_d_e │ │ │ │ +std::ios::openmode OpenMode │ │ │ │ +DDeeffiinniittiioonn _f_i_l_e_._h_:_1_6_5 │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d06/a08474.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Member Functions | │ │ │ List of all members │ │ │
BALL::VIEW::DoubleEditorWidget Class Reference
│ │ │ │ │ │
│ │ │ │ │ │ -

#include <BALL/VIEW/WIDGETS/propertyEditor.h>

│ │ │ +

#include <BALL/VIEW/WIDGETS/propertyEditor.h>

│ │ │
│ │ │ Inheritance diagram for BALL::VIEW::DoubleEditorWidget:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ BALL::VIEW::PropEditorWidget │ │ │ @@ -138,15 +138,15 @@ │ │ │ QString name_ │ │ │   │ │ │ Ui::PropEditorWidget ui_ │ │ │   │ │ │ │ │ │

Detailed Description

│ │ │
│ │ │ -

Definition at line 188 of file propertyEditor.h.

│ │ │ +

Definition at line 188 of file propertyEditor.h.

│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ DoubleEditorWidget()

│ │ │ │ │ │
│ │ │
│ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d0a/a00743.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: graphVertex.h File Reference │ │ │ +BALL: dataset.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,39 +65,98 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │
│ │ │ Classes | │ │ │ -Namespaces
│ │ │ -
graphVertex.h File Reference
│ │ │ +Namespaces | │ │ │ +Macros
│ │ │ +
dataset.h File Reference
│ │ │ │ │ │
│ │ │ -
#include <BALL/common.h>
│ │ │ -#include <BALL/DATATYPE/hashSet.h>
│ │ │ +
#include <BALL/DATATYPE/string.h>
│ │ │ +#include <BALL/DATATYPE/hashMap.h>
│ │ │ +#include <BALL/DATATYPE/hashSet.h>
│ │ │ +#include <BALL/CONCEPT/embeddable.h>
│ │ │ +#include <BALL/VIEW/KERNEL/UIOperationMode.h>
│ │ │ +#include <QtWidgets/QMenu>
│ │ │ +#include <QtWidgets/QTreeWidgetItem>
│ │ │
│ │ │

Go to the source code of this file.

│ │ │
│ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

│ │ │ Classes

class  BALL::GraphVertex< Vertex, Edge, Face >
class  BALL::VIEW::Dataset
 
class  BALL::VIEW::DatasetController
 
│ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ + │ │ │ +

│ │ │ Namespaces

namespace  BALL
 
namespace  BALL::VIEW
 
│ │ │ + │ │ │ + │ │ │ + │ │ │

│ │ │ +Macros

#define BALL_CREATE_DATASET(TYPE)
 
│ │ │ +

Macro Definition Documentation

│ │ │ + │ │ │ +

◆ BALL_CREATE_DATASET

│ │ │ + │ │ │ +
│ │ │ +
│ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
#define BALL_CREATE_DATASET( TYPE)
│ │ │ +
│ │ │ +Value:
class BALL_VIEW_EXPORT TYPE##Dataset\
│ │ │ +
: public Dataset\
│ │ │ +
{\
│ │ │ +
public :\
│ │ │ +
\
│ │ │ +
TYPE##Dataset(TYPE* data = 0)\
│ │ │ +
: Dataset(),\
│ │ │ +
data_(data)\
│ │ │ +
{}\
│ │ │ +
\
│ │ │ +
TYPE##Dataset(const TYPE##Dataset& set)\
│ │ │ +
: Dataset(set),\
│ │ │ +
data_(set.data_)\
│ │ │ +
{}\
│ │ │ +
\
│ │ │ +
TYPE* getData() { return data_;}\
│ │ │ +
\
│ │ │ +
void setData(TYPE* data) { data_ = data;}\
│ │ │ +
\
│ │ │ +
TYPE* data_;\
│ │ │ +
};
│ │ │ +
BALL_VIEW_EXPORT
#define BALL_VIEW_EXPORT
Definition COMMON/global.h:52
│ │ │ +

Macro to create derived Dataset classes

│ │ │ + │ │ │ +

Definition at line 131 of file dataset.h.

│ │ │ + │ │ │ +
│ │ │ +
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ │
│ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,20 +1,63 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -graphVertex.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ + * _V_I_E_W │ │ │ │ + * _D_A_T_A_T_Y_P_E │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s │ │ │ │ +dataset.h File Reference │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ #include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_S_e_t_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_e_m_b_e_d_d_a_b_l_e_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h> │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_<_ _V_e_r_t_e_x_,_ _E_d_g_e_,_ _F_a_c_e_ _> │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │ +  │ │ │ │ +MMaaccrrooss │ │ │ │ +#define  _B_A_L_L___C_R_E_A_T_E___D_A_T_A_S_E_T(TYPE) │ │ │ │ +  │ │ │ │ +********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ +********** _?◆_? BBAALLLL__CCRREEAATTEE__DDAATTAASSEETT ********** │ │ │ │ +#define BALL_CREATE_DATASET (   TYPE ) │ │ │ │ +VVaalluuee:: │ │ │ │ +class _B_A_L_L___V_I_E_W___E_X_P_O_R_T TYPE##Dataset\ │ │ │ │ +: public Dataset\ │ │ │ │ +{\ │ │ │ │ +public :\ │ │ │ │ +\ │ │ │ │ +TYPE##Dataset(TYPE* data = 0)\ │ │ │ │ +: Dataset(),\ │ │ │ │ +data_(data)\ │ │ │ │ +{}\ │ │ │ │ +\ │ │ │ │ +TYPE##Dataset(const TYPE##Dataset& set)\ │ │ │ │ +: Dataset(set),\ │ │ │ │ +data_(set.data_)\ │ │ │ │ +{}\ │ │ │ │ +\ │ │ │ │ +TYPE* getData() { return data_;}\ │ │ │ │ +\ │ │ │ │ +void setData(TYPE* data) { data_ = data;}\ │ │ │ │ +\ │ │ │ │ +TYPE* data_;\ │ │ │ │ +}; │ │ │ │ +_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ +#define BALL_VIEW_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ +Macro to create derived Dataset classes │ │ │ │ +Definition at line _1_3_1 of file _d_a_t_a_s_e_t_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d0a/a00743_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: graphVertex.h Source File │ │ │ +BALL: dataset.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,670 +70,296 @@ │ │ │
│ │ │
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ │ │ │
│ │ │ -
graphVertex.h
│ │ │ +
dataset.h
│ │ │
│ │ │
│ │ │ Go to the documentation of this file.
1// -*- Mode: C++; tab-width: 2; -*-
│ │ │
2// vi: set ts=2:
│ │ │
3//
│ │ │
4
│ │ │ -
5#ifndef BALL_STRUCTURE_GRAPHVERTEX_H
│ │ │ -
6#define BALL_STRUCTURE_GRAPHVERTEX_H
│ │ │ +
5#ifndef BALL_VIEW_DATATYPE_DATASET_H
│ │ │ +
6#define BALL_VIEW_DATATYPE_DATASET_H
│ │ │
7
│ │ │ -
8#ifndef BALL_COMMON_H
│ │ │ -
9# include <BALL/common.h>
│ │ │ +
8#ifndef BALL_DATATYPE_STRING_H
│ │ │ +
9# include <BALL/DATATYPE/string.h>
│ │ │
10#endif
│ │ │
11
│ │ │ -
12#ifndef BALL_DATATYPE_HASHSET_H
│ │ │ -
13# include <BALL/DATATYPE/hashSet.h>
│ │ │ +
12#ifndef BALL_DATATYPE_HASHMAP_H
│ │ │ +
13# include <BALL/DATATYPE/hashMap.h>
│ │ │
14#endif
│ │ │
15
│ │ │ -
16namespace BALL
│ │ │ -
17{
│ │ │ -
18
│ │ │ -
19 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
20 class GraphEdge;
│ │ │ -
21
│ │ │ -
22 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
23 class GraphFace;
│ │ │ -
24
│ │ │ -
25 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
26 class GraphTriangle;
│ │ │ +
16#ifndef BALL_DATATYPE_HASHSET_H
│ │ │ +
17# include <BALL/DATATYPE/hashSet.h>
│ │ │ +
18#endif
│ │ │ +
19
│ │ │ +
20#ifndef BALL_CONCEPT_EMBEDDABLE_H
│ │ │ +
21# include <BALL/CONCEPT/embeddable.h>
│ │ │ +
22#endif
│ │ │ +
23
│ │ │ +
24#ifndef BALL_VIEW_KERNEL_UIOPERATIONMODE_H
│ │ │ +
25# include <BALL/VIEW/KERNEL/UIOperationMode.h>
│ │ │ +
26#endif
│ │ │
27
│ │ │ -
31 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
32 class GraphVertex
│ │ │ -
33 {
│ │ │ -
34 public:
│ │ │ -
35
│ │ │ -
43 friend class GraphEdge<Vertex,Edge,Face>;
│ │ │ -
44 friend class GraphFace<Vertex,Edge,Face>;
│ │ │ -
45 friend class GraphTriangle<Vertex,Edge,Face>;
│ │ │ -
46
│ │ │ -
47 BALL_CREATE(GraphVertex)
│ │ │ -
48
│ │ │ -
49
│ │ │ -
52
│ │ │ -
53 typedef typename HashSet<Edge*>::Iterator EdgeIterator;
│ │ │ -
54 typedef typename HashSet<Edge*>::ConstIterator ConstEdgeIterator;
│ │ │ -
55 typedef typename HashSet<Face*>::Iterator FaceIterator;
│ │ │ -
56 typedef typename HashSet<Face*>::ConstIterator ConstFaceIterator;
│ │ │ -
57
│ │ │ -
59
│ │ │ -
62
│ │ │ -
│ │ │ -
66 GraphVertex()
│ │ │ -
67 ;
│ │ │ -
68
│ │ │ -
│ │ │ -
76 GraphVertex(const GraphVertex<Vertex,Edge,Face>& vertex, bool deep = false)
│ │ │ -
77 ;
│ │ │ -
78
│ │ │ -
│ │ │ -
82 virtual ~GraphVertex()
│ │ │ -
83 ;
│ │ │ +
28#include <QtWidgets/QMenu>
│ │ │ +
29#include <QtWidgets/QTreeWidgetItem>
│ │ │ +
30
│ │ │ +
31namespace BALL
│ │ │ +
32{
│ │ │ +
33 class Composite;
│ │ │ +
34
│ │ │ +
35 namespace VIEW
│ │ │ +
36 {
│ │ │ +
37 class DatasetControl;
│ │ │ +
38 class DatasetMessage;
│ │ │ +
39 class MainControl;
│ │ │ +
40 class DataMessage;
│ │ │ +
41
│ │ │ +
│ │ │ +
60 class BALL_VIEW_EXPORT Dataset
│ │ │ +
61 {
│ │ │ +
62 public:
│ │ │ +
63
│ │ │ +
67
│ │ │ +
70 Dataset();
│ │ │ +
71
│ │ │ +
74 Dataset(const Dataset& dataset);
│ │ │ +
75
│ │ │ +
78 virtual ~Dataset();
│ │ │ +
79
│ │ │ +
82 virtual void clear();
│ │ │ +
83
│ │ │
85
│ │ │ -
89
│ │ │ -
│ │ │ -
97 void set(const GraphVertex<Vertex,Edge,Face>& vertex, bool deep = false)
│ │ │ -
98 ;
│ │ │ -
99
│ │ │ -
│ │ │ -
105 GraphVertex<Vertex,Edge,Face>& operator =
│ │ │ -
106 (const GraphVertex<Vertex,Edge,Face>& vertex)
│ │ │ -
107 ;
│ │ │ -
108
│ │ │ -
110
│ │ │ -
113
│ │ │ -
│ │ │ -
117 void insert(Edge* edge)
│ │ │ -
118 ;
│ │ │ -
119
│ │ │ -
│ │ │ -
123 void insert(Face* face)
│ │ │ -
124 ;
│ │ │ -
125
│ │ │ -
│ │ │ -
129 void remove(Edge* edge)
│ │ │ -
130 ;
│ │ │ -
131
│ │ │ -
│ │ │ -
135 void remove(Face* face)
│ │ │ -
136 ;
│ │ │ -
137
│ │ │ -
│ │ │ -
141 Position numberOfEdges() const
│ │ │ -
142 ;
│ │ │ -
143
│ │ │ -
│ │ │ -
147 Position numberOfFaces() const
│ │ │ -
148 ;
│ │ │ -
149
│ │ │ -
│ │ │ -
153 void setIndex(Index index)
│ │ │ -
154 ;
│ │ │ -
155
│ │ │ -
│ │ │ -
159 Index getIndex() const
│ │ │ -
160 ;
│ │ │ -
161
│ │ │ -
│ │ │ -
168 bool join(const Vertex& vertex)
│ │ │ -
169 ;
│ │ │ -
170
│ │ │ -
│ │ │ -
177 bool substitute(Vertex* vertex)
│ │ │ -
178 ;
│ │ │ -
179
│ │ │ -
180
│ │ │ -
182
│ │ │ -
185
│ │ │ -
│ │ │ -
189 virtual bool operator == (const Vertex&) const
│ │ │ -
190 ;
│ │ │ -
191
│ │ │ -
│ │ │ -
195 virtual bool operator != (const Vertex&) const
│ │ │ -
196 ;
│ │ │ +
88
│ │ │ +
91 void set(const Dataset& v);
│ │ │ +
92
│ │ │ +
96 const Dataset& operator = (const Dataset& v);
│ │ │ +
97
│ │ │ +
99 void setName(String name) { name_ = name;}
│ │ │ +
100
│ │ │ +
102 String getName() const { return name_;}
│ │ │ +
103
│ │ │ +
105 void setType(String type) { type_ = type;}
│ │ │ +
106
│ │ │ +
108 String getType() const { return type_;}
│ │ │ +
109
│ │ │ +
111 void setComposite(Composite* composite) { composite_ = composite;}
│ │ │ +
112
│ │ │ +
114 Composite* getComposite() const { return composite_;}
│ │ │ +
115
│ │ │ +
117 void dump(std::ostream& s, Size depth) const;
│ │ │ +
118 //
│ │ │ +
120
│ │ │ +
121 protected:
│ │ │ +
122
│ │ │ +
123 Composite* composite_;
│ │ │ +
124 String name_;
│ │ │ +
125 String type_;
│ │ │ +
126 };
│ │ │ +
│ │ │ +
127
│ │ │ +
128
│ │ │ +
│ │ │ +
131#define BALL_CREATE_DATASET(TYPE)\
│ │ │ +
132 class BALL_VIEW_EXPORT TYPE##Dataset\
│ │ │ +
133 : public Dataset\
│ │ │ +
134 {\
│ │ │ +
135 public :\
│ │ │ +
136 \
│ │ │ +
137 TYPE##Dataset(TYPE* data = 0)\
│ │ │ +
138 : Dataset(),\
│ │ │ +
139 data_(data)\
│ │ │ +
140 {}\
│ │ │ +
141 \
│ │ │ +
142 TYPE##Dataset(const TYPE##Dataset& set)\
│ │ │ +
143 : Dataset(set),\
│ │ │ +
144 data_(set.data_)\
│ │ │ +
145 {}\
│ │ │ +
146 \
│ │ │ +
147 TYPE* getData() { return data_;}\
│ │ │ +
148 \
│ │ │ +
149 void setData(TYPE* data) { data_ = data;}\
│ │ │ +
150 \
│ │ │ +
151 TYPE* data_;\
│ │ │ +
152 };
│ │ │ +
│ │ │ +
153
│ │ │ +
154
│ │ │ +
│ │ │ +
190 class BALL_VIEW_EXPORT DatasetController
│ │ │ +
191 : public QObject,
│ │ │ +
192 public Embeddable
│ │ │ +
193 {
│ │ │ +
194 Q_OBJECT
│ │ │ +
195
│ │ │ +
196 friend class DatasetControl;
│ │ │
197
│ │ │ -
│ │ │ -
201 virtual bool operator *= (const Vertex&) const
│ │ │ -
202 ;
│ │ │ -
203
│ │ │ -
│ │ │ -
208 Face* has(Face* face) const
│ │ │ -
209 ;
│ │ │ +
198 public:
│ │ │ +
199
│ │ │ +
200 BALL_EMBEDDABLE(DatasetController,Embeddable)
│ │ │ +
201
│ │ │ +
202
│ │ │ +
203 DatasetController();
│ │ │ +
204
│ │ │ +
206 DatasetController(DatasetController& dc);
│ │ │ +
207
│ │ │ +
209 virtual ~DatasetController();
│ │ │
210
│ │ │ -
│ │ │ -
215 Edge* has(Edge* edge) const
│ │ │ -
216 ;
│ │ │ -
217
│ │ │ -
│ │ │ -
220 bool hasEdges() const
│ │ │ -
221 ;
│ │ │ -
222
│ │ │ -
│ │ │ -
225 bool hasFaces() const
│ │ │ -
226 ;
│ │ │ -
227
│ │ │ +
212 void setDatasetControl(DatasetControl* dc) { control_ = dc;}
│ │ │ +
213
│ │ │ +
215 DatasetControl* getDatasetControl() { return control_;}
│ │ │ +
216
│ │ │ +
225 virtual bool handle(DatasetMessage* msg);
│ │ │ +
226
│ │ │ +
228 virtual bool insertDataset(Dataset* set);
│ │ │
229
│ │ │ +
231 virtual bool deleteDataset(Dataset* set);
│ │ │
232
│ │ │ -
│ │ │ -
233 EdgeIterator beginEdge()
│ │ │ -
234 ;
│ │ │ -
│ │ │ -
235 ConstEdgeIterator beginEdge() const
│ │ │ -
236 ;
│ │ │ -
│ │ │ -
237 EdgeIterator endEdge()
│ │ │ -
238 ;
│ │ │ -
│ │ │ -
239 ConstEdgeIterator endEdge() const
│ │ │ -
240 ;
│ │ │ -
│ │ │ -
241 FaceIterator beginFace()
│ │ │ -
242 ;
│ │ │ -
│ │ │ -
243 ConstFaceIterator beginFace() const
│ │ │ -
244 ;
│ │ │ -
│ │ │ -
245 FaceIterator endFace()
│ │ │ -
246 ;
│ │ │ -
│ │ │ -
247 ConstFaceIterator endFace() const
│ │ │ -
248 ;
│ │ │ -
249
│ │ │ -
251
│ │ │ -
252 protected:
│ │ │ -
253
│ │ │ -
254 /*_ @name Attributes
│ │ │ -
255 */
│ │ │ -
257
│ │ │ -
258 /*_ The RSEdges the RSVetex belongs to
│ │ │ -
259 */
│ │ │ -
260 HashSet<Edge*> edges_;
│ │ │ -
261 /*_ The RSFaces the RSVetex belongs to
│ │ │ -
262 */
│ │ │ -
263 HashSet<Face*> faces_;
│ │ │ -
264 /*_ The index of the GraphVertex
│ │ │ -
265 */
│ │ │ -
266 Index index_;
│ │ │ -
267
│ │ │ +
237 virtual bool createMenuEntries();
│ │ │ +
238
│ │ │ +
243 virtual QMenu* buildContextMenu(QTreeWidgetItem* item);
│ │ │ +
244
│ │ │ +
246 vector<Dataset*> getDatasets();
│ │ │ +
247
│ │ │ +
249 vector<Dataset*> getSelectedDatasets();
│ │ │ +
250
│ │ │ +
254 Dataset* getSelectedDataset();
│ │ │ +
255
│ │ │ +
258 bool hasDataset(Dataset* set);
│ │ │ +
259
│ │ │ +
261 bool hasItem(QTreeWidgetItem* item);
│ │ │ +
262
│ │ │ +
264 Dataset* getDataset(QTreeWidgetItem* item);
│ │ │ +
265
│ │ │ +
268 String getType() { return type_;}
│ │ │
269
│ │ │ -
270 };
│ │ │ -
271
│ │ │ -
272
│ │ │ -
273
│ │ │ -
274 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
275 GraphVertex<Vertex,Edge,Face>::GraphVertex()
│ │ │ -
276
│ │ │ -
277 : edges_(),
│ │ │ -
278 faces_(),
│ │ │ -
279 index_(-1)
│ │ │ -
280 {
│ │ │ -
281 }
│ │ │ -
│ │ │ -
282
│ │ │ -
283
│ │ │ -
284 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
285 GraphVertex<Vertex,Edge,Face>::GraphVertex
│ │ │ -
286 (const GraphVertex<Vertex,Edge,Face>& vertex, bool deep)
│ │ │ -
287
│ │ │ -
288 : edges_(),
│ │ │ -
289 faces_(),
│ │ │ -
290 index_(vertex.index_)
│ │ │ -
291 {
│ │ │ -
292 if (deep)
│ │ │ -
293 {
│ │ │ -
294 edges_ = vertex.edges_;
│ │ │ -
295 faces_ = vertex.faces_;
│ │ │ -
296 }
│ │ │ -
297 }
│ │ │ -
│ │ │ +
276 virtual void checkMenu(MainControl& mc);
│ │ │ +
277
│ │ │ +
283 vector<String> getSupportedFileFormats() { return file_formats_;}
│ │ │ +
284
│ │ │ +
285 public Q_SLOTS:
│ │ │ +
286
│ │ │ +
288 virtual bool write();
│ │ │ +
289
│ │ │ +
294 bool open();
│ │ │ +
295
│ │ │ +
297 virtual bool deleteDatasets();
│ │ │
298
│ │ │ -
299
│ │ │ -
300 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
301 GraphVertex<Vertex,Edge,Face>::~GraphVertex()
│ │ │ -
302
│ │ │ -
303 {
│ │ │ -
304 }
│ │ │ -
│ │ │ -
305
│ │ │ -
306
│ │ │ -
307 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
308 void GraphVertex<Vertex,Edge,Face>::set
│ │ │ -
309 (const GraphVertex<Vertex,Edge,Face>& vertex, bool deep)
│ │ │ -
310
│ │ │ -
311 {
│ │ │ -
312 if (this != &vertex)
│ │ │ -
313 {
│ │ │ -
314 if (deep)
│ │ │ -
315 {
│ │ │ -
316 edges_ = vertex.edges_;
│ │ │ -
317 faces_ = vertex.faces_;
│ │ │ -
318 }
│ │ │ -
319 index_ = vertex.index_;
│ │ │ -
320 }
│ │ │ -
321 }
│ │ │ -
│ │ │ -
322
│ │ │ -
323
│ │ │ -
324 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
325 GraphVertex<Vertex,Edge,Face>& GraphVertex<Vertex,Edge,Face>::operator =
│ │ │ -
326 (const GraphVertex<Vertex,Edge,Face>& vertex)
│ │ │ -
327
│ │ │ -
328 {
│ │ │ -
329 if (this != &vertex)
│ │ │ -
330 {
│ │ │ -
331 edges_ = vertex.edges_;
│ │ │ -
332 faces_ = vertex.faces_;
│ │ │ -
333 index_ = vertex.index_;
│ │ │ -
334 }
│ │ │ -
335 return *this;
│ │ │ -
336 }
│ │ │ -
│ │ │ -
337
│ │ │ -
338
│ │ │ -
339 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
340 void GraphVertex<Vertex,Edge,Face>::insert(Edge* edge)
│ │ │ -
341
│ │ │ -
342 {
│ │ │ -
343 edges_.insert(edge);
│ │ │ -
344 }
│ │ │ -
│ │ │ -
345
│ │ │ -
346
│ │ │ -
347 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
348 void GraphVertex<Vertex,Edge,Face>::insert(Face* face)
│ │ │ -
349
│ │ │ -
350 {
│ │ │ -
351 faces_.insert(face);
│ │ │ -
352 }
│ │ │ -
│ │ │ -
353
│ │ │ -
354
│ │ │ -
355 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
356 void GraphVertex<Vertex,Edge,Face>::remove(Edge* edge)
│ │ │ -
357
│ │ │ -
358 {
│ │ │ -
359 edges_.erase(edge);
│ │ │ -
360 }
│ │ │ -
│ │ │ -
361
│ │ │ -
362
│ │ │ -
363 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
364 void GraphVertex<Vertex,Edge,Face>::remove(Face* face)
│ │ │ -
365
│ │ │ -
366 {
│ │ │ -
367 faces_.erase(face);
│ │ │ -
368 }
│ │ │ -
│ │ │ -
369
│ │ │ -
370
│ │ │ -
371 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
372 Position GraphVertex<Vertex,Edge,Face>::numberOfEdges() const
│ │ │ -
373
│ │ │ -
374 {
│ │ │ -
375 return edges_.size();
│ │ │ -
376 }
│ │ │ -
│ │ │ -
377
│ │ │ -
378
│ │ │ -
379 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
380 Position GraphVertex<Vertex,Edge,Face>::numberOfFaces() const
│ │ │ -
381
│ │ │ -
382 {
│ │ │ -
383 return faces_.size();
│ │ │ -
384 }
│ │ │ -
│ │ │ -
385
│ │ │ -
386
│ │ │ -
387 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
388 void GraphVertex<Vertex,Edge,Face>::setIndex(Index index)
│ │ │ -
389
│ │ │ -
390 {
│ │ │ -
391 index_ = index;
│ │ │ -
392 }
│ │ │ -
│ │ │ -
393
│ │ │ -
394
│ │ │ -
395 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
396 Index GraphVertex<Vertex,Edge,Face>::getIndex() const
│ │ │ -
397
│ │ │ -
398 {
│ │ │ -
399 return index_;
│ │ │ -
400 }
│ │ │ -
│ │ │ -
401
│ │ │ -
402
│ │ │ -
403 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
404 bool GraphVertex<Vertex,Edge,Face>::substitute(Vertex* vertex)
│ │ │ -
405
│ │ │ -
406 {
│ │ │ -
407 if (*this *= *vertex)
│ │ │ -
408 {
│ │ │ -
409 typename HashSet<Edge*>::Iterator e;
│ │ │ -
410 for (e = edges_.begin(); e != edges_.end(); e++)
│ │ │ -
411 {
│ │ │ -
412 (*e)->substitute((Vertex*)this,vertex);
│ │ │ -
413 }
│ │ │ -
414 typename HashSet<Face*>::Iterator f;
│ │ │ -
415 for (f = faces_.begin(); f != faces_.end(); f++)
│ │ │ -
416 {
│ │ │ -
417 (*f)->substitute((Vertex*)this,vertex);
│ │ │ -
418 }
│ │ │ -
419 return true;
│ │ │ -
420 }
│ │ │ -
421 return false;
│ │ │ -
422 }
│ │ │ -
│ │ │ -
423
│ │ │ -
424
│ │ │ -
425 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
426 bool GraphVertex<Vertex,Edge,Face>::join(const Vertex& vertex)
│ │ │ -
427
│ │ │ -
428 {
│ │ │ -
429 if (*this *= vertex)
│ │ │ -
430 {
│ │ │ -
431 typename HashSet<Edge*>::ConstIterator e;
│ │ │ -
432 for (e = vertex.edges_.begin(); e != vertex.edges_.end(); e++)
│ │ │ -
433 {
│ │ │ -
434 edges_.insert(*e);
│ │ │ -
435 }
│ │ │ -
436 typename HashSet<Face*>::ConstIterator f;
│ │ │ -
437 for (f = vertex.faces_.begin(); f != vertex.faces_.end(); f++)
│ │ │ -
438 {
│ │ │ -
439 faces_.insert(*f);
│ │ │ -
440 }
│ │ │ -
441 return true;
│ │ │ -
442 }
│ │ │ -
443 else
│ │ │ -
444 {
│ │ │ -
445 return false;
│ │ │ -
446 }
│ │ │ -
447 }
│ │ │ -
│ │ │ -
448
│ │ │ -
449
│ │ │ -
450 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
451 Face* GraphVertex<Vertex,Edge,Face>::has(Face* face) const
│ │ │ -
452
│ │ │ -
453 {
│ │ │ -
454 typename HashSet<Face*>::ConstIterator f;
│ │ │ -
455 for (f = faces_.begin(); f != faces_.end(); f++)
│ │ │ -
456 {
│ │ │ -
457 if (*(*f) == *face)
│ │ │ -
458 {
│ │ │ -
459 return *f;
│ │ │ -
460 }
│ │ │ -
461 }
│ │ │ -
462 return NULL;
│ │ │ -
463 }
│ │ │ -
│ │ │ -
464
│ │ │ -
465
│ │ │ -
466 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
467 Edge* GraphVertex<Vertex,Edge,Face>::has(Edge* edge) const
│ │ │ -
468
│ │ │ -
469 {
│ │ │ -
470 typename HashSet<Edge*>::ConstIterator e;
│ │ │ -
471 for (e = edges_.begin(); e != edges_.end(); e++)
│ │ │ -
472 {
│ │ │ -
473 if (*(*e) == *edge)
│ │ │ -
474 {
│ │ │ -
475 return *e;
│ │ │ -
476 }
│ │ │ -
477 }
│ │ │ -
478 return NULL;
│ │ │ -
479 }
│ │ │ -
│ │ │ -
480
│ │ │ -
481
│ │ │ -
482 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
483 bool GraphVertex<Vertex,Edge,Face>::hasEdges() const
│ │ │ -
484
│ │ │ -
485 {
│ │ │ -
486 return !edges_.isEmpty();
│ │ │ -
487 }
│ │ │ -
│ │ │ -
488
│ │ │ -
489
│ │ │ -
490 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
491 bool GraphVertex<Vertex,Edge,Face>::hasFaces() const
│ │ │ -
492
│ │ │ -
493 {
│ │ │ -
494 return !faces_.isEmpty();
│ │ │ -
495 }
│ │ │ -
│ │ │ -
496
│ │ │ -
497
│ │ │ -
498 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
499 typename GraphVertex<Vertex,Edge,Face>::EdgeIterator
│ │ │ -
│ │ │ -
500 GraphVertex<Vertex,Edge,Face>::beginEdge()
│ │ │ -
501
│ │ │ -
502 {
│ │ │ -
503 return edges_.begin();
│ │ │ -
504 }
│ │ │ -
│ │ │ -
505
│ │ │ -
506
│ │ │ -
507 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
508 typename GraphVertex<Vertex,Edge,Face>::ConstEdgeIterator
│ │ │ -
│ │ │ -
509 GraphVertex<Vertex,Edge,Face>::beginEdge() const
│ │ │ -
510
│ │ │ -
511 {
│ │ │ -
512 return edges_.begin();
│ │ │ -
513 }
│ │ │ -
│ │ │ -
514
│ │ │ -
515
│ │ │ -
516 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
517 typename GraphVertex<Vertex,Edge,Face>::EdgeIterator
│ │ │ -
│ │ │ -
518 GraphVertex<Vertex,Edge,Face>::endEdge()
│ │ │ -
519
│ │ │ -
520 {
│ │ │ -
521 return edges_.end();
│ │ │ -
522 }
│ │ │ -
│ │ │ -
523
│ │ │ -
524
│ │ │ -
525 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
526 typename GraphVertex<Vertex,Edge,Face>::ConstEdgeIterator
│ │ │ -
│ │ │ -
527 GraphVertex<Vertex,Edge,Face>::endEdge() const
│ │ │ -
528
│ │ │ -
529 {
│ │ │ -
530 return edges_.end();
│ │ │ -
531 }
│ │ │ -
│ │ │ -
532
│ │ │ -
533
│ │ │ -
534 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
535 typename GraphVertex<Vertex,Edge,Face>::FaceIterator
│ │ │ -
│ │ │ -
536 GraphVertex<Vertex,Edge,Face>::beginFace()
│ │ │ -
537
│ │ │ -
538 {
│ │ │ -
539 return faces_.begin();
│ │ │ -
540 }
│ │ │ -
│ │ │ -
541
│ │ │ -
542
│ │ │ -
543 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
544 typename GraphVertex<Vertex,Edge,Face>::ConstFaceIterator
│ │ │ -
│ │ │ -
545 GraphVertex<Vertex,Edge,Face>::beginFace() const
│ │ │ -
546
│ │ │ -
547 {
│ │ │ -
548 return faces_.begin();
│ │ │ -
549 }
│ │ │ -
│ │ │ -
550
│ │ │ -
551
│ │ │ -
552 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
553 typename GraphVertex<Vertex,Edge,Face>::FaceIterator
│ │ │ -
│ │ │ -
554 GraphVertex<Vertex,Edge,Face>::endFace()
│ │ │ -
555
│ │ │ -
556 {
│ │ │ -
557 return faces_.end();
│ │ │ -
558 }
│ │ │ -
│ │ │ -
559
│ │ │ -
560
│ │ │ -
561 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
562 typename GraphVertex<Vertex,Edge,Face>::ConstFaceIterator
│ │ │ -
│ │ │ -
563 GraphVertex<Vertex,Edge,Face>::endFace() const
│ │ │ -
564
│ │ │ -
565 {
│ │ │ -
566 return faces_.end();
│ │ │ -
567 }
│ │ │ -
│ │ │ -
│ │ │ -
568
│ │ │ -
569
│ │ │ -
570 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
571 bool GraphVertex<Vertex,Edge,Face>::operator == (const Vertex&) const
│ │ │ -
572
│ │ │ -
573 {
│ │ │ -
574 return true;
│ │ │ -
575 }
│ │ │ -
│ │ │ -
576
│ │ │ -
577
│ │ │ -
578 template <typename Vertex, typename Edge, typename Face>
│ │ │ -
│ │ │ -
579 bool GraphVertex<Vertex,Edge,Face>::operator != (const Vertex&) const
│ │ │ -
580
│ │ │ -
581 {
│ │ │ -
582 return false;
│ │ │ -
583 }
│ │ │ -
│ │ │ -
584
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585
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586 template <typename Vertex, typename Edge, typename Face>
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587 bool GraphVertex<Vertex,Edge,Face>::operator *= (const Vertex&) const
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588
│ │ │ -
589 {
│ │ │ -
590 return true;
│ │ │ -
591 }
│ │ │ -
592
│ │ │ -
593} // namespace BALL
│ │ │ -
594
│ │ │ -
595#endif // BALL_STRUCTURE_GRAPHVERTEX_H
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BALL_CREATE
#define BALL_CREATE(name)
Definition create.h:62
│ │ │ - │ │ │ - │ │ │ -
BALL::ForwardIterator::begin
static ForwardIterator begin(const Container &container)
Definition forwardIterator.h:307
│ │ │ -
BALL::ForwardIterator::end
static ForwardIterator end(const Container &container)
Definition forwardIterator.h:317
│ │ │ - │ │ │ -
BALL::HashSet::begin
Iterator begin()
Definition hashSet.h:536
│ │ │ -
BALL::HashSet::insert
std::pair< Iterator, bool > insert(const ValueType &item)
Definition hashSet.h:896
│ │ │ -
BALL::HashSet::end
Iterator end()
Definition hashSet.h:543
│ │ │ -
BALL::HashSet::ConstIterator
ConstForwardIterator< HashSet< Key >, ValueType, PointerType, IteratorTraits > ConstIterator
Definition hashSet.h:283
│ │ │ - │ │ │ -
BALL::GraphVertex::set
void set(const GraphVertex< Vertex, Edge, Face > &vertex, bool deep=false)
Definition graphVertex.h:309
│ │ │ -
BALL::GraphVertex::operator!=
virtual bool operator!=(const Vertex &) const
Definition graphVertex.h:579
│ │ │ -
BALL::GraphVertex::EdgeIterator
HashSet< Edge * >::Iterator EdgeIterator
Definition graphVertex.h:53
│ │ │ -
BALL::GraphVertex::getIndex
Index getIndex() const
Definition graphVertex.h:396
│ │ │ -
BALL::GraphVertex::substitute
bool substitute(Vertex *vertex)
Definition graphVertex.h:404
│ │ │ - │ │ │ -
BALL::GraphVertex::setIndex
void setIndex(Index index)
Definition graphVertex.h:388
│ │ │ -
BALL::GraphVertex::endEdge
EdgeIterator endEdge()
Definition graphVertex.h:518
│ │ │ -
BALL::GraphVertex::beginFace
FaceIterator beginFace()
Definition graphVertex.h:536
│ │ │ -
BALL::GraphVertex::beginEdge
EdgeIterator beginEdge()
Definition graphVertex.h:500
│ │ │ -
BALL::GraphVertex::ConstEdgeIterator
HashSet< Edge * >::ConstIterator ConstEdgeIterator
Definition graphVertex.h:54
│ │ │ - │ │ │ -
BALL::GraphVertex::insert
void insert(Edge *edge)
Definition graphVertex.h:340
│ │ │ -
BALL::GraphVertex::edges_
HashSet< Edge * > edges_
Definition graphVertex.h:260
│ │ │ -
BALL::GraphVertex::operator==
virtual bool operator==(const Vertex &) const
Definition graphVertex.h:571
│ │ │ -
BALL::GraphVertex::FaceIterator
HashSet< Face * >::Iterator FaceIterator
Definition graphVertex.h:55
│ │ │ -
BALL::GraphVertex::ConstFaceIterator
HashSet< Face * >::ConstIterator ConstFaceIterator
Definition graphVertex.h:56
│ │ │ -
BALL::GraphVertex::hasEdges
bool hasEdges() const
Definition graphVertex.h:483
│ │ │ -
BALL::GraphVertex::faces_
HashSet< Face * > faces_
Definition graphVertex.h:263
│ │ │ -
BALL::GraphVertex::operator*=
virtual bool operator*=(const Vertex &) const
Definition graphVertex.h:587
│ │ │ -
BALL::GraphVertex::join
bool join(const Vertex &vertex)
Definition graphVertex.h:426
│ │ │ -
BALL::GraphVertex::has
Face * has(Face *face) const
Definition graphVertex.h:451
│ │ │ -
BALL::GraphVertex::numberOfEdges
Position numberOfEdges() const
Definition graphVertex.h:372
│ │ │ -
BALL::GraphVertex::remove
void remove(Edge *edge)
Definition graphVertex.h:356
│ │ │ -
BALL::GraphVertex::numberOfFaces
Position numberOfFaces() const
Definition graphVertex.h:380
│ │ │ -
BALL::GraphVertex::hasFaces
bool hasFaces() const
Definition graphVertex.h:491
│ │ │ -
BALL::GraphVertex::endFace
FaceIterator endFace()
Definition graphVertex.h:554
│ │ │ -
BALL::GraphVertex::~GraphVertex
virtual ~GraphVertex()
Definition graphVertex.h:301
│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ +
300 virtual bool deleteDataset();
│ │ │ +
301
│ │ │ +
302 protected:
│ │ │ +
303
│ │ │ +
305 void setStatusbarText(const String& text, bool important = false);
│ │ │ +
306 void setStatusbarText(const QString& text, bool important = false);
│ │ │ +
307
│ │ │ +
308 virtual bool write(Dataset* /*set*/, String /*filetype*/, String /*filename*/);
│ │ │ +
309 virtual Dataset* open(String /*filetype*/, String /*filename*/);
│ │ │ +
310
│ │ │ +
311 String getFileTypes_();
│ │ │ +
312 String getNameFromFileName_(String filename);
│ │ │ +
313 QAction* insertMenuEntry_(Position pid, const QString& name, const char* slot,
│ │ │ +
314 const String& description = "", QKeySequence accel = QKeySequence(),
│ │ │ +
315 const QString& menu_hint = "",
│ │ │ +
316 UIOperationMode::OperationMode initial_mode = UIOperationMode::MODE_ALL);
│ │ │ +
317
│ │ │ +
320 virtual void deleteDataset_(Dataset*) {};
│ │ │ +
321
│ │ │ +
322 String type_;
│ │ │ +
323 vector<String> file_formats_;
│ │ │ +
324 DatasetControl* control_;
│ │ │ +
325 vector<QAction*> actions_;
│ │ │ +
326 HashSet<QAction*> actions_for_one_set_;
│ │ │ +
327 HashMap<QTreeWidgetItem*, Dataset*> item_to_dataset_;
│ │ │ +
328 HashMap<Dataset*, QTreeWidgetItem*> dataset_to_item_;
│ │ │ +
329 };
│ │ │ +
│ │ │ +
330
│ │ │ +
331 } // namespace VIEW
│ │ │ +
332} // namespace BALL
│ │ │ +
333
│ │ │ +
334#endif // BALL_VIEW_DATATYPE_DATASET_H
│ │ │ + │ │ │ + │ │ │ +
BALL_EMBEDDABLE
#define BALL_EMBEDDABLE(TYPE, BASE)
Definition embeddable.h:31
│ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
BALL::HashMap
HashMap class based on the STL map (containing serveral convenience functions)
Definition hashMap.h:74
│ │ │ + │ │ │ + │ │ │ + │ │ │ +
BALL::VIEW::Dataset::getComposite
Composite * getComposite() const
Definition dataset.h:114
│ │ │ +
BALL::VIEW::Dataset::composite_
Composite * composite_
Definition dataset.h:123
│ │ │ + │ │ │ +
BALL::VIEW::Dataset::setName
void setName(String name)
Definition dataset.h:99
│ │ │ + │ │ │ +
BALL::VIEW::Dataset::setType
void setType(String type)
Definition dataset.h:105
│ │ │ + │ │ │ +
BALL::VIEW::Dataset::setComposite
void setComposite(Composite *composite)
Definition dataset.h:111
│ │ │ +
BALL::VIEW::Dataset::Dataset
Dataset(const Dataset &dataset)
│ │ │ +
BALL::VIEW::Dataset::getType
String getType() const
Definition dataset.h:108
│ │ │ +
BALL::VIEW::Dataset::getName
String getName() const
Definition dataset.h:102
│ │ │ + │ │ │ +
BALL::VIEW::Dataset::dump
void dump(std::ostream &s, Size depth) const
│ │ │ +
BALL::VIEW::Dataset::clear
virtual void clear()
│ │ │ +
BALL::VIEW::Dataset::set
void set(const Dataset &v)
│ │ │ + │ │ │ +
BALL::VIEW::DatasetController::deleteDatasets
virtual bool deleteDatasets()
Delete all Datasets.
│ │ │ +
BALL::VIEW::DatasetController::getNameFromFileName_
String getNameFromFileName_(String filename)
│ │ │ +
BALL::VIEW::DatasetController::hasItem
bool hasItem(QTreeWidgetItem *item)
Test if a given QTreeWidgetItem corresponds to a registered Dataset.
│ │ │ +
BALL::VIEW::DatasetController::control_
DatasetControl * control_
Definition dataset.h:324
│ │ │ +
BALL::VIEW::DatasetController::setStatusbarText
void setStatusbarText(const String &text, bool important=false)
│ │ │ +
BALL::VIEW::DatasetController::getDatasets
vector< Dataset * > getDatasets()
Get all Datasets of this type in the DatasetControl.
│ │ │ +
BALL::VIEW::DatasetController::getDataset
Dataset * getDataset(QTreeWidgetItem *item)
Get the Dataset for a QTreeWidgetItem.
│ │ │ +
BALL::VIEW::DatasetController::insertMenuEntry_
QAction * insertMenuEntry_(Position pid, const QString &name, const char *slot, const String &description="", QKeySequence accel=QKeySequence(), const QString &menu_hint="", UIOperationMode::OperationMode initial_mode=UIOperationMode::MODE_ALL)
│ │ │ +
BALL::VIEW::DatasetController::getDatasetControl
DatasetControl * getDatasetControl()
Definition dataset.h:215
│ │ │ +
BALL::VIEW::DatasetController::setStatusbarText
void setStatusbarText(const QString &text, bool important=false)
│ │ │ +
BALL::VIEW::DatasetController::checkMenu
virtual void checkMenu(MainControl &mc)
│ │ │ + │ │ │ + │ │ │ +
BALL::VIEW::DatasetController::write
virtual bool write(Dataset *, String, String)
│ │ │ + │ │ │ +
BALL::VIEW::DatasetController::buildContextMenu
virtual QMenu * buildContextMenu(QTreeWidgetItem *item)
│ │ │ +
BALL::VIEW::DatasetController::getSelectedDatasets
vector< Dataset * > getSelectedDatasets()
Get all selected Datasets of this type in the DatasetControl.
│ │ │ +
BALL::VIEW::DatasetController::item_to_dataset_
HashMap< QTreeWidgetItem *, Dataset * > item_to_dataset_
Definition dataset.h:327
│ │ │ +
BALL::VIEW::DatasetController::dataset_to_item_
HashMap< Dataset *, QTreeWidgetItem * > dataset_to_item_
Definition dataset.h:328
│ │ │ +
BALL::VIEW::DatasetController::write
virtual bool write()
Show a file dialog for writing the selected Dataset.
│ │ │ +
BALL::VIEW::DatasetController::getSupportedFileFormats
vector< String > getSupportedFileFormats()
Definition dataset.h:283
│ │ │ +
BALL::VIEW::DatasetController::deleteDataset
virtual bool deleteDataset()
Delete the currently highlighted Dataset.
│ │ │ +
BALL::VIEW::DatasetController::actions_
vector< QAction * > actions_
Definition dataset.h:325
│ │ │ +
BALL::VIEW::DatasetController::deleteDataset
virtual bool deleteDataset(Dataset *set)
│ │ │ +
BALL::VIEW::DatasetController::insertDataset
virtual bool insertDataset(Dataset *set)
│ │ │ + │ │ │ +
BALL::VIEW::DatasetController::open
virtual Dataset * open(String, String)
│ │ │ +
BALL::VIEW::DatasetController::deleteDataset_
virtual void deleteDataset_(Dataset *)
Definition dataset.h:320
│ │ │ +
BALL::VIEW::DatasetController::handle
virtual bool handle(DatasetMessage *msg)
│ │ │ +
BALL::VIEW::DatasetController::createMenuEntries
virtual bool createMenuEntries()
│ │ │ +
BALL::VIEW::DatasetController::file_formats_
vector< String > file_formats_
Definition dataset.h:323
│ │ │ + │ │ │ +
BALL::VIEW::DatasetController::hasDataset
bool hasDataset(Dataset *set)
│ │ │ +
BALL::VIEW::DatasetController::actions_for_one_set_
HashSet< QAction * > actions_for_one_set_
Definition dataset.h:326
│ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │ + │ │ │ + │ │ │ +
BALL_VIEW_EXPORT
#define BALL_VIEW_EXPORT
Definition COMMON/global.h:52
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ │
│ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,619 +1,380 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ -graphVertex.h │ │ │ │ + * _V_I_E_W │ │ │ │ + * _D_A_T_A_T_Y_P_E │ │ │ │ +dataset.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_STRUCTURE_GRAPHVERTEX_H │ │ │ │ -6#define BALL_STRUCTURE_GRAPHVERTEX_H │ │ │ │ +5#ifndef BALL_VIEW_DATATYPE_DATASET_H │ │ │ │ +6#define BALL_VIEW_DATATYPE_DATASET_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_COMMON_H │ │ │ │ -9# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +8#ifndef BALL_DATATYPE_STRING_H │ │ │ │ +9# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_DATATYPE_HASHSET_H │ │ │ │ -13# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_S_e_t_._h> │ │ │ │ +12#ifndef BALL_DATATYPE_HASHMAP_H │ │ │ │ +13# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16namespace _B_A_L_L │ │ │ │ -17{ │ │ │ │ -18 │ │ │ │ -19 template │ │ │ │ -20 class GraphEdge; │ │ │ │ -21 │ │ │ │ -22 template │ │ │ │ -23 class GraphFace; │ │ │ │ -24 │ │ │ │ -25 template │ │ │ │ -26 class GraphTriangle; │ │ │ │ +16#ifndef BALL_DATATYPE_HASHSET_H │ │ │ │ +17# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_S_e_t_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20#ifndef BALL_CONCEPT_EMBEDDABLE_H │ │ │ │ +21# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_e_m_b_e_d_d_a_b_l_e_._h> │ │ │ │ +22#endif │ │ │ │ +23 │ │ │ │ +24#ifndef BALL_VIEW_KERNEL_UIOPERATIONMODE_H │ │ │ │ +25# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h> │ │ │ │ +26#endif │ │ │ │ 27 │ │ │ │ -31 template │ │ │ │ -_3_2 class _G_r_a_p_h_V_e_r_t_e_x │ │ │ │ -33 { │ │ │ │ -34 public: │ │ │ │ -35 │ │ │ │ -43 friend class _G_r_a_p_h_E_d_g_e<_V_e_r_t_e_x,Edge,Face>; │ │ │ │ -44 friend class _G_r_a_p_h_F_a_c_e<_V_e_r_t_e_x,Edge,Face>; │ │ │ │ -45 friend class _G_r_a_p_h_T_r_i_a_n_g_l_e<_V_e_r_t_e_x,Edge,Face>; │ │ │ │ -46 │ │ │ │ -47 _B_A_L_L___C_R_E_A_T_E(_G_r_a_p_h_V_e_r_t_e_x) │ │ │ │ -48 │ │ │ │ -49 │ │ │ │ -52 │ │ │ │ -_5_3 typedef typename _H_a_s_h_S_e_t::Iterator _E_d_g_e_I_t_e_r_a_t_o_r; │ │ │ │ -_5_4 typedef typename _H_a_s_h_S_e_t::ConstIterator _C_o_n_s_t_E_d_g_e_I_t_e_r_a_t_o_r; │ │ │ │ -_5_5 typedef typename _H_a_s_h_S_e_t::Iterator _F_a_c_e_I_t_e_r_a_t_o_r; │ │ │ │ -_5_6 typedef typename _H_a_s_h_S_e_t::ConstIterator _C_o_n_s_t_F_a_c_e_I_t_e_r_a_t_o_r; │ │ │ │ -57 │ │ │ │ -59 │ │ │ │ -62 │ │ │ │ -_6_6 _G_r_a_p_h_V_e_r_t_e_x() │ │ │ │ -67 ; │ │ │ │ -68 │ │ │ │ -_7_6 _G_r_a_p_h_V_e_r_t_e_x(const _G_r_a_p_h_V_e_r_t_e_x<_V_e_r_t_e_x,Edge,Face>& vertex, bool deep = false) │ │ │ │ -77 ; │ │ │ │ -78 │ │ │ │ -_8_2 virtual ~_G_r_a_p_h_V_e_r_t_e_x() │ │ │ │ -83 ; │ │ │ │ +28#include │ │ │ │ +29#include │ │ │ │ +30 │ │ │ │ +31namespace _B_A_L_L │ │ │ │ +32{ │ │ │ │ +33 class Composite; │ │ │ │ +34 │ │ │ │ +35 namespace VIEW │ │ │ │ +36 { │ │ │ │ +37 class DatasetControl; │ │ │ │ +38 class DatasetMessage; │ │ │ │ +39 class MainControl; │ │ │ │ +40 class DataMessage; │ │ │ │ +41 │ │ │ │ +_6_0 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _D_a_t_a_s_e_t │ │ │ │ +61 { │ │ │ │ +62 public: │ │ │ │ +63 │ │ │ │ +67 │ │ │ │ +_7_0 _D_a_t_a_s_e_t(); │ │ │ │ +71 │ │ │ │ +_7_4 _D_a_t_a_s_e_t(const _D_a_t_a_s_e_t& dataset); │ │ │ │ +75 │ │ │ │ +_7_8 virtual _~_D_a_t_a_s_e_t(); │ │ │ │ +79 │ │ │ │ +_8_2 virtual void _c_l_e_a_r(); │ │ │ │ +83 │ │ │ │ 85 │ │ │ │ -89 │ │ │ │ -_9_7 void set(const _G_r_a_p_h_V_e_r_t_e_x<_V_e_r_t_e_x,Edge,Face>& vertex, bool deep = false) │ │ │ │ -98 ; │ │ │ │ -99 │ │ │ │ -_1_0_5 _G_r_a_p_h_V_e_r_t_e_x<_V_e_r_t_e_x,Edge,Face>& operator = │ │ │ │ -106 (const _G_r_a_p_h_V_e_r_t_e_x<_V_e_r_t_e_x,Edge,Face>& vertex) │ │ │ │ -107 ; │ │ │ │ -108 │ │ │ │ -110 │ │ │ │ -113 │ │ │ │ -_1_1_7 void _i_n_s_e_r_t(Edge* edge) │ │ │ │ -118 ; │ │ │ │ -119 │ │ │ │ -_1_2_3 void _i_n_s_e_r_t(Face* face) │ │ │ │ -124 ; │ │ │ │ -125 │ │ │ │ -_1_2_9 void _r_e_m_o_v_e(Edge* edge) │ │ │ │ -130 ; │ │ │ │ -131 │ │ │ │ -_1_3_5 void _r_e_m_o_v_e(Face* face) │ │ │ │ -136 ; │ │ │ │ -137 │ │ │ │ -_1_4_1 _P_o_s_i_t_i_o_n _n_u_m_b_e_r_O_f_E_d_g_e_s() const │ │ │ │ -142 ; │ │ │ │ -143 │ │ │ │ -_1_4_7 _P_o_s_i_t_i_o_n _n_u_m_b_e_r_O_f_F_a_c_e_s() const │ │ │ │ -148 ; │ │ │ │ -149 │ │ │ │ -_1_5_3 void _s_e_t_I_n_d_e_x(_I_n_d_e_x index) │ │ │ │ -154 ; │ │ │ │ -155 │ │ │ │ -_1_5_9 _I_n_d_e_x _g_e_t_I_n_d_e_x() const │ │ │ │ -160 ; │ │ │ │ -161 │ │ │ │ -_1_6_8 bool _j_o_i_n(const _V_e_r_t_e_x& vertex) │ │ │ │ -169 ; │ │ │ │ -170 │ │ │ │ -_1_7_7 bool _s_u_b_s_t_i_t_u_t_e(_V_e_r_t_e_x* vertex) │ │ │ │ -178 ; │ │ │ │ -179 │ │ │ │ -180 │ │ │ │ -182 │ │ │ │ -185 │ │ │ │ -_1_8_9 virtual bool operator == (const _V_e_r_t_e_x&) const │ │ │ │ -190 ; │ │ │ │ -191 │ │ │ │ -_1_9_5 virtual bool operator != (const _V_e_r_t_e_x&) const │ │ │ │ -196 ; │ │ │ │ +88 │ │ │ │ +_9_1 void _s_e_t(const _D_a_t_a_s_e_t& v); │ │ │ │ +92 │ │ │ │ +_9_6 const _D_a_t_a_s_e_t& operator = (const _D_a_t_a_s_e_t& v); │ │ │ │ +97 │ │ │ │ +_9_9 void _s_e_t_N_a_m_e(_S_t_r_i_n_g name) { name_ = name;} │ │ │ │ +100 │ │ │ │ +_1_0_2 _S_t_r_i_n_g _g_e_t_N_a_m_e() const { return name_;} │ │ │ │ +103 │ │ │ │ +_1_0_5 void _s_e_t_T_y_p_e(_S_t_r_i_n_g type) { type_ = type;} │ │ │ │ +106 │ │ │ │ +_1_0_8 _S_t_r_i_n_g _g_e_t_T_y_p_e() const { return type_;} │ │ │ │ +109 │ │ │ │ +_1_1_1 void _s_e_t_C_o_m_p_o_s_i_t_e(_C_o_m_p_o_s_i_t_e* composite) { composite_ = composite;} │ │ │ │ +112 │ │ │ │ +_1_1_4 _C_o_m_p_o_s_i_t_e* _g_e_t_C_o_m_p_o_s_i_t_e() const { return composite_;} │ │ │ │ +115 │ │ │ │ +_1_1_7 void _d_u_m_p(std::ostream& s, _S_i_z_e depth) const; │ │ │ │ +118 // │ │ │ │ +120 │ │ │ │ +121 protected: │ │ │ │ +122 │ │ │ │ +_1_2_3 _C_o_m_p_o_s_i_t_e* _c_o_m_p_o_s_i_t_e__; │ │ │ │ +_1_2_4 _S_t_r_i_n_g _n_a_m_e__; │ │ │ │ +_1_2_5 _S_t_r_i_n_g _t_y_p_e__; │ │ │ │ +126 }; │ │ │ │ +127 │ │ │ │ +128 │ │ │ │ +_1_3_1#define BALL_CREATE_DATASET(TYPE)\ │ │ │ │ +132 class BALL_VIEW_EXPORT TYPE##Dataset\ │ │ │ │ +133 : public Dataset\ │ │ │ │ +134 {\ │ │ │ │ +135 public :\ │ │ │ │ +136 \ │ │ │ │ +137 TYPE##Dataset(TYPE* data = 0)\ │ │ │ │ +138 : Dataset(),\ │ │ │ │ +139 data_(data)\ │ │ │ │ +140 {}\ │ │ │ │ +141 \ │ │ │ │ +142 TYPE##Dataset(const TYPE##Dataset& set)\ │ │ │ │ +143 : Dataset(set),\ │ │ │ │ +144 data_(set.data_)\ │ │ │ │ +145 {}\ │ │ │ │ +146 \ │ │ │ │ +147 TYPE* getData() { return data_;}\ │ │ │ │ +148 \ │ │ │ │ +149 void setData(TYPE* data) { data_ = data;}\ │ │ │ │ +150 \ │ │ │ │ +151 TYPE* data_;\ │ │ │ │ +152 }; │ │ │ │ +153 │ │ │ │ +154 │ │ │ │ +_1_9_0 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r │ │ │ │ +191 : public _Q_O_b_j_e_c_t, │ │ │ │ +192 public _E_m_b_e_d_d_a_b_l_e │ │ │ │ +193 { │ │ │ │ +194 Q_OBJECT │ │ │ │ +195 │ │ │ │ +_1_9_6 friend class _D_a_t_a_s_e_t_C_o_n_t_r_o_l; │ │ │ │ 197 │ │ │ │ -_2_0_1 virtual bool operator *= (const _V_e_r_t_e_x&) const │ │ │ │ -202 ; │ │ │ │ -203 │ │ │ │ -_2_0_8 Face* _h_a_s(Face* face) const │ │ │ │ -209 ; │ │ │ │ +198 public: │ │ │ │ +199 │ │ │ │ +200 _B_A_L_L___E_M_B_E_D_D_A_B_L_E(_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r,_E_m_b_e_d_d_a_b_l_e) │ │ │ │ +201 │ │ │ │ +202 │ │ │ │ +_2_0_3 _D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r(); │ │ │ │ +204 │ │ │ │ +_2_0_6 _D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r(_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r& dc); │ │ │ │ +207 │ │ │ │ +_2_0_9 virtual ~_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r(); │ │ │ │ 210 │ │ │ │ -_2_1_5 Edge* _h_a_s(Edge* edge) const │ │ │ │ -216 ; │ │ │ │ -217 │ │ │ │ -_2_2_0 bool _h_a_s_E_d_g_e_s() const │ │ │ │ -221 ; │ │ │ │ -222 │ │ │ │ -_2_2_5 bool _h_a_s_F_a_c_e_s() const │ │ │ │ -226 ; │ │ │ │ -227 │ │ │ │ +_2_1_2 void setDatasetControl(_D_a_t_a_s_e_t_C_o_n_t_r_o_l* dc) { control_ = dc;} │ │ │ │ +213 │ │ │ │ +_2_1_5 _D_a_t_a_s_e_t_C_o_n_t_r_o_l* _g_e_t_D_a_t_a_s_e_t_C_o_n_t_r_o_l() { return control_;} │ │ │ │ +216 │ │ │ │ +_2_2_5 virtual bool _h_a_n_d_l_e(_D_a_t_a_s_e_t_M_e_s_s_a_g_e* msg); │ │ │ │ +226 │ │ │ │ +_2_2_8 virtual bool _i_n_s_e_r_t_D_a_t_a_s_e_t(_D_a_t_a_s_e_t* set); │ │ │ │ 229 │ │ │ │ +_2_3_1 virtual bool _d_e_l_e_t_e_D_a_t_a_s_e_t(_D_a_t_a_s_e_t* set); │ │ │ │ 232 │ │ │ │ -_2_3_3 _E_d_g_e_I_t_e_r_a_t_o_r _b_e_g_i_n_E_d_g_e() │ │ │ │ -234 ; │ │ │ │ -_2_3_5 _C_o_n_s_t_E_d_g_e_I_t_e_r_a_t_o_r _b_e_g_i_n_E_d_g_e() const │ │ │ │ -236 ; │ │ │ │ -_2_3_7 _E_d_g_e_I_t_e_r_a_t_o_r _e_n_d_E_d_g_e() │ │ │ │ -238 ; │ │ │ │ -_2_3_9 _C_o_n_s_t_E_d_g_e_I_t_e_r_a_t_o_r _e_n_d_E_d_g_e() const │ │ │ │ -240 ; │ │ │ │ -_2_4_1 _F_a_c_e_I_t_e_r_a_t_o_r _b_e_g_i_n_F_a_c_e() │ │ │ │ -242 ; │ │ │ │ -_2_4_3 _C_o_n_s_t_F_a_c_e_I_t_e_r_a_t_o_r _b_e_g_i_n_F_a_c_e() const │ │ │ │ -244 ; │ │ │ │ -_2_4_5 _F_a_c_e_I_t_e_r_a_t_o_r _e_n_d_F_a_c_e() │ │ │ │ -246 ; │ │ │ │ -_2_4_7 _C_o_n_s_t_F_a_c_e_I_t_e_r_a_t_o_r _e_n_d_F_a_c_e() const │ │ │ │ -248 ; │ │ │ │ -249 │ │ │ │ -251 │ │ │ │ -252 protected: │ │ │ │ -253 │ │ │ │ -254 /*_ @name Attributes │ │ │ │ -255 */ │ │ │ │ -257 │ │ │ │ -258 /*_ The RSEdges the RSVetex belongs to │ │ │ │ -259 */ │ │ │ │ -_2_6_0 _H_a_s_h_S_e_t _e_d_g_e_s__; │ │ │ │ -261 /*_ The RSFaces the RSVetex belongs to │ │ │ │ -262 */ │ │ │ │ -_2_6_3 _H_a_s_h_S_e_t _f_a_c_e_s__; │ │ │ │ -264 /*_ The index of the GraphVertex │ │ │ │ -265 */ │ │ │ │ -_2_6_6 _I_n_d_e_x _i_n_d_e_x__; │ │ │ │ -267 │ │ │ │ +_2_3_7 virtual bool _c_r_e_a_t_e_M_e_n_u_E_n_t_r_i_e_s(); │ │ │ │ +238 │ │ │ │ +_2_4_3 virtual QMenu* _b_u_i_l_d_C_o_n_t_e_x_t_M_e_n_u(_Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m* item); │ │ │ │ +244 │ │ │ │ +_2_4_6 vector _g_e_t_D_a_t_a_s_e_t_s(); │ │ │ │ +247 │ │ │ │ +_2_4_9 vector _g_e_t_S_e_l_e_c_t_e_d_D_a_t_a_s_e_t_s(); │ │ │ │ +250 │ │ │ │ +_2_5_4 _D_a_t_a_s_e_t* _g_e_t_S_e_l_e_c_t_e_d_D_a_t_a_s_e_t(); │ │ │ │ +255 │ │ │ │ +_2_5_8 bool _h_a_s_D_a_t_a_s_e_t(_D_a_t_a_s_e_t* set); │ │ │ │ +259 │ │ │ │ +_2_6_1 bool _h_a_s_I_t_e_m(_Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m* item); │ │ │ │ +262 │ │ │ │ +_2_6_4 _D_a_t_a_s_e_t* _g_e_t_D_a_t_a_s_e_t(_Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m* item); │ │ │ │ +265 │ │ │ │ +_2_6_8 _S_t_r_i_n_g _g_e_t_T_y_p_e() { return type_;} │ │ │ │ 269 │ │ │ │ -270 }; │ │ │ │ -271 │ │ │ │ -272 │ │ │ │ -273 │ │ │ │ -274 template │ │ │ │ -_2_7_5 _G_r_a_p_h_V_e_r_t_e_x<_V_e_r_t_e_x,Edge,Face>::_G_r_a_p_h_V_e_r_t_e_x() │ │ │ │ -276 │ │ │ │ -277 : _e_d_g_e_s__(), │ │ │ │ -278 _f_a_c_e_s__(), │ │ │ │ -279 _i_n_d_e_x__(-1) │ │ │ │ -280 { │ │ │ │ -281 } │ │ │ │ -282 │ │ │ │ -283 │ │ │ │ -284 template │ │ │ │ -_2_8_5 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_G_r_a_p_h_V_e_r_t_e_x │ │ │ │ -286 (const _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>& vertex, bool deep) │ │ │ │ -287 │ │ │ │ -288 : _e_d_g_e_s__(), │ │ │ │ -289 _f_a_c_e_s__(), │ │ │ │ -290 _i_n_d_e_x__(vertex._i_n_d_e_x__) │ │ │ │ -291 { │ │ │ │ -292 if (deep) │ │ │ │ -293 { │ │ │ │ -294 _e_d_g_e_s__ = vertex._e_d_g_e_s__; │ │ │ │ -295 _f_a_c_e_s__ = vertex._f_a_c_e_s__; │ │ │ │ -296 } │ │ │ │ -297 } │ │ │ │ +_2_7_6 virtual void _c_h_e_c_k_M_e_n_u(_M_a_i_n_C_o_n_t_r_o_l& mc); │ │ │ │ +277 │ │ │ │ +_2_8_3 vector _g_e_t_S_u_p_p_o_r_t_e_d_F_i_l_e_F_o_r_m_a_t_s() { return file_formats_;} │ │ │ │ +284 │ │ │ │ +285 public Q_SLOTS: │ │ │ │ +286 │ │ │ │ +_2_8_8 virtual bool _w_r_i_t_e(); │ │ │ │ +289 │ │ │ │ +_2_9_4 bool _o_p_e_n(); │ │ │ │ +295 │ │ │ │ +_2_9_7 virtual bool _d_e_l_e_t_e_D_a_t_a_s_e_t_s(); │ │ │ │ 298 │ │ │ │ -299 │ │ │ │ -300 template │ │ │ │ -_3_0_1 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_~_G_r_a_p_h_V_e_r_t_e_x() │ │ │ │ -302 │ │ │ │ -303 { │ │ │ │ -304 } │ │ │ │ -305 │ │ │ │ -306 │ │ │ │ -307 template │ │ │ │ -_3_0_8 void _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_s_e_t │ │ │ │ -309 (const _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>& vertex, bool deep) │ │ │ │ +_3_0_0 virtual bool _d_e_l_e_t_e_D_a_t_a_s_e_t(); │ │ │ │ +301 │ │ │ │ +302 protected: │ │ │ │ +303 │ │ │ │ +_3_0_5 void _s_e_t_S_t_a_t_u_s_b_a_r_T_e_x_t(const _S_t_r_i_n_g& text, bool important = false); │ │ │ │ +_3_0_6 void _s_e_t_S_t_a_t_u_s_b_a_r_T_e_x_t(const QString& text, bool important = false); │ │ │ │ +307 │ │ │ │ +_3_0_8 virtual bool _w_r_i_t_e(_D_a_t_a_s_e_t* /*set*/, _S_t_r_i_n_g /*filetype*/, _S_t_r_i_n_g / │ │ │ │ +*filename*/); │ │ │ │ +_3_0_9 virtual _D_a_t_a_s_e_t* _o_p_e_n(_S_t_r_i_n_g /*filetype*/, _S_t_r_i_n_g /*filename*/); │ │ │ │ 310 │ │ │ │ -311 { │ │ │ │ -312 if (this != &vertex) │ │ │ │ -313 { │ │ │ │ -314 if (deep) │ │ │ │ -315 { │ │ │ │ -316 edges_ = vertex._e_d_g_e_s__; │ │ │ │ -317 faces_ = vertex._f_a_c_e_s__; │ │ │ │ -318 } │ │ │ │ -319 index_ = vertex._i_n_d_e_x__; │ │ │ │ -320 } │ │ │ │ -321 } │ │ │ │ -322 │ │ │ │ -323 │ │ │ │ -324 template │ │ │ │ -_3_2_5 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>& _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_o_p_e_r_a_t_o_r = │ │ │ │ -326 (const _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>& vertex) │ │ │ │ -327 │ │ │ │ -328 { │ │ │ │ -329 if (this != &vertex) │ │ │ │ -330 { │ │ │ │ -331 edges_ = vertex._e_d_g_e_s__; │ │ │ │ -332 faces_ = vertex.faces_; │ │ │ │ -333 index_ = vertex.index_; │ │ │ │ -334 } │ │ │ │ -335 return *this; │ │ │ │ -336 } │ │ │ │ -337 │ │ │ │ -338 │ │ │ │ -339 template │ │ │ │ -_3_4_0 void _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_i_n_s_e_r_t(Edge* edge) │ │ │ │ -341 │ │ │ │ -342 { │ │ │ │ -343 edges_._i_n_s_e_r_t(edge); │ │ │ │ -344 } │ │ │ │ -345 │ │ │ │ -346 │ │ │ │ -347 template │ │ │ │ -_3_4_8 void _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_i_n_s_e_r_t(Face* face) │ │ │ │ -349 │ │ │ │ -350 { │ │ │ │ -351 faces_.insert(face); │ │ │ │ -352 } │ │ │ │ -353 │ │ │ │ -354 │ │ │ │ -355 template │ │ │ │ -_3_5_6 void _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_r_e_m_o_v_e(Edge* edge) │ │ │ │ -357 │ │ │ │ -358 { │ │ │ │ -359 edges_.erase(edge); │ │ │ │ -360 } │ │ │ │ -361 │ │ │ │ -362 │ │ │ │ -363 template │ │ │ │ -_3_6_4 void _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_r_e_m_o_v_e(Face* face) │ │ │ │ -365 │ │ │ │ -366 { │ │ │ │ -367 faces_.erase(face); │ │ │ │ -368 } │ │ │ │ -369 │ │ │ │ -370 │ │ │ │ -371 template │ │ │ │ -_3_7_2 _P_o_s_i_t_i_o_n _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_n_u_m_b_e_r_O_f_E_d_g_e_s() const │ │ │ │ -373 │ │ │ │ -374 { │ │ │ │ -375 return edges_.size(); │ │ │ │ -376 } │ │ │ │ -377 │ │ │ │ -378 │ │ │ │ -379 template │ │ │ │ -_3_8_0 _P_o_s_i_t_i_o_n _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_n_u_m_b_e_r_O_f_F_a_c_e_s() const │ │ │ │ -381 │ │ │ │ -382 { │ │ │ │ -383 return faces_.size(); │ │ │ │ -384 } │ │ │ │ -385 │ │ │ │ -386 │ │ │ │ -387 template │ │ │ │ -_3_8_8 void _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_s_e_t_I_n_d_e_x(_I_n_d_e_x index) │ │ │ │ -389 │ │ │ │ -390 { │ │ │ │ -391 index_ = index; │ │ │ │ -392 } │ │ │ │ -393 │ │ │ │ -394 │ │ │ │ -395 template │ │ │ │ -_3_9_6 _I_n_d_e_x _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_g_e_t_I_n_d_e_x() const │ │ │ │ -397 │ │ │ │ -398 { │ │ │ │ -399 return index_; │ │ │ │ -400 } │ │ │ │ -401 │ │ │ │ -402 │ │ │ │ -403 template │ │ │ │ -_4_0_4 bool _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_s_u_b_s_t_i_t_u_t_e(_V_e_r_t_e_x* vertex) │ │ │ │ -405 │ │ │ │ -406 { │ │ │ │ -407 if (*this *= *vertex) │ │ │ │ -408 { │ │ │ │ -409 typename _H_a_s_h_S_e_t_<_E_d_g_e_*_>_:_:_I_t_e_r_a_t_o_r e; │ │ │ │ -410 for (e = edges_._b_e_g_i_n(); e != edges_._e_n_d(); e++) │ │ │ │ -411 { │ │ │ │ -412 (*e)->substitute((_V_e_r_t_e_x*)this,vertex); │ │ │ │ -413 } │ │ │ │ -414 typename _H_a_s_h_S_e_t_<_F_a_c_e_*_>_:_:_I_t_e_r_a_t_o_r f; │ │ │ │ -415 for (f = faces_._b_e_g_i_n(); f != faces_._e_n_d(); f++) │ │ │ │ -416 { │ │ │ │ -417 (*f)->substitute((_V_e_r_t_e_x*)this,vertex); │ │ │ │ -418 } │ │ │ │ -419 return true; │ │ │ │ -420 } │ │ │ │ -421 return false; │ │ │ │ -422 } │ │ │ │ -423 │ │ │ │ -424 │ │ │ │ -425 template │ │ │ │ -_4_2_6 bool _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_j_o_i_n(const _V_e_r_t_e_x& vertex) │ │ │ │ -427 │ │ │ │ -428 { │ │ │ │ -429 if (*this *= vertex) │ │ │ │ -430 { │ │ │ │ -431 typename _H_a_s_h_S_e_t_<_E_d_g_e_*_>_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r e; │ │ │ │ -432 for (e = vertex.edges_.begin(); e != vertex.edges_.end(); e++) │ │ │ │ -433 { │ │ │ │ -434 edges_.insert(*e); │ │ │ │ -435 } │ │ │ │ -436 typename _H_a_s_h_S_e_t_<_F_a_c_e_*_>_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r f; │ │ │ │ -437 for (f = vertex.faces_.begin(); f != vertex.faces_.end(); f++) │ │ │ │ -438 { │ │ │ │ -439 faces_.insert(*f); │ │ │ │ -440 } │ │ │ │ -441 return true; │ │ │ │ -442 } │ │ │ │ -443 else │ │ │ │ -444 { │ │ │ │ -445 return false; │ │ │ │ -446 } │ │ │ │ -447 } │ │ │ │ -448 │ │ │ │ -449 │ │ │ │ -450 template │ │ │ │ -_4_5_1 Face* _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_h_a_s(Face* face) const │ │ │ │ -452 │ │ │ │ -453 { │ │ │ │ -454 typename _H_a_s_h_S_e_t_<_F_a_c_e_*_>_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r f; │ │ │ │ -455 for (f = faces_._b_e_g_i_n(); f != faces_._e_n_d(); f++) │ │ │ │ -456 { │ │ │ │ -457 if (*(*f) == *face) │ │ │ │ -458 { │ │ │ │ -459 return *f; │ │ │ │ -460 } │ │ │ │ -461 } │ │ │ │ -462 return NULL; │ │ │ │ -463 } │ │ │ │ -464 │ │ │ │ -465 │ │ │ │ -466 template │ │ │ │ -_4_6_7 Edge* _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_h_a_s(Edge* edge) const │ │ │ │ -468 │ │ │ │ -469 { │ │ │ │ -470 typename _H_a_s_h_S_e_t_<_E_d_g_e_*_>_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r e; │ │ │ │ -471 for (e = edges_._b_e_g_i_n(); e != edges_._e_n_d(); e++) │ │ │ │ -472 { │ │ │ │ -473 if (*(*e) == *edge) │ │ │ │ -474 { │ │ │ │ -475 return *e; │ │ │ │ -476 } │ │ │ │ -477 } │ │ │ │ -478 return NULL; │ │ │ │ -479 } │ │ │ │ -480 │ │ │ │ -481 │ │ │ │ -482 template │ │ │ │ -_4_8_3 bool _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_h_a_s_E_d_g_e_s() const │ │ │ │ -484 │ │ │ │ -485 { │ │ │ │ -486 return !edges_.isEmpty(); │ │ │ │ -487 } │ │ │ │ -488 │ │ │ │ -489 │ │ │ │ -490 template │ │ │ │ -_4_9_1 bool _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_h_a_s_F_a_c_e_s() const │ │ │ │ -492 │ │ │ │ -493 { │ │ │ │ -494 return !faces_.isEmpty(); │ │ │ │ -495 } │ │ │ │ -496 │ │ │ │ -497 │ │ │ │ -498 template │ │ │ │ -499 typename _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_E_d_g_e_I_t_e_r_a_t_o_r │ │ │ │ -_5_0_0 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_b_e_g_i_n_E_d_g_e() │ │ │ │ -501 │ │ │ │ -502 { │ │ │ │ -503 return edges_.begin(); │ │ │ │ -504 } │ │ │ │ -505 │ │ │ │ -506 │ │ │ │ -507 template │ │ │ │ -508 typename _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_C_o_n_s_t_E_d_g_e_I_t_e_r_a_t_o_r │ │ │ │ -_5_0_9 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_b_e_g_i_n_E_d_g_e() const │ │ │ │ -510 │ │ │ │ -511 { │ │ │ │ -512 return edges_.begin(); │ │ │ │ -513 } │ │ │ │ -514 │ │ │ │ -515 │ │ │ │ -516 template │ │ │ │ -517 typename _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_E_d_g_e_I_t_e_r_a_t_o_r │ │ │ │ -_5_1_8 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_e_n_d_E_d_g_e() │ │ │ │ -519 │ │ │ │ -520 { │ │ │ │ -521 return edges_.end(); │ │ │ │ -522 } │ │ │ │ -523 │ │ │ │ -524 │ │ │ │ -525 template │ │ │ │ -526 typename _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_C_o_n_s_t_E_d_g_e_I_t_e_r_a_t_o_r │ │ │ │ -_5_2_7 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_e_n_d_E_d_g_e() const │ │ │ │ -528 │ │ │ │ -529 { │ │ │ │ -530 return edges_.end(); │ │ │ │ -531 } │ │ │ │ -532 │ │ │ │ -533 │ │ │ │ -534 template │ │ │ │ -535 typename _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_F_a_c_e_I_t_e_r_a_t_o_r │ │ │ │ -_5_3_6 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_b_e_g_i_n_F_a_c_e() │ │ │ │ -537 │ │ │ │ -538 { │ │ │ │ -539 return faces_.begin(); │ │ │ │ -540 } │ │ │ │ -541 │ │ │ │ -542 │ │ │ │ -543 template │ │ │ │ -544 typename _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_C_o_n_s_t_F_a_c_e_I_t_e_r_a_t_o_r │ │ │ │ -_5_4_5 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_b_e_g_i_n_F_a_c_e() const │ │ │ │ -546 │ │ │ │ -547 { │ │ │ │ -548 return faces_.begin(); │ │ │ │ -549 } │ │ │ │ -550 │ │ │ │ -551 │ │ │ │ -552 template │ │ │ │ -553 typename _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_F_a_c_e_I_t_e_r_a_t_o_r │ │ │ │ -_5_5_4 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_e_n_d_F_a_c_e() │ │ │ │ -555 │ │ │ │ -556 { │ │ │ │ -557 return faces_.end(); │ │ │ │ -558 } │ │ │ │ -559 │ │ │ │ -560 │ │ │ │ -561 template │ │ │ │ -562 typename _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_C_o_n_s_t_F_a_c_e_I_t_e_r_a_t_o_r │ │ │ │ -_5_6_3 _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_e_n_d_F_a_c_e() const │ │ │ │ -564 │ │ │ │ -565 { │ │ │ │ -566 return faces_.end(); │ │ │ │ -567 } │ │ │ │ -568 │ │ │ │ -569 │ │ │ │ -570 template │ │ │ │ -_5_7_1 bool _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_o_p_e_r_a_t_o_r_ _=_=_ (const _V_e_r_t_e_x&) const │ │ │ │ -572 │ │ │ │ -573 { │ │ │ │ -574 return true; │ │ │ │ -575 } │ │ │ │ -576 │ │ │ │ -577 │ │ │ │ -578 template │ │ │ │ -_5_7_9 bool _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_o_p_e_r_a_t_o_r_ _!_=_ (const _V_e_r_t_e_x&) const │ │ │ │ -580 │ │ │ │ -581 { │ │ │ │ -582 return false; │ │ │ │ -583 } │ │ │ │ -584 │ │ │ │ -585 │ │ │ │ -586 template │ │ │ │ -_5_8_7 bool _G_r_a_p_h_V_e_r_t_e_x_<_V_e_r_t_e_x_,_E_d_g_e_,_F_a_c_e_>_:_:_o_p_e_r_a_t_o_r_ _*_=_ (const _V_e_r_t_e_x&) const │ │ │ │ -588 │ │ │ │ -589 { │ │ │ │ -590 return true; │ │ │ │ -591 } │ │ │ │ -592 │ │ │ │ -593} // namespace BALL │ │ │ │ -594 │ │ │ │ -595#endif // BALL_STRUCTURE_GRAPHVERTEX_H │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ +_3_1_1 _S_t_r_i_n_g _g_e_t_F_i_l_e_T_y_p_e_s__(); │ │ │ │ +_3_1_2 _S_t_r_i_n_g _g_e_t_N_a_m_e_F_r_o_m_F_i_l_e_N_a_m_e__(_S_t_r_i_n_g filename); │ │ │ │ +_3_1_3 QAction* _i_n_s_e_r_t_M_e_n_u_E_n_t_r_y__(_P_o_s_i_t_i_o_n pid, const QString& name, const char* │ │ │ │ +slot, │ │ │ │ +314 const _S_t_r_i_n_g& description = "", QKeySequence accel = QKeySequence(), │ │ │ │ +315 const QString& menu_hint = "", │ │ │ │ +316 _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_O_p_e_r_a_t_i_o_n_M_o_d_e initial_mode = UIOperationMode::MODE_ALL); │ │ │ │ +317 │ │ │ │ +_3_2_0 virtual void _d_e_l_e_t_e_D_a_t_a_s_e_t__(_D_a_t_a_s_e_t*) {}; │ │ │ │ +321 │ │ │ │ +_3_2_2 _S_t_r_i_n_g _t_y_p_e__; │ │ │ │ +_3_2_3 vector _f_i_l_e___f_o_r_m_a_t_s__; │ │ │ │ +_3_2_4 _D_a_t_a_s_e_t_C_o_n_t_r_o_l* _c_o_n_t_r_o_l__; │ │ │ │ +_3_2_5 vector _a_c_t_i_o_n_s__; │ │ │ │ +_3_2_6 _H_a_s_h_S_e_t_<_Q_A_c_t_i_o_n_*_> _a_c_t_i_o_n_s___f_o_r___o_n_e___s_e_t__; │ │ │ │ +_3_2_7 _H_a_s_h_M_a_p_<_Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m_*_,_ _D_a_t_a_s_e_t_*_> _i_t_e_m___t_o___d_a_t_a_s_e_t__; │ │ │ │ +_3_2_8 _H_a_s_h_M_a_p_<_D_a_t_a_s_e_t_*_,_ _Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m_*_> _d_a_t_a_s_e_t___t_o___i_t_e_m__; │ │ │ │ +329 }; │ │ │ │ +330 │ │ │ │ +331 } // namespace VIEW │ │ │ │ +332} // namespace BALL │ │ │ │ +333 │ │ │ │ +334#endif // BALL_VIEW_DATATYPE_DATASET_H │ │ │ │ +_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h │ │ │ │ +_e_m_b_e_d_d_a_b_l_e_._h │ │ │ │ +_B_A_L_L___E_M_B_E_D_D_A_B_L_E │ │ │ │ +#define BALL_EMBEDDABLE(TYPE, BASE) │ │ │ │ +DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_3_1 │ │ │ │ _h_a_s_h_S_e_t_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_s_t_r_i_n_g_._h │ │ │ │ +_h_a_s_h_M_a_p_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_F_o_r_w_a_r_d_I_t_e_r_a_t_o_r │ │ │ │ -DDeeffiinniittiioonn _f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h_:_1_9_9 │ │ │ │ -_B_A_L_L_:_:_F_o_r_w_a_r_d_I_t_e_r_a_t_o_r_:_:_b_e_g_i_n │ │ │ │ -static ForwardIterator begin(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h_:_3_0_7 │ │ │ │ -_B_A_L_L_:_:_F_o_r_w_a_r_d_I_t_e_r_a_t_o_r_:_:_e_n_d │ │ │ │ -static ForwardIterator end(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h_:_3_1_7 │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_E_m_b_e_d_d_a_b_l_e │ │ │ │ +DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_8_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_M_a_p │ │ │ │ +HashMap class based on the STL map (containing serveral convenience functions) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_M_a_p_._h_:_7_4 │ │ │ │ _B_A_L_L_:_:_H_a_s_h_S_e_t │ │ │ │ DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_b_e_g_i_n │ │ │ │ -Iterator begin() │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_5_3_6 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_i_n_s_e_r_t │ │ │ │ -std::pair< Iterator, bool > insert(const ValueType &item) │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_9_6 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_e_n_d │ │ │ │ -Iterator end() │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_5_4_3 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ -ConstForwardIterator< HashSet< Key >, ValueType, PointerType, IteratorTraits > │ │ │ │ -ConstIterator │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_8_3 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_s_e_t │ │ │ │ -void set(const GraphVertex< Vertex, Edge, Face > &vertex, bool deep=false) │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_0_9 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_o_p_e_r_a_t_o_r_!_= │ │ │ │ -virtual bool operator!=(const Vertex &) const │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_7_9 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_E_d_g_e_I_t_e_r_a_t_o_r │ │ │ │ -HashSet< Edge * >::Iterator EdgeIterator │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_g_e_t_I_n_d_e_x │ │ │ │ -Index getIndex() const │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_9_6 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_s_u_b_s_t_i_t_u_t_e │ │ │ │ -bool substitute(Vertex *vertex) │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_4_0_4 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_G_r_a_p_h_V_e_r_t_e_x │ │ │ │ -GraphVertex() │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_2_7_5 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_s_e_t_I_n_d_e_x │ │ │ │ -void setIndex(Index index) │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_8_8 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_e_n_d_E_d_g_e │ │ │ │ -EdgeIterator endEdge() │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_1_8 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_b_e_g_i_n_F_a_c_e │ │ │ │ -FaceIterator beginFace() │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_3_6 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_b_e_g_i_n_E_d_g_e │ │ │ │ -EdgeIterator beginEdge() │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_0_0 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_C_o_n_s_t_E_d_g_e_I_t_e_r_a_t_o_r │ │ │ │ -HashSet< Edge * >::ConstIterator ConstEdgeIterator │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_4 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_i_n_d_e_x__ │ │ │ │ -Index index_ │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_2_6_6 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_i_n_s_e_r_t │ │ │ │ -void insert(Edge *edge) │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_4_0 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_e_d_g_e_s__ │ │ │ │ -HashSet< Edge * > edges_ │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_2_6_0 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_o_p_e_r_a_t_o_r_=_= │ │ │ │ -virtual bool operator==(const Vertex &) const │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_7_1 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_F_a_c_e_I_t_e_r_a_t_o_r │ │ │ │ -HashSet< Face * >::Iterator FaceIterator │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_5 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_C_o_n_s_t_F_a_c_e_I_t_e_r_a_t_o_r │ │ │ │ -HashSet< Face * >::ConstIterator ConstFaceIterator │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_6 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_h_a_s_E_d_g_e_s │ │ │ │ -bool hasEdges() const │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_4_8_3 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_f_a_c_e_s__ │ │ │ │ -HashSet< Face * > faces_ │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_2_6_3 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_o_p_e_r_a_t_o_r_*_= │ │ │ │ -virtual bool operator*=(const Vertex &) const │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_8_7 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_j_o_i_n │ │ │ │ -bool join(const Vertex &vertex) │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_4_2_6 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_h_a_s │ │ │ │ -Face * has(Face *face) const │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_4_5_1 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_n_u_m_b_e_r_O_f_E_d_g_e_s │ │ │ │ -Position numberOfEdges() const │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_7_2 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_r_e_m_o_v_e │ │ │ │ -void remove(Edge *edge) │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_5_6 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_n_u_m_b_e_r_O_f_F_a_c_e_s │ │ │ │ -Position numberOfFaces() const │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_8_0 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_h_a_s_F_a_c_e_s │ │ │ │ -bool hasFaces() const │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_4_9_1 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_e_n_d_F_a_c_e │ │ │ │ -FaceIterator endFace() │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_5_5_4 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x_:_:_~_G_r_a_p_h_V_e_r_t_e_x │ │ │ │ -virtual ~GraphVertex() │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_0_1 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_F_a_c_e │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_F_a_c_e_._h_:_2_9 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_T_r_i_a_n_g_l_e │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_F_a_c_e_._h_:_6_2_5 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_E_d_g_e │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_E_d_g_e_._h_:_3_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_V_e_r_t_e_x │ │ │ │ -DDeeffiinniittiioonn _v_e_r_t_e_x_1_._h_:_3_2 │ │ │ │ -_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_6_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_g_e_t_C_o_m_p_o_s_i_t_e │ │ │ │ +Composite * getComposite() const │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_1_1_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_c_o_m_p_o_s_i_t_e__ │ │ │ │ +Composite * composite_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_1_2_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_t_y_p_e__ │ │ │ │ +String type_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_1_2_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_s_e_t_N_a_m_e │ │ │ │ +void setName(String name) │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_9_9 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_n_a_m_e__ │ │ │ │ +String name_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_1_2_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_s_e_t_T_y_p_e │ │ │ │ +void setType(String type) │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_1_0_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_~_D_a_t_a_s_e_t │ │ │ │ +virtual ~Dataset() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_s_e_t_C_o_m_p_o_s_i_t_e │ │ │ │ +void setComposite(Composite *composite) │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_1_1_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_D_a_t_a_s_e_t │ │ │ │ +Dataset(const Dataset &dataset) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_g_e_t_T_y_p_e │ │ │ │ +String getType() const │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_1_0_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_g_e_t_N_a_m_e │ │ │ │ +String getName() const │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_1_0_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_D_a_t_a_s_e_t │ │ │ │ +Dataset() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_d_u_m_p │ │ │ │ +void dump(std::ostream &s, Size depth) const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_c_l_e_a_r │ │ │ │ +virtual void clear() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_:_:_s_e_t │ │ │ │ +void set(const Dataset &v) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_1_9_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_d_e_l_e_t_e_D_a_t_a_s_e_t_s │ │ │ │ +virtual bool deleteDatasets() │ │ │ │ +Delete all Datasets. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_g_e_t_N_a_m_e_F_r_o_m_F_i_l_e_N_a_m_e__ │ │ │ │ +String getNameFromFileName_(String filename) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_h_a_s_I_t_e_m │ │ │ │ +bool hasItem(QTreeWidgetItem *item) │ │ │ │ +Test if a given QTreeWidgetItem corresponds to a registered Dataset. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_c_o_n_t_r_o_l__ │ │ │ │ +DatasetControl * control_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_3_2_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_s_e_t_S_t_a_t_u_s_b_a_r_T_e_x_t │ │ │ │ +void setStatusbarText(const String &text, bool important=false) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_g_e_t_D_a_t_a_s_e_t_s │ │ │ │ +vector< Dataset * > getDatasets() │ │ │ │ +Get all Datasets of this type in the DatasetControl. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_g_e_t_D_a_t_a_s_e_t │ │ │ │ +Dataset * getDataset(QTreeWidgetItem *item) │ │ │ │ +Get the Dataset for a QTreeWidgetItem. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_i_n_s_e_r_t_M_e_n_u_E_n_t_r_y__ │ │ │ │ +QAction * insertMenuEntry_(Position pid, const QString &name, const char *slot, │ │ │ │ +const String &description="", QKeySequence accel=QKeySequence(), const QString │ │ │ │ +&menu_hint="", UIOperationMode::OperationMode initial_mode=UIOperationMode:: │ │ │ │ +MODE_ALL) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_g_e_t_D_a_t_a_s_e_t_C_o_n_t_r_o_l │ │ │ │ +DatasetControl * getDatasetControl() │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_2_1_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_s_e_t_S_t_a_t_u_s_b_a_r_T_e_x_t │ │ │ │ +void setStatusbarText(const QString &text, bool important=false) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_c_h_e_c_k_M_e_n_u │ │ │ │ +virtual void checkMenu(MainControl &mc) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_t_y_p_e__ │ │ │ │ +String type_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_3_2_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_g_e_t_T_y_p_e │ │ │ │ +String getType() │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_2_6_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_w_r_i_t_e │ │ │ │ +virtual bool write(Dataset *, String, String) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_g_e_t_S_e_l_e_c_t_e_d_D_a_t_a_s_e_t │ │ │ │ +Dataset * getSelectedDataset() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_b_u_i_l_d_C_o_n_t_e_x_t_M_e_n_u │ │ │ │ +virtual QMenu * buildContextMenu(QTreeWidgetItem *item) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_g_e_t_S_e_l_e_c_t_e_d_D_a_t_a_s_e_t_s │ │ │ │ +vector< Dataset * > getSelectedDatasets() │ │ │ │ +Get all selected Datasets of this type in the DatasetControl. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_i_t_e_m___t_o___d_a_t_a_s_e_t__ │ │ │ │ +HashMap< QTreeWidgetItem *, Dataset * > item_to_dataset_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_3_2_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_d_a_t_a_s_e_t___t_o___i_t_e_m__ │ │ │ │ +HashMap< Dataset *, QTreeWidgetItem * > dataset_to_item_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_3_2_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_w_r_i_t_e │ │ │ │ +virtual bool write() │ │ │ │ +Show a file dialog for writing the selected Dataset. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_g_e_t_S_u_p_p_o_r_t_e_d_F_i_l_e_F_o_r_m_a_t_s │ │ │ │ +vector< String > getSupportedFileFormats() │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_2_8_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_d_e_l_e_t_e_D_a_t_a_s_e_t │ │ │ │ +virtual bool deleteDataset() │ │ │ │ +Delete the currently highlighted Dataset. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_a_c_t_i_o_n_s__ │ │ │ │ +vector< QAction * > actions_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_3_2_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_d_e_l_e_t_e_D_a_t_a_s_e_t │ │ │ │ +virtual bool deleteDataset(Dataset *set) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_i_n_s_e_r_t_D_a_t_a_s_e_t │ │ │ │ +virtual bool insertDataset(Dataset *set) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_g_e_t_F_i_l_e_T_y_p_e_s__ │ │ │ │ +String getFileTypes_() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_o_p_e_n │ │ │ │ +virtual Dataset * open(String, String) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_d_e_l_e_t_e_D_a_t_a_s_e_t__ │ │ │ │ +virtual void deleteDataset_(Dataset *) │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_3_2_0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_h_a_n_d_l_e │ │ │ │ +virtual bool handle(DatasetMessage *msg) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_c_r_e_a_t_e_M_e_n_u_E_n_t_r_i_e_s │ │ │ │ +virtual bool createMenuEntries() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_f_i_l_e___f_o_r_m_a_t_s__ │ │ │ │ +vector< String > file_formats_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_3_2_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_o_p_e_n │ │ │ │ +bool open() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_h_a_s_D_a_t_a_s_e_t │ │ │ │ +bool hasDataset(Dataset *set) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l_l_e_r_:_:_a_c_t_i_o_n_s___f_o_r___o_n_e___s_e_t__ │ │ │ │ +HashSet< QAction * > actions_for_one_set_ │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_._h_:_3_2_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_M_e_s_s_a_g_e │ │ │ │ +DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_1_3_9 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_O_p_e_r_a_t_i_o_n_M_o_d_e │ │ │ │ +OperationMode │ │ │ │ +DDeeffiinniittiioonn _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h_:_3_0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_C_o_n_t_r_o_l │ │ │ │ +DDeeffiinniittiioonn _d_a_t_a_s_e_t_C_o_n_t_r_o_l_._h_:_3_8 │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_Q_O_b_j_e_c_t │ │ │ │ +_Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m │ │ │ │ +_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ +#define BALL_VIEW_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d0b/a03910.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
│ │ │
│ │ │ List of all members
│ │ │
BALL::GenericMolFile Class Reference
Molecular Modeling » File Formats » Molecular structure file formats
│ │ │
│ │ │
│ │ │ │ │ │ -

#include <BALL/FORMAT/genericMolFile.h>

│ │ │ +

#include <BALL/FORMAT/genericMolFile.h>

│ │ │
│ │ │ Inheritance diagram for BALL::GenericMolFile:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ BALL::LineBasedFile │ │ │ @@ -396,15 +396,15 @@ │ │ │

Base class for all molecule file format classes. This class provides an interface for all molecular structure formats (except for PDB files, due to their complex and capricious structure and contents).

GenericMolFile supports two type of operations: reading/writing single molecules and reading/writing systems (i.e. collections of molecules).
│ │ │
When reading molecules, the structures are read one at a time from the file in the order they are stored. In contrast, reading systems retrieves all structures contained in the file. For file formats that do not support multiple structure in a file (e.g. the MDL MOLFile ), those two operations are basically equivalent. A fundamental difference however is the fact that reading a molecule create a new molecule, whereas reading a system adds the molecules read to an existing instance of System . This implies that the system has to be cleared prior to reading a system if that incremental behaviour is not desired.
│ │ │
The user interface of the class is mainly provided through the stream operator. A typical example for reading a structure from a HyperChem file might look as follows:
│ │ │
\begin{verbatim} HINFile hinfile(filename); System S; hinfile >> S; \end{verbatim} This interface applies to all derived classes as well, so that file formats can be exchanged conveniently.
│ │ │
GenericMolFile is derived from LineBasedFile since most molecular structure formats are line-based tagged formats, often containing Fortran-style formatted sections. LineBasedFile provides a number of convenient methods to parse that kind of format.
│ │ │
│ │ │ │ │ │ -

Definition at line 56 of file genericMolFile.h.

│ │ │ +

Definition at line 56 of file genericMolFile.h.

│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ GenericMolFile() [1/2]

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ @@ -935,15 +935,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ protected
│ │ │
│ │ │ │ │ │ -

Definition at line 195 of file genericMolFile.h.

│ │ │ +

Definition at line 195 of file genericMolFile.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ gmf_is_closed_

│ │ │ │ │ │
│ │ │ @@ -959,15 +959,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 196 of file genericMolFile.h.

│ │ │ +

Definition at line 196 of file genericMolFile.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ input_is_temporary_

│ │ │ │ │ │
│ │ │ @@ -983,15 +983,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 194 of file genericMolFile.h.

│ │ │ +

Definition at line 194 of file genericMolFile.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ zipped_filename_

│ │ │ │ │ │
│ │ │ @@ -1007,15 +1007,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 197 of file genericMolFile.h.

│ │ │ +

Definition at line 197 of file genericMolFile.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d0b/a08254.html │ │ │ @@ -78,15 +78,15 @@ │ │ │ Protected Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members │ │ │
BALL::VIEW::BufferedRenderer Class Referenceabstract
│ │ │ │ │ │
│ │ │ │ │ │ -

#include <BALL/VIEW/RENDERING/RENDERERS/bufferedRenderer.h>

│ │ │ +

#include <BALL/VIEW/RENDERING/RENDERERS/bufferedRenderer.h>

│ │ │
│ │ │ Inheritance diagram for BALL::VIEW::BufferedRenderer:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ BALL::VIEW::Renderer │ │ │ @@ -301,15 +301,15 @@ │ │ │
│ │ │ } │ │ │   │ │ │ │ │ │

Detailed Description

│ │ │

Interface for Buffered Rendering. BufferedRenderers don't create their own window. Instead, they render the scene to a FrameBuffer which is provided by a RenderTarget. The FrameBuffer contains a pointer to a memory area where the results will be stored, as well as the pixel format and the resolution. Before rendering can start, you have to choose an output format using the setFrameBufferFormat() function. After that, you can call renderToBuffer(), as long as the format of the RenderTarget is the same that you set before.

│ │ │ │ │ │ -

Definition at line 29 of file bufferedRenderer.h.

│ │ │ +

Definition at line 29 of file bufferedRenderer.h.

│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ BufferedRenderer()

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ @@ -326,15 +326,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ inline
│ │ │
│ │ │ │ │ │ -

Definition at line 34 of file bufferedRenderer.h.

│ │ │ +

Definition at line 34 of file bufferedRenderer.h.

│ │ │ │ │ │
│ │ │
│ │ │

Member Function Documentation

│ │ │ │ │ │

◆ formatUpdated()

│ │ │ │ │ │ @@ -383,15 +383,15 @@ │ │ │ │ │ │ inlineprotected │ │ │ │ │ │ │ │ │
│ │ │

Returns the current FrameBufferFormat.

│ │ │ │ │ │ -

Definition at line 125 of file bufferedRenderer.h.

│ │ │ +

Definition at line 125 of file bufferedRenderer.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ getSupportedResolution()

│ │ │ │ │ │
│ │ │ @@ -507,15 +507,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
Exception::InvalidFormatif the FrameBufferFormat is not supported by the renderer
Exception::NoBufferAvailableif the frame buffer was not correctly initialized
│ │ │ │ │ │ │ │ │ │ │ │ -

Definition at line 62 of file bufferedRenderer.h.

│ │ │ +

Definition at line 62 of file bufferedRenderer.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ renderToBufferImpl()

│ │ │ │ │ │
│ │ │ @@ -567,15 +567,15 @@ │ │ │ │ │ │ │ │ │
│ │ │

Tries to choose a format for buffered rendering.

Returns
true if the format could be set,
│ │ │
│ │ │ false if it is not supported.
│ │ │ │ │ │ -

Definition at line 43 of file bufferedRenderer.h.

│ │ │ +

Definition at line 43 of file bufferedRenderer.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ setOffset()

│ │ │ │ │ │
│ │ │ @@ -596,15 +596,15 @@ │ │ │ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
│ │ │

Set an offset into the data buffer

│ │ │ │ │ │ -

Definition at line 94 of file bufferedRenderer.h.

│ │ │ +

Definition at line 94 of file bufferedRenderer.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ setStride()

│ │ │ │ │ │
│ │ │ @@ -625,15 +625,15 @@ │ │ │ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
│ │ │

Set a stride for the data buffer

│ │ │ │ │ │ -

Definition at line 98 of file bufferedRenderer.h.

│ │ │ +

Definition at line 98 of file bufferedRenderer.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ supports() [1/2]

│ │ │ │ │ │
│ │ │ @@ -708,15 +708,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 127 of file bufferedRenderer.h.

│ │ │ +

Definition at line 127 of file bufferedRenderer.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ stride_

│ │ │ │ │ │
│ │ │ @@ -732,15 +732,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 128 of file bufferedRenderer.h.

│ │ │ +

Definition at line 128 of file bufferedRenderer.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d0f/a07170.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
│ │ │
│ │ │ List of all members
│ │ │
BALL::SESVertex Class Reference
Molecular Modeling » Molecular Structure » Molecular Surface Computation
│ │ │
│ │ │
│ │ │ │ │ │ -

#include <BALL/STRUCTURE/SESVertex.h>

│ │ │ +

#include <BALL/STRUCTURE/SESVertex.h>

│ │ │
│ │ │ Inheritance diagram for BALL::SESVertex:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ BALL::GraphVertex< SESVertex, SESEdge, SESFace > │ │ │ @@ -246,15 +246,15 @@ │ │ │   │ │ │ typedef HashSet< SESFace * >::ConstIterator ConstFaceIterator │ │ │   │ │ │ │ │ │

Detailed Description

│ │ │

Generic SESVertex Class. <>

│ │ │ │ │ │ -

Definition at line 29 of file SESVertex.h.

│ │ │ +

Definition at line 29 of file SESVertex.h.

│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ SESVertex() [1/3]

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ @@ -725,15 +725,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ friend
│ │ │
│ │ │ │ │ │ -

Definition at line 47 of file SESVertex.h.

│ │ │ +

Definition at line 47 of file SESVertex.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ SESEdge

│ │ │ │ │ │
│ │ │ @@ -749,15 +749,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 44 of file SESVertex.h.

│ │ │ +

Definition at line 44 of file SESVertex.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ SESFace

│ │ │ │ │ │
│ │ │ @@ -773,15 +773,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 45 of file SESVertex.h.

│ │ │ +

Definition at line 45 of file SESVertex.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ SESSingularityCleaner

│ │ │ │ │ │
│ │ │ @@ -797,15 +797,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 48 of file SESVertex.h.

│ │ │ +

Definition at line 48 of file SESVertex.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ SESTriangulator

│ │ │ │ │ │
│ │ │ @@ -821,15 +821,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 50 of file SESVertex.h.

│ │ │ +

Definition at line 50 of file SESVertex.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ SolventExcludedSurface

│ │ │ │ │ │
│ │ │ @@ -845,15 +845,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 46 of file SESVertex.h.

│ │ │ +

Definition at line 46 of file SESVertex.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ TriangulatedSES

│ │ │ │ │ │
│ │ │ @@ -869,15 +869,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 49 of file SESVertex.h.

│ │ │ +

Definition at line 49 of file SESVertex.h.

│ │ │ │ │ │
│ │ │ │ │ │

Member Data Documentation

│ │ │ │ │ │

◆ atom_

│ │ │ │ │ │ @@ -894,15 +894,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 205 of file SESVertex.h.

│ │ │ +

Definition at line 205 of file SESVertex.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ normal_

│ │ │ │ │ │
│ │ │ @@ -918,15 +918,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 202 of file SESVertex.h.

│ │ │ +

Definition at line 202 of file SESVertex.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ point_

│ │ │ │ │ │
│ │ │ @@ -942,15 +942,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 199 of file SESVertex.h.

│ │ │ +

Definition at line 199 of file SESVertex.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d11/a00842.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: partialBondOrderAssignment.h File Reference │ │ │ +BALL: amberEvaluation.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,36 +65,32 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │
│ │ │ Classes | │ │ │ Namespaces
│ │ │ -
partialBondOrderAssignment.h File Reference
│ │ │ +
amberEvaluation.h File Reference
│ │ │
│ │ │
│ │ │ -
#include <BALL/COMMON/global.h>
│ │ │ -#include <BALL/KERNEL/atom.h>
│ │ │ -#include <BALL/KERNEL/bond.h>
│ │ │ -#include <boost/shared_ptr.hpp>
│ │ │ -#include <vector>
│ │ │ +
#include <BALL/SCORING/FUNCTIONS/forceFieldEvaluation.h>
│ │ │ +#include <BALL/MOLMEC/AMBER/amber.h>
│ │ │
│ │ │

Go to the source code of this file.

│ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

│ │ │ Classes

class  BALL::PartialBondOrderAssignment
 A full or partial solution to the AStar-based bond order assignment problem. More...
class  BALL::AmberEvaluation
 
│ │ │ │ │ │ │ │ │ │ │ │

│ │ │ Namespaces

namespace  BALL
 
│ │ │ ├── html2text {} │ │ │ │ @@ -1,26 +1,21 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ - * _B_O_N_D_O_R_D_E_R_S │ │ │ │ + * _S_C_O_R_I_N_G │ │ │ │ + * _F_U_N_C_T_I_O_N_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -partialBondOrderAssignment.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_b_o_n_d_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ +amberEvaluation.h File Reference │ │ │ │ +#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_F_U_N_C_T_I_O_N_S_/_f_o_r_c_e_F_i_e_l_d_E_v_a_l_u_a_t_i_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_A_M_B_E_R_/_a_m_b_e_r_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t │ │ │ │ -  A full or partial solution to the AStar-based bond order assignment │ │ │ │ - problem. _M_o_r_e_._._. │ │ │ │ +class   _B_A_L_L_:_:_A_m_b_e_r_E_v_a_l_u_a_t_i_o_n │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d11/a00842_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: partialBondOrderAssignment.h Source File │ │ │ +BALL: amberEvaluation.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,149 +70,93 @@ │ │ │
│ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ -
partialBondOrderAssignment.h
│ │ │ +
amberEvaluation.h
│ │ │
│ │ │
│ │ │ -Go to the documentation of this file.
1#ifndef BALL_STRUCTURE_BONDORDERS_PARTIALBONDORDERASSIGNMENT_H
│ │ │ -
2#define BALL_STRUCTURE_BONDORDERS_PARTIALBONDORDERASSIGNMENT_H
│ │ │ -
3
│ │ │ -
4#ifndef BALL_COMMON_GLOBAL_H
│ │ │ -
5# include <BALL/COMMON/global.h>
│ │ │ -
6#endif
│ │ │ -
7
│ │ │ -
8#ifndef BALL_KERNEL_ATOM_H
│ │ │ -
9# include <BALL/KERNEL/atom.h>
│ │ │ -
10#endif
│ │ │ +Go to the documentation of this file.
1// -*- Mode: C++; tab-width: 2; -*-
│ │ │ +
2// vi: set ts=2:
│ │ │ +
3// $Id: amberEvaluation.h,v 1.3.18.2 2007/06/17 07:02:21 oliver Exp $
│ │ │ +
4//
│ │ │ +
5// Author:
│ │ │ +
6//
│ │ │ +
7//
│ │ │ +
8
│ │ │ +
9#ifndef BALL_SCORING_FUNCTIONS_AMBEREVALUATION_H
│ │ │ +
10#define BALL_SCORING_FUNCTIONS_AMBEREVALUATION_H
│ │ │
11
│ │ │ -
12#ifndef BALL_KERNEL_BOND_H
│ │ │ -
13# include <BALL/KERNEL/bond.h>
│ │ │ +
12#ifndef BALL_SCORING_FUNCTIONS_FORCEFIELDEVALUATION_H
│ │ │ +
13# include <BALL/SCORING/FUNCTIONS/forceFieldEvaluation.h>
│ │ │
14#endif
│ │ │
15
│ │ │ -
16#include <boost/shared_ptr.hpp>
│ │ │ -
17#include <vector>
│ │ │ -
18
│ │ │ -
19namespace BALL
│ │ │ -
20{
│ │ │ -
21 class AssignBondOrderProcessor;
│ │ │ -
22 class BondOrderAssignment;
│ │ │ -
23
│ │ │ -
│ │ │ -
33 class BALL_EXPORT PartialBondOrderAssignment
│ │ │ -
34 {
│ │ │ -
35 public:
│ │ │ -
36 // this enum allows faster access to the type of the chosen heuristic than a string compare
│ │ │ -
│ │ │ -
37 enum HEURISTIC_INDEX
│ │ │ -
38 {
│ │ │ -
39 SIMPLE,
│ │ │ -
40 MEDIUM,
│ │ │ -
41 TIGHT
│ │ │ -
42 };
│ │ │ -
│ │ │ -
43
│ │ │ -
44 // Constructor
│ │ │ -
45 PartialBondOrderAssignment(AssignBondOrderProcessor* parent);
│ │ │ -
46
│ │ │ -
47 // Destructor
│ │ │ -
48 ~PartialBondOrderAssignment();
│ │ │ -
49
│ │ │ -
50 boost::shared_ptr<BondOrderAssignment> convertToFullAssignment();
│ │ │ -
51
│ │ │ -
52 //
│ │ │ -
53 void clear();
│ │ │ -
54
│ │ │ -
55 // the less operator.
│ │ │ -
56 // NOTE: we want a reverse sort, hence we actually return a "greater"
│ │ │ -
57 bool operator < (const PartialBondOrderAssignment& b) const;
│ │ │ -
58
│ │ │ -
59 // the penalty
│ │ │ -
60 float coarsePenalty(float atom_type_penalty, float bond_length_penalty) const;
│ │ │ -
61
│ │ │ -
62 // the combined penalty of structure and type penalty
│ │ │ -
63 float coarsePenalty() const;
│ │ │ -
64
│ │ │ -
65 // the bond length penalty
│ │ │ -
66 float finePenalty() const {return estimated_bond_length_penalty;}
│ │ │ -
67
│ │ │ -
69 float getAtomTypePenalty(bool include_heuristic_term = true, HEURISTIC_INDEX heuristic_index = SIMPLE);
│ │ │ -
70
│ │ │ -
78 bool estimatePenalty_(bool include_heuristic_term = true, HEURISTIC_INDEX heuristic_index = SIMPLE);
│ │ │ -
79
│ │ │ -
81 float estimateAtomTypePenalty_(Atom* atom,
│ │ │ -
82 Index atom_index, // the atom index
│ │ │ -
83 int fixed_valence, // its so far fixed valence (incl. virtual H's)
│ │ │ -
84 int fixed_virtual_order, // its so far fixed virtual H's
│ │ │ -
85 int num_free_bonds, // its number of unfixed original bonds
│ │ │ -
86 HEURISTIC_INDEX heuristic_index);
│ │ │ -
87
│ │ │ -
89 // NOTE: virtual bonds are excluded!
│ │ │ -
90 float estimateBondLengthPenalty_(Index atom_index, // the atom index
│ │ │ -
91 const vector<Bond*>& free_bonds,
│ │ │ -
92 int fixed_virtual_order,
│ │ │ -
93 int fixed_valence,
│ │ │ -
94 int num_free_bonds);
│ │ │ -
95
│ │ │ -
96
│ │ │ -
97 // the estimated atom type penalty
│ │ │ -
98 float estimated_atom_type_penalty;
│ │ │ -
99 // the estimated bond length penalty
│ │ │ -
100 float estimated_bond_length_penalty;
│ │ │ -
101
│ │ │ -
102 // the bond orders
│ │ │ -
103 // the i-th entry denotes the bondorder of the i-th bond
│ │ │ -
104 // unset bonds get the order 0
│ │ │ -
105 vector<short> bond_orders;
│ │ │ -
106
│ │ │ -
107 // the index of the bond last considered
│ │ │ -
108 Position last_bond;
│ │ │ -
109
│ │ │ -
110 AssignBondOrderProcessor* abop;
│ │ │ -
111 };
│ │ │ -
│ │ │ -
112}
│ │ │ -
113
│ │ │ -
114#endif // BALL_STRUCTURE_BONDORDERS_PARTIALBONDORDERASSIGNMENT_H
│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
BALL::AssignBondOrderProcessor
Assignment of bond orders from topology information.
Definition assignBondOrderProcessor.h:90
│ │ │ -
BALL::PartialBondOrderAssignment
A full or partial solution to the AStar-based bond order assignment problem.
Definition partialBondOrderAssignment.h:34
│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
BALL::PartialBondOrderAssignment::estimatePenalty_
bool estimatePenalty_(bool include_heuristic_term=true, HEURISTIC_INDEX heuristic_index=SIMPLE)
│ │ │ -
BALL::PartialBondOrderAssignment::coarsePenalty
float coarsePenalty(float atom_type_penalty, float bond_length_penalty) const
│ │ │ -
BALL::PartialBondOrderAssignment::PartialBondOrderAssignment
PartialBondOrderAssignment(AssignBondOrderProcessor *parent)
│ │ │ -
BALL::PartialBondOrderAssignment::getAtomTypePenalty
float getAtomTypePenalty(bool include_heuristic_term=true, HEURISTIC_INDEX heuristic_index=SIMPLE)
Convenience function to obtain total atom type penalty value.
│ │ │ - │ │ │ -
BALL::PartialBondOrderAssignment::estimateAtomTypePenalty_
float estimateAtomTypePenalty_(Atom *atom, Index atom_index, int fixed_valence, int fixed_virtual_order, int num_free_bonds, HEURISTIC_INDEX heuristic_index)
Estimates the atom type penalty for a given unclosed atom.
│ │ │ - │ │ │ -
BALL::PartialBondOrderAssignment::estimateBondLengthPenalty_
float estimateBondLengthPenalty_(Index atom_index, const vector< Bond * > &free_bonds, int fixed_virtual_order, int fixed_valence, int num_free_bonds)
Estimates the bond length penalty for a given unclosed atom.
│ │ │ - │ │ │ -
BALL::PartialBondOrderAssignment::convertToFullAssignment
boost::shared_ptr< BondOrderAssignment > convertToFullAssignment()
│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
│ │ │ +
16#ifndef BALL_MOLMEC_AMBER_AMBER_H
│ │ │ +
17# include <BALL/MOLMEC/AMBER/amber.h>
│ │ │ +
18#endif
│ │ │ +
19
│ │ │ +
20namespace BALL
│ │ │ +
21{
│ │ │ +
│ │ │ +
26 class BALL_EXPORT AmberEvaluation : public ForceFieldEvaluation
│ │ │ +
27 {
│ │ │ +
28 public:
│ │ │ +
29
│ │ │ +
30 // Default constructor.
│ │ │ +
31 AmberEvaluation()
│ │ │ +
32 throw();
│ │ │ +
33
│ │ │ +
34 AmberEvaluation(AmberFF& ff)
│ │ │ +
35 throw();
│ │ │ +
36
│ │ │ +
37 AmberEvaluation(AmberFF& ff, Options& option)
│ │ │ +
38 throw();
│ │ │ +
39
│ │ │ +
40 virtual ~AmberEvaluation()
│ │ │ +
41 throw();
│ │ │ +
42
│ │ │ +
45 void setForceField(ForceField& ff)
│ │ │ +
46 throw();
│ │ │ +
47
│ │ │ +
48 void setOptions(const Options& options)
│ │ │ +
49 throw();
│ │ │ +
50
│ │ │ +
51 ForceField& getForceField()
│ │ │ +
52 throw();
│ │ │ +
53
│ │ │ +
54 const ForceField& getForceField() const
│ │ │ +
55 throw();
│ │ │ +
56
│ │ │ +
57 Options& getOptions()
│ │ │ +
58 throw();
│ │ │ +
59
│ │ │ +
60 const Options& getOptions() const
│ │ │ +
61 throw();
│ │ │ +
62
│ │ │ +
63 };
│ │ │ +
│ │ │ +
64}
│ │ │ +
65
│ │ │ +
66#endif // BALL_SCORING_FUNCTIONS_AMBEREVALUATION_H
│ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ │
│ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,183 +1,91 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ - * _B_O_N_D_O_R_D_E_R_S │ │ │ │ -partialBondOrderAssignment.h │ │ │ │ + * _S_C_O_R_I_N_G │ │ │ │ + * _F_U_N_C_T_I_O_N_S │ │ │ │ +amberEvaluation.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1#ifndef BALL_STRUCTURE_BONDORDERS_PARTIALBONDORDERASSIGNMENT_H │ │ │ │ -2#define BALL_STRUCTURE_BONDORDERS_PARTIALBONDORDERASSIGNMENT_H │ │ │ │ -3 │ │ │ │ -4#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ -5# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -6#endif │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_KERNEL_ATOM_H │ │ │ │ -9# include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_._h> │ │ │ │ -10#endif │ │ │ │ +1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ +2// vi: set ts=2: │ │ │ │ +3// $Id: amberEvaluation.h,v 1.3.18.2 2007/06/17 07:02:21 oliver Exp $ │ │ │ │ +4// │ │ │ │ +5// Author: │ │ │ │ +6// │ │ │ │ +7// │ │ │ │ +8 │ │ │ │ +9#ifndef BALL_SCORING_FUNCTIONS_AMBEREVALUATION_H │ │ │ │ +10#define BALL_SCORING_FUNCTIONS_AMBEREVALUATION_H │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_KERNEL_BOND_H │ │ │ │ -13# include <_B_A_L_L_/_K_E_R_N_E_L_/_b_o_n_d_._h> │ │ │ │ +12#ifndef BALL_SCORING_FUNCTIONS_FORCEFIELDEVALUATION_H │ │ │ │ +13# include <_B_A_L_L_/_S_C_O_R_I_N_G_/_F_U_N_C_T_I_O_N_S_/_f_o_r_c_e_F_i_e_l_d_E_v_a_l_u_a_t_i_o_n_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#include │ │ │ │ -17#include │ │ │ │ -18 │ │ │ │ -19namespace _B_A_L_L │ │ │ │ -20{ │ │ │ │ -21 class AssignBondOrderProcessor; │ │ │ │ -22 class BondOrderAssignment; │ │ │ │ -23 │ │ │ │ -_3_3 class _B_A_L_L___E_X_P_O_R_T _P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t │ │ │ │ -34 { │ │ │ │ -35 public: │ │ │ │ -36 // this enum allows faster access to the type of the chosen heuristic than a │ │ │ │ -string compare │ │ │ │ -_3_7 enum _H_E_U_R_I_S_T_I_C___I_N_D_E_X │ │ │ │ -38 { │ │ │ │ -_3_9 _S_I_M_P_L_E, │ │ │ │ -_4_0 _M_E_D_I_U_M, │ │ │ │ -41 TIGHT │ │ │ │ -_4_2 }; │ │ │ │ -43 │ │ │ │ -44 // Constructor │ │ │ │ -_4_5 _P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t(_A_s_s_i_g_n_B_o_n_d_O_r_d_e_r_P_r_o_c_e_s_s_o_r* parent); │ │ │ │ -46 │ │ │ │ -47 // Destructor │ │ │ │ -_4_8 _~_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t(); │ │ │ │ -49 │ │ │ │ -_5_0 boost::shared_ptr _c_o_n_v_e_r_t_T_o_F_u_l_l_A_s_s_i_g_n_m_e_n_t(); │ │ │ │ -51 │ │ │ │ -52 // │ │ │ │ -_5_3 void _c_l_e_a_r(); │ │ │ │ -54 │ │ │ │ -55 // the less operator. │ │ │ │ -56 // NOTE: we want a reverse sort, hence we actually return a "greater" │ │ │ │ -_5_7 bool operator < (const _P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t& b) const; │ │ │ │ -58 │ │ │ │ -59 // the penalty │ │ │ │ -_6_0 float _c_o_a_r_s_e_P_e_n_a_l_t_y(float atom_type_penalty, float bond_length_penalty) │ │ │ │ -const; │ │ │ │ -61 │ │ │ │ -62 // the combined penalty of structure and type penalty │ │ │ │ -_6_3 float _c_o_a_r_s_e_P_e_n_a_l_t_y() const; │ │ │ │ -64 │ │ │ │ -65 // the bond length penalty │ │ │ │ -_6_6 float _f_i_n_e_P_e_n_a_l_t_y() const {return estimated_bond_length_penalty;} │ │ │ │ -67 │ │ │ │ -_6_9 float _g_e_t_A_t_o_m_T_y_p_e_P_e_n_a_l_t_y(bool include_heuristic_term = true, _H_E_U_R_I_S_T_I_C___I_N_D_E_X │ │ │ │ -heuristic_index = SIMPLE); │ │ │ │ -70 │ │ │ │ -_7_8 bool _e_s_t_i_m_a_t_e_P_e_n_a_l_t_y__(bool include_heuristic_term = true, _H_E_U_R_I_S_T_I_C___I_N_D_E_X │ │ │ │ -heuristic_index = SIMPLE); │ │ │ │ -79 │ │ │ │ -_8_1 float _e_s_t_i_m_a_t_e_A_t_o_m_T_y_p_e_P_e_n_a_l_t_y__(_A_t_o_m* atom, │ │ │ │ -82 _I_n_d_e_x atom_index, // the atom index │ │ │ │ -83 int fixed_valence, // its so far fixed valence (incl. virtual H's) │ │ │ │ -84 int fixed_virtual_order, // its so far fixed virtual H's │ │ │ │ -85 int num_free_bonds, // its number of unfixed original bonds │ │ │ │ -86 _H_E_U_R_I_S_T_I_C___I_N_D_E_X heuristic_index); │ │ │ │ -87 │ │ │ │ -89 // NOTE: virtual bonds are excluded! │ │ │ │ -_9_0 float _e_s_t_i_m_a_t_e_B_o_n_d_L_e_n_g_t_h_P_e_n_a_l_t_y__(_I_n_d_e_x atom_index, // the atom index │ │ │ │ -91 const vector& free_bonds, │ │ │ │ -92 int fixed_virtual_order, │ │ │ │ -93 int fixed_valence, │ │ │ │ -94 int num_free_bonds); │ │ │ │ -95 │ │ │ │ -96 │ │ │ │ -97 // the estimated atom type penalty │ │ │ │ -_9_8 float _e_s_t_i_m_a_t_e_d___a_t_o_m___t_y_p_e___p_e_n_a_l_t_y; │ │ │ │ -99 // the estimated bond length penalty │ │ │ │ -_1_0_0 float _e_s_t_i_m_a_t_e_d___b_o_n_d___l_e_n_g_t_h___p_e_n_a_l_t_y; │ │ │ │ -101 │ │ │ │ -102 // the bond orders │ │ │ │ -103 // the i-th entry denotes the bondorder of the i-th bond │ │ │ │ -104 // unset bonds get the order 0 │ │ │ │ -_1_0_5 vector _b_o_n_d___o_r_d_e_r_s; │ │ │ │ -106 │ │ │ │ -107 // the index of the bond last considered │ │ │ │ -_1_0_8 _P_o_s_i_t_i_o_n _l_a_s_t___b_o_n_d; │ │ │ │ -109 │ │ │ │ -_1_1_0 _A_s_s_i_g_n_B_o_n_d_O_r_d_e_r_P_r_o_c_e_s_s_o_r* _a_b_o_p; │ │ │ │ -111 }; │ │ │ │ -112} │ │ │ │ -113 │ │ │ │ -114#endif // BALL_STRUCTURE_BONDORDERS_PARTIALBONDORDERASSIGNMENT_H │ │ │ │ -_b_o_n_d_._h │ │ │ │ -_a_t_o_m_._h │ │ │ │ +16#ifndef BALL_MOLMEC_AMBER_AMBER_H │ │ │ │ +17# include <_B_A_L_L_/_M_O_L_M_E_C_/_A_M_B_E_R_/_a_m_b_e_r_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20namespace _B_A_L_L │ │ │ │ +21{ │ │ │ │ +_2_6 class _B_A_L_L___E_X_P_O_R_T _A_m_b_e_r_E_v_a_l_u_a_t_i_o_n : public _F_o_r_c_e_F_i_e_l_d_E_v_a_l_u_a_t_i_o_n │ │ │ │ +27 { │ │ │ │ +28 public: │ │ │ │ +29 │ │ │ │ +30 // Default constructor. │ │ │ │ +_3_1 _A_m_b_e_r_E_v_a_l_u_a_t_i_o_n() │ │ │ │ +32 throw(); │ │ │ │ +33 │ │ │ │ +_3_4 _A_m_b_e_r_E_v_a_l_u_a_t_i_o_n(_A_m_b_e_r_F_F& ff) │ │ │ │ +35 throw(); │ │ │ │ +36 │ │ │ │ +_3_7 _A_m_b_e_r_E_v_a_l_u_a_t_i_o_n(_A_m_b_e_r_F_F& ff, _O_p_t_i_o_n_s& option) │ │ │ │ +38 throw(); │ │ │ │ +39 │ │ │ │ +_4_0 virtual ~_A_m_b_e_r_E_v_a_l_u_a_t_i_o_n() │ │ │ │ +41 throw(); │ │ │ │ +42 │ │ │ │ +_4_5 void setForceField(_F_o_r_c_e_F_i_e_l_d& ff) │ │ │ │ +46 throw(); │ │ │ │ +47 │ │ │ │ +_4_8 void setOptions(const _O_p_t_i_o_n_s& options) │ │ │ │ +49 throw(); │ │ │ │ +50 │ │ │ │ +_5_1 _F_o_r_c_e_F_i_e_l_d& getForceField() │ │ │ │ +52 throw(); │ │ │ │ +53 │ │ │ │ +_5_4 const _F_o_r_c_e_F_i_e_l_d& getForceField() const │ │ │ │ +55 throw(); │ │ │ │ +56 │ │ │ │ +_5_7 _O_p_t_i_o_n_s& getOptions() │ │ │ │ +58 throw(); │ │ │ │ +59 │ │ │ │ +_6_0 const _O_p_t_i_o_n_s& getOptions() const │ │ │ │ +61 throw(); │ │ │ │ +62 │ │ │ │ +63 }; │ │ │ │ +64} │ │ │ │ +65 │ │ │ │ +66#endif // BALL_SCORING_FUNCTIONS_AMBEREVALUATION_H │ │ │ │ +_f_o_r_c_e_F_i_e_l_d_E_v_a_l_u_a_t_i_o_n_._h │ │ │ │ +_a_m_b_e_r_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_A_s_s_i_g_n_B_o_n_d_O_r_d_e_r_P_r_o_c_e_s_s_o_r │ │ │ │ -Assignment of bond orders from topology information. │ │ │ │ -DDeeffiinniittiioonn _a_s_s_i_g_n_B_o_n_d_O_r_d_e_r_P_r_o_c_e_s_s_o_r_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t │ │ │ │ -A full or partial solution to the AStar-based bond order assignment problem. │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_3_4 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_b_o_n_d___o_r_d_e_r_s │ │ │ │ -vector< short > bond_orders │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_1_0_5 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_e_s_t_i_m_a_t_e_d___a_t_o_m___t_y_p_e___p_e_n_a_l_t_y │ │ │ │ -float estimated_atom_type_penalty │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_9_8 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_H_E_U_R_I_S_T_I_C___I_N_D_E_X │ │ │ │ -HEURISTIC_INDEX │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_3_8 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_M_E_D_I_U_M │ │ │ │ -@ MEDIUM │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_S_I_M_P_L_E │ │ │ │ -@ SIMPLE │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_3_9 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_f_i_n_e_P_e_n_a_l_t_y │ │ │ │ -float finePenalty() const │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_6_6 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_a_b_o_p │ │ │ │ -AssignBondOrderProcessor * abop │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_1_1_0 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_e_s_t_i_m_a_t_e_P_e_n_a_l_t_y__ │ │ │ │ -bool estimatePenalty_(bool include_heuristic_term=true, HEURISTIC_INDEX │ │ │ │ -heuristic_index=SIMPLE) │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_c_o_a_r_s_e_P_e_n_a_l_t_y │ │ │ │ -float coarsePenalty(float atom_type_penalty, float bond_length_penalty) const │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t │ │ │ │ -PartialBondOrderAssignment(AssignBondOrderProcessor *parent) │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_g_e_t_A_t_o_m_T_y_p_e_P_e_n_a_l_t_y │ │ │ │ -float getAtomTypePenalty(bool include_heuristic_term=true, HEURISTIC_INDEX │ │ │ │ -heuristic_index=SIMPLE) │ │ │ │ -Convenience function to obtain total atom type penalty value. │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_~_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t │ │ │ │ -~PartialBondOrderAssignment() │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_e_s_t_i_m_a_t_e_A_t_o_m_T_y_p_e_P_e_n_a_l_t_y__ │ │ │ │ -float estimateAtomTypePenalty_(Atom *atom, Index atom_index, int fixed_valence, │ │ │ │ -int fixed_virtual_order, int num_free_bonds, HEURISTIC_INDEX heuristic_index) │ │ │ │ -Estimates the atom type penalty for a given unclosed atom. │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_c_l_e_a_r │ │ │ │ -void clear() │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_e_s_t_i_m_a_t_e_B_o_n_d_L_e_n_g_t_h_P_e_n_a_l_t_y__ │ │ │ │ -float estimateBondLengthPenalty_(Index atom_index, const vector< Bond * > │ │ │ │ -&free_bonds, int fixed_virtual_order, int fixed_valence, int num_free_bonds) │ │ │ │ -Estimates the bond length penalty for a given unclosed atom. │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_e_s_t_i_m_a_t_e_d___b_o_n_d___l_e_n_g_t_h___p_e_n_a_l_t_y │ │ │ │ -float estimated_bond_length_penalty │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_1_0_0 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_c_o_n_v_e_r_t_T_o_F_u_l_l_A_s_s_i_g_n_m_e_n_t │ │ │ │ -boost::shared_ptr< BondOrderAssignment > convertToFullAssignment() │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_c_o_a_r_s_e_P_e_n_a_l_t_y │ │ │ │ -float coarsePenalty() const │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_:_:_l_a_s_t___b_o_n_d │ │ │ │ -Position last_bond │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h_:_1_0_8 │ │ │ │ -_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_g_l_o_b_a_l_._h │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_A_m_b_e_r_F_F │ │ │ │ +DDeeffiinniittiioonn _a_m_b_e_r_._h_:_3_3 │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ +_B_A_L_L_:_:_A_m_b_e_r_E_v_a_l_u_a_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _a_m_b_e_r_E_v_a_l_u_a_t_i_o_n_._h_:_2_7 │ │ │ │ +_B_A_L_L_:_:_A_m_b_e_r_E_v_a_l_u_a_t_i_o_n_:_:_A_m_b_e_r_E_v_a_l_u_a_t_i_o_n │ │ │ │ +AmberEvaluation() │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_E_v_a_l_u_a_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_E_v_a_l_u_a_t_i_o_n_._h_:_2_3 │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d12/a05386.html │ │ │ @@ -76,40 +76,40 @@ │ │ │
│ │ │ Public Attributes | │ │ │ List of all members
│ │ │
BALL::LennardJones::Values Struct Reference
│ │ │
│ │ │
│ │ │ │ │ │ -

#include <BALL/MOLMEC/PARAMETER/lennardJones.h>

│ │ │ +

#include <BALL/MOLMEC/PARAMETER/lennardJones.h>

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

│ │ │ Public Attributes

float A
 
float B
 
│ │ │

Detailed Description

│ │ │
│ │ │ -

Definition at line 65 of file lennardJones.h.

│ │ │ +

Definition at line 65 of file lennardJones.h.

│ │ │

Member Data Documentation

│ │ │ │ │ │

◆ A

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │
float BALL::LennardJones::Values::A
│ │ │
│ │ │ │ │ │ -

Definition at line 67 of file lennardJones.h.

│ │ │ +

Definition at line 67 of file lennardJones.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ B

│ │ │ │ │ │
│ │ │ @@ -117,15 +117,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
float BALL::LennardJones::Values::B
│ │ │
│ │ │ │ │ │ -

Definition at line 68 of file lennardJones.h.

│ │ │ +

Definition at line 68 of file lennardJones.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d13/a02139.html │ │ │ @@ -87,15 +87,15 @@ │ │ │

│ │ │ Typedefs

│ │ │ typedef std::list< EnergyProcessor * > BALL::EnergyProcessorList │ │ │   │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

│ │ │ Functions

BALL_EXPORT double BALL::calculateACE (const AtomContainer &atom_container, const string &type_filename="energy/ACE_types.dat", const string &parameter_filename="energy/ACE_parameters.dat")
BALL_EXPORT double BALL::calculateACE (const AtomContainer &atom_container, const string &type_filename="energy/ACE_types.dat", const string &parameter_filename="energy/ACE_parameters.dat")
 
│ │ │

Detailed Description

│ │ │

Typedef Documentation

│ │ │ │ │ │

◆ EnergyProcessorList

│ │ │ │ │ │ @@ -105,27 +105,27 @@ │ │ │ │ │ │ typedef std::list<EnergyProcessor*> BALL::EnergyProcessorList │ │ │ │ │ │ │ │ │
│ │ │

EnergyProcessorList

│ │ │ │ │ │ -

Definition at line 24 of file composedEnergyProcessor.h.

│ │ │ +

Definition at line 24 of file composedEnergyProcessor.h.

│ │ │ │ │ │
│ │ │ │ │ │

Function Documentation

│ │ │ │ │ │

◆ calculateACE()

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d13/a07518.html │ │ │ @@ -80,15 +80,15 @@ │ │ │ Protected Member Functions | │ │ │ Friends | │ │ │ List of all members │ │ │
BALL::VIEW::AmberConfigurationDialog Class Reference
Visualisation » QT Dialogs
│ │ │ │ │ │
│ │ │ │ │ │ -

#include <BALL/VIEW/DIALOGS/amberConfigurationDialog.h>

│ │ │ +

#include <BALL/VIEW/DIALOGS/amberConfigurationDialog.h>

│ │ │
│ │ │ Inheritance diagram for BALL::VIEW::AmberConfigurationDialog:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ QDialog │ │ │ @@ -178,15 +178,15 @@ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -221,15 +221,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
BALL_EXPORT double BALL::calculateACE BALL_EXPORT double BALL::calculateACE (const AtomContainer & atom_container,
- Protected Member Functions inherited from BALL::VIEW::PreferencesEntry
void registerWidgets_ ()
 
void registerObject_ (QObject *widget)
 
void unregisterObject_ (QObject *widget)
 
BALL_DEPRECATED void registerWidgetForHelpSystem_ (const QWidget *, const String &)
BALL_DEPRECATED void registerWidgetForHelpSystem_ (const QWidget *, const String &)
 
void restoreValues_ (bool all, const ValueMap &map)
 
void insertStackEntry_ (QWidget *, const String &name)
 
bool isSupported_ (QObject &widget)
 
 
StackPages stack_pages_
 
│ │ │

Detailed Description

│ │ │

Dialog for changing the options of the AMBER forcefield

│ │ │ │ │ │ -

Definition at line 29 of file amberConfigurationDialog.h.

│ │ │ +

Definition at line 29 of file amberConfigurationDialog.h.

│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ AmberConfigurationDialog()

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ @@ -506,15 +506,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ friend
│ │ │
│ │ │ │ │ │ -

Definition at line 34 of file amberConfigurationDialog.h.

│ │ │ +

Definition at line 34 of file amberConfigurationDialog.h.

│ │ │ │ │ │
│ │ │
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d14/a06358.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
│ │ │ Public Member Functions | │ │ │ List of all members
│ │ │
BALL::RotationalEntropy Class Reference
│ │ │
│ │ │
│ │ │ │ │ │ -

#include <BALL/SCORING/COMPONENTS/rotationalEntropy.h>

│ │ │ +

#include <BALL/SCORING/COMPONENTS/rotationalEntropy.h>

│ │ │
│ │ │ Inheritance diagram for BALL::RotationalEntropy:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ BALL::ScoringComponent │ │ │ @@ -180,15 +180,15 @@ │ │ │ bool enabled_ │ │ │   │ │ │ String type_name_ │ │ │   │ │ │ │ │ │

Detailed Description

│ │ │
│ │ │ -

Definition at line 14 of file rotationalEntropy.h.

│ │ │ +

Definition at line 14 of file rotationalEntropy.h.

│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ RotationalEntropy()

│ │ │ │ │ │
│ │ │
│ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d15/a04574.html │ │ │ @@ -79,15 +79,15 @@ │ │ │
BALL::KernelPredicate< T > Class Template Reference
│ │ │ │ │ │
│ │ │ │ │ │

Kernel predicate class. │ │ │ More...

│ │ │ │ │ │ -

#include <BALL/KERNEL/predicate.h>

│ │ │ +

#include <BALL/KERNEL/predicate.h>

│ │ │
│ │ │ Inheritance diagram for BALL::KernelPredicate< T >:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ BALL::UnaryPredicate< Composite > │ │ │ @@ -117,15 +117,15 @@ │ │ │
│ │ │ │ │ │
virtual bool operator() (const Composite &) const
 
│ │ │

Detailed Description

│ │ │
template<class T>
│ │ │ class BALL::KernelPredicate< T >

Kernel predicate class.

│ │ │ │ │ │ -

Definition at line 64 of file KERNEL/predicate.h.

│ │ │ +

Definition at line 64 of file KERNEL/predicate.h.

│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ ~KernelPredicate()

│ │ │ │ │ │
│ │ │
│ │ │
│ │ │ @@ -144,15 +144,15 @@ │ │ │ │ │ │ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 71 of file KERNEL/predicate.h.

│ │ │ +

Definition at line 71 of file KERNEL/predicate.h.

│ │ │ │ │ │
│ │ │
│ │ │

Member Function Documentation

│ │ │ │ │ │

◆ operator()()

│ │ │ │ │ │ @@ -177,15 +177,15 @@ │ │ │ virtual │ │ │ │ │ │ │ │ │
│ │ │ │ │ │

Constant virtual RTTI evaluation operator.

│ │ │ │ │ │ -

Definition at line 171 of file KERNEL/predicate.h.

│ │ │ +

Definition at line 171 of file KERNEL/predicate.h.

│ │ │ │ │ │
│ │ │
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d18/a04070.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Public Attributes | │ │ │ List of all members
│ │ │
BALL::NMRStarFile::NMRSpectrometer Class Reference
│ │ │
│ │ │
│ │ │ │ │ │ -

#include <BALL/FORMAT/NMRStarFile.h>

│ │ │ +

#include <BALL/FORMAT/NMRStarFile.h>

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │

│ │ │ Public Member Functions

std::ostream & operator>> (std::ostream &s)
 
│ │ │ │ │ │ │ │ │ │ │ │

│ │ │ @@ -98,15 +98,15 @@ │ │ │

 
float field_strength
 
│ │ │

Detailed Description

│ │ │

NMRSpectrometer This class includes all NMR spectrometer information. All members are public for easy access.

│ │ │ │ │ │ -

Definition at line 428 of file NMRStarFile.h.

│ │ │ +

Definition at line 428 of file NMRStarFile.h.

│ │ │

Member Function Documentation

│ │ │ │ │ │

◆ operator>>()

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ @@ -131,15 +131,15 @@ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │
float BALL::NMRStarFile::NMRSpectrometer::field_strength
│ │ │
│ │ │ │ │ │ -

Definition at line 434 of file NMRStarFile.h.

│ │ │ +

Definition at line 434 of file NMRStarFile.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ manufacturer

│ │ │ │ │ │
│ │ │ @@ -147,15 +147,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
String BALL::NMRStarFile::NMRSpectrometer::manufacturer
│ │ │
│ │ │ │ │ │ -

Definition at line 432 of file NMRStarFile.h.

│ │ │ +

Definition at line 432 of file NMRStarFile.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ model

│ │ │ │ │ │
│ │ │ @@ -163,15 +163,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
String BALL::NMRStarFile::NMRSpectrometer::model
│ │ │
│ │ │ │ │ │ -

Definition at line 433 of file NMRStarFile.h.

│ │ │ +

Definition at line 433 of file NMRStarFile.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ name

│ │ │ │ │ │
│ │ │ @@ -179,15 +179,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
String BALL::NMRStarFile::NMRSpectrometer::name
│ │ │
│ │ │ │ │ │ -

Definition at line 431 of file NMRStarFile.h.

│ │ │ +

Definition at line 431 of file NMRStarFile.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d19/a05214.html │ │ │ @@ -76,27 +76,27 @@ │ │ │
│ │ │ Static Public Attributes | │ │ │ List of all members
│ │ │
BALL::StrangLBFGSMinimizer::Option Struct Reference
│ │ │ │ │ │
│ │ │ │ │ │ -

#include <BALL/MOLMEC/MINIMIZATION/strangLBFGS.h>

│ │ │ +

#include <BALL/MOLMEC/MINIMIZATION/strangLBFGS.h>

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

│ │ │ Static Public Attributes

static const char * IMPROVED
 
static const char * NUM_OF_STORED_VECT_PAIRS
 
│ │ │

Detailed Description

│ │ │

Symbolic names for option keys. This struct contains a symbolic name for each recognized key in StrangLBFGSMinimizer::options.

For each symbol the required type is given under parameters.
│ │ │ │ │ │ -

Definition at line 54 of file strangLBFGS.h.

│ │ │ +

Definition at line 54 of file strangLBFGS.h.

│ │ │

Member Data Documentation

│ │ │ │ │ │

◆ IMPROVED

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ @@ -111,15 +111,15 @@ │ │ │ │ │ │ │ │ │
│ │ │ static
│ │ │
│ │ │

Should the improved version be used?

│ │ │ │ │ │ -

Definition at line 58 of file strangLBFGS.h.

│ │ │ +

Definition at line 58 of file strangLBFGS.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ NUM_OF_STORED_VECT_PAIRS

│ │ │ │ │ │
│ │ │ @@ -136,15 +136,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
│ │ │

Maximum number of stored vector pairs

│ │ │ │ │ │ -

Definition at line 62 of file strangLBFGS.h.

│ │ │ +

Definition at line 62 of file strangLBFGS.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d1c/a00605.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: sysinfo.h File Reference │ │ │ +BALL: testFramework.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,51 +65,42 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │
│ │ │ -Namespaces | │ │ │ -Functions
│ │ │ -
sysinfo.h File Reference
│ │ │ +Classes | │ │ │ +Namespaces
│ │ │ +
testFramework.h File Reference
│ │ │ │ │ │
│ │ │ -
#include <BALL/common.h>
│ │ │ +
#include <BALL/VIEW/WIDGETS/dockWidget.h>
│ │ │ +#include <BALL/SYSTEM/file.h>
│ │ │ +#include <BALL/SYSTEM/timer.h>
│ │ │ +#include <QtCore/QThread>
│ │ │
│ │ │

Go to the source code of this file.

│ │ │ │ │ │ + │ │ │ + │ │ │ + │ │ │ +

│ │ │ +Classes

class  BALL::VIEW::TestFramework
 
│ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ -

│ │ │ Namespaces

namespace  BALL
 
namespace  BALL::SysInfo
namespace  BALL::VIEW
 
│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │

│ │ │ -Functions

BALL_EXPORT LongIndex BALL::SysInfo::getAvailableMemory ()
 
BALL_EXPORT LongIndex BALL::SysInfo::getFreeMemory ()
 
BALL_EXPORT LongIndex BALL::SysInfo::getTotalMemory ()
 
BALL_EXPORT LongIndex BALL::SysInfo::getBufferedMemory ()
 
BALL_EXPORT LongIndex BALL::SysInfo::getFreeSwapSpace ()
 
BALL_EXPORT Time BALL::SysInfo::getUptime ()
 
BALL_EXPORT Index BALL::SysInfo::getNumberOfProcessors ()
 
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ │
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,33 +1,25 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_Y_S_T_E_M │ │ │ │ -_N_a_m_e_s_p_a_c_e_s | _F_u_n_c_t_i_o_n_s │ │ │ │ -sysinfo.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ + * _V_I_E_W │ │ │ │ + * _W_I_D_G_E_T_S │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ +testFramework.h File Reference │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_W_I_D_G_E_T_S_/_d_o_c_k_W_i_d_g_e_t_._h> │ │ │ │ +#include <_B_A_L_L_/_S_Y_S_T_E_M_/_f_i_l_e_._h> │ │ │ │ +#include <_B_A_L_L_/_S_Y_S_T_E_M_/_t_i_m_e_r_._h> │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ +CCllaasssseess │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_T_e_s_t_F_r_a_m_e_w_o_r_k │ │ │ │ +  │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_S_y_s_I_n_f_o │ │ │ │ -  │ │ │ │ -FFuunnccttiioonnss │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x  _B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_A_v_a_i_l_a_b_l_e_M_e_m_o_r_y () │ │ │ │ -  │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x  _B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_F_r_e_e_M_e_m_o_r_y () │ │ │ │ -  │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x  _B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_T_o_t_a_l_M_e_m_o_r_y () │ │ │ │ -  │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x  _B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_B_u_f_f_e_r_e_d_M_e_m_o_r_y () │ │ │ │ -  │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x  _B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_F_r_e_e_S_w_a_p_S_p_a_c_e () │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _T_i_m_e  _B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_U_p_t_i_m_e () │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _I_n_d_e_x  _B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_N_u_m_b_e_r_O_f_P_r_o_c_e_s_s_o_r_s () │ │ │ │ +namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d1c/a00605_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: sysinfo.h Source File │ │ │ +BALL: testFramework.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,70 +70,178 @@ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ -
sysinfo.h
│ │ │ +
testFramework.h
│ │ │
│ │ │
│ │ │ Go to the documentation of this file.
1// -*- Mode: C++; tab-width: 2; -*-
│ │ │
2// vi: set ts=2:
│ │ │
3//
│ │ │ -
4// $Id: sysinfo.h,v 1.10 2005/12/23 17:02:07 amoll Exp $
│ │ │ -
5//
│ │ │ -
6
│ │ │ -
7#ifndef BALL_SYSTEM_SYSINFO_H
│ │ │ -
8#define BALL_SYSTEM_SYSINFO_H
│ │ │ -
9
│ │ │ -
10#ifndef BALL_COMMON_H
│ │ │ -
11# include <BALL/common.h>
│ │ │ -
12#endif
│ │ │ -
13
│ │ │ -
14namespace BALL
│ │ │ -
15{
│ │ │ -
│ │ │ -
23 namespace SysInfo
│ │ │ -
24 {
│ │ │ -
28 BALL_EXPORT LongIndex getAvailableMemory();
│ │ │ -
29
│ │ │ -
33 BALL_EXPORT LongIndex getFreeMemory();
│ │ │ -
34
│ │ │ -
38 BALL_EXPORT LongIndex getTotalMemory();
│ │ │ -
39
│ │ │ -
43 BALL_EXPORT LongIndex getBufferedMemory();
│ │ │ -
44
│ │ │ -
48 BALL_EXPORT LongIndex getFreeSwapSpace();
│ │ │ -
49
│ │ │ -
54 BALL_EXPORT Time getUptime();
│ │ │ -
55
│ │ │ -
59 BALL_EXPORT Index getNumberOfProcessors();
│ │ │ -
60 }
│ │ │ -
│ │ │ -
61}
│ │ │ -
62
│ │ │ -
63#endif // BALL_SYSTEM_SYSINFO_H
│ │ │ - │ │ │ - │ │ │ -
BALL::Time
time_t Time
Definition COMMON/global.h:123
│ │ │ -
BALL::LongIndex
BALL_LONG64_TYPE LongIndex
Definition COMMON/global.h:201
│ │ │ -
BALL::SysInfo::getNumberOfProcessors
BALL_EXPORT Index getNumberOfProcessors()
│ │ │ -
BALL::SysInfo::getAvailableMemory
BALL_EXPORT LongIndex getAvailableMemory()
│ │ │ -
BALL::SysInfo::getBufferedMemory
BALL_EXPORT LongIndex getBufferedMemory()
│ │ │ -
BALL::SysInfo::getFreeMemory
BALL_EXPORT LongIndex getFreeMemory()
│ │ │ -
BALL::SysInfo::getFreeSwapSpace
BALL_EXPORT LongIndex getFreeSwapSpace()
│ │ │ -
BALL::SysInfo::getUptime
BALL_EXPORT Time getUptime()
│ │ │ -
BALL::SysInfo::getTotalMemory
BALL_EXPORT LongIndex getTotalMemory()
│ │ │ +
4
│ │ │ +
5#ifndef BALL_VIEW_WIDGETS_TESTFRAMEWORK_H
│ │ │ +
6#define BALL_VIEW_WIDGETS_TESTFRAMEWORK_H
│ │ │ +
7
│ │ │ +
8#ifndef BALL_VIEW_WIDGETS_DOCKWIDGET_H
│ │ │ +
9# include <BALL/VIEW/WIDGETS/dockWidget.h>
│ │ │ +
10#endif
│ │ │ +
11
│ │ │ +
12#ifndef BALL_SYSTEM_FILE_H
│ │ │ +
13# include <BALL/SYSTEM/file.h>
│ │ │ +
14#endif
│ │ │ +
15
│ │ │ +
16#ifndef BALL_SYSTEM_TIMER_H
│ │ │ +
17# include <BALL/SYSTEM/timer.h>
│ │ │ +
18#endif
│ │ │ +
19
│ │ │ +
20#include <QtCore/QThread>
│ │ │ +
21
│ │ │ +
22class QAction;
│ │ │ +
23
│ │ │ +
24namespace BALL
│ │ │ +
25{
│ │ │ +
26 namespace VIEW
│ │ │ +
27 {
│ │ │ +
│ │ │ +
58 class BALL_VIEW_EXPORT TestFramework
│ │ │ +
59 : public QWidget,
│ │ │ +
60 public ModularWidget
│ │ │ +
61 {
│ │ │ +
62 Q_OBJECT
│ │ │ +
63
│ │ │ +
64 class MyMouseEvent
│ │ │ +
65 : public QMouseEvent
│ │ │ +
66 {
│ │ │ +
67 public:
│ │ │ +
68
│ │ │ +
69 MyMouseEvent(Type type, const QPoint & position, Qt::MouseButton button,
│ │ │ +
70 Qt::MouseButtons buttons, Qt::KeyboardModifiers modifiers)
│ │ │ +
71 : QMouseEvent(type, position, button, buttons, modifiers) {}
│ │ │ +
72 };
│ │ │ +
73
│ │ │ +
74 class MyEventThread
│ │ │ +
75 : public QThread
│ │ │ +
76 {
│ │ │ +
77 public:
│ │ │ +
78
│ │ │ +
79 MyEventThread();
│ │ │ +
80
│ │ │ +
81 virtual void run();
│ │ │ +
82
│ │ │ +
83 TestFramework* tf;
│ │ │ +
84 MainControl* mc;
│ │ │ +
85 };
│ │ │ +
86
│ │ │ +
87 friend class MyEventThread;
│ │ │ +
88
│ │ │ +
89 public:
│ │ │ +
90
│ │ │ +
91 BALL_EMBEDDABLE(TestFramework,DockWidget)
│ │ │ +
92
│ │ │ +
93
│ │ │ +
94 TestFramework(QWidget *parent = 0, const char *name = 0);
│ │ │ +
95
│ │ │ +
97 virtual ~TestFramework();
│ │ │ +
98
│ │ │ +
99 //
│ │ │ +
100 virtual void initializeWidget(MainControl& main_control);
│ │ │ +
101
│ │ │ +
103 void setFilename(const String& filename);
│ │ │ +
104
│ │ │ +
106 void checkMenu(MainControl& main_control);
│ │ │ +
107
│ │ │ +
109 virtual bool canHandle(const String& fileformat) const;
│ │ │ +
110
│ │ │ +
112 virtual bool openFile(const String& filename);
│ │ │ +
113
│ │ │ +
114 public Q_SLOTS:
│ │ │ +
115
│ │ │ +
117 void startTest();
│ │ │ +
118
│ │ │ +
120 void stopTest();
│ │ │ +
121
│ │ │ +
123 void runTest();
│ │ │ +
124
│ │ │ +
126 void abortTest();
│ │ │ +
127
│ │ │ +
129 void saveFile();
│ │ │ +
130
│ │ │ +
132 void loadFile();
│ │ │ +
133
│ │ │ +
135 virtual bool eventFilter(QObject*, QEvent* e);
│ │ │ +
136
│ │ │ +
138 virtual void timeOut();
│ │ │ +
139
│ │ │ +
141 void switchRecordMove();
│ │ │ +
142
│ │ │ +
143 protected:
│ │ │ +
144
│ │ │ +
145 virtual bool event(QEvent* e);
│ │ │ +
146
│ │ │ +
147 void storeEvent(QEvent& e);
│ │ │ +
148
│ │ │ +
149 void processEvent_();
│ │ │ +
150
│ │ │ +
151 QAction* start_recording, *stop_recording, *run_test, *abort_test,
│ │ │ +
152 *save_file, *load_file, *switch_move;
│ │ │ +
153 QAction* action_;
│ │ │ +
154
│ │ │ +
155 File outfile_;
│ │ │ +
156 File infile_;
│ │ │ +
157 String filename_;
│ │ │ +
158 Timer timer_, runtime_;
│ │ │ +
159 list<String>lines_;
│ │ │ +
160 QWidget* widget_, *last_widget_;
│ │ │ +
161 float time_;
│ │ │ +
162 bool event_busy_;
│ │ │ +
163 Index x_, y_;
│ │ │ +
164 int modifiers_, type_, our_type_, button_, buttons_;
│ │ │ +
165 bool test_running_, recording_;
│ │ │ +
166 String last_event_string_, last_names_, shortcut_;
│ │ │ +
167 String python_line_;
│ │ │ +
168 String expected_result_;
│ │ │ +
169 MyEventThread thread_;
│ │ │ +
170 Size errors_;
│ │ │ +
171 QEvent* last_event_;
│ │ │ +
172 bool is_command_line_;
│ │ │ +
173 float max_run_time_;
│ │ │ +
174 Position line_nr_;
│ │ │ +
175 };
│ │ │ +
│ │ │ +
176
│ │ │ +
177} } // namespaces
│ │ │ +
178
│ │ │ +
179#endif // BALL_VIEW_WIDGETS_TESTFRAMEWORK_H
│ │ │ + │ │ │ +
BALL_EMBEDDABLE
#define BALL_EMBEDDABLE(TYPE, BASE)
Definition embeddable.h:31
│ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │ -
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
│ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
BALL_VIEW_EXPORT
#define BALL_VIEW_EXPORT
Definition COMMON/global.h:52
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ │
│ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,72 +1,179 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_Y_S_T_E_M │ │ │ │ -sysinfo.h │ │ │ │ + * _V_I_E_W │ │ │ │ + * _W_I_D_G_E_T_S │ │ │ │ +testFramework.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: sysinfo.h,v 1.10 2005/12/23 17:02:07 amoll Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_SYSTEM_SYSINFO_H │ │ │ │ -8#define BALL_SYSTEM_SYSINFO_H │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_COMMON_H │ │ │ │ -11# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -12#endif │ │ │ │ -13 │ │ │ │ -14namespace _B_A_L_L │ │ │ │ -15{ │ │ │ │ -_2_3 namespace SysInfo │ │ │ │ -24 { │ │ │ │ -_2_8 _B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x _g_e_t_A_v_a_i_l_a_b_l_e_M_e_m_o_r_y(); │ │ │ │ -29 │ │ │ │ -_3_3 _B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x _g_e_t_F_r_e_e_M_e_m_o_r_y(); │ │ │ │ -34 │ │ │ │ -_3_8 _B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x _g_e_t_T_o_t_a_l_M_e_m_o_r_y(); │ │ │ │ -39 │ │ │ │ -_4_3 _B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x _g_e_t_B_u_f_f_e_r_e_d_M_e_m_o_r_y(); │ │ │ │ -44 │ │ │ │ -_4_8 _B_A_L_L___E_X_P_O_R_T _L_o_n_g_I_n_d_e_x _g_e_t_F_r_e_e_S_w_a_p_S_p_a_c_e(); │ │ │ │ -49 │ │ │ │ -_5_4 _B_A_L_L___E_X_P_O_R_T _T_i_m_e _g_e_t_U_p_t_i_m_e(); │ │ │ │ -55 │ │ │ │ -_5_9 _B_A_L_L___E_X_P_O_R_T _I_n_d_e_x _g_e_t_N_u_m_b_e_r_O_f_P_r_o_c_e_s_s_o_r_s(); │ │ │ │ -60 } │ │ │ │ -61} │ │ │ │ -62 │ │ │ │ -63#endif // BALL_SYSTEM_SYSINFO_H │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_VIEW_WIDGETS_TESTFRAMEWORK_H │ │ │ │ +6#define BALL_VIEW_WIDGETS_TESTFRAMEWORK_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_VIEW_WIDGETS_DOCKWIDGET_H │ │ │ │ +9# include <_B_A_L_L_/_V_I_E_W_/_W_I_D_G_E_T_S_/_d_o_c_k_W_i_d_g_e_t_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12#ifndef BALL_SYSTEM_FILE_H │ │ │ │ +13# include <_B_A_L_L_/_S_Y_S_T_E_M_/_f_i_l_e_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifndef BALL_SYSTEM_TIMER_H │ │ │ │ +17# include <_B_A_L_L_/_S_Y_S_T_E_M_/_t_i_m_e_r_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20#include │ │ │ │ +21 │ │ │ │ +22class QAction; │ │ │ │ +23 │ │ │ │ +24namespace _B_A_L_L │ │ │ │ +25{ │ │ │ │ +26 namespace VIEW │ │ │ │ +27 { │ │ │ │ +_5_8 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _T_e_s_t_F_r_a_m_e_w_o_r_k │ │ │ │ +59 : public _Q_W_i_d_g_e_t, │ │ │ │ +60 public _M_o_d_u_l_a_r_W_i_d_g_e_t │ │ │ │ +61 { │ │ │ │ +62 Q_OBJECT │ │ │ │ +63 │ │ │ │ +64 class MyMouseEvent │ │ │ │ +65 : public _Q_M_o_u_s_e_E_v_e_n_t │ │ │ │ +66 { │ │ │ │ +67 public: │ │ │ │ +68 │ │ │ │ +69 MyMouseEvent(Type type, const QPoint & position, Qt::MouseButton button, │ │ │ │ +70 Qt::MouseButtons buttons, Qt::KeyboardModifiers modifiers) │ │ │ │ +71 : _Q_M_o_u_s_e_E_v_e_n_t(type, position, button, buttons, modifiers) {} │ │ │ │ +72 }; │ │ │ │ +73 │ │ │ │ +74 class MyEventThread │ │ │ │ +75 : public _Q_T_h_r_e_a_d │ │ │ │ +76 { │ │ │ │ +77 public: │ │ │ │ +78 │ │ │ │ +79 MyEventThread(); │ │ │ │ +80 │ │ │ │ +81 virtual void run(); │ │ │ │ +82 │ │ │ │ +83 _T_e_s_t_F_r_a_m_e_w_o_r_k* tf; │ │ │ │ +84 _M_a_i_n_C_o_n_t_r_o_l* mc; │ │ │ │ +85 }; │ │ │ │ +86 │ │ │ │ +_8_7 friend class MyEventThread; │ │ │ │ +88 │ │ │ │ +89 public: │ │ │ │ +90 │ │ │ │ +91 _B_A_L_L___E_M_B_E_D_D_A_B_L_E(_T_e_s_t_F_r_a_m_e_w_o_r_k,_D_o_c_k_W_i_d_g_e_t) │ │ │ │ +92 │ │ │ │ +93 │ │ │ │ +_9_4 _T_e_s_t_F_r_a_m_e_w_o_r_k(_Q_W_i_d_g_e_t *parent = 0, const char *name = 0); │ │ │ │ +95 │ │ │ │ +_9_7 virtual ~_T_e_s_t_F_r_a_m_e_w_o_r_k(); │ │ │ │ +98 │ │ │ │ +99 // │ │ │ │ +_1_0_0 virtual void initializeWidget(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ +101 │ │ │ │ +_1_0_3 void setFilename(const _S_t_r_i_n_g& filename); │ │ │ │ +104 │ │ │ │ +_1_0_6 void checkMenu(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ +107 │ │ │ │ +_1_0_9 virtual bool canHandle(const _S_t_r_i_n_g& fileformat) const; │ │ │ │ +110 │ │ │ │ +_1_1_2 virtual bool openFile(const _S_t_r_i_n_g& filename); │ │ │ │ +113 │ │ │ │ +114 public Q_SLOTS: │ │ │ │ +115 │ │ │ │ +_1_1_7 void startTest(); │ │ │ │ +118 │ │ │ │ +_1_2_0 void stopTest(); │ │ │ │ +121 │ │ │ │ +_1_2_3 void runTest(); │ │ │ │ +124 │ │ │ │ +_1_2_6 void abortTest(); │ │ │ │ +127 │ │ │ │ +_1_2_9 void saveFile(); │ │ │ │ +130 │ │ │ │ +_1_3_2 void loadFile(); │ │ │ │ +133 │ │ │ │ +_1_3_5 virtual bool eventFilter(_Q_O_b_j_e_c_t*, _Q_E_v_e_n_t* e); │ │ │ │ +136 │ │ │ │ +_1_3_8 virtual void timeOut(); │ │ │ │ +139 │ │ │ │ +_1_4_1 void switchRecordMove(); │ │ │ │ +142 │ │ │ │ +143 protected: │ │ │ │ +144 │ │ │ │ +_1_4_5 virtual bool event(_Q_E_v_e_n_t* e); │ │ │ │ +146 │ │ │ │ +_1_4_7 void storeEvent(_Q_E_v_e_n_t& e); │ │ │ │ +148 │ │ │ │ +_1_4_9 void processEvent_(); │ │ │ │ +150 │ │ │ │ +_1_5_1 QAction* start_recording, *stop_recording, *run_test, *abort_test, │ │ │ │ +_1_5_2 *save_file, *load_file, *switch_move; │ │ │ │ +_1_5_3 QAction* action_; │ │ │ │ +154 │ │ │ │ +_1_5_5 _F_i_l_e outfile_; │ │ │ │ +_1_5_6 _F_i_l_e infile_; │ │ │ │ +_1_5_7 _S_t_r_i_n_g filename_; │ │ │ │ +_1_5_8 _T_i_m_e_r timer_, runtime_; │ │ │ │ +_1_5_9 list<_S_t_r_i_n_g>lines_; │ │ │ │ +_1_6_0 _Q_W_i_d_g_e_t* widget_, *last_widget_; │ │ │ │ +_1_6_1 float time_; │ │ │ │ +_1_6_2 bool event_busy_; │ │ │ │ +_1_6_3 _I_n_d_e_x x_, y_; │ │ │ │ +_1_6_4 int modifiers_, type_, our_type_, button_, buttons_; │ │ │ │ +_1_6_5 bool test_running_, recording_; │ │ │ │ +_1_6_6 _S_t_r_i_n_g last_event_string_, last_names_, shortcut_; │ │ │ │ +_1_6_7 _S_t_r_i_n_g python_line_; │ │ │ │ +_1_6_8 _S_t_r_i_n_g expected_result_; │ │ │ │ +_1_6_9 MyEventThread thread_; │ │ │ │ +_1_7_0 _S_i_z_e errors_; │ │ │ │ +_1_7_1 _Q_E_v_e_n_t* last_event_; │ │ │ │ +_1_7_2 bool is_command_line_; │ │ │ │ +_1_7_3 float max_run_time_; │ │ │ │ +_1_7_4 _P_o_s_i_t_i_o_n line_nr_; │ │ │ │ +175 }; │ │ │ │ +176 │ │ │ │ +177} } // namespaces │ │ │ │ +178 │ │ │ │ +179#endif // BALL_VIEW_WIDGETS_TESTFRAMEWORK_H │ │ │ │ +_d_o_c_k_W_i_d_g_e_t_._h │ │ │ │ +_B_A_L_L___E_M_B_E_D_D_A_B_L_E │ │ │ │ +#define BALL_EMBEDDABLE(TYPE, BASE) │ │ │ │ +DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_3_1 │ │ │ │ +_t_i_m_e_r_._h │ │ │ │ +_f_i_l_e_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_T_i_m_e │ │ │ │ -time_t Time │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_1_2_3 │ │ │ │ -_B_A_L_L_:_:_L_o_n_g_I_n_d_e_x │ │ │ │ -BALL_LONG64_TYPE LongIndex │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_2_0_1 │ │ │ │ -_B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_N_u_m_b_e_r_O_f_P_r_o_c_e_s_s_o_r_s │ │ │ │ -BALL_EXPORT Index getNumberOfProcessors() │ │ │ │ -_B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_A_v_a_i_l_a_b_l_e_M_e_m_o_r_y │ │ │ │ -BALL_EXPORT LongIndex getAvailableMemory() │ │ │ │ -_B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_B_u_f_f_e_r_e_d_M_e_m_o_r_y │ │ │ │ -BALL_EXPORT LongIndex getBufferedMemory() │ │ │ │ -_B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_F_r_e_e_M_e_m_o_r_y │ │ │ │ -BALL_EXPORT LongIndex getFreeMemory() │ │ │ │ -_B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_F_r_e_e_S_w_a_p_S_p_a_c_e │ │ │ │ -BALL_EXPORT LongIndex getFreeSwapSpace() │ │ │ │ -_B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_U_p_t_i_m_e │ │ │ │ -BALL_EXPORT Time getUptime() │ │ │ │ -_B_A_L_L_:_:_S_y_s_I_n_f_o_:_:_g_e_t_T_o_t_a_l_M_e_m_o_r_y │ │ │ │ -BALL_EXPORT LongIndex getTotalMemory() │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_F_i_l_e │ │ │ │ +DDeeffiinniittiioonn _f_i_l_e_._h_:_1_3_6 │ │ │ │ +_B_A_L_L_:_:_T_i_m_e_r │ │ │ │ +DDeeffiinniittiioonn _t_i_m_e_r_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t │ │ │ │ +DDeeffiinniittiioonn _m_o_d_u_l_a_r_W_i_d_g_e_t_._h_:_6_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_D_o_c_k_W_i_d_g_e_t │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_W_i_d_g_e_t_._h_:_2_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_T_e_s_t_F_r_a_m_e_w_o_r_k │ │ │ │ +DDeeffiinniittiioonn _t_e_s_t_F_r_a_m_e_w_o_r_k_._h_:_6_1 │ │ │ │ _B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_Q_O_b_j_e_c_t │ │ │ │ +_Q_T_h_r_e_a_d │ │ │ │ +_Q_W_i_d_g_e_t │ │ │ │ +_Q_E_v_e_n_t │ │ │ │ +_Q_M_o_u_s_e_E_v_e_n_t │ │ │ │ +_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ +#define BALL_VIEW_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d1d/a06954.html │ │ │ @@ -76,28 +76,28 @@ │ │ │
│ │ │ Static Public Attributes | │ │ │ List of all members
│ │ │
BALL::HybridisationProcessor::Method Struct Reference
│ │ │ │ │ │
│ │ │ │ │ │ -

#include <BALL/STRUCTURE/hybridisationProcessor.h>

│ │ │ +

#include <BALL/STRUCTURE/hybridisationProcessor.h>

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

│ │ │ Static Public Attributes

static const String SMART_MATCHING
 
static const String STRUCTURE_BASED
 
static const String FF_BASED
 
│ │ │

Detailed Description

│ │ │
│ │ │ -

Definition at line 94 of file hybridisationProcessor.h.

│ │ │ +

Definition at line 94 of file hybridisationProcessor.h.

│ │ │

Member Data Documentation

│ │ │ │ │ │

◆ FF_BASED

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ @@ -111,15 +111,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ static
│ │ │
│ │ │ │ │ │ -

Definition at line 98 of file hybridisationProcessor.h.

│ │ │ +

Definition at line 98 of file hybridisationProcessor.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ SMART_MATCHING

│ │ │ │ │ │
│ │ │ @@ -135,15 +135,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 96 of file hybridisationProcessor.h.

│ │ │ +

Definition at line 96 of file hybridisationProcessor.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ STRUCTURE_BASED

│ │ │ │ │ │
│ │ │ @@ -159,15 +159,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 97 of file hybridisationProcessor.h.

│ │ │ +

Definition at line 97 of file hybridisationProcessor.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d1e/a03674.html │ │ │ @@ -203,15 +203,15 @@ │ │ │ 00000ca0: 2e20 200a 203c 6120 6872 6566 3d22 2e2e . . │ │ │ 00000cd0: 4d6f 7265 2e2e 2e3c 2f61 3e3c 2f70 3e0a More...

. │ │ │ 00000ce0: 0a3c 703e 3c63 6f64 653e 2369 6e63 6c75 .

#inclu │ │ │ 00000cf0: 6465 2026 6c74 3b3c 6120 636c 6173 733d de <BALL │ │ │ 00000d30: 2f44 4f43 4b49 4e47 2f43 4f4d 4d4f 4e2f /DOCKING/COMMON/ │ │ │ 00000d40: 706f 7365 436c 7573 7465 7269 6e67 2e68 poseClustering.h │ │ │ 00000d50: 3c2f 613e 2667 743b 3c2f 636f 6465 3e3c >< │ │ │ 00000d60: 2f70 3e0a 3c74 6162 6c65 2063 6c61 7373 /p>.. │ │ │ 00000d80: 3c74 7220 636c 6173 733d 2268 6561 6469 Index │ │ │ 00007730: 3c2f 613e 2072 6d73 645f 6c65 7665 6c5f rmsd_level_ │ │ │ 00007740: 6f66 5f64 6574 6169 6c3d 3c61 2063 6c61 of_detail=C_ALPH │ │ │ 000077a0: 413c 2f61 3e29 3c2f 7464 3e3c 2f74 723e A) │ │ │ 000077b0: 0a3c 7472 2063 6c61 7373 3d22 7365 7061 .
..

Definition at l │ │ │ 000108a0: 696e 6520 3c61 2063 6c61 7373 3d22 656c ine │ │ │ 000108e0: 3132 363c 2f61 3e20 6f66 2066 696c 6520 126 of file │ │ │ 000108f0: 3c61 2063 6c61 7373 3d22 656c 2220 6872 poseCluster │ │ │ 00010930: 696e 672e 683c 2f61 3e2e 3c2f 703e 0a3c ing.h.

.< │ │ │ 00010940: 2f64 6976 3e3c 6832 2063 6c61 7373 3d22 /div>

Mem │ │ │ 00010960: 6265 7220 5479 7065 6465 6620 446f 6375 ber Typedef Docu │ │ │ 00010970: 6d65 6e74 6174 696f 6e3c 2f68 323e 0a3c mentation

.< │ │ │ 00010980: 6120 6964 3d22 6139 6163 3337 3538 3963 a id="a9ac37589c │ │ │ @@ -4290,20 +4290,20 @@ │ │ │ 00010c10: 0a20 2020 2020 203c 2f74 6162 6c65 3e0a .
. │ │ │ 00010c20: 3c2f 6469 763e 3c64 6976 2063 6c61 7373

..

Definition at │ │ │ 00010c60: 6c69 6e65 203c 6120 636c 6173 733d 2265 line 277 of file │ │ │ 00010cb0: 203c 6120 636c 6173 733d 2265 6c22 2068 poseCluste │ │ │ 00010cf0: 7269 6e67 2e68 3c2f 613e 2e3c 2f70 3e0a ring.h.

. │ │ │ 00010d00: 0a3c 2f64 6976 3e0a 3c2f 6469 763e 0a3c .
..< │ │ │ 00010d10: 6120 6964 3d22 6162 3863 3561 3065 6136 a id="ab8c5a0ea6 │ │ │ 00010d20: 3631 3830 3764 3630 3637 3135 6334 3137 61807d606715c417 │ │ │ 00010d30: 6532 3063 3263 3222 206e 616d 653d 2261 e20c2c2" name="a │ │ │ 00010d40: 6238 6335 6130 6561 3636 3138 3037 6436 b8c5a0ea661807d6 │ │ │ @@ -4338,20 +4338,20 @@ │ │ │ 00010f10: 2020 203c 2f74 723e 0a20 2020 2020 203c . < │ │ │ 00010f20: 2f74 6162 6c65 3e0a 3c2f 6469 763e 3c64 /table>...

Defini │ │ │ 00010f60: 7469 6f6e 2061 7420 6c69 6e65 203c 6120 tion at line 279 │ │ │ 00010fb0: 206f 6620 6669 6c65 203c 6120 636c 6173 of file po │ │ │ 00010ff0: 7365 436c 7573 7465 7269 6e67 2e68 3c2f seClustering.h.

... │ │ │ 00011010: 3c2f 6469 763e 0a3c 6832 2063 6c61 7373 .

C │ │ │ 00011030: 6f6e 7374 7275 6374 6f72 2026 616d 703b onstructor & │ │ │ 00011040: 2044 6573 7472 7563 746f 7220 446f 6375 Destructor Docu │ │ │ @@ -5143,16 +5143,16 @@ │ │ │ 00014160: 3238 3638 223e 496e 6465 783c 2f61 3e26 2868">Index& │ │ │ 00014170: 2331 3630 3b3c 2f74 643e 0a20 2020 2020 #160;. │ │ │ 00014180: 2020 2020 203c 7464 2063 6c61 7373 3d22 r │ │ │ 000141a0: 6d73 645f 6c65 7665 6c5f 6f66 5f64 6574 msd_level_of_det │ │ │ 000141b0: 6169 6c3c 2f65 6d3e 203d 203c 636f 6465 ail = C_ALPHA . │ │ │ 00014230: 2020 2020 2020 203c 2f74 723e 0a20 2020 . │ │ │ 00014240: 2020 2020 203c 7472 3e0a 2020 2020 2020 . │ │ │ 00014250: 2020 2020 3c74 643e 3c2f 7464 3e0a 2020 . │ │ │ @@ -5900,21 +5900,21 @@ │ │ │ 000170b0: 7265 663d 222e 2e2f 2e2e 2f64 312f 6463 ref="../../d1/dc │ │ │ 000170c0: 392f 6130 3636 3530 2e68 746d 6c22 3e41 9/a06650.html">A │ │ │ 000170d0: 746f 6d42 696a 6563 7469 6f6e 3c2f 613e tomBijection │ │ │ 000170e0: 203c 2f70 3e0a 0a3c 7020 636c 6173 733d

..

Def │ │ │ 00017100: 696e 6974 696f 6e20 6174 206c 696e 6520 inition at line │ │ │ 00017110: 3c61 2063 6c61 7373 3d22 656c 2220 6872 373< │ │ │ 00017150: 2f61 3e20 6f66 2066 696c 6520 3c61 2063 /a> of file poseClustering. │ │ │ 000171a0: 683c 2f61 3e2e 3c2f 703e 0a0a 3c2f 6469 h.

....AtomBi │ │ │ 00017560: 6a65 6374 696f 6e3c 2f61 3e20 3c2f 703e jection

│ │ │ 00017570: 0a0a 3c70 2063 6c61 7373 3d22 6465 6669 ..

Definiti │ │ │ 00017590: 6f6e 2061 7420 6c69 6e65 203c 6120 636c on at line 376 o │ │ │ 000175e0: 6620 6669 6c65 203c 6120 636c 6173 733d f file pose │ │ │ 00017620: 436c 7573 7465 7269 6e67 2e68 3c2f 613e Clustering.h │ │ │ 00017630: 2e3c 2f70 3e0a 0a3c 2f64 6976 3e0a 3c2f .

....D │ │ │ 00017a20: 6566 696e 6974 696f 6e20 6174 206c 696e efinition at lin │ │ │ 00017a30: 6520 3c61 2063 6c61 7373 3d22 656c 2220 e 33 │ │ │ 00017a70: 383c 2f61 3e20 6f66 2066 696c 6520 3c61 8 of file poseClusterin │ │ │ 00017ac0: 672e 683c 2f61 3e2e 3c2f 703e 0a0a 3c2f g.h.

....Definition at │ │ │ 00017ee0: 6c69 6e65 203c 6120 636c 6173 733d 2265 line 341 of file │ │ │ 00017f30: 203c 6120 636c 6173 733d 2265 6c22 2068 poseCluste │ │ │ 00017f70: 7269 6e67 2e68 3c2f 613e 2e3c 2f70 3e0a ring.h.

. │ │ │ 00017f80: 0a3c 2f64 6976 3e0a 3c2f 6469 763e 0a3c ...< │ │ │ 00017f90: 6120 6964 3d22 6162 6661 3331 6334 6233 a id="abfa31c4b3 │ │ │ 00017fa0: 6465 3266 6636 6338 6132 3231 6466 3134 de2ff6c8a221df14 │ │ │ 00017fb0: 3061 6331 3537 3922 206e 616d 653d 2261 0ac1579" name="a │ │ │ 00017fc0: 6266 6133 3163 3462 3364 6532 6666 3663 bfa31c4b3de2ff6c │ │ │ @@ -6618,20 +6618,20 @@ │ │ │ 00019d90: 2e2f 6436 2f64 3831 2f61 3033 3633 302e ./d6/d81/a03630. │ │ │ 00019da0: 6874 6d6c 223e 436f 6e66 6f72 6d61 7469 html">Conformati │ │ │ 00019db0: 6f6e 5365 743c 2f61 3e20 3c2f 703e 0a0a onSet

.. │ │ │ 00019dc0: 3c70 2063 6c61 7373 3d22 6465 6669 6e69

Definition │ │ │ 00019de0: 2061 7420 6c69 6e65 203c 6120 636c 6173 at line 332 of │ │ │ 00019e30: 6669 6c65 203c 6120 636c 6173 733d 2265 file poseCl │ │ │ 00019e70: 7573 7465 7269 6e67 2e68 3c2f 613e 2e3c ustering.h.< │ │ │ 00019e80: 2f70 3e0a 0a3c 2f64 6976 3e0a 3c2f 6469 /p>....ConformationSet │ │ │ 0001a240: 3c2f 613e 203c 2f70 3e0a 0a3c 7020 636c

..

Definition at l │ │ │ 0001a270: 696e 6520 3c61 2063 6c61 7373 3d22 656c ine │ │ │ 0001a2b0: 3332 393c 2f61 3e20 6f66 2066 696c 6520 329 of file │ │ │ 0001a2c0: 3c61 2063 6c61 7373 3d22 656c 2220 6872 poseCluster │ │ │ 0001a300: 696e 672e 683c 2f61 3e2e 3c2f 703e 0a0a ing.h.

.. │ │ │ 0001a310: 3c2f 6469 763e 0a3c 2f64 6976 3e0a 3c61 ..Definitio │ │ │ 0001a6a0: 6e20 6174 206c 696e 6520 3c61 2063 6c61 n at line 353 of │ │ │ 0001a6f0: 2066 696c 6520 3c61 2063 6c61 7373 3d22 file poseC │ │ │ 0001a730: 6c75 7374 6572 696e 672e 683c 2f61 3e2e lustering.h. │ │ │ 0001a740: 3c2f 703e 0a0a 3c2f 6469 763e 0a3c 2f64

......

returns th │ │ │ 0001aa90: 6520 6e75 6d62 6572 206f 6620 706f 7365 e number of pose │ │ │ 0001aaa0: 7320 3c2f 703e 0a0a 3c70 2063 6c61 7373 s

..

De │ │ │ 0001aac0: 6669 6e69 7469 6f6e 2061 7420 6c69 6e65 finition at line │ │ │ 0001aad0: 203c 6120 636c 6173 733d 2265 6c22 2068 350 │ │ │ 0001ab10: 3c2f 613e 206f 6620 6669 6c65 203c 6120 of file poseClustering │ │ │ 0001ab60: 2e68 3c2f 613e 2e3c 2f70 3e0a 0a3c 2f64 .h.

....Po │ │ │ 0001b240: 7365 506f 696e 7465 723c 2f61 3e20 3c2f sePointer ..

Defini │ │ │ 0001b270: 7469 6f6e 2061 7420 6c69 6e65 203c 6120 tion at line 397 │ │ │ 0001b2c0: 206f 6620 6669 6c65 203c 6120 636c 6173 of file po │ │ │ 0001b300: 7365 436c 7573 7465 7269 6e67 2e68 3c2f seClustering.h.

... │ │ │ 0001b320: 3c2f 6469 763e 0a3c 6120 6964 3d22 6134 .Definit │ │ │ 0001c160: 696f 6e20 6174 206c 696e 6520 3c61 2063 ion at line 335 │ │ │ 0001c1b0: 6f66 2066 696c 6520 3c61 2063 6c61 7373 of file pos │ │ │ 0001c1f0: 6543 6c75 7374 6572 696e 672e 683c 2f61 eClustering.h.

...< │ │ │ 0001c210: 2f64 6976 3e0a 3c61 2069 643d 2261 3561 /div>...

Definition at │ │ │ 00022ef0: 206c 696e 6520 3c61 2063 6c61 7373 3d22 line 733 of fil │ │ │ 00022f40: 6520 3c61 2063 6c61 7373 3d22 656c 2220 e poseClust │ │ │ 00022f80: 6572 696e 672e 683c 2f61 3e2e 3c2f 703e ering.h.

│ │ │ 00022f90: 0a0a 3c2f 6469 763e 0a3c 2f64 6976 3e0a .... │ │ │ 00022fa0: 3c61 2069 643d 2261 3738 6561 3766 3433 ..

Defi │ │ │ 00023270: 6e69 7469 6f6e 2061 7420 6c69 6e65 203c nition at line < │ │ │ 00023280: 6120 636c 6173 733d 2265 6c22 2068 7265 a class="el" hre │ │ │ -00023290: 663d 222e 2e2f 2e2e 2f64 392f 6464 352f f="../../d9/dd5/ │ │ │ -000232a0: 6130 3138 3836 5f73 6f75 7263 652e 6874 a01886_source.ht │ │ │ +00023290: 663d 222e 2e2f 2e2e 2f64 382f 6464 302f f="../../d8/dd0/ │ │ │ +000232a0: 6130 3134 3330 5f73 6f75 7263 652e 6874 a01430_source.ht │ │ │ 000232b0: 6d6c 236c 3030 3639 3822 3e36 3938 3c2f ml#l00698">698 of file │ │ │ +000232e0: 2e2f 2e2e 2f64 382f 6464 302f 6130 3134 ./../d8/dd0/a014 │ │ │ +000232f0: 3330 5f73 6f75 7263 652e 6874 6d6c 223e 30_source.html"> │ │ │ 00023300: 706f 7365 436c 7573 7465 7269 6e67 2e68 poseClustering.h │ │ │ 00023310: 3c2f 613e 2e3c 2f70 3e0a 0a3c 2f64 6976 .

..... │ │ │ 000235d0: 0a3c 7020 636c 6173 733d 2264 6566 696e .

Definitio │ │ │ 000235f0: 6e20 6174 206c 696e 6520 3c61 2063 6c61 n at line 695 of │ │ │ 00023640: 2066 696c 6520 3c61 2063 6c61 7373 3d22 file poseC │ │ │ 00023680: 6c75 7374 6572 696e 672e 683c 2f61 3e2e lustering.h. │ │ │ 00023690: 3c2f 703e 0a0a 3c2f 6469 763e 0a3c 2f64

......

│ │ │ 000239b0: 4465 6669 6e69 7469 6f6e 2061 7420 6c69 Definition at li │ │ │ 000239c0: 6e65 203c 6120 636c 6173 733d 2265 6c22 ne 6 │ │ │ 00023a00: 3736 3c2f 613e 206f 6620 6669 6c65 203c 76 of file < │ │ │ 00023a10: 6120 636c 6173 733d 2265 6c22 2068 7265 a class="el" hre │ │ │ -00023a20: 663d 222e 2e2f 2e2e 2f64 392f 6464 352f f="../../d9/dd5/ │ │ │ -00023a30: 6130 3138 3836 5f73 6f75 7263 652e 6874 a01886_source.ht │ │ │ +00023a20: 663d 222e 2e2f 2e2e 2f64 382f 6464 302f f="../../d8/dd0/ │ │ │ +00023a30: 6130 3134 3330 5f73 6f75 7263 652e 6874 a01430_source.ht │ │ │ 00023a40: 6d6c 223e 706f 7365 436c 7573 7465 7269 ml">poseClusteri │ │ │ 00023a50: 6e67 2e68 3c2f 613e 2e3c 2f70 3e0a 0a3c ng.h.

..< │ │ │ 00023a60: 2f64 6976 3e0a 3c2f 6469 763e 0a3c 6120 /div>....< │ │ │ 00023d30: 703e 7468 6520 7363 6f72 6573 206f 6620 p>the scores of │ │ │ 00023d40: 7468 6520 636c 7573 7465 7273 203c 2f70 the clusters

..

Definit │ │ │ 00023d70: 696f 6e20 6174 206c 696e 6520 3c61 2063 ion at line 679 │ │ │ 00023dc0: 6f66 2066 696c 6520 3c61 2063 6c61 7373 of file pos │ │ │ 00023e00: 6543 6c75 7374 6572 696e 672e 683c 2f61 eClustering.h.

...< │ │ │ 00023e20: 2f64 6976 3e0a 3c61 2069 643d 2261 6632 /div>.Definition │ │ │ 00024150: 6174 206c 696e 6520 3c61 2063 6c61 7373 at line 740 of f │ │ │ 000241a0: 696c 6520 3c61 2063 6c61 7373 3d22 656c ile poseClu │ │ │ 000241e0: 7374 6572 696e 672e 683c 2f61 3e2e 3c2f stering.h.......

the │ │ │ 000244f0: 2063 6c75 7374 6572 733a 2073 6574 7320 clusters: sets │ │ │ 00024500: 6f66 2070 6f73 6520 696e 6469 6365 7320 of pose indices │ │ │ 00024510: 3c2f 703e 0a0a 3c70 2063 6c61 7373 3d22

..

Defi │ │ │ 00024530: 6e69 7469 6f6e 2061 7420 6c69 6e65 203c nition at line < │ │ │ 00024540: 6120 636c 6173 733d 2265 6c22 2068 7265 a class="el" hre │ │ │ -00024550: 663d 222e 2e2f 2e2e 2f64 392f 6464 352f f="../../d9/dd5/ │ │ │ -00024560: 6130 3138 3836 5f73 6f75 7263 652e 6874 a01886_source.ht │ │ │ +00024550: 663d 222e 2e2f 2e2e 2f64 382f 6464 302f f="../../d8/dd0/ │ │ │ +00024560: 6130 3134 3330 5f73 6f75 7263 652e 6874 a01430_source.ht │ │ │ 00024570: 6d6c 236c 3030 3637 3422 3e36 3734 3c2f ml#l00674">674 of file │ │ │ +000245a0: 2e2f 2e2e 2f64 382f 6464 302f 6130 3134 ./../d8/dd0/a014 │ │ │ +000245b0: 3330 5f73 6f75 7263 652e 6874 6d6c 223e 30_source.html"> │ │ │ 000245c0: 706f 7365 436c 7573 7465 7269 6e67 2e68 poseClustering.h │ │ │ 000245d0: 3c2f 613e 2e3c 2f70 3e0a 0a3c 2f64 6976 .

......

Def │ │ │ 000248d0: 696e 6974 696f 6e20 6174 206c 696e 6520 inition at line │ │ │ 000248e0: 3c61 2063 6c61 7373 3d22 656c 2220 6872 726< │ │ │ 00024920: 2f61 3e20 6f66 2066 696c 6520 3c61 2063 /a> of file poseClustering. │ │ │ 00024970: 683c 2f61 3e2e 3c2f 703e 0a0a 3c2f 6469 h.

......

Defin │ │ │ 00024c30: 6974 696f 6e20 6174 206c 696e 6520 3c61 ition at line 692 of file p │ │ │ +00024ca0: 2f2e 2e2f 6438 2f64 6430 2f61 3031 3433 /../d8/dd0/a0143 │ │ │ +00024cb0: 305f 736f 7572 6365 2e68 746d 6c22 3e70 0_source.html">p │ │ │ 00024cc0: 6f73 6543 6c75 7374 6572 696e 672e 683c oseClustering.h< │ │ │ 00024cd0: 2f61 3e2e 3c2f 703e 0a0a 3c2f 6469 763e /a>.

.. │ │ │ 00024ce0: 0a3c 2f64 6976 3e0a 3c61 2069 643d 2261 ..Definition at │ │ │ 00025020: 6c69 6e65 203c 6120 636c 6173 733d 2265 line 671 of file │ │ │ 00025070: 203c 6120 636c 6173 733d 2265 6c22 2068 poseCluste │ │ │ 000250b0: 7269 6e67 2e68 3c2f 613e 2e3c 2f70 3e0a ring.h.

. │ │ │ 000250c0: 0a3c 2f64 6976 3e0a 3c2f 6469 763e 0a3c ...< │ │ │ 000250d0: 6120 6964 3d22 6135 3864 3161 3230 3535 a id="a58d1a2055 │ │ │ 000250e0: 6533 6562 3538 6133 3736 3133 3138 3364 e3eb58a37613183d │ │ │ 000250f0: 3338 3266 6662 6322 206e 616d 653d 2261 382ffbc" name="a │ │ │ 00025100: 3538 6431 6132 3035 3565 3365 6235 3861 58d1a2055e3eb58a │ │ │ @@ -9527,20 +9527,20 @@ │ │ │ 00025360: 2020 3c2f 7472 3e0a 3c2f 7461 626c 653e . │ │ │ 00025370: 0a3c 2f64 6976 3e3c 6469 7620 636c 6173 .
..

Definition at │ │ │ 000253b0: 206c 696e 6520 3c61 2063 6c61 7373 3d22 line 705 of fil │ │ │ 00025400: 6520 3c61 2063 6c61 7373 3d22 656c 2220 e poseClust │ │ │ 00025440: 6572 696e 672e 683c 2f61 3e2e 3c2f 703e ering.h.

│ │ │ 00025450: 0a0a 3c2f 6469 763e 0a3c 2f64 6976 3e0a ..
.. │ │ │ 00025460: 3c61 2069 643d 2261 3037 6235 3134 3831 │ │ │ 00025720: 0a0a 3c70 2063 6c61 7373 3d22 6465 6669 ..

Definiti │ │ │ 00025740: 6f6e 2061 7420 6c69 6e65 203c 6120 636c on at line 701 o │ │ │ 00025790: 6620 6669 6c65 203c 6120 636c 6173 733d f file pose │ │ │ 000257d0: 436c 7573 7465 7269 6e67 2e68 3c2f 613e Clustering.h │ │ │ 000257e0: 2e3c 2f70 3e0a 0a3c 2f64 6976 3e0a 3c2f .

......

Defi │ │ │ 00025ac0: 6e69 7469 6f6e 2061 7420 6c69 6e65 203c nition at line < │ │ │ 00025ad0: 6120 636c 6173 733d 2265 6c22 2068 7265 a class="el" hre │ │ │ -00025ae0: 663d 222e 2e2f 2e2e 2f64 392f 6464 352f f="../../d9/dd5/ │ │ │ -00025af0: 6130 3138 3836 5f73 6f75 7263 652e 6874 a01886_source.ht │ │ │ +00025ae0: 663d 222e 2e2f 2e2e 2f64 382f 6464 302f f="../../d8/dd0/ │ │ │ +00025af0: 6130 3134 3330 5f73 6f75 7263 652e 6874 a01430_source.ht │ │ │ 00025b00: 6d6c 236c 3030 3731 3122 3e37 3131 3c2f ml#l00711">711 of file │ │ │ +00025b30: 2e2f 2e2e 2f64 382f 6464 302f 6130 3134 ./../d8/dd0/a014 │ │ │ +00025b40: 3330 5f73 6f75 7263 652e 6874 6d6c 223e 30_source.html"> │ │ │ 00025b50: 706f 7365 436c 7573 7465 7269 6e67 2e68 poseClustering.h │ │ │ 00025b60: 3c2f 613e 2e3c 2f70 3e0a 0a3c 2f64 6976 .

.... │ │ │ 00025e20: 0a0a 3c70 2063 6c61 7373 3d22 6465 6669 ..

Definiti │ │ │ 00025e40: 6f6e 2061 7420 6c69 6e65 203c 6120 636c on at line 717 o │ │ │ 00025e90: 6620 6669 6c65 203c 6120 636c 6173 733d f file pose │ │ │ 00025ed0: 436c 7573 7465 7269 6e67 2e68 3c2f 613e Clustering.h │ │ │ 00025ee0: 2e3c 2f70 3e0a 0a3c 2f64 6976 3e0a 3c2f .

......

Def │ │ │ 000261f0: 696e 6974 696f 6e20 6174 206c 696e 6520 inition at line │ │ │ 00026200: 3c61 2063 6c61 7373 3d22 656c 2220 6872 721< │ │ │ 00026240: 2f61 3e20 6f66 2066 696c 6520 3c61 2063 /a> of file poseClustering. │ │ │ 00026290: 683c 2f61 3e2e 3c2f 703e 0a0a 3c2f 6469 h.

......

options

..< │ │ │ 000264a0: 7020 636c 6173 733d 2264 6566 696e 6974 p class="definit │ │ │ 000264b0: 696f 6e22 3e44 6566 696e 6974 696f 6e20 ion">Definition │ │ │ 000264c0: 6174 206c 696e 6520 3c61 2063 6c61 7373 at line 432 of f │ │ │ 00026510: 696c 6520 3c61 2063 6c61 7373 3d22 656c ile poseClu │ │ │ 00026550: 7374 6572 696e 672e 683c 2f61 3e2e 3c2f stering.h.......

D │ │ │ 00026810: 6566 696e 6974 696f 6e20 6174 206c 696e efinition at lin │ │ │ 00026820: 6520 3c61 2063 6c61 7373 3d22 656c 2220 e 66 │ │ │ 00026860: 383c 2f61 3e20 6f66 2066 696c 6520 3c61 8 of file poseClusterin │ │ │ 000268b0: 672e 683c 2f61 3e2e 3c2f 703e 0a0a 3c2f g.h.

...... │ │ │ 00026b40: 3c70 2063 6c61 7373 3d22 6465 6669 6e69

Definition │ │ │ 00026b60: 2061 7420 6c69 6e65 203c 6120 636c 6173 at line 715 of │ │ │ 00026bb0: 6669 6c65 203c 6120 636c 6173 733d 2265 file poseCl │ │ │ 00026bf0: 7573 7465 7269 6e67 2e68 3c2f 613e 2e3c ustering.h.< │ │ │ 00026c00: 2f70 3e0a 0a3c 2f64 6976 3e0a 3c2f 6469 /p>......

Def │ │ │ 00026ee0: 696e 6974 696f 6e20 6174 206c 696e 6520 inition at line │ │ │ 00026ef0: 3c61 2063 6c61 7373 3d22 656c 2220 6872 687< │ │ │ 00026f30: 2f61 3e20 6f66 2066 696c 6520 3c61 2063 /a> of file poseClustering. │ │ │ 00026f80: 683c 2f61 3e2e 3c2f 703e 0a0a 3c2f 6469 h.

......

the RMSD │ │ │ 00027280: 2064 6566 696e 6974 696f 6e20 7573 6564 definition used │ │ │ 00027290: 2066 6f72 2063 6c75 7374 6572 696e 6720 for clustering │ │ │ 000272a0: 3c2f 703e 0a0a 3c70 2063 6c61 7373 3d22

..

Defi │ │ │ 000272c0: 6e69 7469 6f6e 2061 7420 6c69 6e65 203c nition at line < │ │ │ 000272d0: 6120 636c 6173 733d 2265 6c22 2068 7265 a class="el" hre │ │ │ -000272e0: 663d 222e 2e2f 2e2e 2f64 392f 6464 352f f="../../d9/dd5/ │ │ │ -000272f0: 6130 3138 3836 5f73 6f75 7263 652e 6874 a01886_source.ht │ │ │ +000272e0: 663d 222e 2e2f 2e2e 2f64 382f 6464 302f f="../../d8/dd0/ │ │ │ +000272f0: 6130 3134 3330 5f73 6f75 7263 652e 6874 a01430_source.ht │ │ │ 00027300: 6d6c 236c 3030 3638 3222 3e36 3832 3c2f ml#l00682">682 of file │ │ │ +00027330: 2e2f 2e2e 2f64 382f 6464 302f 6130 3134 ./../d8/dd0/a014 │ │ │ +00027340: 3330 5f73 6f75 7263 652e 6874 6d6c 223e 30_source.html"> │ │ │ 00027350: 706f 7365 436c 7573 7465 7269 6e67 2e68 poseClustering.h │ │ │ 00027360: 3c2f 613e 2e3c 2f70 3e0a 0a3c 2f64 6976 .

......

Definition at l │ │ │ 00027640: 696e 6520 3c61 2063 6c61 7373 3d22 656c ine │ │ │ 00027680: 3733 363c 2f61 3e20 6f66 2066 696c 6520 736 of file │ │ │ 00027690: 3c61 2063 6c61 7373 3d22 656c 2220 6872 poseCluster │ │ │ 000276d0: 696e 672e 683c 2f61 3e2e 3c2f 703e 0a0a ing.h.

.. │ │ │ 000276e0: 3c2f 6469 763e 0a3c 2f64 6976 3e0a 3c61 .... │ │ │ 00027990: 3c70 2063 6c61 7373 3d22 6465 6669 6e69

Definition │ │ │ 000279b0: 2061 7420 6c69 6e65 203c 6120 636c 6173 at line 737 of │ │ │ 00027a00: 6669 6c65 203c 6120 636c 6173 733d 2265 file poseCl │ │ │ 00027a40: 7573 7465 7269 6e67 2e68 3c2f 613e 2e3c ustering.h.< │ │ │ 00027a50: 2f70 3e0a 0a3c 2f64 6976 3e0a 3c2f 6469 /p>......

Definit │ │ │ 00027d50: 696f 6e20 6174 206c 696e 6520 3c61 2063 ion at line 690 │ │ │ 00027da0: 6f66 2066 696c 6520 3c61 2063 6c61 7373 of file pos │ │ │ 00027de0: 6543 6c75 7374 6572 696e 672e 683c 2f61 eClustering.h.

...< │ │ │ 00027e00: 2f64 6976 3e0a 3c2f 6469 763e 3c21 2d2d /div>...
BALL::HybridisationProcessor::Option Struct Reference
│ │ │ │ │ │
│ │ │ │ │ │

Option names. │ │ │ More...

│ │ │ │ │ │ -

#include <BALL/STRUCTURE/hybridisationProcessor.h>

│ │ │ +

#include <BALL/STRUCTURE/hybridisationProcessor.h>

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

│ │ │ Static Public Attributes

static const char * ATOM_TYPE_SMARTS_FILENAME
 
static const char * ATOM_TYPE_FF_FILENAME
 
static const String METHOD
 
│ │ │

Detailed Description

│ │ │

Option names.

│ │ │ │ │ │ -

Definition at line 52 of file hybridisationProcessor.h.

│ │ │ +

Definition at line 52 of file hybridisationProcessor.h.

│ │ │

Member Data Documentation

│ │ │ │ │ │

◆ ATOM_TYPE_FF_FILENAME

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ @@ -116,15 +116,15 @@ │ │ │ │ │ │ │ │ │
│ │ │ static
│ │ │
│ │ │

Name to the file where the atom types, corresponding hybridisation states, and bond angles are stored in (force field based method).

│ │ │ │ │ │ -

Definition at line 62 of file hybridisationProcessor.h.

│ │ │ +

Definition at line 62 of file hybridisationProcessor.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ ATOM_TYPE_SMARTS_FILENAME

│ │ │ │ │ │
│ │ │ @@ -141,15 +141,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
│ │ │

Name to the file where the atom types and corresponding hybridisation states are stored in.

│ │ │ │ │ │ -

Definition at line 57 of file hybridisationProcessor.h.

│ │ │ +

Definition at line 57 of file hybridisationProcessor.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ METHOD

│ │ │ │ │ │
│ │ │ @@ -166,15 +166,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
│ │ │

If true, the existing bonds are deleted before bonds detection begins. If the atoms are in non-bond distance no bonds will be build! Note that the processor cannot rebuild inter-atomcontainer bonds, that will cause problem using it with proteins. Technique to compute the hybridisation states.

│ │ │ │ │ │ -

Definition at line 73 of file hybridisationProcessor.h.

│ │ │ +

Definition at line 73 of file hybridisationProcessor.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d22/a01049.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: diffGridBasedScoring.h File Reference │ │ │ +BALL: visitor.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,32 +65,31 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │
│ │ │ Classes | │ │ │ Namespaces
│ │ │ -
diffGridBasedScoring.h File Reference
│ │ │ +
visitor.h File Reference
│ │ │
│ │ │
│ │ │ -
#include <BALL/SCORING/COMMON/gridBasedScoring.h>
│ │ │ -#include <BALL/MOLMEC/COMMON/forceField.h>
│ │ │ +
#include <BALL/common.h>
│ │ │
│ │ │

Go to the source code of this file.

│ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

│ │ │ Classes

class  BALL::DiffGridBasedScoring
class  BALL::Visitor< Host >
 
│ │ │ │ │ │ │ │ │ │ │ │

│ │ │ Namespaces

namespace  BALL
 
│ │ │ ├── html2text {} │ │ │ │ @@ -1,21 +1,19 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_C_O_R_I_N_G │ │ │ │ - * _C_O_M_M_O_N │ │ │ │ + * _C_O_N_C_E_P_T │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -diffGridBasedScoring.h File Reference │ │ │ │ -#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_M_O_N_/_g_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_._h> │ │ │ │ +visitor.h File Reference │ │ │ │ +#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g │ │ │ │ +class   _B_A_L_L_:_:_V_i_s_i_t_o_r_<_ _H_o_s_t_ _> │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d22/a01049_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: diffGridBasedScoring.h Source File │ │ │ +BALL: visitor.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,81 +70,105 @@ │ │ │
│ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ -
diffGridBasedScoring.h
│ │ │ +
visitor.h
│ │ │
│ │ │
│ │ │ -Go to the documentation of this file.
1// ----------------------------------------------------
│ │ │ -
2// $Maintainer: Marcel Schumann $
│ │ │ -
3// $Authors: Marcel Schumann $
│ │ │ -
4// ----------------------------------------------------
│ │ │ -
5
│ │ │ -
6#ifndef BALL_SCORING_COMMON_DIFFGRIDBASEDSCORING_H
│ │ │ -
7#define BALL_SCORING_COMMON_DIFFGRIDBASEDSCORING_H
│ │ │ -
8
│ │ │ -
9#include <BALL/SCORING/COMMON/gridBasedScoring.h>
│ │ │ -
10#include <BALL/MOLMEC/COMMON/forceField.h>
│ │ │ +Go to the documentation of this file.
1// -*- Mode: C++; tab-width: 2; -*-
│ │ │ +
2// vi: set ts=2:
│ │ │ +
3//
│ │ │ +
4
│ │ │ +
5#ifndef BALL_CONCEPT_VISITOR_H
│ │ │ +
6#define BALL_CONCEPT_VISITOR_H
│ │ │ +
7
│ │ │ +
8#ifndef BALL_COMMON_H
│ │ │ +
9# include <BALL/common.h>
│ │ │ +
10#endif
│ │ │
11
│ │ │ -
12
│ │ │ -
13namespace BALL
│ │ │ -
14{
│ │ │ -
│ │ │ -
15 class BALL_EXPORT DiffGridBasedScoring : public GridBasedScoring
│ │ │ -
16 {
│ │ │ -
17 public:
│ │ │ -
18 DiffGridBasedScoring(AtomContainer& receptor, AtomContainer& ligand, Options& options);
│ │ │ -
19
│ │ │ -
20 DiffGridBasedScoring(AtomContainer& receptor, Vector3& hashgrid_origin, Options& options);
│ │ │ -
21
│ │ │ -
22 ~DiffGridBasedScoring() = default;
│ │ │ -
23
│ │ │ -
24 virtual void setLigand(AtomContainer* sys);
│ │ │ +
12namespace BALL
│ │ │ +
13{
│ │ │ +
14
│ │ │ +
21 template <typename Host>
│ │ │ +
│ │ │ +
22 class Visitor
│ │ │ +
23 {
│ │ │ +
24 public:
│ │ │
25
│ │ │ -
27 void update();
│ │ │ -
28
│ │ │ -
30 virtual double updateScore();
│ │ │ -
31
│ │ │ -
32 void testOverlaps(Vector3& position, HashGrid3<Atom*>* hashg = nullptr);
│ │ │ +
│ │ │ +
31 Visitor()
│ │ │ +
32 ;
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33
│ │ │ -
34 protected:
│ │ │ -
35 //ForceField* force_field_;
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36
│ │ │ -
39 void updatePrecalculatedScore(Size set);
│ │ │ -
40 };
│ │ │ -
│ │ │ -
41}
│ │ │ -
42
│ │ │ -
43#endif // BALL_SCORING_COMMON_DIFFGRIDBASEDSCORING_H
│ │ │ - │ │ │ - │ │ │ - │ │ │ -
BALL::HashGrid3
Three-dimensional Hash Grid Class.
Definition hashGrid.h:755
│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
BALL::DiffGridBasedScoring::setLigand
virtual void setLigand(AtomContainer *sys)
│ │ │ - │ │ │ -
BALL::DiffGridBasedScoring::DiffGridBasedScoring
DiffGridBasedScoring(AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options)
│ │ │ -
BALL::DiffGridBasedScoring::testOverlaps
void testOverlaps(Vector3 &position, HashGrid3< Atom * > *hashg=nullptr)
│ │ │ -
BALL::DiffGridBasedScoring::DiffGridBasedScoring
DiffGridBasedScoring(AtomContainer &receptor, AtomContainer &ligand, Options &options)
│ │ │ -
BALL::DiffGridBasedScoring::updatePrecalculatedScore
void updatePrecalculatedScore(Size set)
│ │ │ -
BALL::DiffGridBasedScoring::updateScore
virtual double updateScore()
│ │ │ - │ │ │ - │ │ │ - │ │ │ -
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
│ │ │ +
│ │ │ +
36 Visitor(const Visitor& visitor)
│ │ │ +
37 ;
│ │ │ +
38
│ │ │ +
│ │ │ +
41 virtual ~Visitor()
│ │ │ +
42 ;
│ │ │ +
43
│ │ │ +
45
│ │ │ +
50 virtual void visit(Host &) = 0;
│ │ │ +
51
│ │ │ +
│ │ │ +
52 virtual void dummy();
│ │ │ +
53 };
│ │ │ +
55
│ │ │ +
56 template <typename T>
│ │ │ +
57 void Visitor<T>::dummy(){}
│ │ │ +
│ │ │ +
58
│ │ │ +
59 template <typename T>
│ │ │ +
60 BALL_INLINE
│ │ │ +
│ │ │ +
61 Visitor<T>::Visitor()
│ │ │ +
62
│ │ │ +
63 {
│ │ │ +
64 }
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│ │ │ +
65
│ │ │ +
66 template <typename Host>
│ │ │ +
67 BALL_INLINE
│ │ │ +
│ │ │ +
68 Visitor<Host>::Visitor(const Visitor<Host>& /* visitor */)
│ │ │ +
69
│ │ │ +
70 {
│ │ │ +
71 }
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│ │ │ +
72
│ │ │ +
73 template <typename T>
│ │ │ +
│ │ │ +
74 Visitor<T>::~Visitor()
│ │ │ +
75
│ │ │ +
76 {
│ │ │ +
77 }
│ │ │ +
│ │ │ +
│ │ │ +
78}
│ │ │ +
79
│ │ │ +
80#endif // BALL_CONCEPT_VISITOR_H
│ │ │ +
│ │ │ +
│ │ │ +
│ │ │ + │ │ │ +
BALL_INLINE
#define BALL_INLINE
Definition debug.h:15
│ │ │ + │ │ │ + │ │ │ +
BALL::Visitor::Visitor
Visitor(const Visitor &visitor)
Definition visitor.h:68
│ │ │ +
BALL::Visitor::~Visitor
virtual ~Visitor()
Definition visitor.h:74
│ │ │ +
BALL::Visitor::dummy
virtual void dummy()
Definition visitor.h:57
│ │ │ + │ │ │ +
BALL::Visitor::visit
virtual void visit(Host &)=0
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ │
│ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,91 +1,92 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_C_O_R_I_N_G │ │ │ │ - * _C_O_M_M_O_N │ │ │ │ -diffGridBasedScoring.h │ │ │ │ + * _C_O_N_C_E_P_T │ │ │ │ +visitor.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// ---------------------------------------------------- │ │ │ │ -2// $Maintainer: Marcel Schumann $ │ │ │ │ -3// $Authors: Marcel Schumann $ │ │ │ │ -4// ---------------------------------------------------- │ │ │ │ -5 │ │ │ │ -6#ifndef BALL_SCORING_COMMON_DIFFGRIDBASEDSCORING_H │ │ │ │ -7#define BALL_SCORING_COMMON_DIFFGRIDBASEDSCORING_H │ │ │ │ -8 │ │ │ │ -9#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_M_O_N_/_g_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_._h> │ │ │ │ -10#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_._h> │ │ │ │ +1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ +2// vi: set ts=2: │ │ │ │ +3// │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_CONCEPT_VISITOR_H │ │ │ │ +6#define BALL_CONCEPT_VISITOR_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_COMMON_H │ │ │ │ +9# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +10#endif │ │ │ │ 11 │ │ │ │ -12 │ │ │ │ -13namespace _B_A_L_L │ │ │ │ -14{ │ │ │ │ -_1_5 class _B_A_L_L___E_X_P_O_R_T _D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g : public _G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g │ │ │ │ -16 { │ │ │ │ -17 public: │ │ │ │ -_1_8 _D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g(_A_t_o_m_C_o_n_t_a_i_n_e_r& receptor, _A_t_o_m_C_o_n_t_a_i_n_e_r& ligand, │ │ │ │ -_O_p_t_i_o_n_s& options); │ │ │ │ -19 │ │ │ │ -_2_0 _D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g(_A_t_o_m_C_o_n_t_a_i_n_e_r& receptor, _V_e_c_t_o_r_3& hashgrid_origin, │ │ │ │ -_O_p_t_i_o_n_s& options); │ │ │ │ -21 │ │ │ │ -_2_2 _~_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g() = default; │ │ │ │ -23 │ │ │ │ -_2_4 virtual void _s_e_t_L_i_g_a_n_d(_A_t_o_m_C_o_n_t_a_i_n_e_r* sys); │ │ │ │ +12namespace _B_A_L_L │ │ │ │ +13{ │ │ │ │ +14 │ │ │ │ +21 template │ │ │ │ +_2_2 class _V_i_s_i_t_o_r │ │ │ │ +23 { │ │ │ │ +24 public: │ │ │ │ 25 │ │ │ │ -_2_7 void _u_p_d_a_t_e(); │ │ │ │ -28 │ │ │ │ -_3_0 virtual double _u_p_d_a_t_e_S_c_o_r_e(); │ │ │ │ -31 │ │ │ │ -_3_2 void _t_e_s_t_O_v_e_r_l_a_p_s(_V_e_c_t_o_r_3& position, _H_a_s_h_G_r_i_d_3_<_A_t_o_m_*_>* hashg = nullptr); │ │ │ │ +_3_1 _V_i_s_i_t_o_r() │ │ │ │ +32 ; │ │ │ │ 33 │ │ │ │ -34 protected: │ │ │ │ -35 //ForceField* force_field_; │ │ │ │ -36 │ │ │ │ -_3_9 void _u_p_d_a_t_e_P_r_e_c_a_l_c_u_l_a_t_e_d_S_c_o_r_e(_S_i_z_e set); │ │ │ │ -40 }; │ │ │ │ -41} │ │ │ │ -42 │ │ │ │ -43#endif // BALL_SCORING_COMMON_DIFFGRIDBASEDSCORING_H │ │ │ │ -_g_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_._h │ │ │ │ -_f_o_r_c_e_F_i_e_l_d_._h │ │ │ │ +_3_6 _V_i_s_i_t_o_r(const _V_i_s_i_t_o_r& visitor) │ │ │ │ +37 ; │ │ │ │ +38 │ │ │ │ +_4_1 virtual _~_V_i_s_i_t_o_r() │ │ │ │ +42 ; │ │ │ │ +43 │ │ │ │ +45 │ │ │ │ +_5_0 virtual void _v_i_s_i_t(Host &) = 0; │ │ │ │ +51 │ │ │ │ +_5_2 virtual void _d_u_m_m_y(); │ │ │ │ +53 }; │ │ │ │ +55 │ │ │ │ +56 template │ │ │ │ +_5_7 void _V_i_s_i_t_o_r_<_T_>_:_:_d_u_m_m_y(){} │ │ │ │ +58 │ │ │ │ +59 template │ │ │ │ +60 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_6_1 _V_i_s_i_t_o_r_<_T_>_:_:_V_i_s_i_t_o_r() │ │ │ │ +62 │ │ │ │ +63 { │ │ │ │ +64 } │ │ │ │ +65 │ │ │ │ +66 template │ │ │ │ +67 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_6_8 _V_i_s_i_t_o_r_<_H_o_s_t_>_:_:_V_i_s_i_t_o_r(const _V_i_s_i_t_o_r_<_H_o_s_t_>& /* visitor */) │ │ │ │ +69 │ │ │ │ +70 { │ │ │ │ +71 } │ │ │ │ +72 │ │ │ │ +73 template │ │ │ │ +_7_4 _V_i_s_i_t_o_r_<_T_>_:_:_~_V_i_s_i_t_o_r() │ │ │ │ +75 │ │ │ │ +76 { │ │ │ │ +77 } │ │ │ │ +78} │ │ │ │ +79 │ │ │ │ +80#endif // BALL_CONCEPT_VISITOR_H │ │ │ │ +_c_o_m_m_o_n_._h │ │ │ │ +_B_A_L_L___I_N_L_I_N_E │ │ │ │ +#define BALL_INLINE │ │ │ │ +DDeeffiinniittiioonn _d_e_b_u_g_._h_:_1_5 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_G_r_i_d_3 │ │ │ │ -Three-dimensional Hash Grid Class. │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_G_r_i_d_._h_:_7_5_5 │ │ │ │ -_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ -DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _d_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_._h_:_1_6 │ │ │ │ -_B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_:_:_s_e_t_L_i_g_a_n_d │ │ │ │ -virtual void setLigand(AtomContainer *sys) │ │ │ │ -_B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_:_:_u_p_d_a_t_e │ │ │ │ -void update() │ │ │ │ -_B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g │ │ │ │ -DiffGridBasedScoring(AtomContainer &receptor, Vector3 &hashgrid_origin, Options │ │ │ │ -&options) │ │ │ │ -_B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_:_:_t_e_s_t_O_v_e_r_l_a_p_s │ │ │ │ -void testOverlaps(Vector3 &position, HashGrid3< Atom * > *hashg=nullptr) │ │ │ │ -_B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g │ │ │ │ -DiffGridBasedScoring(AtomContainer &receptor, AtomContainer &ligand, Options │ │ │ │ -&options) │ │ │ │ -_B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_:_:_u_p_d_a_t_e_P_r_e_c_a_l_c_u_l_a_t_e_d_S_c_o_r_e │ │ │ │ -void updatePrecalculatedScore(Size set) │ │ │ │ -_B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_:_:_u_p_d_a_t_e_S_c_o_r_e │ │ │ │ -virtual double updateScore() │ │ │ │ -_B_A_L_L_:_:_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_:_:_~_D_i_f_f_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g │ │ │ │ -~DiffGridBasedScoring()=default │ │ │ │ -_B_A_L_L_:_:_G_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _g_r_i_d_B_a_s_e_d_S_c_o_r_i_n_g_._h_:_2_2 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_V_i_s_i_t_o_r │ │ │ │ +DDeeffiinniittiioonn _v_i_s_i_t_o_r_._h_:_2_3 │ │ │ │ +_B_A_L_L_:_:_V_i_s_i_t_o_r_:_:_V_i_s_i_t_o_r │ │ │ │ +Visitor(const Visitor &visitor) │ │ │ │ +DDeeffiinniittiioonn _v_i_s_i_t_o_r_._h_:_6_8 │ │ │ │ +_B_A_L_L_:_:_V_i_s_i_t_o_r_:_:_~_V_i_s_i_t_o_r │ │ │ │ +virtual ~Visitor() │ │ │ │ +DDeeffiinniittiioonn _v_i_s_i_t_o_r_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_V_i_s_i_t_o_r_:_:_d_u_m_m_y │ │ │ │ +virtual void dummy() │ │ │ │ +DDeeffiinniittiioonn _v_i_s_i_t_o_r_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_V_i_s_i_t_o_r_:_:_V_i_s_i_t_o_r │ │ │ │ +Visitor() │ │ │ │ +DDeeffiinniittiioonn _v_i_s_i_t_o_r_._h_:_6_1 │ │ │ │ +_B_A_L_L_:_:_V_i_s_i_t_o_r_:_:_v_i_s_i_t │ │ │ │ +virtual void visit(Host &)=0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d22/a03142.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
│ │ │ Public Member Functions | │ │ │ List of all members
│ │ │
BALL::Exception::Postcondition Class Reference
│ │ │
│ │ │
│ │ │ │ │ │ -

#include <BALL/COMMON/exception.h>

│ │ │ +

#include <BALL/COMMON/exception.h>

│ │ │
│ │ │ Inheritance diagram for BALL::Exception::Postcondition:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ BALL::Exception::GeneralException │ │ │ @@ -138,15 +138,15 @@ │ │ │   │ │ │ std::string message_ │ │ │   │ │ │ │ │ │

Detailed Description

│ │ │

Postcondition failed. A postcondition (as defined by BALL_POSTCONDITION_EXCEPTION) has failed.

│ │ │ │ │ │ -

Definition at line 409 of file COMMON/exception.h.

│ │ │ +

Definition at line 409 of file COMMON/exception.h.

│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ Postcondition()

│ │ │ │ │ │
│ │ │
│ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d22/a05526.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
│ │ │
│ │ │ List of all members
│ │ │
BALL::ShiftModel Class Reference
Molecular Modeling » Nuclear Magnetic Resonance Spectroscopy » Shift model classes
│ │ │
│ │ │
│ │ │ │ │ │ -

#include <BALL/NMR/shiftModel.h>

│ │ │ +

#include <BALL/NMR/shiftModel.h>

│ │ │
│ │ │ Inheritance diagram for BALL::ShiftModel:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ BALL::ShiftModule │ │ │ @@ -230,30 +230,30 @@ │ │ │
│ │ │ │ │ │ │ │ │
 
bool valid_
 
│ │ │

Detailed Description

│ │ │

A class representing a complete parameterized NMR shift model. The model consists of a set of single contributions (e.g. ring curent, magnetic anisotropy, etc.). Each of these contributions is calculated by a separate ShiftModule object. ShiftModel contains a list of these processors and is also derived from ShiftModul. Hence, it can be applied to arbitrary kernel objects in the same fashion as ShiftModule s.

│ │ │ │ │ │ -

Definition at line 32 of file shiftModel.h.

│ │ │ +

Definition at line 32 of file shiftModel.h.

│ │ │

Member Typedef Documentation

│ │ │ │ │ │

◆ CreateMethod

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │
typedef void *(* BALL::ShiftModel::CreateMethod) ()
│ │ │
│ │ │

The creation method type. This type describes a method that can construct an object of type ShiftModule.

│ │ │ │ │ │ -

Definition at line 51 of file shiftModel.h.

│ │ │ +

Definition at line 51 of file shiftModel.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ CreateMethodMap

│ │ │ │ │ │
│ │ │ @@ -262,15 +262,15 @@ │ │ │ │ │ │ typedef StringHashMap<CreateMethod> BALL::ShiftModel::CreateMethodMap │ │ │ │ │ │ │ │ │
│ │ │

The creation method hash map type. This type is used internally to store the creation method corresponding to a certain symbolic name (usually the class name).

│ │ │ │ │ │ -

Definition at line 57 of file shiftModel.h.

│ │ │ +

Definition at line 57 of file shiftModel.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ ModuleList

│ │ │ │ │ │
│ │ │ @@ -279,15 +279,15 @@ │ │ │ │ │ │ typedef std::list<ShiftModule*> BALL::ShiftModel::ModuleList │ │ │ │ │ │ │ │ │
│ │ │

The module list type

│ │ │ │ │ │ -

Definition at line 45 of file shiftModel.h.

│ │ │ +

Definition at line 45 of file shiftModel.h.

│ │ │ │ │ │
│ │ │
│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ ShiftModel() [1/3]

│ │ │ │ │ │ @@ -794,15 +794,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
│ │ │

The name of the section containing the module types and names of the model

│ │ │ │ │ │ -

Definition at line 66 of file shiftModel.h.

│ │ │ +

Definition at line 66 of file shiftModel.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ modules_

│ │ │ │ │ │
│ │ │ @@ -818,15 +818,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 205 of file shiftModel.h.

│ │ │ +

Definition at line 205 of file shiftModel.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ options

│ │ │ │ │ │
│ │ │ @@ -835,15 +835,15 @@ │ │ │ │ │ │ Options BALL::ShiftModel::options │ │ │ │ │ │ │ │ │
│ │ │

Options

│ │ │ │ │ │ -

Definition at line 159 of file shiftModel.h.

│ │ │ +

Definition at line 159 of file shiftModel.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ parameters_

│ │ │ │ │ │
│ │ │ @@ -859,15 +859,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 201 of file shiftModel.h.

│ │ │ +

Definition at line 201 of file shiftModel.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ registered_modules_

│ │ │ │ │ │
│ │ │ @@ -883,15 +883,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 209 of file shiftModel.h.

│ │ │ +

Definition at line 209 of file shiftModel.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ valid_

│ │ │ │ │ │
│ │ │ @@ -907,15 +907,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 214 of file shiftModel.h.

│ │ │ +

Definition at line 214 of file shiftModel.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d22/a06722.html │ │ │ @@ -81,15 +81,15 @@ │ │ │
BALL::BondOrderAssignment Class Reference
│ │ │ │ │ │
│ │ │ │ │ │

A solution to the bond order assignment problem. │ │ │ More...

│ │ │ │ │ │ -

#include <BALL/STRUCTURE/BONDORDERS/bondOrderAssignment.h>

│ │ │ +

#include <BALL/STRUCTURE/BONDORDERS/bondOrderAssignment.h>

│ │ │
│ │ │ Inheritance diagram for BALL::BondOrderAssignment:
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ BALL::PartialBondOrderAssignment │ │ │ @@ -184,15 +184,15 @@ │ │ │ } │ │ │   │ │ │ │ │ │

Detailed Description

│ │ │

A solution to the bond order assignment problem.

│ │ │

This class represents a full bond order assignment as it is generated by the AssignBondOrderProcessor through a BondOrderAssignmentStrategy .

│ │ │ │ │ │ -

Definition at line 30 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 30 of file bondOrderAssignment.h.

│ │ │

Constructor & Destructor Documentation

│ │ │ │ │ │

◆ BondOrderAssignment()

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │ @@ -289,15 +289,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ inline
│ │ │
│ │ │ │ │ │ -

Definition at line 49 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 49 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │
│ │ │ │ │ │

◆ getQueueSize()

│ │ │ │ │ │
│ │ │ @@ -316,15 +316,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 52 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 52 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │
│ │ │

Friends And Related Symbol Documentation

│ │ │ │ │ │

◆ AssignBondOrderProcessor

│ │ │ │ │ │ @@ -341,15 +341,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ -

Definition at line 33 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 33 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │
│ │ │

Member Data Documentation

│ │ │ │ │ │

◆ ac

│ │ │ │ │ │ @@ -358,15 +358,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
AtomContainer* BALL::BondOrderAssignment::ac
│ │ │
│ │ │ │ │ │ -

Definition at line 72 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 72 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ atoms_to_delete

│ │ │ │ │ │
│ │ │ @@ -374,15 +374,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
vector<Atom*> BALL::BondOrderAssignment::atoms_to_delete
│ │ │
│ │ │ │ │ │ -

Definition at line 65 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 65 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ bond_order_map

│ │ │ │ │ │
│ │ │ @@ -390,15 +390,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
HashMap<Bond*, int> BALL::BondOrderAssignment::bond_order_map
│ │ │
│ │ │ │ │ │ -

Definition at line 58 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 58 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ node_expansions

│ │ │ │ │ │
│ │ │ @@ -406,15 +406,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
int BALL::BondOrderAssignment::node_expansions
│ │ │
│ │ │ │ │ │ -

Definition at line 69 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 69 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ number_of_virtual_hydrogens

│ │ │ │ │ │
│ │ │ @@ -422,15 +422,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
HashMap<Atom*, int> BALL::BondOrderAssignment::number_of_virtual_hydrogens
│ │ │
│ │ │ │ │ │ -

Definition at line 61 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 61 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ queue_size

│ │ │ │ │ │
│ │ │ @@ -438,15 +438,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
int BALL::BondOrderAssignment::queue_size
│ │ │
│ │ │ │ │ │ -

Definition at line 70 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 70 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ total_charge

│ │ │ │ │ │
│ │ │ @@ -454,15 +454,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
float BALL::BondOrderAssignment::total_charge
│ │ │
│ │ │ │ │ │ -

Definition at line 68 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 68 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │

◆ valid

│ │ │ │ │ │
│ │ │ @@ -470,15 +470,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
bool BALL::BondOrderAssignment::valid
│ │ │
│ │ │ │ │ │ -

Definition at line 55 of file bondOrderAssignment.h.

│ │ │ +

Definition at line 55 of file bondOrderAssignment.h.

│ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d27/a00239.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: modularWidgetPluginHandler.h File Reference │ │ │ +BALL: rotamerLibrary.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,40 +65,40 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │
│ │ │ Classes | │ │ │ Namespaces
│ │ │ -
modularWidgetPluginHandler.h File Reference
│ │ │ +
rotamerLibrary.h File Reference
│ │ │
│ │ │
│ │ │ -
#include <BALL/PLUGIN/pluginHandler.h>
│ │ │ -#include <BALL/VIEW/KERNEL/modularWidget.h>
│ │ │ +
#include <BALL/STRUCTURE/fragmentDB.h>
│ │ │ +#include <BALL/STRUCTURE/residueRotamerSet.h>
│ │ │ +#include <BALL/DATATYPE/hasMap.h>
│ │ │
│ │ │

Go to the source code of this file.

│ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ │ │ │

│ │ │ Classes

class  BALL::VIEW::ModularWidgetPluginHandler
class  BALL::RotamerLibrary
 Rotamer Library Class. More...
 
│ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │

│ │ │ Namespaces

namespace  BALL
 
namespace  BALL::VIEW
 
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ │
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,23 +1,22 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _P_L_U_G_I_N │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -modularWidgetPluginHandler.h File Reference │ │ │ │ -#include <_B_A_L_L_/_P_L_U_G_I_N_/_p_l_u_g_i_n_H_a_n_d_l_e_r_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ +rotamerLibrary.h File Reference │ │ │ │ +#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_f_r_a_g_m_e_n_t_D_B_._h> │ │ │ │ +#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_r_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t_._h> │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r │ │ │ │ +class   _B_A_L_L_:_:_R_o_t_a_m_e_r_L_i_b_r_a_r_y │ │ │ │ +  _R_o_t_a_m_e_r Library Class. _M_o_r_e_._._. │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │ -  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d27/a00239_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: modularWidgetPluginHandler.h Source File │ │ │ +BALL: rotamerLibrary.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,76 +70,135 @@ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │ -
modularWidgetPluginHandler.h
│ │ │ +
rotamerLibrary.h
│ │ │
│ │ │
│ │ │ -Go to the documentation of this file.
1#ifndef BALL_VIEW_PLUGIN_MODULARWIDGETPLUGINHANDLER_H
│ │ │ -
2#define BALL_VIEW_PLUGIN_MODULARWIDGETPLUGINHANDLER_H
│ │ │ -
3
│ │ │ -
4#ifndef BALL_PLUGIN_PLUGINHANDLER_H
│ │ │ -
5# include <BALL/PLUGIN/pluginHandler.h>
│ │ │ -
6#endif
│ │ │ +Go to the documentation of this file.
1// -*- Mode: C++; tab-width: 2; -*-
│ │ │ +
2// vi: set ts=2:
│ │ │ +
3//
│ │ │ +
4
│ │ │ +
5#ifndef BALL_STRUCTURE_ROTAMERLIBRARY_H
│ │ │ +
6#define BALL_STRUCTURE_ROTAMERLIBRARY_H
│ │ │
7
│ │ │ -
8#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H
│ │ │ -
9# include <BALL/VIEW/KERNEL/modularWidget.h>
│ │ │ +
8#ifndef BALL_STRUCTURE_FRAGMENT_DB_H
│ │ │ +
9# include <BALL/STRUCTURE/fragmentDB.h>
│ │ │
10#endif
│ │ │
11
│ │ │ -
12namespace BALL
│ │ │ -
13{
│ │ │ -
14 class BALLPlugin;
│ │ │ +
12#ifndef BALL_STRUCTURE_RESIDUEROTAMERSET_H
│ │ │ +
13 #include <BALL/STRUCTURE/residueRotamerSet.h>
│ │ │ +
14#endif
│ │ │
15
│ │ │ -
16 namespace VIEW
│ │ │ -
17 {
│ │ │ -
18 class MainControl;
│ │ │ +
16#ifndef BALL_DATATYPE_HASHMAP_H
│ │ │ +
17 #include <BALL/DATATYPE/hasMap.h>
│ │ │ +
18#endif
│ │ │
19
│ │ │ -
│ │ │ -
23 class BALL_VIEW_EXPORT ModularWidgetPluginHandler
│ │ │ -
24 : public PluginHandler
│ │ │ -
25 {
│ │ │ -
26 public:
│ │ │ -
27 ModularWidgetPluginHandler(MainControl* parent);
│ │ │ -
28
│ │ │ -
29 virtual bool canHandle(BALLPlugin* plugin) const;
│ │ │ -
30
│ │ │ -
31 protected:
│ │ │ -
32 virtual bool specificSetup_(BALLPlugin* plugin);
│ │ │ -
33 virtual bool specificShutdown_(BALLPlugin* plugin);
│ │ │ -
34
│ │ │ -
35 MainControl* main_control_;
│ │ │ -
36 ModularWidget* modular_widget_;
│ │ │ -
37 };
│ │ │ -
│ │ │ -
38 }
│ │ │ -
39}
│ │ │ -
40
│ │ │ -
41#endif // BALL_VIEW_PLUGIN_MODULARWIDGETPLUGINHANDLER_H
│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
BALL::VIEW::ModularWidgetPluginHandler::canHandle
virtual bool canHandle(BALLPlugin *plugin) const
│ │ │ -
BALL::VIEW::ModularWidgetPluginHandler::ModularWidgetPluginHandler
ModularWidgetPluginHandler(MainControl *parent)
│ │ │ - │ │ │ -
BALL::VIEW::ModularWidgetPluginHandler::specificSetup_
virtual bool specificSetup_(BALLPlugin *plugin)
│ │ │ -
BALL::VIEW::ModularWidgetPluginHandler::specificShutdown_
virtual bool specificShutdown_(BALLPlugin *plugin)
│ │ │ - │ │ │ -
BALL_VIEW_EXPORT
#define BALL_VIEW_EXPORT
Definition COMMON/global.h:52
│ │ │ +
20//#include <map>
│ │ │ +
21
│ │ │ +
22namespace BALL
│ │ │ +
23{
│ │ │ +
24 class FragmentDB;
│ │ │ +
25 class String;
│ │ │ +
26
│ │ │ +
│ │ │ +
33 class BALL_EXPORT RotamerLibrary
│ │ │ +
34 {
│ │ │ +
35 public:
│ │ │ +
36
│ │ │ +
37 BALL_CREATE(RotamerLibrary)
│ │ │ +
38
│ │ │ +
39
│ │ │ +
42
│ │ │ +
43
│ │ │ +
44 static const String DEFAULT_LIBRARY;
│ │ │ +
45
│ │ │ +
47 static const String DEFAULT_FRAGMENT_DB;
│ │ │ +
49
│ │ │ +
57 RotamerLibrary() ;
│ │ │ +
58
│ │ │ +
60 RotamerLibrary(const String& filename, const FragmentDB& fragment_db) ;
│ │ │ +
61
│ │ │ +
63 RotamerLibrary(const FragmentDB& fragment_db) ;
│ │ │ +
64
│ │ │ +
66 RotamerLibrary(const RotamerLibrary& library) ;
│ │ │ +
67
│ │ │ +
69 virtual ~RotamerLibrary();
│ │ │ +
71
│ │ │ +
76 RotamerLibrary& operator = (const RotamerLibrary& rhs);
│ │ │ +
78
│ │ │ +
79
│ │ │ +
84 ResidueRotamerSet* getRotamerSet(const String& name);
│ │ │ +
85
│ │ │ +
87 ResidueRotamerSet* getRotamerSet(const String& name, float phi, float psi);
│ │ │ +
88
│ │ │ +
90 ResidueRotamerSet* getRotamerSet(const Residue& residue);
│ │ │ +
91
│ │ │ +
93 Size getNumberOfRotamers() const;
│ │ │ +
94
│ │ │ +
96 Size getNumberOfRotamers(const String& name) const;
│ │ │ +
97
│ │ │ +
99 Size getNumberOfRotamerSets() const;
│ │ │ +
100
│ │ │ +
102 void addRotamer(const String& name, const Rotamer& rotamer, Size number_of_torsions, Index phi, Index psi);
│ │ │ +
103
│ │ │ +
105 void addRotamer(const String& name, const Rotamer& rotamer, Size number_of_torsions);
│ │ │ +
106
│ │ │ +
108 bool isBackboneDependent() const;
│ │ │ +
109
│ │ │ +
111 void setBackboneDependent(bool dependent);
│ │ │ +
112
│ │ │ +
114 bool hasRotamers(const String& name) const;
│ │ │ +
115
│ │ │ +
117 bool validate();
│ │ │ +
118
│ │ │ +
120 void sort();
│ │ │ +
121
│ │ │ +
125 void clear();
│ │ │ +
127
│ │ │ +
128 protected:
│ │ │ +
129
│ │ │ +
134 HashMap<Index, HashMap<Index, HashMap<String, ResidueRotamerSet> > > bb_dep_sets_;
│ │ │ +
135
│ │ │ +
137 HashMap<String, ResidueRotamerSet> bb_indep_sets_;
│ │ │ +
138
│ │ │ +
140 Index getNearestBackboneTorsion_(double angle) const;
│ │ │ +
141
│ │ │ +
143 Size step_width_;
│ │ │ +
144
│ │ │ +
146 FragmentDB fragment_db_;
│ │ │ +
147
│ │ │ +
149 bool backbone_dependent_;
│ │ │ +
151 };
│ │ │ +
│ │ │ +
152
│ │ │ +
153} // namespace BALL
│ │ │ +
154
│ │ │ +
155#endif // BALL_STRUCTURE_ROTAMERLIBRARY_H
│ │ │ + │ │ │ + │ │ │ +
BALL_CREATE
#define BALL_CREATE(name)
Definition create.h:62
│ │ │ + │ │ │ +
BALL::HashMap
HashMap class based on the STL map (containing serveral convenience functions)
Definition hashMap.h:74
│ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
BALL::RotamerLibrary
Rotamer Library Class.
Definition rotamerLibrary.h:34
│ │ │ + │ │ │ + │ │ │ +
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
│ │ │
│ │ │ │ │ │
│ │ │ Generated by doxygen 1.9.8 │ │ │
│ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,81 +1,140 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _P_L_U_G_I_N │ │ │ │ -modularWidgetPluginHandler.h │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ +rotamerLibrary.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1#ifndef BALL_VIEW_PLUGIN_MODULARWIDGETPLUGINHANDLER_H │ │ │ │ -2#define BALL_VIEW_PLUGIN_MODULARWIDGETPLUGINHANDLER_H │ │ │ │ -3 │ │ │ │ -4#ifndef BALL_PLUGIN_PLUGINHANDLER_H │ │ │ │ -5# include <_B_A_L_L_/_P_L_U_G_I_N_/_p_l_u_g_i_n_H_a_n_d_l_e_r_._h> │ │ │ │ -6#endif │ │ │ │ +1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ +2// vi: set ts=2: │ │ │ │ +3// │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_STRUCTURE_ROTAMERLIBRARY_H │ │ │ │ +6#define BALL_STRUCTURE_ROTAMERLIBRARY_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H │ │ │ │ -9# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ +8#ifndef BALL_STRUCTURE_FRAGMENT_DB_H │ │ │ │ +9# include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_f_r_a_g_m_e_n_t_D_B_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12namespace _B_A_L_L │ │ │ │ -13{ │ │ │ │ -14 class BALLPlugin; │ │ │ │ +12#ifndef BALL_STRUCTURE_RESIDUEROTAMERSET_H │ │ │ │ +13 #include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_r_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t_._h> │ │ │ │ +14#endif │ │ │ │ 15 │ │ │ │ -16 namespace VIEW │ │ │ │ -17 { │ │ │ │ -18 class MainControl; │ │ │ │ +16#ifndef BALL_DATATYPE_HASHMAP_H │ │ │ │ +17 #include │ │ │ │ +18#endif │ │ │ │ 19 │ │ │ │ -_2_3 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r │ │ │ │ -24 : public _P_l_u_g_i_n_H_a_n_d_l_e_r │ │ │ │ -25 { │ │ │ │ -26 public: │ │ │ │ -_2_7 _M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r(_M_a_i_n_C_o_n_t_r_o_l* parent); │ │ │ │ -28 │ │ │ │ -_2_9 virtual bool _c_a_n_H_a_n_d_l_e(_B_A_L_L_P_l_u_g_i_n* plugin) const; │ │ │ │ -30 │ │ │ │ -31 protected: │ │ │ │ -_3_2 virtual bool _s_p_e_c_i_f_i_c_S_e_t_u_p__(_B_A_L_L_P_l_u_g_i_n* plugin); │ │ │ │ -_3_3 virtual bool _s_p_e_c_i_f_i_c_S_h_u_t_d_o_w_n__(_B_A_L_L_P_l_u_g_i_n* plugin); │ │ │ │ -34 │ │ │ │ -_3_5 _M_a_i_n_C_o_n_t_r_o_l* _m_a_i_n___c_o_n_t_r_o_l__; │ │ │ │ -_3_6 _M_o_d_u_l_a_r_W_i_d_g_e_t* _m_o_d_u_l_a_r___w_i_d_g_e_t__; │ │ │ │ -37 }; │ │ │ │ -38 } │ │ │ │ -39} │ │ │ │ -40 │ │ │ │ -41#endif // BALL_VIEW_PLUGIN_MODULARWIDGETPLUGINHANDLER_H │ │ │ │ -_m_o_d_u_l_a_r_W_i_d_g_e_t_._h │ │ │ │ -_p_l_u_g_i_n_H_a_n_d_l_e_r_._h │ │ │ │ +20//#include │ │ │ │ +21 │ │ │ │ +22namespace _B_A_L_L │ │ │ │ +23{ │ │ │ │ +24 class FragmentDB; │ │ │ │ +25 class String; │ │ │ │ +26 │ │ │ │ +_3_3 class _B_A_L_L___E_X_P_O_R_T _R_o_t_a_m_e_r_L_i_b_r_a_r_y │ │ │ │ +34 { │ │ │ │ +35 public: │ │ │ │ +36 │ │ │ │ +37 _B_A_L_L___C_R_E_A_T_E(_R_o_t_a_m_e_r_L_i_b_r_a_r_y) │ │ │ │ +38 │ │ │ │ +39 │ │ │ │ +42 │ │ │ │ +43 │ │ │ │ +_4_4 static const _S_t_r_i_n_g DEFAULT_LIBRARY; │ │ │ │ +45 │ │ │ │ +_4_7 static const _S_t_r_i_n_g DEFAULT_FRAGMENT_DB; │ │ │ │ +49 │ │ │ │ +_5_7 _R_o_t_a_m_e_r_L_i_b_r_a_r_y() ; │ │ │ │ +58 │ │ │ │ +_6_0 _R_o_t_a_m_e_r_L_i_b_r_a_r_y(const _S_t_r_i_n_g& filename, const _F_r_a_g_m_e_n_t_D_B& fragment_db) ; │ │ │ │ +61 │ │ │ │ +_6_3 _R_o_t_a_m_e_r_L_i_b_r_a_r_y(const _F_r_a_g_m_e_n_t_D_B& fragment_db) ; │ │ │ │ +64 │ │ │ │ +_6_6 _R_o_t_a_m_e_r_L_i_b_r_a_r_y(const _R_o_t_a_m_e_r_L_i_b_r_a_r_y& library) ; │ │ │ │ +67 │ │ │ │ +_6_9 virtual ~_R_o_t_a_m_e_r_L_i_b_r_a_r_y(); │ │ │ │ +71 │ │ │ │ +_7_6 _R_o_t_a_m_e_r_L_i_b_r_a_r_y& operator = (const _R_o_t_a_m_e_r_L_i_b_r_a_r_y& rhs); │ │ │ │ +78 │ │ │ │ +79 │ │ │ │ +_8_4 _R_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t* getRotamerSet(const _S_t_r_i_n_g& name); │ │ │ │ +85 │ │ │ │ +_8_7 _R_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t* getRotamerSet(const _S_t_r_i_n_g& name, float phi, float psi); │ │ │ │ +88 │ │ │ │ +_9_0 _R_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t* getRotamerSet(const _R_e_s_i_d_u_e& residue); │ │ │ │ +91 │ │ │ │ +_9_3 _S_i_z_e getNumberOfRotamers() const; │ │ │ │ +94 │ │ │ │ +_9_6 _S_i_z_e getNumberOfRotamers(const _S_t_r_i_n_g& name) const; │ │ │ │ +97 │ │ │ │ +_9_9 _S_i_z_e getNumberOfRotamerSets() const; │ │ │ │ +100 │ │ │ │ +_1_0_2 void addRotamer(const _S_t_r_i_n_g& name, const _R_o_t_a_m_e_r& rotamer, _S_i_z_e │ │ │ │ +number_of_torsions, _I_n_d_e_x phi, _I_n_d_e_x psi); │ │ │ │ +103 │ │ │ │ +_1_0_5 void addRotamer(const _S_t_r_i_n_g& name, const _R_o_t_a_m_e_r& rotamer, _S_i_z_e │ │ │ │ +number_of_torsions); │ │ │ │ +106 │ │ │ │ +_1_0_8 bool isBackboneDependent() const; │ │ │ │ +109 │ │ │ │ +_1_1_1 void setBackboneDependent(bool dependent); │ │ │ │ +112 │ │ │ │ +_1_1_4 bool hasRotamers(const _S_t_r_i_n_g& name) const; │ │ │ │ +115 │ │ │ │ +_1_1_7 bool validate(); │ │ │ │ +118 │ │ │ │ +_1_2_0 void sort(); │ │ │ │ +121 │ │ │ │ +_1_2_5 void clear(); │ │ │ │ +127 │ │ │ │ +128 protected: │ │ │ │ +129 │ │ │ │ +_1_3_4 _H_a_s_h_M_a_p<_I_n_d_e_x, _H_a_s_h_M_a_p<_I_n_d_e_x, _H_a_s_h_M_a_p<_S_t_r_i_n_g, _R_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t> > > │ │ │ │ +bb_dep_sets_; │ │ │ │ +135 │ │ │ │ +_1_3_7 _H_a_s_h_M_a_p<_S_t_r_i_n_g, _R_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t> bb_indep_sets_; │ │ │ │ +138 │ │ │ │ +_1_4_0 _I_n_d_e_x getNearestBackboneTorsion_(double angle) const; │ │ │ │ +141 │ │ │ │ +_1_4_3 _S_i_z_e step_width_; │ │ │ │ +144 │ │ │ │ +_1_4_6 _F_r_a_g_m_e_n_t_D_B fragment_db_; │ │ │ │ +147 │ │ │ │ +_1_4_9 bool backbone_dependent_; │ │ │ │ +151 }; │ │ │ │ +152 │ │ │ │ +153} // namespace BALL │ │ │ │ +154 │ │ │ │ +155#endif // BALL_STRUCTURE_ROTAMERLIBRARY_H │ │ │ │ +_f_r_a_g_m_e_n_t_D_B_._h │ │ │ │ +_r_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_B_A_L_L_P_l_u_g_i_n │ │ │ │ -DDeeffiinniittiioonn _B_A_L_L_P_l_u_g_i_n_._h_:_2_1 │ │ │ │ -_B_A_L_L_:_:_P_l_u_g_i_n_H_a_n_d_l_e_r │ │ │ │ -DDeeffiinniittiioonn _p_l_u_g_i_n_H_a_n_d_l_e_r_._h_:_2_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ -DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _m_o_d_u_l_a_r_W_i_d_g_e_t_._h_:_6_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r │ │ │ │ -DDeeffiinniittiioonn _m_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r_._h_:_2_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r_:_:_c_a_n_H_a_n_d_l_e │ │ │ │ -virtual bool canHandle(BALLPlugin *plugin) const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r │ │ │ │ -ModularWidgetPluginHandler(MainControl *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r_:_:_m_a_i_n___c_o_n_t_r_o_l__ │ │ │ │ -MainControl * main_control_ │ │ │ │ -DDeeffiinniittiioonn _m_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r_:_:_s_p_e_c_i_f_i_c_S_e_t_u_p__ │ │ │ │ -virtual bool specificSetup_(BALLPlugin *plugin) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r_:_:_s_p_e_c_i_f_i_c_S_h_u_t_d_o_w_n__ │ │ │ │ -virtual bool specificShutdown_(BALLPlugin *plugin) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r_:_:_m_o_d_u_l_a_r___w_i_d_g_e_t__ │ │ │ │ -ModularWidget * modular_widget_ │ │ │ │ -DDeeffiinniittiioonn _m_o_d_u_l_a_r_W_i_d_g_e_t_P_l_u_g_i_n_H_a_n_d_l_e_r_._h_:_3_6 │ │ │ │ -_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ -#define BALL_VIEW_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_M_a_p │ │ │ │ +HashMap class based on the STL map (containing serveral convenience functions) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_M_a_p_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_R_e_s_i_d_u_e │ │ │ │ +DDeeffiinniittiioonn _r_e_s_i_d_u_e_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_F_r_a_g_m_e_n_t_D_B │ │ │ │ +DDeeffiinniittiioonn _f_r_a_g_m_e_n_t_D_B_._h_:_4_5 │ │ │ │ +_B_A_L_L_:_:_R_o_t_a_m_e_r │ │ │ │ +DDeeffiinniittiioonn _r_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_R_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t │ │ │ │ +DDeeffiinniittiioonn _r_e_s_i_d_u_e_R_o_t_a_m_e_r_S_e_t_._h_:_8_8 │ │ │ │ +_B_A_L_L_:_:_R_o_t_a_m_e_r_L_i_b_r_a_r_y │ │ │ │ +Rotamer Library Class. │ │ │ │ +DDeeffiinniittiioonn _r_o_t_a_m_e_r_L_i_b_r_a_r_y_._h_:_3_4 │ │ │ │ +_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d29/a00470.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: materialSettings.h File Reference │ │ │ +BALL: mainControlPreferences.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -72,28 +72,29 @@ │ │ │
  • include
  • BALL
  • VIEW
  • DIALOGS
    • │ │ │
    │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    materialSettings.h File Reference
    │ │ │ +
    mainControlPreferences.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/COMMON/global.h>
    │ │ │ -#include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ -#include <BALL/VIEW/UIC/ui_materialSettings.h>
    │ │ │ +
    #include <BALL/COMMON/global.h>
    │ │ │ +#include <BALL/FORMAT/INIFile.h>
    │ │ │ +#include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ +#include <BALL/VIEW/UIC/ui_mainControlPreferences.h>
    │ │ │ #include <QtWidgets/QWidget>
    │ │ │ -#include <QtWidgets/QLabel>
    │ │ │ +#include <QtGui/QFont>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::MaterialSettings
    class  BALL::VIEW::MainControlPreferences
     
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -3,23 +3,24 @@ │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ * _D_I_A_L_O_G_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -materialSettings.h File Reference │ │ │ │ +mainControlPreferences.h File Reference │ │ │ │ #include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +#include <_B_A_L_L_/_F_O_R_M_A_T_/_I_N_I_F_i_l_e_._h> │ │ │ │ #include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h> │ │ │ │ -#include │ │ │ │ +#include │ │ │ │ #include │ │ │ │ -#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d29/a00470_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: materialSettings.h Source File │ │ │ +BALL: mainControlPreferences.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -74,111 +74,127 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    materialSettings.h
    │ │ │ +
    mainControlPreferences.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5#ifndef BALL_VIEW_DIALOGS_MATERIALSETTINGS_H
    │ │ │ -
    6#define BALL_VIEW_DIALOGS_MATERIALSETTINGS_H
    │ │ │ +
    5#ifndef BALL_VIEW_DIALOGS_MAINCONTROLPREFERENCES_H
    │ │ │ +
    6#define BALL_VIEW_DIALOGS_MAINCONTROLPREFERENCES_H
    │ │ │
    7
    │ │ │
    8#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ -
    9# include <BALL/COMMON/global.h>
    │ │ │ +
    9# include <BALL/COMMON/global.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY
    │ │ │ -
    13# include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ +
    12#ifndef BALL_FORMAT_INIFILE_H
    │ │ │ +
    13# include <BALL/FORMAT/INIFile.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │ -
    16#include <BALL/VIEW/UIC/ui_materialSettings.h>
    │ │ │ -
    17
    │ │ │ -
    18#include <QtWidgets/QWidget>
    │ │ │ -
    19#include <QtWidgets/QLabel>
    │ │ │ -
    20
    │ │ │ -
    21namespace BALL
    │ │ │ -
    22{
    │ │ │ -
    23 namespace VIEW
    │ │ │ -
    24 {
    │ │ │ -
    25 class Scene;
    │ │ │ -
    26 class Representation;
    │ │ │ -
    27
    │ │ │ -
    │ │ │ -
    33 class BALL_VIEW_EXPORT MaterialSettings
    │ │ │ -
    34 : public QWidget,
    │ │ │ -
    35 public Ui_MaterialSettingsData,
    │ │ │ -
    36 public PreferencesEntry
    │ │ │ -
    37 {
    │ │ │ -
    38 Q_OBJECT
    │ │ │ -
    39
    │ │ │ -
    40 public:
    │ │ │ -
    41
    │ │ │ -
    43 MaterialSettings( QWidget* parent = 0, const char* name = "MaterialSettings", Qt::WindowFlags fl = 0 );
    │ │ │ -
    44
    │ │ │ -
    46 ~MaterialSettings() {}
    │ │ │ -
    47
    │ │ │ -
    49 void apply();
    │ │ │ -
    50
    │ │ │ -
    52 void setCurrentRepresentation(Representation* representation);
    │ │ │ -
    53
    │ │ │ -
    58 void updateDefaultMaterialsFromStage();
    │ │ │ +
    16#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY
    │ │ │ +
    17# include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ +
    18#endif
    │ │ │ +
    19
    │ │ │ +
    20#include <BALL/VIEW/UIC/ui_mainControlPreferences.h>
    │ │ │ +
    21
    │ │ │ +
    22#include <QtWidgets/QWidget>
    │ │ │ +
    23#include <QtGui/QFont>
    │ │ │ +
    24
    │ │ │ +
    25namespace BALL
    │ │ │ +
    26{
    │ │ │ +
    27 namespace VIEW
    │ │ │ +
    28 {
    │ │ │ +
    29
    │ │ │ +
    │ │ │ +
    37class BALL_VIEW_EXPORT MainControlPreferences
    │ │ │ +
    38 : public QWidget,
    │ │ │ +
    39 public Ui_MainControlPreferencesData,
    │ │ │ +
    40 public PreferencesEntry
    │ │ │ +
    41{
    │ │ │ +
    42 Q_OBJECT
    │ │ │ +
    43
    │ │ │ +
    44 public:
    │ │ │ +
    45
    │ │ │ +
    47 MainControlPreferences(QWidget *parent = NULL, const char *name = "MainControlPreferences",
    │ │ │ +
    48 Qt::WindowFlags fl=0);
    │ │ │ +
    49
    │ │ │ +
    51 virtual ~MainControlPreferences();
    │ │ │ +
    52
    │ │ │ +
    58 QStyle* setStyle();
    │ │ │
    59
    │ │ │ -
    60 public Q_SLOTS:
    │ │ │ -
    61
    │ │ │ -
    62 virtual void ambientFactorChanged();
    │ │ │ -
    63 virtual void specularityFactorChanged();
    │ │ │ -
    64 virtual void reflectivenessFactorChanged();
    │ │ │ -
    65 virtual void shininessFactorChanged();
    │ │ │ -
    66 virtual void transparencyFactorChanged();
    │ │ │ -
    67 virtual void updateDirectlyBoxChanged();
    │ │ │ -
    68 virtual void editAmbientColor();
    │ │ │ -
    69 virtual void editSpecularityColor();
    │ │ │ -
    70 virtual void editReflectivenessColor();
    │ │ │ -
    71 private:
    │ │ │ -
    72
    │ │ │ -
    73 void setLabel_(QLabel& label, float value);
    │ │ │ -
    74 void setValues_(const QSlider& slider, QLabel& label, int divisor);
    │ │ │ -
    75 void setQuadraticValues_(const QSlider& slider, QLabel& label, int divisor);
    │ │ │ -
    76
    │ │ │ -
    77 Representation* current_representation_;
    │ │ │ -
    78 };
    │ │ │ +
    61 void enableLoggingToFile(bool state);
    │ │ │ +
    62
    │ │ │ +
    64 bool loggingToFileEnabled() const;
    │ │ │ +
    65
    │ │ │ +
    67 bool getSkipDriverChecks() const;
    │ │ │ +
    68
    │ │ │ +
    70 QFont getFont();
    │ │ │ +
    71
    │ │ │ +
    │ │ │ +
    72 bool getLanguageChanged() {
    │ │ │ +
    73 return last_index_ != languageComboBox_->currentIndex();
    │ │ │ +
    74 }
    │ │ │ +
    │ │ │ +
    75
    │ │ │ +
    │ │ │ +
    76 void resetLanguageChanged() {
    │ │ │ +
    77 last_index_ = languageComboBox_->currentIndex();
    │ │ │ +
    78 }
    │ │ │
    │ │ │
    79
    │ │ │ -
    80 }
    │ │ │ -
    81}
    │ │ │ +
    81 void writePreferenceEntries(INIFile& inifile);
    │ │ │
    82
    │ │ │ -
    83#endif
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::MaterialSettings::transparencyFactorChanged
    virtual void transparencyFactorChanged()
    │ │ │ -
    BALL::VIEW::MaterialSettings::apply
    void apply()
    Apply the new values to the stage.
    │ │ │ -
    BALL::VIEW::MaterialSettings::setCurrentRepresentation
    void setCurrentRepresentation(Representation *representation)
    set the current representation
    │ │ │ -
    BALL::VIEW::MaterialSettings::editReflectivenessColor
    virtual void editReflectivenessColor()
    │ │ │ -
    BALL::VIEW::MaterialSettings::editSpecularityColor
    virtual void editSpecularityColor()
    │ │ │ -
    BALL::VIEW::MaterialSettings::MaterialSettings
    MaterialSettings(QWidget *parent=0, const char *name="MaterialSettings", Qt::WindowFlags fl=0)
    Constructor.
    │ │ │ -
    BALL::VIEW::MaterialSettings::editAmbientColor
    virtual void editAmbientColor()
    │ │ │ -
    BALL::VIEW::MaterialSettings::shininessFactorChanged
    virtual void shininessFactorChanged()
    │ │ │ -
    BALL::VIEW::MaterialSettings::updateDirectlyBoxChanged
    virtual void updateDirectlyBoxChanged()
    │ │ │ - │ │ │ -
    BALL::VIEW::MaterialSettings::specularityFactorChanged
    virtual void specularityFactorChanged()
    │ │ │ -
    BALL::VIEW::MaterialSettings::ambientFactorChanged
    virtual void ambientFactorChanged()
    │ │ │ -
    BALL::VIEW::MaterialSettings::reflectivenessFactorChanged
    virtual void reflectivenessFactorChanged()
    │ │ │ - │ │ │ - │ │ │ +
    84 void readPreferenceEntries(const INIFile& inifile);
    │ │ │ +
    85
    │ │ │ +
    86 public Q_SLOTS:
    │ │ │ +
    87
    │ │ │ +
    89 void selectFont();
    │ │ │ +
    90
    │ │ │ +
    92 void setFont(QFont font);
    │ │ │ +
    93
    │ │ │ +
    94 protected:
    │ │ │ +
    95
    │ │ │ +
    96 QFont font_;
    │ │ │ +
    97 int last_index_;
    │ │ │ +
    98};
    │ │ │ +
    │ │ │ +
    99
    │ │ │ +
    100} } // namespace
    │ │ │ +
    101
    │ │ │ +
    102#endif // BALL_VIEW_DIALOGS_MAINCONTROLPREFERENCES_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::MainControlPreferences::writePreferenceEntries
    void writePreferenceEntries(INIFile &inifile)
    Store the settings of all registered objects.
    │ │ │ + │ │ │ +
    BALL::VIEW::MainControlPreferences::setFont
    void setFont(QFont font)
    Set the application's default font.
    │ │ │ +
    BALL::VIEW::MainControlPreferences::MainControlPreferences
    MainControlPreferences(QWidget *parent=NULL, const char *name="MainControlPreferences", Qt::WindowFlags fl=0)
    Default Constructor.
    │ │ │ +
    BALL::VIEW::MainControlPreferences::enableLoggingToFile
    void enableLoggingToFile(bool state)
    Enable logging to file.
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::MainControlPreferences::selectFont
    void selectFont()
    Get the application's default font.
    │ │ │ +
    BALL::VIEW::MainControlPreferences::readPreferenceEntries
    void readPreferenceEntries(const INIFile &inifile)
    Restore the settings of all registered objects.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │ - │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ + │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -2,130 +2,148 @@ │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ * _D_I_A_L_O_G_S │ │ │ │ -materialSettings.h │ │ │ │ +mainControlPreferences.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_VIEW_DIALOGS_MATERIALSETTINGS_H │ │ │ │ -6#define BALL_VIEW_DIALOGS_MATERIALSETTINGS_H │ │ │ │ +5#ifndef BALL_VIEW_DIALOGS_MAINCONTROLPREFERENCES_H │ │ │ │ +6#define BALL_VIEW_DIALOGS_MAINCONTROLPREFERENCES_H │ │ │ │ 7 │ │ │ │ 8#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ 9# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY │ │ │ │ -13# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h> │ │ │ │ +12#ifndef BALL_FORMAT_INIFILE_H │ │ │ │ +13# include <_B_A_L_L_/_F_O_R_M_A_T_/_I_N_I_F_i_l_e_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#include │ │ │ │ -17 │ │ │ │ -18#include │ │ │ │ -19#include │ │ │ │ -20 │ │ │ │ -21namespace _B_A_L_L │ │ │ │ -22{ │ │ │ │ -23 namespace VIEW │ │ │ │ -24 { │ │ │ │ -25 class Scene; │ │ │ │ -26 class Representation; │ │ │ │ -27 │ │ │ │ -_3_3 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s │ │ │ │ -34 : public _Q_W_i_d_g_e_t, │ │ │ │ -35 public Ui_MaterialSettingsData, │ │ │ │ -36 public _P_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y │ │ │ │ -37 { │ │ │ │ -38 Q_OBJECT │ │ │ │ -39 │ │ │ │ -40 public: │ │ │ │ -41 │ │ │ │ -_4_3 _M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s( _Q_W_i_d_g_e_t* parent = 0, const char* name = │ │ │ │ -"MaterialSettings", Qt::WindowFlags fl = 0 ); │ │ │ │ -44 │ │ │ │ -_4_6 _~_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s() {} │ │ │ │ -47 │ │ │ │ -_4_9 void _a_p_p_l_y(); │ │ │ │ -50 │ │ │ │ -_5_2 void _s_e_t_C_u_r_r_e_n_t_R_e_p_r_e_s_e_n_t_a_t_i_o_n(_R_e_p_r_e_s_e_n_t_a_t_i_o_n* representation); │ │ │ │ -53 │ │ │ │ -_5_8 void _u_p_d_a_t_e_D_e_f_a_u_l_t_M_a_t_e_r_i_a_l_s_F_r_o_m_S_t_a_g_e(); │ │ │ │ +16#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY │ │ │ │ +17# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20#include │ │ │ │ +21 │ │ │ │ +22#include │ │ │ │ +23#include │ │ │ │ +24 │ │ │ │ +25namespace _B_A_L_L │ │ │ │ +26{ │ │ │ │ +27 namespace VIEW │ │ │ │ +28 { │ │ │ │ +29 │ │ │ │ +_3_7class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ +38 : public _Q_W_i_d_g_e_t, │ │ │ │ +39 public Ui_MainControlPreferencesData, │ │ │ │ +40 public _P_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y │ │ │ │ +41{ │ │ │ │ +42 Q_OBJECT │ │ │ │ +43 │ │ │ │ +44 public: │ │ │ │ +45 │ │ │ │ +_4_7 _M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s(_Q_W_i_d_g_e_t *parent = NULL, const char *name = │ │ │ │ +"MainControlPreferences", │ │ │ │ +48 Qt::WindowFlags fl=0); │ │ │ │ +49 │ │ │ │ +_5_1 virtual _~_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s(); │ │ │ │ +52 │ │ │ │ +_5_8 QStyle* _s_e_t_S_t_y_l_e(); │ │ │ │ 59 │ │ │ │ -60 public Q_SLOTS: │ │ │ │ -61 │ │ │ │ -_6_2 virtual void _a_m_b_i_e_n_t_F_a_c_t_o_r_C_h_a_n_g_e_d(); │ │ │ │ -_6_3 virtual void _s_p_e_c_u_l_a_r_i_t_y_F_a_c_t_o_r_C_h_a_n_g_e_d(); │ │ │ │ -_6_4 virtual void _r_e_f_l_e_c_t_i_v_e_n_e_s_s_F_a_c_t_o_r_C_h_a_n_g_e_d(); │ │ │ │ -_6_5 virtual void _s_h_i_n_i_n_e_s_s_F_a_c_t_o_r_C_h_a_n_g_e_d(); │ │ │ │ -_6_6 virtual void _t_r_a_n_s_p_a_r_e_n_c_y_F_a_c_t_o_r_C_h_a_n_g_e_d(); │ │ │ │ -_6_7 virtual void _u_p_d_a_t_e_D_i_r_e_c_t_l_y_B_o_x_C_h_a_n_g_e_d(); │ │ │ │ -_6_8 virtual void _e_d_i_t_A_m_b_i_e_n_t_C_o_l_o_r(); │ │ │ │ -_6_9 virtual void _e_d_i_t_S_p_e_c_u_l_a_r_i_t_y_C_o_l_o_r(); │ │ │ │ -_7_0 virtual void _e_d_i_t_R_e_f_l_e_c_t_i_v_e_n_e_s_s_C_o_l_o_r(); │ │ │ │ -71 private: │ │ │ │ -72 │ │ │ │ -73 void setLabel_(QLabel& label, float value); │ │ │ │ -74 void setValues_(const QSlider& slider, QLabel& label, int divisor); │ │ │ │ -75 void setQuadraticValues_(const QSlider& slider, QLabel& label, int divisor); │ │ │ │ -76 │ │ │ │ -77 _R_e_p_r_e_s_e_n_t_a_t_i_o_n* current_representation_; │ │ │ │ -78 }; │ │ │ │ +_6_1 void _e_n_a_b_l_e_L_o_g_g_i_n_g_T_o_F_i_l_e(bool state); │ │ │ │ +62 │ │ │ │ +_6_4 bool _l_o_g_g_i_n_g_T_o_F_i_l_e_E_n_a_b_l_e_d() const; │ │ │ │ +65 │ │ │ │ +_6_7 bool _g_e_t_S_k_i_p_D_r_i_v_e_r_C_h_e_c_k_s() const; │ │ │ │ +68 │ │ │ │ +_7_0 QFont _g_e_t_F_o_n_t(); │ │ │ │ +71 │ │ │ │ +_7_2 bool _g_e_t_L_a_n_g_u_a_g_e_C_h_a_n_g_e_d() { │ │ │ │ +73 return last_index_ != languageComboBox_->currentIndex(); │ │ │ │ +74 } │ │ │ │ +75 │ │ │ │ +_7_6 void _r_e_s_e_t_L_a_n_g_u_a_g_e_C_h_a_n_g_e_d() { │ │ │ │ +77 last_index_ = languageComboBox_->currentIndex(); │ │ │ │ +78 } │ │ │ │ 79 │ │ │ │ -80 } │ │ │ │ -81} │ │ │ │ +_8_1 void _w_r_i_t_e_P_r_e_f_e_r_e_n_c_e_E_n_t_r_i_e_s(_I_N_I_F_i_l_e& inifile); │ │ │ │ 82 │ │ │ │ -83#endif │ │ │ │ +_8_4 void _r_e_a_d_P_r_e_f_e_r_e_n_c_e_E_n_t_r_i_e_s(const _I_N_I_F_i_l_e& inifile); │ │ │ │ +85 │ │ │ │ +86 public Q_SLOTS: │ │ │ │ +87 │ │ │ │ +_8_9 void _s_e_l_e_c_t_F_o_n_t(); │ │ │ │ +90 │ │ │ │ +_9_2 void _s_e_t_F_o_n_t(QFont font); │ │ │ │ +93 │ │ │ │ +94 protected: │ │ │ │ +95 │ │ │ │ +_9_6 QFont _f_o_n_t__; │ │ │ │ +_9_7 int _l_a_s_t___i_n_d_e_x__; │ │ │ │ +98}; │ │ │ │ +99 │ │ │ │ +100} } // namespace │ │ │ │ +101 │ │ │ │ +102#endif // BALL_VIEW_DIALOGS_MAINCONTROLPREFERENCES_H │ │ │ │ _p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h │ │ │ │ +_I_N_I_F_i_l_e_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s │ │ │ │ -DDeeffiinniittiioonn _m_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_._h_:_3_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_u_p_d_a_t_e_D_e_f_a_u_l_t_M_a_t_e_r_i_a_l_s_F_r_o_m_S_t_a_g_e │ │ │ │ -void updateDefaultMaterialsFromStage() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_t_r_a_n_s_p_a_r_e_n_c_y_F_a_c_t_o_r_C_h_a_n_g_e_d │ │ │ │ -virtual void transparencyFactorChanged() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_a_p_p_l_y │ │ │ │ -void apply() │ │ │ │ -Apply the new values to the stage. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_s_e_t_C_u_r_r_e_n_t_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -void setCurrentRepresentation(Representation *representation) │ │ │ │ -set the current representation │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_e_d_i_t_R_e_f_l_e_c_t_i_v_e_n_e_s_s_C_o_l_o_r │ │ │ │ -virtual void editReflectivenessColor() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_e_d_i_t_S_p_e_c_u_l_a_r_i_t_y_C_o_l_o_r │ │ │ │ -virtual void editSpecularityColor() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s │ │ │ │ -MaterialSettings(QWidget *parent=0, const char *name="MaterialSettings", Qt:: │ │ │ │ -WindowFlags fl=0) │ │ │ │ -Constructor. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_e_d_i_t_A_m_b_i_e_n_t_C_o_l_o_r │ │ │ │ -virtual void editAmbientColor() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_s_h_i_n_i_n_e_s_s_F_a_c_t_o_r_C_h_a_n_g_e_d │ │ │ │ -virtual void shininessFactorChanged() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_u_p_d_a_t_e_D_i_r_e_c_t_l_y_B_o_x_C_h_a_n_g_e_d │ │ │ │ -virtual void updateDirectlyBoxChanged() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_~_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s │ │ │ │ -~MaterialSettings() │ │ │ │ -Destructor. │ │ │ │ -DDeeffiinniittiioonn _m_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_s_p_e_c_u_l_a_r_i_t_y_F_a_c_t_o_r_C_h_a_n_g_e_d │ │ │ │ -virtual void specularityFactorChanged() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_a_m_b_i_e_n_t_F_a_c_t_o_r_C_h_a_n_g_e_d │ │ │ │ -virtual void ambientFactorChanged() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_:_:_r_e_f_l_e_c_t_i_v_e_n_e_s_s_F_a_c_t_o_r_C_h_a_n_g_e_d │ │ │ │ -virtual void reflectivenessFactorChanged() │ │ │ │ +_B_A_L_L_:_:_I_N_I_F_i_l_e │ │ │ │ +DDeeffiinniittiioonn _I_N_I_F_i_l_e_._h_:_2_9 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_._h_:_4_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_l_o_g_g_i_n_g_T_o_F_i_l_e_E_n_a_b_l_e_d │ │ │ │ +bool loggingToFileEnabled() const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_w_r_i_t_e_P_r_e_f_e_r_e_n_c_e_E_n_t_r_i_e_s │ │ │ │ +void writePreferenceEntries(INIFile &inifile) │ │ │ │ +Store the settings of all registered objects. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_g_e_t_L_a_n_g_u_a_g_e_C_h_a_n_g_e_d │ │ │ │ +bool getLanguageChanged() │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_._h_:_7_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_s_e_t_F_o_n_t │ │ │ │ +void setFont(QFont font) │ │ │ │ +Set the application's default font. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ +MainControlPreferences(QWidget *parent=NULL, const char │ │ │ │ +*name="MainControlPreferences", Qt::WindowFlags fl=0) │ │ │ │ +Default Constructor. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_e_n_a_b_l_e_L_o_g_g_i_n_g_T_o_F_i_l_e │ │ │ │ +void enableLoggingToFile(bool state) │ │ │ │ +Enable logging to file. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_g_e_t_S_k_i_p_D_r_i_v_e_r_C_h_e_c_k_s │ │ │ │ +bool getSkipDriverChecks() const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_s_e_t_S_t_y_l_e │ │ │ │ +QStyle * setStyle() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_s_e_l_e_c_t_F_o_n_t │ │ │ │ +void selectFont() │ │ │ │ +Get the application's default font. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_r_e_a_d_P_r_e_f_e_r_e_n_c_e_E_n_t_r_i_e_s │ │ │ │ +void readPreferenceEntries(const INIFile &inifile) │ │ │ │ +Restore the settings of all registered objects. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_g_e_t_F_o_n_t │ │ │ │ +QFont getFont() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_r_e_s_e_t_L_a_n_g_u_a_g_e_C_h_a_n_g_e_d │ │ │ │ +void resetLanguageChanged() │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_._h_:_7_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_f_o_n_t__ │ │ │ │ +QFont font_ │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_._h_:_9_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_~_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ +virtual ~MainControlPreferences() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_:_:_l_a_s_t___i_n_d_e_x__ │ │ │ │ +int last_index_ │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_P_r_e_f_e_r_e_n_c_e_s_._h_:_9_7 │ │ │ │ _B_A_L_L_:_:_V_I_E_W_:_:_P_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y │ │ │ │ DDeeffiinniittiioonn _p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h_:_6_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h_:_5_9 │ │ │ │ _Q_W_i_d_g_e_t │ │ │ │ _g_l_o_b_a_l_._h │ │ │ │ _B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ #define BALL_VIEW_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d2a/a06142.html │ │ │ @@ -76,26 +76,26 @@ │ │ │
    │ │ │ Static Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::GridBasedScoring::Default Struct Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SCORING/COMMON/gridBasedScoring.h>

    │ │ │ +

    #include <BALL/SCORING/COMMON/gridBasedScoring.h>

    │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Static Public Attributes

    static double SCOREGRID_RESOLUTION
     
    static bool SCOREGRID_INTERPOLATION
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 33 of file gridBasedScoring.h.

    │ │ │ +

    Definition at line 33 of file gridBasedScoring.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ SCOREGRID_INTERPOLATION

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -109,15 +109,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ static
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 36 of file gridBasedScoring.h.

    │ │ │ +

    Definition at line 36 of file gridBasedScoring.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ SCOREGRID_RESOLUTION

    │ │ │ │ │ │
    │ │ │ @@ -133,15 +133,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 35 of file gridBasedScoring.h.

    │ │ │ +

    Definition at line 35 of file gridBasedScoring.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d2b/a01010.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: PLP.h File Reference │ │ │ +BALL: baseFunctor.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,90 +65,40 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces | │ │ │ -Macros
    │ │ │ -
    PLP.h File Reference
    │ │ │ +Namespaces
    │ │ │ +
    baseFunctor.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
    │ │ │ -#include <BALL/MOLMEC/COMMON/forceField.h>
    │ │ │ -#include <BALL/MOLMEC/COMMON/support.h>
    │ │ │ -#include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
    │ │ │ +
    #include <BALL/COMMON/global.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::PLP
    class  BALL::UnaryFunctor< ArgumentType, ResultType >
     
    struct  BALL::PLP::NonBondedPairData
    class  BALL::BinaryFunctor< FirstArgumentType, SecondArgumentType, ResultType >
     
    │ │ │ │ │ │ │ │ │ │ │ │ -

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │

    │ │ │ -Macros

    #define MMFF94_ES_ENABLED   "enable ES"
     flag to enable ES
     
    #define MMFF94_VDW_ENABLED   "enable VDW"
     flag to enable VDW
     
    │ │ │ -

    Macro Definition Documentation

    │ │ │ - │ │ │ -

    ◆ MMFF94_ES_ENABLED

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define MMFF94_ES_ENABLED   "enable ES"
    │ │ │ -
    │ │ │ - │ │ │ -

    flag to enable ES

    │ │ │ - │ │ │ -

    Definition at line 49 of file PLP.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ MMFF94_VDW_ENABLED

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define MMFF94_VDW_ENABLED   "enable VDW"
    │ │ │ -
    │ │ │ - │ │ │ -

    flag to enable VDW

    │ │ │ - │ │ │ -

    Definition at line 52 of file PLP.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,41 +1,22 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_C_O_R_I_N_G │ │ │ │ - * _C_O_M_P_O_N_E_N_T_S │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s │ │ │ │ -PLP.h File Reference │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_s_u_p_p_o_r_t_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_M_F_F_9_4_/_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ + * _C_O_N_C_E_P_T │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ +baseFunctor.h File Reference │ │ │ │ +#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ - class   _B_A_L_L_:_:_P_L_P │ │ │ │ +class   _B_A_L_L_:_:_U_n_a_r_y_F_u_n_c_t_o_r_<_ _A_r_g_u_m_e_n_t_T_y_p_e_,_ _R_e_s_u_l_t_T_y_p_e_ _> │ │ │ │   │ │ │ │ -struct   _B_A_L_L_:_:_P_L_P_:_:_N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a │ │ │ │ +class   _B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_<_ _F_i_r_s_t_A_r_g_u_m_e_n_t_T_y_p_e_,_ _S_e_c_o_n_d_A_r_g_u_m_e_n_t_T_y_p_e_,_ _R_e_s_u_l_t_T_y_p_e │ │ │ │ + _> │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -MMaaccrrooss │ │ │ │ -#define  _M_M_F_F_9_4___E_S___E_N_A_B_L_E_D   "enable ES" │ │ │ │ -  flag to enable ES │ │ │ │ -  │ │ │ │ -#define  _M_M_F_F_9_4___V_D_W___E_N_A_B_L_E_D   "enable VDW" │ │ │ │ -  flag to enable VDW │ │ │ │ -  │ │ │ │ -********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ -********** _?◆_? MMMMFFFF9944__EESS__EENNAABBLLEEDD ********** │ │ │ │ -#define MMFF94_ES_ENABLED   "enable ES" │ │ │ │ -flag to enable ES │ │ │ │ -Definition at line _4_9 of file _P_L_P_._h. │ │ │ │ -********** _?◆_? MMMMFFFF9944__VVDDWW__EENNAABBLLEEDD ********** │ │ │ │ -#define MMFF94_VDW_ENABLED   "enable VDW" │ │ │ │ -flag to enable VDW │ │ │ │ -Definition at line _5_2 of file _P_L_P_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d2b/a01010_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: PLP.h Source File │ │ │ +BALL: baseFunctor.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,187 +70,108 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    PLP.h
    │ │ │ +
    baseFunctor.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// ----------------------------------------------------
    │ │ │ -
    2// $Maintainer: Marcel Schumann $
    │ │ │ -
    3// $Authors: Jan Fuhrmann, Marcel Schumann $
    │ │ │ -
    4// ----------------------------------------------------
    │ │ │ -
    5
    │ │ │ -
    6#ifndef BALL_SCORING_COMPONENTS_PLP_H
    │ │ │ -
    7#define BALL_SCORING_COMPONENTS_PLP_H
    │ │ │ -
    8
    │ │ │ -
    9#include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
    │ │ │ -
    10#include <BALL/MOLMEC/COMMON/forceField.h>
    │ │ │ -
    11#include <BALL/MOLMEC/COMMON/support.h>
    │ │ │ -
    12#include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
    │ │ │ -
    13
    │ │ │ +Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ +
    2// vi: set ts=2:
    │ │ │ +
    3//
    │ │ │ +
    4
    │ │ │ +
    5#ifndef BALL_CONCEPT_BASEFUNCTOR_H
    │ │ │ +
    6#define BALL_CONCEPT_BASEFUNCTOR_H
    │ │ │ +
    7
    │ │ │ +
    8#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ +
    9# include <BALL/COMMON/global.h>
    │ │ │ +
    10#endif
    │ │ │ +
    11
    │ │ │ +
    12namespace BALL
    │ │ │ +
    13{
    │ │ │
    14
    │ │ │ -
    15namespace BALL
    │ │ │ -
    16{
    │ │ │ -
    │ │ │ -
    18 class BALL_EXPORT PLP : public ForceFieldComponent
    │ │ │ -
    19 {
    │ │ │ -
    20 public:
    │ │ │ -
    │ │ │ -
    21 struct NonBondedPairData
    │ │ │ -
    22 {
    │ │ │ -
    23 Size type;
    │ │ │ -
    24
    │ │ │ +
    20
    │ │ │ +
    24 template <class ArgumentType, class ResultType>
    │ │ │
    │ │ │ -
    25 enum Type
    │ │ │ -
    26 {
    │ │ │ -
    27 steric = 0,
    │ │ │ -
    28 hydrogen_bond = 1,
    │ │ │ -
    29 // an atom pair of which both partners are taken from the same ligand molecule in order to evaluate the ligand nonbonded energy
    │ │ │ -
    30 conformation = 2
    │ │ │ -
    31 };
    │ │ │ -
    │ │ │ +
    25 class BALL_EXPORT UnaryFunctor
    │ │ │ +
    26 {
    │ │ │ +
    27 public:
    │ │ │ +
    28
    │ │ │
    32
    │ │ │ -
    33 /*
    │ │ │ -
    34 NonBondedPairData();
    │ │ │ -
    35
    │ │ │ -
    36 double eij;
    │ │ │ -
    37 double rij;
    │ │ │ -
    38 double rij_7;
    │ │ │ -
    39 double vdw_energy; // for debugging
    │ │ │ -
    40 // for electrostatics:
    │ │ │ -
    41 bool is_1_4;
    │ │ │ -
    42 double qi;
    │ │ │ -
    43 double qj;
    │ │ │ -
    44 double es_energy; // for debugging
    │ │ │ -
    45 */
    │ │ │ -
    46 };
    │ │ │ +
    35 typedef ResultType result_type;
    │ │ │ +
    36
    │ │ │ +
    39 typedef ArgumentType argument_type;
    │ │ │ +
    40
    │ │ │ +
    43 typedef ArgumentType& argument_reference;
    │ │ │ +
    44
    │ │ │ +
    47 typedef const ArgumentType& const_argument_reference;
    │ │ │ +
    48
    │ │ │ +
    51 typedef ArgumentType* argument_pointer;
    │ │ │ +
    52
    │ │ │ +
    55 typedef const ArgumentType* const_argument_pointer;
    │ │ │ +
    56
    │ │ │ +
    58 };
    │ │ │ +
    │ │ │ +
    59
    │ │ │ +
    63 template <class FirstArgumentType, class SecondArgumentType, class ResultType>
    │ │ │ +
    │ │ │ +
    64 class BALL_EXPORT BinaryFunctor
    │ │ │ +
    65 {
    │ │ │ +
    66 public:
    │ │ │ +
    67
    │ │ │ +
    71
    │ │ │ +
    74 typedef ResultType result_type;
    │ │ │ +
    75
    │ │ │ +
    78 typedef FirstArgumentType first_argument_type;
    │ │ │ +
    81 typedef FirstArgumentType & first_argument_reference;
    │ │ │ +
    84 typedef const FirstArgumentType & const_first_argument_reference;
    │ │ │ +
    87 typedef FirstArgumentType * first_argument_pointer;
    │ │ │ +
    90 typedef const FirstArgumentType * const_first_argument_pointer;
    │ │ │ +
    91
    │ │ │ +
    94 typedef SecondArgumentType second_argument_type;
    │ │ │ +
    97 typedef SecondArgumentType & second_argument_reference;
    │ │ │ +
    100 typedef const SecondArgumentType & const_second_argument_reference;
    │ │ │ +
    103 typedef SecondArgumentType * second_argument_pointer;
    │ │ │ +
    106 typedef const SecondArgumentType * const_second_argument_pointer;
    │ │ │ +
    107
    │ │ │ +
    109 };
    │ │ │
    │ │ │ -
    47
    │ │ │ -
    49 #define MMFF94_ES_ENABLED "enable ES"
    │ │ │ -
    50
    │ │ │ -
    52 #define MMFF94_VDW_ENABLED "enable VDW"
    │ │ │ -
    53
    │ │ │ -
    54 BALL_CREATE(PLP)
    │ │ │ -
    55
    │ │ │ -
    56
    │ │ │ -
    57 PLP() throw();
    │ │ │ -
    58
    │ │ │ -
    60 PLP(ForceField& force_field) throw();
    │ │ │ -
    61
    │ │ │ -
    63 PLP(const PLP& MMFF94_non_bonded) throw();
    │ │ │ -
    64
    │ │ │ -
    66 virtual ~PLP() throw();
    │ │ │ -
    67
    │ │ │ -
    69 const PLP& operator = (const PLP& anb) throw();
    │ │ │ -
    70
    │ │ │ -
    73 void setRotatableBonds(std::vector<Bond*>& bonds);
    │ │ │ -
    74
    │ │ │ -
    81 static Size getAtomType(const Atom* atom);
    │ │ │ -
    82
    │ │ │ -
    84 void update(const std::vector<std::pair<Atom*, Atom*> >& atom_vector);
    │ │ │ -
    85
    │ │ │ -
    87 virtual void clear() throw();
    │ │ │ -
    88
    │ │ │ -
    90 bool operator == (const PLP& anb) throw();
    │ │ │ -
    91
    │ │ │ -
    93 bool setup(Options& options);
    │ │ │ -
    94
    │ │ │ -
    96 virtual double updateEnergy() throw();
    │ │ │ -
    97
    │ │ │ -
    99 virtual void updateForces() throw();
    │ │ │ -
    100
    │ │ │ -
    107 virtual void update();
    │ │ │ -
    108
    │ │ │ -
    109 double getVDWEnergy() const;
    │ │ │
    110
    │ │ │ -
    111 double getESEnergy() const;
    │ │ │
    112
    │ │ │ -
    113 protected:
    │ │ │ -
    114 //_ Value of the electrostatic energy
    │ │ │ -
    115 double es_energy_;
    │ │ │ -
    116
    │ │ │ -
    117 //_ Value of the vdw energy
    │ │ │ -
    118 double vdw_energy_;
    │ │ │ -
    119
    │ │ │ -
    120 static bool isNSp3(const Atom* at);
    │ │ │ -
    121 static bool isSp3(const Atom* at);
    │ │ │ -
    122
    │ │ │ -
    123 private:
    │ │ │ -
    124 struct GhTorsion
    │ │ │ -
    125 {
    │ │ │ -
    126 Atom* at1;
    │ │ │ -
    127 Atom* at2;
    │ │ │ -
    128 Atom* at3;
    │ │ │ -
    129 Atom* at4;
    │ │ │ -
    130 Size type;
    │ │ │ -
    131 };
    │ │ │ -
    132
    │ │ │ -
    133 void e1(double& d, double& e, double& delta);
    │ │ │ -
    134 void e2(double& d, double& e, double& delta);
    │ │ │ -
    135
    │ │ │ -
    136 std::vector<GhTorsion> ghtorsions_;
    │ │ │ -
    137
    │ │ │ -
    138 ForceField::PairVector atom_pair_vector_;
    │ │ │ -
    139
    │ │ │ -
    140 std::vector<NonBondedPairData> non_bonded_data_;
    │ │ │ -
    141
    │ │ │ -
    142 double cut_off_;
    │ │ │ -
    143 double vdw_cut_on_, vdw_cut_off_;
    │ │ │ -
    144 double es_cut_on_, es_cut_off_;
    │ │ │ -
    145 MMFF94VDWParameters vdw_parameters_;
    │ │ │ -
    146
    │ │ │ -
    147 // dielectric constant
    │ │ │ -
    148 double dc_;
    │ │ │ -
    149 // dielectric model exponent
    │ │ │ -
    150 double n_;
    │ │ │ -
    151 bool es_enabled_;
    │ │ │ -
    152 bool vdw_enabled_;
    │ │ │ -
    153 bool enable_es_switch_;
    │ │ │ -
    154 bool enable_vdw_switch_;
    │ │ │ -
    155 double es_d_on2_, es_d_off2_,
    │ │ │ -
    156 es_d_on_, es_d_off_,
    │ │ │ -
    157 es_ac_, es_bc_,
    │ │ │ -
    158 es_cc_, es_dc_, es_denom_, es_con_, es_cover3_, es_dover5_,
    │ │ │ -
    159 es_eadd_, es_eaddr_, es_const_, es_constr_;
    │ │ │ -
    160
    │ │ │ -
    161 std::vector<bool> dismiss_vector_;
    │ │ │ -
    162
    │ │ │ -
    163 std::vector<double> rotgrad_;
    │ │ │ -
    164 };
    │ │ │ -
    │ │ │ -
    165} //
    │ │ │ -
    166
    │ │ │ -
    167#endif // BALL_SCORING_COMPONENTS_PLP_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ -
    std
    STL namespace.
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::ForceField::PairVector
    std::vector< std::pair< Atom *, Atom * > > PairVector
    Definition forceField.h:99
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    113} // namespace BALL
    │ │ │ +
    114
    │ │ │ +
    115#endif // BALL_CONCEPT_BASEFUNCTOR_H
    │ │ │ + │ │ │ + │ │ │ +
    BALL::UnaryFunctor::result_type
    ResultType result_type
    Definition baseFunctor.h:35
    │ │ │ +
    BALL::UnaryFunctor::argument_reference
    ArgumentType & argument_reference
    Definition baseFunctor.h:43
    │ │ │ +
    BALL::UnaryFunctor::argument_pointer
    ArgumentType * argument_pointer
    Definition baseFunctor.h:51
    │ │ │ +
    BALL::UnaryFunctor::const_argument_pointer
    const ArgumentType * const_argument_pointer
    Definition baseFunctor.h:55
    │ │ │ +
    BALL::UnaryFunctor::argument_type
    ArgumentType argument_type
    Definition baseFunctor.h:39
    │ │ │ +
    BALL::UnaryFunctor::const_argument_reference
    const ArgumentType & const_argument_reference
    Definition baseFunctor.h:47
    │ │ │ + │ │ │ +
    BALL::BinaryFunctor::const_first_argument_reference
    const FirstArgumentType & const_first_argument_reference
    Definition baseFunctor.h:84
    │ │ │ +
    BALL::BinaryFunctor::const_second_argument_pointer
    const SecondArgumentType * const_second_argument_pointer
    Definition baseFunctor.h:106
    │ │ │ +
    BALL::BinaryFunctor::second_argument_type
    SecondArgumentType second_argument_type
    Definition baseFunctor.h:94
    │ │ │ +
    BALL::BinaryFunctor::const_second_argument_reference
    const SecondArgumentType & const_second_argument_reference
    Definition baseFunctor.h:100
    │ │ │ +
    BALL::BinaryFunctor::first_argument_pointer
    FirstArgumentType * first_argument_pointer
    Definition baseFunctor.h:87
    │ │ │ +
    BALL::BinaryFunctor::second_argument_pointer
    SecondArgumentType * second_argument_pointer
    Definition baseFunctor.h:103
    │ │ │ +
    BALL::BinaryFunctor::first_argument_reference
    FirstArgumentType & first_argument_reference
    Definition baseFunctor.h:81
    │ │ │ +
    BALL::BinaryFunctor::first_argument_type
    FirstArgumentType first_argument_type
    Definition baseFunctor.h:78
    │ │ │ +
    BALL::BinaryFunctor::result_type
    ResultType result_type
    Definition baseFunctor.h:74
    │ │ │ +
    BALL::BinaryFunctor::second_argument_reference
    SecondArgumentType & second_argument_reference
    Definition baseFunctor.h:97
    │ │ │ +
    BALL::BinaryFunctor::const_first_argument_pointer
    const FirstArgumentType * const_first_argument_pointer
    Definition baseFunctor.h:90
    │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,193 +1,134 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_C_O_R_I_N_G │ │ │ │ - * _C_O_M_P_O_N_E_N_T_S │ │ │ │ -PLP.h │ │ │ │ + * _C_O_N_C_E_P_T │ │ │ │ +baseFunctor.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// ---------------------------------------------------- │ │ │ │ -2// $Maintainer: Marcel Schumann $ │ │ │ │ -3// $Authors: Jan Fuhrmann, Marcel Schumann $ │ │ │ │ -4// ---------------------------------------------------- │ │ │ │ -5 │ │ │ │ -6#ifndef BALL_SCORING_COMPONENTS_PLP_H │ │ │ │ -7#define BALL_SCORING_COMPONENTS_PLP_H │ │ │ │ -8 │ │ │ │ -9#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ -10#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_._h> │ │ │ │ -11#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_s_u_p_p_o_r_t_._h> │ │ │ │ -12#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_M_F_F_9_4_/_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ -13 │ │ │ │ +1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ +2// vi: set ts=2: │ │ │ │ +3// │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_CONCEPT_BASEFUNCTOR_H │ │ │ │ +6#define BALL_CONCEPT_BASEFUNCTOR_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ +9# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12namespace _B_A_L_L │ │ │ │ +13{ │ │ │ │ 14 │ │ │ │ -15namespace _B_A_L_L │ │ │ │ -16{ │ │ │ │ -_1_8 class _B_A_L_L___E_X_P_O_R_T _P_L_P : public _F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t │ │ │ │ -19 { │ │ │ │ -20 public: │ │ │ │ -_2_1 struct _N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a │ │ │ │ -22 { │ │ │ │ -_2_3 _S_i_z_e _t_y_p_e; │ │ │ │ -24 │ │ │ │ -_2_5 enum _T_y_p_e │ │ │ │ +20 │ │ │ │ +24 template │ │ │ │ +_2_5 class _B_A_L_L___E_X_P_O_R_T _U_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ 26 { │ │ │ │ -_2_7 steric = 0, │ │ │ │ -_2_8 hydrogen_bond = 1, │ │ │ │ -29 // an atom pair of which both partners are taken from the same ligand │ │ │ │ -molecule in order to evaluate the ligand nonbonded energy │ │ │ │ -30 conformation = 2 │ │ │ │ -_3_1 }; │ │ │ │ +27 public: │ │ │ │ +28 │ │ │ │ 32 │ │ │ │ -33 /* │ │ │ │ -34 NonBondedPairData(); │ │ │ │ -35 │ │ │ │ -36 double eij; │ │ │ │ -37 double rij; │ │ │ │ -38 double rij_7; │ │ │ │ -39 double vdw_energy; // for debugging │ │ │ │ -40 // for electrostatics: │ │ │ │ -41 bool is_1_4; │ │ │ │ -42 double qi; │ │ │ │ -43 double qj; │ │ │ │ -44 double es_energy; // for debugging │ │ │ │ -45 */ │ │ │ │ -46 }; │ │ │ │ -47 │ │ │ │ -_4_9 #define MMFF94_ES_ENABLED "enable ES" │ │ │ │ -50 │ │ │ │ -_5_2 #define MMFF94_VDW_ENABLED "enable VDW" │ │ │ │ -53 │ │ │ │ -54 _B_A_L_L___C_R_E_A_T_E(PLP) │ │ │ │ -55 │ │ │ │ +_3_5 typedef ResultType _r_e_s_u_l_t___t_y_p_e; │ │ │ │ +36 │ │ │ │ +_3_9 typedef ArgumentType _a_r_g_u_m_e_n_t___t_y_p_e; │ │ │ │ +40 │ │ │ │ +_4_3 typedef ArgumentType& _a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e; │ │ │ │ +44 │ │ │ │ +_4_7 typedef const ArgumentType& _c_o_n_s_t___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e; │ │ │ │ +48 │ │ │ │ +_5_1 typedef ArgumentType* _a_r_g_u_m_e_n_t___p_o_i_n_t_e_r; │ │ │ │ +52 │ │ │ │ +_5_5 typedef const ArgumentType* _c_o_n_s_t___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r; │ │ │ │ 56 │ │ │ │ -_5_7 _P_L_P() throw(); │ │ │ │ -58 │ │ │ │ -_6_0 _P_L_P(_F_o_r_c_e_F_i_e_l_d& force_field) throw(); │ │ │ │ -61 │ │ │ │ -_6_3 _P_L_P(const _P_L_P& MMFF94_non_bonded) throw(); │ │ │ │ -64 │ │ │ │ -_6_6 virtual ~_P_L_P() throw(); │ │ │ │ +58 }; │ │ │ │ +59 │ │ │ │ +63 template │ │ │ │ +_6_4 class _B_A_L_L___E_X_P_O_R_T _B_i_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ +65 { │ │ │ │ +66 public: │ │ │ │ 67 │ │ │ │ -_6_9 const _P_L_P& operator = (const _P_L_P& anb) throw(); │ │ │ │ -70 │ │ │ │ -_7_3 void setRotatableBonds(_s_t_d::vector<_B_o_n_d*>& bonds); │ │ │ │ -74 │ │ │ │ -_8_1 static _S_i_z_e getAtomType(const _A_t_o_m* atom); │ │ │ │ -82 │ │ │ │ -_8_4 void update(const _s_t_d::vector<_s_t_d::pair<_A_t_o_m*, _A_t_o_m*> >& atom_vector); │ │ │ │ -85 │ │ │ │ -_8_7 virtual void clear() throw(); │ │ │ │ -88 │ │ │ │ -_9_0 bool operator == (const _P_L_P& anb) throw(); │ │ │ │ +71 │ │ │ │ +_7_4 typedef ResultType _r_e_s_u_l_t___t_y_p_e; │ │ │ │ +75 │ │ │ │ +_7_8 typedef FirstArgumentType _f_i_r_s_t___a_r_g_u_m_e_n_t___t_y_p_e; │ │ │ │ +_8_1 typedef FirstArgumentType & _f_i_r_s_t___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e; │ │ │ │ +_8_4 typedef const FirstArgumentType & _c_o_n_s_t___f_i_r_s_t___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e; │ │ │ │ +_8_7 typedef FirstArgumentType * _f_i_r_s_t___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r; │ │ │ │ +_9_0 typedef const FirstArgumentType * _c_o_n_s_t___f_i_r_s_t___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r; │ │ │ │ 91 │ │ │ │ -_9_3 bool setup(_O_p_t_i_o_n_s& options); │ │ │ │ -94 │ │ │ │ -_9_6 virtual double updateEnergy() throw(); │ │ │ │ -97 │ │ │ │ -_9_9 virtual void updateForces() throw(); │ │ │ │ -100 │ │ │ │ -_1_0_7 virtual void update(); │ │ │ │ -108 │ │ │ │ -_1_0_9 double getVDWEnergy() const; │ │ │ │ +_9_4 typedef SecondArgumentType _s_e_c_o_n_d___a_r_g_u_m_e_n_t___t_y_p_e; │ │ │ │ +_9_7 typedef SecondArgumentType & _s_e_c_o_n_d___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e; │ │ │ │ +_1_0_0 typedef const SecondArgumentType & _c_o_n_s_t___s_e_c_o_n_d___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e; │ │ │ │ +_1_0_3 typedef SecondArgumentType * _s_e_c_o_n_d___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r; │ │ │ │ +_1_0_6 typedef const SecondArgumentType * _c_o_n_s_t___s_e_c_o_n_d___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r; │ │ │ │ +107 │ │ │ │ +109 }; │ │ │ │ 110 │ │ │ │ -_1_1_1 double getESEnergy() const; │ │ │ │ 112 │ │ │ │ -113 protected: │ │ │ │ -114 //_ Value of the electrostatic energy │ │ │ │ -_1_1_5 double es_energy_; │ │ │ │ -116 │ │ │ │ -117 //_ Value of the vdw energy │ │ │ │ -_1_1_8 double vdw_energy_; │ │ │ │ -119 │ │ │ │ -_1_2_0 static bool isNSp3(const _A_t_o_m* at); │ │ │ │ -_1_2_1 static bool isSp3(const _A_t_o_m* at); │ │ │ │ -122 │ │ │ │ -123 private: │ │ │ │ -124 struct GhTorsion │ │ │ │ -125 { │ │ │ │ -126 _A_t_o_m* at1; │ │ │ │ -127 _A_t_o_m* at2; │ │ │ │ -128 _A_t_o_m* at3; │ │ │ │ -129 _A_t_o_m* at4; │ │ │ │ -130 _S_i_z_e type; │ │ │ │ -131 }; │ │ │ │ -132 │ │ │ │ -133 void e1(double& d, double& e, double& delta); │ │ │ │ -134 void e2(double& d, double& e, double& delta); │ │ │ │ -135 │ │ │ │ -136 std::vector ghtorsions_; │ │ │ │ -137 │ │ │ │ -138 _F_o_r_c_e_F_i_e_l_d_:_:_P_a_i_r_V_e_c_t_o_r atom_pair_vector_; │ │ │ │ -139 │ │ │ │ -140 std::vector non_bonded_data_; │ │ │ │ -141 │ │ │ │ -142 double cut_off_; │ │ │ │ -143 double vdw_cut_on_, vdw_cut_off_; │ │ │ │ -144 double es_cut_on_, es_cut_off_; │ │ │ │ -145 _M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s vdw_parameters_; │ │ │ │ -146 │ │ │ │ -147 // dielectric constant │ │ │ │ -148 double dc_; │ │ │ │ -149 // dielectric model exponent │ │ │ │ -150 double n_; │ │ │ │ -151 bool es_enabled_; │ │ │ │ -152 bool vdw_enabled_; │ │ │ │ -153 bool enable_es_switch_; │ │ │ │ -154 bool enable_vdw_switch_; │ │ │ │ -155 double es_d_on2_, es_d_off2_, │ │ │ │ -156 es_d_on_, es_d_off_, │ │ │ │ -157 es_ac_, es_bc_, │ │ │ │ -158 es_cc_, es_dc_, es_denom_, es_con_, es_cover3_, es_dover5_, │ │ │ │ -159 es_eadd_, es_eaddr_, es_const_, es_constr_; │ │ │ │ -160 │ │ │ │ -161 std::vector dismiss_vector_; │ │ │ │ -162 │ │ │ │ -163 std::vector rotgrad_; │ │ │ │ -164 }; │ │ │ │ -165} // │ │ │ │ -166 │ │ │ │ -167#endif // BALL_SCORING_COMPONENTS_PLP_H │ │ │ │ -_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h │ │ │ │ -_s_u_p_p_o_r_t_._h │ │ │ │ -_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h │ │ │ │ -_f_o_r_c_e_F_i_e_l_d_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ -_s_t_d │ │ │ │ -STL namespace. │ │ │ │ +113} // namespace BALL │ │ │ │ +114 │ │ │ │ +115#endif // BALL_CONCEPT_BASEFUNCTOR_H │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ -DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_B_o_n_d │ │ │ │ -DDeeffiinniittiioonn _b_o_n_d_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_P_a_i_r_V_e_c_t_o_r │ │ │ │ -std::vector< std::pair< Atom *, Atom * > > PairVector │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_6_0 │ │ │ │ -_B_A_L_L_:_:_P_L_P │ │ │ │ -DDeeffiinniittiioonn _P_L_P_._h_:_1_9 │ │ │ │ -_B_A_L_L_:_:_P_L_P_:_:_N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a │ │ │ │ -DDeeffiinniittiioonn _P_L_P_._h_:_2_2 │ │ │ │ -_B_A_L_L_:_:_P_L_P_:_:_N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a_:_:_T_y_p_e │ │ │ │ -Type │ │ │ │ -DDeeffiinniittiioonn _P_L_P_._h_:_2_6 │ │ │ │ -_B_A_L_L_:_:_P_L_P_:_:_N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a_:_:_t_y_p_e │ │ │ │ -Size type │ │ │ │ -DDeeffiinniittiioonn _P_L_P_._h_:_2_3 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_U_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_2_6 │ │ │ │ +_B_A_L_L_:_:_U_n_a_r_y_F_u_n_c_t_o_r_:_:_r_e_s_u_l_t___t_y_p_e │ │ │ │ +ResultType result_type │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_3_5 │ │ │ │ +_B_A_L_L_:_:_U_n_a_r_y_F_u_n_c_t_o_r_:_:_a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e │ │ │ │ +ArgumentType & argument_reference │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_4_3 │ │ │ │ +_B_A_L_L_:_:_U_n_a_r_y_F_u_n_c_t_o_r_:_:_a_r_g_u_m_e_n_t___p_o_i_n_t_e_r │ │ │ │ +ArgumentType * argument_pointer │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_5_1 │ │ │ │ +_B_A_L_L_:_:_U_n_a_r_y_F_u_n_c_t_o_r_:_:_c_o_n_s_t___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r │ │ │ │ +const ArgumentType * const_argument_pointer │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_5_5 │ │ │ │ +_B_A_L_L_:_:_U_n_a_r_y_F_u_n_c_t_o_r_:_:_a_r_g_u_m_e_n_t___t_y_p_e │ │ │ │ +ArgumentType argument_type │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_3_9 │ │ │ │ +_B_A_L_L_:_:_U_n_a_r_y_F_u_n_c_t_o_r_:_:_c_o_n_s_t___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e │ │ │ │ +const ArgumentType & const_argument_reference │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_4_7 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_6_5 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_c_o_n_s_t___f_i_r_s_t___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e │ │ │ │ +const FirstArgumentType & const_first_argument_reference │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_8_4 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_c_o_n_s_t___s_e_c_o_n_d___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r │ │ │ │ +const SecondArgumentType * const_second_argument_pointer │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_1_0_6 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_s_e_c_o_n_d___a_r_g_u_m_e_n_t___t_y_p_e │ │ │ │ +SecondArgumentType second_argument_type │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_9_4 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_c_o_n_s_t___s_e_c_o_n_d___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e │ │ │ │ +const SecondArgumentType & const_second_argument_reference │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_1_0_0 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_f_i_r_s_t___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r │ │ │ │ +FirstArgumentType * first_argument_pointer │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_8_7 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_s_e_c_o_n_d___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r │ │ │ │ +SecondArgumentType * second_argument_pointer │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_1_0_3 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_f_i_r_s_t___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e │ │ │ │ +FirstArgumentType & first_argument_reference │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_8_1 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_f_i_r_s_t___a_r_g_u_m_e_n_t___t_y_p_e │ │ │ │ +FirstArgumentType first_argument_type │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_7_8 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_r_e_s_u_l_t___t_y_p_e │ │ │ │ +ResultType result_type │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_s_e_c_o_n_d___a_r_g_u_m_e_n_t___r_e_f_e_r_e_n_c_e │ │ │ │ +SecondArgumentType & second_argument_reference │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_9_7 │ │ │ │ +_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r_:_:_c_o_n_s_t___f_i_r_s_t___a_r_g_u_m_e_n_t___p_o_i_n_t_e_r │ │ │ │ +const FirstArgumentType * const_first_argument_pointer │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_9_0 │ │ │ │ +_g_l_o_b_a_l_._h │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d2b/a01997.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: processor.h File Reference │ │ │ +BALL: hashSet.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,41 +65,44 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    processor.h File Reference
    │ │ │ +
    hashSet.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/CONCEPT/baseFunctor.h>
    │ │ │ -#include <BALL/COMMON/global.h>
    │ │ │ +
    #include <BALL/common.h>
    │ │ │ +#include <BALL/COMMON/hash.h>
    │ │ │ +#include <BALL/CONCEPT/forwardIterator.h>
    │ │ │ +#include <BALL/CONCEPT/visitor.h>
    │ │ │ +#include <BALL/DATATYPE/forEach.h>
    │ │ │ +#include <BALL/CONCEPT/predicate.h>
    │ │ │ +#include <BALL/CONCEPT/processor.h>
    │ │ │ +#include <algorithm>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::Processor
    class  BALL::HashSet< Key >
     
    class  BALL::UnaryProcessor< T >
    struct  BALL::HashSet< Key >::Node
     
    class  BALL::ConstUnaryProcessor< T >
    class  BALL::HashSet< Key >::IteratorTraits
     
    class  BALL::BinaryProcessor< T1, T2 >
     
    class  BALL::ConstBinaryProcessor< T1, T2 >
    class  BALL::HashSet< Key >::IllegalKey
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ ├── html2text {} │ │ │ │ @@ -1,29 +1,32 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _C_O_N_C_E_P_T │ │ │ │ + * _D_A_T_A_T_Y_P_E │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -processor.h File Reference │ │ │ │ +hashSet.h File Reference │ │ │ │ #include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_b_a_s_e_F_u_n_c_t_o_r_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_M_M_O_N_/_h_a_s_h_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_v_i_s_i_t_o_r_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_f_o_r_E_a_c_h_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_e_d_i_c_a_t_e_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_P_r_o_c_e_s_s_o_r │ │ │ │ + class   _B_A_L_L_:_:_H_a_s_h_S_e_t_<_ _K_e_y_ _> │ │ │ │   │ │ │ │ -class   _B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r_<_ _T_ _> │ │ │ │ +struct   _B_A_L_L_:_:_H_a_s_h_S_e_t_<_ _K_e_y_ _>_:_:_N_o_d_e │ │ │ │   │ │ │ │ -class   _B_A_L_L_:_:_C_o_n_s_t_U_n_a_r_y_P_r_o_c_e_s_s_o_r_<_ _T_ _> │ │ │ │ + class   _B_A_L_L_:_:_H_a_s_h_S_e_t_<_ _K_e_y_ _>_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │   │ │ │ │ -class   _B_A_L_L_:_:_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_<_ _T_1_,_ _T_2_ _> │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_C_o_n_s_t_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_<_ _T_1_,_ _T_2_ _> │ │ │ │ + class   _B_A_L_L_:_:_H_a_s_h_S_e_t_<_ _K_e_y_ _>_:_:_I_l_l_e_g_a_l_K_e_y │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d2b/a01997_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: processor.h Source File │ │ │ +BALL: hashSet.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,280 +70,1519 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    processor.h
    │ │ │ +
    hashSet.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5#ifndef BALL_CONCEPT_PROCESSOR_H
    │ │ │ -
    6#define BALL_CONCEPT_PROCESSOR_H
    │ │ │ +
    5#ifndef BALL_DATATYPE_HASHSET_H
    │ │ │ +
    6#define BALL_DATATYPE_HASHSET_H
    │ │ │
    7
    │ │ │
    8#ifndef BALL_COMMON_H
    │ │ │ -
    9# include <BALL/common.h>
    │ │ │ +
    9# include <BALL/common.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_CONCEPT_BASEFUNCTOR_H
    │ │ │ -
    13# include <BALL/CONCEPT/baseFunctor.h>
    │ │ │ +
    12#ifndef BALL_COMMON_HASH_H
    │ │ │ +
    13# include <BALL/COMMON/hash.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │ -
    16#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ -
    17# include <BALL/COMMON/global.h>
    │ │ │ +
    16#ifndef BALL_CONCEPT_FORWARDITERATOR_H
    │ │ │ +
    17# include <BALL/CONCEPT/forwardIterator.h>
    │ │ │
    18#endif
    │ │ │
    19
    │ │ │ -
    20namespace BALL
    │ │ │ -
    21{
    │ │ │ -
    22
    │ │ │ -
    28
    │ │ │ -
    │ │ │ -
    31 class BALL_EXPORT Processor
    │ │ │ -
    32 {
    │ │ │ -
    33 public:
    │ │ │ -
    36 typedef int Result;
    │ │ │ +
    20#ifndef BALL_CONCEPT_VISITOR_H
    │ │ │ +
    21# include <BALL/CONCEPT/visitor.h>
    │ │ │ +
    22#endif
    │ │ │ +
    23
    │ │ │ +
    24#ifndef BALL_DATATYPE_FOREACH_H
    │ │ │ +
    25# include <BALL/DATATYPE/forEach.h>
    │ │ │ +
    26#endif
    │ │ │ +
    27
    │ │ │ +
    28#ifndef BALL_CONCEPT_PREDICATE_H
    │ │ │ +
    29# include <BALL/CONCEPT/predicate.h>
    │ │ │ +
    30#endif
    │ │ │ +
    31
    │ │ │ +
    32#ifndef BALL_CONCEPT_PROCESSOR_H
    │ │ │ +
    33# include <BALL/CONCEPT/processor.h>
    │ │ │ +
    34#endif
    │ │ │ +
    35
    │ │ │ +
    36#include <algorithm>
    │ │ │
    37
    │ │ │ -
    40 enum
    │ │ │ -
    41 {
    │ │ │ -
    44 ABORT = 0,
    │ │ │ -
    47 BREAK = 1,
    │ │ │ -
    50 CONTINUE = 2
    │ │ │ -
    51 };
    │ │ │ -
    52 };
    │ │ │ -
    │ │ │ -
    53
    │ │ │ -
    54
    │ │ │ -
    57 template <typename T>
    │ │ │ -
    │ │ │ -
    58 class UnaryProcessor
    │ │ │ -
    59 : public UnaryFunctor<T, Processor::Result>
    │ │ │ -
    60 {
    │ │ │ -
    61 public:
    │ │ │ -
    62
    │ │ │ -
    66 BALL_CREATE(UnaryProcessor)
    │ │ │ -
    │ │ │ -
    69 UnaryProcessor()
    │ │ │ -
    70 {
    │ │ │ -
    71 }
    │ │ │ -
    │ │ │ -
    72
    │ │ │ -
    │ │ │ -
    75 UnaryProcessor
    │ │ │ -
    76 (const UnaryProcessor& /* processor */)
    │ │ │ +
    38
    │ │ │ +
    39namespace BALL
    │ │ │ +
    40{
    │ │ │ +
    44 template <class Key>
    │ │ │ +
    │ │ │ +
    45 class HashSet
    │ │ │ +
    46 {
    │ │ │ +
    47 public:
    │ │ │ +
    48
    │ │ │ +
    51 typedef Key ValueType;
    │ │ │ +
    52
    │ │ │ +
    55 typedef Key KeyType;
    │ │ │ +
    56
    │ │ │ +
    59 typedef Key* PointerType;
    │ │ │ +
    60
    │ │ │ +
    61 // --- EXTERNAL ITERATORS
    │ │ │ +
    │ │ │ +
    62 struct Node
    │ │ │ +
    63 {
    │ │ │ +
    64 Node* next;
    │ │ │ +
    65 ValueType value;
    │ │ │ +
    66
    │ │ │ +
    67 Node(const KeyType& my_key, const Node* my_next)
    │ │ │ +
    68 : next(const_cast<Node*>(my_next)),
    │ │ │ +
    69 value(const_cast<ValueType&>(my_key))
    │ │ │ +
    70 {
    │ │ │ +
    71 }
    │ │ │ +
    72 };
    │ │ │ +
    │ │ │ +
    73
    │ │ │ +
    74 typedef Node* IteratorPosition;
    │ │ │ +
    75
    │ │ │ +
    │ │ │ +
    76 class IteratorTraits
    │ │ │
    77 {
    │ │ │ -
    78 }
    │ │ │ -
    │ │ │ -
    79
    │ │ │ +
    78
    │ │ │ +
    79 friend class HashSet<Key>;
    │ │ │ +
    80 public:
    │ │ │ +
    81
    │ │ │
    │ │ │ -
    82 virtual ~UnaryProcessor()
    │ │ │ -
    83 {
    │ │ │ -
    84 }
    │ │ │ -
    │ │ │ -
    86
    │ │ │ -
    │ │ │ -
    92 virtual bool start()
    │ │ │ -
    93 {
    │ │ │ -
    94 return true;
    │ │ │ -
    95 }
    │ │ │ -
    │ │ │ -
    96
    │ │ │ -
    │ │ │ -
    99 virtual bool finish()
    │ │ │ -
    100 {
    │ │ │ -
    101 return true;
    │ │ │ -
    102 }
    │ │ │ -
    │ │ │ -
    103
    │ │ │ -
    │ │ │ -
    106 virtual Processor::Result operator () (T &)
    │ │ │ -
    107 {
    │ │ │ -
    108 return Processor::CONTINUE;
    │ │ │ -
    109 }
    │ │ │ -
    │ │ │ -
    111 };
    │ │ │ -
    │ │ │ -
    112
    │ │ │ -
    118 template<typename T>
    │ │ │ -
    │ │ │ -
    119 class ConstUnaryProcessor : public UnaryFunctor<T, Processor::Result>
    │ │ │ -
    120 {
    │ │ │ -
    121 public:
    │ │ │ -
    122 BALL_CREATE(ConstUnaryProcessor)
    │ │ │ -
    123
    │ │ │ -
    │ │ │ -
    124 virtual ~ConstUnaryProcessor()
    │ │ │ -
    125 {
    │ │ │ -
    126 }
    │ │ │ -
    │ │ │ -
    127
    │ │ │ -
    │ │ │ -
    128 virtual bool start()
    │ │ │ -
    129 {
    │ │ │ -
    130 return true;
    │ │ │ -
    131 }
    │ │ │ -
    │ │ │ -
    132
    │ │ │ -
    │ │ │ -
    133 virtual bool finish()
    │ │ │ -
    134 {
    │ │ │ -
    135 return true;
    │ │ │ -
    136 }
    │ │ │ -
    │ │ │ -
    137
    │ │ │ -
    │ │ │ -
    138 virtual Processor::Result operator()(const T&)
    │ │ │ -
    139 {
    │ │ │ -
    140 return Processor::CONTINUE;
    │ │ │ -
    141 }
    │ │ │ -
    │ │ │ -
    142 };
    │ │ │ -
    │ │ │ -
    143
    │ │ │ -
    146 template <typename T1, typename T2>
    │ │ │ -
    │ │ │ -
    147 class BinaryProcessor
    │ │ │ -
    148 : public BinaryFunctor<T1, T2, Processor::Result>
    │ │ │ -
    149 {
    │ │ │ -
    150 public:
    │ │ │ -
    151
    │ │ │ -
    155 BALL_CREATE(BinaryProcessor)
    │ │ │ -
    156
    │ │ │ -
    157
    │ │ │ -
    │ │ │ -
    159 BinaryProcessor()
    │ │ │ -
    160 {
    │ │ │ -
    161 }
    │ │ │ -
    │ │ │ -
    162
    │ │ │ -
    │ │ │ -
    165 BinaryProcessor
    │ │ │ -
    166 (const BinaryProcessor& /* processor */)
    │ │ │ -
    167 {
    │ │ │ -
    168 }
    │ │ │ -
    │ │ │ -
    169
    │ │ │ -
    │ │ │ -
    172 virtual ~BinaryProcessor()
    │ │ │ -
    173 {
    │ │ │ -
    174 }
    │ │ │ -
    │ │ │ -
    176
    │ │ │ -
    180
    │ │ │ -
    │ │ │ -
    183 virtual bool start()
    │ │ │ -
    184 {
    │ │ │ -
    185 return true;
    │ │ │ -
    186 }
    │ │ │ -
    │ │ │ -
    187
    │ │ │ -
    │ │ │ -
    190 virtual bool finish()
    │ │ │ -
    191 {
    │ │ │ -
    192 return true;
    │ │ │ -
    193 }
    │ │ │ -
    │ │ │ -
    194
    │ │ │ -
    │ │ │ -
    197 virtual Processor::Result operator () (T1&, T2&)
    │ │ │ -
    198 {
    │ │ │ -
    199 return Processor::CONTINUE;
    │ │ │ -
    200 }
    │ │ │ -
    │ │ │ -
    202 };
    │ │ │ -
    │ │ │ -
    203
    │ │ │ -
    204 template <typename T1, typename T2>
    │ │ │ -
    │ │ │ -
    205 class ConstBinaryProcessor
    │ │ │ -
    206 : public BinaryFunctor<T1, T2, Processor::Result>
    │ │ │ -
    207 {
    │ │ │ -
    208 public:
    │ │ │ -
    209
    │ │ │ -
    213 BALL_CREATE(ConstBinaryProcessor)
    │ │ │ -
    214
    │ │ │ -
    215
    │ │ │ -
    │ │ │ -
    217 virtual ~ConstBinaryProcessor()
    │ │ │ -
    218 {
    │ │ │ -
    219 }
    │ │ │ -
    │ │ │ +
    82 IteratorTraits()
    │ │ │ +
    83 : bound_(0),
    │ │ │ +
    84 position_(0),
    │ │ │ +
    85 bucket_(0)
    │ │ │ +
    86 {
    │ │ │ +
    87 }
    │ │ │ +
    │ │ │ +
    88
    │ │ │ +
    │ │ │ +
    89 IteratorTraits(const HashSet& hash_set)
    │ │ │ +
    90 : bound_(const_cast<HashSet*>(&hash_set)),
    │ │ │ +
    91 position_(0),
    │ │ │ +
    92 bucket_(0)
    │ │ │ +
    93 {
    │ │ │ +
    94 }
    │ │ │ +
    │ │ │ +
    95
    │ │ │ +
    │ │ │ +
    96 IteratorTraits(const IteratorTraits& traits)
    │ │ │ +
    97 : bound_(traits.bound_),
    │ │ │ +
    98 position_(traits.position_),
    │ │ │ +
    99 bucket_(traits.bucket_)
    │ │ │ +
    100 {
    │ │ │ +
    101 }
    │ │ │ +
    │ │ │ +
    102
    │ │ │ +
    │ │ │ +
    103 IteratorTraits& operator = (const IteratorTraits& traits)
    │ │ │ +
    104 {
    │ │ │ +
    105 bound_ = traits.bound_;
    │ │ │ +
    106 position_ = traits.position_;
    │ │ │ +
    107 bucket_ = traits.bucket_;
    │ │ │ +
    108
    │ │ │ +
    109 return *this;
    │ │ │ +
    110 }
    │ │ │ +
    │ │ │ +
    111
    │ │ │ +
    │ │ │ +
    112 HashSet* getContainer()
    │ │ │ +
    113 {
    │ │ │ +
    114 return bound_;
    │ │ │ +
    115 }
    │ │ │ +
    │ │ │ +
    116
    │ │ │ +
    │ │ │ +
    117 const HashSet* getContainer() const
    │ │ │ +
    118 {
    │ │ │ +
    119 return bound_;
    │ │ │ +
    120 }
    │ │ │ +
    │ │ │ +
    121
    │ │ │ +
    │ │ │ +
    122 bool isSingular() const
    │ │ │ +
    123 {
    │ │ │ +
    124 return (bound_ == 0);
    │ │ │ +
    125 }
    │ │ │ +
    │ │ │ +
    126
    │ │ │ +
    │ │ │ +
    127 IteratorPosition& getPosition()
    │ │ │ +
    128 {
    │ │ │ +
    129 return position_;
    │ │ │ +
    130 }
    │ │ │ +
    │ │ │ +
    131
    │ │ │ +
    │ │ │ +
    132 const IteratorPosition& getPosition() const
    │ │ │ +
    133 {
    │ │ │ +
    134 return position_;
    │ │ │ +
    135 }
    │ │ │ +
    │ │ │ +
    136
    │ │ │ +
    │ │ │ +
    137 bool operator == (const IteratorTraits& traits) const
    │ │ │ +
    138 {
    │ │ │ +
    139 return (position_ == traits.position_);
    │ │ │ +
    140 }
    │ │ │ +
    │ │ │ +
    141
    │ │ │ +
    │ │ │ +
    142 bool operator != (const IteratorTraits& traits) const
    │ │ │ +
    143 {
    │ │ │ +
    144 return (position_ != traits.position_);
    │ │ │ +
    145 }
    │ │ │ +
    │ │ │ +
    146
    │ │ │ +
    │ │ │ +
    147 bool isValid() const
    │ │ │ +
    148 {
    │ │ │ +
    149 return ((bound_ != 0) && (position_ != 0)
    │ │ │ +
    150 && (bucket_ < (Position)bound_->bucket_.size()));
    │ │ │ +
    151 }
    │ │ │ +
    │ │ │ +
    152
    │ │ │ +
    │ │ │ +
    153 void invalidate()
    │ │ │ +
    154 {
    │ │ │ +
    155 bound_ = 0;
    │ │ │ +
    156 position_ = 0;
    │ │ │ +
    157 bucket_ = INVALID_Position;
    │ │ │ +
    158 }
    │ │ │ +
    │ │ │ +
    159
    │ │ │ +
    │ │ │ +
    160 void toBegin()
    │ │ │ +
    161 {
    │ │ │ +
    162 for (bucket_ = 0; bucket_ < (Position)bound_->bucket_.size(); ++bucket_)
    │ │ │ +
    163 {
    │ │ │ +
    164 position_ = bound_->bucket_[bucket_];
    │ │ │ +
    165
    │ │ │ +
    166 if (position_ != 0)
    │ │ │ +
    167 {
    │ │ │ +
    168 return;
    │ │ │ +
    169 }
    │ │ │ +
    170 }
    │ │ │ +
    171 }
    │ │ │ +
    │ │ │ +
    172
    │ │ │ +
    │ │ │ +
    173 bool isBegin() const
    │ │ │ +
    174 {
    │ │ │ +
    175 for (Position bucket = 0; bucket < (Position)bound_->bucket_.size(); ++bucket)
    │ │ │ +
    176 {
    │ │ │ +
    177 if (bound_->bucket_[bucket_] != 0)
    │ │ │ +
    178 {
    │ │ │ +
    179 if (position_ == bound_->bucket_[bucket_])
    │ │ │ +
    180 {
    │ │ │ +
    181 return true;
    │ │ │ +
    182 }
    │ │ │ +
    183 else
    │ │ │ +
    184 {
    │ │ │ +
    185 return false;
    │ │ │ +
    186 }
    │ │ │ +
    187 }
    │ │ │ +
    188 }
    │ │ │ +
    189
    │ │ │ +
    190 return false;
    │ │ │ +
    191 }
    │ │ │ +
    │ │ │ +
    192
    │ │ │ +
    │ │ │ +
    193 void toEnd()
    │ │ │ +
    194 {
    │ │ │ +
    195 position_ = 0;
    │ │ │ +
    196 }
    │ │ │ +
    │ │ │ +
    197
    │ │ │ +
    │ │ │ +
    198 bool isEnd() const
    │ │ │ +
    199 {
    │ │ │ +
    200 return (position_ == 0);
    │ │ │ +
    201 }
    │ │ │ +
    │ │ │ +
    202
    │ │ │ +
    │ │ │ +
    203 ValueType& getData()
    │ │ │ +
    204 {
    │ │ │ +
    205 return position_->value;
    │ │ │ +
    206 }
    │ │ │ +
    │ │ │ +
    207
    │ │ │ +
    │ │ │ +
    208 const ValueType& getData() const
    │ │ │ +
    209 {
    │ │ │ +
    210 return position_->value;
    │ │ │ +
    211 }
    │ │ │ +
    │ │ │ +
    212
    │ │ │ +
    │ │ │ +
    213 void forward()
    │ │ │ +
    214 {
    │ │ │ +
    215 position_ = position_->next;
    │ │ │ +
    216
    │ │ │ +
    217 if (position_ != 0)
    │ │ │ +
    218 {
    │ │ │ +
    219 return;
    │ │ │ +
    220 }
    │ │ │
    221
    │ │ │ +
    222 for (++bucket_; bucket_ < (Position)bound_->bucket_.size(); ++bucket_)
    │ │ │ +
    223 {
    │ │ │ +
    224 position_ = bound_->bucket_[bucket_];
    │ │ │
    225
    │ │ │ -
    │ │ │ -
    228 virtual bool start()
    │ │ │ -
    229 {
    │ │ │ -
    230 return true;
    │ │ │ -
    231 }
    │ │ │ +
    226 if (position_ != 0)
    │ │ │ +
    227 {
    │ │ │ +
    228 return;
    │ │ │ +
    229 }
    │ │ │ +
    230 }
    │ │ │ +
    231 }
    │ │ │
    │ │ │
    232
    │ │ │ -
    │ │ │ -
    235 virtual bool finish()
    │ │ │ -
    236 {
    │ │ │ -
    237 return true;
    │ │ │ -
    238 }
    │ │ │ -
    │ │ │ -
    239
    │ │ │ -
    │ │ │ -
    242 virtual Processor::Result operator () (const T1&, const T2&)
    │ │ │ -
    243 {
    │ │ │ -
    244 return Processor::CONTINUE;
    │ │ │ -
    245 }
    │ │ │ -
    │ │ │ -
    247 };
    │ │ │ -
    │ │ │ -
    248
    │ │ │ -
    250// required for MSVC 12/2013 (TODO remove)
    │ │ │ -
    251#ifdef BALL_COMPILER_MSVC
    │ │ │ -
    252class Atom;
    │ │ │ -
    253template class BALL_EXPORT UnaryProcessor<Atom>;
    │ │ │ -
    254template class BALL_EXPORT ConstUnaryProcessor<Atom>;
    │ │ │ -
    255#endif
    │ │ │ -
    256
    │ │ │ -
    257} // namespace BALL
    │ │ │ +
    233 protected:
    │ │ │ +
    234
    │ │ │ +
    235 HashSet* bound_;
    │ │ │ +
    236 IteratorPosition position_;
    │ │ │ +
    237 Position bucket_;
    │ │ │ +
    238 };
    │ │ │ +
    │ │ │ +
    239 friend class IteratorTraits;
    │ │ │ +
    240
    │ │ │ +
    244
    │ │ │ +
    245 enum
    │ │ │ +
    246 {
    │ │ │ +
    248 INITIAL_CAPACITY = 4,
    │ │ │ +
    250 INITIAL_NUMBER_OF_BUCKETS = 3
    │ │ │ +
    251 };
    │ │ │ +
    252
    │ │ │ +
    254
    │ │ │
    258
    │ │ │ -
    259#endif // BALL_CONCEPT_PROCESSOR_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::UnaryProcessor::UnaryProcessor
    UnaryProcessor(const UnaryProcessor &)
    Definition processor.h:76
    │ │ │ -
    BALL::UnaryProcessor::start
    virtual bool start()
    Definition processor.h:92
    │ │ │ -
    BALL::UnaryProcessor::~UnaryProcessor
    virtual ~UnaryProcessor()
    Definition processor.h:82
    │ │ │ -
    BALL::UnaryProcessor::finish
    virtual bool finish()
    Definition processor.h:99
    │ │ │ -
    BALL::UnaryProcessor::operator()
    virtual Processor::Result operator()(T &)
    Definition processor.h:106
    │ │ │ - │ │ │ -
    BALL::ConstUnaryProcessor::finish
    virtual bool finish()
    Definition processor.h:133
    │ │ │ -
    BALL::ConstUnaryProcessor::operator()
    virtual Processor::Result operator()(const T &)
    Definition processor.h:138
    │ │ │ - │ │ │ - │ │ │ -
    BALL::BinaryProcessor::~BinaryProcessor
    virtual ~BinaryProcessor()
    Definition processor.h:172
    │ │ │ -
    BALL::BinaryProcessor::finish
    virtual bool finish()
    Definition processor.h:190
    │ │ │ -
    BALL::BinaryProcessor::operator()
    virtual Processor::Result operator()(T1 &, T2 &)
    Definition processor.h:197
    │ │ │ -
    BALL::BinaryProcessor::BinaryProcessor
    BinaryProcessor(const BinaryProcessor &)
    Definition processor.h:166
    │ │ │ -
    BALL::BinaryProcessor::start
    virtual bool start()
    Definition processor.h:183
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ConstBinaryProcessor::operator()
    virtual Processor::Result operator()(const T1 &, const T2 &)
    Definition processor.h:242
    │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    │ │ │ +
    263 class IllegalKey
    │ │ │ +
    264 : public Exception::GeneralException
    │ │ │ +
    265 {
    │ │ │ +
    266 public:
    │ │ │ +
    │ │ │ +
    267 IllegalKey(const char* file, int line)
    │ │ │ +
    268 : Exception::GeneralException(file, line)
    │ │ │ +
    269 {
    │ │ │ +
    270 }
    │ │ │ +
    │ │ │ +
    271 };
    │ │ │ +
    │ │ │ +
    272
    │ │ │ +
    274
    │ │ │ +
    278
    │ │ │ +
    280 typedef ForwardIterator<HashSet<Key>, ValueType, PointerType, IteratorTraits> Iterator;
    │ │ │ +
    281
    │ │ │ +
    283 typedef ConstForwardIterator <HashSet<Key>, ValueType, PointerType, IteratorTraits> ConstIterator;
    │ │ │ +
    284
    │ │ │ +
    285 // STL compatibility stuff
    │ │ │ +
    287 typedef Iterator iterator;
    │ │ │ +
    289 typedef ConstIterator const_iterator;
    │ │ │ +
    291 typedef Key value_type;
    │ │ │ +
    293 typedef Key key_type;
    │ │ │ +
    295 typedef Key* pointer;
    │ │ │ +
    297 typedef const Key* const_pointer;
    │ │ │ +
    299 typedef Key& reference;
    │ │ │ +
    301 typedef const Key& const_reference;
    │ │ │ +
    303 typedef Size size_type;
    │ │ │ +
    305 typedef Index difference_type;
    │ │ │ +
    307
    │ │ │ +
    311
    │ │ │ +
    │ │ │ +
    314 HashSet(Size initial_capacity = INITIAL_CAPACITY, Size number_of_buckets = INITIAL_NUMBER_OF_BUCKETS);
    │ │ │ +
    315
    │ │ │ +
    │ │ │ +
    318 HashSet(const HashSet& hash_set);
    │ │ │ +
    319
    │ │ │ +
    │ │ │ +
    322 virtual ~HashSet()
    │ │ │ +
    323 {
    │ │ │ +
    324 destroy();
    │ │ │ +
    325 deleteBuckets_();
    │ │ │ +
    326 }
    │ │ │ +
    │ │ │ +
    327
    │ │ │ +
    │ │ │ +
    332 virtual void clear();
    │ │ │ +
    333
    │ │ │ +
    │ │ │ +
    339 void destroy();
    │ │ │ +
    340
    │ │ │ +
    342
    │ │ │ +
    346
    │ │ │ +
    │ │ │ +
    350 void set(const HashSet& hash_set);
    │ │ │ +
    351
    │ │ │ +
    │ │ │ +
    355 const HashSet& operator = (const HashSet& rhs);
    │ │ │ +
    356
    │ │ │ +
    │ │ │ +
    360 void get(HashSet& hash_set) const;
    │ │ │ +
    361
    │ │ │ +
    │ │ │ +
    364 void swap(HashSet& hash_set);
    │ │ │ +
    365
    │ │ │ +
    367
    │ │ │ +
    371
    │ │ │ +
    │ │ │ +
    374 Size getBucketSize() const;
    │ │ │ +
    375
    │ │ │ +
    │ │ │ +
    378 Size getCapacity() const;
    │ │ │ +
    379
    │ │ │ +
    │ │ │ +
    382 Size getSize() const;
    │ │ │ +
    383
    │ │ │ +
    │ │ │ +
    386 Size size() const;
    │ │ │ +
    387
    │ │ │ +
    │ │ │ +
    390 Iterator find(const Key& key);
    │ │ │ +
    391
    │ │ │ +
    │ │ │ +
    394 ConstIterator find(const Key& key) const;
    │ │ │ +
    395
    │ │ │ +
    │ │ │ +
    398 std::pair<Iterator, bool> insert(const ValueType& item);
    │ │ │ +
    399
    │ │ │ +
    403 Iterator insert(Iterator pos, const ValueType& item);
    │ │ │ +
    404
    │ │ │ +
    │ │ │ +
    408 Size erase(const KeyType& key);
    │ │ │ +
    409
    │ │ │ +
    │ │ │ +
    415 void erase(Iterator pos);
    │ │ │ +
    416
    │ │ │ +
    │ │ │ +
    421 void erase(Iterator f, Iterator l);
    │ │ │ +
    422
    │ │ │ +
    424
    │ │ │ +
    │ │ │ +
    432 const HashSet& operator &= (const HashSet& rhs);
    │ │ │ +
    433
    │ │ │ +
    │ │ │ +
    438 const HashSet& operator |= (const HashSet& rhs);
    │ │ │ +
    439
    │ │ │ +
    │ │ │ +
    444 HashSet operator & (const HashSet& rhs) const;
    │ │ │ +
    445
    │ │ │ +
    │ │ │ +
    450 HashSet operator | (const HashSet& rhs) const;
    │ │ │ +
    451
    │ │ │ +
    │ │ │ +
    455 HashSet operator + (const HashSet& rhs) const;
    │ │ │ +
    456
    │ │ │ +
    │ │ │ +
    462 HashSet operator - (const HashSet& rhs) const;
    │ │ │ +
    463
    │ │ │ +
    │ │ │ +
    467 const HashSet& operator += (const HashSet& rhs);
    │ │ │ +
    468
    │ │ │ +
    │ │ │ +
    472 const HashSet& operator -= (const HashSet& rhs);
    │ │ │ +
    474
    │ │ │ +
    478
    │ │ │ +
    │ │ │ +
    481 virtual void host(Visitor<HashSet<Key> >& visitor);
    │ │ │ +
    483
    │ │ │ +
    487
    │ │ │ +
    │ │ │ +
    490 bool has(const Key& key) const;
    │ │ │ +
    491
    │ │ │ +
    │ │ │ +
    494 bool isEmpty() const;
    │ │ │ +
    495
    │ │ │ +
    │ │ │ +
    498 bool operator == (const HashSet& hash_set) const;
    │ │ │ +
    499
    │ │ │ +
    │ │ │ +
    502 bool operator != (const HashSet& hash_set) const;
    │ │ │ +
    504
    │ │ │ +
    508
    │ │ │ +
    │ │ │ +
    513 bool isValid() const;
    │ │ │ +
    514
    │ │ │ +
    │ │ │ +
    517 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ +
    518
    │ │ │ +
    520
    │ │ │ +
    521 // --- INTERNAL ITERATORS
    │ │ │ +
    522
    │ │ │ +
    │ │ │ +
    529 bool apply(UnaryProcessor<ValueType>& processor);
    │ │ │ +
    531
    │ │ │ +
    532
    │ │ │ +
    533
    │ │ │ +
    │ │ │ +
    536 Iterator begin()
    │ │ │ +
    537 {
    │ │ │ +
    538 return Iterator::begin(*this);
    │ │ │ +
    539 }
    │ │ │ +
    │ │ │ +
    540
    │ │ │ +
    │ │ │ +
    543 Iterator end()
    │ │ │ +
    544 {
    │ │ │ +
    545 return Iterator::end(*this);
    │ │ │ +
    546 }
    │ │ │ +
    │ │ │ +
    547
    │ │ │ +
    │ │ │ +
    550 ConstIterator begin() const
    │ │ │ +
    551 {
    │ │ │ +
    552 return ConstIterator::begin(*this);
    │ │ │ +
    553 }
    │ │ │ +
    │ │ │ +
    554
    │ │ │ +
    │ │ │ +
    557 ConstIterator end() const
    │ │ │ +
    558 {
    │ │ │ +
    559 return ConstIterator::end(*this);
    │ │ │ +
    560 }
    │ │ │ +
    │ │ │ +
    561
    │ │ │ +
    562
    │ │ │ +
    563 protected:
    │ │ │ +
    564
    │ │ │ +
    │ │ │ +
    565 virtual Node* newNode_(const ValueType& value, Node* next) const;
    │ │ │ +
    566
    │ │ │ +
    │ │ │ +
    567 virtual void deleteNode_(Node* node) const;
    │ │ │ +
    568
    │ │ │ +
    │ │ │ +
    569 virtual HashIndex hash(const Key& key) const;
    │ │ │ +
    570
    │ │ │ +
    │ │ │ +
    571 virtual bool needRehashing_() const;
    │ │ │ +
    572
    │ │ │ +
    │ │ │ +
    573 virtual void rehash();
    │ │ │ +
    574
    │ │ │ +
    575 private:
    │ │ │ +
    576
    │ │ │ +
    577 void deleteBuckets_();
    │ │ │ +
    578
    │ │ │ +
    579 Position hashBucket_(const Key& key) const;
    │ │ │ +
    580
    │ │ │ +
    581 void rehash_();
    │ │ │ +
    582
    │ │ │ +
    583 // --- ATTRIBUTES
    │ │ │ +
    584
    │ │ │ +
    585 /*_ The number of elements in the hash set
    │ │ │ +
    586 */
    │ │ │ +
    587 Size size_;
    │ │ │ +
    588
    │ │ │ +
    589 /*_ The capacity - usually the number of buckets
    │ │ │ +
    590 */
    │ │ │ +
    591 Size capacity_;
    │ │ │ +
    592
    │ │ │ +
    593 /*_ Buckets are stored as a vector of linked lists of Nodes
    │ │ │ +
    594 */
    │ │ │ +
    595 vector<Node*> bucket_;
    │ │ │ +
    596 };
    │ │ │ +
    597
    │ │ │ +
    598
    │ │ │ +
    599 template <class Key>
    │ │ │ +
    │ │ │ +
    600 HashSet<Key>::HashSet(Size initial_capacity, Size number_of_buckets)
    │ │ │ +
    601 : size_(0),
    │ │ │ +
    602 capacity_(initial_capacity),
    │ │ │ +
    603 bucket_(number_of_buckets)
    │ │ │ +
    604 {
    │ │ │ +
    605 for (Position bucket = 0; bucket < (Position)bucket_.size(); ++bucket)
    │ │ │ +
    606 {
    │ │ │ +
    607 bucket_[bucket] = 0;
    │ │ │ +
    608 }
    │ │ │ +
    609 }
    │ │ │ +
    │ │ │ +
    610
    │ │ │ +
    611 template <class Key>
    │ │ │ +
    │ │ │ +
    612 HashSet<Key>::HashSet(const HashSet& hash_set)
    │ │ │ +
    613 : size_(hash_set.size_),
    │ │ │ +
    614 capacity_(hash_set.capacity_),
    │ │ │ +
    615 bucket_(hash_set.bucket_.size())
    │ │ │ +
    616 {
    │ │ │ +
    617 Node* item = 0;
    │ │ │ +
    618
    │ │ │ +
    619 for (Position bucket = 0; bucket < (Position)bucket_.size(); ++bucket)
    │ │ │ +
    620 {
    │ │ │ +
    621 bucket_[bucket] = 0;
    │ │ │ +
    622
    │ │ │ +
    623 for (item = hash_set.bucket_[bucket]; item != 0; item = item->next)
    │ │ │ +
    624 {
    │ │ │ +
    625 bucket_[bucket] = newNode_(item->value, bucket_[bucket]);
    │ │ │ +
    626 }
    │ │ │ +
    627 }
    │ │ │ +
    628 }
    │ │ │ +
    │ │ │ +
    629
    │ │ │ +
    630 template <class Key>
    │ │ │ +
    │ │ │ +
    631 void HashSet<Key>::set(const HashSet& hash_set)
    │ │ │ +
    632 {
    │ │ │ +
    633 if (&hash_set == this)
    │ │ │ +
    634 {
    │ │ │ +
    635 return;
    │ │ │ +
    636 }
    │ │ │ +
    637
    │ │ │ +
    638 destroy();
    │ │ │ +
    639
    │ │ │ +
    640 deleteBuckets_();
    │ │ │ +
    641
    │ │ │ +
    642 size_ = hash_set.size_;
    │ │ │ +
    643 capacity_ = hash_set.capacity_;
    │ │ │ +
    644 bucket_.resize(hash_set.bucket_.size());
    │ │ │ +
    645
    │ │ │ +
    646 Node* item = 0;
    │ │ │ +
    647
    │ │ │ +
    648 for (Position bucket = 0; bucket < (Position)bucket_.size(); ++bucket)
    │ │ │ +
    649 {
    │ │ │ +
    650 bucket_[bucket] = 0;
    │ │ │ +
    651
    │ │ │ +
    652 for (item = hash_set.bucket_[bucket]; item != 0; item = item->next)
    │ │ │ +
    653 {
    │ │ │ +
    654 bucket_[bucket] = newNode_(item->value, bucket_[bucket]);
    │ │ │ +
    655 }
    │ │ │ +
    656 }
    │ │ │ +
    657 }
    │ │ │ +
    │ │ │ +
    658
    │ │ │ +
    659 template <class Key>
    │ │ │ +
    │ │ │ +
    660 void HashSet<Key>::clear()
    │ │ │ +
    661 {
    │ │ │ +
    662 Node* node = 0;
    │ │ │ +
    663 Node* next_node = 0;
    │ │ │ +
    664
    │ │ │ +
    665 for (Position bucket = 0; bucket < (Position)bucket_.size(); ++bucket)
    │ │ │ +
    666 {
    │ │ │ +
    667 for (node = bucket_[bucket]; node != 0; node = next_node)
    │ │ │ +
    668 {
    │ │ │ +
    669 next_node = node->next;
    │ │ │ +
    670 deleteNode_(node);
    │ │ │ +
    671 }
    │ │ │ +
    672
    │ │ │ +
    673 bucket_[bucket] = 0;
    │ │ │ +
    674 }
    │ │ │ +
    675
    │ │ │ +
    676 size_ = 0;
    │ │ │ +
    677 }
    │ │ │ +
    │ │ │ +
    678
    │ │ │ +
    679 template <class Key>
    │ │ │ +
    680 BALL_INLINE
    │ │ │ +
    │ │ │ +
    681 void HashSet<Key>::destroy()
    │ │ │ +
    682 {
    │ │ │ +
    683 clear();
    │ │ │ +
    684 }
    │ │ │ +
    │ │ │ +
    685
    │ │ │ +
    686 template <class Key>
    │ │ │ +
    687 BALL_INLINE
    │ │ │ +
    │ │ │ +
    688 const HashSet<Key>& HashSet<Key>::operator = (const HashSet& hash_set)
    │ │ │ +
    689 {
    │ │ │ +
    690 set(hash_set);
    │ │ │ +
    691 return *this;
    │ │ │ +
    692 }
    │ │ │ +
    │ │ │ +
    693
    │ │ │ +
    694 template <class Key>
    │ │ │ +
    695 BALL_INLINE
    │ │ │ +
    │ │ │ +
    696 void HashSet<Key>::get(HashSet& hash_set) const
    │ │ │ +
    697
    │ │ │ +
    698 {
    │ │ │ +
    699 hash_set.set(*this);
    │ │ │ +
    700 }
    │ │ │ +
    │ │ │ +
    701
    │ │ │ +
    702 template <class Key>
    │ │ │ +
    703 BALL_INLINE
    │ │ │ +
    │ │ │ +
    704 void HashSet<Key>::swap(HashSet& hash_set)
    │ │ │ +
    705 {
    │ │ │ +
    706 std::swap(size_, hash_set.size_);
    │ │ │ +
    707 std::swap(capacity_, hash_set.capacity_);
    │ │ │ +
    708 std::swap(bucket_, hash_set.bucket_);
    │ │ │ +
    709 }
    │ │ │ +
    │ │ │ +
    710
    │ │ │ +
    711 template <class Key>
    │ │ │ +
    712 BALL_INLINE
    │ │ │ +
    │ │ │ +
    713 const HashSet<Key>& HashSet<Key>::operator &= (const HashSet& rhs)
    │ │ │ +
    714 {
    │ │ │ +
    715 // Store all elements that are not part of the intersection
    │ │ │ +
    716 // in a list for subsequent deletion.
    │ │ │ +
    717 std::list<Key> erase_list;
    │ │ │ +
    718 for (Iterator it = begin(); it != end(); ++it)
    │ │ │ +
    719 {
    │ │ │ +
    720 if (!rhs.has(*it))
    │ │ │ +
    721 {
    │ │ │ +
    722 erase_list.push_back(*it);
    │ │ │ +
    723 }
    │ │ │ +
    724 }
    │ │ │ +
    725
    │ │ │ +
    726 // erase all elements not part of the intersection
    │ │ │ +
    727 typename list<Key>::iterator list_it = erase_list.begin();
    │ │ │ +
    728 for (; list_it != erase_list.end(); ++list_it)
    │ │ │ +
    729 {
    │ │ │ +
    730 erase(*list_it);
    │ │ │ +
    731 }
    │ │ │ +
    732
    │ │ │ +
    733 return *this;
    │ │ │ +
    734 }
    │ │ │ +
    │ │ │ +
    735
    │ │ │ +
    736 template <class Key>
    │ │ │ +
    737 BALL_INLINE
    │ │ │ +
    │ │ │ +
    738 const HashSet<Key>& HashSet<Key>::operator |= (const HashSet<Key>& rhs)
    │ │ │ +
    739 {
    │ │ │ +
    740 // Compute the union of both sets by inserting every element of the
    │ │ │ +
    741 // rhs set.
    │ │ │ +
    742 for (ConstIterator it = rhs.begin(); it != rhs.end(); ++it)
    │ │ │ +
    743 {
    │ │ │ +
    744 insert(*it);
    │ │ │ +
    745 }
    │ │ │ +
    746
    │ │ │ +
    747 return *this;
    │ │ │ +
    748 }
    │ │ │ +
    │ │ │ +
    749
    │ │ │ +
    750 template <class Key>
    │ │ │ +
    751 BALL_INLINE
    │ │ │ +
    │ │ │ +
    752 const HashSet<Key>& HashSet<Key>::operator += (const HashSet<Key>& rhs)
    │ │ │ +
    753 {
    │ │ │ +
    754 return operator |= (rhs);
    │ │ │ +
    755 }
    │ │ │ +
    │ │ │ +
    756
    │ │ │ +
    757 template <class Key>
    │ │ │ +
    758 BALL_INLINE
    │ │ │ +
    │ │ │ +
    759 HashSet<Key> HashSet<Key>::operator & (const HashSet<Key>& rhs) const
    │ │ │ +
    760 {
    │ │ │ +
    761 // Create an empty hash set...
    │ │ │ +
    762 HashSet<Key> tmp;
    │ │ │ +
    763 ConstIterator it = begin();
    │ │ │ +
    764
    │ │ │ +
    765 // ...and copy all the elements contained in the rhs hash set.
    │ │ │ +
    766 for (; +it; ++it)
    │ │ │ +
    767 {
    │ │ │ +
    768 if (rhs.has(*it))
    │ │ │ +
    769 {
    │ │ │ +
    770 tmp.insert(*it);
    │ │ │ +
    771 }
    │ │ │ +
    772 }
    │ │ │ +
    773
    │ │ │ +
    774 return tmp;
    │ │ │ +
    775 }
    │ │ │ +
    │ │ │ +
    776
    │ │ │ +
    777 template <class Key>
    │ │ │ +
    778 BALL_INLINE
    │ │ │ +
    │ │ │ +
    779 HashSet<Key> HashSet<Key>::operator - (const HashSet<Key>& rhs) const
    │ │ │ +
    780 {
    │ │ │ +
    781 // Create an empty hash set...
    │ │ │ +
    782 HashSet<Key> tmp;
    │ │ │ +
    783 ConstIterator it = begin();
    │ │ │ +
    784
    │ │ │ +
    785 // ...and copy all the elements contained in this set and not in the rhs hash set.
    │ │ │ +
    786 for (; +it; ++it)
    │ │ │ +
    787 {
    │ │ │ +
    788 if (!rhs.has(*it))
    │ │ │ +
    789 {
    │ │ │ +
    790 tmp.insert(*it);
    │ │ │ +
    791 }
    │ │ │ +
    792 }
    │ │ │ +
    793
    │ │ │ +
    794 return tmp;
    │ │ │ +
    795 }
    │ │ │ +
    │ │ │ +
    796
    │ │ │ +
    797 template <class Key>
    │ │ │ +
    798 BALL_INLINE
    │ │ │ +
    │ │ │ +
    799 const HashSet<Key>& HashSet<Key>::operator -= (const HashSet<Key>& hash_set)
    │ │ │ +
    800 {
    │ │ │ +
    801 // avoid memory corruption caused by iterating over freed space when
    │ │ │ +
    802 // deleting myself
    │ │ │ +
    803 if (this == &hash_set)
    │ │ │ +
    804 {
    │ │ │ +
    805 clear();
    │ │ │ +
    806 }
    │ │ │ +
    807 else
    │ │ │ +
    808 {
    │ │ │ +
    809 // erase all elements which are contained in this and hash_set
    │ │ │ +
    810 typename HashSet<Key>::ConstIterator it = hash_set.begin();
    │ │ │ +
    811 for (; it != hash_set.end(); ++it)
    │ │ │ +
    812 {
    │ │ │ +
    813 if (has(*it))
    │ │ │ +
    814 {
    │ │ │ +
    815 erase(*it);
    │ │ │ +
    816 }
    │ │ │ +
    817 }
    │ │ │ +
    818 }
    │ │ │ +
    819 return *this;
    │ │ │ +
    820 }
    │ │ │ +
    │ │ │ +
    821
    │ │ │ +
    822 template <class Key>
    │ │ │ +
    823 BALL_INLINE
    │ │ │ +
    │ │ │ +
    824 HashSet<Key> HashSet<Key>::operator | (const HashSet<Key>& rhs) const
    │ │ │ +
    825 {
    │ │ │ +
    826 HashSet<Key> tmp(*this);
    │ │ │ +
    827 tmp |= rhs;
    │ │ │ +
    828
    │ │ │ +
    829 return tmp;
    │ │ │ +
    830 }
    │ │ │ +
    │ │ │ +
    831
    │ │ │ +
    832 template <class Key>
    │ │ │ +
    833 BALL_INLINE
    │ │ │ +
    │ │ │ +
    834 HashSet<Key> HashSet<Key>::operator + (const HashSet<Key>& rhs) const
    │ │ │ +
    835 {
    │ │ │ +
    836 return operator | (rhs);
    │ │ │ +
    837 }
    │ │ │ +
    │ │ │ +
    838
    │ │ │ +
    839 template <class Key>
    │ │ │ +
    840 BALL_INLINE
    │ │ │ +
    │ │ │ +
    841 Size HashSet<Key>::getBucketSize() const
    │ │ │ +
    842 {
    │ │ │ +
    843 return (Size)bucket_.size();
    │ │ │ +
    844 }
    │ │ │ +
    │ │ │ +
    845
    │ │ │ +
    846 template <class Key>
    │ │ │ +
    847 BALL_INLINE
    │ │ │ +
    │ │ │ +
    848 Size HashSet<Key>::getCapacity() const
    │ │ │ +
    849 {
    │ │ │ +
    850 return capacity_;
    │ │ │ +
    851 }
    │ │ │ +
    │ │ │ +
    852
    │ │ │ +
    853 template <class Key>
    │ │ │ +
    854 BALL_INLINE
    │ │ │ +
    │ │ │ +
    855 Size HashSet<Key>::getSize() const
    │ │ │ +
    856 {
    │ │ │ +
    857 return size_;
    │ │ │ +
    858 }
    │ │ │ +
    │ │ │ +
    859
    │ │ │ +
    860 template <class Key>
    │ │ │ +
    861 BALL_INLINE
    │ │ │ +
    │ │ │ +
    862 Size HashSet<Key>::size() const
    │ │ │ +
    863 {
    │ │ │ +
    864 return size_;
    │ │ │ +
    865 }
    │ │ │ +
    │ │ │ +
    866
    │ │ │ +
    867 template <class Key>
    │ │ │ +
    │ │ │ +
    868 typename HashSet<Key>::Iterator HashSet<Key>::find(const Key& key)
    │ │ │ +
    869 {
    │ │ │ +
    870 Iterator it = end();
    │ │ │ +
    871 Position bucket = hashBucket_(key);
    │ │ │ +
    872 Node* node_ptr = bucket_[bucket];
    │ │ │ +
    873 while (node_ptr != 0)
    │ │ │ +
    874 {
    │ │ │ +
    875 if (node_ptr->value == key)
    │ │ │ +
    876 {
    │ │ │ +
    877 it.getTraits().position_ = node_ptr;
    │ │ │ +
    878 it.getTraits().bucket_ = bucket;
    │ │ │ +
    879 break;
    │ │ │ +
    880 }
    │ │ │ +
    881 node_ptr = node_ptr->next;
    │ │ │ +
    882 }
    │ │ │ +
    883
    │ │ │ +
    884 return it;
    │ │ │ +
    885 }
    │ │ │ +
    │ │ │ +
    886
    │ │ │ +
    887 template <class Key>
    │ │ │ +
    888 BALL_INLINE
    │ │ │ +
    │ │ │ +
    889 typename HashSet<Key>::ConstIterator HashSet<Key>::find(const Key& key) const
    │ │ │ +
    890 {
    │ │ │ +
    891 return (const_cast<HashSet*>(this))->find(key);
    │ │ │ +
    892 }
    │ │ │ +
    │ │ │ +
    893
    │ │ │ +
    894 template <class Key>
    │ │ │ +
    │ │ │ +
    895 std::pair<typename HashSet<Key>::Iterator, bool> HashSet<Key>::insert
    │ │ │ +
    896 (const ValueType& item)
    │ │ │ +
    897 {
    │ │ │ +
    898 Iterator it = find(item);
    │ │ │ +
    899 if (it == end())
    │ │ │ +
    900 {
    │ │ │ +
    901 if (needRehashing_() == true)
    │ │ │ +
    902 {
    │ │ │ +
    903 rehash_();
    │ │ │ +
    904 }
    │ │ │ +
    905
    │ │ │ +
    906 Position bucket = hashBucket_(item);
    │ │ │ +
    907
    │ │ │ +
    908 Node* next = bucket_[bucket];
    │ │ │ +
    909 bucket_[bucket] = newNode_(item, next);
    │ │ │ +
    910
    │ │ │ +
    911 ++size_;
    │ │ │ +
    912 it.getTraits().position_ = bucket_[bucket];
    │ │ │ +
    913 it.getTraits().bucket_ = bucket;
    │ │ │ +
    914 }
    │ │ │ +
    915
    │ │ │ +
    916 return std::pair<Iterator, bool>(it, true);
    │ │ │ +
    917 }
    │ │ │ +
    │ │ │ +
    918
    │ │ │ +
    919 template <class Key>
    │ │ │ +
    920 typename HashSet<Key>::Iterator HashSet<Key>::insert
    │ │ │ +
    921 (typename HashSet<Key>::Iterator /* pos */, const ValueType& item)
    │ │ │ +
    922 {
    │ │ │ +
    923 return insert(item).first;
    │ │ │ +
    924 }
    │ │ │ +
    925
    │ │ │ +
    926 template <class Key>
    │ │ │ +
    │ │ │ +
    927 Size HashSet<Key>::erase(const KeyType& key)
    │ │ │ +
    928 {
    │ │ │ +
    929 Position bucket = hashBucket_(key);
    │ │ │ +
    930 Node* previous = 0;
    │ │ │ +
    931 Node* node_ptr = bucket_[bucket];
    │ │ │ +
    932
    │ │ │ +
    933 while (node_ptr != 0 && node_ptr->value != key)
    │ │ │ +
    934 {
    │ │ │ +
    935 previous = node_ptr;
    │ │ │ +
    936 node_ptr = node_ptr->next;
    │ │ │ +
    937 }
    │ │ │ +
    938
    │ │ │ +
    939 if (node_ptr == 0)
    │ │ │ +
    940 {
    │ │ │ +
    941 return false;
    │ │ │ +
    942 }
    │ │ │ +
    943
    │ │ │ +
    944 if (node_ptr == bucket_[bucket])
    │ │ │ +
    945 {
    │ │ │ +
    946 bucket_[bucket] = node_ptr->next;
    │ │ │ +
    947 }
    │ │ │ +
    948 else
    │ │ │ +
    949 {
    │ │ │ +
    950 previous->next = node_ptr->next;
    │ │ │ +
    951 }
    │ │ │ +
    952
    │ │ │ +
    953 deleteNode_(node_ptr);
    │ │ │ +
    954 --size_;
    │ │ │ +
    955
    │ │ │ +
    956 return 1;
    │ │ │ +
    957 }
    │ │ │ +
    │ │ │ +
    958
    │ │ │ +
    959 template <class Key>
    │ │ │ +
    │ │ │ +
    960 void HashSet<Key>::erase(Iterator pos)
    │ │ │ +
    961 {
    │ │ │ +
    962 if (pos.getTraits().bound_ != this)
    │ │ │ +
    963 {
    │ │ │ +
    964 throw Exception::IncompatibleIterators(__FILE__, __LINE__);
    │ │ │ +
    965 }
    │ │ │ +
    966
    │ │ │ +
    967 if ((pos == end()) || (size_ == 0))
    │ │ │ +
    968 {
    │ │ │ +
    969 return;
    │ │ │ +
    970 }
    │ │ │ +
    971
    │ │ │ +
    972 if (pos.getTraits().position_ == bucket_[pos.getTraits().bucket_])
    │ │ │ +
    973 {
    │ │ │ +
    974 bucket_[pos.getTraits().bucket_] = pos.getTraits().position_->next;
    │ │ │ +
    975 }
    │ │ │ +
    976 else
    │ │ │ +
    977 {
    │ │ │ +
    978 // walk over all nodes in this bucket and identify the predecessor
    │ │ │ +
    979 // of the node refered to by the iterator pos
    │ │ │ +
    980 Node* prev = bucket_[pos.getTraits().bucket_];
    │ │ │ +
    981 for (; (prev != 0) && (prev->next != pos.getTraits().position_); prev = prev->next) {};
    │ │ │ +
    982 if (prev != 0)
    │ │ │ +
    983 {
    │ │ │ +
    984 // remove the node and reconnect the list
    │ │ │ +
    985 prev->next = pos.getTraits().position_->next;
    │ │ │ +
    986 }
    │ │ │ +
    987 else
    │ │ │ +
    988 {
    │ │ │ +
    989 throw Exception::InvalidIterator(__FILE__, __LINE__);
    │ │ │ +
    990 }
    │ │ │ +
    991 }
    │ │ │ +
    992
    │ │ │ +
    993 // delete the node and decrement the set size
    │ │ │ +
    994 deleteNode_(pos.getTraits().position_);
    │ │ │ +
    995 --size_;
    │ │ │ +
    996 }
    │ │ │ +
    │ │ │ +
    997
    │ │ │ +
    998 template <class Key>
    │ │ │ +
    │ │ │ +
    999 void HashSet<Key>::erase(Iterator f, Iterator l)
    │ │ │ +
    1000 {
    │ │ │ +
    1001 if (f.getTraits().bound_ != this || l.getTraits().bound_ != this)
    │ │ │ +
    1002 {
    │ │ │ +
    1003 throw Exception::IncompatibleIterators(__FILE__, __LINE__);
    │ │ │ +
    1004 }
    │ │ │ +
    1005
    │ │ │ +
    1006 if (f == end())
    │ │ │ +
    1007 {
    │ │ │ +
    1008 return;
    │ │ │ +
    1009 }
    │ │ │ +
    1010
    │ │ │ +
    1011 Position last_bucket = l.getTraits().bucket_;
    │ │ │ +
    1012 if (l == end())
    │ │ │ +
    1013 {
    │ │ │ +
    1014 last_bucket = (Position)(bucket_.size() - 1);
    │ │ │ +
    1015 }
    │ │ │ +
    1016
    │ │ │ +
    1017 if (f.getTraits().bucket_ > last_bucket)
    │ │ │ +
    1018 {
    │ │ │ +
    1019 // empty range - l < f
    │ │ │ +
    1020 return;
    │ │ │ +
    1021 }
    │ │ │ +
    1022
    │ │ │ +
    1023 // count the deleted entries to correct the set size
    │ │ │ +
    1024 Size no_deletions = 0;
    │ │ │ +
    1025
    │ │ │ +
    1026 Position bucket = f.getTraits().bucket_;
    │ │ │ +
    1027 for (; bucket <= last_bucket; bucket++)
    │ │ │ +
    1028 {
    │ │ │ +
    1029 if (bucket_[bucket] == 0)
    │ │ │ +
    1030 {
    │ │ │ +
    1031 // skip all empty buckets
    │ │ │ +
    1032 continue;
    │ │ │ +
    1033 }
    │ │ │ +
    1034
    │ │ │ +
    1035
    │ │ │ +
    1036 if ((bucket == f.getTraits().bucket_) && (bucket_[bucket] != f.getTraits().position_))
    │ │ │ +
    1037 {
    │ │ │ +
    1038 // find the predecessor of f
    │ │ │ +
    1039 Node* n = bucket_[bucket];
    │ │ │ +
    1040 Node* next;
    │ │ │ +
    1041 for (; (n->next != f.getTraits().position_) && (n->next != 0); n = n->next) {};
    │ │ │ +
    1042
    │ │ │ +
    1043 if (bucket == last_bucket)
    │ │ │ +
    1044 {
    │ │ │ +
    1045 // delete everything from f to l in this bucket
    │ │ │ +
    1046
    │ │ │ +
    1047 next = n->next;
    │ │ │ +
    1048 n->next = l.getTraits().position_;
    │ │ │ +
    1049 for (n = next; (n != 0) && (n != l.getTraits().position_); n = next)
    │ │ │ +
    1050 {
    │ │ │ +
    1051 next = n->next;
    │ │ │ +
    1052 deleteNode_(n);
    │ │ │ +
    1053 no_deletions++;
    │ │ │ +
    1054 }
    │ │ │ +
    1055 }
    │ │ │ +
    1056 else
    │ │ │ +
    1057 {
    │ │ │ +
    1058 // delete everything from f to the end in this bucket
    │ │ │ +
    1059
    │ │ │ +
    1060 if (n != 0)
    │ │ │ +
    1061 {
    │ │ │ +
    1062 // mark the end of the list
    │ │ │ +
    1063 next = n->next;
    │ │ │ +
    1064 n->next = 0;
    │ │ │ +
    1065
    │ │ │ +
    1066 // delete all remaining nodes
    │ │ │ +
    1067 for (n = next; n != 0; n = next)
    │ │ │ +
    1068 {
    │ │ │ +
    1069 next = n->next;
    │ │ │ +
    1070 deleteNode_(n);
    │ │ │ +
    1071 no_deletions++;
    │ │ │ +
    1072 }
    │ │ │ +
    1073 }
    │ │ │ +
    1074 }
    │ │ │ +
    1075 }
    │ │ │ +
    1076 // if the current bucket lies between the first and the last bucket...
    │ │ │ +
    1077 else if (bucket < last_bucket)
    │ │ │ +
    1078 {
    │ │ │ +
    1079 // ...delete the whole bucket
    │ │ │ +
    1080 Node* next;
    │ │ │ +
    1081 for (Node* n = bucket_[bucket]; n != 0; n = next)
    │ │ │ +
    1082 {
    │ │ │ +
    1083 next = n->next;
    │ │ │ +
    1084 deleteNode_(n);
    │ │ │ +
    1085 no_deletions++;
    │ │ │ +
    1086 }
    │ │ │ +
    1087 bucket_[bucket] = 0;
    │ │ │ +
    1088 }
    │ │ │ +
    1089 else if (bucket == last_bucket)
    │ │ │ +
    1090 {
    │ │ │ +
    1091 // we delete everything in this bucket up to the iterator l
    │ │ │ +
    1092
    │ │ │ +
    1093 // find the predecessor of l
    │ │ │ +
    1094 Node* n = bucket_[bucket];
    │ │ │ +
    1095 Node* next;
    │ │ │ +
    1096 for (; (n != 0) && (n != l.getTraits().position_); n = next)
    │ │ │ +
    1097 {
    │ │ │ +
    1098 next = n->next;
    │ │ │ +
    1099 deleteNode_(n);
    │ │ │ +
    1100 no_deletions++;
    │ │ │ +
    1101 }
    │ │ │ +
    1102
    │ │ │ +
    1103 bucket_[bucket] = l.getTraits().position_;
    │ │ │ +
    1104 }
    │ │ │ +
    1105 }
    │ │ │ +
    1106
    │ │ │ +
    1107 // correct the set size
    │ │ │ +
    1108 size_ -= no_deletions;
    │ │ │ +
    1109 }
    │ │ │ +
    │ │ │ +
    1110
    │ │ │ +
    1111 template <class Key>
    │ │ │ +
    1112 BALL_INLINE
    │ │ │ +
    │ │ │ +
    1113 void HashSet<Key>::host(Visitor<HashSet<Key> >& visitor)
    │ │ │ +
    1114 {
    │ │ │ +
    1115 visitor.visit(*this);
    │ │ │ +
    1116 }
    │ │ │ +
    │ │ │ +
    1117
    │ │ │ +
    1118 template <class Key>
    │ │ │ +
    1119 BALL_INLINE
    │ │ │ +
    │ │ │ +
    1120 bool HashSet<Key>::has(const Key& key) const
    │ │ │ +
    1121 {
    │ │ │ +
    1122 return (find(key) != end());
    │ │ │ +
    1123 }
    │ │ │ +
    │ │ │ +
    1124
    │ │ │ +
    1125 template <class Key>
    │ │ │ +
    1126 BALL_INLINE
    │ │ │ +
    │ │ │ +
    1127 bool HashSet<Key>::isEmpty() const
    │ │ │ +
    1128 {
    │ │ │ +
    1129 return (size_ == 0);
    │ │ │ +
    1130 }
    │ │ │ +
    │ │ │ +
    1131
    │ │ │ +
    1132 template <class Key>
    │ │ │ +
    │ │ │ +
    1133 bool HashSet<Key>::operator == (const HashSet& hash_set) const
    │ │ │ +
    1134 {
    │ │ │ +
    1135 if (size_ != hash_set.size_)
    │ │ │ +
    1136 {
    │ │ │ +
    1137 return false;
    │ │ │ +
    1138 }
    │ │ │ +
    1139
    │ │ │ +
    1140 ConstIterator it1 = begin();
    │ │ │ +
    1141 ConstIterator it2 = hash_set.begin();
    │ │ │ +
    1142 while (it1 != end())
    │ │ │ +
    1143 {
    │ │ │ +
    1144 if (*it1 != *it2)
    │ │ │ +
    1145 {
    │ │ │ +
    1146 return false;
    │ │ │ +
    1147 }
    │ │ │ +
    1148 it1++;
    │ │ │ +
    1149 it2++;
    │ │ │ +
    1150 }
    │ │ │ +
    1151 return true;
    │ │ │ +
    1152 }
    │ │ │ +
    │ │ │ +
    1153
    │ │ │ +
    1154 template <class Key>
    │ │ │ +
    1155 BALL_INLINE
    │ │ │ +
    │ │ │ +
    1156 bool HashSet<Key>::operator != (const HashSet& hash_set) const
    │ │ │ +
    1157 {
    │ │ │ +
    1158 return !(*this == hash_set);
    │ │ │ +
    1159 }
    │ │ │ +
    │ │ │ +
    1160
    │ │ │ +
    1161 template <class Key>
    │ │ │ +
    │ │ │ +
    1162 bool HashSet<Key>::isValid() const
    │ │ │ +
    1163 {
    │ │ │ +
    1164 Size size = 0;
    │ │ │ +
    1165 Node* node = 0;
    │ │ │ +
    1166
    │ │ │ +
    1167 for (Position bucket = 0; bucket < (Position)bucket_.size(); ++bucket)
    │ │ │ +
    1168 {
    │ │ │ +
    1169 for (node = bucket_[bucket]; node != 0; node = node->next)
    │ │ │ +
    1170 {
    │ │ │ +
    1171 ++size;
    │ │ │ +
    1172
    │ │ │ +
    1173 if (node->next == 0)
    │ │ │ +
    1174 {
    │ │ │ +
    1175 break;
    │ │ │ +
    1176 }
    │ │ │ +
    1177 }
    │ │ │ +
    1178 }
    │ │ │ +
    1179
    │ │ │ +
    1180 return (size_ == size);
    │ │ │ +
    1181 }
    │ │ │ +
    │ │ │ +
    1182
    │ │ │ +
    1183 template <class Key>
    │ │ │ +
    │ │ │ +
    1184 void HashSet<Key>::dump(std::ostream& s, Size depth) const
    │ │ │ +
    1185 {
    │ │ │ +
    1186 BALL_DUMP_STREAM_PREFIX(s);
    │ │ │ +
    1187
    │ │ │ +
    1188 BALL_DUMP_DEPTH(s, depth);
    │ │ │ +
    1189
    │ │ │ +
    1190 BALL_DUMP_DEPTH(s, depth);
    │ │ │ +
    1191 s << " size: " << getSize() << std::endl;
    │ │ │ +
    1192
    │ │ │ +
    1193 BALL_DUMP_DEPTH(s, depth);
    │ │ │ +
    1194 s << " # buckets: " << getBucketSize() << std::endl;
    │ │ │ +
    1195
    │ │ │ +
    1196 BALL_DUMP_DEPTH(s, depth);
    │ │ │ +
    1197 s << " capacity: " << getCapacity() << std::endl;
    │ │ │ +
    1198
    │ │ │ +
    1199 BALL_DUMP_DEPTH(s, depth);
    │ │ │ +
    1200 s << " load factor: " << (float)size_ / (float)bucket_.size() << std::endl;
    │ │ │ +
    1201
    │ │ │ +
    1202 for (Position bucket = 0; bucket < (Position)bucket_.size(); ++bucket)
    │ │ │ +
    1203 {
    │ │ │ +
    1204 BALL_DUMP_DEPTH(s, depth);
    │ │ │ +
    1205 s << " bucket " << bucket << ": ";
    │ │ │ +
    1206 for (Node* ptr = bucket_[bucket]; ptr != 0; ptr = ptr->next)
    │ │ │ +
    1207 {
    │ │ │ +
    1208 s << "(" << (void*)ptr << ") ";
    │ │ │ +
    1209 }
    │ │ │ +
    1210 s << "(0)" << std::endl;
    │ │ │ +
    1211 }
    │ │ │ +
    1212
    │ │ │ +
    1213 BALL_DUMP_STREAM_SUFFIX(s);
    │ │ │ +
    1214 }
    │ │ │ +
    │ │ │ +
    1215
    │ │ │ +
    1216 template <class Key>
    │ │ │ +
    │ │ │ +
    1217 bool HashSet<Key>::apply(UnaryProcessor<ValueType>& processor)
    │ │ │ +
    1218 {
    │ │ │ +
    1219 if (processor.start() == false)
    │ │ │ +
    1220 {
    │ │ │ +
    1221 return false;
    │ │ │ +
    1222 }
    │ │ │ +
    1223
    │ │ │ +
    1224 Processor::Result result;
    │ │ │ +
    1225
    │ │ │ +
    1226 Iterator it = begin();
    │ │ │ +
    1227 while (it != end())
    │ │ │ +
    1228 {
    │ │ │ +
    1229 result = processor(*it);
    │ │ │ +
    1230 if (result <= Processor::BREAK)
    │ │ │ +
    1231 {
    │ │ │ +
    1232 return (result == Processor::BREAK);
    │ │ │ +
    1233 }
    │ │ │ +
    1234 it++;
    │ │ │ +
    1235 }
    │ │ │ +
    1236
    │ │ │ +
    1237 return processor.finish();
    │ │ │ +
    1238 }
    │ │ │ +
    │ │ │ +
    1239
    │ │ │ +
    1240 template <class Key>
    │ │ │ +
    1241 BALL_INLINE
    │ │ │ +
    │ │ │ +
    1242 HashIndex HashSet<Key>::hash(const Key& key) const
    │ │ │ +
    1243 {
    │ │ │ +
    1244 return (HashIndex)Hash(key);
    │ │ │ +
    1245 }
    │ │ │ +
    │ │ │ +
    1246
    │ │ │ +
    1247 template <class Key>
    │ │ │ +
    1248 BALL_INLINE
    │ │ │ +
    │ │ │ +
    1249 void HashSet<Key>::rehash()
    │ │ │ +
    1250 {
    │ │ │ +
    1251 capacity_ = (Size)getNextPrime((Size)bucket_.size() << 1);
    │ │ │ +
    1252 }
    │ │ │ +
    │ │ │ +
    │ │ │ +
    1253
    │ │ │ +
    1254 template <class Key>
    │ │ │ +
    1255 void HashSet<Key>::deleteBuckets_()
    │ │ │ +
    1256 {
    │ │ │ +
    1257 Size i = 0;
    │ │ │ +
    1258 Node* node = 0;
    │ │ │ +
    1259 Node* next_node = 0;
    │ │ │ +
    1260 for (i = 0; i < bucket_.size(); i++)
    │ │ │ +
    1261 {
    │ │ │ +
    1262 node = bucket_[i];
    │ │ │ +
    1263 while (node != 0)
    │ │ │ +
    1264 {
    │ │ │ +
    1265 next_node = node->next;
    │ │ │ +
    1266 delete node;
    │ │ │ +
    1267 node = next_node;
    │ │ │ +
    1268 }
    │ │ │ +
    1269 bucket_[i] = 0;
    │ │ │ +
    1270 }
    │ │ │ +
    1271 }
    │ │ │ +
    1272
    │ │ │ +
    1273 template <class Key>
    │ │ │ +
    1274 BALL_INLINE
    │ │ │ +
    │ │ │ +
    1275 typename HashSet<Key>::Node* HashSet<Key>::newNode_
    │ │ │ +
    1276 (const ValueType& value, typename HashSet<Key>::Node* next) const
    │ │ │ +
    1277 {
    │ │ │ +
    1278 return new Node(value, next);
    │ │ │ +
    1279 }
    │ │ │ +
    │ │ │ +
    1280
    │ │ │ +
    1281 template <class Key>
    │ │ │ +
    1282 BALL_INLINE
    │ │ │ +
    │ │ │ +
    1283 void HashSet<Key>::deleteNode_(typename HashSet<Key>::Node* node) const
    │ │ │ +
    1284 {
    │ │ │ +
    1285 delete node;
    │ │ │ +
    1286 }
    │ │ │ +
    │ │ │ +
    1287
    │ │ │ +
    1288 template <class Key>
    │ │ │ +
    1289 BALL_INLINE
    │ │ │ +
    │ │ │ +
    1290 bool HashSet<Key>::needRehashing_() const
    │ │ │ +
    1291 {
    │ │ │ +
    1292 return (size_ >= capacity_);
    │ │ │ +
    1293 }
    │ │ │ +
    │ │ │ +
    │ │ │ +
    1294
    │ │ │ +
    1295 template <class Key>
    │ │ │ +
    1296 BALL_INLINE
    │ │ │ +
    1297 HashIndex HashSet<Key>::hashBucket_(const Key& key) const
    │ │ │ +
    1298 {
    │ │ │ +
    1299 return (Position)((HashIndex)hash(key) % (HashIndex)bucket_.size());
    │ │ │ +
    1300 }
    │ │ │ +
    1301
    │ │ │ +
    1302 template <class Key>
    │ │ │ +
    1303 void HashSet<Key>::rehash_()
    │ │ │ +
    1304 {
    │ │ │ +
    1305 // calculate the new number of buckets (in capacity_)
    │ │ │ +
    1306 rehash();
    │ │ │ +
    1307
    │ │ │ +
    1308 // save the old contents
    │ │ │ +
    1309 vector<Node*> old_buckets(bucket_);
    │ │ │ +
    1310
    │ │ │ +
    1311 // resize the bucket vector and initialize it with zero
    │ │ │ +
    1312 bucket_.clear();
    │ │ │ +
    1313 bucket_.resize(capacity_);
    │ │ │ +
    1314 Position i;
    │ │ │ +
    1315 for (i = 0; i < capacity_; i++)
    │ │ │ +
    1316 {
    │ │ │ +
    1317 bucket_[i] = 0;
    │ │ │ +
    1318 }
    │ │ │ +
    1319
    │ │ │ +
    1320 // rehash the old contents into the new buckets
    │ │ │ +
    1321 Node* node;
    │ │ │ +
    1322 Node* next_node;
    │ │ │ +
    1323 for (Position i = 0; i < (Position)old_buckets.size(); ++i)
    │ │ │ +
    1324 {
    │ │ │ +
    1325 for (node = old_buckets[i]; node != 0; node = next_node)
    │ │ │ +
    1326 {
    │ │ │ +
    1327 next_node = node->next;
    │ │ │ +
    1328 Position new_bucket = hashBucket_(node->value);
    │ │ │ +
    1329 node->next = bucket_[new_bucket];
    │ │ │ +
    1330 bucket_[new_bucket] = node;
    │ │ │ +
    1331 }
    │ │ │ +
    1332 }
    │ │ │ +
    1333 }
    │ │ │ +
    1334} // namespace BALL
    │ │ │ +
    1335
    │ │ │ +
    1336#endif // BALL_DATATYPE_HASHSET_H
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
    │ │ │ +
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    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_DUMP_STREAM_PREFIX
    #define BALL_DUMP_STREAM_PREFIX(os)
    Definition macros.h:391
    │ │ │ +
    BALL_DUMP_STREAM_SUFFIX
    #define BALL_DUMP_STREAM_SUFFIX(os)
    Definition macros.h:395
    │ │ │ +
    BALL_DUMP_DEPTH
    #define BALL_DUMP_DEPTH(os, depth)
    Definition macros.h:390
    │ │ │ + │ │ │ +
    BALL_INLINE
    #define BALL_INLINE
    Definition debug.h:15
    │ │ │ + │ │ │ +
    BALL::HashIndex
    BALL_SIZE_TYPE HashIndex
    Definition COMMON/global.h:131
    │ │ │ +
    BALL::INVALID_Position
    static const Position INVALID_Position
    Definition COMMON/global.h:243
    │ │ │ +
    BALL::Size
    BALL_SIZE_TYPE Size
    Definition COMMON/global.h:114
    │ │ │ +
    BALL::Hash
    HashIndex Hash(const T &key)
    Definition hash.h:47
    │ │ │ +
    BALL::Position
    BALL_SIZE_TYPE Position
    Definition COMMON/global.h:140
    │ │ │ +
    BALL::getNextPrime
    BALL_EXPORT HashIndex getNextPrime(HashIndex l)
    │ │ │ + │ │ │ +
    BALL::Exception::GeneralException::GeneralException
    GeneralException()
    Default constructor.
    │ │ │ + │ │ │ + │ │ │ +
    BALL::BaseIterator::getTraits
    BALL_INLINE const Traits & getTraits() const
    Get a constant reference to the traits of this iterator.
    Definition baseIterator.h:130
    │ │ │ + │ │ │ +
    BALL::ForwardIterator::begin
    static ForwardIterator begin(const Container &container)
    Definition forwardIterator.h:307
    │ │ │ +
    BALL::ForwardIterator::end
    static ForwardIterator end(const Container &container)
    Definition forwardIterator.h:317
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::UnaryProcessor::start
    virtual bool start()
    Definition processor.h:92
    │ │ │ +
    BALL::UnaryProcessor::finish
    virtual bool finish()
    Definition processor.h:99
    │ │ │ + │ │ │ + │ │ │ +
    BALL::HashSet::Iterator
    ForwardIterator< HashSet< Key >, ValueType, PointerType, IteratorTraits > Iterator
    Definition hashSet.h:280
    │ │ │ +
    BALL::HashSet::hash
    virtual HashIndex hash(const Key &key) const
    Definition hashSet.h:1242
    │ │ │ +
    BALL::HashSet::size
    Size size() const
    Definition hashSet.h:862
    │ │ │ +
    BALL::HashSet::erase
    void erase(Iterator f, Iterator l)
    Definition hashSet.h:999
    │ │ │ +
    BALL::HashSet::pointer
    Key * pointer
    Definition hashSet.h:295
    │ │ │ +
    BALL::HashSet::const_reference
    const Key & const_reference
    Definition hashSet.h:301
    │ │ │ +
    BALL::HashSet::size_type
    Size size_type
    Definition hashSet.h:303
    │ │ │ +
    BALL::HashSet::set
    void set(const HashSet &hash_set)
    Definition hashSet.h:631
    │ │ │ +
    BALL::HashSet::find
    ConstIterator find(const Key &key) const
    Definition hashSet.h:889
    │ │ │ +
    BALL::HashSet::isValid
    bool isValid() const
    Definition hashSet.h:1162
    │ │ │ +
    BALL::HashSet::isEmpty
    bool isEmpty() const
    Definition hashSet.h:1127
    │ │ │ +
    BALL::HashSet::operator&=
    const HashSet & operator&=(const HashSet &rhs)
    Definition hashSet.h:713
    │ │ │ +
    BALL::HashSet::operator!=
    bool operator!=(const HashSet &hash_set) const
    Definition hashSet.h:1156
    │ │ │ +
    BALL::HashSet::get
    void get(HashSet &hash_set) const
    Definition hashSet.h:696
    │ │ │ +
    BALL::HashSet::newNode_
    virtual Node * newNode_(const ValueType &value, Node *next) const
    Definition hashSet.h:1276
    │ │ │ +
    BALL::HashSet::const_iterator
    ConstIterator const_iterator
    Definition hashSet.h:289
    │ │ │ +
    BALL::HashSet::operator-
    HashSet operator-(const HashSet &rhs) const
    Definition hashSet.h:779
    │ │ │ +
    BALL::HashSet::HashSet
    HashSet(const HashSet &hash_set)
    Definition hashSet.h:612
    │ │ │ +
    BALL::HashSet::end
    ConstIterator end() const
    Definition hashSet.h:557
    │ │ │ +
    BALL::HashSet::begin
    Iterator begin()
    Definition hashSet.h:536
    │ │ │ +
    BALL::HashSet::insert
    std::pair< Iterator, bool > insert(const ValueType &item)
    Definition hashSet.h:896
    │ │ │ +
    BALL::HashSet::operator+
    HashSet operator+(const HashSet &rhs) const
    Definition hashSet.h:834
    │ │ │ +
    BALL::HashSet::begin
    ConstIterator begin() const
    Definition hashSet.h:550
    │ │ │ +
    BALL::HashSet::HashSet
    HashSet(Size initial_capacity=INITIAL_CAPACITY, Size number_of_buckets=INITIAL_NUMBER_OF_BUCKETS)
    Definition hashSet.h:600
    │ │ │ +
    BALL::HashSet::operator+=
    const HashSet & operator+=(const HashSet &rhs)
    Definition hashSet.h:752
    │ │ │ +
    BALL::HashSet::has
    bool has(const Key &key) const
    Definition hashSet.h:1120
    │ │ │ +
    BALL::HashSet::insert
    Iterator insert(Iterator pos, const ValueType &item)
    │ │ │ +
    BALL::HashSet::reference
    Key & reference
    Definition hashSet.h:299
    │ │ │ +
    BALL::HashSet::deleteNode_
    virtual void deleteNode_(Node *node) const
    Definition hashSet.h:1283
    │ │ │ +
    BALL::HashSet::dump
    virtual void dump(std::ostream &s=std::cout, Size depth=0) const
    Definition hashSet.h:1184
    │ │ │ +
    BALL::HashSet::IteratorPosition
    Node * IteratorPosition
    Definition hashSet.h:74
    │ │ │ +
    BALL::HashSet::rehash
    virtual void rehash()
    Definition hashSet.h:1249
    │ │ │ +
    BALL::HashSet::operator=
    const HashSet & operator=(const HashSet &rhs)
    Definition hashSet.h:688
    │ │ │ +
    BALL::HashSet::getSize
    Size getSize() const
    Definition hashSet.h:855
    │ │ │ + │ │ │ +
    BALL::HashSet::ValueType
    Key ValueType
    Definition hashSet.h:51
    │ │ │ +
    BALL::HashSet::~HashSet
    virtual ~HashSet()
    Definition hashSet.h:322
    │ │ │ +
    BALL::HashSet::operator|
    HashSet operator|(const HashSet &rhs) const
    Definition hashSet.h:824
    │ │ │ +
    BALL::HashSet::end
    Iterator end()
    Definition hashSet.h:543
    │ │ │ +
    BALL::HashSet::operator|=
    const HashSet & operator|=(const HashSet &rhs)
    Definition hashSet.h:738
    │ │ │ +
    BALL::HashSet::operator-=
    const HashSet & operator-=(const HashSet &rhs)
    Definition hashSet.h:799
    │ │ │ +
    BALL::HashSet::operator&
    HashSet operator&(const HashSet &rhs) const
    Definition hashSet.h:759
    │ │ │ +
    BALL::HashSet::destroy
    void destroy()
    Definition hashSet.h:681
    │ │ │ +
    BALL::HashSet::operator==
    bool operator==(const HashSet &hash_set) const
    Definition hashSet.h:1133
    │ │ │ +
    BALL::HashSet::getBucketSize
    Size getBucketSize() const
    Definition hashSet.h:841
    │ │ │ +
    BALL::HashSet::host
    virtual void host(Visitor< HashSet< Key > > &visitor)
    Definition hashSet.h:1113
    │ │ │ +
    BALL::HashSet::INITIAL_NUMBER_OF_BUCKETS
    @ INITIAL_NUMBER_OF_BUCKETS
    Initial number of buckets.
    Definition hashSet.h:250
    │ │ │ +
    BALL::HashSet::INITIAL_CAPACITY
    @ INITIAL_CAPACITY
    Initial capacity of the hash set.
    Definition hashSet.h:248
    │ │ │ +
    BALL::HashSet::difference_type
    Index difference_type
    Definition hashSet.h:305
    │ │ │ + │ │ │ +
    BALL::HashSet::apply
    bool apply(UnaryProcessor< ValueType > &processor)
    Definition hashSet.h:1217
    │ │ │ +
    BALL::HashSet::iterator
    Iterator iterator
    Definition hashSet.h:287
    │ │ │ +
    BALL::HashSet::clear
    virtual void clear()
    Definition hashSet.h:660
    │ │ │ + │ │ │ +
    BALL::HashSet::ConstIterator
    ConstForwardIterator< HashSet< Key >, ValueType, PointerType, IteratorTraits > ConstIterator
    Definition hashSet.h:283
    │ │ │ +
    BALL::HashSet::erase
    Size erase(const KeyType &key)
    Definition hashSet.h:927
    │ │ │ +
    BALL::HashSet::swap
    void swap(HashSet &hash_set)
    Definition hashSet.h:704
    │ │ │ +
    BALL::HashSet::erase
    void erase(Iterator pos)
    Definition hashSet.h:960
    │ │ │ +
    BALL::HashSet::PointerType
    Key * PointerType
    Definition hashSet.h:59
    │ │ │ +
    BALL::HashSet::getCapacity
    Size getCapacity() const
    Definition hashSet.h:848
    │ │ │ +
    BALL::HashSet::const_pointer
    const Key * const_pointer
    Definition hashSet.h:297
    │ │ │ +
    BALL::HashSet::needRehashing_
    virtual bool needRehashing_() const
    Definition hashSet.h:1290
    │ │ │ +
    BALL::HashSet::find
    Iterator find(const Key &key)
    Definition hashSet.h:868
    │ │ │ + │ │ │ + │ │ │ +
    BALL::HashSet::Node::value
    ValueType value
    Definition hashSet.h:65
    │ │ │ + │ │ │ +
    BALL::HashSet::IteratorTraits::getContainer
    const HashSet * getContainer() const
    Definition hashSet.h:117
    │ │ │ +
    BALL::HashSet::IteratorTraits::getData
    const ValueType & getData() const
    Definition hashSet.h:208
    │ │ │ + │ │ │ +
    BALL::HashSet::IteratorTraits::operator=
    IteratorTraits & operator=(const IteratorTraits &traits)
    Definition hashSet.h:103
    │ │ │ +
    BALL::HashSet::IteratorTraits::position_
    IteratorPosition position_
    Definition hashSet.h:236
    │ │ │ + │ │ │ +
    BALL::HashSet::IteratorTraits::IteratorTraits
    IteratorTraits(const IteratorTraits &traits)
    Definition hashSet.h:96
    │ │ │ + │ │ │ + │ │ │ +
    BALL::HashSet::IteratorTraits::operator==
    bool operator==(const IteratorTraits &traits) const
    Definition hashSet.h:137
    │ │ │ + │ │ │ + │ │ │ +
    BALL::HashSet::IteratorTraits::getPosition
    IteratorPosition & getPosition()
    Definition hashSet.h:127
    │ │ │ + │ │ │ +
    BALL::HashSet::IteratorTraits::operator!=
    bool operator!=(const IteratorTraits &traits) const
    Definition hashSet.h:142
    │ │ │ +
    BALL::HashSet::IteratorTraits::IteratorTraits
    IteratorTraits(const HashSet &hash_set)
    Definition hashSet.h:89
    │ │ │ + │ │ │ +
    BALL::HashSet::IteratorTraits::getPosition
    const IteratorPosition & getPosition() const
    Definition hashSet.h:132
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::HashSet::IllegalKey::IllegalKey
    IllegalKey(const char *file, int line)
    Definition hashSet.h:267
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,268 +1,1534 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _C_O_N_C_E_P_T │ │ │ │ -processor.h │ │ │ │ + * _D_A_T_A_T_Y_P_E │ │ │ │ +hashSet.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_CONCEPT_PROCESSOR_H │ │ │ │ -6#define BALL_CONCEPT_PROCESSOR_H │ │ │ │ +5#ifndef BALL_DATATYPE_HASHSET_H │ │ │ │ +6#define BALL_DATATYPE_HASHSET_H │ │ │ │ 7 │ │ │ │ 8#ifndef BALL_COMMON_H │ │ │ │ 9# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_CONCEPT_BASEFUNCTOR_H │ │ │ │ -13# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_b_a_s_e_F_u_n_c_t_o_r_._h> │ │ │ │ +12#ifndef BALL_COMMON_HASH_H │ │ │ │ +13# include <_B_A_L_L_/_C_O_M_M_O_N_/_h_a_s_h_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ -17# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +16#ifndef BALL_CONCEPT_FORWARDITERATOR_H │ │ │ │ +17# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h> │ │ │ │ 18#endif │ │ │ │ 19 │ │ │ │ -20namespace _B_A_L_L │ │ │ │ -21{ │ │ │ │ -22 │ │ │ │ -28 │ │ │ │ -_3_1 class _B_A_L_L___E_X_P_O_R_T _P_r_o_c_e_s_s_o_r │ │ │ │ -32 { │ │ │ │ -33 public: │ │ │ │ -_3_6 typedef int _R_e_s_u_l_t; │ │ │ │ +20#ifndef BALL_CONCEPT_VISITOR_H │ │ │ │ +21# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_v_i_s_i_t_o_r_._h> │ │ │ │ +22#endif │ │ │ │ +23 │ │ │ │ +24#ifndef BALL_DATATYPE_FOREACH_H │ │ │ │ +25# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_f_o_r_E_a_c_h_._h> │ │ │ │ +26#endif │ │ │ │ +27 │ │ │ │ +28#ifndef BALL_CONCEPT_PREDICATE_H │ │ │ │ +29# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_e_d_i_c_a_t_e_._h> │ │ │ │ +30#endif │ │ │ │ +31 │ │ │ │ +32#ifndef BALL_CONCEPT_PROCESSOR_H │ │ │ │ +33# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ +34#endif │ │ │ │ +35 │ │ │ │ +36#include │ │ │ │ 37 │ │ │ │ -40 enum │ │ │ │ -41 { │ │ │ │ -_4_4 ABORT = 0, │ │ │ │ -_4_7 BREAK = 1, │ │ │ │ -50 CONTINUE = 2 │ │ │ │ -_5_1 }; │ │ │ │ -52 }; │ │ │ │ -53 │ │ │ │ -54 │ │ │ │ -57 template │ │ │ │ -_5_8 class _U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -59 : public _U_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ -60 { │ │ │ │ -61 public: │ │ │ │ -62 │ │ │ │ -66 _B_A_L_L___C_R_E_A_T_E(_U_n_a_r_y_P_r_o_c_e_s_s_o_r) │ │ │ │ -_6_9 _U_n_a_r_y_P_r_o_c_e_s_s_o_r() │ │ │ │ +38 │ │ │ │ +39namespace _B_A_L_L │ │ │ │ +40{ │ │ │ │ +44 template │ │ │ │ +_4_5 class _H_a_s_h_S_e_t │ │ │ │ +46 { │ │ │ │ +47 public: │ │ │ │ +48 │ │ │ │ +_5_1 typedef Key _V_a_l_u_e_T_y_p_e; │ │ │ │ +52 │ │ │ │ +_5_5 typedef Key _K_e_y_T_y_p_e; │ │ │ │ +56 │ │ │ │ +_5_9 typedef Key* _P_o_i_n_t_e_r_T_y_p_e; │ │ │ │ +60 │ │ │ │ +61 // --- EXTERNAL ITERATORS │ │ │ │ +_6_2 struct _N_o_d_e │ │ │ │ +63 { │ │ │ │ +_6_4 _N_o_d_e* _n_e_x_t; │ │ │ │ +_6_5 _V_a_l_u_e_T_y_p_e _v_a_l_u_e; │ │ │ │ +66 │ │ │ │ +_6_7 _N_o_d_e(const _K_e_y_T_y_p_e& my_key, const _N_o_d_e* my_next) │ │ │ │ +68 : _n_e_x_t(const_cast<_N_o_d_e*>(my_next)), │ │ │ │ +69 _v_a_l_u_e(const_cast<_V_a_l_u_e_T_y_p_e&>(my_key)) │ │ │ │ 70 { │ │ │ │ 71 } │ │ │ │ -72 │ │ │ │ -_7_5 _U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -76 (const _U_n_a_r_y_P_r_o_c_e_s_s_o_r& /* processor */) │ │ │ │ +72 }; │ │ │ │ +73 │ │ │ │ +_7_4 typedef _N_o_d_e* _I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n; │ │ │ │ +75 │ │ │ │ +_7_6 class _I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ 77 { │ │ │ │ -78 } │ │ │ │ -79 │ │ │ │ -_8_2 virtual _~_U_n_a_r_y_P_r_o_c_e_s_s_o_r() │ │ │ │ -83 { │ │ │ │ -84 } │ │ │ │ -86 │ │ │ │ -_9_2 virtual bool _s_t_a_r_t() │ │ │ │ +78 │ │ │ │ +79 friend class _H_a_s_h_S_e_t; │ │ │ │ +80 public: │ │ │ │ +81 │ │ │ │ +_8_2 _I_t_e_r_a_t_o_r_T_r_a_i_t_s() │ │ │ │ +83 : _b_o_u_n_d__(0), │ │ │ │ +84 _p_o_s_i_t_i_o_n__(0), │ │ │ │ +85 _b_u_c_k_e_t__(0) │ │ │ │ +86 { │ │ │ │ +87 } │ │ │ │ +88 │ │ │ │ +_8_9 _I_t_e_r_a_t_o_r_T_r_a_i_t_s(const _H_a_s_h_S_e_t& hash_set) │ │ │ │ +90 : _b_o_u_n_d__(const_cast<_H_a_s_h_S_e_t*>(&hash_set)), │ │ │ │ +91 _p_o_s_i_t_i_o_n__(0), │ │ │ │ +92 _b_u_c_k_e_t__(0) │ │ │ │ 93 { │ │ │ │ -94 return true; │ │ │ │ -95 } │ │ │ │ -96 │ │ │ │ -_9_9 virtual bool _f_i_n_i_s_h() │ │ │ │ +94 } │ │ │ │ +95 │ │ │ │ +_9_6 _I_t_e_r_a_t_o_r_T_r_a_i_t_s(const _I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) │ │ │ │ +97 : _b_o_u_n_d__(traits._b_o_u_n_d__), │ │ │ │ +98 _p_o_s_i_t_i_o_n__(traits._p_o_s_i_t_i_o_n__), │ │ │ │ +99 _b_u_c_k_e_t__(traits._b_u_c_k_e_t__) │ │ │ │ 100 { │ │ │ │ -101 return true; │ │ │ │ -102 } │ │ │ │ -103 │ │ │ │ -_1_0_6 virtual _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t _o_p_e_r_a_t_o_r_ _(_)_ (T &) │ │ │ │ -107 { │ │ │ │ -108 return _P_r_o_c_e_s_s_o_r_:_:_C_O_N_T_I_N_U_E; │ │ │ │ -109 } │ │ │ │ -111 }; │ │ │ │ -112 │ │ │ │ -118 template │ │ │ │ -_1_1_9 class _C_o_n_s_t_U_n_a_r_y_P_r_o_c_e_s_s_o_r : public _U_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ -120 { │ │ │ │ -121 public: │ │ │ │ -122 _B_A_L_L___C_R_E_A_T_E(_C_o_n_s_t_U_n_a_r_y_P_r_o_c_e_s_s_o_r) │ │ │ │ -123 │ │ │ │ -_1_2_4 virtual ~_C_o_n_s_t_U_n_a_r_y_P_r_o_c_e_s_s_o_r() │ │ │ │ -125 { │ │ │ │ -126 } │ │ │ │ -127 │ │ │ │ -_1_2_8 virtual bool _s_t_a_r_t() │ │ │ │ -129 { │ │ │ │ -130 return true; │ │ │ │ -131 } │ │ │ │ -132 │ │ │ │ -_1_3_3 virtual bool _f_i_n_i_s_h() │ │ │ │ -134 { │ │ │ │ -135 return true; │ │ │ │ -136 } │ │ │ │ -137 │ │ │ │ -_1_3_8 virtual _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t _o_p_e_r_a_t_o_r_(_)(const T&) │ │ │ │ -139 { │ │ │ │ -140 return _P_r_o_c_e_s_s_o_r_:_:_C_O_N_T_I_N_U_E; │ │ │ │ -141 } │ │ │ │ -142 }; │ │ │ │ -143 │ │ │ │ -146 template │ │ │ │ -_1_4_7 class _B_i_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -148 : public _B_i_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ -149 { │ │ │ │ -150 public: │ │ │ │ -151 │ │ │ │ -155 _B_A_L_L___C_R_E_A_T_E(_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r) │ │ │ │ -156 │ │ │ │ -157 │ │ │ │ -_1_5_9 _B_i_n_a_r_y_P_r_o_c_e_s_s_o_r() │ │ │ │ -160 { │ │ │ │ -161 } │ │ │ │ -162 │ │ │ │ -_1_6_5 _B_i_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -166 (const _B_i_n_a_r_y_P_r_o_c_e_s_s_o_r& /* processor */) │ │ │ │ +101 } │ │ │ │ +102 │ │ │ │ +_1_0_3 _I_t_e_r_a_t_o_r_T_r_a_i_t_s& _o_p_e_r_a_t_o_r_ _=_ (const _I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) │ │ │ │ +104 { │ │ │ │ +105 _b_o_u_n_d__ = traits._b_o_u_n_d__; │ │ │ │ +106 _p_o_s_i_t_i_o_n__ = traits._p_o_s_i_t_i_o_n__; │ │ │ │ +107 _b_u_c_k_e_t__ = traits._b_u_c_k_e_t__; │ │ │ │ +108 │ │ │ │ +109 return *this; │ │ │ │ +110 } │ │ │ │ +111 │ │ │ │ +_1_1_2 _H_a_s_h_S_e_t* _g_e_t_C_o_n_t_a_i_n_e_r() │ │ │ │ +113 { │ │ │ │ +114 return _b_o_u_n_d__; │ │ │ │ +115 } │ │ │ │ +116 │ │ │ │ +_1_1_7 const _H_a_s_h_S_e_t* _g_e_t_C_o_n_t_a_i_n_e_r() const │ │ │ │ +118 { │ │ │ │ +119 return _b_o_u_n_d__; │ │ │ │ +120 } │ │ │ │ +121 │ │ │ │ +_1_2_2 bool _i_s_S_i_n_g_u_l_a_r() const │ │ │ │ +123 { │ │ │ │ +124 return (_b_o_u_n_d__ == 0); │ │ │ │ +125 } │ │ │ │ +126 │ │ │ │ +_1_2_7 _I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n& _g_e_t_P_o_s_i_t_i_o_n() │ │ │ │ +128 { │ │ │ │ +129 return _p_o_s_i_t_i_o_n__; │ │ │ │ +130 } │ │ │ │ +131 │ │ │ │ +_1_3_2 const _I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n& _g_e_t_P_o_s_i_t_i_o_n() const │ │ │ │ +133 { │ │ │ │ +134 return _p_o_s_i_t_i_o_n__; │ │ │ │ +135 } │ │ │ │ +136 │ │ │ │ +_1_3_7 bool _o_p_e_r_a_t_o_r_ _=_=_ (const _I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) const │ │ │ │ +138 { │ │ │ │ +139 return (_p_o_s_i_t_i_o_n__ == traits._p_o_s_i_t_i_o_n__); │ │ │ │ +140 } │ │ │ │ +141 │ │ │ │ +_1_4_2 bool _o_p_e_r_a_t_o_r_ _!_=_ (const _I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) const │ │ │ │ +143 { │ │ │ │ +144 return (_p_o_s_i_t_i_o_n__ != traits._p_o_s_i_t_i_o_n__); │ │ │ │ +145 } │ │ │ │ +146 │ │ │ │ +_1_4_7 bool _i_s_V_a_l_i_d() const │ │ │ │ +148 { │ │ │ │ +149 return ((_b_o_u_n_d__ != 0) && (_p_o_s_i_t_i_o_n__ != 0) │ │ │ │ +150 && (_b_u_c_k_e_t__ < (_P_o_s_i_t_i_o_n)_b_o_u_n_d__->bucket_.size())); │ │ │ │ +151 } │ │ │ │ +152 │ │ │ │ +_1_5_3 void _i_n_v_a_l_i_d_a_t_e() │ │ │ │ +154 { │ │ │ │ +155 _b_o_u_n_d__ = 0; │ │ │ │ +156 _p_o_s_i_t_i_o_n__ = 0; │ │ │ │ +157 _b_u_c_k_e_t__ = _I_N_V_A_L_I_D___P_o_s_i_t_i_o_n; │ │ │ │ +158 } │ │ │ │ +159 │ │ │ │ +_1_6_0 void _t_o_B_e_g_i_n() │ │ │ │ +161 { │ │ │ │ +162 for (_b_u_c_k_e_t__ = 0; _b_u_c_k_e_t__ < (_P_o_s_i_t_i_o_n)_b_o_u_n_d__->bucket_.size(); ++_b_u_c_k_e_t__) │ │ │ │ +163 { │ │ │ │ +164 _p_o_s_i_t_i_o_n__ = _b_o_u_n_d__->bucket_[_b_u_c_k_e_t__]; │ │ │ │ +165 │ │ │ │ +166 if (_p_o_s_i_t_i_o_n__ != 0) │ │ │ │ 167 { │ │ │ │ -168 } │ │ │ │ -169 │ │ │ │ -_1_7_2 virtual _~_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r() │ │ │ │ -173 { │ │ │ │ -174 } │ │ │ │ -176 │ │ │ │ -180 │ │ │ │ -_1_8_3 virtual bool _s_t_a_r_t() │ │ │ │ +168 return; │ │ │ │ +169 } │ │ │ │ +170 } │ │ │ │ +171 } │ │ │ │ +172 │ │ │ │ +_1_7_3 bool _i_s_B_e_g_i_n() const │ │ │ │ +174 { │ │ │ │ +175 for (_P_o_s_i_t_i_o_n bucket = 0; bucket < (_P_o_s_i_t_i_o_n)_b_o_u_n_d__->bucket_.size(); │ │ │ │ +++bucket) │ │ │ │ +176 { │ │ │ │ +177 if (_b_o_u_n_d__->bucket_[_b_u_c_k_e_t__] != 0) │ │ │ │ +178 { │ │ │ │ +179 if (_p_o_s_i_t_i_o_n__ == _b_o_u_n_d__->bucket_[_b_u_c_k_e_t__]) │ │ │ │ +180 { │ │ │ │ +181 return true; │ │ │ │ +182 } │ │ │ │ +183 else │ │ │ │ 184 { │ │ │ │ -185 return true; │ │ │ │ +185 return false; │ │ │ │ 186 } │ │ │ │ -187 │ │ │ │ -_1_9_0 virtual bool _f_i_n_i_s_h() │ │ │ │ -191 { │ │ │ │ -192 return true; │ │ │ │ -193 } │ │ │ │ -194 │ │ │ │ -_1_9_7 virtual _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t _o_p_e_r_a_t_o_r_ _(_)_ (T1&, T2&) │ │ │ │ -198 { │ │ │ │ -199 return _P_r_o_c_e_s_s_o_r_:_:_C_O_N_T_I_N_U_E; │ │ │ │ -200 } │ │ │ │ -202 }; │ │ │ │ -203 │ │ │ │ -204 template │ │ │ │ -_2_0_5 class _C_o_n_s_t_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -206 : public _B_i_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ -207 { │ │ │ │ -208 public: │ │ │ │ -209 │ │ │ │ -213 _B_A_L_L___C_R_E_A_T_E(_C_o_n_s_t_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r) │ │ │ │ -214 │ │ │ │ -215 │ │ │ │ -_2_1_7 virtual ~_C_o_n_s_t_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r() │ │ │ │ +187 } │ │ │ │ +188 } │ │ │ │ +189 │ │ │ │ +190 return false; │ │ │ │ +191 } │ │ │ │ +192 │ │ │ │ +_1_9_3 void _t_o_E_n_d() │ │ │ │ +194 { │ │ │ │ +195 _p_o_s_i_t_i_o_n__ = 0; │ │ │ │ +196 } │ │ │ │ +197 │ │ │ │ +_1_9_8 bool _i_s_E_n_d() const │ │ │ │ +199 { │ │ │ │ +200 return (_p_o_s_i_t_i_o_n__ == 0); │ │ │ │ +201 } │ │ │ │ +202 │ │ │ │ +_2_0_3 _V_a_l_u_e_T_y_p_e& _g_e_t_D_a_t_a() │ │ │ │ +204 { │ │ │ │ +205 return _p_o_s_i_t_i_o_n__->_v_a_l_u_e; │ │ │ │ +206 } │ │ │ │ +207 │ │ │ │ +_2_0_8 const _V_a_l_u_e_T_y_p_e& _g_e_t_D_a_t_a() const │ │ │ │ +209 { │ │ │ │ +210 return _p_o_s_i_t_i_o_n__->_v_a_l_u_e; │ │ │ │ +211 } │ │ │ │ +212 │ │ │ │ +_2_1_3 void _f_o_r_w_a_r_d() │ │ │ │ +214 { │ │ │ │ +215 _p_o_s_i_t_i_o_n__ = _p_o_s_i_t_i_o_n__->_n_e_x_t; │ │ │ │ +216 │ │ │ │ +217 if (_p_o_s_i_t_i_o_n__ != 0) │ │ │ │ 218 { │ │ │ │ -219 } │ │ │ │ +219 return; │ │ │ │ +220 } │ │ │ │ 221 │ │ │ │ +222 for (++_b_u_c_k_e_t__; _b_u_c_k_e_t__ < (_P_o_s_i_t_i_o_n)_b_o_u_n_d__->bucket_.size(); ++_b_u_c_k_e_t__) │ │ │ │ +223 { │ │ │ │ +224 _p_o_s_i_t_i_o_n__ = _b_o_u_n_d__->bucket_[_b_u_c_k_e_t__]; │ │ │ │ 225 │ │ │ │ -_2_2_8 virtual bool _s_t_a_r_t() │ │ │ │ -229 { │ │ │ │ -230 return true; │ │ │ │ +226 if (_p_o_s_i_t_i_o_n__ != 0) │ │ │ │ +227 { │ │ │ │ +228 return; │ │ │ │ +229 } │ │ │ │ +230 } │ │ │ │ 231 } │ │ │ │ 232 │ │ │ │ -_2_3_5 virtual bool _f_i_n_i_s_h() │ │ │ │ -236 { │ │ │ │ -237 return true; │ │ │ │ -238 } │ │ │ │ -239 │ │ │ │ -_2_4_2 virtual _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t _o_p_e_r_a_t_o_r_ _(_)_ (const T1&, const T2&) │ │ │ │ -243 { │ │ │ │ -244 return _P_r_o_c_e_s_s_o_r_:_:_C_O_N_T_I_N_U_E; │ │ │ │ -245 } │ │ │ │ -247 }; │ │ │ │ -248 │ │ │ │ -250// required for MSVC 12/2013 (TODO remove) │ │ │ │ -251#ifdef BALL_COMPILER_MSVC │ │ │ │ -252class Atom; │ │ │ │ -253template class _B_A_L_L___E_X_P_O_R_T UnaryProcessor; │ │ │ │ -254template class _B_A_L_L___E_X_P_O_R_T ConstUnaryProcessor; │ │ │ │ -255#endif │ │ │ │ -256 │ │ │ │ -257} // namespace BALL │ │ │ │ +233 protected: │ │ │ │ +234 │ │ │ │ +_2_3_5 _H_a_s_h_S_e_t* _b_o_u_n_d__; │ │ │ │ +_2_3_6 _I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n _p_o_s_i_t_i_o_n__; │ │ │ │ +_2_3_7 _P_o_s_i_t_i_o_n _b_u_c_k_e_t__; │ │ │ │ +238 }; │ │ │ │ +_2_3_9 friend class _I_t_e_r_a_t_o_r_T_r_a_i_t_s; │ │ │ │ +240 │ │ │ │ +244 │ │ │ │ +245 enum │ │ │ │ +246 { │ │ │ │ +_2_4_8 _I_N_I_T_I_A_L___C_A_P_A_C_I_T_Y = 4, │ │ │ │ +250 _I_N_I_T_I_A_L___N_U_M_B_E_R___O_F___B_U_C_K_E_T_S = 3 │ │ │ │ +_2_5_1 }; │ │ │ │ +252 │ │ │ │ +254 │ │ │ │ 258 │ │ │ │ -259#endif // BALL_CONCEPT_PROCESSOR_H │ │ │ │ +_2_6_3 class _I_l_l_e_g_a_l_K_e_y │ │ │ │ +264 : public _E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +265 { │ │ │ │ +266 public: │ │ │ │ +_2_6_7 _I_l_l_e_g_a_l_K_e_y(const char* file, int line) │ │ │ │ +268 : Exception::_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n(file, line) │ │ │ │ +269 { │ │ │ │ +270 } │ │ │ │ +271 }; │ │ │ │ +272 │ │ │ │ +274 │ │ │ │ +278 │ │ │ │ +_2_8_0 typedef _F_o_r_w_a_r_d_I_t_e_r_a_t_o_r_<_H_a_s_h_S_e_t_<_K_e_y_>, _V_a_l_u_e_T_y_p_e, _P_o_i_n_t_e_r_T_y_p_e, │ │ │ │ +_I_t_e_r_a_t_o_r_T_r_a_i_t_s> _I_t_e_r_a_t_o_r; │ │ │ │ +281 │ │ │ │ +_2_8_3 typedef ConstForwardIterator , _V_a_l_u_e_T_y_p_e, _P_o_i_n_t_e_r_T_y_p_e, │ │ │ │ +_I_t_e_r_a_t_o_r_T_r_a_i_t_s> _C_o_n_s_t_I_t_e_r_a_t_o_r; │ │ │ │ +284 │ │ │ │ +285 // STL compatibility stuff │ │ │ │ +_2_8_7 typedef _I_t_e_r_a_t_o_r _i_t_e_r_a_t_o_r; │ │ │ │ +_2_8_9 typedef _C_o_n_s_t_I_t_e_r_a_t_o_r _c_o_n_s_t___i_t_e_r_a_t_o_r; │ │ │ │ +_2_9_1 typedef Key _v_a_l_u_e___t_y_p_e; │ │ │ │ +_2_9_3 typedef Key _k_e_y___t_y_p_e; │ │ │ │ +_2_9_5 typedef Key* _p_o_i_n_t_e_r; │ │ │ │ +_2_9_7 typedef const Key* _c_o_n_s_t___p_o_i_n_t_e_r; │ │ │ │ +_2_9_9 typedef Key& _r_e_f_e_r_e_n_c_e; │ │ │ │ +_3_0_1 typedef const Key& _c_o_n_s_t___r_e_f_e_r_e_n_c_e; │ │ │ │ +_3_0_3 typedef _S_i_z_e _s_i_z_e___t_y_p_e; │ │ │ │ +_3_0_5 typedef _I_n_d_e_x _d_i_f_f_e_r_e_n_c_e___t_y_p_e; │ │ │ │ +307 │ │ │ │ +311 │ │ │ │ +_3_1_4 _H_a_s_h_S_e_t(_S_i_z_e initial_capacity = _I_N_I_T_I_A_L___C_A_P_A_C_I_T_Y, _S_i_z_e number_of_buckets = │ │ │ │ +_I_N_I_T_I_A_L___N_U_M_B_E_R___O_F___B_U_C_K_E_T_S); │ │ │ │ +315 │ │ │ │ +_3_1_8 _H_a_s_h_S_e_t(const _H_a_s_h_S_e_t& hash_set); │ │ │ │ +319 │ │ │ │ +_3_2_2 virtual _~_H_a_s_h_S_e_t() │ │ │ │ +323 { │ │ │ │ +324 _d_e_s_t_r_o_y(); │ │ │ │ +325 deleteBuckets_(); │ │ │ │ +326 } │ │ │ │ +327 │ │ │ │ +_3_3_2 virtual void _c_l_e_a_r(); │ │ │ │ +333 │ │ │ │ +_3_3_9 void _d_e_s_t_r_o_y(); │ │ │ │ +340 │ │ │ │ +342 │ │ │ │ +346 │ │ │ │ +_3_5_0 void _s_e_t(const _H_a_s_h_S_e_t& hash_set); │ │ │ │ +351 │ │ │ │ +_3_5_5 const _H_a_s_h_S_e_t& _o_p_e_r_a_t_o_r_ _=_ (const _H_a_s_h_S_e_t& rhs); │ │ │ │ +356 │ │ │ │ +_3_6_0 void _g_e_t(_H_a_s_h_S_e_t& hash_set) const; │ │ │ │ +361 │ │ │ │ +_3_6_4 void _s_w_a_p(_H_a_s_h_S_e_t& hash_set); │ │ │ │ +365 │ │ │ │ +367 │ │ │ │ +371 │ │ │ │ +_3_7_4 _S_i_z_e _g_e_t_B_u_c_k_e_t_S_i_z_e() const; │ │ │ │ +375 │ │ │ │ +_3_7_8 _S_i_z_e _g_e_t_C_a_p_a_c_i_t_y() const; │ │ │ │ +379 │ │ │ │ +_3_8_2 _S_i_z_e _g_e_t_S_i_z_e() const; │ │ │ │ +383 │ │ │ │ +_3_8_6 _S_i_z_e _s_i_z_e() const; │ │ │ │ +387 │ │ │ │ +_3_9_0 _I_t_e_r_a_t_o_r _f_i_n_d(const Key& key); │ │ │ │ +391 │ │ │ │ +_3_9_4 _C_o_n_s_t_I_t_e_r_a_t_o_r _f_i_n_d(const Key& key) const; │ │ │ │ +395 │ │ │ │ +_3_9_8 std::pair _i_n_s_e_r_t(const _V_a_l_u_e_T_y_p_e& item); │ │ │ │ +399 │ │ │ │ +_4_0_3 _I_t_e_r_a_t_o_r _i_n_s_e_r_t(_I_t_e_r_a_t_o_r pos, const _V_a_l_u_e_T_y_p_e& item); │ │ │ │ +404 │ │ │ │ +_4_0_8 _S_i_z_e _e_r_a_s_e(const _K_e_y_T_y_p_e& key); │ │ │ │ +409 │ │ │ │ +_4_1_5 void _e_r_a_s_e(_I_t_e_r_a_t_o_r pos); │ │ │ │ +416 │ │ │ │ +_4_2_1 void _e_r_a_s_e(_I_t_e_r_a_t_o_r f, _I_t_e_r_a_t_o_r l); │ │ │ │ +422 │ │ │ │ +424 │ │ │ │ +_4_3_2 const _H_a_s_h_S_e_t& _o_p_e_r_a_t_o_r_ _&_=_ (const _H_a_s_h_S_e_t& rhs); │ │ │ │ +433 │ │ │ │ +_4_3_8 const _H_a_s_h_S_e_t& _o_p_e_r_a_t_o_r_ _|_=_ (const _H_a_s_h_S_e_t& rhs); │ │ │ │ +439 │ │ │ │ +_4_4_4 _H_a_s_h_S_e_t _o_p_e_r_a_t_o_r_ _&_ (const _H_a_s_h_S_e_t& rhs) const; │ │ │ │ +445 │ │ │ │ +_4_5_0 _H_a_s_h_S_e_t _o_p_e_r_a_t_o_r_ _|_ (const _H_a_s_h_S_e_t& rhs) const; │ │ │ │ +451 │ │ │ │ +_4_5_5 _H_a_s_h_S_e_t _o_p_e_r_a_t_o_r_ _+_ (const _H_a_s_h_S_e_t& rhs) const; │ │ │ │ +456 │ │ │ │ +_4_6_2 _H_a_s_h_S_e_t _o_p_e_r_a_t_o_r_ _-_ (const _H_a_s_h_S_e_t& rhs) const; │ │ │ │ +463 │ │ │ │ +_4_6_7 const _H_a_s_h_S_e_t& _o_p_e_r_a_t_o_r_ _+_=_ (const _H_a_s_h_S_e_t& rhs); │ │ │ │ +468 │ │ │ │ +_4_7_2 const _H_a_s_h_S_e_t& _o_p_e_r_a_t_o_r_ _-_=_ (const _H_a_s_h_S_e_t& rhs); │ │ │ │ +474 │ │ │ │ +478 │ │ │ │ +_4_8_1 virtual void _h_o_s_t(_V_i_s_i_t_o_r<_H_a_s_h_S_e_t_<_K_e_y_> >& visitor); │ │ │ │ +483 │ │ │ │ +487 │ │ │ │ +_4_9_0 bool _h_a_s(const Key& key) const; │ │ │ │ +491 │ │ │ │ +_4_9_4 bool _i_s_E_m_p_t_y() const; │ │ │ │ +495 │ │ │ │ +_4_9_8 bool _o_p_e_r_a_t_o_r_ _=_=_ (const _H_a_s_h_S_e_t& hash_set) const; │ │ │ │ +499 │ │ │ │ +_5_0_2 bool _o_p_e_r_a_t_o_r_ _!_=_ (const _H_a_s_h_S_e_t& hash_set) const; │ │ │ │ +504 │ │ │ │ +508 │ │ │ │ +_5_1_3 bool _i_s_V_a_l_i_d() const; │ │ │ │ +514 │ │ │ │ +_5_1_7 virtual void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const; │ │ │ │ +518 │ │ │ │ +520 │ │ │ │ +521 // --- INTERNAL ITERATORS │ │ │ │ +522 │ │ │ │ +_5_2_9 bool _a_p_p_l_y(_U_n_a_r_y_P_r_o_c_e_s_s_o_r_<_V_a_l_u_e_T_y_p_e_>& processor); │ │ │ │ +531 │ │ │ │ +532 │ │ │ │ +533 │ │ │ │ +_5_3_6 _I_t_e_r_a_t_o_r _b_e_g_i_n() │ │ │ │ +537 { │ │ │ │ +538 return _I_t_e_r_a_t_o_r_:_:_b_e_g_i_n(*this); │ │ │ │ +539 } │ │ │ │ +540 │ │ │ │ +_5_4_3 _I_t_e_r_a_t_o_r _e_n_d() │ │ │ │ +544 { │ │ │ │ +545 return _I_t_e_r_a_t_o_r_:_:_e_n_d(*this); │ │ │ │ +546 } │ │ │ │ +547 │ │ │ │ +_5_5_0 _C_o_n_s_t_I_t_e_r_a_t_o_r _b_e_g_i_n() const │ │ │ │ +551 { │ │ │ │ +552 return ConstIterator::begin(*this); │ │ │ │ +553 } │ │ │ │ +554 │ │ │ │ +_5_5_7 _C_o_n_s_t_I_t_e_r_a_t_o_r _e_n_d() const │ │ │ │ +558 { │ │ │ │ +559 return ConstIterator::end(*this); │ │ │ │ +560 } │ │ │ │ +561 │ │ │ │ +562 │ │ │ │ +563 protected: │ │ │ │ +564 │ │ │ │ +_5_6_5 virtual Node* _n_e_w_N_o_d_e__(const _V_a_l_u_e_T_y_p_e& value, Node* next) const; │ │ │ │ +566 │ │ │ │ +_5_6_7 virtual void _d_e_l_e_t_e_N_o_d_e__(Node* node) const; │ │ │ │ +568 │ │ │ │ +_5_6_9 virtual _H_a_s_h_I_n_d_e_x _h_a_s_h(const Key& key) const; │ │ │ │ +570 │ │ │ │ +_5_7_1 virtual bool _n_e_e_d_R_e_h_a_s_h_i_n_g__() const; │ │ │ │ +572 │ │ │ │ +_5_7_3 virtual void _r_e_h_a_s_h(); │ │ │ │ +574 │ │ │ │ +575 private: │ │ │ │ +576 │ │ │ │ +577 void deleteBuckets_(); │ │ │ │ +578 │ │ │ │ +579 _P_o_s_i_t_i_o_n hashBucket_(const Key& key) const; │ │ │ │ +580 │ │ │ │ +581 void rehash_(); │ │ │ │ +582 │ │ │ │ +583 // --- ATTRIBUTES │ │ │ │ +584 │ │ │ │ +585 /*_ The number of elements in the hash set │ │ │ │ +586 */ │ │ │ │ +587 _S_i_z_e size_; │ │ │ │ +588 │ │ │ │ +589 /*_ The capacity - usually the number of buckets │ │ │ │ +590 */ │ │ │ │ +591 _S_i_z_e capacity_; │ │ │ │ +592 │ │ │ │ +593 /*_ Buckets are stored as a vector of linked lists of Nodes │ │ │ │ +594 */ │ │ │ │ +595 vector bucket_; │ │ │ │ +596 }; │ │ │ │ +597 │ │ │ │ +598 │ │ │ │ +599 template │ │ │ │ +_6_0_0 _H_a_s_h_S_e_t_<_K_e_y_>_:_:_H_a_s_h_S_e_t(_S_i_z_e initial_capacity, _S_i_z_e number_of_buckets) │ │ │ │ +601 : size_(0), │ │ │ │ +602 capacity_(initial_capacity), │ │ │ │ +603 bucket_(number_of_buckets) │ │ │ │ +604 { │ │ │ │ +605 for (_P_o_s_i_t_i_o_n bucket = 0; bucket < (_P_o_s_i_t_i_o_n)bucket_.size(); ++bucket) │ │ │ │ +606 { │ │ │ │ +607 bucket_[bucket] = 0; │ │ │ │ +608 } │ │ │ │ +609 } │ │ │ │ +610 │ │ │ │ +611 template │ │ │ │ +_6_1_2 _H_a_s_h_S_e_t_<_K_e_y_>_:_:_H_a_s_h_S_e_t(const _H_a_s_h_S_e_t& hash_set) │ │ │ │ +613 : size_(hash_set.size_), │ │ │ │ +614 capacity_(hash_set.capacity_), │ │ │ │ +615 bucket_(hash_set.bucket_.size()) │ │ │ │ +616 { │ │ │ │ +617 _N_o_d_e* item = 0; │ │ │ │ +618 │ │ │ │ +619 for (_P_o_s_i_t_i_o_n bucket = 0; bucket < (_P_o_s_i_t_i_o_n)bucket_.size(); ++bucket) │ │ │ │ +620 { │ │ │ │ +621 bucket_[bucket] = 0; │ │ │ │ +622 │ │ │ │ +623 for (item = hash_set.bucket_[bucket]; item != 0; item = item->_n_e_x_t) │ │ │ │ +624 { │ │ │ │ +625 bucket_[bucket] = _n_e_w_N_o_d_e__(item->_v_a_l_u_e, bucket_[bucket]); │ │ │ │ +626 } │ │ │ │ +627 } │ │ │ │ +628 } │ │ │ │ +629 │ │ │ │ +630 template │ │ │ │ +_6_3_1 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_s_e_t(const _H_a_s_h_S_e_t& hash_set) │ │ │ │ +632 { │ │ │ │ +633 if (&hash_set == this) │ │ │ │ +634 { │ │ │ │ +635 return; │ │ │ │ +636 } │ │ │ │ +637 │ │ │ │ +638 destroy(); │ │ │ │ +639 │ │ │ │ +640 deleteBuckets_(); │ │ │ │ +641 │ │ │ │ +642 size_ = hash_set.size_; │ │ │ │ +643 capacity_ = hash_set.capacity_; │ │ │ │ +644 bucket_.resize(hash_set.bucket_.size()); │ │ │ │ +645 │ │ │ │ +646 _N_o_d_e* item = 0; │ │ │ │ +647 │ │ │ │ +648 for (_P_o_s_i_t_i_o_n bucket = 0; bucket < (_P_o_s_i_t_i_o_n)bucket_.size(); ++bucket) │ │ │ │ +649 { │ │ │ │ +650 bucket_[bucket] = 0; │ │ │ │ +651 │ │ │ │ +652 for (item = hash_set.bucket_[bucket]; item != 0; item = item->_n_e_x_t) │ │ │ │ +653 { │ │ │ │ +654 bucket_[bucket] = newNode_(item->_v_a_l_u_e, bucket_[bucket]); │ │ │ │ +655 } │ │ │ │ +656 } │ │ │ │ +657 } │ │ │ │ +658 │ │ │ │ +659 template │ │ │ │ +_6_6_0 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_c_l_e_a_r() │ │ │ │ +661 { │ │ │ │ +662 _N_o_d_e* node = 0; │ │ │ │ +663 _N_o_d_e* next_node = 0; │ │ │ │ +664 │ │ │ │ +665 for (_P_o_s_i_t_i_o_n bucket = 0; bucket < (_P_o_s_i_t_i_o_n)bucket_.size(); ++bucket) │ │ │ │ +666 { │ │ │ │ +667 for (node = bucket_[bucket]; node != 0; node = next_node) │ │ │ │ +668 { │ │ │ │ +669 next_node = node->_n_e_x_t; │ │ │ │ +670 deleteNode_(node); │ │ │ │ +671 } │ │ │ │ +672 │ │ │ │ +673 bucket_[bucket] = 0; │ │ │ │ +674 } │ │ │ │ +675 │ │ │ │ +676 size_ = 0; │ │ │ │ +677 } │ │ │ │ +678 │ │ │ │ +679 template │ │ │ │ +680 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_6_8_1 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_d_e_s_t_r_o_y() │ │ │ │ +682 { │ │ │ │ +683 clear(); │ │ │ │ +684 } │ │ │ │ +685 │ │ │ │ +686 template │ │ │ │ +687 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_6_8_8 const _H_a_s_h_S_e_t_<_K_e_y_>& _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _=_ (const _H_a_s_h_S_e_t& hash_set) │ │ │ │ +689 { │ │ │ │ +690 set(hash_set); │ │ │ │ +691 return *this; │ │ │ │ +692 } │ │ │ │ +693 │ │ │ │ +694 template │ │ │ │ +695 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_6_9_6 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_g_e_t(_H_a_s_h_S_e_t& hash_set) const │ │ │ │ +697 │ │ │ │ +698 { │ │ │ │ +699 hash_set._s_e_t(*this); │ │ │ │ +700 } │ │ │ │ +701 │ │ │ │ +702 template │ │ │ │ +703 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_7_0_4 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_s_w_a_p(_H_a_s_h_S_e_t& hash_set) │ │ │ │ +705 { │ │ │ │ +706 std::swap(size_, hash_set.size_); │ │ │ │ +707 std::swap(capacity_, hash_set.capacity_); │ │ │ │ +708 std::swap(bucket_, hash_set.bucket_); │ │ │ │ +709 } │ │ │ │ +710 │ │ │ │ +711 template │ │ │ │ +712 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_7_1_3 const _H_a_s_h_S_e_t_<_K_e_y_>& _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _&_=_ (const _H_a_s_h_S_e_t& rhs) │ │ │ │ +714 { │ │ │ │ +715 // Store all elements that are not part of the intersection │ │ │ │ +716 // in a list for subsequent deletion. │ │ │ │ +717 std::list erase_list; │ │ │ │ +718 for (_I_t_e_r_a_t_o_r it = begin(); it != end(); ++it) │ │ │ │ +719 { │ │ │ │ +720 if (!rhs._h_a_s(*it)) │ │ │ │ +721 { │ │ │ │ +722 erase_list.push_back(*it); │ │ │ │ +723 } │ │ │ │ +724 } │ │ │ │ +725 │ │ │ │ +726 // erase all elements not part of the intersection │ │ │ │ +727 typename list::iterator list_it = erase_list._b_e_g_i_n(); │ │ │ │ +728 for (; list_it != erase_list.end(); ++list_it) │ │ │ │ +729 { │ │ │ │ +730 erase(*list_it); │ │ │ │ +731 } │ │ │ │ +732 │ │ │ │ +733 return *this; │ │ │ │ +734 } │ │ │ │ +735 │ │ │ │ +736 template │ │ │ │ +737 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_7_3_8 const _H_a_s_h_S_e_t_<_K_e_y_>& _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _|_=_ (const _H_a_s_h_S_e_t_<_K_e_y_>& rhs) │ │ │ │ +739 { │ │ │ │ +740 // Compute the union of both sets by inserting every element of the │ │ │ │ +741 // rhs set. │ │ │ │ +742 for (_C_o_n_s_t_I_t_e_r_a_t_o_r it = rhs._b_e_g_i_n(); it != rhs._e_n_d(); ++it) │ │ │ │ +743 { │ │ │ │ +744 insert(*it); │ │ │ │ +745 } │ │ │ │ +746 │ │ │ │ +747 return *this; │ │ │ │ +748 } │ │ │ │ +749 │ │ │ │ +750 template │ │ │ │ +751 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_7_5_2 const _H_a_s_h_S_e_t_<_K_e_y_>& _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _+_=_ (const _H_a_s_h_S_e_t_<_K_e_y_>& rhs) │ │ │ │ +753 { │ │ │ │ +754 return operator |= (rhs); │ │ │ │ +755 } │ │ │ │ +756 │ │ │ │ +757 template │ │ │ │ +758 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_7_5_9 _H_a_s_h_S_e_t_<_K_e_y_> _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _&_ (const _H_a_s_h_S_e_t_<_K_e_y_>& rhs) const │ │ │ │ +760 { │ │ │ │ +761 // Create an empty hash set... │ │ │ │ +762 _H_a_s_h_S_e_t_<_K_e_y_> tmp; │ │ │ │ +763 _C_o_n_s_t_I_t_e_r_a_t_o_r it = begin(); │ │ │ │ +764 │ │ │ │ +765 // ...and copy all the elements contained in the rhs hash set. │ │ │ │ +766 for (; +it; ++it) │ │ │ │ +767 { │ │ │ │ +768 if (rhs._h_a_s(*it)) │ │ │ │ +769 { │ │ │ │ +770 tmp._i_n_s_e_r_t(*it); │ │ │ │ +771 } │ │ │ │ +772 } │ │ │ │ +773 │ │ │ │ +774 return tmp; │ │ │ │ +775 } │ │ │ │ +776 │ │ │ │ +777 template │ │ │ │ +778 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_7_7_9 _H_a_s_h_S_e_t_<_K_e_y_> _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _-_ (const _H_a_s_h_S_e_t_<_K_e_y_>& rhs) const │ │ │ │ +780 { │ │ │ │ +781 // Create an empty hash set... │ │ │ │ +782 _H_a_s_h_S_e_t_<_K_e_y_> tmp; │ │ │ │ +783 _C_o_n_s_t_I_t_e_r_a_t_o_r it = begin(); │ │ │ │ +784 │ │ │ │ +785 // ...and copy all the elements contained in this set and not in the rhs │ │ │ │ +hash set. │ │ │ │ +786 for (; +it; ++it) │ │ │ │ +787 { │ │ │ │ +788 if (!rhs._h_a_s(*it)) │ │ │ │ +789 { │ │ │ │ +790 tmp._i_n_s_e_r_t(*it); │ │ │ │ +791 } │ │ │ │ +792 } │ │ │ │ +793 │ │ │ │ +794 return tmp; │ │ │ │ +795 } │ │ │ │ +796 │ │ │ │ +797 template │ │ │ │ +798 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_7_9_9 const _H_a_s_h_S_e_t_<_K_e_y_>& _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _-_=_ (const _H_a_s_h_S_e_t_<_K_e_y_>& │ │ │ │ +hash_set) │ │ │ │ +800 { │ │ │ │ +801 // avoid memory corruption caused by iterating over freed space when │ │ │ │ +802 // deleting myself │ │ │ │ +803 if (this == &hash_set) │ │ │ │ +804 { │ │ │ │ +805 clear(); │ │ │ │ +806 } │ │ │ │ +807 else │ │ │ │ +808 { │ │ │ │ +809 // erase all elements which are contained in this and hash_set │ │ │ │ +810 typename _H_a_s_h_S_e_t_<_K_e_y_>_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r it = hash_set._b_e_g_i_n(); │ │ │ │ +811 for (; it != hash_set._e_n_d(); ++it) │ │ │ │ +812 { │ │ │ │ +813 if (has(*it)) │ │ │ │ +814 { │ │ │ │ +815 erase(*it); │ │ │ │ +816 } │ │ │ │ +817 } │ │ │ │ +818 } │ │ │ │ +819 return *this; │ │ │ │ +820 } │ │ │ │ +821 │ │ │ │ +822 template │ │ │ │ +823 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_8_2_4 _H_a_s_h_S_e_t_<_K_e_y_> _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _|_ (const _H_a_s_h_S_e_t_<_K_e_y_>& rhs) const │ │ │ │ +825 { │ │ │ │ +826 _H_a_s_h_S_e_t_<_K_e_y_> tmp(*this); │ │ │ │ +827 tmp |= rhs; │ │ │ │ +828 │ │ │ │ +829 return tmp; │ │ │ │ +830 } │ │ │ │ +831 │ │ │ │ +832 template │ │ │ │ +833 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_8_3_4 _H_a_s_h_S_e_t_<_K_e_y_> _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _+_ (const _H_a_s_h_S_e_t_<_K_e_y_>& rhs) const │ │ │ │ +835 { │ │ │ │ +836 return operator | (rhs); │ │ │ │ +837 } │ │ │ │ +838 │ │ │ │ +839 template │ │ │ │ +840 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_8_4_1 _S_i_z_e _H_a_s_h_S_e_t_<_K_e_y_>_:_:_g_e_t_B_u_c_k_e_t_S_i_z_e() const │ │ │ │ +842 { │ │ │ │ +843 return (_S_i_z_e)bucket_.size(); │ │ │ │ +844 } │ │ │ │ +845 │ │ │ │ +846 template │ │ │ │ +847 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_8_4_8 _S_i_z_e _H_a_s_h_S_e_t_<_K_e_y_>_:_:_g_e_t_C_a_p_a_c_i_t_y() const │ │ │ │ +849 { │ │ │ │ +850 return capacity_; │ │ │ │ +851 } │ │ │ │ +852 │ │ │ │ +853 template │ │ │ │ +854 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_8_5_5 _S_i_z_e _H_a_s_h_S_e_t_<_K_e_y_>_:_:_g_e_t_S_i_z_e() const │ │ │ │ +856 { │ │ │ │ +857 return size_; │ │ │ │ +858 } │ │ │ │ +859 │ │ │ │ +860 template │ │ │ │ +861 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_8_6_2 _S_i_z_e _H_a_s_h_S_e_t_<_K_e_y_>_:_:_s_i_z_e() const │ │ │ │ +863 { │ │ │ │ +864 return size_; │ │ │ │ +865 } │ │ │ │ +866 │ │ │ │ +867 template │ │ │ │ +_8_6_8 typename _H_a_s_h_S_e_t_<_K_e_y_>_:_:_I_t_e_r_a_t_o_r _H_a_s_h_S_e_t_<_K_e_y_>_:_:_f_i_n_d(const Key& key) │ │ │ │ +869 { │ │ │ │ +870 _I_t_e_r_a_t_o_r it = end(); │ │ │ │ +871 _P_o_s_i_t_i_o_n bucket = hashBucket_(key); │ │ │ │ +872 _N_o_d_e* node_ptr = bucket_[bucket]; │ │ │ │ +873 while (node_ptr != 0) │ │ │ │ +874 { │ │ │ │ +875 if (node_ptr->_v_a_l_u_e == key) │ │ │ │ +876 { │ │ │ │ +877 it._g_e_t_T_r_a_i_t_s().position_ = node_ptr; │ │ │ │ +878 it._g_e_t_T_r_a_i_t_s().bucket_ = bucket; │ │ │ │ +879 break; │ │ │ │ +880 } │ │ │ │ +881 node_ptr = node_ptr->_n_e_x_t; │ │ │ │ +882 } │ │ │ │ +883 │ │ │ │ +884 return it; │ │ │ │ +885 } │ │ │ │ +886 │ │ │ │ +887 template │ │ │ │ +888 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_8_8_9 typename _H_a_s_h_S_e_t_<_K_e_y_>_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r _H_a_s_h_S_e_t_<_K_e_y_>_:_:_f_i_n_d(const Key& key) │ │ │ │ +const │ │ │ │ +890 { │ │ │ │ +891 return (const_cast<_H_a_s_h_S_e_t*>(this))->find(key); │ │ │ │ +892 } │ │ │ │ +893 │ │ │ │ +894 template │ │ │ │ +_8_9_5 std::pair::Iterator, bool> _H_a_s_h_S_e_t_<_K_e_y_>_:_:_i_n_s_e_r_t │ │ │ │ +896 (const _V_a_l_u_e_T_y_p_e& item) │ │ │ │ +897 { │ │ │ │ +898 _I_t_e_r_a_t_o_r it = find(item); │ │ │ │ +899 if (it == end()) │ │ │ │ +900 { │ │ │ │ +901 if (needRehashing_() == true) │ │ │ │ +902 { │ │ │ │ +903 rehash_(); │ │ │ │ +904 } │ │ │ │ +905 │ │ │ │ +906 _P_o_s_i_t_i_o_n bucket = hashBucket_(item); │ │ │ │ +907 │ │ │ │ +908 _N_o_d_e* next = bucket_[bucket]; │ │ │ │ +909 bucket_[bucket] = newNode_(item, next); │ │ │ │ +910 │ │ │ │ +911 ++size_; │ │ │ │ +912 it._g_e_t_T_r_a_i_t_s().position_ = bucket_[bucket]; │ │ │ │ +913 it._g_e_t_T_r_a_i_t_s().bucket_ = bucket; │ │ │ │ +914 } │ │ │ │ +915 │ │ │ │ +916 return std::pair(it, true); │ │ │ │ +917 } │ │ │ │ +918 │ │ │ │ +919 template │ │ │ │ +920 typename _H_a_s_h_S_e_t_<_K_e_y_>_:_:_I_t_e_r_a_t_o_r _H_a_s_h_S_e_t_<_K_e_y_>_:_:_i_n_s_e_r_t │ │ │ │ +921 (typename _H_a_s_h_S_e_t_<_K_e_y_>_:_:_I_t_e_r_a_t_o_r /* pos */, const ValueType& item) │ │ │ │ +922 { │ │ │ │ +923 return insert(item).first; │ │ │ │ +924 } │ │ │ │ +925 │ │ │ │ +926 template │ │ │ │ +_9_2_7 _S_i_z_e _H_a_s_h_S_e_t_<_K_e_y_>_:_:_e_r_a_s_e(const _K_e_y_T_y_p_e& key) │ │ │ │ +928 { │ │ │ │ +929 _P_o_s_i_t_i_o_n bucket = hashBucket_(key); │ │ │ │ +930 _N_o_d_e* previous = 0; │ │ │ │ +931 _N_o_d_e* node_ptr = bucket_[bucket]; │ │ │ │ +932 │ │ │ │ +933 while (node_ptr != 0 && node_ptr->_v_a_l_u_e != key) │ │ │ │ +934 { │ │ │ │ +935 previous = node_ptr; │ │ │ │ +936 node_ptr = node_ptr->_n_e_x_t; │ │ │ │ +937 } │ │ │ │ +938 │ │ │ │ +939 if (node_ptr == 0) │ │ │ │ +940 { │ │ │ │ +941 return false; │ │ │ │ +942 } │ │ │ │ +943 │ │ │ │ +944 if (node_ptr == bucket_[bucket]) │ │ │ │ +945 { │ │ │ │ +946 bucket_[bucket] = node_ptr->_n_e_x_t; │ │ │ │ +947 } │ │ │ │ +948 else │ │ │ │ +949 { │ │ │ │ +950 previous->_n_e_x_t = node_ptr->_n_e_x_t; │ │ │ │ +951 } │ │ │ │ +952 │ │ │ │ +953 deleteNode_(node_ptr); │ │ │ │ +954 --size_; │ │ │ │ +955 │ │ │ │ +956 return 1; │ │ │ │ +957 } │ │ │ │ +958 │ │ │ │ +959 template │ │ │ │ +_9_6_0 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_e_r_a_s_e(_I_t_e_r_a_t_o_r pos) │ │ │ │ +961 { │ │ │ │ +962 if (pos._g_e_t_T_r_a_i_t_s().bound_ != this) │ │ │ │ +963 { │ │ │ │ +964 throw _E_x_c_e_p_t_i_o_n_:_:_I_n_c_o_m_p_a_t_i_b_l_e_I_t_e_r_a_t_o_r_s(__FILE__, __LINE__); │ │ │ │ +965 } │ │ │ │ +966 │ │ │ │ +967 if ((pos == end()) || (size_ == 0)) │ │ │ │ +968 { │ │ │ │ +969 return; │ │ │ │ +970 } │ │ │ │ +971 │ │ │ │ +972 if (pos._g_e_t_T_r_a_i_t_s().position_ == bucket_[pos._g_e_t_T_r_a_i_t_s().bucket_]) │ │ │ │ +973 { │ │ │ │ +974 bucket_[pos._g_e_t_T_r_a_i_t_s().bucket_] = pos._g_e_t_T_r_a_i_t_s().position_->next; │ │ │ │ +975 } │ │ │ │ +976 else │ │ │ │ +977 { │ │ │ │ +978 // walk over all nodes in this bucket and identify the predecessor │ │ │ │ +979 // of the node refered to by the iterator pos │ │ │ │ +980 _N_o_d_e* prev = bucket_[pos._g_e_t_T_r_a_i_t_s().bucket_]; │ │ │ │ +981 for (; (prev != 0) && (prev->_n_e_x_t != pos._g_e_t_T_r_a_i_t_s().position_); prev = │ │ │ │ +prev->_n_e_x_t) {}; │ │ │ │ +982 if (prev != 0) │ │ │ │ +983 { │ │ │ │ +984 // remove the node and reconnect the list │ │ │ │ +985 prev->_n_e_x_t = pos._g_e_t_T_r_a_i_t_s().position_->next; │ │ │ │ +986 } │ │ │ │ +987 else │ │ │ │ +988 { │ │ │ │ +989 throw _E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_I_t_e_r_a_t_o_r(__FILE__, __LINE__); │ │ │ │ +990 } │ │ │ │ +991 } │ │ │ │ +992 │ │ │ │ +993 // delete the node and decrement the set size │ │ │ │ +994 deleteNode_(pos._g_e_t_T_r_a_i_t_s().position_); │ │ │ │ +995 --size_; │ │ │ │ +996 } │ │ │ │ +997 │ │ │ │ +998 template │ │ │ │ +_9_9_9 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_e_r_a_s_e(_I_t_e_r_a_t_o_r f, _I_t_e_r_a_t_o_r l) │ │ │ │ +1000 { │ │ │ │ +1001 if (f._g_e_t_T_r_a_i_t_s().bound_ != this || l._g_e_t_T_r_a_i_t_s().bound_ != this) │ │ │ │ +1002 { │ │ │ │ +1003 throw _E_x_c_e_p_t_i_o_n_:_:_I_n_c_o_m_p_a_t_i_b_l_e_I_t_e_r_a_t_o_r_s(__FILE__, __LINE__); │ │ │ │ +1004 } │ │ │ │ +1005 │ │ │ │ +1006 if (f == end()) │ │ │ │ +1007 { │ │ │ │ +1008 return; │ │ │ │ +1009 } │ │ │ │ +1010 │ │ │ │ +1011 _P_o_s_i_t_i_o_n last_bucket = l._g_e_t_T_r_a_i_t_s().bucket_; │ │ │ │ +1012 if (l == end()) │ │ │ │ +1013 { │ │ │ │ +1014 last_bucket = (_P_o_s_i_t_i_o_n)(bucket_.size() - 1); │ │ │ │ +1015 } │ │ │ │ +1016 │ │ │ │ +1017 if (f._g_e_t_T_r_a_i_t_s().bucket_ > last_bucket) │ │ │ │ +1018 { │ │ │ │ +1019 // empty range - l < f │ │ │ │ +1020 return; │ │ │ │ +1021 } │ │ │ │ +1022 │ │ │ │ +1023 // count the deleted entries to correct the set size │ │ │ │ +1024 _S_i_z_e no_deletions = 0; │ │ │ │ +1025 │ │ │ │ +1026 _P_o_s_i_t_i_o_n bucket = f._g_e_t_T_r_a_i_t_s().bucket_; │ │ │ │ +1027 for (; bucket <= last_bucket; bucket++) │ │ │ │ +1028 { │ │ │ │ +1029 if (bucket_[bucket] == 0) │ │ │ │ +1030 { │ │ │ │ +1031 // skip all empty buckets │ │ │ │ +1032 continue; │ │ │ │ +1033 } │ │ │ │ +1034 │ │ │ │ +1035 │ │ │ │ +1036 if ((bucket == f._g_e_t_T_r_a_i_t_s().bucket_) && (bucket_[bucket] != f._g_e_t_T_r_a_i_t_s │ │ │ │ +().position_)) │ │ │ │ +1037 { │ │ │ │ +1038 // find the predecessor of f │ │ │ │ +1039 _N_o_d_e* n = bucket_[bucket]; │ │ │ │ +1040 _N_o_d_e* next; │ │ │ │ +1041 for (; (n->_n_e_x_t != f._g_e_t_T_r_a_i_t_s().position_) && (n->_n_e_x_t != 0); n = n- │ │ │ │ +>_n_e_x_t) {}; │ │ │ │ +1042 │ │ │ │ +1043 if (bucket == last_bucket) │ │ │ │ +1044 { │ │ │ │ +1045 // delete everything from f to l in this bucket │ │ │ │ +1046 │ │ │ │ +1047 next = n->_n_e_x_t; │ │ │ │ +1048 n->_n_e_x_t = l._g_e_t_T_r_a_i_t_s().position_; │ │ │ │ +1049 for (n = next; (n != 0) && (n != l._g_e_t_T_r_a_i_t_s().position_); n = next) │ │ │ │ +1050 { │ │ │ │ +1051 next = n->_n_e_x_t; │ │ │ │ +1052 deleteNode_(n); │ │ │ │ +1053 no_deletions++; │ │ │ │ +1054 } │ │ │ │ +1055 } │ │ │ │ +1056 else │ │ │ │ +1057 { │ │ │ │ +1058 // delete everything from f to the end in this bucket │ │ │ │ +1059 │ │ │ │ +1060 if (n != 0) │ │ │ │ +1061 { │ │ │ │ +1062 // mark the end of the list │ │ │ │ +1063 next = n->_n_e_x_t; │ │ │ │ +1064 n->_n_e_x_t = 0; │ │ │ │ +1065 │ │ │ │ +1066 // delete all remaining nodes │ │ │ │ +1067 for (n = next; n != 0; n = next) │ │ │ │ +1068 { │ │ │ │ +1069 next = n->_n_e_x_t; │ │ │ │ +1070 deleteNode_(n); │ │ │ │ +1071 no_deletions++; │ │ │ │ +1072 } │ │ │ │ +1073 } │ │ │ │ +1074 } │ │ │ │ +1075 } │ │ │ │ +1076 // if the current bucket lies between the first and the last bucket... │ │ │ │ +1077 else if (bucket < last_bucket) │ │ │ │ +1078 { │ │ │ │ +1079 // ...delete the whole bucket │ │ │ │ +1080 _N_o_d_e* next; │ │ │ │ +1081 for (_N_o_d_e* n = bucket_[bucket]; n != 0; n = next) │ │ │ │ +1082 { │ │ │ │ +1083 next = n->_n_e_x_t; │ │ │ │ +1084 deleteNode_(n); │ │ │ │ +1085 no_deletions++; │ │ │ │ +1086 } │ │ │ │ +1087 bucket_[bucket] = 0; │ │ │ │ +1088 } │ │ │ │ +1089 else if (bucket == last_bucket) │ │ │ │ +1090 { │ │ │ │ +1091 // we delete everything in this bucket up to the iterator l │ │ │ │ +1092 │ │ │ │ +1093 // find the predecessor of l │ │ │ │ +1094 _N_o_d_e* n = bucket_[bucket]; │ │ │ │ +1095 _N_o_d_e* next; │ │ │ │ +1096 for (; (n != 0) && (n != l._g_e_t_T_r_a_i_t_s().position_); n = next) │ │ │ │ +1097 { │ │ │ │ +1098 next = n->_n_e_x_t; │ │ │ │ +1099 deleteNode_(n); │ │ │ │ +1100 no_deletions++; │ │ │ │ +1101 } │ │ │ │ +1102 │ │ │ │ +1103 bucket_[bucket] = l._g_e_t_T_r_a_i_t_s().position_; │ │ │ │ +1104 } │ │ │ │ +1105 } │ │ │ │ +1106 │ │ │ │ +1107 // correct the set size │ │ │ │ +1108 size_ -= no_deletions; │ │ │ │ +1109 } │ │ │ │ +1110 │ │ │ │ +1111 template │ │ │ │ +1112 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_1_1_1_3 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_h_o_s_t(_V_i_s_i_t_o_r<_H_a_s_h_S_e_t_<_K_e_y_> >& visitor) │ │ │ │ +1114 { │ │ │ │ +1115 visitor.visit(*this); │ │ │ │ +1116 } │ │ │ │ +1117 │ │ │ │ +1118 template │ │ │ │ +1119 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_1_1_2_0 bool _H_a_s_h_S_e_t_<_K_e_y_>_:_:_h_a_s(const Key& key) const │ │ │ │ +1121 { │ │ │ │ +1122 return (find(key) != end()); │ │ │ │ +1123 } │ │ │ │ +1124 │ │ │ │ +1125 template │ │ │ │ +1126 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_1_1_2_7 bool _H_a_s_h_S_e_t_<_K_e_y_>_:_:_i_s_E_m_p_t_y() const │ │ │ │ +1128 { │ │ │ │ +1129 return (size_ == 0); │ │ │ │ +1130 } │ │ │ │ +1131 │ │ │ │ +1132 template │ │ │ │ +_1_1_3_3 bool _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _=_=_ (const _H_a_s_h_S_e_t& hash_set) const │ │ │ │ +1134 { │ │ │ │ +1135 if (size_ != hash_set.size_) │ │ │ │ +1136 { │ │ │ │ +1137 return false; │ │ │ │ +1138 } │ │ │ │ +1139 │ │ │ │ +1140 _C_o_n_s_t_I_t_e_r_a_t_o_r it1 = begin(); │ │ │ │ +1141 _C_o_n_s_t_I_t_e_r_a_t_o_r it2 = hash_set._b_e_g_i_n(); │ │ │ │ +1142 while (it1 != end()) │ │ │ │ +1143 { │ │ │ │ +1144 if (*it1 != *it2) │ │ │ │ +1145 { │ │ │ │ +1146 return false; │ │ │ │ +1147 } │ │ │ │ +1148 it1++; │ │ │ │ +1149 it2++; │ │ │ │ +1150 } │ │ │ │ +1151 return true; │ │ │ │ +1152 } │ │ │ │ +1153 │ │ │ │ +1154 template │ │ │ │ +1155 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_1_1_5_6 bool _H_a_s_h_S_e_t_<_K_e_y_>_:_:_o_p_e_r_a_t_o_r_ _!_=_ (const _H_a_s_h_S_e_t& hash_set) const │ │ │ │ +1157 { │ │ │ │ +1158 return !(*this == hash_set); │ │ │ │ +1159 } │ │ │ │ +1160 │ │ │ │ +1161 template │ │ │ │ +_1_1_6_2 bool _H_a_s_h_S_e_t_<_K_e_y_>_:_:_i_s_V_a_l_i_d() const │ │ │ │ +1163 { │ │ │ │ +1164 _S_i_z_e size = 0; │ │ │ │ +1165 _N_o_d_e* node = 0; │ │ │ │ +1166 │ │ │ │ +1167 for (_P_o_s_i_t_i_o_n bucket = 0; bucket < (_P_o_s_i_t_i_o_n)bucket_.size(); ++bucket) │ │ │ │ +1168 { │ │ │ │ +1169 for (node = bucket_[bucket]; node != 0; node = node->_n_e_x_t) │ │ │ │ +1170 { │ │ │ │ +1171 ++size; │ │ │ │ +1172 │ │ │ │ +1173 if (node->_n_e_x_t == 0) │ │ │ │ +1174 { │ │ │ │ +1175 break; │ │ │ │ +1176 } │ │ │ │ +1177 } │ │ │ │ +1178 } │ │ │ │ +1179 │ │ │ │ +1180 return (size_ == size); │ │ │ │ +1181 } │ │ │ │ +1182 │ │ │ │ +1183 template │ │ │ │ +_1_1_8_4 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_d_u_m_p(std::ostream& s, _S_i_z_e depth) const │ │ │ │ +1185 { │ │ │ │ +1186 _B_A_L_L___D_U_M_P___S_T_R_E_A_M___P_R_E_F_I_X(s); │ │ │ │ +1187 │ │ │ │ +1188 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ +1189 │ │ │ │ +1190 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ +1191 s << " size: " << getSize() << std::endl; │ │ │ │ +1192 │ │ │ │ +1193 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ +1194 s << " # buckets: " << getBucketSize() << std::endl; │ │ │ │ +1195 │ │ │ │ +1196 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ +1197 s << " capacity: " << getCapacity() << std::endl; │ │ │ │ +1198 │ │ │ │ +1199 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ +1200 s << " load factor: " << (_f_l_o_a_t)size_ / (float)bucket_.size() << std:: │ │ │ │ +endl; │ │ │ │ +1201 │ │ │ │ +1202 for (_P_o_s_i_t_i_o_n bucket = 0; bucket < (_P_o_s_i_t_i_o_n)bucket_.size(); ++bucket) │ │ │ │ +1203 { │ │ │ │ +1204 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ +1205 s << " bucket " << bucket << ": "; │ │ │ │ +1206 for (_N_o_d_e* ptr = bucket_[bucket]; ptr != 0; ptr = ptr->_n_e_x_t) │ │ │ │ +1207 { │ │ │ │ +1208 s << "(" << (void*)ptr << ") "; │ │ │ │ +1209 } │ │ │ │ +1210 s << "(0)" << std::endl; │ │ │ │ +1211 } │ │ │ │ +1212 │ │ │ │ +1213 _B_A_L_L___D_U_M_P___S_T_R_E_A_M___S_U_F_F_I_X(s); │ │ │ │ +1214 } │ │ │ │ +1215 │ │ │ │ +1216 template │ │ │ │ +_1_2_1_7 bool _H_a_s_h_S_e_t_<_K_e_y_>_:_:_a_p_p_l_y(_U_n_a_r_y_P_r_o_c_e_s_s_o_r_<_V_a_l_u_e_T_y_p_e_>& processor) │ │ │ │ +1218 { │ │ │ │ +1219 if (processor._s_t_a_r_t() == false) │ │ │ │ +1220 { │ │ │ │ +1221 return false; │ │ │ │ +1222 } │ │ │ │ +1223 │ │ │ │ +1224 _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t result; │ │ │ │ +1225 │ │ │ │ +1226 _I_t_e_r_a_t_o_r it = begin(); │ │ │ │ +1227 while (it != end()) │ │ │ │ +1228 { │ │ │ │ +1229 result = processor(*it); │ │ │ │ +1230 if (result <= _P_r_o_c_e_s_s_o_r_:_:_B_R_E_A_K) │ │ │ │ +1231 { │ │ │ │ +1232 return (result == _P_r_o_c_e_s_s_o_r_:_:_B_R_E_A_K); │ │ │ │ +1233 } │ │ │ │ +1234 it++; │ │ │ │ +1235 } │ │ │ │ +1236 │ │ │ │ +1237 return processor._f_i_n_i_s_h(); │ │ │ │ +1238 } │ │ │ │ +1239 │ │ │ │ +1240 template │ │ │ │ +1241 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_1_2_4_2 _H_a_s_h_I_n_d_e_x _H_a_s_h_S_e_t_<_K_e_y_>_:_:_h_a_s_h(const Key& key) const │ │ │ │ +1243 { │ │ │ │ +1244 return (_H_a_s_h_I_n_d_e_x)_H_a_s_h(key); │ │ │ │ +1245 } │ │ │ │ +1246 │ │ │ │ +1247 template │ │ │ │ +1248 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_1_2_4_9 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_r_e_h_a_s_h() │ │ │ │ +1250 { │ │ │ │ +1251 capacity_ = (_S_i_z_e)_g_e_t_N_e_x_t_P_r_i_m_e((_S_i_z_e)bucket_.size() << 1); │ │ │ │ +1252 } │ │ │ │ +1253 │ │ │ │ +1254 template │ │ │ │ +1255 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_d_e_l_e_t_e_B_u_c_k_e_t_s__() │ │ │ │ +1256 { │ │ │ │ +1257 _S_i_z_e i = 0; │ │ │ │ +1258 Node* node = 0; │ │ │ │ +1259 Node* next_node = 0; │ │ │ │ +1260 for (i = 0; i < bucket_.size(); i++) │ │ │ │ +1261 { │ │ │ │ +1262 node = bucket_[i]; │ │ │ │ +1263 while (node != 0) │ │ │ │ +1264 { │ │ │ │ +1265 next_node = node->next; │ │ │ │ +1266 delete node; │ │ │ │ +1267 node = next_node; │ │ │ │ +1268 } │ │ │ │ +1269 bucket_[i] = 0; │ │ │ │ +1270 } │ │ │ │ +1271 } │ │ │ │ +1272 │ │ │ │ +1273 template │ │ │ │ +1274 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_1_2_7_5 typename _H_a_s_h_S_e_t_<_K_e_y_>_:_:_N_o_d_e* _H_a_s_h_S_e_t_<_K_e_y_>_:_:_n_e_w_N_o_d_e__ │ │ │ │ +1276 (const _V_a_l_u_e_T_y_p_e& value, typename _H_a_s_h_S_e_t_<_K_e_y_>_:_:_N_o_d_e* next) const │ │ │ │ +1277 { │ │ │ │ +1278 return new _N_o_d_e(value, next); │ │ │ │ +1279 } │ │ │ │ +1280 │ │ │ │ +1281 template │ │ │ │ +1282 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_1_2_8_3 void _H_a_s_h_S_e_t_<_K_e_y_>_:_:_d_e_l_e_t_e_N_o_d_e__(typename _H_a_s_h_S_e_t_<_K_e_y_>_:_:_N_o_d_e* node) const │ │ │ │ +1284 { │ │ │ │ +1285 delete node; │ │ │ │ +1286 } │ │ │ │ +1287 │ │ │ │ +1288 template │ │ │ │ +1289 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +_1_2_9_0 bool _H_a_s_h_S_e_t_<_K_e_y_>_:_:_n_e_e_d_R_e_h_a_s_h_i_n_g__() const │ │ │ │ +1291 { │ │ │ │ +1292 return (size_ >= capacity_); │ │ │ │ +1293 } │ │ │ │ +1294 │ │ │ │ +1295 template │ │ │ │ +1296 _B_A_L_L___I_N_L_I_N_E │ │ │ │ +1297 _H_a_s_h_I_n_d_e_x _H_a_s_h_S_e_t_<_K_e_y_>_:_:_h_a_s_h_B_u_c_k_e_t__(const Key& key) const │ │ │ │ +1298 { │ │ │ │ +1299 return (_P_o_s_i_t_i_o_n)((_H_a_s_h_I_n_d_e_x)hash(key) % (_H_a_s_h_I_n_d_e_x)bucket_.size()); │ │ │ │ +1300 } │ │ │ │ +1301 │ │ │ │ +1302 template │ │ │ │ +1303 void HashSet::rehash_() │ │ │ │ +1304 { │ │ │ │ +1305 // calculate the new number of buckets (in capacity_) │ │ │ │ +1306 rehash(); │ │ │ │ +1307 │ │ │ │ +1308 // save the old contents │ │ │ │ +1309 vector old_buckets(bucket_); │ │ │ │ +1310 │ │ │ │ +1311 // resize the bucket vector and initialize it with zero │ │ │ │ +1312 bucket_.clear(); │ │ │ │ +1313 bucket_.resize(capacity_); │ │ │ │ +1314 _P_o_s_i_t_i_o_n i; │ │ │ │ +1315 for (i = 0; i < capacity_; i++) │ │ │ │ +1316 { │ │ │ │ +1317 bucket_[i] = 0; │ │ │ │ +1318 } │ │ │ │ +1319 │ │ │ │ +1320 // rehash the old contents into the new buckets │ │ │ │ +1321 Node* node; │ │ │ │ +1322 Node* next_node; │ │ │ │ +1323 for (_P_o_s_i_t_i_o_n i = 0; i < (_P_o_s_i_t_i_o_n)old_buckets.size(); ++i) │ │ │ │ +1324 { │ │ │ │ +1325 for (node = old_buckets[i]; node != 0; node = next_node) │ │ │ │ +1326 { │ │ │ │ +1327 next_node = node->next; │ │ │ │ +1328 _P_o_s_i_t_i_o_n new_bucket = hashBucket_(node->value); │ │ │ │ +1329 node->next = bucket_[new_bucket]; │ │ │ │ +1330 bucket_[new_bucket] = node; │ │ │ │ +1331 } │ │ │ │ +1332 } │ │ │ │ +1333 } │ │ │ │ +1334} // namespace BALL │ │ │ │ +1335 │ │ │ │ +1336#endif // BALL_DATATYPE_HASHSET_H │ │ │ │ _c_o_m_m_o_n_._h │ │ │ │ -_b_a_s_e_F_u_n_c_t_o_r_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h │ │ │ │ +_v_i_s_i_t_o_r_._h │ │ │ │ +_p_r_o_c_e_s_s_o_r_._h │ │ │ │ +_B_A_L_L___D_U_M_P___S_T_R_E_A_M___P_R_E_F_I_X │ │ │ │ +#define BALL_DUMP_STREAM_PREFIX(os) │ │ │ │ +DDeeffiinniittiioonn _m_a_c_r_o_s_._h_:_3_9_1 │ │ │ │ +_B_A_L_L___D_U_M_P___S_T_R_E_A_M___S_U_F_F_I_X │ │ │ │ +#define BALL_DUMP_STREAM_SUFFIX(os) │ │ │ │ +DDeeffiinniittiioonn _m_a_c_r_o_s_._h_:_3_9_5 │ │ │ │ +_B_A_L_L___D_U_M_P___D_E_P_T_H │ │ │ │ +#define BALL_DUMP_DEPTH(os, depth) │ │ │ │ +DDeeffiinniittiioonn _m_a_c_r_o_s_._h_:_3_9_0 │ │ │ │ +_h_a_s_h_._h │ │ │ │ +_B_A_L_L___I_N_L_I_N_E │ │ │ │ +#define BALL_INLINE │ │ │ │ +DDeeffiinniittiioonn _d_e_b_u_g_._h_:_1_5 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ -DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_2_6 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_F_u_n_c_t_o_r │ │ │ │ -DDeeffiinniittiioonn _b_a_s_e_F_u_n_c_t_o_r_._h_:_6_5 │ │ │ │ -_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r_:_:_C_O_N_T_I_N_U_E │ │ │ │ -@ CONTINUE │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_I_n_d_e_x │ │ │ │ +BALL_SIZE_TYPE HashIndex │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_1_3_1 │ │ │ │ +_B_A_L_L_:_:_I_N_V_A_L_I_D___P_o_s_i_t_i_o_n │ │ │ │ +static const Position INVALID_Position │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_2_4_3 │ │ │ │ +_B_A_L_L_:_:_S_i_z_e │ │ │ │ +BALL_SIZE_TYPE Size │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_1_1_4 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h │ │ │ │ +HashIndex Hash(const T &key) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_._h_:_4_7 │ │ │ │ +_B_A_L_L_:_:_P_o_s_i_t_i_o_n │ │ │ │ +BALL_SIZE_TYPE Position │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_1_4_0 │ │ │ │ +_B_A_L_L_:_:_g_e_t_N_e_x_t_P_r_i_m_e │ │ │ │ +BALL_EXPORT HashIndex getNextPrime(HashIndex l) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_6_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +GeneralException() │ │ │ │ +Default constructor. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_I_t_e_r_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_7_0 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_c_o_m_p_a_t_i_b_l_e_I_t_e_r_a_t_o_r_s │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_8_1 │ │ │ │ +_B_A_L_L_:_:_B_a_s_e_I_t_e_r_a_t_o_r_:_:_g_e_t_T_r_a_i_t_s │ │ │ │ +BALL_INLINE const Traits & getTraits() const │ │ │ │ +Get a constant reference to the traits of this iterator. │ │ │ │ +DDeeffiinniittiioonn _b_a_s_e_I_t_e_r_a_t_o_r_._h_:_1_3_0 │ │ │ │ +_B_A_L_L_:_:_F_o_r_w_a_r_d_I_t_e_r_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h_:_1_9_9 │ │ │ │ +_B_A_L_L_:_:_F_o_r_w_a_r_d_I_t_e_r_a_t_o_r_:_:_b_e_g_i_n │ │ │ │ +static ForwardIterator begin(const Container &container) │ │ │ │ +DDeeffiinniittiioonn _f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h_:_3_0_7 │ │ │ │ +_B_A_L_L_:_:_F_o_r_w_a_r_d_I_t_e_r_a_t_o_r_:_:_e_n_d │ │ │ │ +static ForwardIterator end(const Container &container) │ │ │ │ +DDeeffiinniittiioonn _f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h_:_3_1_7 │ │ │ │ +_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r_:_:_B_R_E_A_K │ │ │ │ +@ BREAK │ │ │ │ +DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_4_7 │ │ │ │ _B_A_L_L_:_:_P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t │ │ │ │ int Result │ │ │ │ DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_3_6 │ │ │ │ _B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_6_0 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -UnaryProcessor(const UnaryProcessor &) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_7_6 │ │ │ │ _B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_s_t_a_r_t │ │ │ │ virtual bool start() │ │ │ │ DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_9_2 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_~_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -virtual ~UnaryProcessor() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_8_2 │ │ │ │ _B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_f_i_n_i_s_h │ │ │ │ virtual bool finish() │ │ │ │ DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_o_p_e_r_a_t_o_r_(_) │ │ │ │ -virtual Processor::Result operator()(T &) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_0_6 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_2_0 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_f_i_n_i_s_h │ │ │ │ -virtual bool finish() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_3_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_o_p_e_r_a_t_o_r_(_) │ │ │ │ -virtual Processor::Result operator()(const T &) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_3_8 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_s_t_a_r_t │ │ │ │ -virtual bool start() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_2_8 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_4_9 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_~_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -virtual ~BinaryProcessor() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_7_2 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_f_i_n_i_s_h │ │ │ │ -virtual bool finish() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_9_0 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_o_p_e_r_a_t_o_r_(_) │ │ │ │ -virtual Processor::Result operator()(T1 &, T2 &) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_9_7 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -BinaryProcessor(const BinaryProcessor &) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_6_6 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_s_t_a_r_t │ │ │ │ -virtual bool start() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_1_8_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_2_0_7 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_f_i_n_i_s_h │ │ │ │ -virtual bool finish() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_2_3_5 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_o_p_e_r_a_t_o_r_(_) │ │ │ │ -virtual Processor::Result operator()(const T1 &, const T2 &) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_2_4_2 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_s_t_a_r_t │ │ │ │ -virtual bool start() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_2_2_8 │ │ │ │ -_g_l_o_b_a_l_._h │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_V_i_s_i_t_o_r │ │ │ │ +DDeeffiinniittiioonn _v_i_s_i_t_o_r_._h_:_2_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_4_6 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r │ │ │ │ +ForwardIterator< HashSet< Key >, ValueType, PointerType, IteratorTraits > │ │ │ │ +Iterator │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_8_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_h_a_s_h │ │ │ │ +virtual HashIndex hash(const Key &key) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_2_4_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_s_i_z_e │ │ │ │ +Size size() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_6_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_e_r_a_s_e │ │ │ │ +void erase(Iterator f, Iterator l) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_9_9_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_p_o_i_n_t_e_r │ │ │ │ +Key * pointer │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_9_5 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_c_o_n_s_t___r_e_f_e_r_e_n_c_e │ │ │ │ +const Key & const_reference │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_3_0_1 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_s_i_z_e___t_y_p_e │ │ │ │ +Size size_type │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_3_0_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_s_e_t │ │ │ │ +void set(const HashSet &hash_set) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_3_1 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_f_i_n_d │ │ │ │ +ConstIterator find(const Key &key) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_8_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_i_s_V_a_l_i_d │ │ │ │ +bool isValid() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_1_6_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_i_s_E_m_p_t_y │ │ │ │ +bool isEmpty() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_1_2_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_&_= │ │ │ │ +const HashSet & operator&=(const HashSet &rhs) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_7_1_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_!_= │ │ │ │ +bool operator!=(const HashSet &hash_set) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_1_5_6 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_g_e_t │ │ │ │ +void get(HashSet &hash_set) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_9_6 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_n_e_w_N_o_d_e__ │ │ │ │ +virtual Node * newNode_(const ValueType &value, Node *next) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_2_7_6 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_c_o_n_s_t___i_t_e_r_a_t_o_r │ │ │ │ +ConstIterator const_iterator │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_8_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_- │ │ │ │ +HashSet operator-(const HashSet &rhs) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_7_7_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_H_a_s_h_S_e_t │ │ │ │ +HashSet(const HashSet &hash_set) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_1_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_e_n_d │ │ │ │ +ConstIterator end() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_5_5_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_b_e_g_i_n │ │ │ │ +Iterator begin() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_5_3_6 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_i_n_s_e_r_t │ │ │ │ +std::pair< Iterator, bool > insert(const ValueType &item) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_9_6 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_+ │ │ │ │ +HashSet operator+(const HashSet &rhs) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_3_4 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_b_e_g_i_n │ │ │ │ +ConstIterator begin() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_5_5_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_H_a_s_h_S_e_t │ │ │ │ +HashSet(Size initial_capacity=INITIAL_CAPACITY, Size │ │ │ │ +number_of_buckets=INITIAL_NUMBER_OF_BUCKETS) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_0_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_+_= │ │ │ │ +const HashSet & operator+=(const HashSet &rhs) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_7_5_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_h_a_s │ │ │ │ +bool has(const Key &key) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_1_2_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_i_n_s_e_r_t │ │ │ │ +Iterator insert(Iterator pos, const ValueType &item) │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_r_e_f_e_r_e_n_c_e │ │ │ │ +Key & reference │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_9_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_d_e_l_e_t_e_N_o_d_e__ │ │ │ │ +virtual void deleteNode_(Node *node) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_2_8_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_d_u_m_p │ │ │ │ +virtual void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_1_8_4 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n │ │ │ │ +Node * IteratorPosition │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_r_e_h_a_s_h │ │ │ │ +virtual void rehash() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_2_4_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ +const HashSet & operator=(const HashSet &rhs) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_8_8 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_g_e_t_S_i_z_e │ │ │ │ +Size getSize() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_5_5 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_v_a_l_u_e___t_y_p_e │ │ │ │ +Key value_type │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_9_1 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_V_a_l_u_e_T_y_p_e │ │ │ │ +Key ValueType │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_5_1 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_~_H_a_s_h_S_e_t │ │ │ │ +virtual ~HashSet() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_3_2_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_| │ │ │ │ +HashSet operator|(const HashSet &rhs) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_2_4 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_e_n_d │ │ │ │ +Iterator end() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_5_4_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_|_= │ │ │ │ +const HashSet & operator|=(const HashSet &rhs) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_7_3_8 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_-_= │ │ │ │ +const HashSet & operator-=(const HashSet &rhs) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_7_9_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_& │ │ │ │ +HashSet operator&(const HashSet &rhs) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_7_5_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_d_e_s_t_r_o_y │ │ │ │ +void destroy() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_8_1 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_o_p_e_r_a_t_o_r_=_= │ │ │ │ +bool operator==(const HashSet &hash_set) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_1_3_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_g_e_t_B_u_c_k_e_t_S_i_z_e │ │ │ │ +Size getBucketSize() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_4_1 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_h_o_s_t │ │ │ │ +virtual void host(Visitor< HashSet< Key > > &visitor) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_1_1_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_N_I_T_I_A_L___N_U_M_B_E_R___O_F___B_U_C_K_E_T_S │ │ │ │ +@ INITIAL_NUMBER_OF_BUCKETS │ │ │ │ +Initial number of buckets. │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_5_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_N_I_T_I_A_L___C_A_P_A_C_I_T_Y │ │ │ │ +@ INITIAL_CAPACITY │ │ │ │ +Initial capacity of the hash set. │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_4_8 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_d_i_f_f_e_r_e_n_c_e___t_y_p_e │ │ │ │ +Index difference_type │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_3_0_5 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_k_e_y___t_y_p_e │ │ │ │ +Key key_type │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_9_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_a_p_p_l_y │ │ │ │ +bool apply(UnaryProcessor< ValueType > &processor) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_2_1_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_i_t_e_r_a_t_o_r │ │ │ │ +Iterator iterator │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_8_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_c_l_e_a_r │ │ │ │ +virtual void clear() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_6_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_K_e_y_T_y_p_e │ │ │ │ +Key KeyType │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_5_5 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ +ConstForwardIterator< HashSet< Key >, ValueType, PointerType, IteratorTraits > │ │ │ │ +ConstIterator │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_8_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_e_r_a_s_e │ │ │ │ +Size erase(const KeyType &key) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_9_2_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_s_w_a_p │ │ │ │ +void swap(HashSet &hash_set) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_7_0_4 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_e_r_a_s_e │ │ │ │ +void erase(Iterator pos) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_9_6_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_P_o_i_n_t_e_r_T_y_p_e │ │ │ │ +Key * PointerType │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_5_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_g_e_t_C_a_p_a_c_i_t_y │ │ │ │ +Size getCapacity() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_4_8 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_c_o_n_s_t___p_o_i_n_t_e_r │ │ │ │ +const Key * const_pointer │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_9_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_n_e_e_d_R_e_h_a_s_h_i_n_g__ │ │ │ │ +virtual bool needRehashing_() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_2_9_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_f_i_n_d │ │ │ │ +Iterator find(const Key &key) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_6_8 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_N_o_d_e │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_N_o_d_e_:_:_n_e_x_t │ │ │ │ +Node * next │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_4 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_N_o_d_e_:_:_v_a_l_u_e │ │ │ │ +ValueType value │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_6_5 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_7_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_C_o_n_t_a_i_n_e_r │ │ │ │ +const HashSet * getContainer() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_1_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_D_a_t_a │ │ │ │ +const ValueType & getData() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_0_8 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_V_a_l_i_d │ │ │ │ +bool isValid() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_4_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ +IteratorTraits & operator=(const IteratorTraits &traits) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_0_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_p_o_s_i_t_i_o_n__ │ │ │ │ +IteratorPosition position_ │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_3_6 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_b_o_u_n_d__ │ │ │ │ +HashSet * bound_ │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_3_5 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +IteratorTraits(const IteratorTraits &traits) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_9_6 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_t_o_B_e_g_i_n │ │ │ │ +void toBegin() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_6_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_n_v_a_l_i_d_a_t_e │ │ │ │ +void invalidate() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_5_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_o_p_e_r_a_t_o_r_=_= │ │ │ │ +bool operator==(const IteratorTraits &traits) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_3_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_D_a_t_a │ │ │ │ +ValueType & getData() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_0_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_B_e_g_i_n │ │ │ │ +bool isBegin() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_7_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_P_o_s_i_t_i_o_n │ │ │ │ +IteratorPosition & getPosition() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_2_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +IteratorTraits() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_o_p_e_r_a_t_o_r_!_= │ │ │ │ +bool operator!=(const IteratorTraits &traits) const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_4_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +IteratorTraits(const HashSet &hash_set) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_8_9 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_b_u_c_k_e_t__ │ │ │ │ +Position bucket_ │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_3_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_P_o_s_i_t_i_o_n │ │ │ │ +const IteratorPosition & getPosition() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_3_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_C_o_n_t_a_i_n_e_r │ │ │ │ +HashSet * getContainer() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_1_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_f_o_r_w_a_r_d │ │ │ │ +void forward() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_1_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_t_o_E_n_d │ │ │ │ +void toEnd() │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_9_3 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_S_i_n_g_u_l_a_r │ │ │ │ +bool isSingular() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_2_2 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_E_n_d │ │ │ │ +bool isEnd() const │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_1_9_8 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_l_l_e_g_a_l_K_e_y │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_6_5 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_S_e_t_:_:_I_l_l_e_g_a_l_K_e_y_:_:_I_l_l_e_g_a_l_K_e_y │ │ │ │ +IllegalKey(const char *file, int line) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_2_6_7 │ │ │ │ +_B_A_L_L_:_:_R_S_E_d_g_e │ │ │ │ +DDeeffiinniittiioonn _R_S_E_d_g_e_._h_:_4_9 │ │ │ │ +_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_f_l_o_a_t │ │ │ │ +_p_r_e_d_i_c_a_t_e_._h │ │ │ │ +_f_o_r_E_a_c_h_._h │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d2b/a03394.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::Bit::IllegalOperation Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/DATATYPE/bitVector.h>

    │ │ │ +

    #include <BALL/DATATYPE/bitVector.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::Bit::IllegalOperation:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::Exception::GeneralException │ │ │ @@ -138,15 +138,15 @@ │ │ │   │ │ │ std::string message_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Exception thrown if a file could not be processed right.

    │ │ │ │ │ │ -

    Definition at line 52 of file bitVector.h.

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    Definition at line 52 of file bitVector.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ IllegalOperation()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d31/a03558.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::Options Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/DATATYPE/options.h>

    │ │ │ +

    #include <BALL/DATATYPE/options.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::Options:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::StringHashMap< String > │ │ │ @@ -268,15 +268,15 @@ │ │ │
    │ │ │ │ │ │
    typedef Base::const_iterator ConstIterator
     
    │ │ │

    Detailed Description

    │ │ │

    Options class. This object is intended to store options for complex method calls. These options are stored as key/value pairs of String .

    Using this datastructure, options for force fields ( ForceField ), finit difference Poisson Boltzmann calculations ( FDPB ), or the results of calculations can be given, retrieved, stored into a file and retrieved from a file. This simplifies the handling of such complex parameter sets.
    │ │ │
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    Definition at line 46 of file options.h.

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    Definition at line 46 of file options.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ Options() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -1343,15 +1343,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
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    Definition at line 385 of file options.h.

    │ │ │ +

    Definition at line 385 of file options.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ MAX_ENTRY_LENGTH

    │ │ │ │ │ │
    │ │ │ @@ -1368,15 +1368,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │

    Maximum length for each entry (key + value): 1024 byte. @memo

    │ │ │ │ │ │ -

    Definition at line 61 of file options.h.

    │ │ │ +

    Definition at line 61 of file options.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ name_

    │ │ │ │ │ │
    │ │ │ @@ -1392,15 +1392,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
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    Definition at line 384 of file options.h.

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    Definition at line 384 of file options.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ subcategories_

    │ │ │ │ │ │
    │ │ │ @@ -1416,15 +1416,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
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    Definition at line 386 of file options.h.

    │ │ │ +

    Definition at line 386 of file options.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d34/a03874.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Static Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::CommandlineParser Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/FORMAT/commandlineParser.h>

    │ │ │ +

    #include <BALL/FORMAT/commandlineParser.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -191,15 +191,15 @@ │ │ │

    Class for parsing parameters specified on the command line.
    │ │ │ Register the parameters and flags of your tool with registerParameter(), resp. registerFlag() and have the command-line parsed with parse(). After this, you can retrieve the values of all parameters with get().
    │ │ │ In addition to this, you can also register a tool-manual text, define restrictions on parameters and register file-formats that are supported for in- or output-files.
    │ │ │ If the parameter '-write_par somefilename.xml' is given to the program, an xml-based parameter-file will be automatically written, containing the specification the tool, all its parameters and all parameter values used on the commend-line.
    │ │ │ If the parameter '-par somefilename.xml' is used, such a file can be read, so that the parameter-values stored in it will be used. However, if, although this is not necessary, parameters (other than -par) are specified on the command-line, their values will automatically overload those stored in the xml-file.

    │ │ │

    The parameter '-env' allows to differentiate between command line ('cmdline') behaviour and special adaptions to workflow systems like galaxy or knime.

    │ │ │ │ │ │ -

    Definition at line 38 of file commandlineParser.h.

    │ │ │ +

    Definition at line 38 of file commandlineParser.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ CommandlineParser()

    │ │ │ │ │ │
    │ │ │
    │ │ │

    │ │ │ Public Member Functions

     CommandlineParser (String tool_name, String tool_description, String tool_version, String build_date, String category="")
     
    void setToolManual (const String &manual)
     
    │ │ │ @@ -1590,15 +1590,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ static
    │ │ │
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    Definition at line 47 of file commandlineParser.h.

    │ │ │ +

    Definition at line 47 of file commandlineParser.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ NOT_FOUND

    │ │ │ │ │ │
    │ │ │ @@ -1614,15 +1614,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
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    Definition at line 46 of file commandlineParser.h.

    │ │ │ +

    Definition at line 46 of file commandlineParser.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d35/a07306.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::TriangulatedSAS Class Reference
    Molecular Modeling » Molecular Structure » Molecular Surface Computation
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/STRUCTURE/triangulatedSAS.h>

    │ │ │ +

    #include <BALL/STRUCTURE/triangulatedSAS.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::TriangulatedSAS:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::TriangulatedSurface │ │ │ @@ -256,15 +256,15 @@ │ │ │   │ │ │ double density_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Generic TriangulatedSAS Class. <>

    │ │ │ │ │ │ -

    Definition at line 62 of file triangulatedSAS.h.

    │ │ │ +

    Definition at line 62 of file triangulatedSAS.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ TriangulatedSAS() [1/3]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -508,15 +508,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ friend
    │ │ │
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    Definition at line 72 of file triangulatedSAS.h.

    │ │ │ +

    Definition at line 72 of file triangulatedSAS.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ density_

    │ │ │ │ │ │ @@ -533,15 +533,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 148 of file triangulatedSAS.h.

    │ │ │ +

    Definition at line 148 of file triangulatedSAS.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ sas_

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    │ │ │ @@ -557,15 +557,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 146 of file triangulatedSAS.h.

    │ │ │ +

    Definition at line 146 of file triangulatedSAS.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d36/a01388.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: energyMinimizer.h File Reference │ │ │ +BALL: dockProblem.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,36 +65,44 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    energyMinimizer.h File Reference
    │ │ │ +
    dockProblem.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/DATATYPE/options.h>
    │ │ │ -#include <BALL/MOLMEC/COMMON/gradient.h>
    │ │ │ +
    #include <vector>
    │ │ │ +#include <string>
    │ │ │ +#include <BALL/MATHS/vector3.h>
    │ │ │ +#include <BALL/KERNEL/system.h>
    │ │ │ +#include <BALL/KERNEL/molecule.h>
    │ │ │ +#include <BALL/KERNEL/protein.h>
    │ │ │ +#include <BALL/DOCKING/GENETICDOCK/rotateBonds.h>
    │ │ │ +#include <BALL/DOCKING/GENETICDOCK/geneticAlgorithm.h>
    │ │ │ +#include <BALL/DOCKING/GENETICDOCK/evolutionaryDocking.h>
    │ │ │ +#include <BALL/DOCKING/GENETICDOCK/parameter.h>
    │ │ │ +#include <BALL/SCORING/COMMON/scoringFunction.h>
    │ │ │ +#include <BALL/MATHS/matrix44.h>
    │ │ │ +#include <BALL/MATHS/quaternion.h>
    │ │ │ +#include <BALL/DOCKING/COMMON/conformationSet.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::EnergyMinimizer
     
    struct  BALL::EnergyMinimizer::Option
     
    struct  BALL::EnergyMinimizer::Default
    class  BALL::DockProblem
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ ├── html2text {} │ │ │ │ @@ -1,25 +1,33 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _M_O_L_M_E_C │ │ │ │ - * _M_I_N_I_M_I_Z_A_T_I_O_N │ │ │ │ + * _D_O_C_K_I_N_G │ │ │ │ + * _G_E_N_E_T_I_C_D_O_C_K │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -energyMinimizer.h File Reference │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_g_r_a_d_i_e_n_t_._h> │ │ │ │ +dockProblem.h File Reference │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_m_o_l_e_c_u_l_e_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_o_t_e_i_n_._h> │ │ │ │ +#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_r_o_t_a_t_e_B_o_n_d_s_._h> │ │ │ │ +#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_g_e_n_e_t_i_c_A_l_g_o_r_i_t_h_m_._h> │ │ │ │ +#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_e_v_o_l_u_t_i_o_n_a_r_y_D_o_c_k_i_n_g_._h> │ │ │ │ +#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_p_a_r_a_m_e_t_e_r_._h> │ │ │ │ +#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_M_O_N_/_s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_m_a_t_r_i_x_4_4_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_q_u_a_t_e_r_n_i_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_C_O_M_M_O_N_/_c_o_n_f_o_r_m_a_t_i_o_n_S_e_t_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ - class   _B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t │ │ │ │ +class   _B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d36/a01388_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: energyMinimizer.h Source File │ │ │ +BALL: dockProblem.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,313 +70,164 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    energyMinimizer.h
    │ │ │ +
    dockProblem.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ -
    2// vi: set ts=2:
    │ │ │ -
    3//
    │ │ │ -
    4// $Id: energyMinimizer.h,v 1.44.20.3 2007/08/07 09:12:33 aleru Exp $
    │ │ │ -
    5//
    │ │ │ -
    6
    │ │ │ -
    7// Energy Minimizer: A class for minimizing the energy of molecular systems
    │ │ │ +Go to the documentation of this file.
    1// ----------------------------------------------------
    │ │ │ +
    2// $Maintainer: Marcel Schumann $
    │ │ │ +
    3// $Authors: Jan Fuhrmann, Marcel Schumann $
    │ │ │ +
    4// ----------------------------------------------------
    │ │ │ +
    5
    │ │ │ +
    6#ifndef BALL_DOCKING_GENETICDOCK_DOCKPROBLEM_H
    │ │ │ +
    7#define BALL_DOCKING_GENETICDOCK_DOCKPROBLEM_H
    │ │ │
    8
    │ │ │ -
    9#ifndef BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H
    │ │ │ -
    10#define BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H
    │ │ │ +
    9#include <vector>
    │ │ │ +
    10#include <string>
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ -
    13# include <BALL/DATATYPE/options.h>
    │ │ │ -
    14#endif
    │ │ │ -
    15
    │ │ │ -
    16#ifndef BALL_MOLMEC_COMMON_GRADIENT_H
    │ │ │ -
    17# include <BALL/MOLMEC/COMMON/gradient.h>
    │ │ │ -
    18#endif
    │ │ │ -
    19
    │ │ │ -
    20namespace BALL
    │ │ │ -
    21{
    │ │ │ -
    22 class ForceField;
    │ │ │ -
    23 class SnapShotManager;
    │ │ │ -
    24
    │ │ │ -
    │ │ │ -
    29 class BALL_EXPORT EnergyMinimizer
    │ │ │ -
    30 {
    │ │ │ -
    31 public:
    │ │ │ -
    32
    │ │ │ -
    36
    │ │ │ -
    │ │ │ -
    39 struct BALL_EXPORT Option
    │ │ │ -
    40 {
    │ │ │ -
    43 static const char* MAXIMAL_NUMBER_OF_ITERATIONS;
    │ │ │ -
    44
    │ │ │ -
    47 static const char* ENERGY_OUTPUT_FREQUENCY;
    │ │ │ -
    48
    │ │ │ -
    51 static const char* SNAPSHOT_FREQUENCY;
    │ │ │ -
    52
    │ │ │ -
    55 static const char* NUMBER_OF_ITERATION;
    │ │ │ -
    56
    │ │ │ -
    59 static const char* ENERGY_DIFFERENCE_BOUND;
    │ │ │ -
    60
    │ │ │ -
    64 static const char* MAX_SAME_ENERGY;
    │ │ │ -
    65
    │ │ │ -
    69 static const char* MAX_GRADIENT;
    │ │ │ -
    70
    │ │ │ -
    73 static const char* MAXIMUM_DISPLACEMENT;
    │ │ │ -
    74 };
    │ │ │ -
    │ │ │ -
    75
    │ │ │ -
    │ │ │ -
    76 struct BALL_EXPORT Default
    │ │ │ -
    77 {
    │ │ │ -
    80 static Size MAXIMAL_NUMBER_OF_ITERATIONS;
    │ │ │ -
    81
    │ │ │ -
    84 static Size ENERGY_OUTPUT_FREQUENCY;
    │ │ │ -
    85
    │ │ │ -
    88 static Size SNAPSHOT_FREQUENCY;
    │ │ │ -
    89
    │ │ │ -
    92 static Size NUMBER_OF_ITERATION;
    │ │ │ -
    93
    │ │ │ -
    97 static float ENERGY_DIFFERENCE_BOUND;
    │ │ │ -
    98
    │ │ │ -
    103 static Size MAX_SAME_ENERGY;
    │ │ │ -
    104
    │ │ │ -
    108 static float MAX_GRADIENT;
    │ │ │ -
    109
    │ │ │ -
    112 static float MAXIMUM_DISPLACEMENT;
    │ │ │ -
    113 };
    │ │ │ -
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    114
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    116
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    119
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    120 BALL_CREATE(EnergyMinimizer)
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    121
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    122
    │ │ │ -
    124 EnergyMinimizer();
    │ │ │ -
    125
    │ │ │ -
    128 EnergyMinimizer(ForceField& force_field);
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    129
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    132 EnergyMinimizer(ForceField& force_field, const Options& options);
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    133
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    136 EnergyMinimizer(const EnergyMinimizer& energy_minimizer);
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    137
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    140 virtual ~EnergyMinimizer();
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    141
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    143
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    146
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    149 const EnergyMinimizer& operator=(const EnergyMinimizer& energy_minimizer);
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    150
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    152
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    155 bool operator == (const EnergyMinimizer& energy_minimizer) ;
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    156
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    160
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    163 bool isValid() const;
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    164
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    166
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    169
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    172 bool setup(ForceField& force_field);
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    173
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    176 bool setup(ForceField& force_field, SnapShotManager *ssm);
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    177
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    180 bool setup(ForceField& force_field,
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    181 SnapShotManager *ssm, const Options& options);
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    182
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    185 bool setup(ForceField& force_field, const Options& options);
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    186
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    189 virtual bool specificSetup();
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    190
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    192
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    195
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    208 virtual bool isConverged() const;
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    209
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    218 virtual double findStep();
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    219
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    224 virtual void updateDirection();
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    225
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    230 virtual double updateEnergy();
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    231
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    236 virtual void updateForces();
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    237
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    243 void storeGradientEnergy();
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    244
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    252 virtual void printEnergy() const;
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    253
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    262 virtual void takeSnapShot() const;
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    263
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    282 virtual void finishIteration();
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    283
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    286 Size getNumberOfIterations() const;
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    287
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    290 Gradient& getDirection();
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    291
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    294 Gradient& getGradient();
    │ │ │ -
    295
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    298 Gradient& getInitialGradient();
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    299
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    302 double getEnergy() const;
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    303
    │ │ │ -
    306 double& getEnergy();
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    307
    │ │ │ -
    310 double getInitialEnergy() const;
    │ │ │ -
    311
    │ │ │ -
    314 double& getInitialEnergy();
    │ │ │ -
    315
    │ │ │ -
    318 void setNumberOfIterations(Size number_of_iterations);
    │ │ │ -
    319
    │ │ │ -
    322 Size getMaxNumberOfIterations() const;
    │ │ │ -
    323
    │ │ │ -
    326 void setMaxNumberOfIterations(Size number_of_iterations);
    │ │ │ -
    327
    │ │ │ -
    331 void setMaxSameEnergy(Size number);
    │ │ │ -
    332
    │ │ │ -
    336 Size getMaxSameEnergy() const;
    │ │ │ -
    337
    │ │ │ -
    340 void setEnergyOutputFrequency(Size energy_output_frequency);
    │ │ │ -
    341
    │ │ │ -
    344 Size getEnergyOutputFrequency() const;
    │ │ │ -
    345
    │ │ │ -
    348 void setEnergyDifferenceBound(float energy_difference_bound);
    │ │ │ -
    349
    │ │ │ -
    352 float getEnergyDifferenceBound() const;
    │ │ │ -
    353
    │ │ │ -
    357 void setMaxGradient(float max_gradient);
    │ │ │ -
    358
    │ │ │ -
    362 float getMaxGradient() const;
    │ │ │ -
    363
    │ │ │ -
    367 void setMaximumDisplacement(float maximum_displacement);
    │ │ │ -
    368
    │ │ │ -
    371 float getMaximumDisplacement() const;
    │ │ │ -
    372
    │ │ │ -
    375 void setSnapShotFrequency(Size snapshot_frequency);
    │ │ │ -
    376
    │ │ │ -
    379 Size getSnapShotFrequency() const;
    │ │ │ -
    380
    │ │ │ -
    383 ForceField* getForceField();
    │ │ │ -
    384
    │ │ │ -
    387 Size getForceUpdateCounter() const ;
    │ │ │ -
    388
    │ │ │ -
    391 Size getEnergyUpdateCounter() const ;
    │ │ │ -
    392
    │ │ │ -
    404 virtual bool minimize(Size steps = 0, bool resume = false);
    │ │ │ -
    405
    │ │ │ -
    408 void enableEnergyAbortCondition(bool state);
    │ │ │ -
    409
    │ │ │ -
    411 bool energyAbortConditionEnabled() const;
    │ │ │ -
    412
    │ │ │ -
    417 void setEnergyToAbort(float value);
    │ │ │ -
    418
    │ │ │ -
    420 float getEnergyToAbort() const;
    │ │ │ -
    421
    │ │ │ -
    425 bool wasAborted() const ;
    │ │ │ -
    426
    │ │ │ -
    428
    │ │ │ -
    431
    │ │ │ -
    434 Options options;
    │ │ │ -
    436
    │ │ │ -
    437 protected:
    │ │ │ -
    438
    │ │ │ -
    442
    │ │ │ -
    445 Gradient initial_grad_;
    │ │ │ -
    446
    │ │ │ -
    449 Gradient current_grad_;
    │ │ │ -
    450
    │ │ │ -
    453 double initial_energy_;
    │ │ │ -
    454
    │ │ │ -
    457 double current_energy_;
    │ │ │ -
    458
    │ │ │ -
    461 Gradient old_grad_;
    │ │ │ -
    462
    │ │ │ -
    465 double old_energy_;
    │ │ │ -
    466
    │ │ │ -
    469 Gradient direction_;
    │ │ │ -
    470
    │ │ │ -
    473 bool valid_;
    │ │ │ -
    474
    │ │ │ -
    477 SnapShotManager* snapshot_;
    │ │ │ -
    478
    │ │ │ -
    483 ForceField* force_field_;
    │ │ │ -
    484
    │ │ │ -
    487 Size number_of_iterations_;
    │ │ │ -
    488
    │ │ │ -
    491 Size maximal_number_of_iterations_;
    │ │ │ -
    492
    │ │ │ -
    495 Size energy_output_frequency_;
    │ │ │ -
    496
    │ │ │ -
    499 Size snapshot_frequency_;
    │ │ │ -
    500
    │ │ │ -
    504 double energy_difference_bound_;
    │ │ │ -
    505
    │ │ │ -
    508 double max_gradient_;
    │ │ │ -
    509
    │ │ │ -
    514 Size max_same_energy_;
    │ │ │ -
    515
    │ │ │ -
    518 Size same_energy_counter_;
    │ │ │ -
    519
    │ │ │ -
    522 float maximum_displacement_;
    │ │ │ -
    523
    │ │ │ -
    527 Size force_update_counter_;
    │ │ │ -
    528
    │ │ │ -
    532 Size energy_update_counter_;
    │ │ │ -
    533
    │ │ │ -
    537 float cutlo_;
    │ │ │ -
    538
    │ │ │ -
    542 double step_;
    │ │ │ -
    543
    │ │ │ -
    544 //_
    │ │ │ -
    545 bool abort_by_energy_enabled_;
    │ │ │ -
    546
    │ │ │ -
    547 //_
    │ │ │ -
    548 float abort_energy_;
    │ │ │ -
    549
    │ │ │ -
    550 //_
    │ │ │ -
    551 bool aborted_;
    │ │ │ -
    552
    │ │ │ -
    553 //_@}
    │ │ │ -
    554 };
    │ │ │ -
    │ │ │ -
    555
    │ │ │ -
    556} // namespace Ball
    │ │ │ -
    557
    │ │ │ -
    558#endif // BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::EnergyMinimizer::Option::MAXIMAL_NUMBER_OF_ITERATIONS
    static const char * MAXIMAL_NUMBER_OF_ITERATIONS
    Definition energyMinimizer.h:43
    │ │ │ -
    BALL::EnergyMinimizer::Option::ENERGY_OUTPUT_FREQUENCY
    static const char * ENERGY_OUTPUT_FREQUENCY
    Definition energyMinimizer.h:47
    │ │ │ -
    BALL::EnergyMinimizer::Option::SNAPSHOT_FREQUENCY
    static const char * SNAPSHOT_FREQUENCY
    Definition energyMinimizer.h:51
    │ │ │ -
    BALL::EnergyMinimizer::Option::MAX_GRADIENT
    static const char * MAX_GRADIENT
    Definition energyMinimizer.h:69
    │ │ │ -
    BALL::EnergyMinimizer::Option::MAX_SAME_ENERGY
    static const char * MAX_SAME_ENERGY
    Definition energyMinimizer.h:64
    │ │ │ -
    BALL::EnergyMinimizer::Option::MAXIMUM_DISPLACEMENT
    static const char * MAXIMUM_DISPLACEMENT
    Definition energyMinimizer.h:73
    │ │ │ -
    BALL::EnergyMinimizer::Option::ENERGY_DIFFERENCE_BOUND
    static const char * ENERGY_DIFFERENCE_BOUND
    Definition energyMinimizer.h:59
    │ │ │ -
    BALL::EnergyMinimizer::Option::NUMBER_OF_ITERATION
    static const char * NUMBER_OF_ITERATION
    Definition energyMinimizer.h:55
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    12#include <BALL/MATHS/vector3.h>
    │ │ │ +
    13#include <BALL/KERNEL/system.h>
    │ │ │ +
    14#include <BALL/KERNEL/molecule.h>
    │ │ │ +
    15#include <BALL/KERNEL/protein.h>
    │ │ │ +
    16#include <BALL/MATHS/vector3.h>
    │ │ │ +
    17
    │ │ │ +
    18#include <BALL/DOCKING/GENETICDOCK/rotateBonds.h>
    │ │ │ +
    19#include <BALL/DOCKING/GENETICDOCK/geneticAlgorithm.h>
    │ │ │ +
    20#include <BALL/DOCKING/GENETICDOCK/evolutionaryDocking.h>
    │ │ │ +
    21
    │ │ │ +
    22#include <BALL/DOCKING/GENETICDOCK/parameter.h>
    │ │ │ +
    23#include <BALL/SCORING/COMMON/scoringFunction.h>
    │ │ │ +
    24
    │ │ │ +
    25#include <BALL/MATHS/matrix44.h>
    │ │ │ +
    26#include <BALL/MATHS/quaternion.h>
    │ │ │ +
    27
    │ │ │ +
    28#ifndef BALL_DOCKING_COMMON_CONFORMATIONSET_H
    │ │ │ +
    29# include <BALL/DOCKING/COMMON/conformationSet.h>
    │ │ │ +
    30#endif // BALL_DOCKING_COMMON_CONFORMATIONSET_H
    │ │ │ +
    31
    │ │ │ +
    32namespace BALL
    │ │ │ +
    33{
    │ │ │ +
    34
    │ │ │ +
    │ │ │ +
    35 class BALL_EXPORT BALL_DEPRECATED DockProblem
    │ │ │ +
    36 {
    │ │ │ +
    37 public:
    │ │ │ +
    40 DockProblem();
    │ │ │ +
    41
    │ │ │ +
    44 DockProblem(AtomContainer& sys_lig, BALL::ScoringFunction* sf, EvolutionaryDocking* docker, bool post_dock_optimization);
    │ │ │ +
    45
    │ │ │ +
    46
    │ │ │ +
    49 virtual ~DockProblem();
    │ │ │ +
    50
    │ │ │ +
    51
    │ │ │ +
    52 virtual void setup(AtomContainer& sys_lig);
    │ │ │ +
    53
    │ │ │ +
    54
    │ │ │ +
    57 virtual double calculate();
    │ │ │ +
    58
    │ │ │ +
    62 void move();
    │ │ │ +
    63
    │ │ │ +
    66 bool redraw();
    │ │ │ +
    67
    │ │ │ +
    68 AtomContainer* getLigand();
    │ │ │ +
    69
    │ │ │ +
    70
    │ │ │ +
    71 void connectTo(GeneticAlgorithm* opt);
    │ │ │ +
    72
    │ │ │ +
    73
    │ │ │ +
    74 protected:
    │ │ │ +
    75
    │ │ │ +
    76 EvolutionaryDocking* docker_;
    │ │ │ +
    77
    │ │ │ +
    78 DoubleParameter double_parameter_;
    │ │ │ +
    79
    │ │ │ +
    80 QuaternionParameter quaternion_parameter_;
    │ │ │ +
    81
    │ │ │ +
    84 AtomContainer* ligand_, *draw_ligand_;
    │ │ │ +
    85
    │ │ │ +
    88 Vector3 t_origin_, t_extension_;
    │ │ │ +
    89
    │ │ │ +
    90 Vector3 binding_pocket_center_;
    │ │ │ +
    91
    │ │ │ +
    94 BALL::ScoringFunction* scoring_function_;
    │ │ │ +
    95
    │ │ │ +
    98 std::vector<Vector3 > ligand_positions_;
    │ │ │ +
    99
    │ │ │ +
    102 RotateBonds* rb_;
    │ │ │ +
    103
    │ │ │ +
    104
    │ │ │ +
    105
    │ │ │ +
    108 void restore();
    │ │ │ +
    109
    │ │ │ +
    112 Options opt_;
    │ │ │ +
    113
    │ │ │ +
    114 bool redraw_;
    │ │ │ +
    115
    │ │ │ +
    116 bool post_dock_optimization_;
    │ │ │ +
    117
    │ │ │ +
    118 };
    │ │ │ +
    │ │ │ +
    119}
    │ │ │ +
    120
    │ │ │ +
    121#endif /* BALL_DOCKING_GENETICDOCK_DOCKPROBLEM_H */
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::DockProblem::getLigand
    AtomContainer * getLigand()
    │ │ │ +
    BALL::DockProblem::rb_
    RotateBonds * rb_
    Definition dockProblem.h:102
    │ │ │ +
    BALL::DockProblem::double_parameter_
    DoubleParameter double_parameter_
    Definition dockProblem.h:78
    │ │ │ + │ │ │ +
    BALL::DockProblem::binding_pocket_center_
    Vector3 binding_pocket_center_
    Definition dockProblem.h:90
    │ │ │ + │ │ │ +
    BALL::DockProblem::setup
    virtual void setup(AtomContainer &sys_lig)
    │ │ │ + │ │ │ +
    BALL::DockProblem::~DockProblem
    virtual ~DockProblem()
    │ │ │ + │ │ │ + │ │ │ +
    BALL::DockProblem::DockProblem
    DockProblem(AtomContainer &sys_lig, BALL::ScoringFunction *sf, EvolutionaryDocking *docker, bool post_dock_optimization)
    │ │ │ +
    BALL::DockProblem::scoring_function_
    BALL::ScoringFunction * scoring_function_
    Definition dockProblem.h:94
    │ │ │ +
    BALL::DockProblem::ligand_positions_
    std::vector< Vector3 > ligand_positions_
    Definition dockProblem.h:98
    │ │ │ +
    BALL::DockProblem::quaternion_parameter_
    QuaternionParameter quaternion_parameter_
    Definition dockProblem.h:80
    │ │ │ + │ │ │ +
    BALL::DockProblem::calculate
    virtual double calculate()
    │ │ │ + │ │ │ +
    BALL::DockProblem::draw_ligand_
    AtomContainer * draw_ligand_
    Definition dockProblem.h:84
    │ │ │ +
    BALL::DockProblem::docker_
    EvolutionaryDocking * docker_
    Definition dockProblem.h:76
    │ │ │ +
    BALL::DockProblem::connectTo
    void connectTo(GeneticAlgorithm *opt)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_DEPRECATED
    #define BALL_DEPRECATED
    Definition COMMON/global.h:64
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ + │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,342 +1,203 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _M_O_L_M_E_C │ │ │ │ - * _M_I_N_I_M_I_Z_A_T_I_O_N │ │ │ │ -energyMinimizer.h │ │ │ │ + * _D_O_C_K_I_N_G │ │ │ │ + * _G_E_N_E_T_I_C_D_O_C_K │ │ │ │ +dockProblem.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ -2// vi: set ts=2: │ │ │ │ -3// │ │ │ │ -4// $Id: energyMinimizer.h,v 1.44.20.3 2007/08/07 09:12:33 aleru Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7// Energy Minimizer: A class for minimizing the energy of molecular systems │ │ │ │ +1// ---------------------------------------------------- │ │ │ │ +2// $Maintainer: Marcel Schumann $ │ │ │ │ +3// $Authors: Jan Fuhrmann, Marcel Schumann $ │ │ │ │ +4// ---------------------------------------------------- │ │ │ │ +5 │ │ │ │ +6#ifndef BALL_DOCKING_GENETICDOCK_DOCKPROBLEM_H │ │ │ │ +7#define BALL_DOCKING_GENETICDOCK_DOCKPROBLEM_H │ │ │ │ 8 │ │ │ │ -9#ifndef BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H │ │ │ │ -10#define BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H │ │ │ │ +9#include │ │ │ │ +10#include │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ -13# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16#ifndef BALL_MOLMEC_COMMON_GRADIENT_H │ │ │ │ -17# include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_g_r_a_d_i_e_n_t_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20namespace _B_A_L_L │ │ │ │ -21{ │ │ │ │ -22 class ForceField; │ │ │ │ -23 class SnapShotManager; │ │ │ │ +12#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +13#include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ +14#include <_B_A_L_L_/_K_E_R_N_E_L_/_m_o_l_e_c_u_l_e_._h> │ │ │ │ +15#include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_o_t_e_i_n_._h> │ │ │ │ +16#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +17 │ │ │ │ +18#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_r_o_t_a_t_e_B_o_n_d_s_._h> │ │ │ │ +19#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_g_e_n_e_t_i_c_A_l_g_o_r_i_t_h_m_._h> │ │ │ │ +20#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_e_v_o_l_u_t_i_o_n_a_r_y_D_o_c_k_i_n_g_._h> │ │ │ │ +21 │ │ │ │ +22#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_p_a_r_a_m_e_t_e_r_._h> │ │ │ │ +23#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_M_O_N_/_s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h> │ │ │ │ 24 │ │ │ │ -_2_9 class _B_A_L_L___E_X_P_O_R_T _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r │ │ │ │ -30 { │ │ │ │ -31 public: │ │ │ │ -32 │ │ │ │ -36 │ │ │ │ -_3_9 struct _B_A_L_L___E_X_P_O_R_T _O_p_t_i_o_n │ │ │ │ -40 { │ │ │ │ -_4_3 static const char* _M_A_X_I_M_A_L___N_U_M_B_E_R___O_F___I_T_E_R_A_T_I_O_N_S; │ │ │ │ -44 │ │ │ │ -_4_7 static const char* _E_N_E_R_G_Y___O_U_T_P_U_T___F_R_E_Q_U_E_N_C_Y; │ │ │ │ -48 │ │ │ │ -_5_1 static const char* _S_N_A_P_S_H_O_T___F_R_E_Q_U_E_N_C_Y; │ │ │ │ -52 │ │ │ │ -_5_5 static const char* _N_U_M_B_E_R___O_F___I_T_E_R_A_T_I_O_N; │ │ │ │ -56 │ │ │ │ -_5_9 static const char* _E_N_E_R_G_Y___D_I_F_F_E_R_E_N_C_E___B_O_U_N_D; │ │ │ │ -60 │ │ │ │ -_6_4 static const char* _M_A_X___S_A_M_E___E_N_E_R_G_Y; │ │ │ │ -65 │ │ │ │ -_6_9 static const char* _M_A_X___G_R_A_D_I_E_N_T; │ │ │ │ +25#include <_B_A_L_L_/_M_A_T_H_S_/_m_a_t_r_i_x_4_4_._h> │ │ │ │ +26#include <_B_A_L_L_/_M_A_T_H_S_/_q_u_a_t_e_r_n_i_o_n_._h> │ │ │ │ +27 │ │ │ │ +28#ifndef BALL_DOCKING_COMMON_CONFORMATIONSET_H │ │ │ │ +29# include <_B_A_L_L_/_D_O_C_K_I_N_G_/_C_O_M_M_O_N_/_c_o_n_f_o_r_m_a_t_i_o_n_S_e_t_._h> │ │ │ │ +30#endif // BALL_DOCKING_COMMON_CONFORMATIONSET_H │ │ │ │ +31 │ │ │ │ +32namespace _B_A_L_L │ │ │ │ +33{ │ │ │ │ +34 │ │ │ │ +_3_5 class _B_A_L_L___E_X_P_O_R_T _B_A_L_L___D_E_P_R_E_C_A_T_E_D _D_o_c_k_P_r_o_b_l_e_m │ │ │ │ +36 { │ │ │ │ +37 public: │ │ │ │ +_4_0 _D_o_c_k_P_r_o_b_l_e_m(); │ │ │ │ +41 │ │ │ │ +_4_4 _D_o_c_k_P_r_o_b_l_e_m(_A_t_o_m_C_o_n_t_a_i_n_e_r& sys_lig, _B_A_L_L_:_:_S_c_o_r_i_n_g_F_u_n_c_t_i_o_n* sf, │ │ │ │ +_E_v_o_l_u_t_i_o_n_a_r_y_D_o_c_k_i_n_g* docker, bool post_dock_optimization); │ │ │ │ +45 │ │ │ │ +46 │ │ │ │ +_4_9 virtual _~_D_o_c_k_P_r_o_b_l_e_m(); │ │ │ │ +50 │ │ │ │ +51 │ │ │ │ +_5_2 virtual void _s_e_t_u_p(_A_t_o_m_C_o_n_t_a_i_n_e_r& sys_lig); │ │ │ │ +53 │ │ │ │ +54 │ │ │ │ +_5_7 virtual double _c_a_l_c_u_l_a_t_e(); │ │ │ │ +58 │ │ │ │ +_6_2 void _m_o_v_e(); │ │ │ │ +63 │ │ │ │ +_6_6 bool _r_e_d_r_a_w(); │ │ │ │ +67 │ │ │ │ +_6_8 _A_t_o_m_C_o_n_t_a_i_n_e_r* _g_e_t_L_i_g_a_n_d(); │ │ │ │ +69 │ │ │ │ 70 │ │ │ │ -_7_3 static const char* _M_A_X_I_M_U_M___D_I_S_P_L_A_C_E_M_E_N_T; │ │ │ │ -74 }; │ │ │ │ +_7_1 void _c_o_n_n_e_c_t_T_o(_G_e_n_e_t_i_c_A_l_g_o_r_i_t_h_m* opt); │ │ │ │ +72 │ │ │ │ +73 │ │ │ │ +74 protected: │ │ │ │ 75 │ │ │ │ -_7_6 struct _B_A_L_L___E_X_P_O_R_T _D_e_f_a_u_l_t │ │ │ │ -77 { │ │ │ │ -_8_0 static _S_i_z_e _M_A_X_I_M_A_L___N_U_M_B_E_R___O_F___I_T_E_R_A_T_I_O_N_S; │ │ │ │ +_7_6 _E_v_o_l_u_t_i_o_n_a_r_y_D_o_c_k_i_n_g* _d_o_c_k_e_r__; │ │ │ │ +77 │ │ │ │ +_7_8 _D_o_u_b_l_e_P_a_r_a_m_e_t_e_r _d_o_u_b_l_e___p_a_r_a_m_e_t_e_r__; │ │ │ │ +79 │ │ │ │ +_8_0 _Q_u_a_t_e_r_n_i_o_n_P_a_r_a_m_e_t_e_r _q_u_a_t_e_r_n_i_o_n___p_a_r_a_m_e_t_e_r__; │ │ │ │ 81 │ │ │ │ -_8_4 static _S_i_z_e _E_N_E_R_G_Y___O_U_T_P_U_T___F_R_E_Q_U_E_N_C_Y; │ │ │ │ +_8_4 _A_t_o_m_C_o_n_t_a_i_n_e_r* ligand_, *_d_r_a_w___l_i_g_a_n_d__; │ │ │ │ 85 │ │ │ │ -_8_8 static _S_i_z_e _S_N_A_P_S_H_O_T___F_R_E_Q_U_E_N_C_Y; │ │ │ │ +_8_8 _V_e_c_t_o_r_3 t_origin_, _t___e_x_t_e_n_s_i_o_n__; │ │ │ │ 89 │ │ │ │ -_9_2 static _S_i_z_e _N_U_M_B_E_R___O_F___I_T_E_R_A_T_I_O_N; │ │ │ │ -93 │ │ │ │ -_9_7 static float _E_N_E_R_G_Y___D_I_F_F_E_R_E_N_C_E___B_O_U_N_D; │ │ │ │ -98 │ │ │ │ -_1_0_3 static _S_i_z_e _M_A_X___S_A_M_E___E_N_E_R_G_Y; │ │ │ │ +_9_0 _V_e_c_t_o_r_3 _b_i_n_d_i_n_g___p_o_c_k_e_t___c_e_n_t_e_r__; │ │ │ │ +91 │ │ │ │ +_9_4 _B_A_L_L_:_:_S_c_o_r_i_n_g_F_u_n_c_t_i_o_n* _s_c_o_r_i_n_g___f_u_n_c_t_i_o_n__; │ │ │ │ +95 │ │ │ │ +_9_8 std::vector _l_i_g_a_n_d___p_o_s_i_t_i_o_n_s__; │ │ │ │ +99 │ │ │ │ +_1_0_2 _R_o_t_a_t_e_B_o_n_d_s* _r_b__; │ │ │ │ +103 │ │ │ │ 104 │ │ │ │ -_1_0_8 static float _M_A_X___G_R_A_D_I_E_N_T; │ │ │ │ +105 │ │ │ │ +_1_0_8 void _r_e_s_t_o_r_e(); │ │ │ │ 109 │ │ │ │ -_1_1_2 static float _M_A_X_I_M_U_M___D_I_S_P_L_A_C_E_M_E_N_T; │ │ │ │ -113 }; │ │ │ │ -114 │ │ │ │ -116 │ │ │ │ -119 │ │ │ │ -120 _B_A_L_L___C_R_E_A_T_E(_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r) │ │ │ │ -121 │ │ │ │ -122 │ │ │ │ -_1_2_4 _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r(); │ │ │ │ -125 │ │ │ │ -_1_2_8 _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ -129 │ │ │ │ -_1_3_2 _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field, const _O_p_t_i_o_n_s& options); │ │ │ │ -133 │ │ │ │ -_1_3_6 _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r(const _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r& energy_minimizer); │ │ │ │ -137 │ │ │ │ -_1_4_0 virtual ~_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r(); │ │ │ │ -141 │ │ │ │ -143 │ │ │ │ -146 │ │ │ │ -_1_4_9 const _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r& operator=(const _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r& energy_minimizer); │ │ │ │ -150 │ │ │ │ -152 │ │ │ │ -_1_5_5 bool operator == (const _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r& energy_minimizer) ; │ │ │ │ -156 │ │ │ │ -160 │ │ │ │ -_1_6_3 bool isValid() const; │ │ │ │ -164 │ │ │ │ -166 │ │ │ │ -169 │ │ │ │ -_1_7_2 bool setup(_F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ -173 │ │ │ │ -_1_7_6 bool setup(_F_o_r_c_e_F_i_e_l_d& force_field, _S_n_a_p_S_h_o_t_M_a_n_a_g_e_r *ssm); │ │ │ │ -177 │ │ │ │ -_1_8_0 bool setup(_F_o_r_c_e_F_i_e_l_d& force_field, │ │ │ │ -181 _S_n_a_p_S_h_o_t_M_a_n_a_g_e_r *ssm, const _O_p_t_i_o_n_s& options); │ │ │ │ -182 │ │ │ │ -_1_8_5 bool setup(_F_o_r_c_e_F_i_e_l_d& force_field, const _O_p_t_i_o_n_s& options); │ │ │ │ -186 │ │ │ │ -_1_8_9 virtual bool specificSetup(); │ │ │ │ -190 │ │ │ │ -192 │ │ │ │ -195 │ │ │ │ -_2_0_8 virtual bool isConverged() const; │ │ │ │ -209 │ │ │ │ -_2_1_8 virtual double findStep(); │ │ │ │ -219 │ │ │ │ -_2_2_4 virtual void updateDirection(); │ │ │ │ -225 │ │ │ │ -_2_3_0 virtual double updateEnergy(); │ │ │ │ -231 │ │ │ │ -_2_3_6 virtual void updateForces(); │ │ │ │ -237 │ │ │ │ -_2_4_3 void storeGradientEnergy(); │ │ │ │ -244 │ │ │ │ -_2_5_2 virtual void printEnergy() const; │ │ │ │ -253 │ │ │ │ -_2_6_2 virtual void takeSnapShot() const; │ │ │ │ -263 │ │ │ │ -_2_8_2 virtual void finishIteration(); │ │ │ │ -283 │ │ │ │ -_2_8_6 _S_i_z_e getNumberOfIterations() const; │ │ │ │ -287 │ │ │ │ -_2_9_0 _G_r_a_d_i_e_n_t& getDirection(); │ │ │ │ -291 │ │ │ │ -_2_9_4 _G_r_a_d_i_e_n_t& getGradient(); │ │ │ │ -295 │ │ │ │ -_2_9_8 _G_r_a_d_i_e_n_t& getInitialGradient(); │ │ │ │ -299 │ │ │ │ -_3_0_2 double getEnergy() const; │ │ │ │ -303 │ │ │ │ -_3_0_6 double& getEnergy(); │ │ │ │ -307 │ │ │ │ -_3_1_0 double getInitialEnergy() const; │ │ │ │ -311 │ │ │ │ -_3_1_4 double& getInitialEnergy(); │ │ │ │ -315 │ │ │ │ -_3_1_8 void setNumberOfIterations(_S_i_z_e number_of_iterations); │ │ │ │ -319 │ │ │ │ -_3_2_2 _S_i_z_e getMaxNumberOfIterations() const; │ │ │ │ -323 │ │ │ │ -_3_2_6 void setMaxNumberOfIterations(_S_i_z_e number_of_iterations); │ │ │ │ -327 │ │ │ │ -_3_3_1 void setMaxSameEnergy(_S_i_z_e number); │ │ │ │ -332 │ │ │ │ -_3_3_6 _S_i_z_e getMaxSameEnergy() const; │ │ │ │ -337 │ │ │ │ -_3_4_0 void setEnergyOutputFrequency(_S_i_z_e energy_output_frequency); │ │ │ │ -341 │ │ │ │ -_3_4_4 _S_i_z_e getEnergyOutputFrequency() const; │ │ │ │ -345 │ │ │ │ -_3_4_8 void setEnergyDifferenceBound(float energy_difference_bound); │ │ │ │ -349 │ │ │ │ -_3_5_2 float getEnergyDifferenceBound() const; │ │ │ │ -353 │ │ │ │ -_3_5_7 void setMaxGradient(float max_gradient); │ │ │ │ -358 │ │ │ │ -_3_6_2 float getMaxGradient() const; │ │ │ │ -363 │ │ │ │ -_3_6_7 void setMaximumDisplacement(float maximum_displacement); │ │ │ │ -368 │ │ │ │ -_3_7_1 float getMaximumDisplacement() const; │ │ │ │ -372 │ │ │ │ -_3_7_5 void setSnapShotFrequency(_S_i_z_e snapshot_frequency); │ │ │ │ -376 │ │ │ │ -_3_7_9 _S_i_z_e getSnapShotFrequency() const; │ │ │ │ -380 │ │ │ │ -_3_8_3 _F_o_r_c_e_F_i_e_l_d* getForceField(); │ │ │ │ -384 │ │ │ │ -_3_8_7 _S_i_z_e getForceUpdateCounter() const ; │ │ │ │ -388 │ │ │ │ -_3_9_1 _S_i_z_e getEnergyUpdateCounter() const ; │ │ │ │ -392 │ │ │ │ -_4_0_4 virtual bool minimize(_S_i_z_e steps = 0, bool resume = false); │ │ │ │ -405 │ │ │ │ -_4_0_8 void enableEnergyAbortCondition(bool state); │ │ │ │ -409 │ │ │ │ -_4_1_1 bool energyAbortConditionEnabled() const; │ │ │ │ -412 │ │ │ │ -_4_1_7 void setEnergyToAbort(float value); │ │ │ │ -418 │ │ │ │ -_4_2_0 float getEnergyToAbort() const; │ │ │ │ -421 │ │ │ │ -_4_2_5 bool wasAborted() const ; │ │ │ │ -426 │ │ │ │ -428 │ │ │ │ -431 │ │ │ │ -_4_3_4 _O_p_t_i_o_n_s options; │ │ │ │ -436 │ │ │ │ -437 protected: │ │ │ │ -438 │ │ │ │ -442 │ │ │ │ -_4_4_5 _G_r_a_d_i_e_n_t initial_grad_; │ │ │ │ -446 │ │ │ │ -_4_4_9 _G_r_a_d_i_e_n_t current_grad_; │ │ │ │ -450 │ │ │ │ -_4_5_3 double initial_energy_; │ │ │ │ -454 │ │ │ │ -_4_5_7 double current_energy_; │ │ │ │ -458 │ │ │ │ -_4_6_1 _G_r_a_d_i_e_n_t old_grad_; │ │ │ │ -462 │ │ │ │ -_4_6_5 double old_energy_; │ │ │ │ -466 │ │ │ │ -_4_6_9 _G_r_a_d_i_e_n_t direction_; │ │ │ │ -470 │ │ │ │ -_4_7_3 bool valid_; │ │ │ │ -474 │ │ │ │ -_4_7_7 _S_n_a_p_S_h_o_t_M_a_n_a_g_e_r* snapshot_; │ │ │ │ -478 │ │ │ │ -_4_8_3 _F_o_r_c_e_F_i_e_l_d* force_field_; │ │ │ │ -484 │ │ │ │ -_4_8_7 _S_i_z_e number_of_iterations_; │ │ │ │ -488 │ │ │ │ -_4_9_1 _S_i_z_e maximal_number_of_iterations_; │ │ │ │ -492 │ │ │ │ -_4_9_5 _S_i_z_e energy_output_frequency_; │ │ │ │ -496 │ │ │ │ -_4_9_9 _S_i_z_e snapshot_frequency_; │ │ │ │ -500 │ │ │ │ -_5_0_4 double energy_difference_bound_; │ │ │ │ -505 │ │ │ │ -_5_0_8 double max_gradient_; │ │ │ │ -509 │ │ │ │ -_5_1_4 _S_i_z_e max_same_energy_; │ │ │ │ -515 │ │ │ │ -_5_1_8 _S_i_z_e same_energy_counter_; │ │ │ │ -519 │ │ │ │ -_5_2_2 float maximum_displacement_; │ │ │ │ -523 │ │ │ │ -_5_2_7 _S_i_z_e force_update_counter_; │ │ │ │ -528 │ │ │ │ -_5_3_2 _S_i_z_e energy_update_counter_; │ │ │ │ -533 │ │ │ │ -_5_3_7 float cutlo_; │ │ │ │ -538 │ │ │ │ -_5_4_2 double step_; │ │ │ │ -543 │ │ │ │ -544 //_ │ │ │ │ -_5_4_5 bool abort_by_energy_enabled_; │ │ │ │ -546 │ │ │ │ -547 //_ │ │ │ │ -_5_4_8 float abort_energy_; │ │ │ │ -549 │ │ │ │ -550 //_ │ │ │ │ -_5_5_1 bool aborted_; │ │ │ │ -552 │ │ │ │ -553 //_@} │ │ │ │ -554 }; │ │ │ │ -555 │ │ │ │ -556} // namespace Ball │ │ │ │ -557 │ │ │ │ -558#endif // BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H │ │ │ │ -_g_r_a_d_i_e_n_t_._h │ │ │ │ -_o_p_t_i_o_n_s_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_1_1_2 _O_p_t_i_o_n_s _o_p_t__; │ │ │ │ +113 │ │ │ │ +_1_1_4 bool _r_e_d_r_a_w__; │ │ │ │ +115 │ │ │ │ +_1_1_6 bool _p_o_s_t___d_o_c_k___o_p_t_i_m_i_z_a_t_i_o_n__; │ │ │ │ +117 │ │ │ │ +118 }; │ │ │ │ +119} │ │ │ │ +120 │ │ │ │ +121#endif /* BALL_DOCKING_GENETICDOCK_DOCKPROBLEM_H */ │ │ │ │ +_s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h │ │ │ │ +_p_r_o_t_e_i_n_._h │ │ │ │ +_m_o_l_e_c_u_l_e_._h │ │ │ │ +_g_e_n_e_t_i_c_A_l_g_o_r_i_t_h_m_._h │ │ │ │ +_e_v_o_l_u_t_i_o_n_a_r_y_D_o_c_k_i_n_g_._h │ │ │ │ +_p_a_r_a_m_e_t_e_r_._h │ │ │ │ +_r_o_t_a_t_e_B_o_n_d_s_._h │ │ │ │ +_c_o_n_f_o_r_m_a_t_i_o_n_S_e_t_._h │ │ │ │ +_q_u_a_t_e_r_n_i_o_n_._h │ │ │ │ +_m_a_t_r_i_x_4_4_._h │ │ │ │ +_v_e_c_t_o_r_3_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ _B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ -_B_A_L_L_:_:_G_r_a_d_i_e_n_t │ │ │ │ -DDeeffiinniittiioonn _g_r_a_d_i_e_n_t_._h_:_4_5 │ │ │ │ -_B_A_L_L_:_:_S_n_a_p_S_h_o_t_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _s_n_a_p_S_h_o_t_M_a_n_a_g_e_r_._h_:_3_4 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_3_0 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_M_A_X_I_M_A_L___N_U_M_B_E_R___O_F___I_T_E_R_A_T_I_O_N_S │ │ │ │ -static const char * MAXIMAL_NUMBER_OF_ITERATIONS │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_E_N_E_R_G_Y___O_U_T_P_U_T___F_R_E_Q_U_E_N_C_Y │ │ │ │ -static const char * ENERGY_OUTPUT_FREQUENCY │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_4_7 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_S_N_A_P_S_H_O_T___F_R_E_Q_U_E_N_C_Y │ │ │ │ -static const char * SNAPSHOT_FREQUENCY │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_5_1 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_M_A_X___G_R_A_D_I_E_N_T │ │ │ │ -static const char * MAX_GRADIENT │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_6_9 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_M_A_X___S_A_M_E___E_N_E_R_G_Y │ │ │ │ -static const char * MAX_SAME_ENERGY │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_6_4 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_M_A_X_I_M_U_M___D_I_S_P_L_A_C_E_M_E_N_T │ │ │ │ -static const char * MAXIMUM_DISPLACEMENT │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_7_3 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_E_N_E_R_G_Y___D_I_F_F_E_R_E_N_C_E___B_O_U_N_D │ │ │ │ -static const char * ENERGY_DIFFERENCE_BOUND │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_5_9 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_N_U_M_B_E_R___O_F___I_T_E_R_A_T_I_O_N │ │ │ │ -static const char * NUMBER_OF_ITERATION │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_5_5 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_7_7 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_S_N_A_P_S_H_O_T___F_R_E_Q_U_E_N_C_Y │ │ │ │ -static Size SNAPSHOT_FREQUENCY │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_8_8 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_M_A_X___S_A_M_E___E_N_E_R_G_Y │ │ │ │ -static Size MAX_SAME_ENERGY │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_1_0_3 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_M_A_X_I_M_A_L___N_U_M_B_E_R___O_F___I_T_E_R_A_T_I_O_N_S │ │ │ │ -static Size MAXIMAL_NUMBER_OF_ITERATIONS │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_8_0 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_E_N_E_R_G_Y___O_U_T_P_U_T___F_R_E_Q_U_E_N_C_Y │ │ │ │ -static Size ENERGY_OUTPUT_FREQUENCY │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_8_4 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_E_N_E_R_G_Y___D_I_F_F_E_R_E_N_C_E___B_O_U_N_D │ │ │ │ -static float ENERGY_DIFFERENCE_BOUND │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_9_7 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_N_U_M_B_E_R___O_F___I_T_E_R_A_T_I_O_N │ │ │ │ -static Size NUMBER_OF_ITERATION │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_9_2 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_M_A_X___G_R_A_D_I_E_N_T │ │ │ │ -static float MAX_GRADIENT │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_1_0_8 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_M_A_X_I_M_U_M___D_I_S_P_L_A_C_E_M_E_N_T │ │ │ │ -static float MAXIMUM_DISPLACEMENT │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_1_1_2 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_3_6 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_p_o_s_t___d_o_c_k___o_p_t_i_m_i_z_a_t_i_o_n__ │ │ │ │ +bool post_dock_optimization_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_1_1_6 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_g_e_t_L_i_g_a_n_d │ │ │ │ +AtomContainer * getLigand() │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_r_b__ │ │ │ │ +RotateBonds * rb_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_1_0_2 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_d_o_u_b_l_e___p_a_r_a_m_e_t_e_r__ │ │ │ │ +DoubleParameter double_parameter_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_7_8 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_r_e_s_t_o_r_e │ │ │ │ +void restore() │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_b_i_n_d_i_n_g___p_o_c_k_e_t___c_e_n_t_e_r__ │ │ │ │ +Vector3 binding_pocket_center_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_9_0 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_o_p_t__ │ │ │ │ +Options opt_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_1_1_2 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_s_e_t_u_p │ │ │ │ +virtual void setup(AtomContainer &sys_lig) │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_m_o_v_e │ │ │ │ +void move() │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_~_D_o_c_k_P_r_o_b_l_e_m │ │ │ │ +virtual ~DockProblem() │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_D_o_c_k_P_r_o_b_l_e_m │ │ │ │ +DockProblem() │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_r_e_d_r_a_w__ │ │ │ │ +bool redraw_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_1_1_4 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_D_o_c_k_P_r_o_b_l_e_m │ │ │ │ +DockProblem(AtomContainer &sys_lig, BALL::ScoringFunction *sf, │ │ │ │ +EvolutionaryDocking *docker, bool post_dock_optimization) │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_s_c_o_r_i_n_g___f_u_n_c_t_i_o_n__ │ │ │ │ +BALL::ScoringFunction * scoring_function_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_9_4 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_l_i_g_a_n_d___p_o_s_i_t_i_o_n_s__ │ │ │ │ +std::vector< Vector3 > ligand_positions_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_9_8 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_q_u_a_t_e_r_n_i_o_n___p_a_r_a_m_e_t_e_r__ │ │ │ │ +QuaternionParameter quaternion_parameter_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_8_0 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_r_e_d_r_a_w │ │ │ │ +bool redraw() │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_c_a_l_c_u_l_a_t_e │ │ │ │ +virtual double calculate() │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_t___e_x_t_e_n_s_i_o_n__ │ │ │ │ +Vector3 t_extension_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_8_8 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_d_r_a_w___l_i_g_a_n_d__ │ │ │ │ +AtomContainer * draw_ligand_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_8_4 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_d_o_c_k_e_r__ │ │ │ │ +EvolutionaryDocking * docker_ │ │ │ │ +DDeeffiinniittiioonn _d_o_c_k_P_r_o_b_l_e_m_._h_:_7_6 │ │ │ │ +_B_A_L_L_:_:_D_o_c_k_P_r_o_b_l_e_m_:_:_c_o_n_n_e_c_t_T_o │ │ │ │ +void connectTo(GeneticAlgorithm *opt) │ │ │ │ +_B_A_L_L_:_:_E_v_o_l_u_t_i_o_n_a_r_y_D_o_c_k_i_n_g │ │ │ │ +DDeeffiinniittiioonn _e_v_o_l_u_t_i_o_n_a_r_y_D_o_c_k_i_n_g_._h_:_3_5 │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_A_l_g_o_r_i_t_h_m │ │ │ │ +DDeeffiinniittiioonn _g_e_n_e_t_i_c_A_l_g_o_r_i_t_h_m_._h_:_2_4 │ │ │ │ +_B_A_L_L_:_:_D_o_u_b_l_e_P_a_r_a_m_e_t_e_r │ │ │ │ +DDeeffiinniittiioonn _p_a_r_a_m_e_t_e_r_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_P_a_r_a_m_e_t_e_r │ │ │ │ +DDeeffiinniittiioonn _p_a_r_a_m_e_t_e_r_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_R_o_t_a_t_e_B_o_n_d_s │ │ │ │ +DDeeffiinniittiioonn _r_o_t_a_t_e_B_o_n_d_s_._h_:_2_3 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_F_u_n_c_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h_:_2_9 │ │ │ │ +_B_A_L_L___D_E_P_R_E_C_A_T_E_D │ │ │ │ +#define BALL_DEPRECATED │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_6_4 │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_s_y_s_t_e_m_._h │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d36/a01916.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: triple.h File Reference │ │ │ +BALL: directory.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,38 +65,66 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces
    │ │ │ -
    triple.h File Reference
    │ │ │ +Namespaces | │ │ │ +Macros
    │ │ │ +
    directory.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ +
    #include <BALL/common.h>
    │ │ │ +#include <BALL/CONCEPT/processor.h>
    │ │ │ +#include <BALL/DATATYPE/string.h>
    │ │ │ +#include <BALL/SYSTEM/fileSystem.h>
    │ │ │ +#include <cstdio>
    │ │ │ +#include <BALL/SYSTEM/directory.iC>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::Triple< T1, T2, T3 >
    class  BALL::Directory
     
    │ │ │ │ │ │ │ │ │ │ │ │ +

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ +Macros

    #define INVALID_HANDLE_VALUE   0
     
    │ │ │ +

    Macro Definition Documentation

    │ │ │ + │ │ │ +

    ◆ INVALID_HANDLE_VALUE

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define INVALID_HANDLE_VALUE   0
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 53 of file directory.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,19 +1,31 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _D_A_T_A_T_Y_P_E │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -triple.h File Reference │ │ │ │ + * _S_Y_S_T_E_M │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s │ │ │ │ +directory.h File Reference │ │ │ │ #include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ +#include <_B_A_L_L_/_S_Y_S_T_E_M_/_f_i_l_e_S_y_s_t_e_m_._h> │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_T_r_i_p_l_e_<_ _T_1_,_ _T_2_,_ _T_3_ _> │ │ │ │ +class   _B_A_L_L_:_:_D_i_r_e_c_t_o_r_y │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +MMaaccrrooss │ │ │ │ +#define  _I_N_V_A_L_I_D___H_A_N_D_L_E___V_A_L_U_E   0 │ │ │ │ +  │ │ │ │ +********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ +********** _?◆_? IINNVVAALLIIDD__HHAANNDDLLEE__VVAALLUUEE ********** │ │ │ │ +#define INVALID_HANDLE_VALUE   0 │ │ │ │ +Definition at line _5_3 of file _d_i_r_e_c_t_o_r_y_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d36/a01916_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: triple.h Source File │ │ │ +BALL: directory.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,266 +70,222 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    triple.h
    │ │ │ +
    directory.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4// $Id: triple.h,v 1.9 2003/08/26 08:04:12 oliver Exp $
    │ │ │ +
    4// $Id: directory.h,v 1.29.16.1 2007/03/25 21:25:38 oliver Exp $
    │ │ │
    5//
    │ │ │
    6
    │ │ │ -
    7#ifndef BALL_DATATYPE_TRIPLE_H
    │ │ │ -
    8#define BALL_DATATYPE_TRIPLE_H
    │ │ │ +
    7#ifndef BALL_SYSTEM_DIRECTORY_H
    │ │ │ +
    8#define BALL_SYSTEM_DIRECTORY_H
    │ │ │
    9
    │ │ │
    10#ifndef BALL_COMMON_H
    │ │ │ -
    11# include <BALL/common.h>
    │ │ │ +
    11# include <BALL/common.h>
    │ │ │
    12#endif
    │ │ │
    13
    │ │ │ -
    14namespace BALL
    │ │ │ -
    15{
    │ │ │ -
    23 template <typename T1, typename T2, typename T3>
    │ │ │ -
    │ │ │ -
    24 class Triple
    │ │ │ -
    25 {
    │ │ │ -
    26 public:
    │ │ │ -
    27
    │ │ │ -
    31
    │ │ │ -
    32 BALL_CREATE(Triple)
    │ │ │ -
    33
    │ │ │ -
    34
    │ │ │ -
    37 Triple();
    │ │ │ -
    38
    │ │ │ -
    44 Triple(const Triple& triple, bool deep = true);
    │ │ │ -
    45
    │ │ │ -
    53 Triple(const T1& new_first, const T2& new_second, const T3& new_third);
    │ │ │ -
    54
    │ │ │ -
    58 virtual ~Triple();
    │ │ │ -
    60
    │ │ │ -
    63 virtual void clear();
    │ │ │ -
    64
    │ │ │ -
    68
    │ │ │ -
    73 const Triple& operator = (const Triple& triple);
    │ │ │ -
    74
    │ │ │ -
    77 void set(const T1& t1, const T2& t2, const T3& t3);
    │ │ │ -
    78
    │ │ │ -
    81 void get(T1& first, T2& second, T3& third) const;
    │ │ │ -
    82
    │ │ │ -
    84
    │ │ │ -
    87
    │ │ │ -
    91 bool operator == (const Triple& triple) const;
    │ │ │ -
    92
    │ │ │ -
    95 bool operator != (const Triple& triple) const;
    │ │ │ -
    96
    │ │ │ -
    102 bool operator < (const Triple& triple) const;
    │ │ │ -
    103
    │ │ │ -
    106 bool operator <= (const Triple& triple) const;
    │ │ │ +
    14#ifndef BALL_CONCEPT_PROCESSOR_H
    │ │ │ +
    15# include <BALL/CONCEPT/processor.h>
    │ │ │ +
    16#endif
    │ │ │ +
    17
    │ │ │ +
    18#ifndef BALL_DATATYPE_STRING_H
    │ │ │ +
    19# include <BALL/DATATYPE/string.h>
    │ │ │ +
    20#endif
    │ │ │ +
    21
    │ │ │ +
    22#ifndef BALL_SYSTEM_FILESYSTEM_H
    │ │ │ +
    23# include <BALL/SYSTEM/fileSystem.h>
    │ │ │ +
    24#endif
    │ │ │ +
    25
    │ │ │ +
    26#ifdef BALL_HAS_DIRENT_H
    │ │ │ +
    27# include <dirent.h>
    │ │ │ +
    28#endif
    │ │ │ +
    29#ifdef BALL_HAS_UNISTD_H
    │ │ │ +
    30# include <unistd.h>
    │ │ │ +
    31#endif
    │ │ │ +
    32#ifdef BALL_HAS_SYS_STAT_H
    │ │ │ +
    33# include <sys/stat.h>
    │ │ │ +
    34#endif
    │ │ │ +
    35#ifdef BALL_HAS_DIRECT_H
    │ │ │ +
    36# include <direct.h>
    │ │ │ +
    37#endif
    │ │ │ +
    38#include <cstdio>
    │ │ │ +
    39#ifdef BALL_COMPILER_MSVC
    │ │ │ +
    40#define WINDOWS_LEAN_AND_MEAN
    │ │ │ +
    41#include <windows.h>
    │ │ │ +
    42#define mode_t int
    │ │ │ +
    43#endif
    │ │ │ +
    44
    │ │ │ +
    45namespace BALL
    │ │ │ +
    46{
    │ │ │ +
    │ │ │ +
    50 class BALL_EXPORT Directory
    │ │ │ +
    51 {
    │ │ │ +
    52#ifndef BALL_OS_WINDOWS
    │ │ │ +
    53# define INVALID_HANDLE_VALUE 0
    │ │ │ +
    54#endif
    │ │ │ +
    55
    │ │ │ +
    56 public:
    │ │ │ +
    57
    │ │ │ +
    61
    │ │ │ +
    66 static const Size MAX_PATH_LENGTH;
    │ │ │ +
    67
    │ │ │ +
    69
    │ │ │ +
    72
    │ │ │ +
    79 Directory();
    │ │ │ +
    80
    │ │ │ +
    89 Directory(const String& directory_path, bool set_current = false);
    │ │ │ +
    90
    │ │ │ +
    96 Directory(const Directory& directory);
    │ │ │ +
    97
    │ │ │ +
    100 ~Directory();
    │ │ │ +
    101
    │ │ │ +
    106 void clear();
    │ │ │
    107
    │ │ │ -
    110 bool operator >= (const Triple& triple) const;
    │ │ │ +
    110 void destroy();
    │ │ │
    111
    │ │ │ -
    114 bool operator > (const Triple& triple) const;
    │ │ │ -
    115
    │ │ │ -
    117
    │ │ │ -
    121
    │ │ │ -
    124 T1 first;
    │ │ │ +
    113
    │ │ │ +
    116
    │ │ │ +
    124 bool set(const String& directory_path, bool set_current = false);
    │ │ │
    125
    │ │ │ -
    128 T2 second;
    │ │ │ -
    129
    │ │ │ -
    132 T3 third;
    │ │ │ -
    134 };
    │ │ │ -
    │ │ │ -
    135
    │ │ │ -
    136 template <typename T1, typename T2, typename T3>
    │ │ │ -
    │ │ │ -
    137 Triple<T1, T2, T3>::Triple()
    │ │ │ -
    138 {
    │ │ │ -
    139 }
    │ │ │ -
    │ │ │ -
    140
    │ │ │ -
    141 template <typename T1, typename T2, typename T3>
    │ │ │ -
    │ │ │ -
    142 Triple<T1, T2, T3>::Triple
    │ │ │ -
    143 (const Triple<T1, T2, T3>& triple, bool /* deep */)
    │ │ │ -
    144 : first(triple.first),
    │ │ │ -
    145 second(triple.second),
    │ │ │ -
    146 third(triple.third) {
    │ │ │ -
    147 }
    │ │ │ -
    │ │ │ -
    148
    │ │ │ -
    149 template <typename T1, typename T2, typename T3>
    │ │ │ -
    │ │ │ -
    150 Triple<T1, T2, T3>::Triple
    │ │ │ -
    151 (const T1& new_first, const T2& new_second, const T3& new_third)
    │ │ │ -
    152 : first(new_first),
    │ │ │ -
    153 second(new_second),
    │ │ │ -
    154 third(new_third)
    │ │ │ -
    155 {
    │ │ │ -
    156 }
    │ │ │ -
    │ │ │ -
    157
    │ │ │ -
    158 template <typename T1, typename T2, typename T3>
    │ │ │ -
    │ │ │ -
    159 Triple<T1, T2, T3>::~Triple()
    │ │ │ -
    160 {
    │ │ │ -
    161 }
    │ │ │ -
    │ │ │ -
    162
    │ │ │ -
    163 template <typename T1, typename T2, typename T3>
    │ │ │ -
    164 BALL_INLINE
    │ │ │ -
    │ │ │ -
    165 void Triple<T1, T2, T3>::set(const T1& new_first, const T2& new_second, const T3& new_third)
    │ │ │ -
    166 {
    │ │ │ -
    167 first = new_first;
    │ │ │ -
    168 second = new_second;
    │ │ │ -
    169 third = new_third;
    │ │ │ -
    170 }
    │ │ │ -
    │ │ │ -
    171
    │ │ │ -
    172 template <typename T1, typename T2, typename T3>
    │ │ │ -
    173 BALL_INLINE
    │ │ │ -
    │ │ │ -
    174 const Triple<T1, T2, T3>& Triple<T1, T2, T3>::operator =
    │ │ │ -
    175 (const Triple<T1, T2, T3>& triple)
    │ │ │ -
    176 {
    │ │ │ -
    177 first = triple.first;
    │ │ │ -
    178 second = triple.second;
    │ │ │ -
    179 third = triple.third;
    │ │ │ +
    130 void set(const Directory& directory);
    │ │ │ +
    131
    │ │ │ +
    135 Directory& operator = (const Directory& directory);
    │ │ │ +
    136
    │ │ │ +
    141 void get(Directory& directory) const;
    │ │ │ +
    143
    │ │ │ +
    147
    │ │ │ +
    153 const String& getPath() const;
    │ │ │ +
    154
    │ │ │ +
    162 bool rename(String old_path, String new_path);
    │ │ │ +
    163
    │ │ │ +
    168 bool renameTo(String new_path);
    │ │ │ +
    169
    │ │ │ +
    174 bool setCurrent(String directory_path);
    │ │ │ +
    175
    │ │ │ +
    179 bool setCurrent();
    │ │ │
    180
    │ │ │ -
    181 return *this;
    │ │ │ -
    182 }
    │ │ │ -
    │ │ │ -
    183
    │ │ │ -
    184 template <typename T1, typename T2, typename T3>
    │ │ │ -
    185 BALL_INLINE
    │ │ │ -
    │ │ │ -
    186 void Triple<T1, T2, T3>::get(T1& t1, T2& t2, T3& t3)
    │ │ │ -
    187 const
    │ │ │ -
    188 {
    │ │ │ -
    189 t1 = first;
    │ │ │ -
    190 t2 = second;
    │ │ │ -
    191 t3 = third;
    │ │ │ -
    192 }
    │ │ │ -
    │ │ │ -
    193
    │ │ │ -
    194 template <typename T1, typename T2, typename T3>
    │ │ │ -
    195 BALL_INLINE
    │ │ │ -
    │ │ │ -
    196 bool Triple<T1, T2, T3>::operator == (const Triple& triple)
    │ │ │ -
    197 const
    │ │ │ -
    198 {
    │ │ │ -
    199 return (first == triple.first
    │ │ │ -
    200 && second == triple.second
    │ │ │ -
    201 && third == triple.third);
    │ │ │ -
    202 }
    │ │ │ -
    │ │ │ +
    188 bool create(String path, const mode_t& mode = 0777);
    │ │ │ +
    189
    │ │ │ +
    196 bool remove(String old_path);
    │ │ │ +
    197
    │ │ │ +
    202 bool remove();
    │ │ │
    203
    │ │ │ -
    204 template <typename T1, typename T2, typename T3>
    │ │ │ -
    205 BALL_INLINE
    │ │ │ -
    │ │ │ -
    206 bool Triple<T1, T2, T3>::operator != (const Triple& triple)
    │ │ │ -
    207 const
    │ │ │ -
    208 {
    │ │ │ -
    209 return (first != triple.first
    │ │ │ -
    210 || second != triple.second
    │ │ │ -
    211 || third != triple.third);
    │ │ │ -
    212 }
    │ │ │ -
    │ │ │ -
    213
    │ │ │ -
    214 template <typename T1, typename T2, typename T3>
    │ │ │ -
    215 BALL_INLINE
    │ │ │ -
    │ │ │ -
    216 void Triple<T1, T2, T3>::clear()
    │ │ │ -
    217 {
    │ │ │ -
    218 first = T1();
    │ │ │ -
    219 second = T2();
    │ │ │ -
    220 third = T3();
    │ │ │ -
    221 }
    │ │ │ -
    │ │ │ -
    222
    │ │ │ -
    223 template <typename T1, typename T2, typename T3>
    │ │ │ -
    224 BALL_INLINE
    │ │ │ -
    │ │ │ -
    225 bool Triple<T1, T2, T3>::operator <
    │ │ │ -
    226 (const Triple<T1, T2, T3>& triple) const
    │ │ │ -
    227 {
    │ │ │ -
    228 return ((first < triple.first)
    │ │ │ -
    229 || ((first == triple.first) && (second < triple.second))
    │ │ │ -
    230 || ((first == triple.first) && (second == triple.second) && (third < triple.third)));
    │ │ │ -
    231 }
    │ │ │ -
    │ │ │ -
    232
    │ │ │ -
    233 template <typename T1, typename T2, typename T3>
    │ │ │ -
    234 BALL_INLINE
    │ │ │ -
    │ │ │ -
    235 bool Triple<T1, T2, T3>::operator <=
    │ │ │ -
    236 (const Triple<T1, T2, T3>& triple) const
    │ │ │ -
    237 {
    │ │ │ -
    238 return ((first < triple.first)
    │ │ │ -
    239 || ((first == triple.first) && (second < triple.second))
    │ │ │ -
    240 || ((first == triple.first) && (second == triple.second) && (third < triple.third))
    │ │ │ -
    241 || ((first == triple.first) && (second == triple.second) && (third == triple.third)));
    │ │ │ -
    242 }
    │ │ │ -
    │ │ │ -
    243
    │ │ │ -
    244 template <typename T1, typename T2, typename T3>
    │ │ │ -
    245 BALL_INLINE
    │ │ │ -
    │ │ │ -
    246 bool Triple<T1, T2, T3>::operator >=
    │ │ │ -
    247 (const Triple<T1, T2, T3>& triple) const
    │ │ │ -
    248 {
    │ │ │ -
    249 return ((first > triple.first)
    │ │ │ -
    250 || ((first == triple.first) && (second > triple.second))
    │ │ │ -
    251 || ((first == triple.first) && (second == triple.second) && (third > triple.third))
    │ │ │ -
    252 || ((first == triple.first) && (second == triple.second) && (third == triple.third)));
    │ │ │ -
    253 }
    │ │ │ -
    │ │ │ -
    254
    │ │ │ -
    255 template <typename T1, typename T2, typename T3>
    │ │ │ -
    256 BALL_INLINE
    │ │ │ -
    │ │ │ -
    257 bool Triple<T1, T2, T3>::operator >
    │ │ │ -
    258 (const Triple<T1, T2, T3>& triple) const
    │ │ │ -
    259 {
    │ │ │ -
    260 return ((first > triple.first)
    │ │ │ -
    261 || ((first == triple.first) && (second > triple.second))
    │ │ │ -
    262 || ((first == triple.first) && (second == triple.second) && (third > triple.third)));
    │ │ │ -
    263 }
    │ │ │ -
    │ │ │ -
    264} // namespace BALL
    │ │ │ -
    265
    │ │ │ -
    266#endif // BALL_DATATYPE_TRIPLE_H
    │ │ │ - │ │ │ -
    BALL_INLINE
    #define BALL_INLINE
    Definition debug.h:15
    │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Triple::operator>
    bool operator>(const Triple &triple) const
    Definition triple.h:258
    │ │ │ - │ │ │ -
    BALL::Triple::set
    void set(const T1 &t1, const T2 &t2, const T3 &t3)
    Definition triple.h:165
    │ │ │ - │ │ │ -
    BALL::Triple::get
    void get(T1 &first, T2 &second, T3 &third) const
    Definition triple.h:186
    │ │ │ -
    BALL::Triple::operator=
    const Triple & operator=(const Triple &triple)
    Definition triple.h:175
    │ │ │ -
    BALL::Triple::operator<
    bool operator<(const Triple &triple) const
    Definition triple.h:226
    │ │ │ -
    BALL::Triple::clear
    virtual void clear()
    Definition triple.h:216
    │ │ │ -
    BALL::Triple::operator==
    bool operator==(const Triple &triple) const
    Definition triple.h:196
    │ │ │ -
    BALL::Triple::operator>=
    bool operator>=(const Triple &triple) const
    Definition triple.h:247
    │ │ │ -
    BALL::Triple::operator!=
    bool operator!=(const Triple &triple) const
    Definition triple.h:206
    │ │ │ -
    BALL::Triple::operator<=
    bool operator<=(const Triple &triple) const
    Definition triple.h:236
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Triple::~Triple
    virtual ~Triple()
    Definition triple.h:159
    │ │ │ +
    208 bool getFirstEntry(String& entry);
    │ │ │ +
    209
    │ │ │ +
    214 bool getNextEntry(String& entry);
    │ │ │ +
    215
    │ │ │ +
    219 Size countItems();
    │ │ │ +
    220
    │ │ │ +
    224 Size countFiles();
    │ │ │ +
    225
    │ │ │ +
    229 Size countDirectories();
    │ │ │ +
    230
    │ │ │ +
    237 bool find(const String& filename, String& filepath);
    │ │ │ +
    238
    │ │ │ +
    240
    │ │ │ +
    243
    │ │ │ +
    248 bool has(const String& item);
    │ │ │ +
    249
    │ │ │ +
    255 bool isValid() const;
    │ │ │ +
    256
    │ │ │ +
    260 bool isCurrent() const;
    │ │ │ +
    261
    │ │ │ +
    265 bool isEmpty();
    │ │ │ +
    266
    │ │ │ +
    270 bool operator == (const Directory& directory) const;
    │ │ │ +
    271
    │ │ │ +
    275 bool operator != (const Directory& directory) const;
    │ │ │ +
    276
    │ │ │ +
    278 static String getUserHomeDir();
    │ │ │ +
    279
    │ │ │ +
    281 static bool changeToUserHomeDir();
    │ │ │ +
    282
    │ │ │ +
    284
    │ │ │ +
    285 private:
    │ │ │ +
    286
    │ │ │ +
    287 //_wrapper function around getcwd to handle different naming conventions in different OS
    │ │ │ +
    288 String getcwd_();
    │ │ │ +
    289
    │ │ │ +
    290 //_wrapper function around chdir to handle different naming conventions in different OS
    │ │ │ +
    291 int chdir_(const String& new_dir);
    │ │ │ +
    292
    │ │ │ +
    293 //_switch to this dir
    │ │ │ +
    294 void synchronize_();
    │ │ │ +
    295
    │ │ │ +
    296 //_switch back to the working directory
    │ │ │ +
    297 bool desynchronize_(bool result = true);
    │ │ │ +
    298#ifdef BALL_COMPILER_MSVC
    │ │ │ +
    299 HANDLE dirent_;
    │ │ │ +
    300 HANDLE dir_;
    │ │ │ +
    301#else
    │ │ │ +
    302 DIR* dir_;
    │ │ │ +
    303 dirent* dirent_;
    │ │ │ +
    304#endif
    │ │ │ +
    305 String directory_path_;
    │ │ │ +
    306 String backup_path_;
    │ │ │ +
    307 };
    │ │ │ +
    │ │ │ +
    308
    │ │ │ +
    309# ifndef BALL_NO_INLINE_FUNCTIONS
    │ │ │ +
    310# include <BALL/SYSTEM/directory.iC>
    │ │ │ +
    311# endif
    │ │ │ +
    312
    │ │ │ +
    313} // namespace BALL
    │ │ │ +
    314
    │ │ │ +
    315#endif // BALL_SYSTEM_DIRECTORY_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Directory::MAX_PATH_LENGTH
    static const Size MAX_PATH_LENGTH
    Definition directory.h:66
    │ │ │ +
    BALL::Directory::changeToUserHomeDir
    static bool changeToUserHomeDir()
    Goto the home directory of the current user.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Directory::getNextEntry
    bool getNextEntry(String &entry)
    │ │ │ + │ │ │ +
    BALL::Directory::Directory
    Directory(const Directory &directory)
    │ │ │ +
    BALL::Directory::getFirstEntry
    bool getFirstEntry(String &entry)
    │ │ │ + │ │ │ +
    BALL::Directory::countDirectories
    Size countDirectories()
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Directory::setCurrent
    bool setCurrent(String directory_path)
    │ │ │ +
    BALL::Directory::find
    bool find(const String &filename, String &filepath)
    │ │ │ +
    BALL::Directory::Directory
    Directory(const String &directory_path, bool set_current=false)
    │ │ │ +
    BALL::Directory::rename
    bool rename(String old_path, String new_path)
    │ │ │ +
    BALL::Directory::renameTo
    bool renameTo(String new_path)
    │ │ │ +
    BALL::Directory::remove
    bool remove(String old_path)
    │ │ │ +
    BALL::Directory::set
    void set(const Directory &directory)
    │ │ │ +
    BALL::Directory::has
    bool has(const String &item)
    │ │ │ +
    BALL::Directory::isValid
    bool isValid() const
    │ │ │ +
    BALL::Directory::getPath
    const String & getPath() const
    │ │ │ +
    BALL::Directory::create
    bool create(String path, const mode_t &mode=0777)
    │ │ │ + │ │ │ +
    BALL::Directory::get
    void get(Directory &directory) const
    │ │ │ +
    BALL::Directory::set
    bool set(const String &directory_path, bool set_current=false)
    │ │ │ + │ │ │ +
    BALL::Directory::isCurrent
    bool isCurrent() const
    │ │ │ +
    BALL::Directory::getUserHomeDir
    static String getUserHomeDir()
    Get the home directory of the current user.
    │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,269 +1,250 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _D_A_T_A_T_Y_P_E │ │ │ │ -triple.h │ │ │ │ + * _S_Y_S_T_E_M │ │ │ │ +directory.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: triple.h,v 1.9 2003/08/26 08:04:12 oliver Exp $ │ │ │ │ +4// $Id: directory.h,v 1.29.16.1 2007/03/25 21:25:38 oliver Exp $ │ │ │ │ 5// │ │ │ │ 6 │ │ │ │ -7#ifndef BALL_DATATYPE_TRIPLE_H │ │ │ │ -8#define BALL_DATATYPE_TRIPLE_H │ │ │ │ +7#ifndef BALL_SYSTEM_DIRECTORY_H │ │ │ │ +8#define BALL_SYSTEM_DIRECTORY_H │ │ │ │ 9 │ │ │ │ 10#ifndef BALL_COMMON_H │ │ │ │ 11# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ 12#endif │ │ │ │ 13 │ │ │ │ -14namespace _B_A_L_L │ │ │ │ -15{ │ │ │ │ -23 template │ │ │ │ -_2_4 class _T_r_i_p_l_e │ │ │ │ -25 { │ │ │ │ -26 public: │ │ │ │ -27 │ │ │ │ -31 │ │ │ │ -32 _B_A_L_L___C_R_E_A_T_E(_T_r_i_p_l_e) │ │ │ │ -33 │ │ │ │ -34 │ │ │ │ -37 _T_r_i_p_l_e(); │ │ │ │ -38 │ │ │ │ -44 _T_r_i_p_l_e(const _T_r_i_p_l_e& triple, bool deep = true); │ │ │ │ -45 │ │ │ │ -53 _T_r_i_p_l_e(const T1& new_first, const T2& new_second, const T3& new_third); │ │ │ │ -54 │ │ │ │ -58 virtual _~_T_r_i_p_l_e(); │ │ │ │ -60 │ │ │ │ -63 virtual void _c_l_e_a_r(); │ │ │ │ -64 │ │ │ │ -68 │ │ │ │ -73 const _T_r_i_p_l_e& _o_p_e_r_a_t_o_r_ _=_ (const _T_r_i_p_l_e& triple); │ │ │ │ -74 │ │ │ │ -77 void _s_e_t(const T1& t1, const T2& t2, const T3& t3); │ │ │ │ -78 │ │ │ │ -81 void _g_e_t(T1& _f_i_r_s_t, T2& _s_e_c_o_n_d, T3& _t_h_i_r_d) const; │ │ │ │ -82 │ │ │ │ -84 │ │ │ │ -87 │ │ │ │ -91 bool _o_p_e_r_a_t_o_r_ _=_=_ (const _T_r_i_p_l_e& triple) const; │ │ │ │ -92 │ │ │ │ -95 bool _o_p_e_r_a_t_o_r_ _!_=_ (const _T_r_i_p_l_e& triple) const; │ │ │ │ -96 │ │ │ │ -102 bool _o_p_e_r_a_t_o_r_ _<_ (const _T_r_i_p_l_e& triple) const; │ │ │ │ -103 │ │ │ │ -106 bool _o_p_e_r_a_t_o_r_ _<_=_ (const _T_r_i_p_l_e& triple) const; │ │ │ │ +14#ifndef BALL_CONCEPT_PROCESSOR_H │ │ │ │ +15# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ +16#endif │ │ │ │ +17 │ │ │ │ +18#ifndef BALL_DATATYPE_STRING_H │ │ │ │ +19# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ +20#endif │ │ │ │ +21 │ │ │ │ +22#ifndef BALL_SYSTEM_FILESYSTEM_H │ │ │ │ +23# include <_B_A_L_L_/_S_Y_S_T_E_M_/_f_i_l_e_S_y_s_t_e_m_._h> │ │ │ │ +24#endif │ │ │ │ +25 │ │ │ │ +26#ifdef BALL_HAS_DIRENT_H │ │ │ │ +27# include │ │ │ │ +28#endif │ │ │ │ +29#ifdef BALL_HAS_UNISTD_H │ │ │ │ +30# include │ │ │ │ +31#endif │ │ │ │ +32#ifdef BALL_HAS_SYS_STAT_H │ │ │ │ +33# include │ │ │ │ +34#endif │ │ │ │ +35#ifdef BALL_HAS_DIRECT_H │ │ │ │ +36# include │ │ │ │ +37#endif │ │ │ │ +38#include │ │ │ │ +39#ifdef BALL_COMPILER_MSVC │ │ │ │ +40#define WINDOWS_LEAN_AND_MEAN │ │ │ │ +41#include │ │ │ │ +42#define mode_t int │ │ │ │ +43#endif │ │ │ │ +44 │ │ │ │ +45namespace _B_A_L_L │ │ │ │ +46{ │ │ │ │ +_5_0 class _B_A_L_L___E_X_P_O_R_T _D_i_r_e_c_t_o_r_y │ │ │ │ +51 { │ │ │ │ +52#ifndef BALL_OS_WINDOWS │ │ │ │ +_5_3# define INVALID_HANDLE_VALUE 0 │ │ │ │ +54#endif │ │ │ │ +55 │ │ │ │ +56 public: │ │ │ │ +57 │ │ │ │ +61 │ │ │ │ +_6_6 static const _S_i_z_e _M_A_X___P_A_T_H___L_E_N_G_T_H; │ │ │ │ +67 │ │ │ │ +69 │ │ │ │ +72 │ │ │ │ +_7_9 _D_i_r_e_c_t_o_r_y(); │ │ │ │ +80 │ │ │ │ +_8_9 _D_i_r_e_c_t_o_r_y(const _S_t_r_i_n_g& directory_path, bool set_current = false); │ │ │ │ +90 │ │ │ │ +_9_6 _D_i_r_e_c_t_o_r_y(const _D_i_r_e_c_t_o_r_y& directory); │ │ │ │ +97 │ │ │ │ +_1_0_0 _~_D_i_r_e_c_t_o_r_y(); │ │ │ │ +101 │ │ │ │ +_1_0_6 void _c_l_e_a_r(); │ │ │ │ 107 │ │ │ │ -110 bool _o_p_e_r_a_t_o_r_ _>_=_ (const _T_r_i_p_l_e& triple) const; │ │ │ │ +_1_1_0 void _d_e_s_t_r_o_y(); │ │ │ │ 111 │ │ │ │ -114 bool _o_p_e_r_a_t_o_r_ _>_ (const _T_r_i_p_l_e& triple) const; │ │ │ │ -115 │ │ │ │ -117 │ │ │ │ -121 │ │ │ │ -_1_2_4 T1 _f_i_r_s_t; │ │ │ │ +113 │ │ │ │ +116 │ │ │ │ +_1_2_4 bool _s_e_t(const _S_t_r_i_n_g& directory_path, bool set_current = false); │ │ │ │ 125 │ │ │ │ -_1_2_8 T2 _s_e_c_o_n_d; │ │ │ │ -129 │ │ │ │ -_1_3_2 T3 _t_h_i_r_d; │ │ │ │ -134 }; │ │ │ │ -135 │ │ │ │ -136 template │ │ │ │ -_1_3_7 _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_T_r_i_p_l_e() │ │ │ │ -138 { │ │ │ │ -139 } │ │ │ │ -140 │ │ │ │ -141 template │ │ │ │ -_1_4_2 _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_T_r_i_p_l_e │ │ │ │ -143 (const _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>& triple, bool /* deep */) │ │ │ │ -144 : first(triple.first), │ │ │ │ -145 second(triple.second), │ │ │ │ -146 third(triple.third) { │ │ │ │ -147 } │ │ │ │ -148 │ │ │ │ -149 template │ │ │ │ -_1_5_0 _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_T_r_i_p_l_e │ │ │ │ -151 (const T1& new_first, const T2& new_second, const T3& new_third) │ │ │ │ -152 : first(new_first), │ │ │ │ -153 second(new_second), │ │ │ │ -154 third(new_third) │ │ │ │ -155 { │ │ │ │ -156 } │ │ │ │ -157 │ │ │ │ -158 template │ │ │ │ -_1_5_9 _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_~_T_r_i_p_l_e() │ │ │ │ -160 { │ │ │ │ -161 } │ │ │ │ -162 │ │ │ │ -163 template │ │ │ │ -164 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_6_5 void _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_s_e_t(const T1& new_first, const T2& new_second, │ │ │ │ -const T3& new_third) │ │ │ │ -166 { │ │ │ │ -167 first = new_first; │ │ │ │ -168 second = new_second; │ │ │ │ -169 third = new_third; │ │ │ │ -170 } │ │ │ │ -171 │ │ │ │ -172 template │ │ │ │ -173 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_7_4 const _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>& _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_o_p_e_r_a_t_o_r = │ │ │ │ -175 (const _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>& triple) │ │ │ │ -176 { │ │ │ │ -177 first = triple._f_i_r_s_t; │ │ │ │ -178 second = triple.second; │ │ │ │ -179 third = triple.third; │ │ │ │ +_1_3_0 void _s_e_t(const _D_i_r_e_c_t_o_r_y& directory); │ │ │ │ +131 │ │ │ │ +_1_3_5 _D_i_r_e_c_t_o_r_y& operator = (const _D_i_r_e_c_t_o_r_y& directory); │ │ │ │ +136 │ │ │ │ +_1_4_1 void _g_e_t(_D_i_r_e_c_t_o_r_y& directory) const; │ │ │ │ +143 │ │ │ │ +147 │ │ │ │ +_1_5_3 const _S_t_r_i_n_g& _g_e_t_P_a_t_h() const; │ │ │ │ +154 │ │ │ │ +_1_6_2 bool _r_e_n_a_m_e(_S_t_r_i_n_g old_path, _S_t_r_i_n_g new_path); │ │ │ │ +163 │ │ │ │ +_1_6_8 bool _r_e_n_a_m_e_T_o(_S_t_r_i_n_g new_path); │ │ │ │ +169 │ │ │ │ +_1_7_4 bool _s_e_t_C_u_r_r_e_n_t(_S_t_r_i_n_g directory_path); │ │ │ │ +175 │ │ │ │ +_1_7_9 bool _s_e_t_C_u_r_r_e_n_t(); │ │ │ │ 180 │ │ │ │ -181 return *this; │ │ │ │ -182 } │ │ │ │ -183 │ │ │ │ -184 template │ │ │ │ -185 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_8_6 void _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_g_e_t(T1& t1, T2& t2, T3& t3) │ │ │ │ -187 const │ │ │ │ -188 { │ │ │ │ -189 t1 = first; │ │ │ │ -190 t2 = second; │ │ │ │ -191 t3 = third; │ │ │ │ -192 } │ │ │ │ -193 │ │ │ │ -194 template │ │ │ │ -195 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_9_6 bool _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_o_p_e_r_a_t_o_r_ _=_=_ (const _T_r_i_p_l_e& triple) │ │ │ │ -197 const │ │ │ │ -198 { │ │ │ │ -199 return (first == triple._f_i_r_s_t │ │ │ │ -200 && second == triple._s_e_c_o_n_d │ │ │ │ -201 && third == triple._t_h_i_r_d); │ │ │ │ -202 } │ │ │ │ +_1_8_8 bool _c_r_e_a_t_e(_S_t_r_i_n_g path, const mode_t& mode = 0777); │ │ │ │ +189 │ │ │ │ +_1_9_6 bool _r_e_m_o_v_e(_S_t_r_i_n_g old_path); │ │ │ │ +197 │ │ │ │ +_2_0_2 bool _r_e_m_o_v_e(); │ │ │ │ 203 │ │ │ │ -204 template │ │ │ │ -205 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_0_6 bool _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_o_p_e_r_a_t_o_r_ _!_=_ (const _T_r_i_p_l_e& triple) │ │ │ │ -207 const │ │ │ │ -208 { │ │ │ │ -209 return (first != triple._f_i_r_s_t │ │ │ │ -210 || second != triple._s_e_c_o_n_d │ │ │ │ -211 || third != triple._t_h_i_r_d); │ │ │ │ -212 } │ │ │ │ -213 │ │ │ │ -214 template │ │ │ │ -215 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_1_6 void _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_c_l_e_a_r() │ │ │ │ -217 { │ │ │ │ -218 first = T1(); │ │ │ │ -219 second = T2(); │ │ │ │ -220 third = T3(); │ │ │ │ -221 } │ │ │ │ -222 │ │ │ │ -223 template │ │ │ │ -224 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_2_5 bool _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_o_p_e_r_a_t_o_r < │ │ │ │ -226 (const _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>& triple) const │ │ │ │ -227 { │ │ │ │ -228 return ((first < triple.first) │ │ │ │ -229 || ((first == triple.first) && (second < triple.second)) │ │ │ │ -230 || ((first == triple.first) && (second == triple.second) && (third < │ │ │ │ -triple.third))); │ │ │ │ -231 } │ │ │ │ -232 │ │ │ │ -233 template │ │ │ │ -234 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_3_5 bool _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_o_p_e_r_a_t_o_r <= │ │ │ │ -236 (const _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>& triple) const │ │ │ │ -237 { │ │ │ │ -238 return ((first < triple.first) │ │ │ │ -239 || ((first == triple.first) && (second < triple.second)) │ │ │ │ -240 || ((first == triple.first) && (second == triple.second) && (third < │ │ │ │ -triple.third)) │ │ │ │ -241 || ((first == triple.first) && (second == triple.second) && (third == │ │ │ │ -triple.third))); │ │ │ │ -242 } │ │ │ │ +_2_0_8 bool _g_e_t_F_i_r_s_t_E_n_t_r_y(_S_t_r_i_n_g& entry); │ │ │ │ +209 │ │ │ │ +_2_1_4 bool _g_e_t_N_e_x_t_E_n_t_r_y(_S_t_r_i_n_g& entry); │ │ │ │ +215 │ │ │ │ +_2_1_9 _S_i_z_e _c_o_u_n_t_I_t_e_m_s(); │ │ │ │ +220 │ │ │ │ +_2_2_4 _S_i_z_e _c_o_u_n_t_F_i_l_e_s(); │ │ │ │ +225 │ │ │ │ +_2_2_9 _S_i_z_e _c_o_u_n_t_D_i_r_e_c_t_o_r_i_e_s(); │ │ │ │ +230 │ │ │ │ +_2_3_7 bool _f_i_n_d(const _S_t_r_i_n_g& filename, _S_t_r_i_n_g& filepath); │ │ │ │ +238 │ │ │ │ +240 │ │ │ │ 243 │ │ │ │ -244 template │ │ │ │ -245 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_4_6 bool _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_o_p_e_r_a_t_o_r >= │ │ │ │ -247 (const _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>& triple) const │ │ │ │ -248 { │ │ │ │ -249 return ((first > triple.first) │ │ │ │ -250 || ((first == triple.first) && (second > triple.second)) │ │ │ │ -251 || ((first == triple.first) && (second == triple.second) && (third > │ │ │ │ -triple.third)) │ │ │ │ -252 || ((first == triple.first) && (second == triple.second) && (third == │ │ │ │ -triple.third))); │ │ │ │ -253 } │ │ │ │ -254 │ │ │ │ -255 template │ │ │ │ -256 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_5_7 bool _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>_:_:_o_p_e_r_a_t_o_r > │ │ │ │ -258 (const _T_r_i_p_l_e_<_T_1_,_ _T_2_,_ _T_3_>& triple) const │ │ │ │ -259 { │ │ │ │ -260 return ((first > triple.first) │ │ │ │ -261 || ((first == triple.first) && (second > triple.second)) │ │ │ │ -262 || ((first == triple.first) && (second == triple.second) && (third > │ │ │ │ -triple.third))); │ │ │ │ -263 } │ │ │ │ -264} // namespace BALL │ │ │ │ -265 │ │ │ │ -266#endif // BALL_DATATYPE_TRIPLE_H │ │ │ │ +_2_4_8 bool _h_a_s(const _S_t_r_i_n_g& item); │ │ │ │ +249 │ │ │ │ +_2_5_5 bool _i_s_V_a_l_i_d() const; │ │ │ │ +256 │ │ │ │ +_2_6_0 bool _i_s_C_u_r_r_e_n_t() const; │ │ │ │ +261 │ │ │ │ +_2_6_5 bool _i_s_E_m_p_t_y(); │ │ │ │ +266 │ │ │ │ +_2_7_0 bool operator == (const _D_i_r_e_c_t_o_r_y& directory) const; │ │ │ │ +271 │ │ │ │ +_2_7_5 bool operator != (const _D_i_r_e_c_t_o_r_y& directory) const; │ │ │ │ +276 │ │ │ │ +_2_7_8 static _S_t_r_i_n_g _g_e_t_U_s_e_r_H_o_m_e_D_i_r(); │ │ │ │ +279 │ │ │ │ +_2_8_1 static bool _c_h_a_n_g_e_T_o_U_s_e_r_H_o_m_e_D_i_r(); │ │ │ │ +282 │ │ │ │ +284 │ │ │ │ +285 private: │ │ │ │ +286 │ │ │ │ +287 //_wrapper function around getcwd to handle different naming conventions in │ │ │ │ +different OS │ │ │ │ +288 _S_t_r_i_n_g getcwd_(); │ │ │ │ +289 │ │ │ │ +290 //_wrapper function around chdir to handle different naming conventions in │ │ │ │ +different OS │ │ │ │ +291 int chdir_(const _S_t_r_i_n_g& new_dir); │ │ │ │ +292 │ │ │ │ +293 //_switch to this dir │ │ │ │ +294 void synchronize_(); │ │ │ │ +295 │ │ │ │ +296 //_switch back to the working directory │ │ │ │ +297 bool desynchronize_(bool result = true); │ │ │ │ +298#ifdef BALL_COMPILER_MSVC │ │ │ │ +299 HANDLE dirent_; │ │ │ │ +300 HANDLE dir_; │ │ │ │ +301#else │ │ │ │ +302 DIR* dir_; │ │ │ │ +303 dirent* dirent_; │ │ │ │ +304#endif │ │ │ │ +305 _S_t_r_i_n_g directory_path_; │ │ │ │ +306 _S_t_r_i_n_g backup_path_; │ │ │ │ +307 }; │ │ │ │ +308 │ │ │ │ +309# ifndef BALL_NO_INLINE_FUNCTIONS │ │ │ │ +310# include │ │ │ │ +311# endif │ │ │ │ +312 │ │ │ │ +313} // namespace BALL │ │ │ │ +314 │ │ │ │ +315#endif // BALL_SYSTEM_DIRECTORY_H │ │ │ │ _c_o_m_m_o_n_._h │ │ │ │ -_B_A_L_L___I_N_L_I_N_E │ │ │ │ -#define BALL_INLINE │ │ │ │ -DDeeffiinniittiioonn _d_e_b_u_g_._h_:_1_5 │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_p_r_o_c_e_s_s_o_r_._h │ │ │ │ +_f_i_l_e_S_y_s_t_e_m_._h │ │ │ │ +_s_t_r_i_n_g_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_2_5 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_o_p_e_r_a_t_o_r_> │ │ │ │ -bool operator>(const Triple &triple) const │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_2_5_8 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_s_e_c_o_n_d │ │ │ │ -T2 second │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_1_2_8 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_s_e_t │ │ │ │ -void set(const T1 &t1, const T2 &t2, const T3 &t3) │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_1_6_5 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_t_h_i_r_d │ │ │ │ -T3 third │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_1_3_2 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_g_e_t │ │ │ │ -void get(T1 &first, T2 &second, T3 &third) const │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_1_8_6 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ -const Triple & operator=(const Triple &triple) │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_1_7_5 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_o_p_e_r_a_t_o_r_< │ │ │ │ -bool operator<(const Triple &triple) const │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_2_2_6 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_c_l_e_a_r │ │ │ │ -virtual void clear() │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_2_1_6 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_o_p_e_r_a_t_o_r_=_= │ │ │ │ -bool operator==(const Triple &triple) const │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_1_9_6 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_o_p_e_r_a_t_o_r_>_= │ │ │ │ -bool operator>=(const Triple &triple) const │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_2_4_7 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_o_p_e_r_a_t_o_r_!_= │ │ │ │ -bool operator!=(const Triple &triple) const │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_2_0_6 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_o_p_e_r_a_t_o_r_<_= │ │ │ │ -bool operator<=(const Triple &triple) const │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_2_3_6 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_T_r_i_p_l_e │ │ │ │ -Triple() │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_1_3_7 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_f_i_r_s_t │ │ │ │ -T1 first │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_1_2_4 │ │ │ │ -_B_A_L_L_:_:_T_r_i_p_l_e_:_:_~_T_r_i_p_l_e │ │ │ │ -virtual ~Triple() │ │ │ │ -DDeeffiinniittiioonn _t_r_i_p_l_e_._h_:_1_5_9 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y │ │ │ │ +DDeeffiinniittiioonn _d_i_r_e_c_t_o_r_y_._h_:_5_1 │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_M_A_X___P_A_T_H___L_E_N_G_T_H │ │ │ │ +static const Size MAX_PATH_LENGTH │ │ │ │ +DDeeffiinniittiioonn _d_i_r_e_c_t_o_r_y_._h_:_6_6 │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_c_h_a_n_g_e_T_o_U_s_e_r_H_o_m_e_D_i_r │ │ │ │ +static bool changeToUserHomeDir() │ │ │ │ +Goto the home directory of the current user. │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_s_e_t_C_u_r_r_e_n_t │ │ │ │ +bool setCurrent() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_c_o_u_n_t_F_i_l_e_s │ │ │ │ +Size countFiles() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_c_o_u_n_t_I_t_e_m_s │ │ │ │ +Size countItems() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_g_e_t_N_e_x_t_E_n_t_r_y │ │ │ │ +bool getNextEntry(String &entry) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_d_e_s_t_r_o_y │ │ │ │ +void destroy() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_D_i_r_e_c_t_o_r_y │ │ │ │ +Directory(const Directory &directory) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_g_e_t_F_i_r_s_t_E_n_t_r_y │ │ │ │ +bool getFirstEntry(String &entry) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_c_l_e_a_r │ │ │ │ +void clear() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_c_o_u_n_t_D_i_r_e_c_t_o_r_i_e_s │ │ │ │ +Size countDirectories() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_~_D_i_r_e_c_t_o_r_y │ │ │ │ +~Directory() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_D_i_r_e_c_t_o_r_y │ │ │ │ +Directory() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_s_e_t_C_u_r_r_e_n_t │ │ │ │ +bool setCurrent(String directory_path) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_f_i_n_d │ │ │ │ +bool find(const String &filename, String &filepath) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_D_i_r_e_c_t_o_r_y │ │ │ │ +Directory(const String &directory_path, bool set_current=false) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_r_e_n_a_m_e │ │ │ │ +bool rename(String old_path, String new_path) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_r_e_n_a_m_e_T_o │ │ │ │ +bool renameTo(String new_path) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_r_e_m_o_v_e │ │ │ │ +bool remove(String old_path) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_s_e_t │ │ │ │ +void set(const Directory &directory) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_h_a_s │ │ │ │ +bool has(const String &item) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_i_s_V_a_l_i_d │ │ │ │ +bool isValid() const │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_g_e_t_P_a_t_h │ │ │ │ +const String & getPath() const │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_c_r_e_a_t_e │ │ │ │ +bool create(String path, const mode_t &mode=0777) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_i_s_E_m_p_t_y │ │ │ │ +bool isEmpty() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_g_e_t │ │ │ │ +void get(Directory &directory) const │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_s_e_t │ │ │ │ +bool set(const String &directory_path, bool set_current=false) │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_r_e_m_o_v_e │ │ │ │ +bool remove() │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_i_s_C_u_r_r_e_n_t │ │ │ │ +bool isCurrent() const │ │ │ │ +_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_g_e_t_U_s_e_r_H_o_m_e_D_i_r │ │ │ │ +static String getUserHomeDir() │ │ │ │ +Get the home directory of the current user. │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d36/a07986.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members │ │ │
    BALL::VIEW::CalculateFDPBThread Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/threads.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/threads.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::CalculateFDPBThread:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::BALLThread │ │ │ @@ -132,15 +132,15 @@ │ │ │  Sends the string as outout to Log.info.
    │ │ │   │ │ │ void waitForUpdateOfRepresentations_ () │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 120 of file threads.h.

    │ │ │ +

    Definition at line 120 of file threads.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ CalculateFDPBThread()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -204,15 +204,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 132 of file threads.h.

    │ │ │ +

    Definition at line 132 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ dialog_

    │ │ │ │ │ │ @@ -229,15 +229,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 135 of file threads.h.

    │ │ │ +

    Definition at line 135 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d39/a00314.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: representationManager.h File Reference │ │ │ +BALL: undoManagerDialog.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,35 +65,35 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    representationManager.h File Reference
    │ │ │ +
    undoManagerDialog.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/VIEW/KERNEL/representation.h>
    │ │ │ -#include <BALL/SYSTEM/mutex.h>
    │ │ │ -#include <QtCore/QCoreApplication>
    │ │ │ -#include <QtCore/QWaitCondition>
    │ │ │ -#include <vector>
    │ │ │ +
    #include <BALL/COMMON/global.h>
    │ │ │ +#include <BALL/VIEW/KERNEL/modularWidget.h>
    │ │ │ +#include <BALL/VIEW/KERNEL/snapshotManagerInterface.h>
    │ │ │ +#include <QtWidgets/QDialog>
    │ │ │ +#include <BALL/VIEW/UIC/ui_undoManagerDialog.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::RepresentationManager
    class  BALL::VIEW::UndoManagerDialog
     
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,25 +1,25 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ + * _D_I_A_L_O_G_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -representationManager.h File Reference │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_S_Y_S_T_E_M_/_m_u_t_e_x_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ +undoManagerDialog.h File Reference │ │ │ │ +#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_s_n_a_p_s_h_o_t_M_a_n_a_g_e_r_I_n_t_e_r_f_a_c_e_._h> │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d39/a00314_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: representationManager.h Source File │ │ │ +BALL: undoManagerDialog.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,252 +70,118 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    representationManager.h
    │ │ │ +
    undoManagerDialog.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4// $Id: representationManager.h,v 1.1.4.2 2007/03/28 13:11:43 amoll Exp $
    │ │ │ -
    5
    │ │ │ -
    6#ifndef BALL_VIEW_KERNEL_REPRESENTATIONMANAGER_H
    │ │ │ -
    7#define BALL_VIEW_KERNEL_REPRESENTATIONMANAGER_H
    │ │ │ -
    8
    │ │ │ -
    9#ifndef BALL_VIEW_KERNEL_REPRESENTATION_H
    │ │ │ -
    10# include <BALL/VIEW/KERNEL/representation.h>
    │ │ │ -
    11#endif
    │ │ │ -
    12
    │ │ │ -
    13#ifndef BALL_SYSTEM_MUTEX_H
    │ │ │ -
    14#include <BALL/SYSTEM/mutex.h>
    │ │ │ -
    15#endif
    │ │ │ -
    16
    │ │ │ -
    17#include <QtCore/QCoreApplication>
    │ │ │ -
    18#include <QtCore/QWaitCondition>
    │ │ │ +
    4
    │ │ │ +
    5#ifndef BALL_VIEW_DIALOGS_UNDOMANAGERDIALOG_H
    │ │ │ +
    6#define BALL_VIEW_DIALOGS_UNDOMANAGERDIALOG_H
    │ │ │ +
    7
    │ │ │ +
    8#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ +
    9# include <BALL/COMMON/global.h>
    │ │ │ +
    10#endif
    │ │ │ +
    11
    │ │ │ +
    12#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H
    │ │ │ +
    13# include <BALL/VIEW/KERNEL/modularWidget.h>
    │ │ │ +
    14#endif
    │ │ │ +
    15
    │ │ │ +
    16#ifndef BALL_VIEW_KERNEL_SNAPSHOT_MANAGER_INTERFACE_H
    │ │ │ +
    17# include <BALL/VIEW/KERNEL/snapshotManagerInterface.h>
    │ │ │ +
    18#endif
    │ │ │
    19
    │ │ │ -
    20#include <vector>
    │ │ │ +
    20#include <QtWidgets/QDialog>
    │ │ │
    21
    │ │ │ -
    22using std::vector;
    │ │ │ +
    22#include <BALL/VIEW/UIC/ui_undoManagerDialog.h>
    │ │ │
    23
    │ │ │
    24namespace BALL
    │ │ │
    25{
    │ │ │ -
    26 class Composite;
    │ │ │ -
    27 class INIFile;
    │ │ │ -
    28
    │ │ │ -
    29 namespace VIEW
    │ │ │ -
    30 {
    │ │ │ -
    31 class MainControl;
    │ │ │ -
    32 class UpdateRepresentationThread;
    │ │ │ -
    33 class ClippingPlane;
    │ │ │ -
    34
    │ │ │ -
    │ │ │ -
    45 class BALL_VIEW_EXPORT RepresentationManager
    │ │ │ -
    46 : public Object
    │ │ │ -
    47 {
    │ │ │ -
    48 friend class Representation;
    │ │ │ -
    49 friend class UpdateRepresentationThread;
    │ │ │ -
    50 friend class BALLThread;
    │ │ │ -
    51 friend class MainControl;
    │ │ │ -
    52
    │ │ │ -
    53 public:
    │ │ │ -
    54
    │ │ │ -
    55 BALL_CREATE(RepresentationManager)
    │ │ │ +
    26 namespace VIEW
    │ │ │ +
    27 {
    │ │ │ +
    │ │ │ +
    31 class BALL_VIEW_EXPORT UndoManagerDialog
    │ │ │ +
    32 : public QDialog,
    │ │ │ +
    33 public Ui_UndoManagerDialogData,
    │ │ │ +
    34 public ModularWidget
    │ │ │ +
    35 {
    │ │ │ +
    36 Q_OBJECT
    │ │ │ +
    37
    │ │ │ +
    38 public:
    │ │ │ +
    39
    │ │ │ +
    40 BALL_EMBEDDABLE(UndoManagerDialog,ModularWidget)
    │ │ │ +
    41
    │ │ │ +
    42
    │ │ │ +
    43 UndoManagerDialog( QWidget* parent = 0, const char* name = "UndoManagerDialog", Qt::WindowFlags fl = 0 );
    │ │ │ +
    44
    │ │ │ +
    46 ~UndoManagerDialog() {}
    │ │ │ +
    47
    │ │ │ +
    49 virtual void initializeWidget(MainControl& main_control);
    │ │ │ +
    50
    │ │ │ +
    52 virtual void checkMenu(MainControl& main_control);
    │ │ │ +
    53
    │ │ │ +
    55 virtual void onNotify(Message* message);
    │ │ │
    56
    │ │ │ -
    57
    │ │ │ -
    62 typedef HashSet<Representation*> RepresentationSet;
    │ │ │ -
    63
    │ │ │ -
    65 typedef RepresentationList::iterator RepresentationsIterator;
    │ │ │ -
    66
    │ │ │ -
    68 typedef RepresentationList::const_iterator RepresentationsConstIterator;
    │ │ │ -
    69
    │ │ │ -
    71
    │ │ │ -
    74
    │ │ │ -
    78 RepresentationManager(MainControl* mc = 0);
    │ │ │ -
    79
    │ │ │ -
    82 RepresentationManager(const RepresentationManager& pm);
    │ │ │ -
    83
    │ │ │ -
    86 virtual ~RepresentationManager();
    │ │ │ -
    87
    │ │ │ -
    89
    │ │ │ -
    92
    │ │ │ -
    94 const RepresentationManager& operator = (const RepresentationManager& pm);
    │ │ │ -
    95
    │ │ │ -
    97 bool operator == (const RepresentationManager& pm) const;
    │ │ │ -
    98
    │ │ │ -
    100 void clear();
    │ │ │ -
    101
    │ │ │ -
    108 bool remove(Representation& representation, bool send_message = true);
    │ │ │ -
    109
    │ │ │ -
    114 bool insert(Representation& representation, bool send_message = true);
    │ │ │ -
    115
    │ │ │ -
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    117 const RepresentationList& getRepresentations() const
    │ │ │ -
    118 { return representations_;}
    │ │ │ -
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    119
    │ │ │ -
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    121 Size getNumberOfRepresentations() const
    │ │ │ -
    122 { return representations_.size();}
    │ │ │ -
    │ │ │ -
    123
    │ │ │ -
    125 Representation* createRepresentation();
    │ │ │ -
    126
    │ │ │ -
    128 bool has(const Representation& representation) const;
    │ │ │ -
    129
    │ │ │ -
    131 void dump(std::ostream& s, Size depth = 0) const;
    │ │ │ -
    132
    │ │ │ -
    │ │ │ -
    134 RepresentationsIterator begin()
    │ │ │ -
    135 { return representations_.begin();}
    │ │ │ -
    │ │ │ -
    136
    │ │ │ -
    │ │ │ -
    138 RepresentationsConstIterator begin() const
    │ │ │ -
    139 { return representations_.begin();}
    │ │ │ +
    57 public Q_SLOTS:
    │ │ │ +
    58
    │ │ │ +
    60 void show();
    │ │ │ +
    61
    │ │ │ +
    63 void close_pressed();
    │ │ │ +
    64
    │ │ │ +
    66 void resetTo_pressed();
    │ │ │ +
    67
    │ │ │ +
    69 void takeSnapshot_pressed();
    │ │ │ +
    70
    │ │ │ +
    71 protected:
    │ │ │ +
    72
    │ │ │ +
    73 QAction* action_;
    │ │ │ +
    74 SnapshotManagerInterface snapshot_interface_;
    │ │ │ +
    75
    │ │ │ +
    76 bool first_run;
    │ │ │ +
    77
    │ │ │ +
    78 };
    │ │ │
    │ │ │ -
    140
    │ │ │ -
    │ │ │ -
    142 RepresentationsIterator end()
    │ │ │ -
    143 { return representations_.end();}
    │ │ │ -
    │ │ │ -
    144
    │ │ │ -
    │ │ │ -
    146 RepresentationsConstIterator end() const
    │ │ │ -
    147 { return representations_.end();}
    │ │ │ -
    │ │ │ -
    148
    │ │ │ -
    156 RepresentationList removedComposite(const Composite& composite, bool update = true);
    │ │ │ -
    157
    │ │ │ -
    162 RepresentationList getRepresentationsOf(const Composite& composite);
    │ │ │ -
    163
    │ │ │ -
    165 void rebuildAllRepresentations();
    │ │ │ -
    166
    │ │ │ -
    168 const vector<ClippingPlane*>& getClippingPlanes() const { return clipping_planes_;}
    │ │ │ -
    169
    │ │ │ -
    171 bool removeClippingPlane(ClippingPlane* plane);
    │ │ │ -
    172
    │ │ │ -
    174 void insertClippingPlane(ClippingPlane* plane);
    │ │ │ -
    175
    │ │ │ -
    177 void storeRepresentations(INIFile& out);
    │ │ │ -
    178
    │ │ │ -
    180 void restoreRepresentations(const INIFile& in, const vector<const Composite*>& new_systems);
    │ │ │ -
    181
    │ │ │ -
    183 void focusRepresentation(const Representation& rep);
    │ │ │ -
    184
    │ │ │ -
    186 bool willBeUpdated(const Representation& rep) const;
    │ │ │ -
    187
    │ │ │ -
    189 bool updateRunning() const ;
    │ │ │ -
    190
    │ │ │ -
    192 bool startRendering(Representation* rep);
    │ │ │ -
    193
    │ │ │ -
    195 void finishedRendering(Representation* rep);
    │ │ │ -
    196
    │ │ │ -
    198 bool isBeeingRendered(const Representation* rep) const;
    │ │ │ -
    199
    │ │ │ -
    200 protected:
    │ │ │ -
    201
    │ │ │ -
    203 Representation* popRepresentationToUpdate();
    │ │ │ -
    204
    │ │ │ -
    205 void finishedUpdate_(Representation* rep);
    │ │ │ -
    206
    │ │ │ -
    207 /*_ Called by Representation::update() to start a multithreaded
    │ │ │ -
    208 Update of the Representation.
    │ │ │ -
    209 (Only used in Multithreaded code.)
    │ │ │ -
    210 */
    │ │ │ -
    211 void update_(Representation& rep);
    │ │ │ -
    212
    │ │ │ -
    213 //_ List with all representations
    │ │ │ -
    214 RepresentationList representations_;
    │ │ │ -
    215
    │ │ │ -
    216 HashSet<Representation*> beeing_rendered_;
    │ │ │ -
    217 HashSet<Representation*> beeing_updated_;
    │ │ │ -
    218 HashSet<Representation*> to_update_;
    │ │ │ -
    219
    │ │ │ -
    220 vector<ClippingPlane*> clipping_planes_;
    │ │ │ -
    221
    │ │ │ -
    222 // we need to ensure that the mutex is always created correctly before
    │ │ │ -
    223 // the thread that tries to access it!
    │ │ │ -
    224 mutable Mutex update_mutex_;
    │ │ │ -
    225
    │ │ │ -
    226 UpdateRepresentationThread* thread_;
    │ │ │ -
    227 bool no_update_;
    │ │ │ -
    228 bool still_to_notify_;
    │ │ │ -
    229
    │ │ │ -
    230 MainControl* main_control_;
    │ │ │ -
    231 };
    │ │ │ -
    │ │ │ -
    232
    │ │ │ -
    233 } // namespace VIEW
    │ │ │ -
    234} // namespace BALL
    │ │ │ -
    235
    │ │ │ -
    236#endif // BALL_VIEW_KERNEL_REPRESENTATIONMANAGER_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ -
    BALL::VIEW::RepresentationList
    std::list< Representation * > RepresentationList
    Definition representation.h:342
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::RepresentationManager::end
    RepresentationsConstIterator end() const
    Const Iterator pointing behind the last Representation.
    Definition representationManager.h:146
    │ │ │ - │ │ │ -
    BALL::VIEW::RepresentationManager::removedComposite
    RepresentationList removedComposite(const Composite &composite, bool update=true)
    │ │ │ -
    BALL::VIEW::RepresentationManager::beeing_rendered_
    HashSet< Representation * > beeing_rendered_
    Definition representationManager.h:216
    │ │ │ -
    BALL::VIEW::RepresentationManager::clipping_planes_
    vector< ClippingPlane * > clipping_planes_
    Definition representationManager.h:220
    │ │ │ -
    BALL::VIEW::RepresentationManager::popRepresentationToUpdate
    Representation * popRepresentationToUpdate()
    │ │ │ -
    BALL::VIEW::RepresentationManager::beeing_updated_
    HashSet< Representation * > beeing_updated_
    Definition representationManager.h:217
    │ │ │ - │ │ │ -
    BALL::VIEW::RepresentationManager::removeClippingPlane
    bool removeClippingPlane(ClippingPlane *plane)
    │ │ │ - │ │ │ -
    BALL::VIEW::RepresentationManager::createRepresentation
    Representation * createRepresentation()
    Create a Representation and insert it.
    │ │ │ - │ │ │ -
    BALL::VIEW::RepresentationManager::dump
    void dump(std::ostream &s, Size depth=0) const
    Dump the internal state to an output stream.
    │ │ │ -
    BALL::VIEW::RepresentationManager::willBeUpdated
    bool willBeUpdated(const Representation &rep) const
    Return true if a Representation will be updated.
    │ │ │ -
    BALL::VIEW::RepresentationManager::insertClippingPlane
    void insertClippingPlane(ClippingPlane *plane)
    │ │ │ -
    BALL::VIEW::RepresentationManager::to_update_
    HashSet< Representation * > to_update_
    Definition representationManager.h:218
    │ │ │ -
    BALL::VIEW::RepresentationManager::restoreRepresentations
    void restoreRepresentations(const INIFile &in, const vector< const Composite * > &new_systems)
    │ │ │ -
    BALL::VIEW::RepresentationManager::thread_
    UpdateRepresentationThread * thread_
    Definition representationManager.h:226
    │ │ │ -
    BALL::VIEW::RepresentationManager::RepresentationSet
    HashSet< Representation * > RepresentationSet
    Definition representationManager.h:62
    │ │ │ -
    BALL::VIEW::RepresentationManager::getClippingPlanes
    const vector< ClippingPlane * > & getClippingPlanes() const
    Definition representationManager.h:168
    │ │ │ -
    BALL::VIEW::RepresentationManager::update_
    void update_(Representation &rep)
    │ │ │ -
    BALL::VIEW::RepresentationManager::finishedUpdate_
    void finishedUpdate_(Representation *rep)
    │ │ │ -
    BALL::VIEW::RepresentationManager::RepresentationsIterator
    RepresentationList::iterator RepresentationsIterator
    Iteration to the Representations.
    Definition representationManager.h:65
    │ │ │ -
    BALL::VIEW::RepresentationManager::startRendering
    bool startRendering(Representation *rep)
    │ │ │ -
    BALL::VIEW::RepresentationManager::RepresentationsConstIterator
    RepresentationList::const_iterator RepresentationsConstIterator
    ConstIterator to the Representations.
    Definition representationManager.h:68
    │ │ │ -
    BALL::VIEW::RepresentationManager::begin
    RepresentationsConstIterator begin() const
    ConstIterator to the first Representation.
    Definition representationManager.h:138
    │ │ │ -
    BALL::VIEW::RepresentationManager::finishedRendering
    void finishedRendering(Representation *rep)
    │ │ │ -
    BALL::VIEW::RepresentationManager::end
    RepresentationsIterator end()
    Iterator pointing behind the last Representation.
    Definition representationManager.h:142
    │ │ │ -
    BALL::VIEW::RepresentationManager::has
    bool has(const Representation &representation) const
    Test if a Representation is inserted.
    │ │ │ -
    BALL::VIEW::RepresentationManager::getRepresentationsOf
    RepresentationList getRepresentationsOf(const Composite &composite)
    │ │ │ - │ │ │ -
    BALL::VIEW::RepresentationManager::focusRepresentation
    void focusRepresentation(const Representation &rep)
    │ │ │ - │ │ │ -
    BALL::VIEW::RepresentationManager::getNumberOfRepresentations
    Size getNumberOfRepresentations() const
    Get the number of the Representations.
    Definition representationManager.h:121
    │ │ │ -
    BALL::VIEW::RepresentationManager::begin
    RepresentationsIterator begin()
    Iterator to the first Representation.
    Definition representationManager.h:134
    │ │ │ -
    BALL::VIEW::RepresentationManager::isBeeingRendered
    bool isBeeingRendered(const Representation *rep) const
    Used by UpdateRepresentationThread.
    │ │ │ -
    BALL::VIEW::RepresentationManager::storeRepresentations
    void storeRepresentations(INIFile &out)
    │ │ │ -
    BALL::VIEW::RepresentationManager::updateRunning
    bool updateRunning() const
    Return true, if a Representation is currently beeing updated.
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ +
    79
    │ │ │ +
    80 }
    │ │ │ +
    81} // namespaces
    │ │ │ +
    82
    │ │ │ +
    83#endif
    │ │ │ + │ │ │ + │ │ │ +
    BALL_EMBEDDABLE
    #define BALL_EMBEDDABLE(TYPE, BASE)
    Definition embeddable.h:31
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::UndoManagerDialog::show
    void show()
    Show and raise dialog.
    │ │ │ +
    BALL::VIEW::UndoManagerDialog::initializeWidget
    virtual void initializeWidget(MainControl &main_control)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::UndoManagerDialog::snapshot_interface_
    SnapshotManagerInterface snapshot_interface_
    Definition undoManagerDialog.h:74
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::UndoManagerDialog::checkMenu
    virtual void checkMenu(MainControl &main_control)
    │ │ │ +
    BALL::VIEW::UndoManagerDialog::onNotify
    virtual void onNotify(Message *message)
    Overrides message in order to intercept system changed events.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
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    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,321 +1,133 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ -representationManager.h │ │ │ │ + * _D_I_A_L_O_G_S │ │ │ │ +undoManagerDialog.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: representationManager.h,v 1.1.4.2 2007/03/28 13:11:43 amoll Exp $ │ │ │ │ -5 │ │ │ │ -6#ifndef BALL_VIEW_KERNEL_REPRESENTATIONMANAGER_H │ │ │ │ -7#define BALL_VIEW_KERNEL_REPRESENTATIONMANAGER_H │ │ │ │ -8 │ │ │ │ -9#ifndef BALL_VIEW_KERNEL_REPRESENTATION_H │ │ │ │ -10# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h> │ │ │ │ -11#endif │ │ │ │ -12 │ │ │ │ -13#ifndef BALL_SYSTEM_MUTEX_H │ │ │ │ -14#include <_B_A_L_L_/_S_Y_S_T_E_M_/_m_u_t_e_x_._h> │ │ │ │ -15#endif │ │ │ │ -16 │ │ │ │ -17#include │ │ │ │ -18#include │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_VIEW_DIALOGS_UNDOMANAGERDIALOG_H │ │ │ │ +6#define BALL_VIEW_DIALOGS_UNDOMANAGERDIALOG_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ +9# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H │ │ │ │ +13# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifndef BALL_VIEW_KERNEL_SNAPSHOT_MANAGER_INTERFACE_H │ │ │ │ +17# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_s_n_a_p_s_h_o_t_M_a_n_a_g_e_r_I_n_t_e_r_f_a_c_e_._h> │ │ │ │ +18#endif │ │ │ │ 19 │ │ │ │ -20#include │ │ │ │ +20#include │ │ │ │ 21 │ │ │ │ -22using std::vector; │ │ │ │ +22#include │ │ │ │ 23 │ │ │ │ 24namespace _B_A_L_L │ │ │ │ 25{ │ │ │ │ -26 class Composite; │ │ │ │ -27 class INIFile; │ │ │ │ -28 │ │ │ │ -29 namespace VIEW │ │ │ │ -30 { │ │ │ │ -31 class MainControl; │ │ │ │ -32 class UpdateRepresentationThread; │ │ │ │ -33 class ClippingPlane; │ │ │ │ -34 │ │ │ │ -_4_5 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r │ │ │ │ -46 : public _O_b_j_e_c_t │ │ │ │ -47 { │ │ │ │ -_4_8 friend class _R_e_p_r_e_s_e_n_t_a_t_i_o_n; │ │ │ │ -_4_9 friend class _U_p_d_a_t_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n_T_h_r_e_a_d; │ │ │ │ -_5_0 friend class _B_A_L_L_T_h_r_e_a_d; │ │ │ │ -_5_1 friend class _M_a_i_n_C_o_n_t_r_o_l; │ │ │ │ -52 │ │ │ │ -53 public: │ │ │ │ -54 │ │ │ │ -55 _B_A_L_L___C_R_E_A_T_E(_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r) │ │ │ │ +26 namespace VIEW │ │ │ │ +27 { │ │ │ │ +_3_1 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g │ │ │ │ +32 : public _Q_D_i_a_l_o_g, │ │ │ │ +33 public Ui_UndoManagerDialogData, │ │ │ │ +34 public _M_o_d_u_l_a_r_W_i_d_g_e_t │ │ │ │ +35 { │ │ │ │ +36 Q_OBJECT │ │ │ │ +37 │ │ │ │ +38 public: │ │ │ │ +39 │ │ │ │ +40 _B_A_L_L___E_M_B_E_D_D_A_B_L_E(_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g,_M_o_d_u_l_a_r_W_i_d_g_e_t) │ │ │ │ +41 │ │ │ │ +42 │ │ │ │ +_4_3 _U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g( _Q_W_i_d_g_e_t* parent = 0, const char* name = │ │ │ │ +"_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g", Qt::WindowFlags fl = 0 ); │ │ │ │ +44 │ │ │ │ +_4_6 ~_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g() {} │ │ │ │ +47 │ │ │ │ +_4_9 virtual void _i_n_i_t_i_a_l_i_z_e_W_i_d_g_e_t(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ +50 │ │ │ │ +_5_2 virtual void _c_h_e_c_k_M_e_n_u(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ +53 │ │ │ │ +_5_5 virtual void _o_n_N_o_t_i_f_y(_M_e_s_s_a_g_e* message); │ │ │ │ 56 │ │ │ │ -57 │ │ │ │ -_6_2 typedef _H_a_s_h_S_e_t<_R_e_p_r_e_s_e_n_t_a_t_i_o_n*> _R_e_p_r_e_s_e_n_t_a_t_i_o_n_S_e_t; │ │ │ │ -63 │ │ │ │ -_6_5 typedef _R_e_p_r_e_s_e_n_t_a_t_i_o_n_L_i_s_t::iterator _R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_I_t_e_r_a_t_o_r; │ │ │ │ -66 │ │ │ │ -_6_8 typedef _R_e_p_r_e_s_e_n_t_a_t_i_o_n_L_i_s_t::const_iterator _R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_C_o_n_s_t_I_t_e_r_a_t_o_r; │ │ │ │ -69 │ │ │ │ -71 │ │ │ │ -74 │ │ │ │ -_7_8 _R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r(_M_a_i_n_C_o_n_t_r_o_l* mc = 0); │ │ │ │ +57 public Q_SLOTS: │ │ │ │ +58 │ │ │ │ +_6_0 void _s_h_o_w(); │ │ │ │ +61 │ │ │ │ +_6_3 void _c_l_o_s_e___p_r_e_s_s_e_d(); │ │ │ │ +64 │ │ │ │ +_6_6 void _r_e_s_e_t_T_o___p_r_e_s_s_e_d(); │ │ │ │ +67 │ │ │ │ +_6_9 void _t_a_k_e_S_n_a_p_s_h_o_t___p_r_e_s_s_e_d(); │ │ │ │ +70 │ │ │ │ +71 protected: │ │ │ │ +72 │ │ │ │ +_7_3 QAction* _a_c_t_i_o_n__; │ │ │ │ +_7_4 _S_n_a_p_s_h_o_t_M_a_n_a_g_e_r_I_n_t_e_r_f_a_c_e _s_n_a_p_s_h_o_t___i_n_t_e_r_f_a_c_e__; │ │ │ │ +75 │ │ │ │ +_7_6 bool _f_i_r_s_t___r_u_n; │ │ │ │ +77 │ │ │ │ +78 }; │ │ │ │ 79 │ │ │ │ -_8_2 _R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r(const _R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r& pm); │ │ │ │ -83 │ │ │ │ -_8_6 virtual ~_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r(); │ │ │ │ -87 │ │ │ │ -89 │ │ │ │ -92 │ │ │ │ -_9_4 const _R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r& operator = (const _R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r& pm); │ │ │ │ -95 │ │ │ │ -_9_7 bool operator == (const _R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r& pm) const; │ │ │ │ -98 │ │ │ │ -_1_0_0 void clear(); │ │ │ │ -101 │ │ │ │ -_1_0_8 bool remove(_R_e_p_r_e_s_e_n_t_a_t_i_o_n& representation, bool send_message = true); │ │ │ │ -109 │ │ │ │ -_1_1_4 bool insert(_R_e_p_r_e_s_e_n_t_a_t_i_o_n& representation, bool send_message = true); │ │ │ │ -115 │ │ │ │ -_1_1_7 const _R_e_p_r_e_s_e_n_t_a_t_i_o_n_L_i_s_t& getRepresentations() const │ │ │ │ -118 { return representations_;} │ │ │ │ -119 │ │ │ │ -_1_2_1 _S_i_z_e _g_e_t_N_u_m_b_e_r_O_f_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s() const │ │ │ │ -122 { return representations_.size();} │ │ │ │ -123 │ │ │ │ -_1_2_5 _R_e_p_r_e_s_e_n_t_a_t_i_o_n* _c_r_e_a_t_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n(); │ │ │ │ -126 │ │ │ │ -_1_2_8 bool _h_a_s(const _R_e_p_r_e_s_e_n_t_a_t_i_o_n& representation) const; │ │ │ │ -129 │ │ │ │ -_1_3_1 void _d_u_m_p(std::ostream& s, _S_i_z_e depth = 0) const; │ │ │ │ -132 │ │ │ │ -_1_3_4 _R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_I_t_e_r_a_t_o_r _b_e_g_i_n() │ │ │ │ -135 { return representations_.begin();} │ │ │ │ -136 │ │ │ │ -_1_3_8 _R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_C_o_n_s_t_I_t_e_r_a_t_o_r _b_e_g_i_n() const │ │ │ │ -139 { return representations_.begin();} │ │ │ │ -140 │ │ │ │ -_1_4_2 _R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_I_t_e_r_a_t_o_r _e_n_d() │ │ │ │ -143 { return representations_.end();} │ │ │ │ -144 │ │ │ │ -_1_4_6 _R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_C_o_n_s_t_I_t_e_r_a_t_o_r _e_n_d() const │ │ │ │ -147 { return representations_.end();} │ │ │ │ -148 │ │ │ │ -_1_5_6 _R_e_p_r_e_s_e_n_t_a_t_i_o_n_L_i_s_t _r_e_m_o_v_e_d_C_o_m_p_o_s_i_t_e(const _C_o_m_p_o_s_i_t_e& composite, bool update │ │ │ │ -= true); │ │ │ │ -157 │ │ │ │ -_1_6_2 _R_e_p_r_e_s_e_n_t_a_t_i_o_n_L_i_s_t _g_e_t_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_O_f(const _C_o_m_p_o_s_i_t_e& composite); │ │ │ │ -163 │ │ │ │ -_1_6_5 void _r_e_b_u_i_l_d_A_l_l_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s(); │ │ │ │ -166 │ │ │ │ -_1_6_8 const vector& _g_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e_s() const { return │ │ │ │ -clipping_planes_;} │ │ │ │ -169 │ │ │ │ -_1_7_1 bool _r_e_m_o_v_e_C_l_i_p_p_i_n_g_P_l_a_n_e(_C_l_i_p_p_i_n_g_P_l_a_n_e* plane); │ │ │ │ -172 │ │ │ │ -_1_7_4 void _i_n_s_e_r_t_C_l_i_p_p_i_n_g_P_l_a_n_e(_C_l_i_p_p_i_n_g_P_l_a_n_e* plane); │ │ │ │ -175 │ │ │ │ -_1_7_7 void _s_t_o_r_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s(_I_N_I_F_i_l_e& out); │ │ │ │ -178 │ │ │ │ -_1_8_0 void _r_e_s_t_o_r_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s(const _I_N_I_F_i_l_e& in, const vector& new_systems); │ │ │ │ -181 │ │ │ │ -_1_8_3 void _f_o_c_u_s_R_e_p_r_e_s_e_n_t_a_t_i_o_n(const _R_e_p_r_e_s_e_n_t_a_t_i_o_n& rep); │ │ │ │ -184 │ │ │ │ -_1_8_6 bool _w_i_l_l_B_e_U_p_d_a_t_e_d(const _R_e_p_r_e_s_e_n_t_a_t_i_o_n& rep) const; │ │ │ │ -187 │ │ │ │ -_1_8_9 bool _u_p_d_a_t_e_R_u_n_n_i_n_g() const ; │ │ │ │ -190 │ │ │ │ -_1_9_2 bool _s_t_a_r_t_R_e_n_d_e_r_i_n_g(_R_e_p_r_e_s_e_n_t_a_t_i_o_n* rep); │ │ │ │ -193 │ │ │ │ -_1_9_5 void _f_i_n_i_s_h_e_d_R_e_n_d_e_r_i_n_g(_R_e_p_r_e_s_e_n_t_a_t_i_o_n* rep); │ │ │ │ -196 │ │ │ │ -_1_9_8 bool _i_s_B_e_e_i_n_g_R_e_n_d_e_r_e_d(const _R_e_p_r_e_s_e_n_t_a_t_i_o_n* rep) const; │ │ │ │ -199 │ │ │ │ -200 protected: │ │ │ │ -201 │ │ │ │ -_2_0_3 _R_e_p_r_e_s_e_n_t_a_t_i_o_n* _p_o_p_R_e_p_r_e_s_e_n_t_a_t_i_o_n_T_o_U_p_d_a_t_e(); │ │ │ │ -204 │ │ │ │ -_2_0_5 void _f_i_n_i_s_h_e_d_U_p_d_a_t_e__(_R_e_p_r_e_s_e_n_t_a_t_i_o_n* rep); │ │ │ │ -206 │ │ │ │ -207 /*_ Called by Representation::update() to start a multithreaded │ │ │ │ -208 Update of the Representation. │ │ │ │ -209 (Only used in Multithreaded code.) │ │ │ │ -210 */ │ │ │ │ -_2_1_1 void _u_p_d_a_t_e__(_R_e_p_r_e_s_e_n_t_a_t_i_o_n& rep); │ │ │ │ -212 │ │ │ │ -213 //_ List with all representations │ │ │ │ -_2_1_4 _R_e_p_r_e_s_e_n_t_a_t_i_o_n_L_i_s_t _r_e_p_r_e_s_e_n_t_a_t_i_o_n_s__; │ │ │ │ -215 │ │ │ │ -_2_1_6 _H_a_s_h_S_e_t_<_R_e_p_r_e_s_e_n_t_a_t_i_o_n_*_> _b_e_e_i_n_g___r_e_n_d_e_r_e_d__; │ │ │ │ -_2_1_7 _H_a_s_h_S_e_t_<_R_e_p_r_e_s_e_n_t_a_t_i_o_n_*_> _b_e_e_i_n_g___u_p_d_a_t_e_d__; │ │ │ │ -_2_1_8 _H_a_s_h_S_e_t_<_R_e_p_r_e_s_e_n_t_a_t_i_o_n_*_> _t_o___u_p_d_a_t_e__; │ │ │ │ -219 │ │ │ │ -_2_2_0 vector _c_l_i_p_p_i_n_g___p_l_a_n_e_s__; │ │ │ │ -221 │ │ │ │ -222 // we need to ensure that the mutex is always created correctly before │ │ │ │ -223 // the thread that tries to access it! │ │ │ │ -_2_2_4 mutable _M_u_t_e_x _u_p_d_a_t_e___m_u_t_e_x__; │ │ │ │ -225 │ │ │ │ -_2_2_6 _U_p_d_a_t_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n_T_h_r_e_a_d* _t_h_r_e_a_d__; │ │ │ │ -_2_2_7 bool _n_o___u_p_d_a_t_e__; │ │ │ │ -_2_2_8 bool _s_t_i_l_l___t_o___n_o_t_i_f_y__; │ │ │ │ -229 │ │ │ │ -_2_3_0 _M_a_i_n_C_o_n_t_r_o_l* _m_a_i_n___c_o_n_t_r_o_l__; │ │ │ │ -231 }; │ │ │ │ -232 │ │ │ │ -233 } // namespace VIEW │ │ │ │ -234} // namespace BALL │ │ │ │ -235 │ │ │ │ -236#endif // BALL_VIEW_KERNEL_REPRESENTATIONMANAGER_H │ │ │ │ -_r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h │ │ │ │ -_m_u_t_e_x_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +80 } │ │ │ │ +81} // namespaces │ │ │ │ +82 │ │ │ │ +83#endif │ │ │ │ +_m_o_d_u_l_a_r_W_i_d_g_e_t_._h │ │ │ │ +_s_n_a_p_s_h_o_t_M_a_n_a_g_e_r_I_n_t_e_r_f_a_c_e_._h │ │ │ │ +_B_A_L_L___E_M_B_E_D_D_A_B_L_E │ │ │ │ +#define BALL_EMBEDDABLE(TYPE, BASE) │ │ │ │ +DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_3_1 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_L_i_s_t │ │ │ │ -std::list< Representation * > RepresentationList │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h_:_3_4_2 │ │ │ │ -_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ -DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_O_b_j_e_c_t │ │ │ │ -DDeeffiinniittiioonn _o_b_j_e_c_t_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_S_e_t │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_I_N_I_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _I_N_I_F_i_l_e_._h_:_2_9 │ │ │ │ -_B_A_L_L_:_:_T_M_u_t_e_x_<_ _B_A_L_L___D_E_F_A_U_L_T___M_U_T_E_X___T_Y_P_E_ _> │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_C_l_i_p_p_i_n_g_P_l_a_n_e │ │ │ │ -DDeeffiinniittiioonn _c_l_i_p_p_i_n_g_P_l_a_n_e_._h_:_2_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g │ │ │ │ +DDeeffiinniittiioonn _u_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_._h_:_3_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_s_h_o_w │ │ │ │ +void show() │ │ │ │ +Show and raise dialog. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_i_n_i_t_i_a_l_i_z_e_W_i_d_g_e_t │ │ │ │ +virtual void initializeWidget(MainControl &main_control) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_t_a_k_e_S_n_a_p_s_h_o_t___p_r_e_s_s_e_d │ │ │ │ +void takeSnapshot_pressed() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_a_c_t_i_o_n__ │ │ │ │ +QAction * action_ │ │ │ │ +DDeeffiinniittiioonn _u_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_s_n_a_p_s_h_o_t___i_n_t_e_r_f_a_c_e__ │ │ │ │ +SnapshotManagerInterface snapshot_interface_ │ │ │ │ +DDeeffiinniittiioonn _u_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_r_e_s_e_t_T_o___p_r_e_s_s_e_d │ │ │ │ +void resetTo_pressed() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_f_i_r_s_t___r_u_n │ │ │ │ +bool first_run │ │ │ │ +DDeeffiinniittiioonn _u_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_._h_:_7_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_c_h_e_c_k_M_e_n_u │ │ │ │ +virtual void checkMenu(MainControl &main_control) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_o_n_N_o_t_i_f_y │ │ │ │ +virtual void onNotify(Message *message) │ │ │ │ +Overrides message in order to intercept system changed events. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_n_d_o_M_a_n_a_g_e_r_D_i_a_l_o_g_:_:_c_l_o_s_e___p_r_e_s_s_e_d │ │ │ │ +void close_pressed() │ │ │ │ _B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h_:_5_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_4_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_e_n_d │ │ │ │ -RepresentationsConstIterator end() const │ │ │ │ -Const Iterator pointing behind the last Representation. │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_1_4_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_m_a_i_n___c_o_n_t_r_o_l__ │ │ │ │ -MainControl * main_control_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_3_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_r_e_m_o_v_e_d_C_o_m_p_o_s_i_t_e │ │ │ │ -RepresentationList removedComposite(const Composite &composite, bool │ │ │ │ -update=true) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_b_e_e_i_n_g___r_e_n_d_e_r_e_d__ │ │ │ │ -HashSet< Representation * > beeing_rendered_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_1_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_c_l_i_p_p_i_n_g___p_l_a_n_e_s__ │ │ │ │ -vector< ClippingPlane * > clipping_planes_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_2_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_p_o_p_R_e_p_r_e_s_e_n_t_a_t_i_o_n_T_o_U_p_d_a_t_e │ │ │ │ -Representation * popRepresentationToUpdate() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_b_e_e_i_n_g___u_p_d_a_t_e_d__ │ │ │ │ -HashSet< Representation * > beeing_updated_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_1_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_n_o___u_p_d_a_t_e__ │ │ │ │ -bool no_update_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_2_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_r_e_m_o_v_e_C_l_i_p_p_i_n_g_P_l_a_n_e │ │ │ │ -bool removeClippingPlane(ClippingPlane *plane) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_r_e_p_r_e_s_e_n_t_a_t_i_o_n_s__ │ │ │ │ -RepresentationList representations_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_1_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_c_r_e_a_t_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -Representation * createRepresentation() │ │ │ │ -Create a Representation and insert it. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_s_t_i_l_l___t_o___n_o_t_i_f_y__ │ │ │ │ -bool still_to_notify_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_2_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_d_u_m_p │ │ │ │ -void dump(std::ostream &s, Size depth=0) const │ │ │ │ -Dump the internal state to an output stream. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_w_i_l_l_B_e_U_p_d_a_t_e_d │ │ │ │ -bool willBeUpdated(const Representation &rep) const │ │ │ │ -Return true if a Representation will be updated. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_i_n_s_e_r_t_C_l_i_p_p_i_n_g_P_l_a_n_e │ │ │ │ -void insertClippingPlane(ClippingPlane *plane) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_t_o___u_p_d_a_t_e__ │ │ │ │ -HashSet< Representation * > to_update_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_1_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_r_e_s_t_o_r_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s │ │ │ │ -void restoreRepresentations(const INIFile &in, const vector< const Composite * │ │ │ │ -> &new_systems) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_t_h_r_e_a_d__ │ │ │ │ -UpdateRepresentationThread * thread_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_2_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_S_e_t │ │ │ │ -HashSet< Representation * > RepresentationSet │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_6_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_g_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e_s │ │ │ │ -const vector< ClippingPlane * > & getClippingPlanes() const │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_1_6_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_u_p_d_a_t_e__ │ │ │ │ -void update_(Representation &rep) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_f_i_n_i_s_h_e_d_U_p_d_a_t_e__ │ │ │ │ -void finishedUpdate_(Representation *rep) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_I_t_e_r_a_t_o_r │ │ │ │ -RepresentationList::iterator RepresentationsIterator │ │ │ │ -Iteration to the Representations. │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_6_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_s_t_a_r_t_R_e_n_d_e_r_i_n_g │ │ │ │ -bool startRendering(Representation *rep) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ -RepresentationList::const_iterator RepresentationsConstIterator │ │ │ │ -ConstIterator to the Representations. │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_6_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_b_e_g_i_n │ │ │ │ -RepresentationsConstIterator begin() const │ │ │ │ -ConstIterator to the first Representation. │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_1_3_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_f_i_n_i_s_h_e_d_R_e_n_d_e_r_i_n_g │ │ │ │ -void finishedRendering(Representation *rep) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_e_n_d │ │ │ │ -RepresentationsIterator end() │ │ │ │ -Iterator pointing behind the last Representation. │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_1_4_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_h_a_s │ │ │ │ -bool has(const Representation &representation) const │ │ │ │ -Test if a Representation is inserted. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_g_e_t_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_O_f │ │ │ │ -RepresentationList getRepresentationsOf(const Composite &composite) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_u_p_d_a_t_e___m_u_t_e_x__ │ │ │ │ -Mutex update_mutex_ │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_2_2_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_f_o_c_u_s_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -void focusRepresentation(const Representation &rep) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_r_e_b_u_i_l_d_A_l_l_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s │ │ │ │ -void rebuildAllRepresentations() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_g_e_t_N_u_m_b_e_r_O_f_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s │ │ │ │ -Size getNumberOfRepresentations() const │ │ │ │ -Get the number of the Representations. │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_1_2_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_b_e_g_i_n │ │ │ │ -RepresentationsIterator begin() │ │ │ │ -Iterator to the first Representation. │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_._h_:_1_3_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_i_s_B_e_e_i_n_g_R_e_n_d_e_r_e_d │ │ │ │ -bool isBeeingRendered(const Representation *rep) const │ │ │ │ -Used by UpdateRepresentationThread. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_s_t_o_r_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s │ │ │ │ -void storeRepresentations(INIFile &out) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_a_n_a_g_e_r_:_:_u_p_d_a_t_e_R_u_n_n_i_n_g │ │ │ │ -bool updateRunning() const │ │ │ │ -Return true, if a Representation is currently beeing updated. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_B_A_L_L_T_h_r_e_a_d │ │ │ │ -DDeeffiinniittiioonn _t_h_r_e_a_d_s_._h_:_7_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_U_p_d_a_t_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n_T_h_r_e_a_d │ │ │ │ -DDeeffiinniittiioonn _t_h_r_e_a_d_s_._h_:_1_6_1 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_e_s_s_a_g_e │ │ │ │ +DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_5_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t │ │ │ │ +DDeeffiinniittiioonn _m_o_d_u_l_a_r_W_i_d_g_e_t_._h_:_6_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_S_n_a_p_s_h_o_t_M_a_n_a_g_e_r_I_n_t_e_r_f_a_c_e │ │ │ │ +DDeeffiinniittiioonn _s_n_a_p_s_h_o_t_M_a_n_a_g_e_r_I_n_t_e_r_f_a_c_e_._h_:_1_6 │ │ │ │ +_Q_D_i_a_l_o_g │ │ │ │ +_Q_W_i_d_g_e_t │ │ │ │ +_g_l_o_b_a_l_._h │ │ │ │ _B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ #define BALL_VIEW_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d39/a01112.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: partialChargeBase.h File Reference │ │ │ +BALL: reissCavFreeEnergyProcessor.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,31 +65,37 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    partialChargeBase.h File Reference
    │ │ │ +
    reissCavFreeEnergyProcessor.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/QSAR/descriptor.h>
    │ │ │ +
    #include <BALL/common.h>
    │ │ │ +#include <BALL/ENERGY/energyProcessor.h>
    │ │ │ +#include <BALL/DATATYPE/options.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
    │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::PartialChargeBase
    class  BALL::ReissCavFreeEnergyProcessor
     
    struct  BALL::ReissCavFreeEnergyProcessor::Option
     
    struct  BALL::ReissCavFreeEnergyProcessor::Default
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ ├── html2text {} │ │ │ │ @@ -1,19 +1,25 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ + * _S_O_L_V_A_T_I_O_N │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -partialChargeBase.h File Reference │ │ │ │ -#include <_B_A_L_L_/_Q_S_A_R_/_d_e_s_c_r_i_p_t_o_r_._h> │ │ │ │ +reissCavFreeEnergyProcessor.h File Reference │ │ │ │ +#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_E_N_E_R_G_Y_/_e_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e │ │ │ │ + class   _B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d39/a01112_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: partialChargeBase.h Source File │ │ │ +BALL: reissCavFreeEnergyProcessor.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,90 +70,145 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    partialChargeBase.h
    │ │ │ +
    reissCavFreeEnergyProcessor.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-wdith: 2: -*-
    │ │ │ +Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4//
    │ │ │ -
    5
    │ │ │ -
    6#ifndef BALL_QSAR_PARTIALCHARGEBASE_H
    │ │ │ -
    7#define BALL_QSAR_PARTIALCHARGEBASE_H
    │ │ │ -
    8
    │ │ │ -
    9#ifndef BALL_QSAR_DESCRIPTOR_H
    │ │ │ -
    10#include <BALL/QSAR/descriptor.h>
    │ │ │ -
    11#endif
    │ │ │ -
    12
    │ │ │ -
    13namespace BALL
    │ │ │ -
    14{
    │ │ │ -
    │ │ │ -
    18 class BALL_EXPORT PartialChargeBase
    │ │ │ -
    19 : public Descriptor
    │ │ │ -
    20 {
    │ │ │ -
    21 public:
    │ │ │ -
    27 PartialChargeBase();
    │ │ │ -
    28
    │ │ │ -
    31 PartialChargeBase(const PartialChargeBase& pcb);
    │ │ │ -
    32
    │ │ │ -
    35 PartialChargeBase(const String& name);
    │ │ │ -
    36
    │ │ │ -
    39 PartialChargeBase(const String& name, const String& unit);
    │ │ │ -
    40
    │ │ │ -
    43 virtual ~PartialChargeBase();
    │ │ │ -
    45
    │ │ │ -
    49 void computeAllDescriptors(AtomContainer& ac);
    │ │ │ -
    50
    │ │ │ -
    51 void setDataFolder(const char* folder);
    │ │ │ -
    53
    │ │ │ -
    59 PartialChargeBase& operator = (const PartialChargeBase& pcb);
    │ │ │ -
    61
    │ │ │ -
    62
    │ │ │ -
    63 protected:
    │ │ │ -
    64
    │ │ │ -
    69 bool isValid_(AtomContainer& ac);
    │ │ │ -
    71
    │ │ │ -
    76 void calculate_(AtomContainer& ac);
    │ │ │ -
    78
    │ │ │ -
    79 String data_folder_;
    │ │ │ -
    80
    │ │ │ -
    81 };
    │ │ │ -
    │ │ │ -
    82
    │ │ │ -
    83} // namespace BALL
    │ │ │ -
    84
    │ │ │ -
    85#endif
    │ │ │ +
    4// $Id: reissCavFreeEnergyProcessor.h,v 1.18 2005/12/23 17:02:00 amoll Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_SOLVATION_REISSCAVFREEENERGYPROCESSOR_H
    │ │ │ +
    8#define BALL_SOLVATION_REISSCAVFREEENERGYPROCESSOR_H
    │ │ │ +
    9
    │ │ │ +
    10#ifndef BALL_COMMON_H
    │ │ │ +
    11# include <BALL/common.h>
    │ │ │ +
    12#endif
    │ │ │ +
    13
    │ │ │ +
    14#ifndef BALL_ENERGY_ENERGYPROCESSOR_H
    │ │ │ +
    15# include <BALL/ENERGY/energyProcessor.h>
    │ │ │ +
    16#endif
    │ │ │ +
    17
    │ │ │ +
    18#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ +
    19# include <BALL/DATATYPE/options.h>
    │ │ │ +
    20#endif
    │ │ │ +
    21
    │ │ │ +
    22namespace BALL
    │ │ │ +
    23{
    │ │ │ +
    │ │ │ +
    33 class BALL_EXPORT ReissCavFreeEnergyProcessor
    │ │ │ +
    34 : public EnergyProcessor
    │ │ │ +
    35 {
    │ │ │ +
    36
    │ │ │ +
    37 public:
    │ │ │ +
    38
    │ │ │ +
    │ │ │ +
    43 struct Option
    │ │ │ +
    44 {
    │ │ │ +
    50 static const char* VERBOSITY;
    │ │ │ +
    51
    │ │ │ +
    58 static const char* SOLVENT_NUMBER_DENSITY;
    │ │ │ +
    59
    │ │ │ +
    67 static const char* PRESSURE;
    │ │ │ +
    68
    │ │ │ +
    75 static const char* ABSOLUTE_TEMPERATURE;
    │ │ │ +
    76
    │ │ │ +
    84 static const char* PROBE_RADIUS;
    │ │ │ +
    85 };
    │ │ │ +
    │ │ │
    86
    │ │ │ -
    87
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::PartialChargeBase::setDataFolder
    void setDataFolder(const char *folder)
    │ │ │ -
    BALL::PartialChargeBase::calculate_
    void calculate_(AtomContainer &ac)
    │ │ │ -
    BALL::PartialChargeBase::isValid_
    bool isValid_(AtomContainer &ac)
    │ │ │ - │ │ │ -
    BALL::PartialChargeBase::computeAllDescriptors
    void computeAllDescriptors(AtomContainer &ac)
    │ │ │ -
    BALL::PartialChargeBase::PartialChargeBase
    PartialChargeBase(const PartialChargeBase &pcb)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::PartialChargeBase::PartialChargeBase
    PartialChargeBase(const String &name, const String &unit)
    │ │ │ -
    BALL::PartialChargeBase::PartialChargeBase
    PartialChargeBase(const String &name)
    │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    │ │ │ +
    91 struct Default
    │ │ │ +
    92 {
    │ │ │ +
    96 static const int VERBOSITY;
    │ │ │ +
    97
    │ │ │ +
    103 static const float SOLVENT_NUMBER_DENSITY;
    │ │ │ +
    104
    │ │ │ +
    109 static const float PRESSURE;
    │ │ │ +
    110
    │ │ │ +
    115 static const float ABSOLUTE_TEMPERATURE;
    │ │ │ +
    116
    │ │ │ +
    122 static const float PROBE_RADIUS;
    │ │ │ +
    123 };
    │ │ │ +
    │ │ │ +
    124
    │ │ │ +
    125
    │ │ │ +
    129
    │ │ │ +
    132 ReissCavFreeEnergyProcessor();
    │ │ │ +
    133
    │ │ │ +
    136 ReissCavFreeEnergyProcessor(const ReissCavFreeEnergyProcessor& proc);
    │ │ │ +
    137
    │ │ │ +
    140 virtual ~ReissCavFreeEnergyProcessor();
    │ │ │ +
    141
    │ │ │ +
    143
    │ │ │ +
    146
    │ │ │ +
    149 const ReissCavFreeEnergyProcessor& operator =
    │ │ │ +
    150 (const ReissCavFreeEnergyProcessor& proc);
    │ │ │ +
    151
    │ │ │ +
    154 virtual void clear();
    │ │ │ +
    155
    │ │ │ +
    157
    │ │ │ +
    160
    │ │ │ +
    163 bool operator == (const ReissCavFreeEnergyProcessor& proc) const;
    │ │ │ +
    164
    │ │ │ +
    166
    │ │ │ +
    169
    │ │ │ +
    172 virtual bool finish();
    │ │ │ +
    173
    │ │ │ +
    175
    │ │ │ +
    178
    │ │ │ +
    181 Options options;
    │ │ │ +
    182
    │ │ │ +
    184
    │ │ │ +
    185 private:
    │ │ │ +
    186
    │ │ │ +
    187 void setDefaultOptions();
    │ │ │ +
    188
    │ │ │ +
    189 };
    │ │ │ +
    │ │ │ +
    190
    │ │ │ +
    191}
    │ │ │ +
    192
    │ │ │ +
    193#endif // BALL_SOLVATION_REISSCAVFREEENERGYPROCESSOR_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::ReissCavFreeEnergyProcessor::ReissCavFreeEnergyProcessor
    ReissCavFreeEnergyProcessor(const ReissCavFreeEnergyProcessor &proc)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,96 +1,164 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ -partialChargeBase.h │ │ │ │ + * _S_O_L_V_A_T_I_O_N │ │ │ │ +reissCavFreeEnergyProcessor.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-wdith: 2: -*- │ │ │ │ +1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// │ │ │ │ -5 │ │ │ │ -6#ifndef BALL_QSAR_PARTIALCHARGEBASE_H │ │ │ │ -7#define BALL_QSAR_PARTIALCHARGEBASE_H │ │ │ │ -8 │ │ │ │ -9#ifndef BALL_QSAR_DESCRIPTOR_H │ │ │ │ -10#include <_B_A_L_L_/_Q_S_A_R_/_d_e_s_c_r_i_p_t_o_r_._h> │ │ │ │ -11#endif │ │ │ │ -12 │ │ │ │ -13namespace _B_A_L_L │ │ │ │ -14{ │ │ │ │ -_1_8 class _B_A_L_L___E_X_P_O_R_T _P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e │ │ │ │ -19 : public _D_e_s_c_r_i_p_t_o_r │ │ │ │ -20 { │ │ │ │ -21 public: │ │ │ │ -_2_7 _P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e(); │ │ │ │ -28 │ │ │ │ -_3_1 _P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e(const _P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e& pcb); │ │ │ │ -32 │ │ │ │ -_3_5 _P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e(const _S_t_r_i_n_g& name); │ │ │ │ +4// $Id: reissCavFreeEnergyProcessor.h,v 1.18 2005/12/23 17:02:00 amoll Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_SOLVATION_REISSCAVFREEENERGYPROCESSOR_H │ │ │ │ +8#define BALL_SOLVATION_REISSCAVFREEENERGYPROCESSOR_H │ │ │ │ +9 │ │ │ │ +10#ifndef BALL_COMMON_H │ │ │ │ +11# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +12#endif │ │ │ │ +13 │ │ │ │ +14#ifndef BALL_ENERGY_ENERGYPROCESSOR_H │ │ │ │ +15# include <_B_A_L_L_/_E_N_E_R_G_Y_/_e_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h> │ │ │ │ +16#endif │ │ │ │ +17 │ │ │ │ +18#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ +19# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +20#endif │ │ │ │ +21 │ │ │ │ +22namespace _B_A_L_L │ │ │ │ +23{ │ │ │ │ +_3_3 class _B_A_L_L___E_X_P_O_R_T _R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +34 : public _E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +35 { │ │ │ │ 36 │ │ │ │ -_3_9 _P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e(const _S_t_r_i_n_g& name, const _S_t_r_i_n_g& unit); │ │ │ │ -40 │ │ │ │ -_4_3 virtual _~_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e(); │ │ │ │ -45 │ │ │ │ -_4_9 void _c_o_m_p_u_t_e_A_l_l_D_e_s_c_r_i_p_t_o_r_s(_A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ -50 │ │ │ │ -_5_1 void _s_e_t_D_a_t_a_F_o_l_d_e_r(const char* folder); │ │ │ │ -53 │ │ │ │ -_5_9 _P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e& operator = (const _P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e& pcb); │ │ │ │ -61 │ │ │ │ -62 │ │ │ │ -63 protected: │ │ │ │ -64 │ │ │ │ -_6_9 bool _i_s_V_a_l_i_d__(_A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ -71 │ │ │ │ -_7_6 void _c_a_l_c_u_l_a_t_e__(_A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ -78 │ │ │ │ -_7_9 _S_t_r_i_n_g _d_a_t_a___f_o_l_d_e_r__; │ │ │ │ -80 │ │ │ │ -81 }; │ │ │ │ -82 │ │ │ │ -83} // namespace BALL │ │ │ │ -84 │ │ │ │ -85#endif │ │ │ │ +37 public: │ │ │ │ +38 │ │ │ │ +_4_3 struct _O_p_t_i_o_n │ │ │ │ +44 { │ │ │ │ +_5_0 static const char* _V_E_R_B_O_S_I_T_Y; │ │ │ │ +51 │ │ │ │ +_5_8 static const char* _S_O_L_V_E_N_T___N_U_M_B_E_R___D_E_N_S_I_T_Y; │ │ │ │ +59 │ │ │ │ +_6_7 static const char* _P_R_E_S_S_U_R_E; │ │ │ │ +68 │ │ │ │ +_7_5 static const char* _A_B_S_O_L_U_T_E___T_E_M_P_E_R_A_T_U_R_E; │ │ │ │ +76 │ │ │ │ +_8_4 static const char* _P_R_O_B_E___R_A_D_I_U_S; │ │ │ │ +85 }; │ │ │ │ 86 │ │ │ │ -87 │ │ │ │ -_d_e_s_c_r_i_p_t_o_r_._h │ │ │ │ +_9_1 struct _D_e_f_a_u_l_t │ │ │ │ +92 { │ │ │ │ +_9_6 static const int _V_E_R_B_O_S_I_T_Y; │ │ │ │ +97 │ │ │ │ +_1_0_3 static const float _S_O_L_V_E_N_T___N_U_M_B_E_R___D_E_N_S_I_T_Y; │ │ │ │ +104 │ │ │ │ +_1_0_9 static const float _P_R_E_S_S_U_R_E; │ │ │ │ +110 │ │ │ │ +_1_1_5 static const float _A_B_S_O_L_U_T_E___T_E_M_P_E_R_A_T_U_R_E; │ │ │ │ +116 │ │ │ │ +_1_2_2 static const float _P_R_O_B_E___R_A_D_I_U_S; │ │ │ │ +123 }; │ │ │ │ +124 │ │ │ │ +125 │ │ │ │ +129 │ │ │ │ +_1_3_2 _R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r(); │ │ │ │ +133 │ │ │ │ +_1_3_6 _R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r(const _R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r& proc); │ │ │ │ +137 │ │ │ │ +_1_4_0 virtual _~_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r(); │ │ │ │ +141 │ │ │ │ +143 │ │ │ │ +146 │ │ │ │ +_1_4_9 const _R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r& operator = │ │ │ │ +150 (const _R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r& proc); │ │ │ │ +151 │ │ │ │ +_1_5_4 virtual void _c_l_e_a_r(); │ │ │ │ +155 │ │ │ │ +157 │ │ │ │ +160 │ │ │ │ +_1_6_3 bool operator == (const _R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r& proc) const; │ │ │ │ +164 │ │ │ │ +166 │ │ │ │ +169 │ │ │ │ +_1_7_2 virtual bool _f_i_n_i_s_h(); │ │ │ │ +173 │ │ │ │ +175 │ │ │ │ +178 │ │ │ │ +_1_8_1 _O_p_t_i_o_n_s _o_p_t_i_o_n_s; │ │ │ │ +182 │ │ │ │ +184 │ │ │ │ +185 private: │ │ │ │ +186 │ │ │ │ +187 void setDefaultOptions(); │ │ │ │ +188 │ │ │ │ +189 }; │ │ │ │ +190 │ │ │ │ +191} │ │ │ │ +192 │ │ │ │ +193#endif // BALL_SOLVATION_REISSCAVFREEENERGYPROCESSOR_H │ │ │ │ +_c_o_m_m_o_n_._h │ │ │ │ +_o_p_t_i_o_n_s_._h │ │ │ │ +_e_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_D_e_s_c_r_i_p_t_o_r │ │ │ │ -DDeeffiinniittiioonn _d_e_s_c_r_i_p_t_o_r_._h_:_2_7 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_._h_:_2_0 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_s_e_t_D_a_t_a_F_o_l_d_e_r │ │ │ │ -void setDataFolder(const char *folder) │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_c_a_l_c_u_l_a_t_e__ │ │ │ │ -void calculate_(AtomContainer &ac) │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_i_s_V_a_l_i_d__ │ │ │ │ -bool isValid_(AtomContainer &ac) │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e │ │ │ │ -PartialChargeBase() │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_c_o_m_p_u_t_e_A_l_l_D_e_s_c_r_i_p_t_o_r_s │ │ │ │ -void computeAllDescriptors(AtomContainer &ac) │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e │ │ │ │ -PartialChargeBase(const PartialChargeBase &pcb) │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_~_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e │ │ │ │ -virtual ~PartialChargeBase() │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_d_a_t_a___f_o_l_d_e_r__ │ │ │ │ -String data_folder_ │ │ │ │ -DDeeffiinniittiioonn _p_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_._h_:_7_9 │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e │ │ │ │ -PartialChargeBase(const String &name, const String &unit) │ │ │ │ -_B_A_L_L_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e_:_:_P_a_r_t_i_a_l_C_h_a_r_g_e_B_a_s_e │ │ │ │ -PartialChargeBase(const String &name) │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _e_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_3_5 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_o_p_t_i_o_n_s │ │ │ │ +Options options │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_1_8_1 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_c_l_e_a_r │ │ │ │ +virtual void clear() │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_~_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +virtual ~ReissCavFreeEnergyProcessor() │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +ReissCavFreeEnergyProcessor() │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +ReissCavFreeEnergyProcessor(const ReissCavFreeEnergyProcessor &proc) │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_f_i_n_i_s_h │ │ │ │ +virtual bool finish() │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_4_4 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_S_O_L_V_E_N_T___N_U_M_B_E_R___D_E_N_S_I_T_Y │ │ │ │ +static const char * SOLVENT_NUMBER_DENSITY │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_5_8 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_R_O_B_E___R_A_D_I_U_S │ │ │ │ +static const char * PROBE_RADIUS │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_8_4 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_A_B_S_O_L_U_T_E___T_E_M_P_E_R_A_T_U_R_E │ │ │ │ +static const char * ABSOLUTE_TEMPERATURE │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_7_5 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_V_E_R_B_O_S_I_T_Y │ │ │ │ +static const char * VERBOSITY │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_R_E_S_S_U_R_E │ │ │ │ +static const char * PRESSURE │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_6_7 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_9_2 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_R_O_B_E___R_A_D_I_U_S │ │ │ │ +static const float PROBE_RADIUS │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_1_2_2 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_R_E_S_S_U_R_E │ │ │ │ +static const float PRESSURE │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_1_0_9 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_S_O_L_V_E_N_T___N_U_M_B_E_R___D_E_N_S_I_T_Y │ │ │ │ +static const float SOLVENT_NUMBER_DENSITY │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_1_0_3 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_V_E_R_B_O_S_I_T_Y │ │ │ │ +static const int VERBOSITY │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_9_6 │ │ │ │ +_B_A_L_L_:_:_R_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_A_B_S_O_L_U_T_E___T_E_M_P_E_R_A_T_U_R_E │ │ │ │ +static const float ABSOLUTE_TEMPERATURE │ │ │ │ +DDeeffiinniittiioonn _r_e_i_s_s_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_1_1_5 │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d3c/a00971.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: polarity.h File Reference │ │ │ +BALL: scoringOptimizer.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,33 +65,33 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    polarity.h File Reference
    │ │ │ +
    scoringOptimizer.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/SCORING/COMMON/scoringComponent.h>
    │ │ │ -#include <BALL/SCORING/COMMON/scoringFunction.h>
    │ │ │ -#include <BALL/SCORING/COMPONENTS/fresnoTypes.h>
    │ │ │ +
    #include <BALL/SCORING/COMMON/scoringFunction.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::Polarity
    class  BALL::ScoringOptimizer
     
    struct  BALL::ScoringOptimizer::Result
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ ├── html2text {} │ │ │ │ @@ -1,22 +1,22 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _S_C_O_R_I_N_G │ │ │ │ - * _C_O_M_P_O_N_E_N_T_S │ │ │ │ + * _C_O_M_M_O_N │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -polarity.h File Reference │ │ │ │ -#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_M_O_N_/_s_c_o_r_i_n_g_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ +scoringOptimizer.h File Reference │ │ │ │ #include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_M_O_N_/_s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_P_O_N_E_N_T_S_/_f_r_e_s_n_o_T_y_p_e_s_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_P_o_l_a_r_i_t_y │ │ │ │ + class   _B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_R_e_s_u_l_t │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d3c/a00971_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: polarity.h Source File │ │ │ +BALL: scoringOptimizer.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,109 +70,106 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    polarity.h
    │ │ │ +
    scoringOptimizer.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// ----------------------------------------------------
    │ │ │
    2// $Maintainer: Marcel Schumann $
    │ │ │
    3// $Authors: Marcel Schumann $
    │ │ │
    4// ----------------------------------------------------
    │ │ │
    5
    │ │ │ -
    6#ifndef BALL_SCORING_COMPONENTS_POLARITY_H
    │ │ │ -
    7#define BALL_SCORING_COMPONENTS_POLARITY_H
    │ │ │ +
    6#ifndef BALL_SCORING_COMMON_SCORINGOPTIMIZER_H
    │ │ │ +
    7#define BALL_SCORING_COMMON_SCORINGOPTIMIZER_H
    │ │ │
    8
    │ │ │ -
    9#include <BALL/SCORING/COMMON/scoringComponent.h>
    │ │ │ -
    10#include <BALL/SCORING/COMMON/scoringFunction.h>
    │ │ │ -
    11#include <BALL/SCORING/COMPONENTS/fresnoTypes.h>
    │ │ │ -
    12
    │ │ │ -
    13
    │ │ │ -
    14namespace BALL
    │ │ │ -
    15{
    │ │ │ -
    │ │ │ -
    19 class BALL_EXPORT Polarity
    │ │ │ -
    20 : public ScoringComponent
    │ │ │ -
    21 {
    │ │ │ -
    22 public:
    │ │ │ -
    23 static const double POL_ES_THRESHOLD;
    │ │ │ -
    24 static const double LIP_ES_THRESHOLD;
    │ │ │ +
    9#include <BALL/SCORING/COMMON/scoringFunction.h>
    │ │ │ +
    10
    │ │ │ +
    11
    │ │ │ +
    12namespace BALL
    │ │ │ +
    13{
    │ │ │ +
    │ │ │ +
    15 class BALL_EXPORT ScoringOptimizer
    │ │ │ +
    16 {
    │ │ │ +
    17 public:
    │ │ │ +
    18 ScoringOptimizer(Options& options, bool train);
    │ │ │ +
    19
    │ │ │ +
    20 void addComplex(String name, String receptor_file, String ligand_file, double binding_free_energy);
    │ │ │ +
    21
    │ │ │ +
    22 void evaluate(double* correlation = 0, double* R2 = 0, double* RMSE = 0, Size* no_valid_complexes = 0);
    │ │ │ +
    23
    │ │ │ +
    24 void printMatrix(std::ostream& out = std::cout);
    │ │ │
    25
    │ │ │ -
    29
    │ │ │ -
    32 Polarity(ScoringFunction& sf);
    │ │ │ -
    33
    │ │ │ -
    36 Polarity(const Polarity& bp);
    │ │ │ -
    37
    │ │ │ -
    40 virtual ~Polarity();
    │ │ │ -
    41
    │ │ │ -
    43
    │ │ │ -
    46
    │ │ │ -
    49 const Polarity& operator = (const Polarity& bp);
    │ │ │ +
    │ │ │ +
    26 struct Result
    │ │ │ +
    27 {
    │ │ │ +
    28 std::list<double> predictions;
    │ │ │ +
    29 std::list<double> expected_affinities;
    │ │ │ +
    30 std::list<String> target_names;
    │ │ │ +
    31 std::vector<std::vector<double> > score_contributions;
    │ │ │ +
    32 std::vector<String> score_contribution_names;
    │ │ │ +
    33 };
    │ │ │ +
    │ │ │ +
    34
    │ │ │ +
    35 const Result* getResult();
    │ │ │ +
    36
    │ │ │ +
    37 private:
    │ │ │ +
    38 struct Complex
    │ │ │ +
    39 {
    │ │ │ +
    40 String name;
    │ │ │ +
    41 String receptor_file;
    │ │ │ +
    42 String ligand_file;
    │ │ │ +
    43 double binding_free_energy;
    │ │ │ +
    44 };
    │ │ │ +
    45
    │ │ │ +
    46 list<Complex> complexes_;
    │ │ │ +
    47
    │ │ │ +
    48 Options options_;
    │ │ │ +
    49 String scoring_function_name_;
    │ │ │
    50
    │ │ │ -
    53 void clear();
    │ │ │ -
    54
    │ │ │ +
    51 Result result_;
    │ │ │ +
    52
    │ │ │ +
    54 bool train_;
    │ │ │
    55
    │ │ │ -
    57
    │ │ │ +
    56 ScoringFunction* createScoringFunction(System& receptor, System& ligand);
    │ │ │ +
    57 };
    │ │ │ +
    │ │ │ +
    58}
    │ │ │ +
    59
    │ │ │
    60
    │ │ │ -
    63 bool setup();
    │ │ │ -
    64
    │ │ │ -
    65 void setupLigand();
    │ │ │ -
    66
    │ │ │ -
    68
    │ │ │ -
    71
    │ │ │ -
    74 double updateScore();
    │ │ │ -
    75
    │ │ │ -
    76 void update(const vector<std::pair<Atom*, Atom*> >& /* pair_vector */);
    │ │ │ -
    77
    │ │ │ -
    79
    │ │ │ -
    80 private:
    │ │ │ -
    81
    │ │ │ -
    82 Size getType_(const Atom* atom);
    │ │ │ -
    83
    │ │ │ -
    84 bool isPolar_(const Atom* atom);
    │ │ │ -
    85
    │ │ │ -
    86 bool isLipophilic_(const Atom* atom);
    │ │ │ -
    87
    │ │ │ -
    88 bool isBackboneAtom_(const Atom* atom);
    │ │ │ -
    89
    │ │ │ -
    90 FresnoTypes* receptor_fresno_types_;
    │ │ │ -
    91 FresnoTypes* ligand_fresno_types_;
    │ │ │ -
    92 };
    │ │ │ -
    │ │ │ -
    93} // namespace BALL
    │ │ │ -
    94
    │ │ │ -
    95#endif // BALL_SCORING_COMPONENTS_POLARITY_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Polarity::POL_ES_THRESHOLD
    static const double POL_ES_THRESHOLD
    Definition polarity.h:23
    │ │ │ -
    BALL::Polarity::Polarity
    Polarity(ScoringFunction &sf)
    │ │ │ -
    BALL::Polarity::Polarity
    Polarity(const Polarity &bp)
    │ │ │ - │ │ │ -
    BALL::Polarity::setupLigand
    void setupLigand()
    │ │ │ -
    BALL::Polarity::LIP_ES_THRESHOLD
    static const double LIP_ES_THRESHOLD
    Definition polarity.h:24
    │ │ │ - │ │ │ -
    BALL::Polarity::update
    void update(const vector< std::pair< Atom *, Atom * > > &)
    │ │ │ -
    BALL::Polarity::updateScore
    double updateScore()
    │ │ │ -
    BALL::Polarity::~Polarity
    virtual ~Polarity()
    │ │ │ +
    61#endif // BALL_SCORING_COMMON_SCORINGOPTIMIZER_H
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Complex
    std::complex< BALL_COMPLEX_PRECISION > Complex
    Definition complex.h:21
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::ScoringOptimizer::printMatrix
    void printMatrix(std::ostream &out=std::cout)
    │ │ │ +
    BALL::ScoringOptimizer::getResult
    const Result * getResult()
    │ │ │ +
    BALL::ScoringOptimizer::ScoringOptimizer
    ScoringOptimizer(Options &options, bool train)
    │ │ │ +
    BALL::ScoringOptimizer::addComplex
    void addComplex(String name, String receptor_file, String ligand_file, double binding_free_energy)
    │ │ │ +
    BALL::ScoringOptimizer::evaluate
    void evaluate(double *correlation=0, double *R2=0, double *RMSE=0, Size *no_valid_complexes=0)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::ScoringOptimizer::Result::score_contribution_names
    std::vector< String > score_contribution_names
    Definition scoringOptimizer.h:32
    │ │ │ +
    BALL::ScoringOptimizer::Result::score_contributions
    std::vector< std::vector< double > > score_contributions
    Definition scoringOptimizer.h:31
    │ │ │ + │ │ │ +
    BALL::ScoringOptimizer::Result::expected_affinities
    std::list< double > expected_affinities
    Definition scoringOptimizer.h:29
    │ │ │ │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,118 +1,124 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _S_C_O_R_I_N_G │ │ │ │ - * _C_O_M_P_O_N_E_N_T_S │ │ │ │ -polarity.h │ │ │ │ + * _C_O_M_M_O_N │ │ │ │ +scoringOptimizer.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// ---------------------------------------------------- │ │ │ │ 2// $Maintainer: Marcel Schumann $ │ │ │ │ 3// $Authors: Marcel Schumann $ │ │ │ │ 4// ---------------------------------------------------- │ │ │ │ 5 │ │ │ │ -6#ifndef BALL_SCORING_COMPONENTS_POLARITY_H │ │ │ │ -7#define BALL_SCORING_COMPONENTS_POLARITY_H │ │ │ │ +6#ifndef BALL_SCORING_COMMON_SCORINGOPTIMIZER_H │ │ │ │ +7#define BALL_SCORING_COMMON_SCORINGOPTIMIZER_H │ │ │ │ 8 │ │ │ │ -9#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_M_O_N_/_s_c_o_r_i_n_g_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ -10#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_M_O_N_/_s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h> │ │ │ │ -11#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_P_O_N_E_N_T_S_/_f_r_e_s_n_o_T_y_p_e_s_._h> │ │ │ │ -12 │ │ │ │ -13 │ │ │ │ -14namespace _B_A_L_L │ │ │ │ -15{ │ │ │ │ -_1_9 class _B_A_L_L___E_X_P_O_R_T _P_o_l_a_r_i_t_y │ │ │ │ -20 : public _S_c_o_r_i_n_g_C_o_m_p_o_n_e_n_t │ │ │ │ -21 { │ │ │ │ -22 public: │ │ │ │ -_2_3 static const double _P_O_L___E_S___T_H_R_E_S_H_O_L_D; │ │ │ │ -_2_4 static const double _L_I_P___E_S___T_H_R_E_S_H_O_L_D; │ │ │ │ +9#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_C_O_M_M_O_N_/_s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h> │ │ │ │ +10 │ │ │ │ +11 │ │ │ │ +12namespace _B_A_L_L │ │ │ │ +13{ │ │ │ │ +_1_5 class _B_A_L_L___E_X_P_O_R_T _S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r │ │ │ │ +16 { │ │ │ │ +17 public: │ │ │ │ +_1_8 _S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r(_O_p_t_i_o_n_s& options, bool train); │ │ │ │ +19 │ │ │ │ +_2_0 void _a_d_d_C_o_m_p_l_e_x(_S_t_r_i_n_g name, _S_t_r_i_n_g receptor_file, _S_t_r_i_n_g ligand_file, │ │ │ │ +double binding_free_energy); │ │ │ │ +21 │ │ │ │ +_2_2 void _e_v_a_l_u_a_t_e(double* correlation = 0, double* R2 = 0, double* RMSE = 0, │ │ │ │ +_S_i_z_e* no_valid_complexes = 0); │ │ │ │ +23 │ │ │ │ +_2_4 void _p_r_i_n_t_M_a_t_r_i_x(std::ostream& out = std::cout); │ │ │ │ 25 │ │ │ │ -29 │ │ │ │ -_3_2 _P_o_l_a_r_i_t_y(_S_c_o_r_i_n_g_F_u_n_c_t_i_o_n& sf); │ │ │ │ -33 │ │ │ │ -_3_6 _P_o_l_a_r_i_t_y(const _P_o_l_a_r_i_t_y& bp); │ │ │ │ -37 │ │ │ │ -_4_0 virtual _~_P_o_l_a_r_i_t_y(); │ │ │ │ -41 │ │ │ │ -43 │ │ │ │ -46 │ │ │ │ -_4_9 const _P_o_l_a_r_i_t_y& operator = (const _P_o_l_a_r_i_t_y& bp); │ │ │ │ +_2_6 struct _R_e_s_u_l_t │ │ │ │ +27 { │ │ │ │ +_2_8 std::list _p_r_e_d_i_c_t_i_o_n_s; │ │ │ │ +_2_9 std::list _e_x_p_e_c_t_e_d___a_f_f_i_n_i_t_i_e_s; │ │ │ │ +_3_0 std::list _t_a_r_g_e_t___n_a_m_e_s; │ │ │ │ +_3_1 std::vector > _s_c_o_r_e___c_o_n_t_r_i_b_u_t_i_o_n_s; │ │ │ │ +_3_2 std::vector _s_c_o_r_e___c_o_n_t_r_i_b_u_t_i_o_n___n_a_m_e_s; │ │ │ │ +33 }; │ │ │ │ +34 │ │ │ │ +_3_5 const _R_e_s_u_l_t* _g_e_t_R_e_s_u_l_t(); │ │ │ │ +36 │ │ │ │ +37 private: │ │ │ │ +38 struct _C_o_m_p_l_e_x │ │ │ │ +39 { │ │ │ │ +40 _S_t_r_i_n_g name; │ │ │ │ +41 _S_t_r_i_n_g receptor_file; │ │ │ │ +42 _S_t_r_i_n_g ligand_file; │ │ │ │ +43 double binding_free_energy; │ │ │ │ +44 }; │ │ │ │ +45 │ │ │ │ +46 list complexes_; │ │ │ │ +47 │ │ │ │ +48 _O_p_t_i_o_n_s options_; │ │ │ │ +49 _S_t_r_i_n_g scoring_function_name_; │ │ │ │ 50 │ │ │ │ -_5_3 void _c_l_e_a_r(); │ │ │ │ -54 │ │ │ │ +51 _R_e_s_u_l_t result_; │ │ │ │ +52 │ │ │ │ +54 bool train_; │ │ │ │ 55 │ │ │ │ -57 │ │ │ │ +56 _S_c_o_r_i_n_g_F_u_n_c_t_i_o_n* createScoringFunction(_S_y_s_t_e_m& receptor, _S_y_s_t_e_m& ligand); │ │ │ │ +57 }; │ │ │ │ +58} │ │ │ │ +59 │ │ │ │ 60 │ │ │ │ -_6_3 bool _s_e_t_u_p(); │ │ │ │ -64 │ │ │ │ -_6_5 void _s_e_t_u_p_L_i_g_a_n_d(); │ │ │ │ -66 │ │ │ │ -68 │ │ │ │ -71 │ │ │ │ -_7_4 double _u_p_d_a_t_e_S_c_o_r_e(); │ │ │ │ -75 │ │ │ │ -_7_6 void _u_p_d_a_t_e(const vector >& /* pair_vector */); │ │ │ │ -77 │ │ │ │ -79 │ │ │ │ -80 private: │ │ │ │ -81 │ │ │ │ -82 _S_i_z_e getType_(const _A_t_o_m* atom); │ │ │ │ -83 │ │ │ │ -84 bool isPolar_(const _A_t_o_m* atom); │ │ │ │ -85 │ │ │ │ -86 bool isLipophilic_(const _A_t_o_m* atom); │ │ │ │ -87 │ │ │ │ -88 bool isBackboneAtom_(const _A_t_o_m* atom); │ │ │ │ -89 │ │ │ │ -90 _F_r_e_s_n_o_T_y_p_e_s* receptor_fresno_types_; │ │ │ │ -91 _F_r_e_s_n_o_T_y_p_e_s* ligand_fresno_types_; │ │ │ │ -92 }; │ │ │ │ -93} // namespace BALL │ │ │ │ -94 │ │ │ │ -95#endif // BALL_SCORING_COMPONENTS_POLARITY_H │ │ │ │ -_f_r_e_s_n_o_T_y_p_e_s_._h │ │ │ │ +61#endif // BALL_SCORING_COMMON_SCORINGOPTIMIZER_H │ │ │ │ _s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h │ │ │ │ -_s_c_o_r_i_n_g_C_o_m_p_o_n_e_n_t_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_S_c_o_r_i_n_g_C_o_m_p_o_n_e_n_t │ │ │ │ -DDeeffiinniittiioonn _s_c_o_r_i_n_g_C_o_m_p_o_n_e_n_t_._h_:_2_1 │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_l_e_x │ │ │ │ +std::complex< BALL_COMPLEX_PRECISION > Complex │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_l_e_x_._h_:_2_1 │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_R_e_s_u_l_t │ │ │ │ +DDeeffiinniittiioonn _r_e_s_u_l_t_._h_:_2_2 │ │ │ │ +_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ +DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ _B_A_L_L_:_:_S_c_o_r_i_n_g_F_u_n_c_t_i_o_n │ │ │ │ DDeeffiinniittiioonn _s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h_:_2_9 │ │ │ │ -_B_A_L_L_:_:_F_r_e_s_n_o_T_y_p_e_s │ │ │ │ -DDeeffiinniittiioonn _f_r_e_s_n_o_T_y_p_e_s_._h_:_1_6 │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y │ │ │ │ -DDeeffiinniittiioonn _p_o_l_a_r_i_t_y_._h_:_2_1 │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_P_O_L___E_S___T_H_R_E_S_H_O_L_D │ │ │ │ -static const double POL_ES_THRESHOLD │ │ │ │ -DDeeffiinniittiioonn _p_o_l_a_r_i_t_y_._h_:_2_3 │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_P_o_l_a_r_i_t_y │ │ │ │ -Polarity(ScoringFunction &sf) │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_P_o_l_a_r_i_t_y │ │ │ │ -Polarity(const Polarity &bp) │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_s_e_t_u_p │ │ │ │ -bool setup() │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_s_e_t_u_p_L_i_g_a_n_d │ │ │ │ -void setupLigand() │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_L_I_P___E_S___T_H_R_E_S_H_O_L_D │ │ │ │ -static const double LIP_ES_THRESHOLD │ │ │ │ -DDeeffiinniittiioonn _p_o_l_a_r_i_t_y_._h_:_2_4 │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_c_l_e_a_r │ │ │ │ -void clear() │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_u_p_d_a_t_e │ │ │ │ -void update(const vector< std::pair< Atom *, Atom * > > &) │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_u_p_d_a_t_e_S_c_o_r_e │ │ │ │ -double updateScore() │ │ │ │ -_B_A_L_L_:_:_P_o_l_a_r_i_t_y_:_:_~_P_o_l_a_r_i_t_y │ │ │ │ -virtual ~Polarity() │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r │ │ │ │ +DDeeffiinniittiioonn _s_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_._h_:_1_6 │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_p_r_i_n_t_M_a_t_r_i_x │ │ │ │ +void printMatrix(std::ostream &out=std::cout) │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_g_e_t_R_e_s_u_l_t │ │ │ │ +const Result * getResult() │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r │ │ │ │ +ScoringOptimizer(Options &options, bool train) │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_a_d_d_C_o_m_p_l_e_x │ │ │ │ +void addComplex(String name, String receptor_file, String ligand_file, double │ │ │ │ +binding_free_energy) │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_e_v_a_l_u_a_t_e │ │ │ │ +void evaluate(double *correlation=0, double *R2=0, double *RMSE=0, Size │ │ │ │ +*no_valid_complexes=0) │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_R_e_s_u_l_t │ │ │ │ +DDeeffiinniittiioonn _s_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_._h_:_2_7 │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_R_e_s_u_l_t_:_:_p_r_e_d_i_c_t_i_o_n_s │ │ │ │ +std::list< double > predictions │ │ │ │ +DDeeffiinniittiioonn _s_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_._h_:_2_8 │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_R_e_s_u_l_t_:_:_s_c_o_r_e___c_o_n_t_r_i_b_u_t_i_o_n___n_a_m_e_s │ │ │ │ +std::vector< String > score_contribution_names │ │ │ │ +DDeeffiinniittiioonn _s_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_R_e_s_u_l_t_:_:_s_c_o_r_e___c_o_n_t_r_i_b_u_t_i_o_n_s │ │ │ │ +std::vector< std::vector< double > > score_contributions │ │ │ │ +DDeeffiinniittiioonn _s_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_R_e_s_u_l_t_:_:_t_a_r_g_e_t___n_a_m_e_s │ │ │ │ +std::list< String > target_names │ │ │ │ +DDeeffiinniittiioonn _s_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_._h_:_3_0 │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_:_:_R_e_s_u_l_t_:_:_e_x_p_e_c_t_e_d___a_f_f_i_n_i_t_i_e_s │ │ │ │ +std::list< double > expected_affinities │ │ │ │ +DDeeffiinniittiioonn _s_c_o_r_i_n_g_O_p_t_i_m_i_z_e_r_._h_:_2_9 │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d3d/a05482.html │ │ │ @@ -80,15 +80,15 @@ │ │ │ Protected Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members │ │ │
    BALL::EmpiricalHSShiftProcessor::PropertiesForShift_ Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/NMR/empiricalHSShiftProcessor.h>

    │ │ │ +

    #include <BALL/NMR/empiricalHSShiftProcessor.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -141,15 +141,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

     PropertiesForShift_ (int verbosity_=EmpiricalHSShiftProcessor::VERBOSITY_LEVEL_CRITICAL)
     
    bool computeProperties_ (Atom *atom, std::set< String > properties)
     
    std::map< String, float > properties_real_
     
    std::map< String, String > properties_string_
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 195 of file empiricalHSShiftProcessor.h.

    │ │ │ +

    Definition at line 195 of file empiricalHSShiftProcessor.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ PropertiesForShift_()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -618,15 +618,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    Atom* BALL::EmpiricalHSShiftProcessor::PropertiesForShift_::current_atom
    │ │ │
    │ │ │

    A pointer to the atom, whose properties are computed and stored.

    │ │ │ │ │ │ -

    Definition at line 205 of file empiricalHSShiftProcessor.h.

    │ │ │ +

    Definition at line 205 of file empiricalHSShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ properties_real_

    │ │ │ │ │ │
    │ │ │ @@ -642,15 +642,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 253 of file empiricalHSShiftProcessor.h.

    │ │ │ +

    Definition at line 253 of file empiricalHSShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ properties_string_

    │ │ │ │ │ │
    │ │ │ @@ -666,15 +666,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 255 of file empiricalHSShiftProcessor.h.

    │ │ │ +

    Definition at line 255 of file empiricalHSShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d3e/a00566.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: vertex1.h File Reference │ │ │ +BALL: labelModel.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,33 +65,34 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    vertex1.h File Reference
    │ │ │ +
    labelModel.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/MATHS/vector3.h>
    │ │ │ -#include <BALL/VIEW/DATATYPE/vertex1.iC>
    │ │ │ +
    #include <BALL/VIEW/MODELS/modelProcessor.h>
    │ │ │ +#include <BALL/VIEW/DATATYPE/colorRGBA.h>
    │ │ │ +#include <BALL/STRUCTURE/geometricProperties.h>
    │ │ │ +#include <QtGui/QFont>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::Vertex
    class  BALL::VIEW::LabelModel
     
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,23 +1,24 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ - * _D_A_T_A_T_Y_P_E │ │ │ │ + * _M_O_D_E_L_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -vertex1.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ -#include │ │ │ │ +labelModel.h File Reference │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_M_O_D_E_L_S_/_m_o_d_e_l_P_r_o_c_e_s_s_o_r_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_c_o_l_o_r_R_G_B_A_._h> │ │ │ │ +#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_g_e_o_m_e_t_r_i_c_P_r_o_p_e_r_t_i_e_s_._h> │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_V_e_r_t_e_x │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d3e/a00566_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: vertex1.h Source File │ │ │ +BALL: labelModel.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,129 +70,151 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    vertex1.h
    │ │ │ +
    labelModel.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4// $Id: vertex1.h,v 1.10.20.1 2007/03/25 21:25:42 oliver Exp $
    │ │ │ -
    5//
    │ │ │ -
    6
    │ │ │ -
    7#ifndef BALL_VIEW_DATATYPE_VERTEX1_H
    │ │ │ -
    8#define BALL_VIEW_DATATYPE_VERTEX1_H
    │ │ │ -
    9
    │ │ │ -
    10#ifndef BALL_COMMON_H
    │ │ │ -
    11# include <BALL/common.h>
    │ │ │ -
    12#endif
    │ │ │ -
    13
    │ │ │ -
    14#ifndef BALL_MATHS_VECTOR3_H
    │ │ │ -
    15# include <BALL/MATHS/vector3.h>
    │ │ │ -
    16#endif
    │ │ │ -
    17
    │ │ │ -
    18namespace BALL
    │ │ │ -
    19{
    │ │ │ -
    20 namespace VIEW
    │ │ │ -
    21 {
    │ │ │ -
    │ │ │ -
    31 class BALL_VIEW_EXPORT Vertex
    │ │ │ -
    32 {
    │ │ │ -
    33 public:
    │ │ │ -
    34
    │ │ │ -
    35 BALL_CREATE(Vertex)
    │ │ │ -
    36
    │ │ │ -
    37
    │ │ │ -
    40
    │ │ │ -
    41
    │ │ │ -
    45 Vertex();
    │ │ │ -
    46
    │ │ │ -
    52 Vertex(const Vertex& vertex);
    │ │ │ -
    53
    │ │ │ +
    4
    │ │ │ +
    5#ifndef BALL_VIEW_MODELS_LABELMODEL_H
    │ │ │ +
    6#define BALL_VIEW_MODELS_LABELMODEL_H
    │ │ │ +
    7
    │ │ │ +
    8#ifndef BALL_VIEW_MODELS_MODELPROCESSOR_H
    │ │ │ +
    9# include <BALL/VIEW/MODELS/modelProcessor.h>
    │ │ │ +
    10#endif
    │ │ │ +
    11
    │ │ │ +
    12#ifndef BALL_VIEW_DATATYPE_COLORRGBA_H
    │ │ │ +
    13# include <BALL/VIEW/DATATYPE/colorRGBA.h>
    │ │ │ +
    14#endif
    │ │ │ +
    15
    │ │ │ +
    16#ifndef BALL_STRUCTURE_GEOMETRICPROPERTIES_H
    │ │ │ +
    17# include <BALL/STRUCTURE/geometricProperties.h>
    │ │ │ +
    18#endif
    │ │ │ +
    19
    │ │ │ +
    20
    │ │ │ +
    21#include <QtGui/QFont>
    │ │ │ +
    22
    │ │ │ +
    23namespace BALL
    │ │ │ +
    24{
    │ │ │ +
    25 namespace VIEW
    │ │ │ +
    26 {
    │ │ │ +
    27
    │ │ │ +
    │ │ │ +
    36 class BALL_VIEW_EXPORT LabelModel: public ModelProcessor
    │ │ │ +
    37 {
    │ │ │ +
    38 public:
    │ │ │ +
    39
    │ │ │ +
    40 BALL_CREATE(LabelModel)
    │ │ │ +
    41
    │ │ │ +
    42
    │ │ │ +
    │ │ │ +
    43 enum Mode
    │ │ │ +
    44 {
    │ │ │ +
    46 ALL_ITEMS,
    │ │ │ +
    48 ALL_ATOMS,
    │ │ │ +
    50 ALL_RESIDUES,
    │ │ │ +
    52 ONE_LABEL
    │ │ │ +
    53 };
    │ │ │ +
    │ │ │ +
    54
    │ │ │
    55
    │ │ │ -
    58
    │ │ │ -
    61 virtual ~Vertex();
    │ │ │ -
    62
    │ │ │ -
    68 virtual void clear();
    │ │ │ -
    69
    │ │ │ +
    59
    │ │ │ +
    62 LabelModel();
    │ │ │ +
    63
    │ │ │ +
    66 LabelModel(const LabelModel& model);
    │ │ │ +
    67
    │ │ │ +
    70 virtual ~LabelModel();
    │ │ │
    71
    │ │ │ +
    73 void setFont(const QFont& font) { font_ = font;}
    │ │ │
    74
    │ │ │ -
    79 void set(const Vertex& v);
    │ │ │ +
    76 const QFont& getFont() const { return font_;}
    │ │ │ +
    77
    │ │ │ +
    79 void setColor(const ColorRGBA& color) { color_ = color;}
    │ │ │
    80
    │ │ │ -
    86 const Vertex& operator = (const Vertex& v);
    │ │ │ -
    87
    │ │ │ -
    92 void swap(Vertex& v);
    │ │ │ -
    93
    │ │ │ +
    82 const ColorRGBA& getColor() const { return color_;}
    │ │ │ +
    83
    │ │ │ +
    85 void setMode(Mode mode) { mode_ = mode;}
    │ │ │ +
    86
    │ │ │ +
    88 Mode getType() const { return mode_;}
    │ │ │ +
    89
    │ │ │ +
    91 void setText(const String& text) { text_ = text;}
    │ │ │ +
    92
    │ │ │ +
    94 const String& getText() const { return text_;}
    │ │ │
    95
    │ │ │ +
    96
    │ │ │
    98
    │ │ │ -
    102 void setVertex(const Vector3& v);
    │ │ │ -
    103
    │ │ │ -
    107 void setVertex(const float x, const float y, const float z);
    │ │ │ -
    108
    │ │ │ -
    112 Vector3& getVertex();
    │ │ │ -
    113
    │ │ │ -
    117 const Vector3& getVertex() const;
    │ │ │ -
    118
    │ │ │ -
    122 void getVertex(Vector3& v) const;
    │ │ │ +
    101
    │ │ │ +
    104 virtual Processor::Result operator() (Composite& composite);
    │ │ │ +
    105
    │ │ │ +
    107 virtual bool createGeometricObjects();
    │ │ │ +
    109
    │ │ │ +
    110 protected:
    │ │ │ +
    111
    │ │ │ +
    112 QFont font_;
    │ │ │ +
    113 ColorRGBA color_;
    │ │ │ +
    114 Mode mode_;
    │ │ │ +
    115 String text_;
    │ │ │ +
    116 Size nr_objects_;
    │ │ │ +
    117 Vector3 center_;
    │ │ │ +
    118 GeometricCenterProcessor center_processor_;
    │ │ │ +
    119 };
    │ │ │ +
    │ │ │ +
    120
    │ │ │ +
    121 } // namespace VIEW
    │ │ │ +
    122} // namspace BALL
    │ │ │
    123
    │ │ │ -
    127 void getVertex(float& x, float& y, float& z) const;
    │ │ │ -
    128
    │ │ │ -
    142 void setVertexAddress(const Vector3& v);
    │ │ │ -
    143
    │ │ │ -
    152 void setDefaultVertexAddress();
    │ │ │ -
    153
    │ │ │ -
    158 Vector3* getVertexAddress() const;
    │ │ │ -
    159
    │ │ │ -
    161
    │ │ │ -
    164
    │ │ │ -
    172 bool isDefaultVertexAddress() const;
    │ │ │ -
    173
    │ │ │ -
    175
    │ │ │ -
    178
    │ │ │ -
    182 virtual bool isValid() const;
    │ │ │ -
    183
    │ │ │ -
    191 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ -
    192
    │ │ │ -
    194
    │ │ │ -
    195 private:
    │ │ │ -
    196
    │ │ │ -
    197 /* vertex */
    │ │ │ -
    198 Vector3 vertex1_;
    │ │ │ -
    199
    │ │ │ -
    200 /* vertex pointer */
    │ │ │ -
    201 Vector3* vertex1_ptr_;
    │ │ │ -
    202 };
    │ │ │ -
    │ │ │ -
    203
    │ │ │ -
    204
    │ │ │ -
    205# ifndef BALL_NO_INLINE_FUNCTIONS
    │ │ │ -
    206# include <BALL/VIEW/DATATYPE/vertex1.iC>
    │ │ │ -
    207# endif
    │ │ │ -
    208
    │ │ │ -
    209 } // namespace VIEW
    │ │ │ -
    210} // namespace BALL
    │ │ │ -
    211
    │ │ │ -
    212#endif // BALL_VIEW_DATATYPE_VERTEX1_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ -
    std
    STL namespace.
    │ │ │ - │ │ │ +
    124#endif // BALL_VIEW_MODELS_LabelMODEL_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::LabelModel::getType
    Mode getType() const
    Definition labelModel.h:88
    │ │ │ +
    BALL::VIEW::LabelModel::setText
    void setText(const String &text)
    Definition labelModel.h:91
    │ │ │ + │ │ │ +
    BALL::VIEW::LabelModel::center_processor_
    GeometricCenterProcessor center_processor_
    Definition labelModel.h:118
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::LabelModel::setColor
    void setColor(const ColorRGBA &color)
    Definition labelModel.h:79
    │ │ │ +
    BALL::VIEW::LabelModel::LabelModel
    LabelModel(const LabelModel &model)
    │ │ │ +
    BALL::VIEW::LabelModel::setMode
    void setMode(Mode mode)
    Definition labelModel.h:85
    │ │ │ +
    BALL::VIEW::LabelModel::createGeometricObjects
    virtual bool createGeometricObjects()
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::LabelModel::getText
    const String & getText() const
    Definition labelModel.h:94
    │ │ │ + │ │ │ +
    BALL::VIEW::LabelModel::setFont
    void setFont(const QFont &font)
    Definition labelModel.h:73
    │ │ │ +
    BALL::VIEW::LabelModel::getFont
    const QFont & getFont() const
    Definition labelModel.h:76
    │ │ │ + │ │ │ +
    BALL::VIEW::LabelModel::getColor
    const ColorRGBA & getColor() const
    Definition labelModel.h:82
    │ │ │ + │ │ │ │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,125 +1,193 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ - * _D_A_T_A_T_Y_P_E │ │ │ │ -vertex1.h │ │ │ │ + * _M_O_D_E_L_S │ │ │ │ +labelModel.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: vertex1.h,v 1.10.20.1 2007/03/25 21:25:42 oliver Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_VIEW_DATATYPE_VERTEX1_H │ │ │ │ -8#define BALL_VIEW_DATATYPE_VERTEX1_H │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_COMMON_H │ │ │ │ -11# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -12#endif │ │ │ │ -13 │ │ │ │ -14#ifndef BALL_MATHS_VECTOR3_H │ │ │ │ -15# include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ -16#endif │ │ │ │ -17 │ │ │ │ -18namespace _B_A_L_L │ │ │ │ -19{ │ │ │ │ -20 namespace VIEW │ │ │ │ -21 { │ │ │ │ -_3_1 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _V_e_r_t_e_x │ │ │ │ -32 { │ │ │ │ -33 public: │ │ │ │ -34 │ │ │ │ -35 _B_A_L_L___C_R_E_A_T_E(_V_e_r_t_e_x) │ │ │ │ -36 │ │ │ │ -37 │ │ │ │ -40 │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_VIEW_MODELS_LABELMODEL_H │ │ │ │ +6#define BALL_VIEW_MODELS_LABELMODEL_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_VIEW_MODELS_MODELPROCESSOR_H │ │ │ │ +9# include <_B_A_L_L_/_V_I_E_W_/_M_O_D_E_L_S_/_m_o_d_e_l_P_r_o_c_e_s_s_o_r_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12#ifndef BALL_VIEW_DATATYPE_COLORRGBA_H │ │ │ │ +13# include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_c_o_l_o_r_R_G_B_A_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifndef BALL_STRUCTURE_GEOMETRICPROPERTIES_H │ │ │ │ +17# include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_g_e_o_m_e_t_r_i_c_P_r_o_p_e_r_t_i_e_s_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20 │ │ │ │ +21#include │ │ │ │ +22 │ │ │ │ +23namespace _B_A_L_L │ │ │ │ +24{ │ │ │ │ +25 namespace VIEW │ │ │ │ +26 { │ │ │ │ +27 │ │ │ │ +_3_6 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _L_a_b_e_l_M_o_d_e_l: public _M_o_d_e_l_P_r_o_c_e_s_s_o_r │ │ │ │ +37 { │ │ │ │ +38 public: │ │ │ │ +39 │ │ │ │ +40 _B_A_L_L___C_R_E_A_T_E(_L_a_b_e_l_M_o_d_e_l) │ │ │ │ 41 │ │ │ │ -_4_5 _V_e_r_t_e_x(); │ │ │ │ -46 │ │ │ │ -_5_2 _V_e_r_t_e_x(const _V_e_r_t_e_x& vertex); │ │ │ │ -53 │ │ │ │ +42 │ │ │ │ +_4_3 enum _M_o_d_e │ │ │ │ +44 { │ │ │ │ +_4_6 _A_L_L___I_T_E_M_S, │ │ │ │ +_4_8 _A_L_L___A_T_O_M_S, │ │ │ │ +_5_0 _A_L_L___R_E_S_I_D_U_E_S, │ │ │ │ +52 ONE_LABEL │ │ │ │ +_5_3 }; │ │ │ │ +54 │ │ │ │ 55 │ │ │ │ -58 │ │ │ │ -_6_1 virtual ~_V_e_r_t_e_x(); │ │ │ │ -62 │ │ │ │ -_6_8 virtual void clear(); │ │ │ │ -69 │ │ │ │ +59 │ │ │ │ +_6_2 _L_a_b_e_l_M_o_d_e_l(); │ │ │ │ +63 │ │ │ │ +_6_6 _L_a_b_e_l_M_o_d_e_l(const _L_a_b_e_l_M_o_d_e_l& model); │ │ │ │ +67 │ │ │ │ +_7_0 virtual _~_L_a_b_e_l_M_o_d_e_l(); │ │ │ │ 71 │ │ │ │ +_7_3 void _s_e_t_F_o_n_t(const QFont& font) { font_ = font;} │ │ │ │ 74 │ │ │ │ -_7_9 void set(const _V_e_r_t_e_x& v); │ │ │ │ +_7_6 const QFont& _g_e_t_F_o_n_t() const { return font_;} │ │ │ │ +77 │ │ │ │ +_7_9 void _s_e_t_C_o_l_o_r(const _C_o_l_o_r_R_G_B_A& color) { color_ = color;} │ │ │ │ 80 │ │ │ │ -_8_6 const _V_e_r_t_e_x& operator = (const _V_e_r_t_e_x& v); │ │ │ │ -87 │ │ │ │ -_9_2 void swap(_V_e_r_t_e_x& v); │ │ │ │ -93 │ │ │ │ +_8_2 const _C_o_l_o_r_R_G_B_A& _g_e_t_C_o_l_o_r() const { return color_;} │ │ │ │ +83 │ │ │ │ +_8_5 void _s_e_t_M_o_d_e(_M_o_d_e mode) { mode_ = mode;} │ │ │ │ +86 │ │ │ │ +_8_8 _M_o_d_e _g_e_t_T_y_p_e() const { return mode_;} │ │ │ │ +89 │ │ │ │ +_9_1 void _s_e_t_T_e_x_t(const _S_t_r_i_n_g& text) { text_ = text;} │ │ │ │ +92 │ │ │ │ +_9_4 const _S_t_r_i_n_g& _g_e_t_T_e_x_t() const { return text_;} │ │ │ │ 95 │ │ │ │ +96 │ │ │ │ 98 │ │ │ │ -_1_0_2 void setVertex(const _V_e_c_t_o_r_3& v); │ │ │ │ -103 │ │ │ │ -_1_0_7 void setVertex(const float x, const float y, const float z); │ │ │ │ -108 │ │ │ │ -_1_1_2 _V_e_c_t_o_r_3& getVertex(); │ │ │ │ -113 │ │ │ │ -_1_1_7 const _V_e_c_t_o_r_3& getVertex() const; │ │ │ │ -118 │ │ │ │ -_1_2_2 void getVertex(_V_e_c_t_o_r_3& v) const; │ │ │ │ +101 │ │ │ │ +_1_0_4 virtual _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t operator() (_C_o_m_p_o_s_i_t_e& composite); │ │ │ │ +105 │ │ │ │ +_1_0_7 virtual bool _c_r_e_a_t_e_G_e_o_m_e_t_r_i_c_O_b_j_e_c_t_s(); │ │ │ │ +109 │ │ │ │ +110 protected: │ │ │ │ +111 │ │ │ │ +_1_1_2 QFont _f_o_n_t__; │ │ │ │ +_1_1_3 _C_o_l_o_r_R_G_B_A _c_o_l_o_r__; │ │ │ │ +_1_1_4 _M_o_d_e _m_o_d_e__; │ │ │ │ +_1_1_5 _S_t_r_i_n_g _t_e_x_t__; │ │ │ │ +_1_1_6 _S_i_z_e _n_r___o_b_j_e_c_t_s__; │ │ │ │ +_1_1_7 _V_e_c_t_o_r_3 _c_e_n_t_e_r__; │ │ │ │ +_1_1_8 _G_e_o_m_e_t_r_i_c_C_e_n_t_e_r_P_r_o_c_e_s_s_o_r _c_e_n_t_e_r___p_r_o_c_e_s_s_o_r__; │ │ │ │ +119 }; │ │ │ │ +120 │ │ │ │ +121 } // namespace VIEW │ │ │ │ +122} // namspace BALL │ │ │ │ 123 │ │ │ │ -_1_2_7 void getVertex(float& x, float& y, float& z) const; │ │ │ │ -128 │ │ │ │ -_1_4_2 void setVertexAddress(const _V_e_c_t_o_r_3& v); │ │ │ │ -143 │ │ │ │ -_1_5_2 void setDefaultVertexAddress(); │ │ │ │ -153 │ │ │ │ -_1_5_8 _V_e_c_t_o_r_3* getVertexAddress() const; │ │ │ │ -159 │ │ │ │ -161 │ │ │ │ -164 │ │ │ │ -_1_7_2 bool isDefaultVertexAddress() const; │ │ │ │ -173 │ │ │ │ -175 │ │ │ │ -178 │ │ │ │ -_1_8_2 virtual bool isValid() const; │ │ │ │ -183 │ │ │ │ -_1_9_1 virtual void dump(_s_t_d::ostream& s = _s_t_d::cout, _S_i_z_e depth = 0) const; │ │ │ │ -192 │ │ │ │ -194 │ │ │ │ -195 private: │ │ │ │ -196 │ │ │ │ -197 /* vertex */ │ │ │ │ -198 _V_e_c_t_o_r_3 vertex1_; │ │ │ │ -199 │ │ │ │ -200 /* vertex pointer */ │ │ │ │ -201 _V_e_c_t_o_r_3* vertex1_ptr_; │ │ │ │ -202 }; │ │ │ │ -203 │ │ │ │ -204 │ │ │ │ -205# ifndef BALL_NO_INLINE_FUNCTIONS │ │ │ │ -206# include │ │ │ │ -207# endif │ │ │ │ -208 │ │ │ │ -209 } // namespace VIEW │ │ │ │ -210} // namespace BALL │ │ │ │ -211 │ │ │ │ -212#endif // BALL_VIEW_DATATYPE_VERTEX1_H │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_v_e_c_t_o_r_3_._h │ │ │ │ +124#endif // BALL_VIEW_MODELS_LabelMODEL_H │ │ │ │ +_g_e_o_m_e_t_r_i_c_P_r_o_p_e_r_t_i_e_s_._h │ │ │ │ +_m_o_d_e_l_P_r_o_c_e_s_s_o_r_._h │ │ │ │ +_c_o_l_o_r_R_G_B_A_._h │ │ │ │ _B_A_L_L___C_R_E_A_T_E │ │ │ │ #define BALL_CREATE(name) │ │ │ │ DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ -_s_t_d │ │ │ │ -STL namespace. │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t │ │ │ │ +int Result │ │ │ │ +DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_3_6 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ _B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_V_e_r_t_e_x │ │ │ │ -DDeeffiinniittiioonn _v_e_r_t_e_x_1_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_G_e_o_m_e_t_r_i_c_C_e_n_t_e_r_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_P_r_o_p_e_r_t_i_e_s_._h_:_1_3_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_C_o_l_o_r_R_G_B_A │ │ │ │ +DDeeffiinniittiioonn _c_o_l_o_r_R_G_B_A_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_3_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_m_o_d_e__ │ │ │ │ +Mode mode_ │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_1_1_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_g_e_t_T_y_p_e │ │ │ │ +Mode getType() const │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_8_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_s_e_t_T_e_x_t │ │ │ │ +void setText(const String &text) │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_9_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_t_e_x_t__ │ │ │ │ +String text_ │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_1_1_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_c_e_n_t_e_r___p_r_o_c_e_s_s_o_r__ │ │ │ │ +GeometricCenterProcessor center_processor_ │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_1_1_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_c_o_l_o_r__ │ │ │ │ +ColorRGBA color_ │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_1_1_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_n_r___o_b_j_e_c_t_s__ │ │ │ │ +Size nr_objects_ │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_1_1_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_s_e_t_C_o_l_o_r │ │ │ │ +void setColor(const ColorRGBA &color) │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_7_9 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_L_a_b_e_l_M_o_d_e_l │ │ │ │ +LabelModel(const LabelModel &model) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_s_e_t_M_o_d_e │ │ │ │ +void setMode(Mode mode) │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_8_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_c_r_e_a_t_e_G_e_o_m_e_t_r_i_c_O_b_j_e_c_t_s │ │ │ │ +virtual bool createGeometricObjects() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_M_o_d_e │ │ │ │ +Mode │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_4_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_A_L_L___A_T_O_M_S │ │ │ │ +@ ALL_ATOMS │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_A_L_L___R_E_S_I_D_U_E_S │ │ │ │ +@ ALL_RESIDUES │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_A_L_L___I_T_E_M_S │ │ │ │ +@ ALL_ITEMS │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_4_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_f_o_n_t__ │ │ │ │ +QFont font_ │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_1_1_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_~_L_a_b_e_l_M_o_d_e_l │ │ │ │ +virtual ~LabelModel() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_g_e_t_T_e_x_t │ │ │ │ +const String & getText() const │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_9_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_c_e_n_t_e_r__ │ │ │ │ +Vector3 center_ │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_1_1_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_s_e_t_F_o_n_t │ │ │ │ +void setFont(const QFont &font) │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_g_e_t_F_o_n_t │ │ │ │ +const QFont & getFont() const │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_7_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_L_a_b_e_l_M_o_d_e_l │ │ │ │ +LabelModel() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_M_o_d_e_l_:_:_g_e_t_C_o_l_o_r │ │ │ │ +const ColorRGBA & getColor() const │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_M_o_d_e_l_._h_:_8_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_e_l_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _m_o_d_e_l_P_r_o_c_e_s_s_o_r_._h_:_4_0 │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ #define BALL_VIEW_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d41/a06442.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Static Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::SLICKEnergy::Option Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SCORING/FUNCTIONS/slickEnergy.h>

    │ │ │ +

    #include <BALL/SCORING/FUNCTIONS/slickEnergy.h>

    │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -96,15 +96,15 @@ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Static Public Attributes

    static const char * CONST
     
    static const char * CHPI
     
     
    static const char * POLAR
     
    │ │ │

    Detailed Description

    │ │ │

    Option names

    │ │ │ │ │ │ -

    Definition at line 36 of file slickEnergy.h.

    │ │ │ +

    Definition at line 36 of file slickEnergy.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ CHPI

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -118,15 +118,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ static
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 44 of file slickEnergy.h.

    │ │ │ +

    Definition at line 44 of file slickEnergy.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ CONST

    │ │ │ │ │ │
    │ │ │ @@ -143,15 +143,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │

    The additive constant (

    See also
    Default::CONST)
    │ │ │ │ │ │ -

    Definition at line 40 of file slickEnergy.h.

    │ │ │ +

    Definition at line 40 of file slickEnergy.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ HB

    │ │ │ │ │ │
    │ │ │ @@ -167,15 +167,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 48 of file slickEnergy.h.

    │ │ │ +

    Definition at line 48 of file slickEnergy.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ NONPOLAR

    │ │ │ │ │ │
    │ │ │ @@ -191,15 +191,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 56 of file slickEnergy.h.

    │ │ │ +

    Definition at line 56 of file slickEnergy.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ POLAR

    │ │ │ │ │ │
    │ │ │ @@ -215,15 +215,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 60 of file slickEnergy.h.

    │ │ │ +

    Definition at line 60 of file slickEnergy.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ VDW

    │ │ │ │ │ │
    │ │ │ @@ -239,15 +239,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 52 of file slickEnergy.h.

    │ │ │ +

    Definition at line 52 of file slickEnergy.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d44/a06302.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Classes | │ │ │ List of all members
    │ │ │
    BALL::Lipophilic Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SCORING/COMPONENTS/lipophilic.h>

    │ │ │ +

    #include <BALL/SCORING/COMPONENTS/lipophilic.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::Lipophilic:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::ScoringComponent │ │ │ @@ -204,15 +204,15 @@ │ │ │   │ │ │ String type_name_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Fresno lipophilic component

    │ │ │ │ │ │ -

    Definition at line 17 of file lipophilic.h.

    │ │ │ +

    Definition at line 17 of file lipophilic.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ Lipophilic() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d49/a07962.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Types | │ │ │ List of all members
    │ │ │
    BALL::VIEW::LightSource Class Reference
    Visualisation » Kernel » Setup of the Stage, Camera and LightSources
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/stage.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/stage.h>

    │ │ │
    │ │ │ │ │ │ │ │ │ @@ -177,15 +177,15 @@ │ │ │

    │ │ │ Public Types

    enum  Types { AMBIENT = 0 │ │ │ , POSITIONAL │ │ │ , DIRECTIONAL │ │ │ }
    │ │ │

    Detailed Description

    │ │ │

    Light source is mainly used for Renderer classes (e.g. OpenGL and POVRay). Currently we support ambient, positional and directional light sources. The Position and direction of lights can be stored twofold:

      │ │ │
    • Either with absolute room coordinates and a direction vector or \
      • │ │ │
    • Relative to a Camera. In this case, the position and direction vector are stored as multiples of look right, look up and view vector.
      • │ │ │
    │ │ │ │ │ │ -

    Definition at line 53 of file stage.h.

    │ │ │ +

    Definition at line 53 of file stage.h.

    │ │ │

    Member Enumeration Documentation

    │ │ │ │ │ │

    ◆ Types

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -200,15 +200,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    Enumerator
    AMBIENT 

    Ambient light doesn't come from any particular direction. All the objects in the scene will be lit up by the ambient light.

    │ │ │
    POSITIONAL 

    Diffuse light is created the light source and is reflected off the surface of any object in the scene. Any surface of an object that the light hits directly will be very bright, and areas the light barely gets to will be darker.

    │ │ │
    DIRECTIONAL 
    │ │ │ │ │ │ -

    Definition at line 58 of file stage.h.

    │ │ │ +

    Definition at line 58 of file stage.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ LightSource() [1/2]

    │ │ │ │ │ │ @@ -266,15 +266,15 @@ │ │ │ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
    │ │ │

    Destructor

    │ │ │ │ │ │ -

    Definition at line 91 of file stage.h.

    │ │ │ +

    Definition at line 91 of file stage.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ dump()

    │ │ │ │ │ │ @@ -339,15 +339,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the angle of the light cone.

    │ │ │ │ │ │ -

    Definition at line 124 of file stage.h.

    │ │ │ +

    Definition at line 124 of file stage.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getAttenuation()

    │ │ │ │ │ │
    │ │ │ @@ -368,15 +368,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the attenuation parameters of the light.

    │ │ │ │ │ │ -

    Definition at line 115 of file stage.h.

    │ │ │ +

    Definition at line 115 of file stage.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getColor()

    │ │ │ │ │ │
    │ │ │ @@ -396,15 +396,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Get the color of the light. The alpha channel of the color is ignored.

    │ │ │ │ │ │ -

    Definition at line 146 of file stage.h.

    │ │ │ +

    Definition at line 146 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getDirection()

    │ │ │ │ │ │
    │ │ │ @@ -425,15 +425,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the direction vector of the light.

    │ │ │ │ │ │ -

    Definition at line 107 of file stage.h.

    │ │ │ +

    Definition at line 107 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getIntensity()

    │ │ │ │ │ │
    │ │ │ @@ -453,15 +453,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Get the light intensity. 0 is the minumum, 1 is the maximum.

    │ │ │ │ │ │ -

    Definition at line 134 of file stage.h.

    │ │ │ +

    Definition at line 134 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getPosition()

    │ │ │ │ │ │
    │ │ │ @@ -482,15 +482,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get position.

    │ │ │ │ │ │ -

    Definition at line 99 of file stage.h.

    │ │ │ +

    Definition at line 99 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getType()

    │ │ │ │ │ │
    │ │ │ @@ -510,15 +510,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Get the type of the light.

    See also
    Types
    │ │ │ │ │ │ -

    Definition at line 158 of file stage.h.

    │ │ │ +

    Definition at line 158 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ isRelativeToCamera()

    │ │ │ │ │ │
    │ │ │ @@ -539,15 +539,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Test if a LightSource will move with the Camera.

    │ │ │ │ │ │ -

    Definition at line 172 of file stage.h.

    │ │ │ +

    Definition at line 172 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator<()

    │ │ │ │ │ │
    │ │ │ @@ -625,15 +625,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Set the angle of the light cone.

    │ │ │ │ │ │ -

    Definition at line 128 of file stage.h.

    │ │ │ +

    Definition at line 128 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setAttenuation()

    │ │ │ │ │ │
    │ │ │ @@ -655,15 +655,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Set the attenuation parameters of the light.

    │ │ │ │ │ │ -

    Definition at line 119 of file stage.h.

    │ │ │ +

    Definition at line 119 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setColor()

    │ │ │ │ │ │
    │ │ │ @@ -684,15 +684,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Set the color of the light. The alpha channel of the color is ignored.

    │ │ │ │ │ │ -

    Definition at line 152 of file stage.h.

    │ │ │ +

    Definition at line 152 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setDirection()

    │ │ │ │ │ │
    │ │ │ @@ -714,15 +714,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Set the direction vector of the light.

    │ │ │ │ │ │ -

    Definition at line 111 of file stage.h.

    │ │ │ +

    Definition at line 111 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setIntensity()

    │ │ │ │ │ │
    │ │ │ @@ -743,15 +743,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Set the intensity. 0 is the minumum, 1 is the maximum.

    │ │ │ │ │ │ -

    Definition at line 140 of file stage.h.

    │ │ │ +

    Definition at line 140 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setPosition()

    │ │ │ │ │ │
    │ │ │ @@ -773,15 +773,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Set position.

    │ │ │ │ │ │ -

    Definition at line 103 of file stage.h.

    │ │ │ +

    Definition at line 103 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setRelativeToCamera()

    │ │ │ │ │ │
    │ │ │ @@ -803,15 +803,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    If set to true, the LightSource will move with the Camera.

    │ │ │ │ │ │ -

    Definition at line 168 of file stage.h.

    │ │ │ +

    Definition at line 168 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setType()

    │ │ │ │ │ │
    │ │ │ @@ -832,15 +832,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Set the type of the light.

    See also
    Types
    │ │ │ │ │ │ -

    Definition at line 164 of file stage.h.

    │ │ │ +

    Definition at line 164 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ angle_

    │ │ │ │ │ │ @@ -857,15 +857,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 217 of file stage.h.

    │ │ │ +

    Definition at line 217 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ attenuation_

    │ │ │ │ │ │
    │ │ │ @@ -881,15 +881,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 208 of file stage.h.

    │ │ │ +

    Definition at line 208 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ color_

    │ │ │ │ │ │
    │ │ │ @@ -905,15 +905,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 223 of file stage.h.

    │ │ │ +

    Definition at line 223 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ direction_

    │ │ │ │ │ │
    │ │ │ @@ -929,15 +929,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 205 of file stage.h.

    │ │ │ +

    Definition at line 205 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ intensity_

    │ │ │ │ │ │
    │ │ │ @@ -953,15 +953,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 220 of file stage.h.

    │ │ │ +

    Definition at line 220 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ position_

    │ │ │ │ │ │
    │ │ │ @@ -977,15 +977,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 202 of file stage.h.

    │ │ │ +

    Definition at line 202 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ r_direction_

    │ │ │ │ │ │
    │ │ │ @@ -1001,15 +1001,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 214 of file stage.h.

    │ │ │ +

    Definition at line 214 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ r_position_

    │ │ │ │ │ │
    │ │ │ @@ -1025,15 +1025,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 211 of file stage.h.

    │ │ │ +

    Definition at line 211 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ relative_

    │ │ │ │ │ │
    │ │ │ @@ -1049,15 +1049,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 229 of file stage.h.

    │ │ │ +

    Definition at line 229 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ type_

    │ │ │ │ │ │
    │ │ │ @@ -1073,15 +1073,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 226 of file stage.h.

    │ │ │ +

    Definition at line 226 of file stage.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d4a/a01862.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: genes.h File Reference │ │ │ +BALL: periodicBoundary.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,37 +65,38 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    genes.h File Reference
    │ │ │ +
    periodicBoundary.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/MATHS/quaternion.h>
    │ │ │ -#include <vector>
    │ │ │ -#include <random>
    │ │ │ +
    #include <BALL/common.h>
    │ │ │ +#include <BALL/DATATYPE/options.h>
    │ │ │ +#include <BALL/MATHS/simpleBox3.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::GenericGene
    class  BALL::PeriodicBoundary
     
    class  BALL::DoubleGene
    struct  BALL::PeriodicBoundary::Option
     
    class  BALL::QuaternionGene
    struct  BALL::PeriodicBoundary::Default
     Default values. More...
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ ├── html2text {} │ │ │ │ @@ -1,26 +1,27 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _D_O_C_K_I_N_G │ │ │ │ - * _G_E_N_E_T_I_C_D_O_C_K │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _C_O_M_M_O_N │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -genes.h File Reference │ │ │ │ -#include <_B_A_L_L_/_M_A_T_H_S_/_q_u_a_t_e_r_n_i_o_n_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ +periodicBoundary.h File Reference │ │ │ │ +#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_s_i_m_p_l_e_B_o_x_3_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e │ │ │ │ + class   _B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y │ │ │ │   │ │ │ │ -class   _B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e │ │ │ │ +struct   _B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n │ │ │ │   │ │ │ │ -class   _B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e │ │ │ │ +struct   _B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t │ │ │ │ +  _D_e_f_a_u_l_t values. _M_o_r_e_._._. │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d4a/a01862_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: genes.h Source File │ │ │ +BALL: periodicBoundary.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,153 +70,234 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    genes.h
    │ │ │ +
    periodicBoundary.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// ----------------------------------------------------
    │ │ │ -
    2// $Maintainer: Marcel Schumann $
    │ │ │ -
    3// $Authors: Jan Fuhrmann, Marcel Schumann $
    │ │ │ -
    4// ----------------------------------------------------
    │ │ │ -
    5
    │ │ │ -
    6#ifndef BALL_DOCKING_GENETICDOCK_GENES_H
    │ │ │ -
    7#define BALL_DOCKING_GENETICDOCK_GENES_H
    │ │ │ -
    8
    │ │ │ -
    9#include <BALL/MATHS/quaternion.h>
    │ │ │ -
    10
    │ │ │ -
    11#include <vector>
    │ │ │ -
    12#include <random>
    │ │ │ +Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ +
    2// vi: set ts=2:
    │ │ │ +
    3//
    │ │ │ +
    4// $Id: periodicBoundary.h,v 1.22 2005/12/23 17:01:51 amoll Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_MOLMEC_COMMON_PERIODICBOUNDARY_H
    │ │ │ +
    8#define BALL_MOLMEC_COMMON_PERIODICBOUNDARY_H
    │ │ │ +
    9
    │ │ │ +
    10#ifndef BALL_COMMON_H
    │ │ │ +
    11# include <BALL/common.h>
    │ │ │ +
    12#endif
    │ │ │
    13
    │ │ │ -
    14namespace BALL
    │ │ │ -
    15{
    │ │ │ -
    │ │ │ -
    18 class BALL_EXPORT BALL_DEPRECATED GenericGene
    │ │ │ -
    19 {
    │ │ │ -
    20 public:
    │ │ │ +
    14#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ +
    15# include <BALL/DATATYPE/options.h>
    │ │ │ +
    16#endif
    │ │ │ +
    17
    │ │ │ +
    18#ifndef BALL_MATHS_SIMPLEBOX3_H
    │ │ │ +
    19# include <BALL/MATHS/simpleBox3.h>
    │ │ │ +
    20#endif
    │ │ │
    21
    │ │ │ -
    24 GenericGene();
    │ │ │ +
    22namespace BALL
    │ │ │ +
    23{
    │ │ │ +
    24 class ForceField;
    │ │ │
    25
    │ │ │ -
    28 virtual ~GenericGene(){};
    │ │ │ -
    29
    │ │ │ -
    32 virtual GenericGene* mate(GenericGene* gg) = 0;
    │ │ │ -
    33
    │ │ │ -
    36 virtual void mutate() = 0;
    │ │ │ +
    26 class PeriodicBoundary;
    │ │ │ +
    27
    │ │ │ +
    │ │ │ +
    34 class BALL_EXPORT PeriodicBoundary
    │ │ │ +
    35 {
    │ │ │ +
    36 public:
    │ │ │
    37
    │ │ │ -
    40 virtual GenericGene* clone() = 0;
    │ │ │ -
    41
    │ │ │ -
    44 virtual void randomize() = 0;
    │ │ │ -
    45
    │ │ │ -
    46 protected:
    │ │ │ -
    47 double randomGeneValue();
    │ │ │ -
    48 int randomGenePosition(int from, int to);
    │ │ │ +
    38 BALL_CREATE(PeriodicBoundary)
    │ │ │ +
    39
    │ │ │ +
    40
    │ │ │ +
    43
    │ │ │ +
    44
    │ │ │ +
    45 typedef std::pair<Size, Size> AtomIndexPair;
    │ │ │ +
    46
    │ │ │ +
    48 typedef std::vector<AtomIndexPair> AtomIndexArray;
    │ │ │
    49
    │ │ │ -
    50 private:
    │ │ │ -
    51 std::mt19937 rng_;
    │ │ │ -
    52 std::uniform_real_distribution<double> dist_;
    │ │ │ -
    53 };
    │ │ │ -
    │ │ │ +
    51
    │ │ │
    54
    │ │ │ -
    │ │ │ -
    57 class BALL_EXPORT BALL_DEPRECATED DoubleGene: public GenericGene
    │ │ │ -
    58 {
    │ │ │ -
    59 public:
    │ │ │ +
    │ │ │ +
    56 struct BALL_EXPORT Option
    │ │ │ +
    57 {
    │ │ │ +
    59 static const char* PERIODIC_BOX_LOWER;
    │ │ │
    60
    │ │ │ -
    63 DoubleGene();
    │ │ │ -
    64
    │ │ │ -
    67 virtual ~DoubleGene();
    │ │ │ -
    68
    │ │ │ -
    71 DoubleGene(Size i);
    │ │ │ -
    72
    │ │ │ -
    75 virtual GenericGene *mate(GenericGene * gg);
    │ │ │ -
    76
    │ │ │ -
    79 virtual void mutate();
    │ │ │ -
    80
    │ │ │ -
    83 std::vector<double> getValues();
    │ │ │ -
    84
    │ │ │ -
    87 void setValue(std::vector<double> v);
    │ │ │ -
    88
    │ │ │ -
    91 virtual GenericGene *clone();
    │ │ │ -
    92
    │ │ │ -
    95 void randomize();
    │ │ │ -
    96
    │ │ │ -
    97 private:
    │ │ │ -
    98
    │ │ │ -
    101 std::vector<double> values_;
    │ │ │ -
    102 };
    │ │ │ +
    62 static const char* PERIODIC_BOX_UPPER;
    │ │ │ +
    63
    │ │ │ +
    65 static const char* PERIODIC_BOX_ENABLED;
    │ │ │ +
    66
    │ │ │ +
    68 static const char* PERIODIC_BOX_DISTANCE;
    │ │ │ +
    69
    │ │ │ +
    71 static const char* PERIODIC_BOX_ADD_SOLVENT;
    │ │ │ +
    72
    │ │ │ +
    77 static const char* PERIODIC_BOX_SOLVENT_FILE;
    │ │ │ +
    78
    │ │ │ +
    81 static const char* PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE;
    │ │ │ +
    82
    │ │ │ +
    85 static const char* PERIODIC_WATER_FILE;
    │ │ │ +
    86
    │ │ │ +
    87 };
    │ │ │
    │ │ │ +
    88
    │ │ │ +
    │ │ │ +
    90 struct BALL_EXPORT Default
    │ │ │ +
    91 {
    │ │ │ +
    93 static const Vector3 PERIODIC_BOX_LOWER;
    │ │ │ +
    94
    │ │ │ +
    96 static const Vector3 PERIODIC_BOX_UPPER;
    │ │ │ +
    97
    │ │ │ +
    99 static const bool PERIODIC_BOX_ENABLED;
    │ │ │ +
    100
    │ │ │ +
    102 static const float PERIODIC_BOX_DISTANCE;
    │ │ │
    103
    │ │ │ -
    104
    │ │ │ -
    │ │ │ -
    107 class BALL_EXPORT BALL_DEPRECATED QuaternionGene: public GenericGene
    │ │ │ -
    108 {
    │ │ │ -
    109 public:
    │ │ │ -
    110
    │ │ │ -
    113 QuaternionGene();
    │ │ │ -
    114
    │ │ │ -
    117 virtual ~QuaternionGene();
    │ │ │ -
    118
    │ │ │ -
    121 virtual GenericGene *mate(GenericGene *gg);
    │ │ │ -
    122
    │ │ │ -
    125 virtual void mutate();
    │ │ │ -
    126
    │ │ │ -
    129 Quaternion getValue();
    │ │ │ -
    130
    │ │ │ -
    133 virtual GenericGene *clone();
    │ │ │ -
    134
    │ │ │ -
    137 void randomize();
    │ │ │ -
    138
    │ │ │ -
    139 private:
    │ │ │ +
    105 static const bool PERIODIC_BOX_ADD_SOLVENT;
    │ │ │ +
    106
    │ │ │ +
    111 static const char* PERIODIC_BOX_SOLVENT_FILE;
    │ │ │ +
    112
    │ │ │ +
    114 static const float PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE;
    │ │ │ +
    115
    │ │ │ +
    117 static const char* PERIODIC_WATER_FILE;
    │ │ │ +
    118 };
    │ │ │ +
    │ │ │ +
    119
    │ │ │ +
    121
    │ │ │ +
    124
    │ │ │ +
    127 PeriodicBoundary();
    │ │ │ +
    128
    │ │ │ +
    131 PeriodicBoundary(const ForceField& force_field);
    │ │ │ +
    132
    │ │ │ +
    135 PeriodicBoundary(const PeriodicBoundary& periodic_boundary);
    │ │ │ +
    136
    │ │ │ +
    139 virtual ~PeriodicBoundary();
    │ │ │
    140
    │ │ │ -
    143 Quaternion quat_;
    │ │ │ -
    144 };
    │ │ │ +
    142
    │ │ │ +
    145
    │ │ │ +
    148 PeriodicBoundary& operator = (const PeriodicBoundary& periodic_boundary);
    │ │ │ +
    149
    │ │ │ +
    152 virtual void clear();
    │ │ │ +
    153
    │ │ │ +
    155
    │ │ │ +
    158
    │ │ │ +
    161 bool setup();
    │ │ │ +
    162
    │ │ │ +
    165 Size generateMoleculesVector();
    │ │ │ +
    166
    │ │ │ +
    168
    │ │ │ +
    171
    │ │ │ +
    173 void enable();
    │ │ │ +
    174
    │ │ │ +
    176 void disable();
    │ │ │ +
    177
    │ │ │ +
    180 SimpleBox3 getBox() const;
    │ │ │ +
    181
    │ │ │ +
    186 void setBox(const SimpleBox3& box);
    │ │ │ +
    187
    │ │ │ +
    204 Size addSolvent(const String& filename);
    │ │ │ +
    205
    │ │ │ +
    212 Size removeSolvent();
    │ │ │ +
    213
    │ │ │ +
    215
    │ │ │ +
    218
    │ │ │ +
    223 bool isEnabled() const;
    │ │ │ +
    224
    │ │ │ +
    226
    │ │ │ +
    229
    │ │ │ +
    234 void updateMolecules();
    │ │ │ +
    235
    │ │ │ +
    237
    │ │ │ +
    240
    │ │ │ +
    245 Options* options;
    │ │ │ +
    246
    │ │ │ +
    248
    │ │ │ +
    249 protected:
    │ │ │ +
    250
    │ │ │ +
    251 private:
    │ │ │ +
    252
    │ │ │ +
    253 /*_ @name Private Attributes
    │ │ │ +
    254 */
    │ │ │ +
    255 //_@{
    │ │ │ +
    256
    │ │ │ +
    257 //_ Pointer to the force field of the periodic boundary
    │ │ │ +
    258 ForceField* force_field_;
    │ │ │ +
    259
    │ │ │ +
    260 //_ Indicates if periodic boundary is enabled or not
    │ │ │ +
    261 bool enabled_;
    │ │ │ +
    262
    │ │ │ +
    263 //_ The box of the periodic boundary
    │ │ │ +
    264 SimpleBox3 box_;
    │ │ │ +
    265
    │ │ │ +
    266 //_ An pair vector with the start and end indices of all molecules (atoms of the molecules)
    │ │ │ +
    267 AtomIndexArray molecules_;
    │ │ │ +
    268
    │ │ │ +
    269 //_@}
    │ │ │ +
    270
    │ │ │ +
    271 };
    │ │ │
    │ │ │ -
    145}
    │ │ │ -
    146
    │ │ │ -
    147#endif /* BALL_DOCKING_GENETICDOCK_GENES_H */
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::GenericGene::randomize
    virtual void randomize()=0
    │ │ │ -
    BALL::GenericGene::mutate
    virtual void mutate()=0
    │ │ │ -
    BALL::GenericGene::clone
    virtual GenericGene * clone()=0
    │ │ │ -
    BALL::GenericGene::randomGenePosition
    int randomGenePosition(int from, int to)
    │ │ │ -
    BALL::GenericGene::~GenericGene
    virtual ~GenericGene()
    Definition genes.h:28
    │ │ │ -
    BALL::GenericGene::mate
    virtual GenericGene * mate(GenericGene *gg)=0
    │ │ │ - │ │ │ -
    BALL::GenericGene::randomGeneValue
    double randomGeneValue()
    │ │ │ - │ │ │ -
    BALL::DoubleGene::mutate
    virtual void mutate()
    │ │ │ -
    BALL::DoubleGene::getValues
    std::vector< double > getValues()
    │ │ │ -
    BALL::DoubleGene::~DoubleGene
    virtual ~DoubleGene()
    │ │ │ - │ │ │ - │ │ │ -
    BALL::DoubleGene::clone
    virtual GenericGene * clone()
    │ │ │ -
    BALL::DoubleGene::setValue
    void setValue(std::vector< double > v)
    │ │ │ - │ │ │ -
    BALL::DoubleGene::mate
    virtual GenericGene * mate(GenericGene *gg)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::QuaternionGene::clone
    virtual GenericGene * clone()
    │ │ │ -
    BALL::QuaternionGene::mutate
    virtual void mutate()
    │ │ │ -
    BALL::QuaternionGene::mate
    virtual GenericGene * mate(GenericGene *gg)
    │ │ │ - │ │ │ -
    BALL::QuaternionGene::getValue
    Quaternion getValue()
    │ │ │ -
    BALL::QuaternionGene::~QuaternionGene
    virtual ~QuaternionGene()
    │ │ │ - │ │ │ +
    272
    │ │ │ +
    273} // namespace BALL
    │ │ │ +
    274
    │ │ │ +
    275#endif // BALL_MOLMEC_COMMON_PERIODICBOUNDARY_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ +
    std
    STL namespace.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::PeriodicBoundary::enable
    void enable()
    Enable periodic boundary conditions.
    │ │ │ + │ │ │ + │ │ │ +
    BALL::PeriodicBoundary::addSolvent
    Size addSolvent(const String &filename)
    │ │ │ +
    BALL::PeriodicBoundary::PeriodicBoundary
    PeriodicBoundary(const PeriodicBoundary &periodic_boundary)
    │ │ │ + │ │ │ +
    BALL::PeriodicBoundary::PeriodicBoundary
    PeriodicBoundary(const ForceField &force_field)
    │ │ │ + │ │ │ +
    BALL::PeriodicBoundary::getBox
    SimpleBox3 getBox() const
    │ │ │ +
    BALL::PeriodicBoundary::isEnabled
    bool isEnabled() const
    │ │ │ +
    BALL::PeriodicBoundary::disable
    void disable()
    Disable periodic boundary conditions.
    │ │ │ +
    BALL::PeriodicBoundary::AtomIndexPair
    std::pair< Size, Size > AtomIndexPair
    Definition periodicBoundary.h:45
    │ │ │ +
    BALL::PeriodicBoundary::setBox
    void setBox(const SimpleBox3 &box)
    │ │ │ + │ │ │ +
    BALL::PeriodicBoundary::clear
    virtual void clear()
    │ │ │ +
    BALL::PeriodicBoundary::AtomIndexArray
    std::vector< AtomIndexPair > AtomIndexArray
    Definition periodicBoundary.h:48
    │ │ │ + │ │ │ +
    BALL::PeriodicBoundary::Option::PERIODIC_BOX_UPPER
    static const char * PERIODIC_BOX_UPPER
    Vector containing the upper corner of the box.
    Definition periodicBoundary.h:62
    │ │ │ +
    BALL::PeriodicBoundary::Option::PERIODIC_BOX_SOLVENT_FILE
    static const char * PERIODIC_BOX_SOLVENT_FILE
    Definition periodicBoundary.h:77
    │ │ │ +
    BALL::PeriodicBoundary::Option::PERIODIC_BOX_LOWER
    static const char * PERIODIC_BOX_LOWER
    Vector containing the lower corner of the box.
    Definition periodicBoundary.h:59
    │ │ │ +
    BALL::PeriodicBoundary::Option::PERIODIC_BOX_ADD_SOLVENT
    static const char * PERIODIC_BOX_ADD_SOLVENT
    Flag to initiate the addition of solvent to the box.
    Definition periodicBoundary.h:71
    │ │ │ +
    BALL::PeriodicBoundary::Option::PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE
    static const char * PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE
    Definition periodicBoundary.h:81
    │ │ │ +
    BALL::PeriodicBoundary::Option::PERIODIC_BOX_DISTANCE
    static const char * PERIODIC_BOX_DISTANCE
    Minimum distance between solute molecules and the box in Angstrom.
    Definition periodicBoundary.h:68
    │ │ │ +
    BALL::PeriodicBoundary::Option::PERIODIC_WATER_FILE
    static const char * PERIODIC_WATER_FILE
    Definition periodicBoundary.h:85
    │ │ │ +
    BALL::PeriodicBoundary::Option::PERIODIC_BOX_ENABLED
    static const char * PERIODIC_BOX_ENABLED
    Bool that indicates whether periodic boundary is enabled or not.
    Definition periodicBoundary.h:65
    │ │ │ + │ │ │ +
    BALL::PeriodicBoundary::Default::PERIODIC_BOX_ADD_SOLVENT
    static const bool PERIODIC_BOX_ADD_SOLVENT
    Default value of the flag to initiate the addition of solvent to the box.
    Definition periodicBoundary.h:105
    │ │ │ +
    BALL::PeriodicBoundary::Default::PERIODIC_BOX_UPPER
    static const Vector3 PERIODIC_BOX_UPPER
    Default vector for the upper corner of the box.
    Definition periodicBoundary.h:96
    │ │ │ +
    BALL::PeriodicBoundary::Default::PERIODIC_WATER_FILE
    static const char * PERIODIC_WATER_FILE
    Default file for default solvent.
    Definition periodicBoundary.h:117
    │ │ │ +
    BALL::PeriodicBoundary::Default::PERIODIC_BOX_LOWER
    static const Vector3 PERIODIC_BOX_LOWER
    Default vector for the lower corner of the box.
    Definition periodicBoundary.h:93
    │ │ │ +
    BALL::PeriodicBoundary::Default::PERIODIC_BOX_ENABLED
    static const bool PERIODIC_BOX_ENABLED
    Default bool value for periodic boundary (enabled or not)
    Definition periodicBoundary.h:99
    │ │ │ +
    BALL::PeriodicBoundary::Default::PERIODIC_BOX_DISTANCE
    static const float PERIODIC_BOX_DISTANCE
    Default minimum distance between solute molecules and the box in Angstrom.
    Definition periodicBoundary.h:102
    │ │ │ +
    BALL::PeriodicBoundary::Default::PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE
    static const float PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE
    Default minimum distance between solvent and solute for added solvent.
    Definition periodicBoundary.h:114
    │ │ │ +
    BALL::PeriodicBoundary::Default::PERIODIC_BOX_SOLVENT_FILE
    static const char * PERIODIC_BOX_SOLVENT_FILE
    Definition periodicBoundary.h:111
    │ │ │ │ │ │ -
    BALL_DEPRECATED
    #define BALL_DEPRECATED
    Definition COMMON/global.h:64
    │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,171 +1,300 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _D_O_C_K_I_N_G │ │ │ │ - * _G_E_N_E_T_I_C_D_O_C_K │ │ │ │ -genes.h │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _C_O_M_M_O_N │ │ │ │ +periodicBoundary.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// ---------------------------------------------------- │ │ │ │ -2// $Maintainer: Marcel Schumann $ │ │ │ │ -3// $Authors: Jan Fuhrmann, Marcel Schumann $ │ │ │ │ -4// ---------------------------------------------------- │ │ │ │ -5 │ │ │ │ -6#ifndef BALL_DOCKING_GENETICDOCK_GENES_H │ │ │ │ -7#define BALL_DOCKING_GENETICDOCK_GENES_H │ │ │ │ -8 │ │ │ │ -9#include <_B_A_L_L_/_M_A_T_H_S_/_q_u_a_t_e_r_n_i_o_n_._h> │ │ │ │ -10 │ │ │ │ -11#include │ │ │ │ -12#include │ │ │ │ +1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ +2// vi: set ts=2: │ │ │ │ +3// │ │ │ │ +4// $Id: periodicBoundary.h,v 1.22 2005/12/23 17:01:51 amoll Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_MOLMEC_COMMON_PERIODICBOUNDARY_H │ │ │ │ +8#define BALL_MOLMEC_COMMON_PERIODICBOUNDARY_H │ │ │ │ +9 │ │ │ │ +10#ifndef BALL_COMMON_H │ │ │ │ +11# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +12#endif │ │ │ │ 13 │ │ │ │ -14namespace _B_A_L_L │ │ │ │ -15{ │ │ │ │ -_1_8 class _B_A_L_L___E_X_P_O_R_T _B_A_L_L___D_E_P_R_E_C_A_T_E_D _G_e_n_e_r_i_c_G_e_n_e │ │ │ │ -19 { │ │ │ │ -20 public: │ │ │ │ +14#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ +15# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +16#endif │ │ │ │ +17 │ │ │ │ +18#ifndef BALL_MATHS_SIMPLEBOX3_H │ │ │ │ +19# include <_B_A_L_L_/_M_A_T_H_S_/_s_i_m_p_l_e_B_o_x_3_._h> │ │ │ │ +20#endif │ │ │ │ 21 │ │ │ │ -_2_4 _G_e_n_e_r_i_c_G_e_n_e(); │ │ │ │ +22namespace _B_A_L_L │ │ │ │ +23{ │ │ │ │ +24 class ForceField; │ │ │ │ 25 │ │ │ │ -_2_8 virtual _~_G_e_n_e_r_i_c_G_e_n_e(){}; │ │ │ │ -29 │ │ │ │ -_3_2 virtual _G_e_n_e_r_i_c_G_e_n_e* _m_a_t_e(_G_e_n_e_r_i_c_G_e_n_e* gg) = 0; │ │ │ │ -33 │ │ │ │ -_3_6 virtual void _m_u_t_a_t_e() = 0; │ │ │ │ +26 class PeriodicBoundary; │ │ │ │ +27 │ │ │ │ +_3_4 class _B_A_L_L___E_X_P_O_R_T _P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y │ │ │ │ +35 { │ │ │ │ +36 public: │ │ │ │ 37 │ │ │ │ -_4_0 virtual _G_e_n_e_r_i_c_G_e_n_e* _c_l_o_n_e() = 0; │ │ │ │ -41 │ │ │ │ -_4_4 virtual void _r_a_n_d_o_m_i_z_e() = 0; │ │ │ │ -45 │ │ │ │ -46 protected: │ │ │ │ -_4_7 double _r_a_n_d_o_m_G_e_n_e_V_a_l_u_e(); │ │ │ │ -_4_8 int _r_a_n_d_o_m_G_e_n_e_P_o_s_i_t_i_o_n(int from, int to); │ │ │ │ +38 _B_A_L_L___C_R_E_A_T_E(_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y) │ │ │ │ +39 │ │ │ │ +40 │ │ │ │ +43 │ │ │ │ +44 │ │ │ │ +_4_5 typedef _s_t_d::pair<_S_i_z_e, _S_i_z_e> _A_t_o_m_I_n_d_e_x_P_a_i_r; │ │ │ │ +46 │ │ │ │ +_4_8 typedef _s_t_d::vector<_A_t_o_m_I_n_d_e_x_P_a_i_r> _A_t_o_m_I_n_d_e_x_A_r_r_a_y; │ │ │ │ 49 │ │ │ │ -50 private: │ │ │ │ -51 std::mt19937 rng_; │ │ │ │ -52 std::uniform_real_distribution dist_; │ │ │ │ -53 }; │ │ │ │ +51 │ │ │ │ 54 │ │ │ │ -_5_7 class _B_A_L_L___E_X_P_O_R_T _B_A_L_L___D_E_P_R_E_C_A_T_E_D _D_o_u_b_l_e_G_e_n_e: public _G_e_n_e_r_i_c_G_e_n_e │ │ │ │ -58 { │ │ │ │ -59 public: │ │ │ │ +_5_6 struct _B_A_L_L___E_X_P_O_R_T _O_p_t_i_o_n │ │ │ │ +57 { │ │ │ │ +_5_9 static const char* _P_E_R_I_O_D_I_C___B_O_X___L_O_W_E_R; │ │ │ │ 60 │ │ │ │ -_6_3 _D_o_u_b_l_e_G_e_n_e(); │ │ │ │ -64 │ │ │ │ -_6_7 virtual _~_D_o_u_b_l_e_G_e_n_e(); │ │ │ │ -68 │ │ │ │ -_7_1 _D_o_u_b_l_e_G_e_n_e(_S_i_z_e i); │ │ │ │ +_6_2 static const char* _P_E_R_I_O_D_I_C___B_O_X___U_P_P_E_R; │ │ │ │ +63 │ │ │ │ +_6_5 static const char* _P_E_R_I_O_D_I_C___B_O_X___E_N_A_B_L_E_D; │ │ │ │ +66 │ │ │ │ +_6_8 static const char* _P_E_R_I_O_D_I_C___B_O_X___D_I_S_T_A_N_C_E; │ │ │ │ +69 │ │ │ │ +_7_1 static const char* _P_E_R_I_O_D_I_C___B_O_X___A_D_D___S_O_L_V_E_N_T; │ │ │ │ 72 │ │ │ │ -_7_5 virtual _G_e_n_e_r_i_c_G_e_n_e *_m_a_t_e(_G_e_n_e_r_i_c_G_e_n_e * gg); │ │ │ │ -76 │ │ │ │ -_7_9 virtual void _m_u_t_a_t_e(); │ │ │ │ -80 │ │ │ │ -_8_3 std::vector _g_e_t_V_a_l_u_e_s(); │ │ │ │ -84 │ │ │ │ -_8_7 void _s_e_t_V_a_l_u_e(std::vector v); │ │ │ │ +_7_7 static const char* _P_E_R_I_O_D_I_C___B_O_X___S_O_L_V_E_N_T___F_I_L_E; │ │ │ │ +78 │ │ │ │ +_8_1 static const char* _P_E_R_I_O_D_I_C___B_O_X___S_O_L_V_E_N_T___S_O_L_U_T_E___D_I_S_T_A_N_C_E; │ │ │ │ +82 │ │ │ │ +_8_5 static const char* _P_E_R_I_O_D_I_C___W_A_T_E_R___F_I_L_E; │ │ │ │ +86 │ │ │ │ +87 }; │ │ │ │ 88 │ │ │ │ -_9_1 virtual _G_e_n_e_r_i_c_G_e_n_e *_c_l_o_n_e(); │ │ │ │ -92 │ │ │ │ -_9_5 void _r_a_n_d_o_m_i_z_e(); │ │ │ │ -96 │ │ │ │ -97 private: │ │ │ │ -98 │ │ │ │ -101 std::vector values_; │ │ │ │ -102 }; │ │ │ │ +_9_0 struct _B_A_L_L___E_X_P_O_R_T _D_e_f_a_u_l_t │ │ │ │ +91 { │ │ │ │ +_9_3 static const _V_e_c_t_o_r_3 _P_E_R_I_O_D_I_C___B_O_X___L_O_W_E_R; │ │ │ │ +94 │ │ │ │ +_9_6 static const _V_e_c_t_o_r_3 _P_E_R_I_O_D_I_C___B_O_X___U_P_P_E_R; │ │ │ │ +97 │ │ │ │ +_9_9 static const bool _P_E_R_I_O_D_I_C___B_O_X___E_N_A_B_L_E_D; │ │ │ │ +100 │ │ │ │ +_1_0_2 static const float _P_E_R_I_O_D_I_C___B_O_X___D_I_S_T_A_N_C_E; │ │ │ │ 103 │ │ │ │ -104 │ │ │ │ -_1_0_7 class _B_A_L_L___E_X_P_O_R_T _B_A_L_L___D_E_P_R_E_C_A_T_E_D _Q_u_a_t_e_r_n_i_o_n_G_e_n_e: public _G_e_n_e_r_i_c_G_e_n_e │ │ │ │ -108 { │ │ │ │ -109 public: │ │ │ │ -110 │ │ │ │ -_1_1_3 _Q_u_a_t_e_r_n_i_o_n_G_e_n_e(); │ │ │ │ -114 │ │ │ │ -_1_1_7 virtual _~_Q_u_a_t_e_r_n_i_o_n_G_e_n_e(); │ │ │ │ -118 │ │ │ │ -_1_2_1 virtual _G_e_n_e_r_i_c_G_e_n_e *_m_a_t_e(_G_e_n_e_r_i_c_G_e_n_e *gg); │ │ │ │ -122 │ │ │ │ -_1_2_5 virtual void _m_u_t_a_t_e(); │ │ │ │ -126 │ │ │ │ -_1_2_9 _Q_u_a_t_e_r_n_i_o_n _g_e_t_V_a_l_u_e(); │ │ │ │ -130 │ │ │ │ -_1_3_3 virtual _G_e_n_e_r_i_c_G_e_n_e *_c_l_o_n_e(); │ │ │ │ -134 │ │ │ │ -_1_3_7 void _r_a_n_d_o_m_i_z_e(); │ │ │ │ -138 │ │ │ │ -139 private: │ │ │ │ +_1_0_5 static const bool _P_E_R_I_O_D_I_C___B_O_X___A_D_D___S_O_L_V_E_N_T; │ │ │ │ +106 │ │ │ │ +_1_1_1 static const char* _P_E_R_I_O_D_I_C___B_O_X___S_O_L_V_E_N_T___F_I_L_E; │ │ │ │ +112 │ │ │ │ +_1_1_4 static const float _P_E_R_I_O_D_I_C___B_O_X___S_O_L_V_E_N_T___S_O_L_U_T_E___D_I_S_T_A_N_C_E; │ │ │ │ +115 │ │ │ │ +_1_1_7 static const char* _P_E_R_I_O_D_I_C___W_A_T_E_R___F_I_L_E; │ │ │ │ +118 }; │ │ │ │ +119 │ │ │ │ +121 │ │ │ │ +124 │ │ │ │ +_1_2_7 _P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y(); │ │ │ │ +128 │ │ │ │ +_1_3_1 _P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y(const _F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ +132 │ │ │ │ +_1_3_5 _P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y(const _P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y& periodic_boundary); │ │ │ │ +136 │ │ │ │ +_1_3_9 virtual _~_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y(); │ │ │ │ 140 │ │ │ │ -143 _Q_u_a_t_e_r_n_i_o_n quat_; │ │ │ │ -144 }; │ │ │ │ -145} │ │ │ │ -146 │ │ │ │ -147#endif /* BALL_DOCKING_GENETICDOCK_GENES_H */ │ │ │ │ -_q_u_a_t_e_r_n_i_o_n_._h │ │ │ │ +142 │ │ │ │ +145 │ │ │ │ +_1_4_8 _P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y& operator = (const _P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y& periodic_boundary); │ │ │ │ +149 │ │ │ │ +_1_5_2 virtual void _c_l_e_a_r(); │ │ │ │ +153 │ │ │ │ +155 │ │ │ │ +158 │ │ │ │ +_1_6_1 bool _s_e_t_u_p(); │ │ │ │ +162 │ │ │ │ +_1_6_5 _S_i_z_e _g_e_n_e_r_a_t_e_M_o_l_e_c_u_l_e_s_V_e_c_t_o_r(); │ │ │ │ +166 │ │ │ │ +168 │ │ │ │ +171 │ │ │ │ +_1_7_3 void _e_n_a_b_l_e(); │ │ │ │ +174 │ │ │ │ +_1_7_6 void _d_i_s_a_b_l_e(); │ │ │ │ +177 │ │ │ │ +_1_8_0 _S_i_m_p_l_e_B_o_x_3 _g_e_t_B_o_x() const; │ │ │ │ +181 │ │ │ │ +_1_8_6 void _s_e_t_B_o_x(const _S_i_m_p_l_e_B_o_x_3& box); │ │ │ │ +187 │ │ │ │ +_2_0_4 _S_i_z_e _a_d_d_S_o_l_v_e_n_t(const _S_t_r_i_n_g& filename); │ │ │ │ +205 │ │ │ │ +_2_1_2 _S_i_z_e _r_e_m_o_v_e_S_o_l_v_e_n_t(); │ │ │ │ +213 │ │ │ │ +215 │ │ │ │ +218 │ │ │ │ +_2_2_3 bool _i_s_E_n_a_b_l_e_d() const; │ │ │ │ +224 │ │ │ │ +226 │ │ │ │ +229 │ │ │ │ +_2_3_4 void _u_p_d_a_t_e_M_o_l_e_c_u_l_e_s(); │ │ │ │ +235 │ │ │ │ +237 │ │ │ │ +240 │ │ │ │ +_2_4_5 _O_p_t_i_o_n_s* _o_p_t_i_o_n_s; │ │ │ │ +246 │ │ │ │ +248 │ │ │ │ +249 protected: │ │ │ │ +250 │ │ │ │ +251 private: │ │ │ │ +252 │ │ │ │ +253 /*_ @name Private Attributes │ │ │ │ +254 */ │ │ │ │ +255 //_@{ │ │ │ │ +256 │ │ │ │ +257 //_ Pointer to the force field of the periodic boundary │ │ │ │ +258 _F_o_r_c_e_F_i_e_l_d* force_field_; │ │ │ │ +259 │ │ │ │ +260 //_ Indicates if periodic boundary is enabled or not │ │ │ │ +261 bool enabled_; │ │ │ │ +262 │ │ │ │ +263 //_ The box of the periodic boundary │ │ │ │ +264 _S_i_m_p_l_e_B_o_x_3 box_; │ │ │ │ +265 │ │ │ │ +266 //_ An pair vector with the start and end indices of all molecules (atoms │ │ │ │ +of the molecules) │ │ │ │ +267 _A_t_o_m_I_n_d_e_x_A_r_r_a_y molecules_; │ │ │ │ +268 │ │ │ │ +269 //_@} │ │ │ │ +270 │ │ │ │ +271 }; │ │ │ │ +272 │ │ │ │ +273} // namespace BALL │ │ │ │ +274 │ │ │ │ +275#endif // BALL_MOLMEC_COMMON_PERIODICBOUNDARY_H │ │ │ │ +_c_o_m_m_o_n_._h │ │ │ │ +_s_i_m_p_l_e_B_o_x_3_._h │ │ │ │ +_o_p_t_i_o_n_s_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_s_t_d │ │ │ │ +STL namespace. │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e │ │ │ │ -DDeeffiinniittiioonn _g_e_n_e_s_._h_:_1_9 │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e_:_:_r_a_n_d_o_m_i_z_e │ │ │ │ -virtual void randomize()=0 │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e_:_:_m_u_t_a_t_e │ │ │ │ -virtual void mutate()=0 │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e_:_:_c_l_o_n_e │ │ │ │ -virtual GenericGene * clone()=0 │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e_:_:_r_a_n_d_o_m_G_e_n_e_P_o_s_i_t_i_o_n │ │ │ │ -int randomGenePosition(int from, int to) │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e_:_:_~_G_e_n_e_r_i_c_G_e_n_e │ │ │ │ -virtual ~GenericGene() │ │ │ │ -DDeeffiinniittiioonn _g_e_n_e_s_._h_:_2_8 │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e_:_:_m_a_t_e │ │ │ │ -virtual GenericGene * mate(GenericGene *gg)=0 │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e_:_:_G_e_n_e_r_i_c_G_e_n_e │ │ │ │ -GenericGene() │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e_:_:_r_a_n_d_o_m_G_e_n_e_V_a_l_u_e │ │ │ │ -double randomGeneValue() │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e │ │ │ │ -DDeeffiinniittiioonn _g_e_n_e_s_._h_:_5_8 │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e_:_:_m_u_t_a_t_e │ │ │ │ -virtual void mutate() │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e_:_:_g_e_t_V_a_l_u_e_s │ │ │ │ -std::vector< double > getValues() │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e_:_:_~_D_o_u_b_l_e_G_e_n_e │ │ │ │ -virtual ~DoubleGene() │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e_:_:_r_a_n_d_o_m_i_z_e │ │ │ │ -void randomize() │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e_:_:_D_o_u_b_l_e_G_e_n_e │ │ │ │ -DoubleGene(Size i) │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e_:_:_c_l_o_n_e │ │ │ │ -virtual GenericGene * clone() │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e_:_:_s_e_t_V_a_l_u_e │ │ │ │ -void setValue(std::vector< double > v) │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e_:_:_D_o_u_b_l_e_G_e_n_e │ │ │ │ -DoubleGene() │ │ │ │ -_B_A_L_L_:_:_D_o_u_b_l_e_G_e_n_e_:_:_m_a_t_e │ │ │ │ -virtual GenericGene * mate(GenericGene *gg) │ │ │ │ -_B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e │ │ │ │ -DDeeffiinniittiioonn _g_e_n_e_s_._h_:_1_0_8 │ │ │ │ -_B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e │ │ │ │ -QuaternionGene() │ │ │ │ -_B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e_:_:_c_l_o_n_e │ │ │ │ -virtual GenericGene * clone() │ │ │ │ -_B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e_:_:_m_u_t_a_t_e │ │ │ │ -virtual void mutate() │ │ │ │ -_B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e_:_:_m_a_t_e │ │ │ │ -virtual GenericGene * mate(GenericGene *gg) │ │ │ │ -_B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e_:_:_r_a_n_d_o_m_i_z_e │ │ │ │ -void randomize() │ │ │ │ -_B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e_:_:_g_e_t_V_a_l_u_e │ │ │ │ -Quaternion getValue() │ │ │ │ -_B_A_L_L_:_:_Q_u_a_t_e_r_n_i_o_n_G_e_n_e_:_:_~_Q_u_a_t_e_r_n_i_o_n_G_e_n_e │ │ │ │ -virtual ~QuaternionGene() │ │ │ │ -_B_A_L_L_:_:_T_Q_u_a_t_e_r_n_i_o_n_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_T_S_i_m_p_l_e_B_o_x_3_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_3_5 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y │ │ │ │ +PeriodicBoundary() │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_g_e_n_e_r_a_t_e_M_o_l_e_c_u_l_e_s_V_e_c_t_o_r │ │ │ │ +Size generateMoleculesVector() │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_e_n_a_b_l_e │ │ │ │ +void enable() │ │ │ │ +Enable periodic boundary conditions. │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_r_e_m_o_v_e_S_o_l_v_e_n_t │ │ │ │ +Size removeSolvent() │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_o_p_t_i_o_n_s │ │ │ │ +Options * options │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_2_4_5 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_a_d_d_S_o_l_v_e_n_t │ │ │ │ +Size addSolvent(const String &filename) │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y │ │ │ │ +PeriodicBoundary(const PeriodicBoundary &periodic_boundary) │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_~_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y │ │ │ │ +virtual ~PeriodicBoundary() │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y │ │ │ │ +PeriodicBoundary(const ForceField &force_field) │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_s_e_t_u_p │ │ │ │ +bool setup() │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_g_e_t_B_o_x │ │ │ │ +SimpleBox3 getBox() const │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_i_s_E_n_a_b_l_e_d │ │ │ │ +bool isEnabled() const │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_d_i_s_a_b_l_e │ │ │ │ +void disable() │ │ │ │ +Disable periodic boundary conditions. │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_A_t_o_m_I_n_d_e_x_P_a_i_r │ │ │ │ +std::pair< Size, Size > AtomIndexPair │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_4_5 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_s_e_t_B_o_x │ │ │ │ +void setBox(const SimpleBox3 &box) │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_u_p_d_a_t_e_M_o_l_e_c_u_l_e_s │ │ │ │ +void updateMolecules() │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_c_l_e_a_r │ │ │ │ +virtual void clear() │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_A_t_o_m_I_n_d_e_x_A_r_r_a_y │ │ │ │ +std::vector< AtomIndexPair > AtomIndexArray │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n_:_:_P_E_R_I_O_D_I_C___B_O_X___U_P_P_E_R │ │ │ │ +static const char * PERIODIC_BOX_UPPER │ │ │ │ +Vector containing the upper corner of the box. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_6_2 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n_:_:_P_E_R_I_O_D_I_C___B_O_X___S_O_L_V_E_N_T___F_I_L_E │ │ │ │ +static const char * PERIODIC_BOX_SOLVENT_FILE │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_7_7 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n_:_:_P_E_R_I_O_D_I_C___B_O_X___L_O_W_E_R │ │ │ │ +static const char * PERIODIC_BOX_LOWER │ │ │ │ +Vector containing the lower corner of the box. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_5_9 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n_:_:_P_E_R_I_O_D_I_C___B_O_X___A_D_D___S_O_L_V_E_N_T │ │ │ │ +static const char * PERIODIC_BOX_ADD_SOLVENT │ │ │ │ +Flag to initiate the addition of solvent to the box. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_7_1 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n_:_:_P_E_R_I_O_D_I_C___B_O_X___S_O_L_V_E_N_T___S_O_L_U_T_E___D_I_S_T_A_N_C_E │ │ │ │ +static const char * PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_8_1 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n_:_:_P_E_R_I_O_D_I_C___B_O_X___D_I_S_T_A_N_C_E │ │ │ │ +static const char * PERIODIC_BOX_DISTANCE │ │ │ │ +Minimum distance between solute molecules and the box in Angstrom. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_6_8 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n_:_:_P_E_R_I_O_D_I_C___W_A_T_E_R___F_I_L_E │ │ │ │ +static const char * PERIODIC_WATER_FILE │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_8_5 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_O_p_t_i_o_n_:_:_P_E_R_I_O_D_I_C___B_O_X___E_N_A_B_L_E_D │ │ │ │ +static const char * PERIODIC_BOX_ENABLED │ │ │ │ +Bool that indicates whether periodic boundary is enabled or not. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_6_5 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t │ │ │ │ +Default values. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_9_1 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t_:_:_P_E_R_I_O_D_I_C___B_O_X___A_D_D___S_O_L_V_E_N_T │ │ │ │ +static const bool PERIODIC_BOX_ADD_SOLVENT │ │ │ │ +Default value of the flag to initiate the addition of solvent to the box. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_1_0_5 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t_:_:_P_E_R_I_O_D_I_C___B_O_X___U_P_P_E_R │ │ │ │ +static const Vector3 PERIODIC_BOX_UPPER │ │ │ │ +Default vector for the upper corner of the box. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_9_6 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t_:_:_P_E_R_I_O_D_I_C___W_A_T_E_R___F_I_L_E │ │ │ │ +static const char * PERIODIC_WATER_FILE │ │ │ │ +Default file for default solvent. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_1_1_7 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t_:_:_P_E_R_I_O_D_I_C___B_O_X___L_O_W_E_R │ │ │ │ +static const Vector3 PERIODIC_BOX_LOWER │ │ │ │ +Default vector for the lower corner of the box. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_9_3 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t_:_:_P_E_R_I_O_D_I_C___B_O_X___E_N_A_B_L_E_D │ │ │ │ +static const bool PERIODIC_BOX_ENABLED │ │ │ │ +Default bool value for periodic boundary (enabled or not) │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_9_9 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t_:_:_P_E_R_I_O_D_I_C___B_O_X___D_I_S_T_A_N_C_E │ │ │ │ +static const float PERIODIC_BOX_DISTANCE │ │ │ │ +Default minimum distance between solute molecules and the box in Angstrom. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_1_0_2 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t_:_:_P_E_R_I_O_D_I_C___B_O_X___S_O_L_V_E_N_T___S_O_L_U_T_E___D_I_S_T_A_N_C_E │ │ │ │ +static const float PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE │ │ │ │ +Default minimum distance between solvent and solute for added solvent. │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_1_1_4 │ │ │ │ +_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_:_:_D_e_f_a_u_l_t_:_:_P_E_R_I_O_D_I_C___B_O_X___S_O_L_V_E_N_T___F_I_L_E │ │ │ │ +static const char * PERIODIC_BOX_SOLVENT_FILE │ │ │ │ +DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_1_1_1 │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_B_A_L_L___D_E_P_R_E_C_A_T_E_D │ │ │ │ -#define BALL_DEPRECATED │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_6_4 │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d4c/a04422.html │ │ │ @@ -79,30 +79,30 @@ │ │ │
    BALL::PubChemDownloader Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │

    Downloads PubChem entries. │ │ │ More...

    │ │ │ │ │ │ -

    #include <BALL/FORMAT/pubchemDownloader.h>

    │ │ │ +

    #include <BALL/FORMAT/pubchemDownloader.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

     PubChemDownloader ()
     
    bool downloadSDFByName (const String &query, const String &filename)
     
    bool downloadSDFByCID (int cid, const String &filename)
     
    │ │ │

    Detailed Description

    │ │ │

    Downloads PubChem entries.

    │ │ │

    This class provides a simplistic, blocking interface to the PubChem REST query interface. It downloads the obtained records in SDF format and

    │ │ │ │ │ │ -

    Definition at line 20 of file pubchemDownloader.h.

    │ │ │ +

    Definition at line 20 of file pubchemDownloader.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ PubChemDownloader()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d51/a04710.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Member Functions | │ │ │ List of all members │ │ │
    BALL::NumberOfBondsPredicate Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/KERNEL/standardPredicates.h>

    │ │ │ +

    #include <BALL/KERNEL/standardPredicates.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::NumberOfBondsPredicate:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::ExpressionPredicate │ │ │ @@ -138,15 +138,15 @@ │ │ │
    │ │ │ │ │ │ │ │ │
    - Protected Attributes inherited from BALL::ExpressionPredicate
    String argument_
     
    │ │ │

    Detailed Description

    │ │ │

    Predicate class for atoms bearing a certain number of bonds. Arguments of this class are required to consist of an relational operator and a number between 1 and 8. The default is ">0" which means that the atom under siege has to bear at least one bond to make this predicate's operator () () return true.

    │ │ │ │ │ │ -

    Definition at line 353 of file standardPredicates.h.

    │ │ │ +

    Definition at line 353 of file standardPredicates.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ NumberOfBondsPredicate()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d54/a01691.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: PTE.h File Reference │ │ │ +BALL: modelFactory.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,260 +65,42 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces | │ │ │ -Macros | │ │ │ -Functions | │ │ │ -Variables
    │ │ │ -
    PTE.h File Reference
    │ │ │ +Namespaces
    │ │ │ +
    modelFactory.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/COMMON/create.h>
    │ │ │ -#include <BALL/DATATYPE/string.h>
    │ │ │ -#include <BALL/CONCEPT/processor.h>
    │ │ │ -#include <BALL/KERNEL/PTE.iC>
    │ │ │ +
    #include <BALL/CONCEPT/factory.h>
    │ │ │ +#include <BALL/QSAR/Model.h>
    │ │ │ +#include <BALL/QSAR/QSARData.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │
    │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::Element
     
    class  BALL::PTE_
     
    struct  BALL::PTE_::SymbolToElement
    class  BALL::QSAR::ModelFactory< T >
     
    │ │ │ │ │ │ │ │ │ │ │ │ -

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -

    │ │ │ -Macros

    #define BALL_ELEMENT_NAME_DEFAULT   "Unknown"
     
    #define BALL_ELEMENT_SYMBOL_DEFAULT   "?"
     
    #define BALL_ELEMENT_GROUP_DEFAULT   0
     
    #define BALL_ELEMENT_PERIOD_DEFAULT   0
     
    #define BALL_ELEMENT_ATOMICNUMBER_DEFAULT   0
     
    #define BALL_ELEMENT_ATOMICWEIGHT_DEFAULT   0
     
    #define BALL_ELEMENT_ATOMICRADIUS_DEFAULT   0
     
    #define BALL_ELEMENT_COVALENTRADIUS_DEFAULT   0
     
    #define BALL_ELEMENT_VANDERWAALSRADIUS_DEFAULT   0
     
    #define BALL_ELEMENT_ELECTRONEGATIVITY_DEFAULT   0
     
    #define BALL_ELEMENT_IS_METAL_DEFAULT   false
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -

    │ │ │ -Functions

    BALL_EXPORT std::ostream & BALL::operator<< (std::ostream &s, const Element &element)
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ + │ │ │

    │ │ │ -Variables

    BALL_EXPORT PTE_ BALL::PTE
     
    namespace  BALL::QSAR
     
    │ │ │ -

    Macro Definition Documentation

    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_ATOMICNUMBER_DEFAULT

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_ATOMICNUMBER_DEFAULT   0
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 26 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_ATOMICRADIUS_DEFAULT

    │ │ │ - │ │ │ -
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    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_ATOMICRADIUS_DEFAULT   0
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 28 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_ATOMICWEIGHT_DEFAULT

    │ │ │ - │ │ │ -
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    #define BALL_ELEMENT_ATOMICWEIGHT_DEFAULT   0
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 27 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_COVALENTRADIUS_DEFAULT

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_COVALENTRADIUS_DEFAULT   0
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 29 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_ELECTRONEGATIVITY_DEFAULT

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_ELECTRONEGATIVITY_DEFAULT   0
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 31 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_GROUP_DEFAULT

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_GROUP_DEFAULT   0
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 24 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_IS_METAL_DEFAULT

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_IS_METAL_DEFAULT   false
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 32 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_NAME_DEFAULT

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_NAME_DEFAULT   "Unknown"
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 22 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_PERIOD_DEFAULT

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_PERIOD_DEFAULT   0
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 25 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_SYMBOL_DEFAULT

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_SYMBOL_DEFAULT   "?"
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 23 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ BALL_ELEMENT_VANDERWAALSRADIUS_DEFAULT

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define BALL_ELEMENT_VANDERWAALSRADIUS_DEFAULT   0
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 30 of file PTE.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,90 +1,23 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s | _F_u_n_c_t_i_o_n_s | _V_a_r_i_a_b_l_e_s │ │ │ │ -PTE.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_M_M_O_N_/_c_r_e_a_t_e_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ -#include │ │ │ │ + * _Q_S_A_R │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ +modelFactory.h File Reference │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_f_a_c_t_o_r_y_._h> │ │ │ │ +#include <_B_A_L_L_/_Q_S_A_R_/_M_o_d_e_l_._h> │ │ │ │ +#include <_B_A_L_L_/_Q_S_A_R_/_Q_S_A_R_D_a_t_a_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ - class   _B_A_L_L_:_:_E_l_e_m_e_n_t │ │ │ │ -  │ │ │ │ - class   _B_A_L_L_:_:_P_T_E__ │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_P_T_E___:_:_S_y_m_b_o_l_T_o_E_l_e_m_e_n_t │ │ │ │ +class   _B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y_<_ _T_ _> │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -MMaaccrrooss │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___N_A_M_E___D_E_F_A_U_L_T   "Unknown" │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___S_Y_M_B_O_L___D_E_F_A_U_L_T   "?" │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___G_R_O_U_P___D_E_F_A_U_L_T   0 │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___P_E_R_I_O_D___D_E_F_A_U_L_T   0 │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___A_T_O_M_I_C_N_U_M_B_E_R___D_E_F_A_U_L_T   0 │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___A_T_O_M_I_C_W_E_I_G_H_T___D_E_F_A_U_L_T   0 │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___A_T_O_M_I_C_R_A_D_I_U_S___D_E_F_A_U_L_T   0 │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___C_O_V_A_L_E_N_T_R_A_D_I_U_S___D_E_F_A_U_L_T   0 │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___V_A_N_D_E_R_W_A_A_L_S_R_A_D_I_U_S___D_E_F_A_U_L_T   0 │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___E_L_E_C_T_R_O_N_E_G_A_T_I_V_I_T_Y___D_E_F_A_U_L_T   0 │ │ │ │ -  │ │ │ │ -#define  _B_A_L_L___E_L_E_M_E_N_T___I_S___M_E_T_A_L___D_E_F_A_U_L_T   false │ │ │ │ -  │ │ │ │ -FFuunnccttiioonnss │ │ │ │ -_B_A_L_L___E_X_P_O_R_T std::ostream &  _B_A_L_L_:_:_o_p_e_r_a_t_o_r_<_< (std::ostream &s, const _E_l_e_m_e_n_t │ │ │ │ - &element) │ │ │ │ -  │ │ │ │ -VVaarriiaabblleess │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _P_T_E__  _B_A_L_L_:_:_P_T_E │ │ │ │ +namespace   _B_A_L_L_:_:_Q_S_A_R │ │ │ │   │ │ │ │ -********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__AATTOOMMIICCNNUUMMBBEERR__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_ATOMICNUMBER_DEFAULT   0 │ │ │ │ -Definition at line _2_6 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__AATTOOMMIICCRRAADDIIUUSS__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_ATOMICRADIUS_DEFAULT   0 │ │ │ │ -Definition at line _2_8 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__AATTOOMMIICCWWEEIIGGHHTT__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_ATOMICWEIGHT_DEFAULT   0 │ │ │ │ -Definition at line _2_7 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__CCOOVVAALLEENNTTRRAADDIIUUSS__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_COVALENTRADIUS_DEFAULT   0 │ │ │ │ -Definition at line _2_9 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__EELLEECCTTRROONNEEGGAATTIIVVIITTYY__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_ELECTRONEGATIVITY_DEFAULT   0 │ │ │ │ -Definition at line _3_1 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__GGRROOUUPP__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_GROUP_DEFAULT   0 │ │ │ │ -Definition at line _2_4 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__IISS__MMEETTAALL__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_IS_METAL_DEFAULT   false │ │ │ │ -Definition at line _3_2 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__NNAAMMEE__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_NAME_DEFAULT   "Unknown" │ │ │ │ -Definition at line _2_2 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__PPEERRIIOODD__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_PERIOD_DEFAULT   0 │ │ │ │ -Definition at line _2_5 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__SSYYMMBBOOLL__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_SYMBOL_DEFAULT   "?" │ │ │ │ -Definition at line _2_3 of file _P_T_E_._h. │ │ │ │ -********** _?◆_? BBAALLLL__EELLEEMMEENNTT__VVAANNDDEERRWWAAAALLSSRRAADDIIUUSS__DDEEFFAAUULLTT ********** │ │ │ │ -#define BALL_ELEMENT_VANDERWAALSRADIUS_DEFAULT   0 │ │ │ │ -Definition at line _3_0 of file _P_T_E_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d54/a01691_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: PTE.h Source File │ │ │ +BALL: modelFactory.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,780 +70,88 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    PTE.h
    │ │ │ +
    modelFactory.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4// $Id: PTE.h,v 1.30.16.1 2007/03/25 21:23:42 oliver Exp $
    │ │ │ -
    5//
    │ │ │ -
    6
    │ │ │ -
    7#ifndef BALL_KERNEL_PTE_H
    │ │ │ -
    8#define BALL_KERNEL_PTE_H
    │ │ │ -
    9
    │ │ │ -
    10#ifndef BALL_COMMON_CREATE_H
    │ │ │ -
    11# include <BALL/COMMON/create.h>
    │ │ │ -
    12#endif
    │ │ │ -
    13
    │ │ │ -
    14#ifndef BALL_DATATYPE_STRING_H
    │ │ │ -
    15# include <BALL/DATATYPE/string.h>
    │ │ │ -
    16#endif
    │ │ │ -
    17
    │ │ │ -
    18#ifndef BALL_CONCEPT_PROCESSOR_H
    │ │ │ -
    19# include <BALL/CONCEPT/processor.h>
    │ │ │ -
    20#endif
    │ │ │ -
    21
    │ │ │ -
    22#define BALL_ELEMENT_NAME_DEFAULT "Unknown"
    │ │ │ -
    23#define BALL_ELEMENT_SYMBOL_DEFAULT "?"
    │ │ │ -
    24#define BALL_ELEMENT_GROUP_DEFAULT 0
    │ │ │ -
    25#define BALL_ELEMENT_PERIOD_DEFAULT 0
    │ │ │ -
    26#define BALL_ELEMENT_ATOMICNUMBER_DEFAULT 0
    │ │ │ -
    27#define BALL_ELEMENT_ATOMICWEIGHT_DEFAULT 0
    │ │ │ -
    28#define BALL_ELEMENT_ATOMICRADIUS_DEFAULT 0
    │ │ │ -
    29#define BALL_ELEMENT_COVALENTRADIUS_DEFAULT 0
    │ │ │ -
    30#define BALL_ELEMENT_VANDERWAALSRADIUS_DEFAULT 0
    │ │ │ -
    31#define BALL_ELEMENT_ELECTRONEGATIVITY_DEFAULT 0
    │ │ │ -
    32#define BALL_ELEMENT_IS_METAL_DEFAULT false
    │ │ │ -
    33
    │ │ │ -
    34
    │ │ │ -
    35namespace BALL
    │ │ │ -
    36{
    │ │ │ +
    4
    │ │ │ +
    5#ifndef BALL_QSAR_MODELFACTORY_H
    │ │ │ +
    6#define BALL_QSAR_MODELFACTORY_H
    │ │ │ +
    7
    │ │ │ +
    8#ifndef BALL_CONCEPT_FACTORY_H
    │ │ │ +
    9#include <BALL/CONCEPT/factory.h>
    │ │ │ +
    10#endif
    │ │ │ +
    11
    │ │ │ +
    12#ifndef MODEL
    │ │ │ +
    13#include <BALL/QSAR/Model.h>
    │ │ │ +
    14#endif
    │ │ │ +
    15
    │ │ │ +
    16#ifndef QSARH
    │ │ │ +
    17#include <BALL/QSAR/QSARData.h>
    │ │ │ +
    18#endif
    │ │ │ +
    19
    │ │ │ +
    20namespace BALL
    │ │ │ +
    21{
    │ │ │ +
    22 namespace QSAR
    │ │ │ +
    23 {
    │ │ │ +
    24 //typedef Model* (*CreateMethod) (const QSARData& q);
    │ │ │ +
    25
    │ │ │ +
    28 template <typename T>
    │ │ │ +
    │ │ │ +
    29 class ModelFactory
    │ │ │ +
    30 {
    │ │ │ +
    31 public:
    │ │ │ +
    32
    │ │ │ +
    │ │ │ +
    33 static T* create(const QSARData& q)
    │ │ │ +
    34 {
    │ │ │ +
    35 return new T(q);
    │ │ │ +
    36 }
    │ │ │ +
    │ │ │ +
    37
    │ │ │ +
    │ │ │ +
    38 static T* createKernel1(const QSARData& q, int k, double p1, double p2)
    │ │ │ +
    39 {
    │ │ │ +
    40 return new T(q,k,p1,p2);
    │ │ │ +
    41 }
    │ │ │ +
    │ │ │ +
    42
    │ │ │ +
    │ │ │ +
    43 static T* createKernel2(const QSARData& q, String s1, String s2)
    │ │ │ +
    44 {
    │ │ │ +
    45 return new T(q,s1,s2);
    │ │ │ +
    46 }
    │ │ │ +
    │ │ │ +
    47 };
    │ │ │ +
    │ │ │ +
    48 }
    │ │ │ +
    49}
    │ │ │
    50
    │ │ │ -
    │ │ │ -
    54 class BALL_EXPORT Element
    │ │ │ -
    55 {
    │ │ │ -
    56 public:
    │ │ │ -
    57
    │ │ │ -
    58 BALL_CREATE(Element)
    │ │ │ -
    59
    │ │ │ -
    60
    │ │ │ -
    62 typedef short Group;
    │ │ │ -
    63
    │ │ │ -
    66 typedef short Period;
    │ │ │ -
    67
    │ │ │ -
    70 typedef short AtomicNumber;
    │ │ │ -
    71
    │ │ │ -
    │ │ │ -
    75 enum Name
    │ │ │ -
    76 {
    │ │ │ -
    77 ACTINIUM = 0,
    │ │ │ -
    78 ALUMINUM,
    │ │ │ -
    79 AMERICIUM,
    │ │ │ -
    80 ANTIMONY, STIBIUM = ANTIMONY,
    │ │ │ -
    81 ARGON,
    │ │ │ -
    82 ARSENIC,
    │ │ │ -
    83 ASTATINE,
    │ │ │ -
    84 BARIUM,
    │ │ │ -
    85 BERKELIUM,
    │ │ │ -
    86 BERYLLIUM,
    │ │ │ -
    87 BISMUTH, WISMUT = BISMUTH,
    │ │ │ -
    88 BOHRIUM,
    │ │ │ -
    89 BORON,
    │ │ │ -
    90 BROMINE,
    │ │ │ -
    91 CADMIUM,
    │ │ │ -
    92 CAESIUM,
    │ │ │ -
    93 CALCIUM,
    │ │ │ -
    94 CALIFORNIUM,
    │ │ │ -
    95 CARBON, CARBONEUM = CARBON,
    │ │ │ -
    96 CERIUM,
    │ │ │ -
    97 CHLORINE,
    │ │ │ -
    98 CHROMIUM,
    │ │ │ -
    99 COBALT,
    │ │ │ -
    100 COPPER, CUPRUM = COPPER,
    │ │ │ -
    101 CURIUM,
    │ │ │ -
    102 DUBNIUM,
    │ │ │ -
    103 DYSPROSIUM,
    │ │ │ -
    104 EINSTEINIUM,
    │ │ │ -
    105 ERBIUM,
    │ │ │ -
    106 EUROPIUM,
    │ │ │ -
    107 FERMIUM,
    │ │ │ -
    108 FLUORINE,
    │ │ │ -
    109 FRANCIUM,
    │ │ │ -
    110 GADOLINIUM,
    │ │ │ -
    111 GALLIUM,
    │ │ │ -
    112 GERMANIUM,
    │ │ │ -
    113 GOLD, AURUM = GOLD,
    │ │ │ -
    114 HAFNIUM,
    │ │ │ -
    115 HAHNIUM,
    │ │ │ -
    116 HELIUM,
    │ │ │ -
    117 HOLMIUM,
    │ │ │ -
    118 HYDROGEN, HYDROGENIUM = HYDROGEN,
    │ │ │ -
    119 INDIUM,
    │ │ │ -
    120 IODINE, JOD = IODINE,
    │ │ │ -
    121 IRIDIUM,
    │ │ │ -
    122 IRON, FERRUM = IRON,
    │ │ │ -
    123 JOLIOTIUM,
    │ │ │ -
    124 KRYPTON,
    │ │ │ -
    125 LANTHANUM,
    │ │ │ -
    126 LAWRENCIUM,
    │ │ │ -
    127 LEAD, PLUMBUM = LEAD,
    │ │ │ -
    128 LITHIUM,
    │ │ │ -
    129 LUTETIUM,
    │ │ │ -
    130 MAGNESIUM,
    │ │ │ -
    131 MANGANESE, MANGAN = MANGANESE,
    │ │ │ -
    132 MEITNERIUM,
    │ │ │ -
    133 MENDELEVIUM,
    │ │ │ -
    134 MERCURY, HYDRARGYRUM = MERCURY, MERCURIUM = MERCURY,
    │ │ │ -
    135 MOLYBDENUM,
    │ │ │ -
    136 NEODYMIUM,
    │ │ │ -
    137 NEON,
    │ │ │ -
    138 NEPTUNIUM,
    │ │ │ -
    139 NICKEL,
    │ │ │ -
    140 NIOBIUM,
    │ │ │ -
    141 NITROGEN, NITROGENIUM = NITROGEN,
    │ │ │ -
    142 NOBELIUM,
    │ │ │ -
    143 OSMIUM,
    │ │ │ -
    144 OXYGEN, OXYGENIUM = OXYGEN,
    │ │ │ -
    145 PALLADIUM,
    │ │ │ -
    146 PHOSPHORUS,
    │ │ │ -
    147 PLATINUM,
    │ │ │ -
    148 PLUTONIUM,
    │ │ │ -
    149 POLONIUM,
    │ │ │ -
    150 POTASSIUM, KALIUM = POTASSIUM,
    │ │ │ -
    151 PRASEODYMIUM,
    │ │ │ -
    152 PROMETHIUM,
    │ │ │ -
    153 PROTACTINIUM,
    │ │ │ -
    154 RADIUM,
    │ │ │ -
    155 RADON,
    │ │ │ -
    156 RHENIUM,
    │ │ │ -
    157 RHODIUM,
    │ │ │ -
    158 RUBIDIUM,
    │ │ │ -
    159 RUTHENIUM,
    │ │ │ -
    160 RUTHERFORDIUM,
    │ │ │ -
    161 SAMARIUM,
    │ │ │ -
    162 SCANDIUM,
    │ │ │ -
    163 SELENIUM,
    │ │ │ -
    164 SILICON, SILICIUM = SILICON,
    │ │ │ -
    165 SILVER, ARGENTUM = SILVER,
    │ │ │ -
    166 SODIUM, NATRIUM = SODIUM,
    │ │ │ -
    167 STRONTIUM,
    │ │ │ -
    168 SULPHUR, SULFUR = SULPHUR,
    │ │ │ -
    169 TANTALUM,
    │ │ │ -
    170 TECHNETIUM,
    │ │ │ -
    171 TELLURIUM,
    │ │ │ -
    172 TERBIUM,
    │ │ │ -
    173 THALLIUM,
    │ │ │ -
    174 THORIUM,
    │ │ │ -
    175 THULIUM,
    │ │ │ -
    176 TIN, STANNUM = TIN,
    │ │ │ -
    177 TITANIUM,
    │ │ │ -
    178 TUNGSTEN, WOLFRAM = TUNGSTEN,
    │ │ │ -
    179 UNUNBIUM,
    │ │ │ -
    180 UNUNNILIUM,
    │ │ │ -
    181 UNUNNINIUM,
    │ │ │ -
    182 URANIUM,
    │ │ │ -
    183 VANADIUM,
    │ │ │ -
    184 XENON,
    │ │ │ -
    185 YTTERBIUM,
    │ │ │ -
    186 YTTRIUM,
    │ │ │ -
    187 ZINC, ZINCUM = ZINC,
    │ │ │ -
    188 ZIRCONIUM,
    │ │ │ -
    189
    │ │ │ -
    190 NUMBER_OF_ELEMENTS // 111
    │ │ │ -
    191 };
    │ │ │ -
    │ │ │ -
    192
    │ │ │ -
    │ │ │ -
    196 enum Symbol
    │ │ │ -
    197 {
    │ │ │ -
    198 Ac = 0,
    │ │ │ -
    199 Al,
    │ │ │ -
    200 Am,
    │ │ │ -
    201 Sb,
    │ │ │ -
    202 Ar,
    │ │ │ -
    203 As,
    │ │ │ -
    204 At,
    │ │ │ -
    205 Ba,
    │ │ │ -
    206 Bk,
    │ │ │ -
    207 Be,
    │ │ │ -
    208 Bi,
    │ │ │ -
    209 Bh,
    │ │ │ -
    210 B,
    │ │ │ -
    211 Br,
    │ │ │ -
    212 Cd,
    │ │ │ -
    213 Cs,
    │ │ │ -
    214 Ca,
    │ │ │ -
    215 Cf,
    │ │ │ -
    216 C,
    │ │ │ -
    217 Ce,
    │ │ │ -
    218 Cl,
    │ │ │ -
    219 Cr,
    │ │ │ -
    220 Co,
    │ │ │ -
    221 Cu,
    │ │ │ -
    222 Cm,
    │ │ │ -
    223 Db,
    │ │ │ -
    224 Dy,
    │ │ │ -
    225 Es,
    │ │ │ -
    226 Er,
    │ │ │ -
    227 Eu,
    │ │ │ -
    228 Fm,
    │ │ │ -
    229 F,
    │ │ │ -
    230 Fr,
    │ │ │ -
    231 Gd,
    │ │ │ -
    232 Ga,
    │ │ │ -
    233 Ge,
    │ │ │ -
    234 Au,
    │ │ │ -
    235 Hf,
    │ │ │ -
    236 Hn,
    │ │ │ -
    237 He,
    │ │ │ -
    238 Ho,
    │ │ │ -
    239 H,
    │ │ │ -
    240 In,
    │ │ │ -
    241 I,
    │ │ │ -
    242 Ir,
    │ │ │ -
    243 Fe,
    │ │ │ -
    244 Jl,
    │ │ │ -
    245 Kr,
    │ │ │ -
    246 La,
    │ │ │ -
    247 Lr,
    │ │ │ -
    248 Pb,
    │ │ │ -
    249 Li,
    │ │ │ -
    250 Lu,
    │ │ │ -
    251 Mg,
    │ │ │ -
    252 Mn,
    │ │ │ -
    253 Mt,
    │ │ │ -
    254 Md,
    │ │ │ -
    255 Hg,
    │ │ │ -
    256 Mo,
    │ │ │ -
    257 Nd,
    │ │ │ -
    258 Ne,
    │ │ │ -
    259 Np,
    │ │ │ -
    260 Ni,
    │ │ │ -
    261 Nb,
    │ │ │ -
    262 N,
    │ │ │ -
    263 No,
    │ │ │ -
    264 Os,
    │ │ │ -
    265 O,
    │ │ │ -
    266 Pd,
    │ │ │ -
    267 P,
    │ │ │ -
    268 Pt,
    │ │ │ -
    269 Pu,
    │ │ │ -
    270 Po,
    │ │ │ -
    271 K,
    │ │ │ -
    272 Pr,
    │ │ │ -
    273 Pm,
    │ │ │ -
    274 Pa,
    │ │ │ -
    275 Ra,
    │ │ │ -
    276 Rn,
    │ │ │ -
    277 Re,
    │ │ │ -
    278 Rh,
    │ │ │ -
    279 Rb,
    │ │ │ -
    280 Ru,
    │ │ │ -
    281 Rf,
    │ │ │ -
    282 Sm,
    │ │ │ -
    283 Sc,
    │ │ │ -
    284 Se,
    │ │ │ -
    285 Si,
    │ │ │ -
    286 Ag,
    │ │ │ -
    287 Na,
    │ │ │ -
    288 Sr,
    │ │ │ -
    289 S,
    │ │ │ -
    290 Ta,
    │ │ │ -
    291 Tc,
    │ │ │ -
    292 Te,
    │ │ │ -
    293 Tb,
    │ │ │ -
    294 Tl,
    │ │ │ -
    295 Th,
    │ │ │ -
    296 Tm,
    │ │ │ -
    297 Sn,
    │ │ │ -
    298 Ti,
    │ │ │ -
    299 W,
    │ │ │ -
    300 Uub,
    │ │ │ -
    301 Uun,
    │ │ │ -
    302 Uuu,
    │ │ │ -
    303 U,
    │ │ │ -
    304 V,
    │ │ │ -
    305 Xe,
    │ │ │ -
    306 Yb,
    │ │ │ -
    307 Y,
    │ │ │ -
    308 Zn,
    │ │ │ -
    309 Zr
    │ │ │ -
    310 };
    │ │ │ -
    │ │ │ -
    311
    │ │ │ -
    315
    │ │ │ -
    320 Element();
    │ │ │ -
    321
    │ │ │ -
    324 Element(const Element& element);
    │ │ │ -
    325
    │ │ │ -
    328 Element
    │ │ │ -
    329 (const String& name,
    │ │ │ -
    330 const String& symbol,
    │ │ │ -
    331 Group group,
    │ │ │ -
    332 Period period,
    │ │ │ -
    333 AtomicNumber atomic_umber,
    │ │ │ -
    334 float atomic_weight,
    │ │ │ -
    335 float atomic_radius,
    │ │ │ -
    336 float covalent_radius,
    │ │ │ -
    337 float van_der_waals_radius,
    │ │ │ -
    338 bool is_metal,
    │ │ │ -
    339 float electronegativity);
    │ │ │ -
    340
    │ │ │ -
    343 virtual ~Element();
    │ │ │ -
    344
    │ │ │ -
    349 virtual void clear();
    │ │ │ -
    350
    │ │ │ -
    352
    │ │ │ -
    355
    │ │ │ -
    360 Element& operator = (const Element& element);
    │ │ │ -
    361
    │ │ │ -
    363
    │ │ │ -
    366
    │ │ │ -
    370 void setName(const String& name);
    │ │ │ -
    371
    │ │ │ -
    377 const String& getName() const;
    │ │ │ -
    378
    │ │ │ -
    382 void setSymbol(const String& symbol);
    │ │ │ -
    383
    │ │ │ -
    387 const String& getSymbol() const;
    │ │ │ -
    388
    │ │ │ -
    392 void setGroup(Group group);
    │ │ │ -
    393
    │ │ │ -
    397 Group getGroup() const;
    │ │ │ -
    398
    │ │ │ -
    402 void setPeriod(Period period);
    │ │ │ -
    403
    │ │ │ -
    407 Period getPeriod() const;
    │ │ │ -
    408
    │ │ │ -
    412 void setAtomicNumber(AtomicNumber atomic_number);
    │ │ │ -
    413
    │ │ │ -
    417 AtomicNumber getAtomicNumber() const;
    │ │ │ -
    418
    │ │ │ -
    422 void setAtomicWeight(float atomic_weight);
    │ │ │ -
    423
    │ │ │ -
    427 float getAtomicWeight() const;
    │ │ │ -
    428
    │ │ │ -
    432 void setAtomicRadius(float atomic_radius);
    │ │ │ -
    433
    │ │ │ -
    437 float getAtomicRadius() const;
    │ │ │ -
    438
    │ │ │ -
    442 void setCovalentRadius(float covalent_radius);
    │ │ │ -
    443
    │ │ │ -
    447 float getCovalentRadius() const;
    │ │ │ -
    448
    │ │ │ -
    452 void setVanDerWaalsRadius(float van_der_waals_radius);
    │ │ │ -
    453
    │ │ │ -
    457 float getVanDerWaalsRadius() const;
    │ │ │ -
    458
    │ │ │ -
    462 void setElectronegativity(float electronegativity);
    │ │ │ -
    463
    │ │ │ -
    467 float getElectronegativity() const;
    │ │ │ -
    468
    │ │ │ -
    470
    │ │ │ -
    473
    │ │ │ -
    479 bool operator == (const Element& element) const;
    │ │ │ -
    480
    │ │ │ -
    486 bool operator != (const Element& element) const;
    │ │ │ -
    487
    │ │ │ -
    494 bool operator < (const Element& element) const;
    │ │ │ -
    495
    │ │ │ -
    502 bool operator <= (const Element& element) const;
    │ │ │ -
    503
    │ │ │ -
    510 bool operator >= (const Element& element) const;
    │ │ │ -
    511
    │ │ │ -
    518 bool operator >(const Element& element) const;
    │ │ │ -
    519
    │ │ │ -
    523 BALL_EXPORT
    │ │ │ -
    524 friend std::ostream& operator << (std::ostream& s, const Element& element);
    │ │ │ -
    525
    │ │ │ -
    527
    │ │ │ -
    530
    │ │ │ -
    536 bool isUnknown() const;
    │ │ │ -
    537
    │ │ │ -
    543 bool isMetal() const;
    │ │ │ -
    544
    │ │ │ -
    546
    │ │ │ -
    550 static Element UNKNOWN;
    │ │ │ -
    551
    │ │ │ -
    552
    │ │ │ -
    553 private:
    │ │ │ -
    554
    │ │ │ -
    557 String name_;
    │ │ │ -
    558
    │ │ │ -
    561 String symbol_;
    │ │ │ -
    562
    │ │ │ -
    600 Group group_;
    │ │ │ -
    601
    │ │ │ -
    604 Period period_;
    │ │ │ -
    605
    │ │ │ -
    609 AtomicNumber atomic_number_;
    │ │ │ -
    610
    │ │ │ -
    618 float atomic_weight_;
    │ │ │ -
    619
    │ │ │ -
    622 float atomic_radius_;
    │ │ │ -
    623
    │ │ │ -
    626 float covalent_radius_;
    │ │ │ -
    627
    │ │ │ -
    630 float van_der_waals_radius_;
    │ │ │ -
    631
    │ │ │ -
    634 bool is_metal_;
    │ │ │ -
    635
    │ │ │ -
    638 float electronegativity_;
    │ │ │ -
    639 };
    │ │ │ -
    │ │ │ -
    640
    │ │ │ -
    641
    │ │ │ -
    645 BALL_EXPORT
    │ │ │ -
    646 std::ostream& operator << (std::ostream& s, const Element& element);
    │ │ │ -
    647
    │ │ │ -
    648
    │ │ │ -
    │ │ │ -
    651 class BALL_EXPORT PTE_
    │ │ │ -
    652 {
    │ │ │ -
    653 public:
    │ │ │ -
    654
    │ │ │ -
    655 BALL_CREATE(PTE_)
    │ │ │ -
    656
    │ │ │ -
    657
    │ │ │ -
    660
    │ │ │ -
    661
    │ │ │ -
    663 PTE_();
    │ │ │ -
    664
    │ │ │ -
    667 PTE_(const PTE_& pse);
    │ │ │ -
    668
    │ │ │ -
    671 virtual ~PTE_();
    │ │ │ -
    672
    │ │ │ -
    675 virtual void clear();
    │ │ │ -
    676
    │ │ │ -
    678
    │ │ │ -
    681
    │ │ │ -
    686 PTE_& operator = (const PTE_& /*pte*/);
    │ │ │ -
    687
    │ │ │ -
    689
    │ │ │ -
    692
    │ │ │ -
    695 static Element& getElement(Position atomic_number);
    │ │ │ -
    696
    │ │ │ -
    700 static Element& getElement(const String& symbol);
    │ │ │ -
    701
    │ │ │ -
    703
    │ │ │ -
    706
    │ │ │ -
    711 bool operator == (const PTE_& pte) const;
    │ │ │ -
    712
    │ │ │ -
    716 Element& operator [] (const String& symbol);
    │ │ │ -
    717
    │ │ │ -
    721 const Element& operator [] (const String& symbol) const;
    │ │ │ -
    722
    │ │ │ -
    726 Element& operator [] (Element::Name name);
    │ │ │ -
    727
    │ │ │ -
    731 const Element& operator [] (Element::Name name) const;
    │ │ │ -
    732
    │ │ │ -
    736 Element& operator [] (Element::Symbol symbol);
    │ │ │ -
    737
    │ │ │ -
    741 const Element& operator [] (Element::Symbol symbol) const;
    │ │ │ -
    742
    │ │ │ -
    746 Element& operator [] (Position position);
    │ │ │ -
    747
    │ │ │ -
    751 const Element& operator [] (Position position) const;
    │ │ │ -
    752
    │ │ │ -
    754
    │ │ │ -
    757
    │ │ │ -
    763 static bool apply(UnaryProcessor<Element>& applicator);
    │ │ │ -
    764
    │ │ │ -
    766
    │ │ │ -
    │ │ │ -
    768 struct SymbolToElement
    │ │ │ -
    769 {
    │ │ │ -
    771 const char* symbol;
    │ │ │ -
    772
    │ │ │ -
    774 Element* element;
    │ │ │ -
    775 };
    │ │ │ -
    │ │ │ -
    776
    │ │ │ -
    777 private:
    │ │ │ -
    778
    │ │ │ -
    780 static Element element_[];
    │ │ │ -
    781
    │ │ │ -
    783 static SymbolToElement symbol_to_element_[];
    │ │ │ -
    784
    │ │ │ -
    786 static Element* atomic_number_to_element_[];
    │ │ │ -
    787 };
    │ │ │ -
    │ │ │ -
    788
    │ │ │ -
    789
    │ │ │ -
    793 BALL_EXPORT extern PTE_ PTE;
    │ │ │ -
    794
    │ │ │ -
    795
    │ │ │ -
    796
    │ │ │ -
    797# ifndef BALL_NO_INLINE_FUNCTIONS
    │ │ │ -
    798# include <BALL/KERNEL/PTE.iC>
    │ │ │ -
    799# endif
    │ │ │ -
    800} //namespace BALL
    │ │ │ -
    801
    │ │ │ -
    802
    │ │ │ -
    803#endif // BALL_KERNEL_PTE_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ -
    BALL::operator<<
    BALL_EXPORT std::ostream & operator<<(std::ostream &os, const Exception::GeneralException &e)
    │ │ │ -
    BALL::PTE
    BALL_EXPORT PTE_ PTE
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::AtomicNumber
    short AtomicNumber
    Definition PTE.h:70
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::GADOLINIUM
    @ GADOLINIUM
    Definition PTE.h:110
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::NEODYMIUM
    @ NEODYMIUM
    Definition PTE.h:136
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::ALUMINUM
    @ ALUMINUM
    Definition PTE.h:78
    │ │ │ -
    BALL::Element::CALIFORNIUM
    @ CALIFORNIUM
    Definition PTE.h:94
    │ │ │ - │ │ │ -
    BALL::Element::CHROMIUM
    @ CHROMIUM
    Definition PTE.h:98
    │ │ │ -
    BALL::Element::PLUTONIUM
    @ PLUTONIUM
    Definition PTE.h:148
    │ │ │ -
    BALL::Element::ASTATINE
    @ ASTATINE
    Definition PTE.h:83
    │ │ │ -
    BALL::Element::BERYLLIUM
    @ BERYLLIUM
    Definition PTE.h:86
    │ │ │ - │ │ │ -
    BALL::Element::TECHNETIUM
    @ TECHNETIUM
    Definition PTE.h:170
    │ │ │ -
    BALL::Element::BOHRIUM
    @ BOHRIUM
    Definition PTE.h:88
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::RUTHENIUM
    @ RUTHENIUM
    Definition PTE.h:159
    │ │ │ -
    BALL::Element::JOLIOTIUM
    @ JOLIOTIUM
    Definition PTE.h:123
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::CALCIUM
    @ CALCIUM
    Definition PTE.h:93
    │ │ │ -
    BALL::Element::PHOSPHORUS
    @ PHOSPHORUS
    Definition PTE.h:146
    │ │ │ - │ │ │ -
    BALL::Element::PROTACTINIUM
    @ PROTACTINIUM
    Definition PTE.h:153
    │ │ │ -
    BALL::Element::RUTHERFORDIUM
    @ RUTHERFORDIUM
    Definition PTE.h:160
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::PALLADIUM
    @ PALLADIUM
    Definition PTE.h:145
    │ │ │ - │ │ │ -
    BALL::Element::MEITNERIUM
    @ MEITNERIUM
    Definition PTE.h:132
    │ │ │ -
    BALL::Element::NEPTUNIUM
    @ NEPTUNIUM
    Definition PTE.h:138
    │ │ │ - │ │ │ -
    BALL::Element::ARSENIC
    @ ARSENIC
    Definition PTE.h:82
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::DYSPROSIUM
    @ DYSPROSIUM
    Definition PTE.h:103
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::CHLORINE
    @ CHLORINE
    Definition PTE.h:97
    │ │ │ -
    BALL::Element::CAESIUM
    @ CAESIUM
    Definition PTE.h:92
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::TELLURIUM
    @ TELLURIUM
    Definition PTE.h:171
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::UNUNNILIUM
    @ UNUNNILIUM
    Definition PTE.h:180
    │ │ │ -
    BALL::Element::STRONTIUM
    @ STRONTIUM
    Definition PTE.h:167
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::ANTIMONY
    @ ANTIMONY
    Definition PTE.h:80
    │ │ │ -
    BALL::Element::PRASEODYMIUM
    @ PRASEODYMIUM
    Definition PTE.h:151
    │ │ │ - │ │ │ -
    BALL::Element::PROMETHIUM
    @ PROMETHIUM
    Definition PTE.h:152
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::UNUNNINIUM
    @ UNUNNINIUM
    Definition PTE.h:181
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::AMERICIUM
    @ AMERICIUM
    Definition PTE.h:79
    │ │ │ -
    BALL::Element::ZIRCONIUM
    @ ZIRCONIUM
    Definition PTE.h:188
    │ │ │ -
    BALL::Element::BISMUTH
    @ BISMUTH
    Definition PTE.h:87
    │ │ │ -
    BALL::Element::MENDELEVIUM
    @ MENDELEVIUM
    Definition PTE.h:133
    │ │ │ - │ │ │ -
    BALL::Element::CADMIUM
    @ CADMIUM
    Definition PTE.h:91
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::LAWRENCIUM
    @ LAWRENCIUM
    Definition PTE.h:126
    │ │ │ -
    BALL::Element::MOLYBDENUM
    @ MOLYBDENUM
    Definition PTE.h:135
    │ │ │ -
    BALL::Element::LANTHANUM
    @ LANTHANUM
    Definition PTE.h:125
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::EINSTEINIUM
    @ EINSTEINIUM
    Definition PTE.h:104
    │ │ │ -
    BALL::Element::MAGNESIUM
    @ MAGNESIUM
    Definition PTE.h:130
    │ │ │ - │ │ │ -
    BALL::Element::BERKELIUM
    @ BERKELIUM
    Definition PTE.h:85
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::YTTERBIUM
    @ YTTERBIUM
    Definition PTE.h:185
    │ │ │ -
    BALL::Element::GERMANIUM
    @ GERMANIUM
    Definition PTE.h:112
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::BROMINE
    @ BROMINE
    Definition PTE.h:90
    │ │ │ - │ │ │ -
    BALL::Element::setName
    void setName(const String &name)
    │ │ │ -
    BALL::Element::getAtomicRadius
    float getAtomicRadius() const
    │ │ │ -
    BALL::Element::setAtomicRadius
    void setAtomicRadius(float atomic_radius)
    │ │ │ -
    BALL::Element::setPeriod
    void setPeriod(Period period)
    │ │ │ -
    BALL::Element::clear
    virtual void clear()
    │ │ │ -
    BALL::Element::getSymbol
    const String & getSymbol() const
    │ │ │ -
    BALL::Element::setAtomicWeight
    void setAtomicWeight(float atomic_weight)
    │ │ │ -
    BALL::Element::getName
    const String & getName() const
    │ │ │ -
    BALL::Element::getAtomicNumber
    AtomicNumber getAtomicNumber() const
    │ │ │ -
    BALL::Element::setCovalentRadius
    void setCovalentRadius(float covalent_radius)
    │ │ │ -
    BALL::Element::setGroup
    void setGroup(Group group)
    │ │ │ -
    BALL::Element::setElectronegativity
    void setElectronegativity(float electronegativity)
    │ │ │ -
    BALL::Element::UNKNOWN
    static Element UNKNOWN
    Definition PTE.h:550
    │ │ │ -
    BALL::Element::Group
    short Group
    Definition PTE.h:62
    │ │ │ -
    BALL::Element::isMetal
    bool isMetal() const
    │ │ │ -
    BALL::Element::getPeriod
    Period getPeriod() const
    │ │ │ -
    BALL::Element::Element
    Element(const String &name, const String &symbol, Group group, Period period, AtomicNumber atomic_umber, float atomic_weight, float atomic_radius, float covalent_radius, float van_der_waals_radius, bool is_metal, float electronegativity)
    │ │ │ -
    BALL::Element::getVanDerWaalsRadius
    float getVanDerWaalsRadius() const
    │ │ │ -
    BALL::Element::Period
    short Period
    Definition PTE.h:66
    │ │ │ -
    BALL::Element::getAtomicWeight
    float getAtomicWeight() const
    │ │ │ -
    BALL::Element::Element
    Element(const Element &element)
    │ │ │ -
    BALL::Element::getGroup
    Group getGroup() const
    │ │ │ -
    BALL::Element::~Element
    virtual ~Element()
    │ │ │ -
    BALL::Element::setSymbol
    void setSymbol(const String &symbol)
    │ │ │ -
    BALL::Element::getElectronegativity
    float getElectronegativity() const
    │ │ │ -
    BALL::Element::setAtomicNumber
    void setAtomicNumber(AtomicNumber atomic_number)
    │ │ │ -
    BALL::Element::setVanDerWaalsRadius
    void setVanDerWaalsRadius(float van_der_waals_radius)
    │ │ │ -
    BALL::Element::getCovalentRadius
    float getCovalentRadius() const
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Element::isUnknown
    bool isUnknown() const
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::PTE_::SymbolToElement::symbol
    const char * symbol
    Definition PTE.h:771
    │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    51#endif // BALL_QSAR_MODELFACTORY_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::QSAR::ModelFactory::createKernel1
    static T * createKernel1(const QSARData &q, int k, double p1, double p2)
    Definition modelFactory.h:38
    │ │ │ +
    BALL::QSAR::ModelFactory::createKernel2
    static T * createKernel2(const QSARData &q, String s1, String s2)
    Definition modelFactory.h:43
    │ │ │ +
    BALL::QSAR::ModelFactory::create
    static T * create(const QSARData &q)
    Definition modelFactory.h:33
    │ │ │ + │ │ │
    │ │ │ │ │ │
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    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,1241 +1,80 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ -PTE.h │ │ │ │ + * _Q_S_A_R │ │ │ │ +modelFactory.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: PTE.h,v 1.30.16.1 2007/03/25 21:23:42 oliver Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_KERNEL_PTE_H │ │ │ │ -8#define BALL_KERNEL_PTE_H │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_COMMON_CREATE_H │ │ │ │ -11# include <_B_A_L_L_/_C_O_M_M_O_N_/_c_r_e_a_t_e_._h> │ │ │ │ -12#endif │ │ │ │ -13 │ │ │ │ -14#ifndef BALL_DATATYPE_STRING_H │ │ │ │ -15# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ -16#endif │ │ │ │ -17 │ │ │ │ -18#ifndef BALL_CONCEPT_PROCESSOR_H │ │ │ │ -19# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ -20#endif │ │ │ │ -21 │ │ │ │ -_2_2#define BALL_ELEMENT_NAME_DEFAULT "Unknown" │ │ │ │ -_2_3#define BALL_ELEMENT_SYMBOL_DEFAULT "?" │ │ │ │ -_2_4#define BALL_ELEMENT_GROUP_DEFAULT 0 │ │ │ │ -_2_5#define BALL_ELEMENT_PERIOD_DEFAULT 0 │ │ │ │ -_2_6#define BALL_ELEMENT_ATOMICNUMBER_DEFAULT 0 │ │ │ │ -_2_7#define BALL_ELEMENT_ATOMICWEIGHT_DEFAULT 0 │ │ │ │ -_2_8#define BALL_ELEMENT_ATOMICRADIUS_DEFAULT 0 │ │ │ │ -_2_9#define BALL_ELEMENT_COVALENTRADIUS_DEFAULT 0 │ │ │ │ -_3_0#define BALL_ELEMENT_VANDERWAALSRADIUS_DEFAULT 0 │ │ │ │ -_3_1#define BALL_ELEMENT_ELECTRONEGATIVITY_DEFAULT 0 │ │ │ │ -_3_2#define BALL_ELEMENT_IS_METAL_DEFAULT false │ │ │ │ -33 │ │ │ │ -34 │ │ │ │ -35namespace _B_A_L_L │ │ │ │ -36{ │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_QSAR_MODELFACTORY_H │ │ │ │ +6#define BALL_QSAR_MODELFACTORY_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_CONCEPT_FACTORY_H │ │ │ │ +9#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_f_a_c_t_o_r_y_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12#ifndef MODEL │ │ │ │ +13#include <_B_A_L_L_/_Q_S_A_R_/_M_o_d_e_l_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifndef QSARH │ │ │ │ +17#include <_B_A_L_L_/_Q_S_A_R_/_Q_S_A_R_D_a_t_a_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20namespace _B_A_L_L │ │ │ │ +21{ │ │ │ │ +22 namespace QSAR │ │ │ │ +23 { │ │ │ │ +24 //typedef Model* (*CreateMethod) (const QSARData& q); │ │ │ │ +25 │ │ │ │ +28 template │ │ │ │ +_2_9 class _M_o_d_e_l_F_a_c_t_o_r_y │ │ │ │ +30 { │ │ │ │ +31 public: │ │ │ │ +32 │ │ │ │ +_3_3 static T* _c_r_e_a_t_e(const _Q_S_A_R_D_a_t_a& q) │ │ │ │ +34 { │ │ │ │ +35 return new T(q); │ │ │ │ +36 } │ │ │ │ +37 │ │ │ │ +_3_8 static T* _c_r_e_a_t_e_K_e_r_n_e_l_1(const _Q_S_A_R_D_a_t_a& q, int k, double p1, double p2) │ │ │ │ +39 { │ │ │ │ +40 return new T(q,k,p1,p2); │ │ │ │ +41 } │ │ │ │ +42 │ │ │ │ +_4_3 static T* _c_r_e_a_t_e_K_e_r_n_e_l_2(const _Q_S_A_R_D_a_t_a& q, _S_t_r_i_n_g s1, _S_t_r_i_n_g s2) │ │ │ │ +44 { │ │ │ │ +45 return new T(q,s1,s2); │ │ │ │ +46 } │ │ │ │ +47 }; │ │ │ │ +48 } │ │ │ │ +49} │ │ │ │ 50 │ │ │ │ -_5_4 class _B_A_L_L___E_X_P_O_R_T _E_l_e_m_e_n_t │ │ │ │ -55 { │ │ │ │ -56 public: │ │ │ │ -57 │ │ │ │ -58 _B_A_L_L___C_R_E_A_T_E(_E_l_e_m_e_n_t) │ │ │ │ -59 │ │ │ │ -60 │ │ │ │ -_6_2 typedef short _G_r_o_u_p; │ │ │ │ -63 │ │ │ │ -_6_6 typedef short _P_e_r_i_o_d; │ │ │ │ -67 │ │ │ │ -_7_0 typedef short _A_t_o_m_i_c_N_u_m_b_e_r; │ │ │ │ -71 │ │ │ │ -_7_5 enum _N_a_m_e │ │ │ │ -76 { │ │ │ │ -_7_7 ACTINIUM = 0, │ │ │ │ -_7_8 _A_L_U_M_I_N_U_M, │ │ │ │ -_7_9 _A_M_E_R_I_C_I_U_M, │ │ │ │ -_8_0 _A_N_T_I_M_O_N_Y, STIBIUM = _A_N_T_I_M_O_N_Y, │ │ │ │ -_8_1 _A_R_G_O_N, │ │ │ │ -_8_2 _A_R_S_E_N_I_C, │ │ │ │ -_8_3 _A_S_T_A_T_I_N_E, │ │ │ │ -_8_4 _B_A_R_I_U_M, │ │ │ │ -_8_5 _B_E_R_K_E_L_I_U_M, │ │ │ │ -_8_6 _B_E_R_Y_L_L_I_U_M, │ │ │ │ -_8_7 _B_I_S_M_U_T_H, WISMUT = _B_I_S_M_U_T_H, │ │ │ │ -_8_8 _B_O_H_R_I_U_M, │ │ │ │ -_8_9 _B_O_R_O_N, │ │ │ │ -_9_0 _B_R_O_M_I_N_E, │ │ │ │ -_9_1 _C_A_D_M_I_U_M, │ │ │ │ -_9_2 _C_A_E_S_I_U_M, │ │ │ │ -_9_3 _C_A_L_C_I_U_M, │ │ │ │ -_9_4 _C_A_L_I_F_O_R_N_I_U_M, │ │ │ │ -_9_5 _C_A_R_B_O_N, CARBONEUM = _C_A_R_B_O_N, │ │ │ │ -_9_6 _C_E_R_I_U_M, │ │ │ │ -_9_7 _C_H_L_O_R_I_N_E, │ │ │ │ -_9_8 _C_H_R_O_M_I_U_M, │ │ │ │ -_9_9 _C_O_B_A_L_T, │ │ │ │ -_1_0_0 _C_O_P_P_E_R, CUPRUM = _C_O_P_P_E_R, │ │ │ │ -_1_0_1 _C_U_R_I_U_M, │ │ │ │ -_1_0_2 _D_U_B_N_I_U_M, │ │ │ │ -_1_0_3 _D_Y_S_P_R_O_S_I_U_M, │ │ │ │ -_1_0_4 _E_I_N_S_T_E_I_N_I_U_M, │ │ │ │ -_1_0_5 _E_R_B_I_U_M, │ │ │ │ -_1_0_6 _E_U_R_O_P_I_U_M, │ │ │ │ -_1_0_7 _F_E_R_M_I_U_M, │ │ │ │ -_1_0_8 _F_L_U_O_R_I_N_E, │ │ │ │ -_1_0_9 _F_R_A_N_C_I_U_M, │ │ │ │ -_1_1_0 _G_A_D_O_L_I_N_I_U_M, │ │ │ │ -_1_1_1 _G_A_L_L_I_U_M, │ │ │ │ -_1_1_2 _G_E_R_M_A_N_I_U_M, │ │ │ │ -_1_1_3 GOLD, AURUM = GOLD, │ │ │ │ -_1_1_4 _H_A_F_N_I_U_M, │ │ │ │ -_1_1_5 _H_A_H_N_I_U_M, │ │ │ │ -_1_1_6 _H_E_L_I_U_M, │ │ │ │ -_1_1_7 _H_O_L_M_I_U_M, │ │ │ │ -_1_1_8 _H_Y_D_R_O_G_E_N, HYDROGENIUM = _H_Y_D_R_O_G_E_N, │ │ │ │ -_1_1_9 _I_N_D_I_U_M, │ │ │ │ -_1_2_0 _I_O_D_I_N_E, JOD = _I_O_D_I_N_E, │ │ │ │ -_1_2_1 _I_R_I_D_I_U_M, │ │ │ │ -_1_2_2 IRON, FERRUM = IRON, │ │ │ │ -_1_2_3 _J_O_L_I_O_T_I_U_M, │ │ │ │ -_1_2_4 _K_R_Y_P_T_O_N, │ │ │ │ -_1_2_5 _L_A_N_T_H_A_N_U_M, │ │ │ │ -_1_2_6 _L_A_W_R_E_N_C_I_U_M, │ │ │ │ -_1_2_7 _L_E_A_D, PLUMBUM = _L_E_A_D, │ │ │ │ -_1_2_8 _L_I_T_H_I_U_M, │ │ │ │ -_1_2_9 _L_U_T_E_T_I_U_M, │ │ │ │ -_1_3_0 _M_A_G_N_E_S_I_U_M, │ │ │ │ -_1_3_1 MANGANESE, MANGAN = MANGANESE, │ │ │ │ -_1_3_2 _M_E_I_T_N_E_R_I_U_M, │ │ │ │ -_1_3_3 _M_E_N_D_E_L_E_V_I_U_M, │ │ │ │ -_1_3_4 MERCURY, HYDRARGYRUM = MERCURY, MERCURIUM = MERCURY, │ │ │ │ -_1_3_5 _M_O_L_Y_B_D_E_N_U_M, │ │ │ │ -_1_3_6 _N_E_O_D_Y_M_I_U_M, │ │ │ │ -_1_3_7 _N_E_O_N, │ │ │ │ -_1_3_8 _N_E_P_T_U_N_I_U_M, │ │ │ │ -_1_3_9 _N_I_C_K_E_L, │ │ │ │ -_1_4_0 _N_I_O_B_I_U_M, │ │ │ │ -_1_4_1 _N_I_T_R_O_G_E_N, NITROGENIUM = _N_I_T_R_O_G_E_N, │ │ │ │ -_1_4_2 _N_O_B_E_L_I_U_M, │ │ │ │ -_1_4_3 _O_S_M_I_U_M, │ │ │ │ -_1_4_4 _O_X_Y_G_E_N, OXYGENIUM = _O_X_Y_G_E_N, │ │ │ │ -_1_4_5 _P_A_L_L_A_D_I_U_M, │ │ │ │ -_1_4_6 _P_H_O_S_P_H_O_R_U_S, │ │ │ │ -_1_4_7 _P_L_A_T_I_N_U_M, │ │ │ │ -_1_4_8 _P_L_U_T_O_N_I_U_M, │ │ │ │ -_1_4_9 _P_O_L_O_N_I_U_M, │ │ │ │ -_1_5_0 POTASSIUM, KALIUM = POTASSIUM, │ │ │ │ -_1_5_1 _P_R_A_S_E_O_D_Y_M_I_U_M, │ │ │ │ -_1_5_2 _P_R_O_M_E_T_H_I_U_M, │ │ │ │ -_1_5_3 _P_R_O_T_A_C_T_I_N_I_U_M, │ │ │ │ -_1_5_4 _R_A_D_I_U_M, │ │ │ │ -_1_5_5 _R_A_D_O_N, │ │ │ │ -_1_5_6 _R_H_E_N_I_U_M, │ │ │ │ -_1_5_7 _R_H_O_D_I_U_M, │ │ │ │ -_1_5_8 _R_U_B_I_D_I_U_M, │ │ │ │ -_1_5_9 _R_U_T_H_E_N_I_U_M, │ │ │ │ -_1_6_0 _R_U_T_H_E_R_F_O_R_D_I_U_M, │ │ │ │ -_1_6_1 _S_A_M_A_R_I_U_M, │ │ │ │ -_1_6_2 _S_C_A_N_D_I_U_M, │ │ │ │ -_1_6_3 _S_E_L_E_N_I_U_M, │ │ │ │ -_1_6_4 SILICON, SILICIUM = SILICON, │ │ │ │ -_1_6_5 SILVER, ARGENTUM = SILVER, │ │ │ │ -_1_6_6 SODIUM, NATRIUM = SODIUM, │ │ │ │ -_1_6_7 _S_T_R_O_N_T_I_U_M, │ │ │ │ -_1_6_8 SULPHUR, SULFUR = SULPHUR, │ │ │ │ -_1_6_9 _T_A_N_T_A_L_U_M, │ │ │ │ -_1_7_0 _T_E_C_H_N_E_T_I_U_M, │ │ │ │ -_1_7_1 _T_E_L_L_U_R_I_U_M, │ │ │ │ -_1_7_2 _T_E_R_B_I_U_M, │ │ │ │ -_1_7_3 _T_H_A_L_L_I_U_M, │ │ │ │ -_1_7_4 _T_H_O_R_I_U_M, │ │ │ │ -_1_7_5 _T_H_U_L_I_U_M, │ │ │ │ -_1_7_6 TIN, STANNUM = TIN, │ │ │ │ -_1_7_7 _T_I_T_A_N_I_U_M, │ │ │ │ -_1_7_8 _T_U_N_G_S_T_E_N, WOLFRAM = _T_U_N_G_S_T_E_N, │ │ │ │ -_1_7_9 _U_N_U_N_B_I_U_M, │ │ │ │ -_1_8_0 _U_N_U_N_N_I_L_I_U_M, │ │ │ │ -_1_8_1 _U_N_U_N_N_I_N_I_U_M, │ │ │ │ -_1_8_2 _U_R_A_N_I_U_M, │ │ │ │ -_1_8_3 _V_A_N_A_D_I_U_M, │ │ │ │ -_1_8_4 _X_E_N_O_N, │ │ │ │ -_1_8_5 _Y_T_T_E_R_B_I_U_M, │ │ │ │ -_1_8_6 _Y_T_T_R_I_U_M, │ │ │ │ -_1_8_7 _Z_I_N_C, ZINCUM = _Z_I_N_C, │ │ │ │ -_1_8_8 _Z_I_R_C_O_N_I_U_M, │ │ │ │ -189 │ │ │ │ -190 NUMBER_OF_ELEMENTS // 111 │ │ │ │ -_1_9_1 }; │ │ │ │ -192 │ │ │ │ -_1_9_6 enum _S_y_m_b_o_l │ │ │ │ -197 { │ │ │ │ -_1_9_8 Ac = 0, │ │ │ │ -_1_9_9 _A_l, │ │ │ │ -_2_0_0 _A_m, │ │ │ │ -_2_0_1 _S_b, │ │ │ │ -_2_0_2 _A_r, │ │ │ │ -_2_0_3 _A_s, │ │ │ │ -_2_0_4 _A_t, │ │ │ │ -_2_0_5 _B_a, │ │ │ │ -_2_0_6 _B_k, │ │ │ │ -_2_0_7 _B_e, │ │ │ │ -_2_0_8 _B_i, │ │ │ │ -_2_0_9 _B_h, │ │ │ │ -_2_1_0 _B, │ │ │ │ -_2_1_1 _B_r, │ │ │ │ -_2_1_2 _C_d, │ │ │ │ -_2_1_3 _C_s, │ │ │ │ -_2_1_4 _C_a, │ │ │ │ -_2_1_5 _C_f, │ │ │ │ -_2_1_6 _C, │ │ │ │ -_2_1_7 _C_e, │ │ │ │ -_2_1_8 _C_l, │ │ │ │ -_2_1_9 _C_r, │ │ │ │ -_2_2_0 _C_o, │ │ │ │ -_2_2_1 _C_u, │ │ │ │ -_2_2_2 _C_m, │ │ │ │ -_2_2_3 _D_b, │ │ │ │ -_2_2_4 _D_y, │ │ │ │ -_2_2_5 _E_s, │ │ │ │ -_2_2_6 _E_r, │ │ │ │ -_2_2_7 _E_u, │ │ │ │ -_2_2_8 _F_m, │ │ │ │ -_2_2_9 _F, │ │ │ │ -_2_3_0 _F_r, │ │ │ │ -_2_3_1 _G_d, │ │ │ │ -_2_3_2 _G_a, │ │ │ │ -_2_3_3 _G_e, │ │ │ │ -_2_3_4 _A_u, │ │ │ │ -_2_3_5 _H_f, │ │ │ │ -_2_3_6 _H_n, │ │ │ │ -_2_3_7 _H_e, │ │ │ │ -_2_3_8 _H_o, │ │ │ │ -_2_3_9 _H, │ │ │ │ -_2_4_0 _I_n, │ │ │ │ -_2_4_1 _I, │ │ │ │ -_2_4_2 _I_r, │ │ │ │ -_2_4_3 _F_e, │ │ │ │ -_2_4_4 _J_l, │ │ │ │ -_2_4_5 _K_r, │ │ │ │ -_2_4_6 _L_a, │ │ │ │ -_2_4_7 _L_r, │ │ │ │ -_2_4_8 _P_b, │ │ │ │ -_2_4_9 _L_i, │ │ │ │ -_2_5_0 _L_u, │ │ │ │ -_2_5_1 _M_g, │ │ │ │ -_2_5_2 _M_n, │ │ │ │ -_2_5_3 _M_t, │ │ │ │ -_2_5_4 _M_d, │ │ │ │ -_2_5_5 _H_g, │ │ │ │ -_2_5_6 _M_o, │ │ │ │ -_2_5_7 _N_d, │ │ │ │ -_2_5_8 _N_e, │ │ │ │ -_2_5_9 _N_p, │ │ │ │ -_2_6_0 _N_i, │ │ │ │ -_2_6_1 _N_b, │ │ │ │ -_2_6_2 _N, │ │ │ │ -_2_6_3 _N_o, │ │ │ │ -_2_6_4 _O_s, │ │ │ │ -_2_6_5 _O, │ │ │ │ -_2_6_6 _P_d, │ │ │ │ -_2_6_7 _P, │ │ │ │ -_2_6_8 _P_t, │ │ │ │ -_2_6_9 _P_u, │ │ │ │ -_2_7_0 _P_o, │ │ │ │ -_2_7_1 _K, │ │ │ │ -_2_7_2 _P_r, │ │ │ │ -_2_7_3 _P_m, │ │ │ │ -_2_7_4 _P_a, │ │ │ │ -_2_7_5 _R_a, │ │ │ │ -_2_7_6 _R_n, │ │ │ │ -_2_7_7 _R_e, │ │ │ │ -_2_7_8 _R_h, │ │ │ │ -_2_7_9 _R_b, │ │ │ │ -_2_8_0 _R_u, │ │ │ │ -_2_8_1 _R_f, │ │ │ │ -_2_8_2 _S_m, │ │ │ │ -_2_8_3 _S_c, │ │ │ │ -_2_8_4 _S_e, │ │ │ │ -_2_8_5 _S_i, │ │ │ │ -_2_8_6 _A_g, │ │ │ │ -_2_8_7 _N_a, │ │ │ │ -_2_8_8 _S_r, │ │ │ │ -_2_8_9 _S, │ │ │ │ -_2_9_0 _T_a, │ │ │ │ -_2_9_1 _T_c, │ │ │ │ -_2_9_2 _T_e, │ │ │ │ -_2_9_3 _T_b, │ │ │ │ -_2_9_4 _T_l, │ │ │ │ -_2_9_5 _T_h, │ │ │ │ -_2_9_6 _T_m, │ │ │ │ -_2_9_7 _S_n, │ │ │ │ -_2_9_8 _T_i, │ │ │ │ -_2_9_9 _W, │ │ │ │ -_3_0_0 _U_u_b, │ │ │ │ -_3_0_1 _U_u_n, │ │ │ │ -_3_0_2 _U_u_u, │ │ │ │ -_3_0_3 _U, │ │ │ │ -_3_0_4 _V, │ │ │ │ -_3_0_5 _X_e, │ │ │ │ -_3_0_6 _Y_b, │ │ │ │ -_3_0_7 _Y, │ │ │ │ -_3_0_8 _Z_n, │ │ │ │ -309 Zr │ │ │ │ -_3_1_0 }; │ │ │ │ -311 │ │ │ │ -315 │ │ │ │ -_3_2_0 _E_l_e_m_e_n_t(); │ │ │ │ -321 │ │ │ │ -_3_2_4 _E_l_e_m_e_n_t(const _E_l_e_m_e_n_t& element); │ │ │ │ -325 │ │ │ │ -_3_2_8 _E_l_e_m_e_n_t │ │ │ │ -329 (const _S_t_r_i_n_g& name, │ │ │ │ -330 const _S_t_r_i_n_g& symbol, │ │ │ │ -331 _G_r_o_u_p group, │ │ │ │ -332 _P_e_r_i_o_d period, │ │ │ │ -333 _A_t_o_m_i_c_N_u_m_b_e_r atomic_umber, │ │ │ │ -334 float atomic_weight, │ │ │ │ -335 float atomic_radius, │ │ │ │ -336 float covalent_radius, │ │ │ │ -337 float van_der_waals_radius, │ │ │ │ -338 bool is_metal, │ │ │ │ -339 float electronegativity); │ │ │ │ -340 │ │ │ │ -_3_4_3 virtual _~_E_l_e_m_e_n_t(); │ │ │ │ -344 │ │ │ │ -_3_4_9 virtual void _c_l_e_a_r(); │ │ │ │ -350 │ │ │ │ -352 │ │ │ │ -355 │ │ │ │ -_3_6_0 _E_l_e_m_e_n_t& operator = (const _E_l_e_m_e_n_t& element); │ │ │ │ -361 │ │ │ │ -363 │ │ │ │ -366 │ │ │ │ -_3_7_0 void _s_e_t_N_a_m_e(const _S_t_r_i_n_g& name); │ │ │ │ -371 │ │ │ │ -_3_7_7 const _S_t_r_i_n_g& _g_e_t_N_a_m_e() const; │ │ │ │ -378 │ │ │ │ -_3_8_2 void _s_e_t_S_y_m_b_o_l(const _S_t_r_i_n_g& symbol); │ │ │ │ -383 │ │ │ │ -_3_8_7 const _S_t_r_i_n_g& _g_e_t_S_y_m_b_o_l() const; │ │ │ │ -388 │ │ │ │ -_3_9_2 void _s_e_t_G_r_o_u_p(_G_r_o_u_p group); │ │ │ │ -393 │ │ │ │ -_3_9_7 _G_r_o_u_p _g_e_t_G_r_o_u_p() const; │ │ │ │ -398 │ │ │ │ -_4_0_2 void _s_e_t_P_e_r_i_o_d(_P_e_r_i_o_d period); │ │ │ │ -403 │ │ │ │ -_4_0_7 _P_e_r_i_o_d _g_e_t_P_e_r_i_o_d() const; │ │ │ │ -408 │ │ │ │ -_4_1_2 void _s_e_t_A_t_o_m_i_c_N_u_m_b_e_r(_A_t_o_m_i_c_N_u_m_b_e_r atomic_number); │ │ │ │ -413 │ │ │ │ -_4_1_7 _A_t_o_m_i_c_N_u_m_b_e_r _g_e_t_A_t_o_m_i_c_N_u_m_b_e_r() const; │ │ │ │ -418 │ │ │ │ -_4_2_2 void _s_e_t_A_t_o_m_i_c_W_e_i_g_h_t(float atomic_weight); │ │ │ │ -423 │ │ │ │ -_4_2_7 float _g_e_t_A_t_o_m_i_c_W_e_i_g_h_t() const; │ │ │ │ -428 │ │ │ │ -_4_3_2 void _s_e_t_A_t_o_m_i_c_R_a_d_i_u_s(float atomic_radius); │ │ │ │ -433 │ │ │ │ -_4_3_7 float _g_e_t_A_t_o_m_i_c_R_a_d_i_u_s() const; │ │ │ │ -438 │ │ │ │ -_4_4_2 void _s_e_t_C_o_v_a_l_e_n_t_R_a_d_i_u_s(float covalent_radius); │ │ │ │ -443 │ │ │ │ -_4_4_7 float _g_e_t_C_o_v_a_l_e_n_t_R_a_d_i_u_s() const; │ │ │ │ -448 │ │ │ │ -_4_5_2 void _s_e_t_V_a_n_D_e_r_W_a_a_l_s_R_a_d_i_u_s(float van_der_waals_radius); │ │ │ │ -453 │ │ │ │ -_4_5_7 float _g_e_t_V_a_n_D_e_r_W_a_a_l_s_R_a_d_i_u_s() const; │ │ │ │ -458 │ │ │ │ -_4_6_2 void _s_e_t_E_l_e_c_t_r_o_n_e_g_a_t_i_v_i_t_y(float electronegativity); │ │ │ │ -463 │ │ │ │ -_4_6_7 float _g_e_t_E_l_e_c_t_r_o_n_e_g_a_t_i_v_i_t_y() const; │ │ │ │ -468 │ │ │ │ -470 │ │ │ │ -473 │ │ │ │ -_4_7_9 bool operator == (const _E_l_e_m_e_n_t& element) const; │ │ │ │ -480 │ │ │ │ -_4_8_6 bool operator != (const _E_l_e_m_e_n_t& element) const; │ │ │ │ -487 │ │ │ │ -_4_9_4 bool operator < (const _E_l_e_m_e_n_t& element) const; │ │ │ │ -495 │ │ │ │ -_5_0_2 bool operator <= (const _E_l_e_m_e_n_t& element) const; │ │ │ │ -503 │ │ │ │ -_5_1_0 bool operator >= (const _E_l_e_m_e_n_t& element) const; │ │ │ │ -511 │ │ │ │ -_5_1_8 bool operator >(const _E_l_e_m_e_n_t& element) const; │ │ │ │ -519 │ │ │ │ -523 _B_A_L_L___E_X_P_O_R_T │ │ │ │ -_5_2_4 friend std::ostream& operator << (std::ostream& s, const _E_l_e_m_e_n_t& element); │ │ │ │ -525 │ │ │ │ -527 │ │ │ │ -530 │ │ │ │ -_5_3_6 bool _i_s_U_n_k_n_o_w_n() const; │ │ │ │ -537 │ │ │ │ -_5_4_3 bool _i_s_M_e_t_a_l() const; │ │ │ │ -544 │ │ │ │ -546 │ │ │ │ -_5_5_0 static _E_l_e_m_e_n_t _U_N_K_N_O_W_N; │ │ │ │ -551 │ │ │ │ -552 │ │ │ │ -553 private: │ │ │ │ -554 │ │ │ │ -557 _S_t_r_i_n_g name_; │ │ │ │ -558 │ │ │ │ -561 _S_t_r_i_n_g symbol_; │ │ │ │ -562 │ │ │ │ -600 _G_r_o_u_p group_; │ │ │ │ -601 │ │ │ │ -604 _P_e_r_i_o_d period_; │ │ │ │ -605 │ │ │ │ -609 _A_t_o_m_i_c_N_u_m_b_e_r atomic_number_; │ │ │ │ -610 │ │ │ │ -618 float atomic_weight_; │ │ │ │ -619 │ │ │ │ -622 float atomic_radius_; │ │ │ │ -623 │ │ │ │ -626 float covalent_radius_; │ │ │ │ -627 │ │ │ │ -630 float van_der_waals_radius_; │ │ │ │ -631 │ │ │ │ -634 bool is_metal_; │ │ │ │ -635 │ │ │ │ -638 float electronegativity_; │ │ │ │ -639 }; │ │ │ │ -640 │ │ │ │ -641 │ │ │ │ -645 _B_A_L_L___E_X_P_O_R_T │ │ │ │ -_6_4_6 std::ostream& _o_p_e_r_a_t_o_r_ _<_<_ (std::ostream& s, const _E_l_e_m_e_n_t& element); │ │ │ │ -647 │ │ │ │ -648 │ │ │ │ -_6_5_1 class _B_A_L_L___E_X_P_O_R_T _P_T_E__ │ │ │ │ -652 { │ │ │ │ -653 public: │ │ │ │ -654 │ │ │ │ -655 _B_A_L_L___C_R_E_A_T_E(_P_T_E__) │ │ │ │ -656 │ │ │ │ -657 │ │ │ │ -660 │ │ │ │ -661 │ │ │ │ -_6_6_3 _P_T_E__(); │ │ │ │ -664 │ │ │ │ -_6_6_7 _P_T_E__(const _P_T_E__& pse); │ │ │ │ -668 │ │ │ │ -_6_7_1 virtual ~_P_T_E__(); │ │ │ │ -672 │ │ │ │ -_6_7_5 virtual void clear(); │ │ │ │ -676 │ │ │ │ -678 │ │ │ │ -681 │ │ │ │ -_6_8_6 _P_T_E__& operator = (const _P_T_E__& /*pte*/); │ │ │ │ -687 │ │ │ │ -689 │ │ │ │ -692 │ │ │ │ -_6_9_5 static _E_l_e_m_e_n_t& getElement(_P_o_s_i_t_i_o_n atomic_number); │ │ │ │ -696 │ │ │ │ -_7_0_0 static _E_l_e_m_e_n_t& getElement(const _S_t_r_i_n_g& symbol); │ │ │ │ -701 │ │ │ │ -703 │ │ │ │ -706 │ │ │ │ -_7_1_1 bool operator == (const _P_T_E__& pte) const; │ │ │ │ -712 │ │ │ │ -_7_1_6 _E_l_e_m_e_n_t& operator [] (const _S_t_r_i_n_g& symbol); │ │ │ │ -717 │ │ │ │ -_7_2_1 const _E_l_e_m_e_n_t& operator [] (const _S_t_r_i_n_g& symbol) const; │ │ │ │ -722 │ │ │ │ -_7_2_6 _E_l_e_m_e_n_t& operator [] (_E_l_e_m_e_n_t::Name name); │ │ │ │ -727 │ │ │ │ -_7_3_1 const _E_l_e_m_e_n_t& operator [] (_E_l_e_m_e_n_t::Name name) const; │ │ │ │ -732 │ │ │ │ -_7_3_6 _E_l_e_m_e_n_t& operator [] (_E_l_e_m_e_n_t::Symbol symbol); │ │ │ │ -737 │ │ │ │ -_7_4_1 const _E_l_e_m_e_n_t& operator [] (_E_l_e_m_e_n_t::Symbol symbol) const; │ │ │ │ -742 │ │ │ │ -_7_4_6 _E_l_e_m_e_n_t& operator [] (_P_o_s_i_t_i_o_n position); │ │ │ │ -747 │ │ │ │ -_7_5_1 const _E_l_e_m_e_n_t& operator [] (_P_o_s_i_t_i_o_n position) const; │ │ │ │ -752 │ │ │ │ -754 │ │ │ │ -757 │ │ │ │ -_7_6_3 static bool apply(_U_n_a_r_y_P_r_o_c_e_s_s_o_r<_E_l_e_m_e_n_t>& applicator); │ │ │ │ -764 │ │ │ │ -766 │ │ │ │ -_7_6_8 struct _S_y_m_b_o_l_T_o_E_l_e_m_e_n_t │ │ │ │ -769 { │ │ │ │ -_7_7_1 const char* _s_y_m_b_o_l; │ │ │ │ -772 │ │ │ │ -_7_7_4 _E_l_e_m_e_n_t* _e_l_e_m_e_n_t; │ │ │ │ -775 }; │ │ │ │ -776 │ │ │ │ -777 private: │ │ │ │ -778 │ │ │ │ -780 static _E_l_e_m_e_n_t element_[]; │ │ │ │ -781 │ │ │ │ -783 static _S_y_m_b_o_l_T_o_E_l_e_m_e_n_t symbol_to_element_[]; │ │ │ │ -784 │ │ │ │ -786 static _E_l_e_m_e_n_t* atomic_number_to_element_[]; │ │ │ │ -787 }; │ │ │ │ -788 │ │ │ │ -789 │ │ │ │ -793 _B_A_L_L___E_X_P_O_R_T extern _P_T_E__ _P_T_E; │ │ │ │ -794 │ │ │ │ -795 │ │ │ │ -796 │ │ │ │ -797# ifndef BALL_NO_INLINE_FUNCTIONS │ │ │ │ -798# include │ │ │ │ -799# endif │ │ │ │ -800} //namespace BALL │ │ │ │ -801 │ │ │ │ -802 │ │ │ │ -803#endif // BALL_KERNEL_PTE_H │ │ │ │ -_s_t_r_i_n_g_._h │ │ │ │ -_p_r_o_c_e_s_s_o_r_._h │ │ │ │ -_c_r_e_a_t_e_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ -_B_A_L_L_:_:_o_p_e_r_a_t_o_r_<_< │ │ │ │ -BALL_EXPORT std::ostream & operator<<(std::ostream &os, const Exception:: │ │ │ │ -GeneralException &e) │ │ │ │ -_B_A_L_L_:_:_P_T_E │ │ │ │ -BALL_EXPORT PTE_ PTE │ │ │ │ +51#endif // BALL_QSAR_MODELFACTORY_H │ │ │ │ +_f_a_c_t_o_r_y_._h │ │ │ │ +_Q_S_A_R_D_a_t_a_._h │ │ │ │ +_M_o_d_e_l_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_6_0 │ │ │ │ _B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_5_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_t_o_m_i_c_N_u_m_b_e_r │ │ │ │ -short AtomicNumber │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_7_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_a_m_e │ │ │ │ -Name │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_7_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_A_R_I_U_M │ │ │ │ -@ BARIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_U_R_I_U_M │ │ │ │ -@ CURIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_G_A_D_O_L_I_N_I_U_M │ │ │ │ -@ GADOLINIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_1_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_E_L_E_N_I_U_M │ │ │ │ -@ SELENIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_6_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_O_X_Y_G_E_N │ │ │ │ -@ OXYGEN │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_E_R_I_U_M │ │ │ │ -@ CERIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_E_O_D_Y_M_I_U_M │ │ │ │ -@ NEODYMIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_3_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_U_B_I_D_I_U_M │ │ │ │ -@ RUBIDIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_5_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_V_A_N_A_D_I_U_M │ │ │ │ -@ VANADIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_8_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_I_O_D_I_N_E │ │ │ │ -@ IODINE │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_2_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_I_T_R_O_G_E_N │ │ │ │ -@ NITROGEN │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_L_U_M_I_N_U_M │ │ │ │ -@ ALUMINUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_7_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_A_L_I_F_O_R_N_I_U_M │ │ │ │ -@ CALIFORNIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_I_R_I_D_I_U_M │ │ │ │ -@ IRIDIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_2_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_H_R_O_M_I_U_M │ │ │ │ -@ CHROMIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_L_U_T_O_N_I_U_M │ │ │ │ -@ PLUTONIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_S_T_A_T_I_N_E │ │ │ │ -@ ASTATINE │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_E_R_Y_L_L_I_U_M │ │ │ │ -@ BERYLLIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_Z_I_N_C │ │ │ │ -@ ZINC │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_8_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_E_C_H_N_E_T_I_U_M │ │ │ │ -@ TECHNETIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_7_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_O_H_R_I_U_M │ │ │ │ -@ BOHRIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_U_R_A_N_I_U_M │ │ │ │ -@ URANIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_8_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_O_L_O_N_I_U_M │ │ │ │ -@ POLONIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_U_T_H_E_N_I_U_M │ │ │ │ -@ RUTHENIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_5_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_J_O_L_I_O_T_I_U_M │ │ │ │ -@ JOLIOTIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_2_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_E_O_N │ │ │ │ -@ NEON │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_3_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_O_B_E_L_I_U_M │ │ │ │ -@ NOBELIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_A_L_C_I_U_M │ │ │ │ -@ CALCIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_H_O_S_P_H_O_R_U_S │ │ │ │ -@ PHOSPHORUS │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_L_U_T_E_T_I_U_M │ │ │ │ -@ LUTETIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_2_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_R_O_T_A_C_T_I_N_I_U_M │ │ │ │ -@ PROTACTINIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_5_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_U_T_H_E_R_F_O_R_D_I_U_M │ │ │ │ -@ RUTHERFORDIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_6_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_U_N_U_N_B_I_U_M │ │ │ │ -@ UNUNBIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_7_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_A_R_B_O_N │ │ │ │ -@ CARBON │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_A_L_L_A_D_I_U_M │ │ │ │ -@ PALLADIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_O_B_A_L_T │ │ │ │ -@ COBALT │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_M_E_I_T_N_E_R_I_U_M │ │ │ │ -@ MEITNERIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_3_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_E_P_T_U_N_I_U_M │ │ │ │ -@ NEPTUNIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_3_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_H_E_N_I_U_M │ │ │ │ -@ RHENIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_5_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_R_S_E_N_I_C │ │ │ │ -@ ARSENIC │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_G_A_L_L_I_U_M │ │ │ │ -@ GALLIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_1_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_L_E_A_D │ │ │ │ -@ LEAD │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_2_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_A_D_I_U_M │ │ │ │ -@ RADIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_5_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_I_C_K_E_L │ │ │ │ -@ NICKEL │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_3_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_D_Y_S_P_R_O_S_I_U_M │ │ │ │ -@ DYSPROSIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_I_N_D_I_U_M │ │ │ │ -@ INDIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_1_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_O_R_O_N │ │ │ │ -@ BORON │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_H_L_O_R_I_N_E │ │ │ │ -@ CHLORINE │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_A_E_S_I_U_M │ │ │ │ -@ CAESIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_E_L_I_U_M │ │ │ │ -@ HELIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_1_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_I_O_B_I_U_M │ │ │ │ -@ NIOBIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_E_L_L_U_R_I_U_M │ │ │ │ -@ TELLURIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_7_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_F_E_R_M_I_U_M │ │ │ │ -@ FERMIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_E_U_R_O_P_I_U_M │ │ │ │ -@ EUROPIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_E_R_B_I_U_M │ │ │ │ -@ TERBIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_7_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_Y_T_T_R_I_U_M │ │ │ │ -@ YTTRIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_8_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_O_S_M_I_U_M │ │ │ │ -@ OSMIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_U_N_U_N_N_I_L_I_U_M │ │ │ │ -@ UNUNNILIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_8_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_T_R_O_N_T_I_U_M │ │ │ │ -@ STRONTIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_6_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_A_F_N_I_U_M │ │ │ │ -@ HAFNIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_1_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_U_N_G_S_T_E_N │ │ │ │ -@ TUNGSTEN │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_7_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_R_G_O_N │ │ │ │ -@ ARGON │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_N_T_I_M_O_N_Y │ │ │ │ -@ ANTIMONY │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_R_A_S_E_O_D_Y_M_I_U_M │ │ │ │ -@ PRASEODYMIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_5_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_F_R_A_N_C_I_U_M │ │ │ │ -@ FRANCIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_R_O_M_E_T_H_I_U_M │ │ │ │ -@ PROMETHIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_5_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_D_U_B_N_I_U_M │ │ │ │ -@ DUBNIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_H_A_L_L_I_U_M │ │ │ │ -@ THALLIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_7_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_X_E_N_O_N │ │ │ │ -@ XENON │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_8_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_U_N_U_N_N_I_N_I_U_M │ │ │ │ -@ UNUNNINIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_8_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_L_A_T_I_N_U_M │ │ │ │ -@ PLATINUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_4_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_O_P_P_E_R │ │ │ │ -@ COPPER │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_H_U_L_I_U_M │ │ │ │ -@ THULIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_7_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_M_E_R_I_C_I_U_M │ │ │ │ -@ AMERICIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_7_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_Z_I_R_C_O_N_I_U_M │ │ │ │ -@ ZIRCONIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_8_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_I_S_M_U_T_H │ │ │ │ -@ BISMUTH │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_M_E_N_D_E_L_E_V_I_U_M │ │ │ │ -@ MENDELEVIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_3_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_L_I_T_H_I_U_M │ │ │ │ -@ LITHIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_2_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_A_D_M_I_U_M │ │ │ │ -@ CADMIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_I_T_A_N_I_U_M │ │ │ │ -@ TITANIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_7_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_A_H_N_I_U_M │ │ │ │ -@ HAHNIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_1_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_L_A_W_R_E_N_C_I_U_M │ │ │ │ -@ LAWRENCIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_2_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_M_O_L_Y_B_D_E_N_U_M │ │ │ │ -@ MOLYBDENUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_3_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_L_A_N_T_H_A_N_U_M │ │ │ │ -@ LANTHANUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_2_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_O_L_M_I_U_M │ │ │ │ -@ HOLMIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_1_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_E_R_B_I_U_M │ │ │ │ -@ ERBIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_E_I_N_S_T_E_I_N_I_U_M │ │ │ │ -@ EINSTEINIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_M_A_G_N_E_S_I_U_M │ │ │ │ -@ MAGNESIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_3_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_Y_D_R_O_G_E_N │ │ │ │ -@ HYDROGEN │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_1_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_E_R_K_E_L_I_U_M │ │ │ │ -@ BERKELIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_8_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_C_A_N_D_I_U_M │ │ │ │ -@ SCANDIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_6_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_A_N_T_A_L_U_M │ │ │ │ -@ TANTALUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_6_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_Y_T_T_E_R_B_I_U_M │ │ │ │ -@ YTTERBIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_8_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_G_E_R_M_A_N_I_U_M │ │ │ │ -@ GERMANIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_1_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_H_O_D_I_U_M │ │ │ │ -@ RHODIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_5_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_A_M_A_R_I_U_M │ │ │ │ -@ SAMARIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_6_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_F_L_U_O_R_I_N_E │ │ │ │ -@ FLUORINE │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_0_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_H_O_R_I_U_M │ │ │ │ -@ THORIUM │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_7_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_A_D_O_N │ │ │ │ -@ RADON │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_5_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_K_R_Y_P_T_O_N │ │ │ │ -@ KRYPTON │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_2_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_R_O_M_I_N_E │ │ │ │ -@ BROMINE │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_E_l_e_m_e_n_t │ │ │ │ -Element() │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_N_a_m_e │ │ │ │ -void setName(const String &name) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_A_t_o_m_i_c_R_a_d_i_u_s │ │ │ │ -float getAtomicRadius() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_A_t_o_m_i_c_R_a_d_i_u_s │ │ │ │ -void setAtomicRadius(float atomic_radius) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_P_e_r_i_o_d │ │ │ │ -void setPeriod(Period period) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_c_l_e_a_r │ │ │ │ -virtual void clear() │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_S_y_m_b_o_l │ │ │ │ -const String & getSymbol() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_A_t_o_m_i_c_W_e_i_g_h_t │ │ │ │ -void setAtomicWeight(float atomic_weight) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_N_a_m_e │ │ │ │ -const String & getName() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_A_t_o_m_i_c_N_u_m_b_e_r │ │ │ │ -AtomicNumber getAtomicNumber() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_C_o_v_a_l_e_n_t_R_a_d_i_u_s │ │ │ │ -void setCovalentRadius(float covalent_radius) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_G_r_o_u_p │ │ │ │ -void setGroup(Group group) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_E_l_e_c_t_r_o_n_e_g_a_t_i_v_i_t_y │ │ │ │ -void setElectronegativity(float electronegativity) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_U_N_K_N_O_W_N │ │ │ │ -static Element UNKNOWN │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_5_5_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_G_r_o_u_p │ │ │ │ -short Group │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_6_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_i_s_M_e_t_a_l │ │ │ │ -bool isMetal() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_P_e_r_i_o_d │ │ │ │ -Period getPeriod() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_E_l_e_m_e_n_t │ │ │ │ -Element(const String &name, const String &symbol, Group group, Period period, │ │ │ │ -AtomicNumber atomic_umber, float atomic_weight, float atomic_radius, float │ │ │ │ -covalent_radius, float van_der_waals_radius, bool is_metal, float │ │ │ │ -electronegativity) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_V_a_n_D_e_r_W_a_a_l_s_R_a_d_i_u_s │ │ │ │ -float getVanDerWaalsRadius() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_e_r_i_o_d │ │ │ │ -short Period │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_6_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_A_t_o_m_i_c_W_e_i_g_h_t │ │ │ │ -float getAtomicWeight() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_E_l_e_m_e_n_t │ │ │ │ -Element(const Element &element) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_G_r_o_u_p │ │ │ │ -Group getGroup() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_~_E_l_e_m_e_n_t │ │ │ │ -virtual ~Element() │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_S_y_m_b_o_l │ │ │ │ -void setSymbol(const String &symbol) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_E_l_e_c_t_r_o_n_e_g_a_t_i_v_i_t_y │ │ │ │ -float getElectronegativity() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_A_t_o_m_i_c_N_u_m_b_e_r │ │ │ │ -void setAtomicNumber(AtomicNumber atomic_number) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_s_e_t_V_a_n_D_e_r_W_a_a_l_s_R_a_d_i_u_s │ │ │ │ -void setVanDerWaalsRadius(float van_der_waals_radius) │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_g_e_t_C_o_v_a_l_e_n_t_R_a_d_i_u_s │ │ │ │ -float getCovalentRadius() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_y_m_b_o_l │ │ │ │ -Symbol │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_9_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_e │ │ │ │ -@ Ce │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_b │ │ │ │ -@ Rb │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_G_e │ │ │ │ -@ Ge │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_X_e │ │ │ │ -@ Xe │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_3_0_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_F_r │ │ │ │ -@ Fr │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_g │ │ │ │ -@ Hg │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_Z_n │ │ │ │ -@ Zn │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_3_0_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_r │ │ │ │ -@ Br │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_K_r │ │ │ │ -@ Kr │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_e │ │ │ │ -@ Re │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_d │ │ │ │ -@ Cd │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S │ │ │ │ -@ S │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_Y │ │ │ │ -@ Y │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_3_0_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_I │ │ │ │ -@ I │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_F_e │ │ │ │ -@ Fe │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_m │ │ │ │ -@ Pm │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_f │ │ │ │ -@ Rf │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_G_a │ │ │ │ -@ Ga │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P │ │ │ │ -@ P │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_b │ │ │ │ -@ Nb │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_M_t │ │ │ │ -@ Mt │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_m │ │ │ │ -@ Tm │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_K │ │ │ │ -@ K │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_d │ │ │ │ -@ Nd │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_i │ │ │ │ -@ Bi │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_b │ │ │ │ -@ Pb │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_J_l │ │ │ │ -@ Jl │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_b │ │ │ │ -@ Tb │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N │ │ │ │ -@ N │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_U_u_u │ │ │ │ -@ Uuu │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_3_0_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_O │ │ │ │ -@ O │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_a │ │ │ │ -@ Ra │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_o │ │ │ │ -@ Co │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_W │ │ │ │ -@ W │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_m │ │ │ │ -@ Cm │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_e │ │ │ │ -@ Te │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_U │ │ │ │ -@ U │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_3_0_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_m │ │ │ │ -@ Am │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_l │ │ │ │ -@ Tl │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_e │ │ │ │ -@ He │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_a │ │ │ │ -@ Ta │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_s │ │ │ │ -@ Cs │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_f │ │ │ │ -@ Cf │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_L_i │ │ │ │ -@ Li │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_l │ │ │ │ -@ Cl │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_V │ │ │ │ -@ V │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_3_0_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B │ │ │ │ -@ B │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_i │ │ │ │ -@ Si │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_e │ │ │ │ -@ Be │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_b │ │ │ │ -@ Sb │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_n │ │ │ │ -@ Hn │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_O_s │ │ │ │ -@ Os │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_G_d │ │ │ │ -@ Gd │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_k │ │ │ │ -@ Bk │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_Y_b │ │ │ │ -@ Yb │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_3_0_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_p │ │ │ │ -@ Np │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_a │ │ │ │ -@ Pa │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_I_n │ │ │ │ -@ In │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_m │ │ │ │ -@ Sm │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_e │ │ │ │ -@ Se │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_D_y │ │ │ │ -@ Dy │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_E_r │ │ │ │ -@ Er │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_r │ │ │ │ -@ Sr │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_E_s │ │ │ │ -@ Es │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_M_g │ │ │ │ -@ Mg │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_F_m │ │ │ │ -@ Fm │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_L_a │ │ │ │ -@ La │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_L_r │ │ │ │ -@ Lr │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_e │ │ │ │ -@ Ne │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_g │ │ │ │ -@ Ag │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_t │ │ │ │ -@ Pt │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C │ │ │ │ -@ C │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_h │ │ │ │ -@ Th │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_n │ │ │ │ -@ Sn │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_F │ │ │ │ -@ F │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_i │ │ │ │ -@ Ni │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_a │ │ │ │ -@ Na │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_u │ │ │ │ -@ Cu │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_s │ │ │ │ -@ As │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_S_c │ │ │ │ -@ Sc │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_d │ │ │ │ -@ Pd │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_a │ │ │ │ -@ Ba │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_h │ │ │ │ -@ Rh │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_c │ │ │ │ -@ Tc │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_B_h │ │ │ │ -@ Bh │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_L_u │ │ │ │ -@ Lu │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_M_d │ │ │ │ -@ Md │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_o │ │ │ │ -@ Po │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_r │ │ │ │ -@ Cr │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_E_u │ │ │ │ -@ Eu │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_u │ │ │ │ -@ Pu │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_D_b │ │ │ │ -@ Db │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_2_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_U_u_b │ │ │ │ -@ Uub │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_3_0_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H │ │ │ │ -@ H │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_P_r │ │ │ │ -@ Pr │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_u │ │ │ │ -@ Au │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_o │ │ │ │ -@ Ho │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_N_o │ │ │ │ -@ No │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_6_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_C_a │ │ │ │ -@ Ca │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_1_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_n │ │ │ │ -@ Rn │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_7_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_R_u │ │ │ │ -@ Ru │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_8_0 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_r │ │ │ │ -@ Ar │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_T_i │ │ │ │ -@ Ti │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_9_8 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_t │ │ │ │ -@ At │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_0_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_U_u_n │ │ │ │ -@ Uun │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_3_0_1 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_I_r │ │ │ │ -@ Ir │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_4_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_M_n │ │ │ │ -@ Mn │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_2 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_H_f │ │ │ │ -@ Hf │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_3_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_A_l │ │ │ │ -@ Al │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_1_9_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_M_o │ │ │ │ -@ Mo │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_2_5_6 │ │ │ │ -_B_A_L_L_:_:_E_l_e_m_e_n_t_:_:_i_s_U_n_k_n_o_w_n │ │ │ │ -bool isUnknown() const │ │ │ │ -_B_A_L_L_:_:_P_T_E__ │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_6_5_2 │ │ │ │ -_B_A_L_L_:_:_P_T_E___:_:_S_y_m_b_o_l_T_o_E_l_e_m_e_n_t │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_7_6_9 │ │ │ │ -_B_A_L_L_:_:_P_T_E___:_:_S_y_m_b_o_l_T_o_E_l_e_m_e_n_t_:_:_e_l_e_m_e_n_t │ │ │ │ -Element * element │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_7_7_4 │ │ │ │ -_B_A_L_L_:_:_P_T_E___:_:_S_y_m_b_o_l_T_o_E_l_e_m_e_n_t_:_:_s_y_m_b_o_l │ │ │ │ -const char * symbol │ │ │ │ -DDeeffiinniittiioonn _P_T_E_._h_:_7_7_1 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y │ │ │ │ +DDeeffiinniittiioonn _m_o_d_e_l_F_a_c_t_o_r_y_._h_:_3_0 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y_:_:_c_r_e_a_t_e_K_e_r_n_e_l_1 │ │ │ │ +static T * createKernel1(const QSARData &q, int k, double p1, double p2) │ │ │ │ +DDeeffiinniittiioonn _m_o_d_e_l_F_a_c_t_o_r_y_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y_:_:_c_r_e_a_t_e_K_e_r_n_e_l_2 │ │ │ │ +static T * createKernel2(const QSARData &q, String s1, String s2) │ │ │ │ +DDeeffiinniittiioonn _m_o_d_e_l_F_a_c_t_o_r_y_._h_:_4_3 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y_:_:_c_r_e_a_t_e │ │ │ │ +static T * create(const QSARData &q) │ │ │ │ +DDeeffiinniittiioonn _m_o_d_e_l_F_a_c_t_o_r_y_._h_:_3_3 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_Q_S_A_R_D_a_t_a │ │ │ │ +DDeeffiinniittiioonn _Q_S_A_R_D_a_t_a_._h_:_5_6 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d5a/a01199.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: NMRDescriptors.h File Reference │ │ │ +BALL: chain.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,52 +65,62 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ +Classes | │ │ │ Namespaces | │ │ │ -Functions
    │ │ │ -
    NMRDescriptors.h File Reference
    │ │ │ +Macros
    │ │ │ +
    chain.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/DATATYPE/hashMap.h>
    │ │ │ -#include <BALL/KERNEL/residue.h>
    │ │ │ -#include <BALL/KERNEL/protein.h>
    │ │ │ -#include <BALL/KERNEL/atomContainer.h>
    │ │ │ +
    #include <BALL/KERNEL/residue.h>
    │ │ │ +#include <BALL/KERNEL/secondaryStructureIterator.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ + │ │ │ + │ │ │ + │ │ │ +

    │ │ │ +Classes

    class  BALL::Chain
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ -Functions

    BALL_EXPORT void BALL::calculateResidueChiAngles (const Protein &protein, HashMap< const Residue *, float > &residue_angles)
     
    BALL_EXPORT void BALL::calculateResidueChiAngles (const Chain &fragment, HashMap< const Residue *, float > &residue_angles)
     
    BALL_EXPORT float BALL::calculateResidueChiAngles (const Residue &residue)
     
    BALL_EXPORT void BALL::calculateResidueChi2Angles (const Protein &protein, HashMap< const Residue *, float > &residue_angles)
     
    BALL_EXPORT void BALL::calculateResidueChi2Angles (const Chain &fragment, HashMap< const Residue *, float > &residue_angles)
     
    BALL_EXPORT float BALL::calculateResidueChi2Angles (const Residue &residue)
     

    │ │ │ +Macros

    #define BALL_CHAIN_DEFAULT_NAME   ' '
     
    │ │ │ +

    Macro Definition Documentation

    │ │ │ + │ │ │ +

    ◆ BALL_CHAIN_DEFAULT_NAME

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_CHAIN_DEFAULT_NAME   ' '
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 17 of file chain.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,37 +1,27 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ -_N_a_m_e_s_p_a_c_e_s | _F_u_n_c_t_i_o_n_s │ │ │ │ -NMRDescriptors.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s │ │ │ │ +chain.h File Reference │ │ │ │ #include <_B_A_L_L_/_K_E_R_N_E_L_/_r_e_s_i_d_u_e_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_o_t_e_i_n_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_s_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_I_t_e_r_a_t_o_r_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ +CCllaasssseess │ │ │ │ +class   _B_A_L_L_:_:_C_h_a_i_n │ │ │ │ +  │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -FFuunnccttiioonnss │ │ │ │ - _B_A_L_L___E_X_P_O_R_T void  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s (const _P_r_o_t_e_i_n &protein, │ │ │ │ - _H_a_s_h_M_a_p< const _R_e_s_i_d_u_e *, _f_l_o_a_t > &residue_angles) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T void  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s (const _C_h_a_i_n &fragment, │ │ │ │ - _H_a_s_h_M_a_p< const _R_e_s_i_d_u_e *, _f_l_o_a_t > &residue_angles) │ │ │ │ -  │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _f_l_o_a_t  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s (const _R_e_s_i_d_u_e &residue) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T void  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s (const _P_r_o_t_e_i_n &protein, │ │ │ │ - _H_a_s_h_M_a_p< const _R_e_s_i_d_u_e *, _f_l_o_a_t > &residue_angles) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T void  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s (const _C_h_a_i_n &fragment, │ │ │ │ - _H_a_s_h_M_a_p< const _R_e_s_i_d_u_e *, _f_l_o_a_t > &residue_angles) │ │ │ │ -  │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _f_l_o_a_t  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s (const _R_e_s_i_d_u_e &residue) │ │ │ │ +MMaaccrrooss │ │ │ │ +#define  _B_A_L_L___C_H_A_I_N___D_E_F_A_U_L_T___N_A_M_E   ' ' │ │ │ │   │ │ │ │ +********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ +********** _?◆_? BBAALLLL__CCHHAAIINN__DDEEFFAAUULLTT__NNAAMMEE ********** │ │ │ │ +#define BALL_CHAIN_DEFAULT_NAME   ' ' │ │ │ │ +Definition at line _1_7 of file _c_h_a_i_n_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d5a/a01199_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: NMRDescriptors.h Source File │ │ │ +BALL: chain.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,79 +70,280 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    NMRDescriptors.h
    │ │ │ +
    chain.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1#ifndef BALL_QSAR_NMRDESCRIPTORS_H
    │ │ │ -
    2#define BALL_QSAR_NMRDESCRIPTORS_H
    │ │ │ -
    3
    │ │ │ -
    4#ifndef BALL_COMMON_H
    │ │ │ -
    5# include <BALL/common.h>
    │ │ │ -
    6#endif
    │ │ │ +Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ +
    2// vi: set ts=2:
    │ │ │ +
    3//
    │ │ │ +
    4
    │ │ │ +
    5#ifndef BALL_KERNEL_CHAIN_H
    │ │ │ +
    6#define BALL_KERNEL_CHAIN_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_DATATYPE_H
    │ │ │ -
    9# include <BALL/DATATYPE/hashMap.h>
    │ │ │ +
    8#ifndef BALL_KERNEL_RESIDUE_H
    │ │ │ +
    9# include <BALL/KERNEL/residue.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_KERNEL_RESIDUE_H
    │ │ │ -
    13# include <BALL/KERNEL/residue.h>
    │ │ │ +
    12#ifndef BALL_KERNEL_SECONDARYSTRUCTUREITERATOR_H
    │ │ │ +
    13# include <BALL/KERNEL/secondaryStructureIterator.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │ -
    16#ifndef BALL_KERNEL_PROTEIN_H
    │ │ │ -
    17# include <BALL/KERNEL/protein.h>
    │ │ │ -
    18#endif
    │ │ │ -
    19
    │ │ │ -
    20#ifndef BALL_KERNEL_ATOMCONTAINER_H
    │ │ │ -
    21# include <BALL/KERNEL/atomContainer.h>
    │ │ │ -
    22#endif
    │ │ │ -
    23
    │ │ │ -
    24namespace BALL
    │ │ │ -
    25{
    │ │ │ -
    26
    │ │ │ -
    34 BALL_EXPORT void calculateResidueChiAngles(const Protein& protein, HashMap<const Residue*, float>& residue_angles);
    │ │ │ -
    35
    │ │ │ -
    43 BALL_EXPORT void calculateResidueChiAngles( const Chain& fragment,
    │ │ │ -
    44 HashMap<const Residue*,float>& residue_angles);
    │ │ │ -
    45
    │ │ │ -
    49 BALL_EXPORT float calculateResidueChiAngles(const Residue& residue);
    │ │ │ -
    50
    │ │ │ -
    51
    │ │ │ -
    59 BALL_EXPORT void calculateResidueChi2Angles(const Protein& protein, HashMap<const Residue*, float>& residue_angles);
    │ │ │ -
    60
    │ │ │ -
    68 BALL_EXPORT void calculateResidueChi2Angles( const Chain& fragment,
    │ │ │ -
    69 HashMap<const Residue*,float>& residue_angles);
    │ │ │ -
    70
    │ │ │ -
    71
    │ │ │ -
    75 BALL_EXPORT float calculateResidueChi2Angles(const Residue& residue);
    │ │ │ -
    76
    │ │ │ -
    77}
    │ │ │ -
    78
    │ │ │ -
    79#endif
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::calculateResidueChiAngles
    BALL_EXPORT void calculateResidueChiAngles(const Protein &protein, HashMap< const Residue *, float > &residue_angles)
    │ │ │ -
    BALL::calculateResidueChi2Angles
    BALL_EXPORT void calculateResidueChi2Angles(const Protein &protein, HashMap< const Residue *, float > &residue_angles)
    │ │ │ -
    BALL::HashMap
    HashMap class based on the STL map (containing serveral convenience functions)
    Definition hashMap.h:74
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    16
    │ │ │ +
    17#define BALL_CHAIN_DEFAULT_NAME ' '
    │ │ │ +
    18
    │ │ │ +
    19namespace BALL
    │ │ │ +
    20{
    │ │ │ +
    21 class Protein;
    │ │ │ +
    22
    │ │ │ +
    │ │ │ +
    30 class BALL_EXPORT Chain
    │ │ │ +
    31 : public AtomContainer
    │ │ │ +
    32 {
    │ │ │ +
    33 public:
    │ │ │ +
    34
    │ │ │ +
    35 BALL_CREATE_DEEP(Chain)
    │ │ │ +
    36
    │ │ │ +
    37
    │ │ │ +
    40
    │ │ │ +
    41
    │ │ │ +
    │ │ │ +
    43 enum Property
    │ │ │ +
    44 {
    │ │ │ +
    45 NUMBER_OF_PROPERTIES = AtomContainer::NUMBER_OF_PROPERTIES
    │ │ │ +
    46 };
    │ │ │ +
    │ │ │ +
    47
    │ │ │ +
    49
    │ │ │ +
    52
    │ │ │ +
    54 Chain();
    │ │ │ +
    55
    │ │ │ +
    57 Chain(const Chain& chain, bool deep = true);
    │ │ │ +
    58
    │ │ │ +
    60 Chain(const String& name);
    │ │ │ +
    61
    │ │ │ +
    63 virtual ~Chain();
    │ │ │ +
    64
    │ │ │ +
    66
    │ │ │ +
    69
    │ │ │ +
    73 void persistentWrite(PersistenceManager& pm, const char* name = 0) const;
    │ │ │ +
    74
    │ │ │ +
    78 void persistentRead(PersistenceManager& pm);
    │ │ │ +
    79
    │ │ │ +
    81
    │ │ │ +
    84
    │ │ │ +
    90 void set(const Chain& chain, bool deep = true);
    │ │ │ +
    91
    │ │ │ +
    98 Chain& operator = (const Chain& chain);
    │ │ │ +
    99
    │ │ │ +
    105 void get(Chain& chain, bool deep = true) const;
    │ │ │ +
    106
    │ │ │ +
    110 void swap(Chain& chain);
    │ │ │ +
    111
    │ │ │ +
    113
    │ │ │ +
    118 bool operator == (const Chain& chain) const;
    │ │ │ +
    119
    │ │ │ +
    123 bool operator != (const Chain& chain) const;
    │ │ │ +
    124
    │ │ │ +
    125
    │ │ │ +
    129
    │ │ │ +
    134 Protein* getProtein();
    │ │ │ +
    135
    │ │ │ +
    140 const Protein* getProtein() const;
    │ │ │ +
    141
    │ │ │ +
    148 SecondaryStructure* getSecondaryStructure(Position position);
    │ │ │ +
    149
    │ │ │ +
    156 const SecondaryStructure* getSecondaryStructure(Position position) const;
    │ │ │ +
    157
    │ │ │ +
    163 Residue* getResidue(Position position);
    │ │ │ +
    164
    │ │ │ +
    170 const Residue* getResidue(Position position) const;
    │ │ │ +
    171
    │ │ │ +
    177 Residue* getNTerminal();
    │ │ │ +
    178
    │ │ │ +
    184 const Residue* getNTerminal() const;
    │ │ │ +
    185
    │ │ │ +
    191 Residue* getCTerminal();
    │ │ │ +
    192
    │ │ │ +
    198 const Residue* getCTerminal() const;
    │ │ │ +
    199
    │ │ │ +
    205 PDBAtom* getPDBAtom(Position position);
    │ │ │ +
    206
    │ │ │ +
    212 const PDBAtom* getPDBAtom(Position position) const;
    │ │ │ +
    213
    │ │ │ +
    217 Size countSecondaryStructures() const;
    │ │ │ +
    218
    │ │ │ +
    222 Size countResidues() const;
    │ │ │ +
    223
    │ │ │ +
    227 Size countPDBAtoms() const;
    │ │ │ +
    228
    │ │ │ +
    232 void prepend(SecondaryStructure& secondary_structure);
    │ │ │ +
    233
    │ │ │ +
    237 void append(SecondaryStructure& secondary_structure);
    │ │ │ +
    238
    │ │ │ +
    242 void insert(SecondaryStructure& secondary_structure);
    │ │ │ +
    243
    │ │ │ +
    248 void insertBefore(SecondaryStructure& secondary_structure, Composite& before);
    │ │ │ +
    249
    │ │ │ +
    254 void insertAfter(SecondaryStructure& secondary_structure, Composite& after);
    │ │ │ +
    255
    │ │ │ +
    259 bool remove(SecondaryStructure& secondary_structure);
    │ │ │ +
    260
    │ │ │ +
    264 void prepend(Residue& residue);
    │ │ │ +
    265
    │ │ │ +
    269 void append(Residue& residue);
    │ │ │ +
    270
    │ │ │ +
    274 void insert(Residue& residue);
    │ │ │ +
    275
    │ │ │ +
    280 void insertBefore(Residue& residue, Composite& before);
    │ │ │ +
    281
    │ │ │ +
    286 void insertAfter(Residue& residue, Composite& after);
    │ │ │ +
    287
    │ │ │ +
    291 bool remove(Residue& residue);
    │ │ │ +
    292
    │ │ │ +
    296 void spliceBefore(Chain& chain);
    │ │ │ +
    297
    │ │ │ +
    301 void spliceAfter(Chain &chain);
    │ │ │ +
    302
    │ │ │ +
    306 void splice(Chain &chain);
    │ │ │ +
    307
    │ │ │ +
    309
    │ │ │ +
    313 virtual bool isChain() const { return true; }
    │ │ │ +
    315
    │ │ │ +
    319
    │ │ │ +
    326 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const
    │ │ │ +
    327;
    │ │ │ +
    328
    │ │ │ +
    330
    │ │ │ +
    331 // --- EXTERNAL ITERATORS
    │ │ │ +
    332
    │ │ │ +
    333 BALL_KERNEL_DEFINE_ITERATOR_CREATORS(SecondaryStructure)
    │ │ │ +
    334 BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Residue)
    │ │ │ +
    335 BALL_KERNEL_DEFINE_ITERATOR_CREATORS(PDBAtom)
    │ │ │ +
    336
    │ │ │ +
    337 BALL_DECLARE_STD_ITERATOR_WRAPPER(Chain, SecondaryStructure, secondaryStructures)
    │ │ │ +
    338 BALL_DECLARE_STD_ITERATOR_WRAPPER(Chain, Residue , residues)
    │ │ │ +
    339 BALL_DECLARE_STD_ITERATOR_WRAPPER(Chain, PDBAtom , pdbAtoms)
    │ │ │ +
    340
    │ │ │ +
    341 protected:
    │ │ │ +
    342
    │ │ │ +
    343 private:
    │ │ │ +
    344 AtomContainer* getAtomContainer(Position position);
    │ │ │ +
    345
    │ │ │ +
    346 const AtomContainer* getAtomContainer(Position position) const;
    │ │ │ +
    347
    │ │ │ +
    348 Atom* getAtom(Position position);
    │ │ │ +
    349
    │ │ │ +
    350 const Atom* getAtom(Position position) const;
    │ │ │ +
    351
    │ │ │ +
    352 void prepend(Atom& atom);
    │ │ │ +
    353
    │ │ │ +
    354 void append(Atom& atom);
    │ │ │ +
    355
    │ │ │ +
    356 void insert(Atom& atom);
    │ │ │ +
    357
    │ │ │ +
    358 void insertBefore(Atom& atom, Composite& before);
    │ │ │ +
    359
    │ │ │ +
    360 void insertAfter(Atom& atom, Composite& after);
    │ │ │ +
    361
    │ │ │ +
    362 bool remove(Atom& atom);
    │ │ │ +
    363
    │ │ │ +
    364 void prepend(AtomContainer& atom_container);
    │ │ │ +
    365
    │ │ │ +
    366 void append(AtomContainer& atom_container);
    │ │ │ +
    367
    │ │ │ +
    368 void insert(AtomContainer& atom_container);
    │ │ │ +
    369
    │ │ │ +
    370 void insertBefore(AtomContainer& atom_container, Composite& before);
    │ │ │ +
    371
    │ │ │ +
    372 void insertAfter(AtomContainer& atom_container, Composite& after);
    │ │ │ +
    373
    │ │ │ +
    374 void spliceBefore(AtomContainer& atom_container);
    │ │ │ +
    375
    │ │ │ +
    376 void spliceAfter(AtomContainer& atom_container);
    │ │ │ +
    377
    │ │ │ +
    378 void splice(AtomContainer& atom_container);
    │ │ │ +
    379
    │ │ │ +
    380 bool remove(AtomContainer& atom_container);
    │ │ │ +
    381
    │ │ │ +
    382 BALL_KERNEL_DEFINE_ITERATOR_CREATORS(AtomContainer)
    │ │ │ +
    383 BALL_DECLARE_STD_ITERATOR_WRAPPER(Chain, AtomContainer, atomContainers)
    │ │ │ +
    384 };
    │ │ │ +
    │ │ │ +
    385} // namespace BALL
    │ │ │ +
    386
    │ │ │ +
    387#endif // BALL_KERNEL_CHAIN_H
    │ │ │ +
    BALL_DECLARE_STD_ITERATOR_WRAPPER
    #define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
    Definition stdIteratorWrapper.h:30
    │ │ │ + │ │ │ +
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS
    #define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
    Definition iterator.h:25
    │ │ │ + │ │ │ +
    BALL_CREATE_DEEP
    #define BALL_CREATE_DEEP(name)
    Definition create.h:26
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Chain::insert
    void insert(SecondaryStructure &secondary_structure)
    │ │ │ +
    BALL::Chain::remove
    bool remove(SecondaryStructure &secondary_structure)
    │ │ │ +
    BALL::Chain::insertAfter
    void insertAfter(SecondaryStructure &secondary_structure, Composite &after)
    │ │ │ +
    BALL::Chain::insertBefore
    void insertBefore(SecondaryStructure &secondary_structure, Composite &before)
    │ │ │ +
    BALL::Chain::set
    void set(const Chain &chain, bool deep=true)
    │ │ │ +
    BALL::Chain::isChain
    virtual bool isChain() const
    Definition chain.h:313
    │ │ │ + │ │ │ +
    BALL::Chain::Chain
    Chain(const Chain &chain, bool deep=true)
    Copy constructor.
    │ │ │ +
    BALL::Chain::spliceAfter
    void spliceAfter(Chain &chain)
    │ │ │ +
    BALL::Chain::countPDBAtoms
    Size countPDBAtoms() const
    │ │ │ +
    BALL::Chain::getCTerminal
    Residue * getCTerminal()
    │ │ │ +
    BALL::Chain::getPDBAtom
    PDBAtom * getPDBAtom(Position position)
    │ │ │ +
    BALL::Chain::splice
    void splice(Chain &chain)
    │ │ │ +
    BALL::Chain::persistentRead
    void persistentRead(PersistenceManager &pm)
    │ │ │ +
    BALL::Chain::append
    void append(SecondaryStructure &secondary_structure)
    │ │ │ +
    BALL::Chain::insertBefore
    void insertBefore(Residue &residue, Composite &before)
    │ │ │ +
    BALL::Chain::getProtein
    const Protein * getProtein() const
    │ │ │ +
    BALL::Chain::append
    void append(Residue &residue)
    │ │ │ +
    BALL::Chain::remove
    bool remove(Residue &residue)
    │ │ │ +
    BALL::Chain::insert
    void insert(Residue &residue)
    │ │ │ +
    BALL::Chain::dump
    virtual void dump(std::ostream &s=std::cout, Size depth=0) const
    │ │ │ +
    BALL::Chain::getSecondaryStructure
    SecondaryStructure * getSecondaryStructure(Position position)
    │ │ │ +
    BALL::Chain::countResidues
    Size countResidues() const
    │ │ │ +
    BALL::Chain::~Chain
    virtual ~Chain()
    Destructor.
    │ │ │ +
    BALL::Chain::prepend
    void prepend(Residue &residue)
    │ │ │ +
    BALL::Chain::swap
    void swap(Chain &chain)
    │ │ │ +
    BALL::Chain::spliceBefore
    void spliceBefore(Chain &chain)
    │ │ │ +
    BALL::Chain::getNTerminal
    Residue * getNTerminal()
    │ │ │ +
    BALL::Chain::get
    void get(Chain &chain, bool deep=true) const
    │ │ │ +
    BALL::Chain::persistentWrite
    void persistentWrite(PersistenceManager &pm, const char *name=0) const
    │ │ │ +
    BALL::Chain::getSecondaryStructure
    const SecondaryStructure * getSecondaryStructure(Position position) const
    │ │ │ +
    BALL::Chain::getPDBAtom
    const PDBAtom * getPDBAtom(Position position) const
    │ │ │ +
    BALL::Chain::insertAfter
    void insertAfter(Residue &residue, Composite &after)
    │ │ │ +
    BALL::Chain::prepend
    void prepend(SecondaryStructure &secondary_structure)
    │ │ │ +
    BALL::Chain::getResidue
    const Residue * getResidue(Position position) const
    │ │ │ +
    BALL::Chain::getCTerminal
    const Residue * getCTerminal() const
    │ │ │ +
    BALL::Chain::Chain
    Chain(const String &name)
    Detailled constructor.
    │ │ │ +
    BALL::Chain::getNTerminal
    const Residue * getNTerminal() const
    │ │ │ +
    BALL::Chain::Chain
    Chain()
    Default constrcutor.
    │ │ │ +
    BALL::Chain::getProtein
    Protein * getProtein()
    │ │ │ +
    BALL::Chain::countSecondaryStructures
    Size countSecondaryStructures() const
    │ │ │ +
    BALL::Chain::getResidue
    Residue * getResidue(Position position)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
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    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,83 +1,336 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ -NMRDescriptors.h │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ +chain.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1#ifndef BALL_QSAR_NMRDESCRIPTORS_H │ │ │ │ -2#define BALL_QSAR_NMRDESCRIPTORS_H │ │ │ │ -3 │ │ │ │ -4#ifndef BALL_COMMON_H │ │ │ │ -5# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -6#endif │ │ │ │ +1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ +2// vi: set ts=2: │ │ │ │ +3// │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_KERNEL_CHAIN_H │ │ │ │ +6#define BALL_KERNEL_CHAIN_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_DATATYPE_H │ │ │ │ -9# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ +8#ifndef BALL_KERNEL_RESIDUE_H │ │ │ │ +9# include <_B_A_L_L_/_K_E_R_N_E_L_/_r_e_s_i_d_u_e_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_KERNEL_RESIDUE_H │ │ │ │ -13# include <_B_A_L_L_/_K_E_R_N_E_L_/_r_e_s_i_d_u_e_._h> │ │ │ │ +12#ifndef BALL_KERNEL_SECONDARYSTRUCTUREITERATOR_H │ │ │ │ +13# include <_B_A_L_L_/_K_E_R_N_E_L_/_s_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_I_t_e_r_a_t_o_r_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#ifndef BALL_KERNEL_PROTEIN_H │ │ │ │ -17# include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_o_t_e_i_n_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20#ifndef BALL_KERNEL_ATOMCONTAINER_H │ │ │ │ -21# include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ -22#endif │ │ │ │ -23 │ │ │ │ -24namespace _B_A_L_L │ │ │ │ -25{ │ │ │ │ -26 │ │ │ │ -_3_4 _B_A_L_L___E_X_P_O_R_T void _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s(const _P_r_o_t_e_i_n& protein, │ │ │ │ -_H_a_s_h_M_a_p_<_c_o_n_s_t_ _R_e_s_i_d_u_e_*_,_ _f_l_o_a_t_>& residue_angles); │ │ │ │ -35 │ │ │ │ -_4_3 _B_A_L_L___E_X_P_O_R_T void _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s( const _C_h_a_i_n& fragment, │ │ │ │ -44 _H_a_s_h_M_a_p_<_c_o_n_s_t_ _R_e_s_i_d_u_e_*_,_f_l_o_a_t_>& residue_angles); │ │ │ │ -45 │ │ │ │ -_4_9 _B_A_L_L___E_X_P_O_R_T float _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s(const _R_e_s_i_d_u_e& residue); │ │ │ │ -50 │ │ │ │ -51 │ │ │ │ -_5_9 _B_A_L_L___E_X_P_O_R_T void _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s(const _P_r_o_t_e_i_n& protein, │ │ │ │ -_H_a_s_h_M_a_p_<_c_o_n_s_t_ _R_e_s_i_d_u_e_*_,_ _f_l_o_a_t_>& residue_angles); │ │ │ │ -60 │ │ │ │ -_6_8 _B_A_L_L___E_X_P_O_R_T void _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s( const _C_h_a_i_n& fragment, │ │ │ │ -69 _H_a_s_h_M_a_p_<_c_o_n_s_t_ _R_e_s_i_d_u_e_*_,_f_l_o_a_t_>& residue_angles); │ │ │ │ -70 │ │ │ │ -71 │ │ │ │ -_7_5 _B_A_L_L___E_X_P_O_R_T float _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s(const _R_e_s_i_d_u_e& residue); │ │ │ │ -76 │ │ │ │ -77} │ │ │ │ -78 │ │ │ │ -79#endif │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ +16 │ │ │ │ +_1_7#define BALL_CHAIN_DEFAULT_NAME ' ' │ │ │ │ +18 │ │ │ │ +19namespace _B_A_L_L │ │ │ │ +20{ │ │ │ │ +21 class Protein; │ │ │ │ +22 │ │ │ │ +_3_0 class _B_A_L_L___E_X_P_O_R_T _C_h_a_i_n │ │ │ │ +31 : public _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ +32 { │ │ │ │ +33 public: │ │ │ │ +34 │ │ │ │ +35 _B_A_L_L___C_R_E_A_T_E___D_E_E_P(_C_h_a_i_n) │ │ │ │ +36 │ │ │ │ +37 │ │ │ │ +40 │ │ │ │ +41 │ │ │ │ +_4_3 enum _P_r_o_p_e_r_t_y │ │ │ │ +44 { │ │ │ │ +45 NUMBER_OF_PROPERTIES = AtomContainer::NUMBER_OF_PROPERTIES │ │ │ │ +_4_6 }; │ │ │ │ +47 │ │ │ │ +49 │ │ │ │ +52 │ │ │ │ +_5_4 _C_h_a_i_n(); │ │ │ │ +55 │ │ │ │ +_5_7 _C_h_a_i_n(const _C_h_a_i_n& chain, bool deep = true); │ │ │ │ +58 │ │ │ │ +_6_0 _C_h_a_i_n(const _S_t_r_i_n_g& name); │ │ │ │ +61 │ │ │ │ +_6_3 virtual _~_C_h_a_i_n(); │ │ │ │ +64 │ │ │ │ +66 │ │ │ │ +69 │ │ │ │ +_7_3 void _p_e_r_s_i_s_t_e_n_t_W_r_i_t_e(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm, const char* name = 0) const; │ │ │ │ +74 │ │ │ │ +_7_8 void _p_e_r_s_i_s_t_e_n_t_R_e_a_d(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm); │ │ │ │ +79 │ │ │ │ +81 │ │ │ │ +84 │ │ │ │ +_9_0 void _s_e_t(const _C_h_a_i_n& chain, bool deep = true); │ │ │ │ +91 │ │ │ │ +_9_8 _C_h_a_i_n& operator = (const _C_h_a_i_n& chain); │ │ │ │ +99 │ │ │ │ +_1_0_5 void _g_e_t(_C_h_a_i_n& chain, bool deep = true) const; │ │ │ │ +106 │ │ │ │ +_1_1_0 void _s_w_a_p(_C_h_a_i_n& chain); │ │ │ │ +111 │ │ │ │ +113 │ │ │ │ +_1_1_8 bool operator == (const _C_h_a_i_n& chain) const; │ │ │ │ +119 │ │ │ │ +_1_2_3 bool operator != (const _C_h_a_i_n& chain) const; │ │ │ │ +124 │ │ │ │ +125 │ │ │ │ +129 │ │ │ │ +_1_3_4 _P_r_o_t_e_i_n* _g_e_t_P_r_o_t_e_i_n(); │ │ │ │ +135 │ │ │ │ +_1_4_0 const _P_r_o_t_e_i_n* _g_e_t_P_r_o_t_e_i_n() const; │ │ │ │ +141 │ │ │ │ +_1_4_8 _S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e* _g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e(_P_o_s_i_t_i_o_n position); │ │ │ │ +149 │ │ │ │ +_1_5_6 const _S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e* _g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e(_P_o_s_i_t_i_o_n position) const; │ │ │ │ +157 │ │ │ │ +_1_6_3 _R_e_s_i_d_u_e* _g_e_t_R_e_s_i_d_u_e(_P_o_s_i_t_i_o_n position); │ │ │ │ +164 │ │ │ │ +_1_7_0 const _R_e_s_i_d_u_e* _g_e_t_R_e_s_i_d_u_e(_P_o_s_i_t_i_o_n position) const; │ │ │ │ +171 │ │ │ │ +_1_7_7 _R_e_s_i_d_u_e* _g_e_t_N_T_e_r_m_i_n_a_l(); │ │ │ │ +178 │ │ │ │ +_1_8_4 const _R_e_s_i_d_u_e* _g_e_t_N_T_e_r_m_i_n_a_l() const; │ │ │ │ +185 │ │ │ │ +_1_9_1 _R_e_s_i_d_u_e* _g_e_t_C_T_e_r_m_i_n_a_l(); │ │ │ │ +192 │ │ │ │ +_1_9_8 const _R_e_s_i_d_u_e* _g_e_t_C_T_e_r_m_i_n_a_l() const; │ │ │ │ +199 │ │ │ │ +_2_0_5 _P_D_B_A_t_o_m* _g_e_t_P_D_B_A_t_o_m(_P_o_s_i_t_i_o_n position); │ │ │ │ +206 │ │ │ │ +_2_1_2 const _P_D_B_A_t_o_m* _g_e_t_P_D_B_A_t_o_m(_P_o_s_i_t_i_o_n position) const; │ │ │ │ +213 │ │ │ │ +_2_1_7 _S_i_z_e _c_o_u_n_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_s() const; │ │ │ │ +218 │ │ │ │ +_2_2_2 _S_i_z_e _c_o_u_n_t_R_e_s_i_d_u_e_s() const; │ │ │ │ +223 │ │ │ │ +_2_2_7 _S_i_z_e _c_o_u_n_t_P_D_B_A_t_o_m_s() const; │ │ │ │ +228 │ │ │ │ +_2_3_2 void _p_r_e_p_e_n_d(_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e& secondary_structure); │ │ │ │ +233 │ │ │ │ +_2_3_7 void _a_p_p_e_n_d(_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e& secondary_structure); │ │ │ │ +238 │ │ │ │ +_2_4_2 void _i_n_s_e_r_t(_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e& secondary_structure); │ │ │ │ +243 │ │ │ │ +_2_4_8 void _i_n_s_e_r_t_B_e_f_o_r_e(_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e& secondary_structure, _C_o_m_p_o_s_i_t_e& │ │ │ │ +before); │ │ │ │ +249 │ │ │ │ +_2_5_4 void _i_n_s_e_r_t_A_f_t_e_r(_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e& secondary_structure, _C_o_m_p_o_s_i_t_e& │ │ │ │ +after); │ │ │ │ +255 │ │ │ │ +_2_5_9 bool _r_e_m_o_v_e(_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e& secondary_structure); │ │ │ │ +260 │ │ │ │ +_2_6_4 void _p_r_e_p_e_n_d(_R_e_s_i_d_u_e& residue); │ │ │ │ +265 │ │ │ │ +_2_6_9 void _a_p_p_e_n_d(_R_e_s_i_d_u_e& residue); │ │ │ │ +270 │ │ │ │ +_2_7_4 void _i_n_s_e_r_t(_R_e_s_i_d_u_e& residue); │ │ │ │ +275 │ │ │ │ +_2_8_0 void _i_n_s_e_r_t_B_e_f_o_r_e(_R_e_s_i_d_u_e& residue, _C_o_m_p_o_s_i_t_e& before); │ │ │ │ +281 │ │ │ │ +_2_8_6 void _i_n_s_e_r_t_A_f_t_e_r(_R_e_s_i_d_u_e& residue, _C_o_m_p_o_s_i_t_e& after); │ │ │ │ +287 │ │ │ │ +_2_9_1 bool _r_e_m_o_v_e(_R_e_s_i_d_u_e& residue); │ │ │ │ +292 │ │ │ │ +_2_9_6 void _s_p_l_i_c_e_B_e_f_o_r_e(_C_h_a_i_n& chain); │ │ │ │ +297 │ │ │ │ +_3_0_1 void _s_p_l_i_c_e_A_f_t_e_r(_C_h_a_i_n &chain); │ │ │ │ +302 │ │ │ │ +_3_0_6 void _s_p_l_i_c_e(_C_h_a_i_n &chain); │ │ │ │ +307 │ │ │ │ +309 │ │ │ │ +_3_1_3 virtual bool _i_s_C_h_a_i_n() const { return true; } │ │ │ │ +315 │ │ │ │ +319 │ │ │ │ +_3_2_6 virtual void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const │ │ │ │ +327; │ │ │ │ +328 │ │ │ │ +330 │ │ │ │ +331 // --- EXTERNAL ITERATORS │ │ │ │ +332 │ │ │ │ +333 _B_A_L_L___K_E_R_N_E_L___D_E_F_I_N_E___I_T_E_R_A_T_O_R___C_R_E_A_T_O_R_S(_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e) │ │ │ │ +334 _B_A_L_L___K_E_R_N_E_L___D_E_F_I_N_E___I_T_E_R_A_T_O_R___C_R_E_A_T_O_R_S(_R_e_s_i_d_u_e) │ │ │ │ +335 _B_A_L_L___K_E_R_N_E_L___D_E_F_I_N_E___I_T_E_R_A_T_O_R___C_R_E_A_T_O_R_S(_P_D_B_A_t_o_m) │ │ │ │ +336 │ │ │ │ +337 _B_A_L_L___D_E_C_L_A_R_E___S_T_D___I_T_E_R_A_T_O_R___W_R_A_P_P_E_R(_C_h_a_i_n, _S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e, │ │ │ │ +secondaryStructures) │ │ │ │ +338 _B_A_L_L___D_E_C_L_A_R_E___S_T_D___I_T_E_R_A_T_O_R___W_R_A_P_P_E_R(_C_h_a_i_n, _R_e_s_i_d_u_e , residues) │ │ │ │ +339 _B_A_L_L___D_E_C_L_A_R_E___S_T_D___I_T_E_R_A_T_O_R___W_R_A_P_P_E_R(_C_h_a_i_n, _P_D_B_A_t_o_m , pdbAtoms) │ │ │ │ +340 │ │ │ │ +341 protected: │ │ │ │ +342 │ │ │ │ +343 private: │ │ │ │ +344 _A_t_o_m_C_o_n_t_a_i_n_e_r* getAtomContainer(_P_o_s_i_t_i_o_n position); │ │ │ │ +345 │ │ │ │ +346 const _A_t_o_m_C_o_n_t_a_i_n_e_r* getAtomContainer(_P_o_s_i_t_i_o_n position) const; │ │ │ │ +347 │ │ │ │ +348 _A_t_o_m* getAtom(_P_o_s_i_t_i_o_n position); │ │ │ │ +349 │ │ │ │ +350 const _A_t_o_m* getAtom(_P_o_s_i_t_i_o_n position) const; │ │ │ │ +351 │ │ │ │ +352 void prepend(_A_t_o_m& atom); │ │ │ │ +353 │ │ │ │ +354 void append(_A_t_o_m& atom); │ │ │ │ +355 │ │ │ │ +356 void insert(_A_t_o_m& atom); │ │ │ │ +357 │ │ │ │ +358 void insertBefore(_A_t_o_m& atom, _C_o_m_p_o_s_i_t_e& before); │ │ │ │ +359 │ │ │ │ +360 void insertAfter(_A_t_o_m& atom, _C_o_m_p_o_s_i_t_e& after); │ │ │ │ +361 │ │ │ │ +362 bool remove(_A_t_o_m& atom); │ │ │ │ +363 │ │ │ │ +364 void prepend(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +365 │ │ │ │ +366 void append(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +367 │ │ │ │ +368 void insert(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +369 │ │ │ │ +370 void insertBefore(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container, _C_o_m_p_o_s_i_t_e& before); │ │ │ │ +371 │ │ │ │ +372 void insertAfter(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container, _C_o_m_p_o_s_i_t_e& after); │ │ │ │ +373 │ │ │ │ +374 void spliceBefore(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +375 │ │ │ │ +376 void spliceAfter(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +377 │ │ │ │ +378 void splice(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +379 │ │ │ │ +380 bool remove(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +381 │ │ │ │ +382 _B_A_L_L___K_E_R_N_E_L___D_E_F_I_N_E___I_T_E_R_A_T_O_R___C_R_E_A_T_O_R_S(_A_t_o_m_C_o_n_t_a_i_n_e_r) │ │ │ │ +383 _B_A_L_L___D_E_C_L_A_R_E___S_T_D___I_T_E_R_A_T_O_R___W_R_A_P_P_E_R(_C_h_a_i_n, _A_t_o_m_C_o_n_t_a_i_n_e_r, atomContainers) │ │ │ │ +384 }; │ │ │ │ +385} // namespace BALL │ │ │ │ +386 │ │ │ │ +387#endif // BALL_KERNEL_CHAIN_H │ │ │ │ +_B_A_L_L___D_E_C_L_A_R_E___S_T_D___I_T_E_R_A_T_O_R___W_R_A_P_P_E_R │ │ │ │ +#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name) │ │ │ │ +DDeeffiinniittiioonn _s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h_:_3_0 │ │ │ │ _r_e_s_i_d_u_e_._h │ │ │ │ -_p_r_o_t_e_i_n_._h │ │ │ │ -_a_t_o_m_C_o_n_t_a_i_n_e_r_._h │ │ │ │ -_h_a_s_h_M_a_p_._h │ │ │ │ +_B_A_L_L___K_E_R_N_E_L___D_E_F_I_N_E___I_T_E_R_A_T_O_R___C_R_E_A_T_O_R_S │ │ │ │ +#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type) │ │ │ │ +DDeeffiinniittiioonn _i_t_e_r_a_t_o_r_._h_:_2_5 │ │ │ │ +_s_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_I_t_e_r_a_t_o_r_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E___D_E_E_P │ │ │ │ +#define BALL_CREATE_DEEP(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_2_6 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s │ │ │ │ -BALL_EXPORT void calculateResidueChiAngles(const Protein &protein, HashMap< │ │ │ │ -const Residue *, float > &residue_angles) │ │ │ │ -_B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s │ │ │ │ -BALL_EXPORT void calculateResidueChi2Angles(const Protein &protein, HashMap< │ │ │ │ -const Residue *, float > &residue_angles) │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_M_a_p │ │ │ │ -HashMap class based on the STL map (containing serveral convenience functions) │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_M_a_p_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r │ │ │ │ +DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ _B_A_L_L_:_:_C_h_a_i_n │ │ │ │ DDeeffiinniittiioonn _c_h_a_i_n_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_i_n_s_e_r_t │ │ │ │ +void insert(SecondaryStructure &secondary_structure) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_r_e_m_o_v_e │ │ │ │ +bool remove(SecondaryStructure &secondary_structure) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_i_n_s_e_r_t_A_f_t_e_r │ │ │ │ +void insertAfter(SecondaryStructure &secondary_structure, Composite &after) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_i_n_s_e_r_t_B_e_f_o_r_e │ │ │ │ +void insertBefore(SecondaryStructure &secondary_structure, Composite &before) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_s_e_t │ │ │ │ +void set(const Chain &chain, bool deep=true) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_i_s_C_h_a_i_n │ │ │ │ +virtual bool isChain() const │ │ │ │ +DDeeffiinniittiioonn _c_h_a_i_n_._h_:_3_1_3 │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_P_r_o_p_e_r_t_y │ │ │ │ +Property │ │ │ │ +DDeeffiinniittiioonn _c_h_a_i_n_._h_:_4_4 │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_C_h_a_i_n │ │ │ │ +Chain(const Chain &chain, bool deep=true) │ │ │ │ +Copy constructor. │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_s_p_l_i_c_e_A_f_t_e_r │ │ │ │ +void spliceAfter(Chain &chain) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_c_o_u_n_t_P_D_B_A_t_o_m_s │ │ │ │ +Size countPDBAtoms() const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_C_T_e_r_m_i_n_a_l │ │ │ │ +Residue * getCTerminal() │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_P_D_B_A_t_o_m │ │ │ │ +PDBAtom * getPDBAtom(Position position) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_s_p_l_i_c_e │ │ │ │ +void splice(Chain &chain) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_p_e_r_s_i_s_t_e_n_t_R_e_a_d │ │ │ │ +void persistentRead(PersistenceManager &pm) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_a_p_p_e_n_d │ │ │ │ +void append(SecondaryStructure &secondary_structure) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_i_n_s_e_r_t_B_e_f_o_r_e │ │ │ │ +void insertBefore(Residue &residue, Composite &before) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_P_r_o_t_e_i_n │ │ │ │ +const Protein * getProtein() const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_a_p_p_e_n_d │ │ │ │ +void append(Residue &residue) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_r_e_m_o_v_e │ │ │ │ +bool remove(Residue &residue) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_i_n_s_e_r_t │ │ │ │ +void insert(Residue &residue) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_d_u_m_p │ │ │ │ +virtual void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e │ │ │ │ +SecondaryStructure * getSecondaryStructure(Position position) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_c_o_u_n_t_R_e_s_i_d_u_e_s │ │ │ │ +Size countResidues() const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_~_C_h_a_i_n │ │ │ │ +virtual ~Chain() │ │ │ │ +Destructor. │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_p_r_e_p_e_n_d │ │ │ │ +void prepend(Residue &residue) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_s_w_a_p │ │ │ │ +void swap(Chain &chain) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_s_p_l_i_c_e_B_e_f_o_r_e │ │ │ │ +void spliceBefore(Chain &chain) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_N_T_e_r_m_i_n_a_l │ │ │ │ +Residue * getNTerminal() │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t │ │ │ │ +void get(Chain &chain, bool deep=true) const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_p_e_r_s_i_s_t_e_n_t_W_r_i_t_e │ │ │ │ +void persistentWrite(PersistenceManager &pm, const char *name=0) const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e │ │ │ │ +const SecondaryStructure * getSecondaryStructure(Position position) const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_P_D_B_A_t_o_m │ │ │ │ +const PDBAtom * getPDBAtom(Position position) const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_i_n_s_e_r_t_A_f_t_e_r │ │ │ │ +void insertAfter(Residue &residue, Composite &after) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_p_r_e_p_e_n_d │ │ │ │ +void prepend(SecondaryStructure &secondary_structure) │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_R_e_s_i_d_u_e │ │ │ │ +const Residue * getResidue(Position position) const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_C_T_e_r_m_i_n_a_l │ │ │ │ +const Residue * getCTerminal() const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_C_h_a_i_n │ │ │ │ +Chain(const String &name) │ │ │ │ +Detailled constructor. │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_N_T_e_r_m_i_n_a_l │ │ │ │ +const Residue * getNTerminal() const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_C_h_a_i_n │ │ │ │ +Chain() │ │ │ │ +Default constrcutor. │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_P_r_o_t_e_i_n │ │ │ │ +Protein * getProtein() │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_c_o_u_n_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_s │ │ │ │ +Size countSecondaryStructures() const │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n_:_:_g_e_t_R_e_s_i_d_u_e │ │ │ │ +Residue * getResidue(Position position) │ │ │ │ +_B_A_L_L_:_:_P_D_B_A_t_o_m │ │ │ │ +DDeeffiinniittiioonn _P_D_B_A_t_o_m_._h_:_4_0 │ │ │ │ _B_A_L_L_:_:_P_r_o_t_e_i_n │ │ │ │ DDeeffiinniittiioonn _p_r_o_t_e_i_n_._h_:_3_0 │ │ │ │ _B_A_L_L_:_:_R_e_s_i_d_u_e │ │ │ │ DDeeffiinniittiioonn _r_e_s_i_d_u_e_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e │ │ │ │ +DDeeffiinniittiioonn _s_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_._h_:_3_1 │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d5c/a00668.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: smilesParser.h File Reference │ │ │ +BALL: HTMLPage.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,46 +65,41 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    smilesParser.h File Reference
    │ │ │ +
    HTMLPage.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/KERNEL/atom.h>
    │ │ │ -#include <BALL/KERNEL/bond.h>
    │ │ │ -#include <BALL/KERNEL/system.h>
    │ │ │ +
    #include <BALL/COMMON/global.h>
    │ │ │ +#include <QtCore/QHash>
    │ │ │ +#include <QtWebEngineWidgets/QWebEnginePage>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::SmilesParser
     
    class  BALL::SmilesParser::SPBond
     
    class  BALL::SmilesParser::SPAtom
     
    struct  BALL::SmilesParser::State
    class  BALL::VIEW::HTMLPage
     
    │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ + │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,28 +1,24 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ + * _V_I_E_W │ │ │ │ + * _W_I_D_G_E_T_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -smilesParser.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_b_o_n_d_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ +HTMLPage.h File Reference │ │ │ │ +#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ - class   _B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r │ │ │ │ -  │ │ │ │ - class   _B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_B_o_n_d │ │ │ │ -  │ │ │ │ - class   _B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_t_a_t_e │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_H_T_M_L_P_a_g_e │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │ +  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d5c/a00668_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: smilesParser.h Source File │ │ │ +BALL: HTMLPage.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,244 +70,70 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    smilesParser.h
    │ │ │ +
    HTMLPage.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ -
    2// vi: set ts=2:
    │ │ │ -
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_STRUCTURE_SMILES_PARSER_H
    │ │ │ -
    6#define BALL_STRUCTURE_SMILES_PARSER_H
    │ │ │ -
    7
    │ │ │ -
    8#ifndef BALL_COMMON_H
    │ │ │ -
    9# include <BALL/common.h>
    │ │ │ -
    10#endif
    │ │ │ -
    11
    │ │ │ -
    12#ifndef BALL_KERNEL_ATOM_H
    │ │ │ -
    13# include <BALL/KERNEL/atom.h>
    │ │ │ -
    14#endif
    │ │ │ -
    15
    │ │ │ -
    16#ifndef BALL_KERNEL_BOND_H
    │ │ │ -
    17# include <BALL/KERNEL/bond.h>
    │ │ │ -
    18#endif
    │ │ │ -
    19
    │ │ │ -
    20#ifndef BALL_KERNEL_SYSTEM_H
    │ │ │ -
    21# include <BALL/KERNEL/system.h>
    │ │ │ -
    22#endif
    │ │ │ -
    23
    │ │ │ -
    24namespace BALL
    │ │ │ -
    25{
    │ │ │ +Go to the documentation of this file.
    1#ifndef BALL_VIEW_WIDGETS_HTMLPAGE_H
    │ │ │ +
    2#define BALL_VIEW_WIDGETS_HTMLPAGE_H
    │ │ │ +
    3
    │ │ │ +
    4#include <BALL/COMMON/global.h>
    │ │ │ +
    5
    │ │ │ +
    6#include <QtCore/QHash>
    │ │ │ +
    7#include <QtWebEngineWidgets/QWebEnginePage>
    │ │ │ +
    8
    │ │ │ +
    9namespace BALL
    │ │ │ +
    10{
    │ │ │ +
    11 namespace VIEW
    │ │ │ +
    12 {
    │ │ │ +
    │ │ │ +
    13 class BALL_VIEW_EXPORT HTMLPage: public QWebEnginePage
    │ │ │ +
    14 {
    │ │ │ +
    15 Q_OBJECT
    │ │ │ +
    16
    │ │ │ +
    17 public:
    │ │ │ +
    18 HTMLPage(QObject* parent = 0, bool ignore_ssl_errors = false);
    │ │ │ +
    19 HTMLPage(QWebEngineProfile* profile, QObject* parent = 0, bool ignore_ssl_errors = false);
    │ │ │ +
    20 ~HTMLPage() override = default;
    │ │ │ +
    21
    │ │ │ +
    22 protected:
    │ │ │ +
    23 bool acceptNavigationRequest(const QUrl& url, NavigationType type, bool isMainFrame) override;
    │ │ │ +
    24 bool certificateError(const QWebEngineCertificateError& /* certificateError */) override;
    │ │ │ +
    25 void javaScriptConsoleMessage(JavaScriptConsoleMessageLevel level, const QString& message, int lineNumber, const QString& /* sourceID */) override;
    │ │ │
    26
    │ │ │ -
    │ │ │ -
    36 class BALL_EXPORT SmilesParser
    │ │ │ -
    37 {
    │ │ │ -
    38 public:
    │ │ │ -
    │ │ │ -
    39 enum ZEIsomerType
    │ │ │ -
    40 {
    │ │ │ -
    41 NONE,
    │ │ │ -
    42 Z,
    │ │ │ -
    43 E
    │ │ │ -
    44 };
    │ │ │ -
    │ │ │ -
    45
    │ │ │ -
    │ │ │ -
    46 enum ChiralClass
    │ │ │ -
    47 {
    │ │ │ -
    48 NONCHIRAL,
    │ │ │ -
    49 TH,
    │ │ │ -
    50 AL,
    │ │ │ -
    51 SP,
    │ │ │ -
    52 TB,
    │ │ │ -
    53 OH
    │ │ │ -
    54 };
    │ │ │ -
    │ │ │ -
    55
    │ │ │ -
    56 enum
    │ │ │ -
    57 {
    │ │ │ -
    58 MAX_CONNECTIONS = 100
    │ │ │ -
    59 };
    │ │ │ -
    60
    │ │ │ -
    61 typedef std::pair<ChiralClass, Position> ChiralDef;
    │ │ │ -
    62
    │ │ │ -
    63 class SPAtom;
    │ │ │ -
    │ │ │ -
    64 class BALL_EXPORT SPBond
    │ │ │ -
    65 : public Bond
    │ │ │ -
    66 {
    │ │ │ -
    67 public:
    │ │ │ -
    68 virtual ~SPBond() ;
    │ │ │ -
    69
    │ │ │ -
    70 SPBond(SPAtom* first, SPAtom* second, Index order = 1);
    │ │ │ -
    71
    │ │ │ -
    72 ZEIsomerType getZEType() const;
    │ │ │ -
    73 void setZEType(ZEIsomerType type);
    │ │ │ -
    74
    │ │ │ -
    75 protected:
    │ │ │ -
    76 ZEIsomerType ze_type_;
    │ │ │ -
    77 };
    │ │ │ -
    │ │ │ -
    78
    │ │ │ -
    │ │ │ -
    79 class BALL_EXPORT SPAtom
    │ │ │ -
    80 : public Atom
    │ │ │ -
    81 {
    │ │ │ -
    82 public:
    │ │ │ -
    83
    │ │ │ -
    84 SPAtom(const String& symbol, bool in_brackets);
    │ │ │ -
    85 virtual ~SPAtom() ;
    │ │ │ -
    86
    │ │ │ -
    87 Size getDefaultValence() const;
    │ │ │ -
    88 Size countRealValences() const;
    │ │ │ -
    89
    │ │ │ -
    90 Size getIsotope() const { return isotope_; }
    │ │ │ -
    91 void setIsotope(Size isotope) { isotope_ = isotope; };
    │ │ │ -
    92
    │ │ │ -
    93 Index getFormalCharge() const { return formal_charge_; }
    │ │ │ -
    94 void setFormalCharge(Index charge) { formal_charge_ = charge; }
    │ │ │ -
    95
    │ │ │ -
    96 const ChiralDef& getChirality() const { return chirality_; }
    │ │ │ -
    97 void setChirality(const ChiralDef& chirality) { chirality_ = chirality; }
    │ │ │ -
    98
    │ │ │ -
    99 bool isAromatic() const { return is_aromatic_; }
    │ │ │ -
    100 void setAromatic(bool is_aromatic) { is_aromatic_ = is_aromatic; };
    │ │ │ -
    101 bool isInBrackets() const { return in_brackets_; }
    │ │ │ -
    102 void setInBrackets(bool in_brackets) { in_brackets_ = in_brackets; };
    │ │ │ -
    103
    │ │ │ -
    104 protected:
    │ │ │ -
    105 Size isotope_;
    │ │ │ -
    106 Index formal_charge_;
    │ │ │ -
    107 ChiralDef chirality_;
    │ │ │ -
    108 bool is_aromatic_;
    │ │ │ -
    109 bool in_brackets_;
    │ │ │ -
    110 };
    │ │ │ -
    │ │ │ -
    111
    │ │ │ -
    112 typedef std::list<Position> ConnectionList;
    │ │ │ -
    113
    │ │ │ -
    117
    │ │ │ -
    119 SmilesParser();
    │ │ │ -
    120
    │ │ │ -
    122 SmilesParser(const SmilesParser& parser);
    │ │ │ -
    123
    │ │ │ -
    125 virtual ~SmilesParser();
    │ │ │ -
    127
    │ │ │ -
    134 void parse(const String& s);
    │ │ │ -
    135
    │ │ │ -
    138 const System& getSystem() const;
    │ │ │ -
    140
    │ │ │ -
    145 SPAtom* createAtom(const String& symbol, bool in_bracket = false);
    │ │ │ -
    146
    │ │ │ -
    148 void createBonds(SPAtom* atom, const ConnectionList* list);
    │ │ │ -
    149
    │ │ │ -
    151 void createBond(SPAtom* left, SPAtom* right, Index order);
    │ │ │ -
    152
    │ │ │ -
    154 void addMissingHydrogens();
    │ │ │ -
    156
    │ │ │ -
    157
    │ │ │ -
    │ │ │ -
    158 struct State
    │ │ │ -
    159 {
    │ │ │ -
    160 Size char_count;
    │ │ │ -
    161 SmilesParser* current_parser;
    │ │ │ -
    162 const char* buffer;
    │ │ │ -
    163 };
    │ │ │ -
    │ │ │ -
    164
    │ │ │ -
    165 static State state;
    │ │ │ -
    166
    │ │ │ -
    167 protected:
    │ │ │ -
    168 System system_;
    │ │ │ -
    169 std::vector<SPAtom*> connections_;
    │ │ │ -
    170 std::vector<SPAtom*> all_atoms_;
    │ │ │ -
    171 static SmilesParser* current_parser_;
    │ │ │ -
    172 };
    │ │ │ -
    │ │ │ -
    173
    │ │ │ -
    174} // namespace BALL
    │ │ │ -
    175
    │ │ │ -
    176#endif // BALL_STRUCTURE_SMILES_PARSER_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::SmilesParser::SmilesParser
    SmilesParser(const SmilesParser &parser)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::SmilesParser::getSystem
    const System & getSystem() const
    │ │ │ - │ │ │ -
    BALL::SmilesParser::createBond
    void createBond(SPAtom *left, SPAtom *right, Index order)
    │ │ │ - │ │ │ -
    BALL::SmilesParser::parse
    void parse(const String &s)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::SmilesParser::ChiralDef
    std::pair< ChiralClass, Position > ChiralDef
    Definition smilesParser.h:61
    │ │ │ -
    BALL::SmilesParser::createBonds
    void createBonds(SPAtom *atom, const ConnectionList *list)
    │ │ │ -
    BALL::SmilesParser::all_atoms_
    std::vector< SPAtom * > all_atoms_
    Definition smilesParser.h:170
    │ │ │ -
    BALL::SmilesParser::createAtom
    SPAtom * createAtom(const String &symbol, bool in_bracket=false)
    │ │ │ -
    BALL::SmilesParser::ConnectionList
    std::list< Position > ConnectionList
    Definition smilesParser.h:112
    │ │ │ -
    BALL::SmilesParser::~SmilesParser
    virtual ~SmilesParser()
    │ │ │ -
    BALL::SmilesParser::connections_
    std::vector< SPAtom * > connections_
    Definition smilesParser.h:169
    │ │ │ -
    BALL::SmilesParser::addMissingHydrogens
    void addMissingHydrogens()
    │ │ │ -
    BALL::SmilesParser::current_parser_
    static SmilesParser * current_parser_
    Definition smilesParser.h:171
    │ │ │ -
    BALL::SmilesParser::state
    static State state
    Definition smilesParser.h:165
    │ │ │ - │ │ │ -
    BALL::SmilesParser::SPBond::SPBond
    SPBond(SPAtom *first, SPAtom *second, Index order=1)
    │ │ │ -
    BALL::SmilesParser::SPBond::getZEType
    ZEIsomerType getZEType() const
    │ │ │ -
    BALL::SmilesParser::SPBond::setZEType
    void setZEType(ZEIsomerType type)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::SmilesParser::SPAtom::setInBrackets
    void setInBrackets(bool in_brackets)
    Definition smilesParser.h:102
    │ │ │ -
    BALL::SmilesParser::SPAtom::setIsotope
    void setIsotope(Size isotope)
    Definition smilesParser.h:91
    │ │ │ -
    BALL::SmilesParser::SPAtom::SPAtom
    SPAtom(const String &symbol, bool in_brackets)
    │ │ │ - │ │ │ -
    BALL::SmilesParser::SPAtom::getChirality
    const ChiralDef & getChirality() const
    Definition smilesParser.h:96
    │ │ │ -
    BALL::SmilesParser::SPAtom::setAromatic
    void setAromatic(bool is_aromatic)
    Definition smilesParser.h:100
    │ │ │ - │ │ │ - │ │ │ -
    BALL::SmilesParser::SPAtom::getDefaultValence
    Size getDefaultValence() const
    │ │ │ -
    BALL::SmilesParser::SPAtom::countRealValences
    Size countRealValences() const
    │ │ │ - │ │ │ -
    BALL::SmilesParser::SPAtom::setChirality
    void setChirality(const ChiralDef &chirality)
    Definition smilesParser.h:97
    │ │ │ -
    BALL::SmilesParser::SPAtom::setFormalCharge
    void setFormalCharge(Index charge)
    Definition smilesParser.h:94
    │ │ │ - │ │ │ - │ │ │ -
    BALL::SmilesParser::SPAtom::getFormalCharge
    Index getFormalCharge() const
    Definition smilesParser.h:93
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::SmilesParser::State::current_parser
    SmilesParser * current_parser
    Definition smilesParser.h:161
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ - │ │ │ +
    27 virtual void executeLink(const QUrl& url);
    │ │ │ +
    28
    │ │ │ +
    29 private:
    │ │ │ +
    30 bool ignore_ssl_errors_;
    │ │ │ +
    31 };
    │ │ │ +
    │ │ │ +
    32 }
    │ │ │ +
    33}
    │ │ │ +
    34#endif // BALL_VIEW_WIDGETS_HTMLPAGE_H
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::HTMLPage::~HTMLPage
    ~HTMLPage() override=default
    │ │ │ +
    BALL::VIEW::HTMLPage::javaScriptConsoleMessage
    void javaScriptConsoleMessage(JavaScriptConsoleMessageLevel level, const QString &message, int lineNumber, const QString &) override
    │ │ │ +
    BALL::VIEW::HTMLPage::certificateError
    bool certificateError(const QWebEngineCertificateError &) override
    │ │ │ +
    BALL::VIEW::HTMLPage::acceptNavigationRequest
    bool acceptNavigationRequest(const QUrl &url, NavigationType type, bool isMainFrame) override
    │ │ │ +
    BALL::VIEW::HTMLPage::HTMLPage
    HTMLPage(QWebEngineProfile *profile, QObject *parent=0, bool ignore_ssl_errors=false)
    │ │ │ +
    BALL::VIEW::HTMLPage::HTMLPage
    HTMLPage(QObject *parent=0, bool ignore_ssl_errors=false)
    │ │ │ +
    BALL::VIEW::HTMLPage::executeLink
    virtual void executeLink(const QUrl &url)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,320 +1,77 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ -smilesParser.h │ │ │ │ + * _V_I_E_W │ │ │ │ + * _W_I_D_G_E_T_S │ │ │ │ +HTMLPage.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ -2// vi: set ts=2: │ │ │ │ -3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_STRUCTURE_SMILES_PARSER_H │ │ │ │ -6#define BALL_STRUCTURE_SMILES_PARSER_H │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_COMMON_H │ │ │ │ -9# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12#ifndef BALL_KERNEL_ATOM_H │ │ │ │ -13# include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16#ifndef BALL_KERNEL_BOND_H │ │ │ │ -17# include <_B_A_L_L_/_K_E_R_N_E_L_/_b_o_n_d_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20#ifndef BALL_KERNEL_SYSTEM_H │ │ │ │ -21# include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ -22#endif │ │ │ │ -23 │ │ │ │ -24namespace _B_A_L_L │ │ │ │ -25{ │ │ │ │ +1#ifndef BALL_VIEW_WIDGETS_HTMLPAGE_H │ │ │ │ +2#define BALL_VIEW_WIDGETS_HTMLPAGE_H │ │ │ │ +3 │ │ │ │ +4#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +5 │ │ │ │ +6#include │ │ │ │ +7#include │ │ │ │ +8 │ │ │ │ +9namespace _B_A_L_L │ │ │ │ +10{ │ │ │ │ +11 namespace VIEW │ │ │ │ +12 { │ │ │ │ +_1_3 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _H_T_M_L_P_a_g_e: public _Q_W_e_b_E_n_g_i_n_e_P_a_g_e │ │ │ │ +14 { │ │ │ │ +15 Q_OBJECT │ │ │ │ +16 │ │ │ │ +17 public: │ │ │ │ +_1_8 _H_T_M_L_P_a_g_e(_Q_O_b_j_e_c_t* parent = 0, bool ignore_ssl_errors = false); │ │ │ │ +_1_9 _H_T_M_L_P_a_g_e(QWebEngineProfile* profile, _Q_O_b_j_e_c_t* parent = 0, bool │ │ │ │ +ignore_ssl_errors = false); │ │ │ │ +_2_0 _~_H_T_M_L_P_a_g_e() override = default; │ │ │ │ +21 │ │ │ │ +22 protected: │ │ │ │ +_2_3 bool _a_c_c_e_p_t_N_a_v_i_g_a_t_i_o_n_R_e_q_u_e_s_t(const QUrl& url, NavigationType type, bool │ │ │ │ +isMainFrame) override; │ │ │ │ +_2_4 bool _c_e_r_t_i_f_i_c_a_t_e_E_r_r_o_r(const QWebEngineCertificateError& /* certificateError │ │ │ │ +*/) override; │ │ │ │ +_2_5 void _j_a_v_a_S_c_r_i_p_t_C_o_n_s_o_l_e_M_e_s_s_a_g_e(JavaScriptConsoleMessageLevel level, const │ │ │ │ +QString& message, int lineNumber, const QString& /* sourceID */) override; │ │ │ │ 26 │ │ │ │ -_3_6 class _B_A_L_L___E_X_P_O_R_T _S_m_i_l_e_s_P_a_r_s_e_r │ │ │ │ -37 { │ │ │ │ -38 public: │ │ │ │ -_3_9 enum _Z_E_I_s_o_m_e_r_T_y_p_e │ │ │ │ -40 { │ │ │ │ -_4_1 _N_O_N_E, │ │ │ │ -_4_2 _Z, │ │ │ │ -43 E │ │ │ │ -_4_4 }; │ │ │ │ -45 │ │ │ │ -_4_6 enum _C_h_i_r_a_l_C_l_a_s_s │ │ │ │ -47 { │ │ │ │ -_4_8 _N_O_N_C_H_I_R_A_L, │ │ │ │ -_4_9 _T_H, │ │ │ │ -_5_0 _A_L, │ │ │ │ -_5_1 _S_P, │ │ │ │ -_5_2 _T_B, │ │ │ │ -53 OH │ │ │ │ -_5_4 }; │ │ │ │ -55 │ │ │ │ -56 enum │ │ │ │ -57 { │ │ │ │ -58 MAX_CONNECTIONS = 100 │ │ │ │ -_5_9 }; │ │ │ │ -60 │ │ │ │ -_6_1 typedef std::pair _C_h_i_r_a_l_D_e_f; │ │ │ │ -62 │ │ │ │ -63 class _S_P_A_t_o_m; │ │ │ │ -_6_4 class _B_A_L_L___E_X_P_O_R_T _S_P_B_o_n_d │ │ │ │ -65 : public _B_o_n_d │ │ │ │ -66 { │ │ │ │ -67 public: │ │ │ │ -_6_8 virtual _~_S_P_B_o_n_d() ; │ │ │ │ -69 │ │ │ │ -_7_0 _S_P_B_o_n_d(_S_P_A_t_o_m* first, _S_P_A_t_o_m* second, _I_n_d_e_x order = 1); │ │ │ │ -71 │ │ │ │ -_7_2 _Z_E_I_s_o_m_e_r_T_y_p_e _g_e_t_Z_E_T_y_p_e() const; │ │ │ │ -_7_3 void _s_e_t_Z_E_T_y_p_e(_Z_E_I_s_o_m_e_r_T_y_p_e type); │ │ │ │ -74 │ │ │ │ -75 protected: │ │ │ │ -_7_6 _Z_E_I_s_o_m_e_r_T_y_p_e _z_e___t_y_p_e__; │ │ │ │ -77 }; │ │ │ │ -78 │ │ │ │ -_7_9 class _B_A_L_L___E_X_P_O_R_T _S_P_A_t_o_m │ │ │ │ -80 : public _A_t_o_m │ │ │ │ -81 { │ │ │ │ -82 public: │ │ │ │ -83 │ │ │ │ -_8_4 _S_P_A_t_o_m(const _S_t_r_i_n_g& symbol, bool in_brackets); │ │ │ │ -_8_5 virtual _~_S_P_A_t_o_m() ; │ │ │ │ -86 │ │ │ │ -_8_7 _S_i_z_e _g_e_t_D_e_f_a_u_l_t_V_a_l_e_n_c_e() const; │ │ │ │ -_8_8 _S_i_z_e _c_o_u_n_t_R_e_a_l_V_a_l_e_n_c_e_s() const; │ │ │ │ -89 │ │ │ │ -_9_0 _S_i_z_e _g_e_t_I_s_o_t_o_p_e() const { return isotope_; } │ │ │ │ -_9_1 void _s_e_t_I_s_o_t_o_p_e(_S_i_z_e isotope) { isotope_ = isotope; }; │ │ │ │ -92 │ │ │ │ -_9_3 _I_n_d_e_x _g_e_t_F_o_r_m_a_l_C_h_a_r_g_e() const { return formal_charge_; } │ │ │ │ -_9_4 void _s_e_t_F_o_r_m_a_l_C_h_a_r_g_e(_I_n_d_e_x charge) { formal_charge_ = charge; } │ │ │ │ -95 │ │ │ │ -_9_6 const _C_h_i_r_a_l_D_e_f& _g_e_t_C_h_i_r_a_l_i_t_y() const { return chirality_; } │ │ │ │ -_9_7 void _s_e_t_C_h_i_r_a_l_i_t_y(const _C_h_i_r_a_l_D_e_f& chirality) { chirality_ = chirality; } │ │ │ │ -98 │ │ │ │ -_9_9 bool _i_s_A_r_o_m_a_t_i_c() const { return is_aromatic_; } │ │ │ │ -_1_0_0 void _s_e_t_A_r_o_m_a_t_i_c(bool is_aromatic) { is_aromatic_ = is_aromatic; }; │ │ │ │ -_1_0_1 bool _i_s_I_n_B_r_a_c_k_e_t_s() const { return in_brackets_; } │ │ │ │ -_1_0_2 void _s_e_t_I_n_B_r_a_c_k_e_t_s(bool in_brackets) { in_brackets_ = in_brackets; }; │ │ │ │ -103 │ │ │ │ -104 protected: │ │ │ │ -_1_0_5 _S_i_z_e _i_s_o_t_o_p_e__; │ │ │ │ -_1_0_6 _I_n_d_e_x _f_o_r_m_a_l___c_h_a_r_g_e__; │ │ │ │ -_1_0_7 _C_h_i_r_a_l_D_e_f _c_h_i_r_a_l_i_t_y__; │ │ │ │ -_1_0_8 bool _i_s___a_r_o_m_a_t_i_c__; │ │ │ │ -_1_0_9 bool _i_n___b_r_a_c_k_e_t_s__; │ │ │ │ -110 }; │ │ │ │ -111 │ │ │ │ -_1_1_2 typedef std::list _C_o_n_n_e_c_t_i_o_n_L_i_s_t; │ │ │ │ -113 │ │ │ │ -117 │ │ │ │ -_1_1_9 _S_m_i_l_e_s_P_a_r_s_e_r(); │ │ │ │ -120 │ │ │ │ -_1_2_2 _S_m_i_l_e_s_P_a_r_s_e_r(const _S_m_i_l_e_s_P_a_r_s_e_r& parser); │ │ │ │ -123 │ │ │ │ -_1_2_5 virtual _~_S_m_i_l_e_s_P_a_r_s_e_r(); │ │ │ │ -127 │ │ │ │ -_1_3_4 void _p_a_r_s_e(const _S_t_r_i_n_g& s); │ │ │ │ -135 │ │ │ │ -_1_3_8 const _S_y_s_t_e_m& _g_e_t_S_y_s_t_e_m() const; │ │ │ │ -140 │ │ │ │ -_1_4_5 _S_P_A_t_o_m* _c_r_e_a_t_e_A_t_o_m(const _S_t_r_i_n_g& symbol, bool in_bracket = false); │ │ │ │ -146 │ │ │ │ -_1_4_8 void _c_r_e_a_t_e_B_o_n_d_s(_S_P_A_t_o_m* atom, const _C_o_n_n_e_c_t_i_o_n_L_i_s_t* list); │ │ │ │ -149 │ │ │ │ -_1_5_1 void _c_r_e_a_t_e_B_o_n_d(_S_P_A_t_o_m* left, _S_P_A_t_o_m* right, _I_n_d_e_x order); │ │ │ │ -152 │ │ │ │ -_1_5_4 void _a_d_d_M_i_s_s_i_n_g_H_y_d_r_o_g_e_n_s(); │ │ │ │ -156 │ │ │ │ -157 │ │ │ │ -_1_5_8 struct _S_t_a_t_e │ │ │ │ -159 { │ │ │ │ -_1_6_0 _S_i_z_e _c_h_a_r___c_o_u_n_t; │ │ │ │ -_1_6_1 _S_m_i_l_e_s_P_a_r_s_e_r* _c_u_r_r_e_n_t___p_a_r_s_e_r; │ │ │ │ -_1_6_2 const char* _b_u_f_f_e_r; │ │ │ │ -163 }; │ │ │ │ -164 │ │ │ │ -_1_6_5 static _S_t_a_t_e _s_t_a_t_e; │ │ │ │ -166 │ │ │ │ -167 protected: │ │ │ │ -_1_6_8 _S_y_s_t_e_m _s_y_s_t_e_m__; │ │ │ │ -_1_6_9 std::vector _c_o_n_n_e_c_t_i_o_n_s__; │ │ │ │ -_1_7_0 std::vector _a_l_l___a_t_o_m_s__; │ │ │ │ -_1_7_1 static _S_m_i_l_e_s_P_a_r_s_e_r* _c_u_r_r_e_n_t___p_a_r_s_e_r__; │ │ │ │ -172 }; │ │ │ │ -173 │ │ │ │ -174} // namespace BALL │ │ │ │ -175 │ │ │ │ -176#endif // BALL_STRUCTURE_SMILES_PARSER_H │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_b_o_n_d_._h │ │ │ │ -_a_t_o_m_._h │ │ │ │ +_2_7 virtual void _e_x_e_c_u_t_e_L_i_n_k(const QUrl& url); │ │ │ │ +28 │ │ │ │ +29 private: │ │ │ │ +30 bool ignore_ssl_errors_; │ │ │ │ +31 }; │ │ │ │ +32 } │ │ │ │ +33} │ │ │ │ +34#endif // BALL_VIEW_WIDGETS_HTMLPAGE_H │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_B_o_n_d │ │ │ │ -DDeeffiinniittiioonn _b_o_n_d_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ -DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_3_7 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_m_i_l_e_s_P_a_r_s_e_r │ │ │ │ -SmilesParser(const SmilesParser &parser) │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_Z_E_I_s_o_m_e_r_T_y_p_e │ │ │ │ -ZEIsomerType │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_N_O_N_E │ │ │ │ -@ NONE │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_4_1 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_Z │ │ │ │ -@ Z │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_4_2 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_g_e_t_S_y_s_t_e_m │ │ │ │ -const System & getSystem() const │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_m_i_l_e_s_P_a_r_s_e_r │ │ │ │ -SmilesParser() │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_c_r_e_a_t_e_B_o_n_d │ │ │ │ -void createBond(SPAtom *left, SPAtom *right, Index order) │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_s_y_s_t_e_m__ │ │ │ │ -System system_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_6_8 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_p_a_r_s_e │ │ │ │ -void parse(const String &s) │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_C_h_i_r_a_l_C_l_a_s_s │ │ │ │ -ChiralClass │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_4_7 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_T_H │ │ │ │ -@ TH │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_4_9 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_A_L │ │ │ │ -@ AL │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_5_0 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P │ │ │ │ -@ SP │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_5_1 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_N_O_N_C_H_I_R_A_L │ │ │ │ -@ NONCHIRAL │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_T_B │ │ │ │ -@ TB │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_5_2 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_C_h_i_r_a_l_D_e_f │ │ │ │ -std::pair< ChiralClass, Position > ChiralDef │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_6_1 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_c_r_e_a_t_e_B_o_n_d_s │ │ │ │ -void createBonds(SPAtom *atom, const ConnectionList *list) │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_a_l_l___a_t_o_m_s__ │ │ │ │ -std::vector< SPAtom * > all_atoms_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_7_0 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_c_r_e_a_t_e_A_t_o_m │ │ │ │ -SPAtom * createAtom(const String &symbol, bool in_bracket=false) │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_C_o_n_n_e_c_t_i_o_n_L_i_s_t │ │ │ │ -std::list< Position > ConnectionList │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_1_2 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_~_S_m_i_l_e_s_P_a_r_s_e_r │ │ │ │ -virtual ~SmilesParser() │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_c_o_n_n_e_c_t_i_o_n_s__ │ │ │ │ -std::vector< SPAtom * > connections_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_6_9 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_a_d_d_M_i_s_s_i_n_g_H_y_d_r_o_g_e_n_s │ │ │ │ -void addMissingHydrogens() │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_c_u_r_r_e_n_t___p_a_r_s_e_r__ │ │ │ │ -static SmilesParser * current_parser_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_7_1 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_s_t_a_t_e │ │ │ │ -static State state │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_6_5 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_B_o_n_d │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_6_6 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_B_o_n_d_:_:_S_P_B_o_n_d │ │ │ │ -SPBond(SPAtom *first, SPAtom *second, Index order=1) │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_B_o_n_d_:_:_g_e_t_Z_E_T_y_p_e │ │ │ │ -ZEIsomerType getZEType() const │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_B_o_n_d_:_:_s_e_t_Z_E_T_y_p_e │ │ │ │ -void setZEType(ZEIsomerType type) │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_B_o_n_d_:_:_~_S_P_B_o_n_d │ │ │ │ -virtual ~SPBond() │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_B_o_n_d_:_:_z_e___t_y_p_e__ │ │ │ │ -ZEIsomerType ze_type_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_7_6 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_8_1 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_i_s_o_t_o_p_e__ │ │ │ │ -Size isotope_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_0_5 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_i_s_I_n_B_r_a_c_k_e_t_s │ │ │ │ -bool isInBrackets() const │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_0_1 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_s_e_t_I_n_B_r_a_c_k_e_t_s │ │ │ │ -void setInBrackets(bool in_brackets) │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_0_2 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_s_e_t_I_s_o_t_o_p_e │ │ │ │ -void setIsotope(Size isotope) │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_9_1 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_S_P_A_t_o_m │ │ │ │ -SPAtom(const String &symbol, bool in_brackets) │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_c_h_i_r_a_l_i_t_y__ │ │ │ │ -ChiralDef chirality_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_0_7 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_g_e_t_C_h_i_r_a_l_i_t_y │ │ │ │ -const ChiralDef & getChirality() const │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_9_6 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_s_e_t_A_r_o_m_a_t_i_c │ │ │ │ -void setAromatic(bool is_aromatic) │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_0_0 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_~_S_P_A_t_o_m │ │ │ │ -virtual ~SPAtom() │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_i_n___b_r_a_c_k_e_t_s__ │ │ │ │ -bool in_brackets_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_0_9 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_g_e_t_D_e_f_a_u_l_t_V_a_l_e_n_c_e │ │ │ │ -Size getDefaultValence() const │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_c_o_u_n_t_R_e_a_l_V_a_l_e_n_c_e_s │ │ │ │ -Size countRealValences() const │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_g_e_t_I_s_o_t_o_p_e │ │ │ │ -Size getIsotope() const │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_s_e_t_C_h_i_r_a_l_i_t_y │ │ │ │ -void setChirality(const ChiralDef &chirality) │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_9_7 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_s_e_t_F_o_r_m_a_l_C_h_a_r_g_e │ │ │ │ -void setFormalCharge(Index charge) │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_9_4 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_i_s___a_r_o_m_a_t_i_c__ │ │ │ │ -bool is_aromatic_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_0_8 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_i_s_A_r_o_m_a_t_i_c │ │ │ │ -bool isAromatic() const │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_g_e_t_F_o_r_m_a_l_C_h_a_r_g_e │ │ │ │ -Index getFormalCharge() const │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_9_3 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_P_A_t_o_m_:_:_f_o_r_m_a_l___c_h_a_r_g_e__ │ │ │ │ -Index formal_charge_ │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_0_6 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_t_a_t_e │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_5_9 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_t_a_t_e_:_:_c_h_a_r___c_o_u_n_t │ │ │ │ -Size char_count │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_6_0 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_t_a_t_e_:_:_c_u_r_r_e_n_t___p_a_r_s_e_r │ │ │ │ -SmilesParser * current_parser │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_6_1 │ │ │ │ -_B_A_L_L_:_:_S_m_i_l_e_s_P_a_r_s_e_r_:_:_S_t_a_t_e_:_:_b_u_f_f_e_r │ │ │ │ -const char * buffer │ │ │ │ -DDeeffiinniittiioonn _s_m_i_l_e_s_P_a_r_s_e_r_._h_:_1_6_2 │ │ │ │ -_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ -_s_y_s_t_e_m_._h │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_H_T_M_L_P_a_g_e │ │ │ │ +DDeeffiinniittiioonn _H_T_M_L_P_a_g_e_._h_:_1_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_H_T_M_L_P_a_g_e_:_:_~_H_T_M_L_P_a_g_e │ │ │ │ +~HTMLPage() override=default │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_H_T_M_L_P_a_g_e_:_:_j_a_v_a_S_c_r_i_p_t_C_o_n_s_o_l_e_M_e_s_s_a_g_e │ │ │ │ +void javaScriptConsoleMessage(JavaScriptConsoleMessageLevel level, const │ │ │ │ +QString &message, int lineNumber, const QString &) override │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_H_T_M_L_P_a_g_e_:_:_c_e_r_t_i_f_i_c_a_t_e_E_r_r_o_r │ │ │ │ +bool certificateError(const QWebEngineCertificateError &) override │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_H_T_M_L_P_a_g_e_:_:_a_c_c_e_p_t_N_a_v_i_g_a_t_i_o_n_R_e_q_u_e_s_t │ │ │ │ +bool acceptNavigationRequest(const QUrl &url, NavigationType type, bool │ │ │ │ +isMainFrame) override │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_H_T_M_L_P_a_g_e_:_:_H_T_M_L_P_a_g_e │ │ │ │ +HTMLPage(QWebEngineProfile *profile, QObject *parent=0, bool │ │ │ │ +ignore_ssl_errors=false) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_H_T_M_L_P_a_g_e_:_:_H_T_M_L_P_a_g_e │ │ │ │ +HTMLPage(QObject *parent=0, bool ignore_ssl_errors=false) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_H_T_M_L_P_a_g_e_:_:_e_x_e_c_u_t_e_L_i_n_k │ │ │ │ +virtual void executeLink(const QUrl &url) │ │ │ │ +_Q_O_b_j_e_c_t │ │ │ │ +_Q_W_e_b_E_n_g_i_n_e_P_a_g_e │ │ │ │ +_g_l_o_b_a_l_._h │ │ │ │ +_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ +#define BALL_VIEW_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d5e/a05570.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::PyDatasetVector Class Reference
    Python » Python extensions
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/PYTHON/EXTENSIONS/pyDatasetVector.h>

    │ │ │ +

    #include <BALL/PYTHON/EXTENSIONS/pyDatasetVector.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::PyDatasetVector:
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ │ │ │ @@ -116,30 +116,30 @@ │ │ │ │ │ │ │ │ │ │ │ │
    virtual ~PyDatasetVector () throw ()
     Destructor.
     
    │ │ │

    Detailed Description

    │ │ │

    Equivalent for a STL::Vector of Dataset Pointers in Python

    │ │ │ │ │ │ -

    Definition at line 23 of file pyDatasetVector.h.

    │ │ │ +

    Definition at line 23 of file pyDatasetVector.h.

    │ │ │

    Member Typedef Documentation

    │ │ │ │ │ │

    ◆ ConstIterator

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef vector<BALL::VIEW::Dataset*>::const_iterator BALL::PyDatasetVector::ConstIterator
    │ │ │
    │ │ │

    Constant iterator type.

    │ │ │ │ │ │ -

    Definition at line 48 of file pyDatasetVector.h.

    │ │ │ +

    Definition at line 48 of file pyDatasetVector.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ Iterator

    │ │ │ │ │ │
    │ │ │ @@ -148,15 +148,15 @@ │ │ │ │ │ │ typedef vector<BALL::VIEW::Dataset*>::iterator BALL::PyDatasetVector::Iterator │ │ │ │ │ │ │ │ │
    │ │ │

    Iterator type.

    │ │ │ │ │ │ -

    Definition at line 44 of file pyDatasetVector.h.

    │ │ │ +

    Definition at line 44 of file pyDatasetVector.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ PointerType

    │ │ │ │ │ │
    │ │ │ @@ -165,15 +165,15 @@ │ │ │ │ │ │ typedef BALL::VIEW::Dataset** BALL::PyDatasetVector::PointerType │ │ │ │ │ │ │ │ │
    │ │ │

    Pointer type

    │ │ │ │ │ │ -

    Definition at line 40 of file pyDatasetVector.h.

    │ │ │ +

    Definition at line 40 of file pyDatasetVector.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ ValueType

    │ │ │ │ │ │
    │ │ │ @@ -182,15 +182,15 @@ │ │ │ │ │ │ typedef BALL::VIEW::Dataset* BALL::PyDatasetVector::ValueType │ │ │ │ │ │ │ │ │
    │ │ │

    Dataset* type

    │ │ │ │ │ │ -

    Definition at line 36 of file pyDatasetVector.h.

    │ │ │ +

    Definition at line 36 of file pyDatasetVector.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ PyDatasetVector() [1/3]

    │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d60/a03878.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::DCDFile Class Reference
    Molecular Modeling » File Formats » Molecular Dynamics Trajectory File Formats
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/FORMAT/DCDFile.h>

    │ │ │ +

    #include <BALL/FORMAT/DCDFile.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::DCDFile:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::TrajectoryFile │ │ │ @@ -377,15 +377,15 @@ │ │ │ Each such "record" begins with 4 bytes containing the integer value │ │ │ of the number of bytes in the following record. It ends with a │ │ │ record containing the same 4 bytes." │ │ │
    The header consists of several blocks. Each block starts and ends with the number of bytes enclosed between those numbers, i. e. a block consisting of 8 bytes starts with the number 8 followed by 8 bytes of data and ends with the number 8.
    │ │ │
    TODO: complete header description
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 37 of file DCDFile.h.

    │ │ │ +

    Definition at line 37 of file DCDFile.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ DCDFile() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -939,15 +939,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inlineprotected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 148 of file DCDFile.h.

    │ │ │ +

    Definition at line 148 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ writeHeader()

    │ │ │ │ │ │
    │ │ │ @@ -995,15 +995,15 @@ │ │ │ │ │ │ │ │ │ inlineprotected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 144 of file DCDFile.h.

    │ │ │ +

    Definition at line 144 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ writeVector_()

    │ │ │ │ │ │
    │ │ │ @@ -1046,15 +1046,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 204 of file DCDFile.h.

    │ │ │ +

    Definition at line 204 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ adapt_size_

    │ │ │ │ │ │
    │ │ │ @@ -1070,15 +1070,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 203 of file DCDFile.h.

    │ │ │ +

    Definition at line 203 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ charmm_extra_block_A_

    │ │ │ │ │ │
    │ │ │ @@ -1094,15 +1094,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 176 of file DCDFile.h.

    │ │ │ +

    Definition at line 176 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ charmm_extra_block_B_

    │ │ │ │ │ │
    │ │ │ @@ -1118,15 +1118,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 179 of file DCDFile.h.

    │ │ │ +

    Definition at line 179 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ CORD_

    │ │ │ │ │ │
    │ │ │ @@ -1142,15 +1142,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 182 of file DCDFile.h.

    │ │ │ +

    Definition at line 182 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ current_snapshot_

    │ │ │ │ │ │
    │ │ │ @@ -1166,15 +1166,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 201 of file DCDFile.h.

    │ │ │ +

    Definition at line 201 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ has_velocities_

    │ │ │ │ │ │
    │ │ │ @@ -1190,15 +1190,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 173 of file DCDFile.h.

    │ │ │ +

    Definition at line 173 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ number_of_comments_

    │ │ │ │ │ │
    │ │ │ @@ -1214,15 +1214,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 194 of file DCDFile.h.

    │ │ │ +

    Definition at line 194 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ step_number_of_starting_time_

    │ │ │ │ │ │
    │ │ │ @@ -1238,15 +1238,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 185 of file DCDFile.h.

    │ │ │ +

    Definition at line 185 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ steps_between_saves_

    │ │ │ │ │ │
    │ │ │ @@ -1262,15 +1262,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 188 of file DCDFile.h.

    │ │ │ +

    Definition at line 188 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ swap_bytes_

    │ │ │ │ │ │
    │ │ │ @@ -1286,15 +1286,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 170 of file DCDFile.h.

    │ │ │ +

    Definition at line 170 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ time_step_length_

    │ │ │ │ │ │
    │ │ │ @@ -1310,15 +1310,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 191 of file DCDFile.h.

    │ │ │ +

    Definition at line 191 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ verbosity_

    │ │ │ │ │ │
    │ │ │ @@ -1334,15 +1334,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 167 of file DCDFile.h.

    │ │ │ +

    Definition at line 167 of file DCDFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d61/a00302.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: stage.h File Reference │ │ │ +BALL: fakeDriver.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,44 +65,31 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    stage.h File Reference
    │ │ │ +
    fakeDriver.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/MATHS/vector3.h>
    │ │ │ -#include <BALL/MATHS/quaternion.h>
    │ │ │ -#include <BALL/MATHS/matrix44.h>
    │ │ │ -#include <BALL/MATHS/angle.h>
    │ │ │ -#include <BALL/VIEW/DATATYPE/colorRGBA.h>
    │ │ │ -#include <BALL/VIEW/KERNEL/representation.h>
    │ │ │ -#include <BALL/COMMON/exception.h>
    │ │ │ -#include <BALL/VIEW/RENDERING/camera.h>
    │ │ │ +
    #include <BALL/VIEW/INPUT/inputDeviceDriver.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::LightSource
     
    class  BALL::VIEW::Stage
     
    class  BALL::VIEW::Stage::Material
     
    class  BALL::VIEW::Stage::RaytracingMaterial
    class  BALL::VIEW::FakeDriver
     
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,34 +1,21 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ + * _I_N_P_U_T │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -stage.h File Reference │ │ │ │ -#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ -#include <_B_A_L_L_/_M_A_T_H_S_/_q_u_a_t_e_r_n_i_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_M_A_T_H_S_/_m_a_t_r_i_x_4_4_._h> │ │ │ │ -#include <_B_A_L_L_/_M_A_T_H_S_/_a_n_g_l_e_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_c_o_l_o_r_R_G_B_A_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_c_a_m_e_r_a_._h> │ │ │ │ +fakeDriver.h File Reference │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_I_N_P_U_T_/_i_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_M_a_t_e_r_i_a_l │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_R_a_y_t_r_a_c_i_n_g_M_a_t_e_r_i_a_l │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_F_a_k_e_D_r_i_v_e_r │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d61/a00302_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: stage.h Source File │ │ │ +BALL: fakeDriver.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,539 +70,58 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    stage.h
    │ │ │ +
    fakeDriver.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ -
    2// vi: set ts=2:
    │ │ │ -
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_VIEW_KERNEL_STAGE_H
    │ │ │ -
    6#define BALL_VIEW_KERNEL_STAGE_H
    │ │ │ -
    7
    │ │ │ -
    8#ifndef BALL_MATHS_VECTOR3_H
    │ │ │ -
    9# include <BALL/MATHS/vector3.h>
    │ │ │ -
    10#endif
    │ │ │ -
    11
    │ │ │ -
    12#ifndef BALL_MATHS_QUATERNION_H
    │ │ │ -
    13# include <BALL/MATHS/quaternion.h>
    │ │ │ -
    14#endif
    │ │ │ -
    15
    │ │ │ -
    16#ifndef BALL_MATHS_MATRIX44_H
    │ │ │ -
    17# include <BALL/MATHS/matrix44.h>
    │ │ │ -
    18#endif
    │ │ │ -
    19
    │ │ │ -
    20#ifndef BALL_MATHS_ANGLE_H
    │ │ │ -
    21# include <BALL/MATHS/angle.h>
    │ │ │ -
    22#endif
    │ │ │ -
    23
    │ │ │ -
    24#ifndef BALL_VIEW_DATATYPE_COLORRGBA_H
    │ │ │ -
    25# include <BALL/VIEW/DATATYPE/colorRGBA.h>
    │ │ │ -
    26#endif
    │ │ │ -
    27
    │ │ │ -
    28#ifndef BALL_VIEW_KERNEL_REPRESENTATION_H
    │ │ │ -
    29# include <BALL/VIEW/KERNEL/representation.h>
    │ │ │ -
    30#endif
    │ │ │ -
    31
    │ │ │ -
    32#ifndef BALL_COMMON_EXCEPTION_H
    │ │ │ -
    33# include <BALL/COMMON/exception.h>
    │ │ │ -
    34#endif
    │ │ │ -
    35
    │ │ │ -
    36#ifndef BALL_VIEW_RENDERING_CAMERA_H
    │ │ │ -
    37# include <BALL/VIEW/RENDERING/camera.h>
    │ │ │ -
    38#endif
    │ │ │ -
    39
    │ │ │ -
    40namespace BALL
    │ │ │ -
    41{
    │ │ │ -
    42 namespace VIEW
    │ │ │ -
    43 {
    │ │ │ -
    │ │ │ -
    53 class BALL_VIEW_EXPORT LightSource
    │ │ │ -
    54 {
    │ │ │ -
    55 public:
    │ │ │ -
    56
    │ │ │ -
    │ │ │ -
    58 enum Types
    │ │ │ -
    59 {
    │ │ │ -
    60
    │ │ │ -
    64 AMBIENT = 0,
    │ │ │ -
    65
    │ │ │ -
    70 POSITIONAL,
    │ │ │ -
    71
    │ │ │ -
    74 DIRECTIONAL
    │ │ │ -
    75 };
    │ │ │ -
    │ │ │ -
    76
    │ │ │ -
    80
    │ │ │ -
    83 LightSource();
    │ │ │ -
    84
    │ │ │ -
    87 LightSource(const LightSource& light_source);
    │ │ │ -
    88
    │ │ │ -
    91 virtual ~LightSource(){}
    │ │ │ -
    92
    │ │ │ -
    94
    │ │ │ -
    97
    │ │ │ -
    │ │ │ -
    99 const Vector3& getPosition() const
    │ │ │ -
    100 { return position_;}
    │ │ │ -
    │ │ │ -
    101
    │ │ │ -
    │ │ │ -
    103 void setPosition(const Vector3& position)
    │ │ │ -
    104 { position_ = position; }
    │ │ │ -
    │ │ │ -
    105
    │ │ │ -
    │ │ │ -
    107 const Vector3& getDirection() const
    │ │ │ -
    108 { return direction_;}
    │ │ │ -
    │ │ │ -
    109
    │ │ │ -
    │ │ │ -
    111 void setDirection(const Vector3& direction)
    │ │ │ -
    112 { direction_ = direction;}
    │ │ │ -
    │ │ │ -
    113
    │ │ │ -
    │ │ │ -
    115 const Vector3& getAttenuation() const
    │ │ │ -
    116 { return attenuation_;}
    │ │ │ -
    │ │ │ -
    117
    │ │ │ -
    │ │ │ -
    119 void setAttenuation(const Vector3& attenuation)
    │ │ │ -
    120 { attenuation_ = attenuation;}
    │ │ │ -
    │ │ │ -
    121
    │ │ │ -
    122
    │ │ │ -
    │ │ │ -
    124 const Angle& getAngle() const
    │ │ │ -
    125 { return angle_;}
    │ │ │ -
    │ │ │ -
    126
    │ │ │ -
    │ │ │ -
    128 void setAngle(const Angle& angle)
    │ │ │ -
    129 { angle_ = angle;}
    │ │ │ -
    │ │ │ -
    130
    │ │ │ -
    │ │ │ -
    134 float getIntensity() const
    │ │ │ -
    135 { return intensity_;}
    │ │ │ -
    │ │ │ -
    136
    │ │ │ -
    │ │ │ -
    140 void setIntensity(float intensity)
    │ │ │ -
    141 { intensity_ = intensity;}
    │ │ │ -
    │ │ │ -
    142
    │ │ │ -
    │ │ │ -
    146 const ColorRGBA& getColor() const
    │ │ │ -
    147 { return color_;}
    │ │ │ -
    │ │ │ -
    148
    │ │ │ -
    │ │ │ -
    152 void setColor(const ColorRGBA& color)
    │ │ │ -
    153 { color_ = color;}
    │ │ │ -
    │ │ │ -
    154
    │ │ │ -
    │ │ │ -
    158 Index getType() const
    │ │ │ -
    159 { return type_;}
    │ │ │ -
    │ │ │ -
    160
    │ │ │ -
    │ │ │ -
    164 void setType(Types type)
    │ │ │ -
    165 { type_ = type;}
    │ │ │ -
    │ │ │ -
    166
    │ │ │ -
    │ │ │ -
    168 void setRelativeToCamera(bool state)
    │ │ │ -
    169 { relative_ = state;}
    │ │ │ -
    │ │ │ -
    170
    │ │ │ -
    │ │ │ -
    172 bool isRelativeToCamera() const
    │ │ │ -
    173 { return relative_;}
    │ │ │ -
    │ │ │ -
    174
    │ │ │ -
    176 LightSource& operator = (const LightSource& light);
    │ │ │ -
    177
    │ │ │ -
    179 bool operator < (const LightSource& light) const;
    │ │ │ -
    180
    │ │ │ -
    182
    │ │ │ -
    185
    │ │ │ -
    187 bool operator == (const LightSource& light_source) const;
    │ │ │ -
    188
    │ │ │ -
    190
    │ │ │ -
    197 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ -
    198
    │ │ │ -
    199 protected:
    │ │ │ -
    200
    │ │ │ -
    201 //_ Position of the light source
    │ │ │ -
    202 Vector3 position_;
    │ │ │ -
    203
    │ │ │ -
    204 //_ Direction of the light cone
    │ │ │ -
    205 Vector3 direction_;
    │ │ │ -
    206
    │ │ │ -
    207 //_ Attenuation parameters of the light
    │ │ │ -
    208 Vector3 attenuation_;
    │ │ │ -
    209
    │ │ │ -
    210 //_
    │ │ │ -
    211 Vector3 r_position_;
    │ │ │ -
    212
    │ │ │ -
    213 //_
    │ │ │ -
    214 Vector3 r_direction_;
    │ │ │ -
    215
    │ │ │ -
    216 //_ Angle of the light cone
    │ │ │ -
    217 Angle angle_;
    │ │ │ -
    218
    │ │ │ -
    219 //_ Intensity of the light
    │ │ │ -
    220 float intensity_;
    │ │ │ -
    221
    │ │ │ -
    222 //_ Color of the light
    │ │ │ -
    223 ColorRGBA color_;
    │ │ │ -
    224
    │ │ │ -
    225 //_ Enumeration of types for further usage
    │ │ │ -
    226 Index type_;
    │ │ │ -
    227
    │ │ │ -
    228 //_ Relative to camera
    │ │ │ -
    229 bool relative_;
    │ │ │ -
    230 };
    │ │ │ -
    │ │ │ -
    231
    │ │ │ -
    232
    │ │ │ -
    │ │ │ -
    238 class BALL_VIEW_EXPORT Stage
    │ │ │ -
    239 {
    │ │ │ -
    240 public:
    │ │ │ -
    241
    │ │ │ -
    │ │ │ -
    244 class BALL_VIEW_EXPORT Material
    │ │ │ -
    245 : public PersistentObject
    │ │ │ -
    246 {
    │ │ │ -
    247 public:
    │ │ │ -
    248
    │ │ │ -
    249 BALL_CREATE(Material)
    │ │ │ -
    250
    │ │ │ -
    251 Material();
    │ │ │ -
    252
    │ │ │ -
    256
    │ │ │ -
    261 virtual void persistentWrite(PersistenceManager& pm, const char* name = 0) const;
    │ │ │ -
    262
    │ │ │ -
    267 virtual void persistentRead(PersistenceManager& pm);
    │ │ │ -
    268
    │ │ │ -
    270
    │ │ │ -
    271 ColorRGBA ambient_color;
    │ │ │ -
    272 float ambient_intensity;
    │ │ │ -
    273
    │ │ │ -
    274 ColorRGBA specular_color;
    │ │ │ -
    275 float specular_intensity;
    │ │ │ -
    276
    │ │ │ -
    277 ColorRGBA reflective_color;
    │ │ │ -
    278 float reflective_intensity;
    │ │ │ -
    279
    │ │ │ -
    280 float shininess;
    │ │ │ -
    281 float transparency;
    │ │ │ -
    282 };
    │ │ │ -
    │ │ │ -
    283
    │ │ │ -
    284 // needed for backwards compatibilty of project files
    │ │ │ -
    │ │ │ -
    285 class BALL_VIEW_EXPORT RaytracingMaterial : public Material
    │ │ │ -
    286 {
    │ │ │ -
    287 public:
    │ │ │ -
    288
    │ │ │ -
    289 BALL_CREATE(RaytracingMaterial)
    │ │ │ -
    290 };
    │ │ │ -
    │ │ │ -
    291
    │ │ │ -
    295
    │ │ │ -
    298 Stage();
    │ │ │ -
    299
    │ │ │ -
    301 Stage(const Stage& stage);
    │ │ │ -
    302
    │ │ │ -
    304 virtual ~Stage(){}
    │ │ │ -
    305
    │ │ │ -
    307 virtual void clear();
    │ │ │ -
    308
    │ │ │ -
    310
    │ │ │ -
    313
    │ │ │ -
    │ │ │ -
    315 virtual const std::list<LightSource>& getLightSources() const
    │ │ │ -
    316 { return light_sources_;}
    │ │ │ -
    │ │ │ -
    317
    │ │ │ -
    │ │ │ -
    319 virtual LightSource& getLightSource(Position i)
    │ │ │ -
    320 {
    │ │ │ -
    321 if (i >= light_sources_.size())
    │ │ │ -
    322 {
    │ │ │ -
    323 Exception::OutOfRange e(__FILE__, __LINE__);
    │ │ │ -
    324 throw(e);
    │ │ │ -
    325 }
    │ │ │ -
    326
    │ │ │ -
    327 std::list<LightSource>::iterator l_it;
    │ │ │ -
    328
    │ │ │ -
    329 Position current_light = 0;
    │ │ │ -
    330 for (l_it = light_sources_.begin();
    │ │ │ -
    331 (current_light < i) && (l_it != light_sources_.end());
    │ │ │ -
    332 ++l_it, ++current_light)
    │ │ │ -
    333 { }
    │ │ │ -
    334
    │ │ │ -
    335 return *l_it;
    │ │ │ -
    336 }
    │ │ │ -
    │ │ │ -
    338 virtual void addLightSource(const LightSource& light_source);
    │ │ │ -
    339
    │ │ │ -
    341 virtual void removeLightSource(const LightSource& light_source) ;
    │ │ │ -
    342
    │ │ │ -
    344 void clearLightSources();
    │ │ │ -
    345
    │ │ │ -
    │ │ │ -
    347 virtual Camera& getCamera()
    │ │ │ -
    348 { return camera_;}
    │ │ │ -
    │ │ │ -
    349
    │ │ │ -
    │ │ │ -
    351 virtual const Camera& getCamera() const
    │ │ │ -
    352 { return camera_;}
    │ │ │ -
    │ │ │ -
    353
    │ │ │ -
    │ │ │ -
    356 virtual void setCamera(const Camera& camera)
    │ │ │ -
    357 { camera_ = camera;}
    │ │ │ -
    │ │ │ -
    358
    │ │ │ -
    │ │ │ -
    360 virtual const ColorRGBA& getBackgroundColor() const
    │ │ │ -
    361 { return background_color_;}
    │ │ │ -
    │ │ │ -
    362
    │ │ │ -
    │ │ │ -
    364 virtual void setBackgroundColor(const ColorRGBA& color)
    │ │ │ -
    365 { background_color_ = color;}
    │ │ │ -
    │ │ │ -
    366
    │ │ │ -
    │ │ │ -
    368 virtual const ColorRGBA& getInfoColor() const
    │ │ │ -
    369 { return info_color_;}
    │ │ │ -
    │ │ │ -
    370
    │ │ │ -
    │ │ │ -
    372 virtual void setInfoColor(const ColorRGBA& color)
    │ │ │ -
    373 { info_color_ = color;}
    │ │ │ -
    │ │ │ -
    374
    │ │ │ -
    │ │ │ -
    376 void showCoordinateSystem(bool state)
    │ │ │ -
    377 { show_coordinate_system_ = state;}
    │ │ │ -
    │ │ │ -
    378
    │ │ │ -
    │ │ │ -
    380 bool coordinateSystemEnabled() const
    │ │ │ -
    381 { return show_coordinate_system_;}
    │ │ │ -
    │ │ │ -
    382
    │ │ │ -
    │ │ │ -
    384 void setEyeDistance(float value)
    │ │ │ -
    385 { eye_distance_ = value;}
    │ │ │ -
    │ │ │ -
    386
    │ │ │ -
    │ │ │ -
    388 float getEyeDistance() const
    │ │ │ -
    389 { return eye_distance_;}
    │ │ │ -
    │ │ │ -
    390
    │ │ │ -
    │ │ │ -
    392 void setFocalDistance(float value)
    │ │ │ -
    393 { focal_distance_ = value;}
    │ │ │ -
    │ │ │ -
    394
    │ │ │ -
    │ │ │ -
    396 float getFocalDistance() const
    │ │ │ -
    397 { return focal_distance_;}
    │ │ │ -
    │ │ │ -
    398
    │ │ │ -
    │ │ │ -
    400 void setSwapSideBySideStereo(bool state)
    │ │ │ -
    401 { swap_side_by_side_stereo_ = state;}
    │ │ │ -
    │ │ │ -
    402
    │ │ │ -
    │ │ │ -
    404 bool swapSideBySideStereo() const
    │ │ │ -
    405 { return swap_side_by_side_stereo_;}
    │ │ │ -
    │ │ │ -
    406
    │ │ │ -
    │ │ │ -
    408 float getFogIntensity() const
    │ │ │ -
    409 { return fog_intensity_;}
    │ │ │ -
    │ │ │ -
    410
    │ │ │ -
    │ │ │ -
    412 void setFogIntensity(float value)
    │ │ │ -
    413 { fog_intensity_ = value;}
    │ │ │ -
    │ │ │ -
    414
    │ │ │ -
    416
    │ │ │ -
    419
    │ │ │ -
    421 bool operator == (const Stage& stage) const;
    │ │ │ -
    422
    │ │ │ -
    430 Vector3 calculateRelativeCoordinates(Vector3 pos) const;
    │ │ │ -
    431
    │ │ │ -
    435 Vector3 calculateAbsoluteCoordinates(Vector3 pos) const;
    │ │ │ -
    436
    │ │ │ -
    438
    │ │ │ -
    445 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ -
    446
    │ │ │ -
    448 Material& getMaterial() { return material_; }
    │ │ │ -
    449
    │ │ │ -
    451 const Material& getMaterial() const { return material_; }
    │ │ │ -
    452
    │ │ │ -
    453 protected:
    │ │ │ -
    454
    │ │ │ -
    455 //_
    │ │ │ -
    456 ColorRGBA background_color_;
    │ │ │ -
    457
    │ │ │ -
    458 //_
    │ │ │ -
    459 ColorRGBA info_color_;
    │ │ │ -
    460
    │ │ │ -
    461 //_
    │ │ │ -
    462 std::list<LightSource> light_sources_;
    │ │ │ -
    463
    │ │ │ -
    464 //_
    │ │ │ -
    465 Camera camera_;
    │ │ │ -
    466
    │ │ │ -
    467 //_
    │ │ │ -
    468 bool show_coordinate_system_;
    │ │ │ -
    469
    │ │ │ -
    470 //_
    │ │ │ -
    471 float fog_intensity_;
    │ │ │ -
    472
    │ │ │ -
    473 //_
    │ │ │ -
    474 float eye_distance_;
    │ │ │ -
    475
    │ │ │ -
    476 //_
    │ │ │ -
    477 float focal_distance_;
    │ │ │ -
    478
    │ │ │ -
    479 //_
    │ │ │ -
    480 bool swap_side_by_side_stereo_;
    │ │ │ -
    481
    │ │ │ -
    482 // the current default materials used for raytracing
    │ │ │ -
    483 Material material_;
    │ │ │ -
    484 };
    │ │ │ -
    │ │ │ -
    485
    │ │ │ -
    486 } // namespace VIEW
    │ │ │ -
    487} // namespace BALL
    │ │ │ -
    488
    │ │ │ -
    489#endif // BALL_VIEW_KERNEL_STAGE_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::LightSource::getPosition
    const Vector3 & getPosition() const
    Get position.
    Definition stage.h:99
    │ │ │ -
    BALL::VIEW::LightSource::getType
    Index getType() const
    Definition stage.h:158
    │ │ │ -
    BALL::VIEW::LightSource::getAngle
    const Angle & getAngle() const
    Get the angle of the light cone.
    Definition stage.h:124
    │ │ │ -
    BALL::VIEW::LightSource::setAngle
    void setAngle(const Angle &angle)
    Set the angle of the light cone.
    Definition stage.h:128
    │ │ │ -
    BALL::VIEW::LightSource::setColor
    void setColor(const ColorRGBA &color)
    Definition stage.h:152
    │ │ │ -
    BALL::VIEW::LightSource::setDirection
    void setDirection(const Vector3 &direction)
    Set the direction vector of the light.
    Definition stage.h:111
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::LightSource::getColor
    const ColorRGBA & getColor() const
    Definition stage.h:146
    │ │ │ -
    BALL::VIEW::LightSource::getIntensity
    float getIntensity() const
    Definition stage.h:134
    │ │ │ -
    BALL::VIEW::LightSource::getDirection
    const Vector3 & getDirection() const
    Get the direction vector of the light.
    Definition stage.h:107
    │ │ │ -
    BALL::VIEW::LightSource::setRelativeToCamera
    void setRelativeToCamera(bool state)
    If set to true, the LightSource will move with the Camera.
    Definition stage.h:168
    │ │ │ -
    BALL::VIEW::LightSource::LightSource
    LightSource(const LightSource &light_source)
    │ │ │ -
    BALL::VIEW::LightSource::setType
    void setType(Types type)
    Definition stage.h:164
    │ │ │ -
    BALL::VIEW::LightSource::dump
    virtual void dump(std::ostream &s=std::cout, Size depth=0) const
    │ │ │ -
    BALL::VIEW::LightSource::setIntensity
    void setIntensity(float intensity)
    Definition stage.h:140
    │ │ │ - │ │ │ -
    BALL::VIEW::LightSource::setPosition
    void setPosition(const Vector3 &position)
    Set position.
    Definition stage.h:103
    │ │ │ - │ │ │ -
    BALL::VIEW::LightSource::getAttenuation
    const Vector3 & getAttenuation() const
    Get the attenuation parameters of the light.
    Definition stage.h:115
    │ │ │ -
    BALL::VIEW::LightSource::setAttenuation
    void setAttenuation(const Vector3 &attenuation)
    Set the attenuation parameters of the light.
    Definition stage.h:119
    │ │ │ - │ │ │ -
    BALL::VIEW::LightSource::~LightSource
    virtual ~LightSource()
    Definition stage.h:91
    │ │ │ - │ │ │ -
    BALL::VIEW::LightSource::Types
    Types
    Enumeration of different types of lights.
    Definition stage.h:59
    │ │ │ - │ │ │ -
    BALL::VIEW::LightSource::isRelativeToCamera
    bool isRelativeToCamera() const
    Test if a LightSource will move with the Camera.
    Definition stage.h:172
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::Stage::setFogIntensity
    void setFogIntensity(float value)
    Definition stage.h:412
    │ │ │ -
    BALL::VIEW::Stage::coordinateSystemEnabled
    bool coordinateSystemEnabled() const
    Shows coordinate system.
    Definition stage.h:380
    │ │ │ -
    BALL::VIEW::Stage::setSwapSideBySideStereo
    void setSwapSideBySideStereo(bool state)
    Settings for side by side stereo side swapping.
    Definition stage.h:400
    │ │ │ -
    BALL::VIEW::Stage::getMaterial
    Material & getMaterial()
    Gives access to the default material parameters.
    Definition stage.h:448
    │ │ │ -
    BALL::VIEW::Stage::swapSideBySideStereo
    bool swapSideBySideStereo() const
    Get settings for side by side stereo side swapping.
    Definition stage.h:404
    │ │ │ -
    BALL::VIEW::Stage::getFocalDistance
    float getFocalDistance() const
    Get the focal distance for the stereo view.
    Definition stage.h:396
    │ │ │ -
    BALL::VIEW::Stage::eye_distance_
    float eye_distance_
    Definition stage.h:474
    │ │ │ -
    BALL::VIEW::Stage::getCamera
    virtual Camera & getCamera()
    Get the camera.
    Definition stage.h:347
    │ │ │ -
    BALL::VIEW::Stage::getMaterial
    const Material & getMaterial() const
    Gives access to the default material parameters, const version.
    Definition stage.h:451
    │ │ │ -
    BALL::VIEW::Stage::Stage
    Stage(const Stage &stage)
    Copy constructor.
    │ │ │ -
    BALL::VIEW::Stage::setFocalDistance
    void setFocalDistance(float value)
    Set the focal distance for the stereo view.
    Definition stage.h:392
    │ │ │ -
    BALL::VIEW::Stage::getLightSource
    virtual LightSource & getLightSource(Position i)
    Get a reference to the i-th light source.
    Definition stage.h:319
    │ │ │ -
    BALL::VIEW::Stage::material_
    Material material_
    Definition stage.h:483
    │ │ │ -
    BALL::VIEW::Stage::getCamera
    virtual const Camera & getCamera() const
    Get the camera (const)
    Definition stage.h:351
    │ │ │ -
    BALL::VIEW::Stage::background_color_
    ColorRGBA background_color_
    Definition stage.h:456
    │ │ │ -
    BALL::VIEW::Stage::getBackgroundColor
    virtual const ColorRGBA & getBackgroundColor() const
    Get the background color.
    Definition stage.h:360
    │ │ │ -
    BALL::VIEW::Stage::show_coordinate_system_
    bool show_coordinate_system_
    Definition stage.h:468
    │ │ │ -
    BALL::VIEW::Stage::setInfoColor
    virtual void setInfoColor(const ColorRGBA &color)
    Set the background color.
    Definition stage.h:372
    │ │ │ -
    BALL::VIEW::Stage::clear
    virtual void clear()
    Explicit default initialization.
    │ │ │ -
    BALL::VIEW::Stage::info_color_
    ColorRGBA info_color_
    Definition stage.h:459
    │ │ │ -
    BALL::VIEW::Stage::camera_
    Camera camera_
    Definition stage.h:465
    │ │ │ -
    BALL::VIEW::Stage::setCamera
    virtual void setCamera(const Camera &camera)
    Definition stage.h:356
    │ │ │ -
    BALL::VIEW::Stage::focal_distance_
    float focal_distance_
    Definition stage.h:477
    │ │ │ -
    BALL::VIEW::Stage::getInfoColor
    virtual const ColorRGBA & getInfoColor() const
    Get the background color.
    Definition stage.h:368
    │ │ │ -
    BALL::VIEW::Stage::fog_intensity_
    float fog_intensity_
    Definition stage.h:471
    │ │ │ -
    BALL::VIEW::Stage::calculateAbsoluteCoordinates
    Vector3 calculateAbsoluteCoordinates(Vector3 pos) const
    │ │ │ -
    BALL::VIEW::Stage::setBackgroundColor
    virtual void setBackgroundColor(const ColorRGBA &color)
    Set the background color.
    Definition stage.h:364
    │ │ │ -
    BALL::VIEW::Stage::getFogIntensity
    float getFogIntensity() const
    Definition stage.h:408
    │ │ │ -
    BALL::VIEW::Stage::calculateRelativeCoordinates
    Vector3 calculateRelativeCoordinates(Vector3 pos) const
    │ │ │ -
    BALL::VIEW::Stage::removeLightSource
    virtual void removeLightSource(const LightSource &light_source)
    Remove a light source.
    │ │ │ -
    BALL::VIEW::Stage::getLightSources
    virtual const std::list< LightSource > & getLightSources() const
    Get the light sources (const)
    Definition stage.h:315
    │ │ │ -
    BALL::VIEW::Stage::dump
    virtual void dump(std::ostream &s=std::cout, Size depth=0) const
    │ │ │ - │ │ │ -
    BALL::VIEW::Stage::~Stage
    virtual ~Stage()
    Destructor.
    Definition stage.h:304
    │ │ │ -
    BALL::VIEW::Stage::getEyeDistance
    float getEyeDistance() const
    Get the eye distance for the stereo view.
    Definition stage.h:388
    │ │ │ -
    BALL::VIEW::Stage::addLightSource
    virtual void addLightSource(const LightSource &light_source)
    Add a light source.
    │ │ │ -
    BALL::VIEW::Stage::setEyeDistance
    void setEyeDistance(float value)
    Set the eye distance for the stereo view.
    Definition stage.h:384
    │ │ │ -
    BALL::VIEW::Stage::showCoordinateSystem
    void showCoordinateSystem(bool state)
    Show coordinate system.
    Definition stage.h:376
    │ │ │ -
    BALL::VIEW::Stage::swap_side_by_side_stereo_
    bool swap_side_by_side_stereo_
    Definition stage.h:480
    │ │ │ -
    BALL::VIEW::Stage::clearLightSources
    void clearLightSources()
    │ │ │ -
    BALL::VIEW::Stage::light_sources_
    std::list< LightSource > light_sources_
    Definition stage.h:462
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ - │ │ │ +Go to the documentation of this file.
    1#include <BALL/VIEW/INPUT/inputDeviceDriver.h>
    │ │ │ +
    2
    │ │ │ +
    3namespace BALL
    │ │ │ +
    4{
    │ │ │ +
    5 namespace VIEW
    │ │ │ +
    6 {
    │ │ │ +
    │ │ │ +
    7 class FakeDriver : public InputDeviceDriver, protected QThread
    │ │ │ +
    8 {
    │ │ │ +
    9 public:
    │ │ │ +
    │ │ │ +
    10 FakeDriver(Scene* receiver)
    │ │ │ +
    11 : InputDeviceDriver(receiver) {}
    │ │ │ +
    │ │ │ +
    12 bool setUp() { return true; }
    │ │ │ +
    13 bool tearDown() { return true; }
    │ │ │ +
    14
    │ │ │ +
    15 void setEnabled(bool enabled) { InputDeviceDriver::setEnabled(enabled); if(enabled) start(); }
    │ │ │ +
    16
    │ │ │ +
    17 private:
    │ │ │ +
    18 void run() { while(true) { emitPositionChange(1,2,-3,4,5,6); msleep(20); } }
    │ │ │ +
    19 };
    │ │ │ +
    │ │ │ +
    20 }
    │ │ │ +
    21}
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::FakeDriver::FakeDriver
    FakeDriver(Scene *receiver)
    Definition fakeDriver.h:10
    │ │ │ + │ │ │ +
    BALL::VIEW::FakeDriver::setEnabled
    void setEnabled(bool enabled)
    Definition fakeDriver.h:15
    │ │ │ + │ │ │ +
    BALL::VIEW::InputDeviceDriver::emitPositionChange
    void emitPositionChange(double x, double y, double z, double a, double b, double c)
    │ │ │ +
    BALL::VIEW::InputDeviceDriver::setEnabled
    void setEnabled(bool enabled)
    │ │ │ + │ │ │ + │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,633 +1,61 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ -stage.h │ │ │ │ + * _I_N_P_U_T │ │ │ │ +fakeDriver.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ -2// vi: set ts=2: │ │ │ │ -3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_VIEW_KERNEL_STAGE_H │ │ │ │ -6#define BALL_VIEW_KERNEL_STAGE_H │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_MATHS_VECTOR3_H │ │ │ │ -9# include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12#ifndef BALL_MATHS_QUATERNION_H │ │ │ │ -13# include <_B_A_L_L_/_M_A_T_H_S_/_q_u_a_t_e_r_n_i_o_n_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16#ifndef BALL_MATHS_MATRIX44_H │ │ │ │ -17# include <_B_A_L_L_/_M_A_T_H_S_/_m_a_t_r_i_x_4_4_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20#ifndef BALL_MATHS_ANGLE_H │ │ │ │ -21# include <_B_A_L_L_/_M_A_T_H_S_/_a_n_g_l_e_._h> │ │ │ │ -22#endif │ │ │ │ -23 │ │ │ │ -24#ifndef BALL_VIEW_DATATYPE_COLORRGBA_H │ │ │ │ -25# include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_c_o_l_o_r_R_G_B_A_._h> │ │ │ │ -26#endif │ │ │ │ -27 │ │ │ │ -28#ifndef BALL_VIEW_KERNEL_REPRESENTATION_H │ │ │ │ -29# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h> │ │ │ │ -30#endif │ │ │ │ -31 │ │ │ │ -32#ifndef BALL_COMMON_EXCEPTION_H │ │ │ │ -33# include <_B_A_L_L_/_C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h> │ │ │ │ -34#endif │ │ │ │ -35 │ │ │ │ -36#ifndef BALL_VIEW_RENDERING_CAMERA_H │ │ │ │ -37# include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_c_a_m_e_r_a_._h> │ │ │ │ -38#endif │ │ │ │ -39 │ │ │ │ -40namespace _B_A_L_L │ │ │ │ -41{ │ │ │ │ -42 namespace VIEW │ │ │ │ -43 { │ │ │ │ -_5_3 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _L_i_g_h_t_S_o_u_r_c_e │ │ │ │ -54 { │ │ │ │ -55 public: │ │ │ │ -56 │ │ │ │ -_5_8 enum _T_y_p_e_s │ │ │ │ -59 { │ │ │ │ -60 │ │ │ │ -_6_4 AMBIENT = 0, │ │ │ │ -65 │ │ │ │ -_7_0 _P_O_S_I_T_I_O_N_A_L, │ │ │ │ -71 │ │ │ │ -74 DIRECTIONAL │ │ │ │ -_7_5 }; │ │ │ │ -76 │ │ │ │ -80 │ │ │ │ -_8_3 _L_i_g_h_t_S_o_u_r_c_e(); │ │ │ │ -84 │ │ │ │ -_8_7 _L_i_g_h_t_S_o_u_r_c_e(const _L_i_g_h_t_S_o_u_r_c_e& light_source); │ │ │ │ -88 │ │ │ │ -_9_1 virtual _~_L_i_g_h_t_S_o_u_r_c_e(){} │ │ │ │ -92 │ │ │ │ -94 │ │ │ │ -97 │ │ │ │ -_9_9 const _V_e_c_t_o_r_3& _g_e_t_P_o_s_i_t_i_o_n() const │ │ │ │ -100 { return position_;} │ │ │ │ -101 │ │ │ │ -_1_0_3 void _s_e_t_P_o_s_i_t_i_o_n(const _V_e_c_t_o_r_3& position) │ │ │ │ -104 { position_ = position; } │ │ │ │ -105 │ │ │ │ -_1_0_7 const _V_e_c_t_o_r_3& _g_e_t_D_i_r_e_c_t_i_o_n() const │ │ │ │ -108 { return direction_;} │ │ │ │ -109 │ │ │ │ -_1_1_1 void _s_e_t_D_i_r_e_c_t_i_o_n(const _V_e_c_t_o_r_3& direction) │ │ │ │ -112 { direction_ = direction;} │ │ │ │ -113 │ │ │ │ -_1_1_5 const _V_e_c_t_o_r_3& _g_e_t_A_t_t_e_n_u_a_t_i_o_n() const │ │ │ │ -116 { return attenuation_;} │ │ │ │ -117 │ │ │ │ -_1_1_9 void _s_e_t_A_t_t_e_n_u_a_t_i_o_n(const _V_e_c_t_o_r_3& attenuation) │ │ │ │ -120 { attenuation_ = attenuation;} │ │ │ │ -121 │ │ │ │ -122 │ │ │ │ -_1_2_4 const _A_n_g_l_e& _g_e_t_A_n_g_l_e() const │ │ │ │ -125 { return angle_;} │ │ │ │ -126 │ │ │ │ -_1_2_8 void _s_e_t_A_n_g_l_e(const _A_n_g_l_e& angle) │ │ │ │ -129 { angle_ = angle;} │ │ │ │ -130 │ │ │ │ -_1_3_4 float _g_e_t_I_n_t_e_n_s_i_t_y() const │ │ │ │ -135 { return intensity_;} │ │ │ │ -136 │ │ │ │ -_1_4_0 void _s_e_t_I_n_t_e_n_s_i_t_y(float intensity) │ │ │ │ -141 { intensity_ = intensity;} │ │ │ │ -142 │ │ │ │ -_1_4_6 const _C_o_l_o_r_R_G_B_A& _g_e_t_C_o_l_o_r() const │ │ │ │ -147 { return color_;} │ │ │ │ -148 │ │ │ │ -_1_5_2 void _s_e_t_C_o_l_o_r(const _C_o_l_o_r_R_G_B_A& color) │ │ │ │ -153 { color_ = color;} │ │ │ │ -154 │ │ │ │ -_1_5_8 _I_n_d_e_x _g_e_t_T_y_p_e() const │ │ │ │ -159 { return type_;} │ │ │ │ -160 │ │ │ │ -_1_6_4 void _s_e_t_T_y_p_e(_T_y_p_e_s type) │ │ │ │ -165 { type_ = type;} │ │ │ │ -166 │ │ │ │ -_1_6_8 void _s_e_t_R_e_l_a_t_i_v_e_T_o_C_a_m_e_r_a(bool state) │ │ │ │ -169 { relative_ = state;} │ │ │ │ -170 │ │ │ │ -_1_7_2 bool _i_s_R_e_l_a_t_i_v_e_T_o_C_a_m_e_r_a() const │ │ │ │ -173 { return relative_;} │ │ │ │ -174 │ │ │ │ -_1_7_6 _L_i_g_h_t_S_o_u_r_c_e& operator = (const _L_i_g_h_t_S_o_u_r_c_e& light); │ │ │ │ -177 │ │ │ │ -_1_7_9 bool operator < (const _L_i_g_h_t_S_o_u_r_c_e& light) const; │ │ │ │ -180 │ │ │ │ -182 │ │ │ │ -185 │ │ │ │ -_1_8_7 bool operator == (const _L_i_g_h_t_S_o_u_r_c_e& light_source) const; │ │ │ │ -188 │ │ │ │ -190 │ │ │ │ -_1_9_7 virtual void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const; │ │ │ │ -198 │ │ │ │ -199 protected: │ │ │ │ -200 │ │ │ │ -201 //_ Position of the light source │ │ │ │ -_2_0_2 _V_e_c_t_o_r_3 _p_o_s_i_t_i_o_n__; │ │ │ │ -203 │ │ │ │ -204 //_ Direction of the light cone │ │ │ │ -_2_0_5 _V_e_c_t_o_r_3 _d_i_r_e_c_t_i_o_n__; │ │ │ │ -206 │ │ │ │ -207 //_ Attenuation parameters of the light │ │ │ │ -_2_0_8 _V_e_c_t_o_r_3 _a_t_t_e_n_u_a_t_i_o_n__; │ │ │ │ -209 │ │ │ │ -210 //_ │ │ │ │ -_2_1_1 _V_e_c_t_o_r_3 _r___p_o_s_i_t_i_o_n__; │ │ │ │ -212 │ │ │ │ -213 //_ │ │ │ │ -_2_1_4 _V_e_c_t_o_r_3 _r___d_i_r_e_c_t_i_o_n__; │ │ │ │ -215 │ │ │ │ -216 //_ Angle of the light cone │ │ │ │ -_2_1_7 _A_n_g_l_e _a_n_g_l_e__; │ │ │ │ -218 │ │ │ │ -219 //_ Intensity of the light │ │ │ │ -_2_2_0 float _i_n_t_e_n_s_i_t_y__; │ │ │ │ -221 │ │ │ │ -222 //_ Color of the light │ │ │ │ -_2_2_3 _C_o_l_o_r_R_G_B_A _c_o_l_o_r__; │ │ │ │ -224 │ │ │ │ -225 //_ Enumeration of types for further usage │ │ │ │ -_2_2_6 _I_n_d_e_x _t_y_p_e__; │ │ │ │ -227 │ │ │ │ -228 //_ Relative to camera │ │ │ │ -_2_2_9 bool _r_e_l_a_t_i_v_e__; │ │ │ │ -230 }; │ │ │ │ -231 │ │ │ │ -232 │ │ │ │ -_2_3_8 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _S_t_a_g_e │ │ │ │ -239 { │ │ │ │ -240 public: │ │ │ │ -241 │ │ │ │ -_2_4_4 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _M_a_t_e_r_i_a_l │ │ │ │ -245 : public _P_e_r_s_i_s_t_e_n_t_O_b_j_e_c_t │ │ │ │ -246 { │ │ │ │ -247 public: │ │ │ │ -248 │ │ │ │ -249 _B_A_L_L___C_R_E_A_T_E(_M_a_t_e_r_i_a_l) │ │ │ │ -250 │ │ │ │ -_2_5_1 _M_a_t_e_r_i_a_l(); │ │ │ │ -252 │ │ │ │ -256 │ │ │ │ -_2_6_1 virtual void persistentWrite(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm, const char* name = 0) │ │ │ │ -const; │ │ │ │ -262 │ │ │ │ -_2_6_7 virtual void persistentRead(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm); │ │ │ │ -268 │ │ │ │ -270 │ │ │ │ -_2_7_1 _C_o_l_o_r_R_G_B_A ambient_color; │ │ │ │ -_2_7_2 float ambient_intensity; │ │ │ │ -273 │ │ │ │ -_2_7_4 _C_o_l_o_r_R_G_B_A specular_color; │ │ │ │ -_2_7_5 float specular_intensity; │ │ │ │ -276 │ │ │ │ -_2_7_7 _C_o_l_o_r_R_G_B_A reflective_color; │ │ │ │ -_2_7_8 float reflective_intensity; │ │ │ │ -279 │ │ │ │ -_2_8_0 float shininess; │ │ │ │ -_2_8_1 float transparency; │ │ │ │ -282 }; │ │ │ │ -283 │ │ │ │ -284 // needed for backwards compatibilty of project files │ │ │ │ -_2_8_5 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _R_a_y_t_r_a_c_i_n_g_M_a_t_e_r_i_a_l : public _M_a_t_e_r_i_a_l │ │ │ │ -286 { │ │ │ │ -287 public: │ │ │ │ -288 │ │ │ │ -289 _B_A_L_L___C_R_E_A_T_E(_R_a_y_t_r_a_c_i_n_g_M_a_t_e_r_i_a_l) │ │ │ │ -290 }; │ │ │ │ -291 │ │ │ │ -295 │ │ │ │ -_2_9_8 _S_t_a_g_e(); │ │ │ │ -299 │ │ │ │ -_3_0_1 _S_t_a_g_e(const _S_t_a_g_e& stage); │ │ │ │ -302 │ │ │ │ -_3_0_4 virtual _~_S_t_a_g_e(){} │ │ │ │ -305 │ │ │ │ -_3_0_7 virtual void _c_l_e_a_r(); │ │ │ │ -308 │ │ │ │ -310 │ │ │ │ -313 │ │ │ │ -_3_1_5 virtual const std::list& _g_e_t_L_i_g_h_t_S_o_u_r_c_e_s() const │ │ │ │ -316 { return light_sources_;} │ │ │ │ -317 │ │ │ │ -_3_1_9 virtual _L_i_g_h_t_S_o_u_r_c_e& _g_e_t_L_i_g_h_t_S_o_u_r_c_e(_P_o_s_i_t_i_o_n i) │ │ │ │ -320 { │ │ │ │ -321 if (i >= light_sources_.size()) │ │ │ │ -322 { │ │ │ │ -323 _E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_R_a_n_g_e e(__FILE__, __LINE__); │ │ │ │ -324 throw(e); │ │ │ │ -325 } │ │ │ │ -326 │ │ │ │ -327 std::list::iterator l_it; │ │ │ │ -328 │ │ │ │ -329 _P_o_s_i_t_i_o_n current_light = 0; │ │ │ │ -330 for (l_it = light_sources_.begin(); │ │ │ │ -331 (current_light < i) && (l_it != light_sources_.end()); │ │ │ │ -332 ++l_it, ++current_light) │ │ │ │ -333 { } │ │ │ │ -334 │ │ │ │ -335 return *l_it; │ │ │ │ -336 } │ │ │ │ -_3_3_8 virtual void _a_d_d_L_i_g_h_t_S_o_u_r_c_e(const _L_i_g_h_t_S_o_u_r_c_e& light_source); │ │ │ │ -339 │ │ │ │ -_3_4_1 virtual void _r_e_m_o_v_e_L_i_g_h_t_S_o_u_r_c_e(const _L_i_g_h_t_S_o_u_r_c_e& light_source) ; │ │ │ │ -342 │ │ │ │ -_3_4_4 void _c_l_e_a_r_L_i_g_h_t_S_o_u_r_c_e_s(); │ │ │ │ -345 │ │ │ │ -_3_4_7 virtual _C_a_m_e_r_a& _g_e_t_C_a_m_e_r_a() │ │ │ │ -348 { return camera_;} │ │ │ │ -349 │ │ │ │ -_3_5_1 virtual const _C_a_m_e_r_a& _g_e_t_C_a_m_e_r_a() const │ │ │ │ -352 { return camera_;} │ │ │ │ -353 │ │ │ │ -_3_5_6 virtual void _s_e_t_C_a_m_e_r_a(const _C_a_m_e_r_a& camera) │ │ │ │ -357 { camera_ = camera;} │ │ │ │ -358 │ │ │ │ -_3_6_0 virtual const _C_o_l_o_r_R_G_B_A& _g_e_t_B_a_c_k_g_r_o_u_n_d_C_o_l_o_r() const │ │ │ │ -361 { return background_color_;} │ │ │ │ -362 │ │ │ │ -_3_6_4 virtual void _s_e_t_B_a_c_k_g_r_o_u_n_d_C_o_l_o_r(const _C_o_l_o_r_R_G_B_A& color) │ │ │ │ -365 { background_color_ = color;} │ │ │ │ -366 │ │ │ │ -_3_6_8 virtual const _C_o_l_o_r_R_G_B_A& _g_e_t_I_n_f_o_C_o_l_o_r() const │ │ │ │ -369 { return info_color_;} │ │ │ │ -370 │ │ │ │ -_3_7_2 virtual void _s_e_t_I_n_f_o_C_o_l_o_r(const _C_o_l_o_r_R_G_B_A& color) │ │ │ │ -373 { info_color_ = color;} │ │ │ │ -374 │ │ │ │ -_3_7_6 void _s_h_o_w_C_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m(bool state) │ │ │ │ -377 { show_coordinate_system_ = state;} │ │ │ │ -378 │ │ │ │ -_3_8_0 bool _c_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m_E_n_a_b_l_e_d() const │ │ │ │ -381 { return show_coordinate_system_;} │ │ │ │ -382 │ │ │ │ -_3_8_4 void _s_e_t_E_y_e_D_i_s_t_a_n_c_e(float value) │ │ │ │ -385 { eye_distance_ = value;} │ │ │ │ -386 │ │ │ │ -_3_8_8 float _g_e_t_E_y_e_D_i_s_t_a_n_c_e() const │ │ │ │ -389 { return eye_distance_;} │ │ │ │ -390 │ │ │ │ -_3_9_2 void _s_e_t_F_o_c_a_l_D_i_s_t_a_n_c_e(float value) │ │ │ │ -393 { focal_distance_ = value;} │ │ │ │ -394 │ │ │ │ -_3_9_6 float _g_e_t_F_o_c_a_l_D_i_s_t_a_n_c_e() const │ │ │ │ -397 { return focal_distance_;} │ │ │ │ -398 │ │ │ │ -_4_0_0 void _s_e_t_S_w_a_p_S_i_d_e_B_y_S_i_d_e_S_t_e_r_e_o(bool state) │ │ │ │ -401 { swap_side_by_side_stereo_ = state;} │ │ │ │ -402 │ │ │ │ -_4_0_4 bool _s_w_a_p_S_i_d_e_B_y_S_i_d_e_S_t_e_r_e_o() const │ │ │ │ -405 { return swap_side_by_side_stereo_;} │ │ │ │ -406 │ │ │ │ -_4_0_8 float _g_e_t_F_o_g_I_n_t_e_n_s_i_t_y() const │ │ │ │ -409 { return fog_intensity_;} │ │ │ │ -410 │ │ │ │ -_4_1_2 void _s_e_t_F_o_g_I_n_t_e_n_s_i_t_y(float value) │ │ │ │ -413 { fog_intensity_ = value;} │ │ │ │ -414 │ │ │ │ -416 │ │ │ │ -419 │ │ │ │ -_4_2_1 bool operator == (const _S_t_a_g_e& stage) const; │ │ │ │ -422 │ │ │ │ -_4_3_0 _V_e_c_t_o_r_3 _c_a_l_c_u_l_a_t_e_R_e_l_a_t_i_v_e_C_o_o_r_d_i_n_a_t_e_s(_V_e_c_t_o_r_3 pos) const; │ │ │ │ -431 │ │ │ │ -_4_3_5 _V_e_c_t_o_r_3 _c_a_l_c_u_l_a_t_e_A_b_s_o_l_u_t_e_C_o_o_r_d_i_n_a_t_e_s(_V_e_c_t_o_r_3 pos) const; │ │ │ │ -436 │ │ │ │ -438 │ │ │ │ -_4_4_5 virtual void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const; │ │ │ │ -446 │ │ │ │ -_4_4_8 _M_a_t_e_r_i_a_l& _g_e_t_M_a_t_e_r_i_a_l() { return material_; } │ │ │ │ -449 │ │ │ │ -_4_5_1 const _M_a_t_e_r_i_a_l& _g_e_t_M_a_t_e_r_i_a_l() const { return material_; } │ │ │ │ -452 │ │ │ │ -453 protected: │ │ │ │ -454 │ │ │ │ -455 //_ │ │ │ │ -_4_5_6 _C_o_l_o_r_R_G_B_A _b_a_c_k_g_r_o_u_n_d___c_o_l_o_r__; │ │ │ │ -457 │ │ │ │ -458 //_ │ │ │ │ -_4_5_9 _C_o_l_o_r_R_G_B_A _i_n_f_o___c_o_l_o_r__; │ │ │ │ -460 │ │ │ │ -461 //_ │ │ │ │ -_4_6_2 std::list _l_i_g_h_t___s_o_u_r_c_e_s__; │ │ │ │ -463 │ │ │ │ -464 //_ │ │ │ │ -_4_6_5 _C_a_m_e_r_a _c_a_m_e_r_a__; │ │ │ │ -466 │ │ │ │ -467 //_ │ │ │ │ -_4_6_8 bool _s_h_o_w___c_o_o_r_d_i_n_a_t_e___s_y_s_t_e_m__; │ │ │ │ -469 │ │ │ │ -470 //_ │ │ │ │ -_4_7_1 float _f_o_g___i_n_t_e_n_s_i_t_y__; │ │ │ │ -472 │ │ │ │ -473 //_ │ │ │ │ -_4_7_4 float _e_y_e___d_i_s_t_a_n_c_e__; │ │ │ │ -475 │ │ │ │ -476 //_ │ │ │ │ -_4_7_7 float _f_o_c_a_l___d_i_s_t_a_n_c_e__; │ │ │ │ -478 │ │ │ │ -479 //_ │ │ │ │ -_4_8_0 bool _s_w_a_p___s_i_d_e___b_y___s_i_d_e___s_t_e_r_e_o__; │ │ │ │ -481 │ │ │ │ -482 // the current default materials used for raytracing │ │ │ │ -_4_8_3 _M_a_t_e_r_i_a_l _m_a_t_e_r_i_a_l__; │ │ │ │ -484 }; │ │ │ │ -485 │ │ │ │ -486 } // namespace VIEW │ │ │ │ -487} // namespace BALL │ │ │ │ -488 │ │ │ │ -489#endif // BALL_VIEW_KERNEL_STAGE_H │ │ │ │ -_c_a_m_e_r_a_._h │ │ │ │ -_r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h │ │ │ │ -_c_o_l_o_r_R_G_B_A_._h │ │ │ │ -_v_e_c_t_o_r_3_._h │ │ │ │ -_q_u_a_t_e_r_n_i_o_n_._h │ │ │ │ -_m_a_t_r_i_x_4_4_._h │ │ │ │ -_a_n_g_l_e_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +1#include <_B_A_L_L_/_V_I_E_W_/_I_N_P_U_T_/_i_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r_._h> │ │ │ │ +2 │ │ │ │ +3namespace _B_A_L_L │ │ │ │ +4{ │ │ │ │ +5 namespace VIEW │ │ │ │ +6 { │ │ │ │ +_7 class _F_a_k_e_D_r_i_v_e_r : public _I_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r, protected _Q_T_h_r_e_a_d │ │ │ │ +8 { │ │ │ │ +9 public: │ │ │ │ +_1_0 _F_a_k_e_D_r_i_v_e_r(_S_c_e_n_e* receiver) │ │ │ │ +11 : _I_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r(receiver) {} │ │ │ │ +_1_2 bool _s_e_t_U_p() { return true; } │ │ │ │ +_1_3 bool _t_e_a_r_D_o_w_n() { return true; } │ │ │ │ +14 │ │ │ │ +_1_5 void _s_e_t_E_n_a_b_l_e_d(bool enabled) { _I_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r_:_:_s_e_t_E_n_a_b_l_e_d(enabled); if │ │ │ │ +(enabled) start(); } │ │ │ │ +16 │ │ │ │ +17 private: │ │ │ │ +18 void run() { while(true) { _e_m_i_t_P_o_s_i_t_i_o_n_C_h_a_n_g_e(1,2,-3,4,5,6); msleep(20); } } │ │ │ │ +19 }; │ │ │ │ +20 } │ │ │ │ +21} │ │ │ │ +_i_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_R_a_n_g_e │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_1_9 │ │ │ │ -_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h_:_7_3 │ │ │ │ -_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_t_O_b_j_e_c_t │ │ │ │ -DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_t_O_b_j_e_c_t_._h_:_2_9 │ │ │ │ -_B_A_L_L_:_:_T_A_n_g_l_e_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_C_o_l_o_r_R_G_B_A │ │ │ │ -DDeeffiinniittiioonn _c_o_l_o_r_R_G_B_A_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_5_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_g_e_t_P_o_s_i_t_i_o_n │ │ │ │ -const Vector3 & getPosition() const │ │ │ │ -Get position. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_g_e_t_T_y_p_e │ │ │ │ -Index getType() const │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_5_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_g_e_t_A_n_g_l_e │ │ │ │ -const Angle & getAngle() const │ │ │ │ -Get the angle of the light cone. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_2_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_s_e_t_A_n_g_l_e │ │ │ │ -void setAngle(const Angle &angle) │ │ │ │ -Set the angle of the light cone. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_2_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_s_e_t_C_o_l_o_r │ │ │ │ -void setColor(const ColorRGBA &color) │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_5_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_s_e_t_D_i_r_e_c_t_i_o_n │ │ │ │ -void setDirection(const Vector3 &direction) │ │ │ │ -Set the direction vector of the light. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_1_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_r___d_i_r_e_c_t_i_o_n__ │ │ │ │ -Vector3 r_direction_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_1_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_c_o_l_o_r__ │ │ │ │ -ColorRGBA color_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_2_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_g_e_t_C_o_l_o_r │ │ │ │ -const ColorRGBA & getColor() const │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_4_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_g_e_t_I_n_t_e_n_s_i_t_y │ │ │ │ -float getIntensity() const │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_3_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_g_e_t_D_i_r_e_c_t_i_o_n │ │ │ │ -const Vector3 & getDirection() const │ │ │ │ -Get the direction vector of the light. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_0_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_s_e_t_R_e_l_a_t_i_v_e_T_o_C_a_m_e_r_a │ │ │ │ -void setRelativeToCamera(bool state) │ │ │ │ -If set to true, the LightSource will move with the Camera. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_6_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_L_i_g_h_t_S_o_u_r_c_e │ │ │ │ -LightSource(const LightSource &light_source) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_s_e_t_T_y_p_e │ │ │ │ -void setType(Types type) │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_6_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_d_u_m_p │ │ │ │ -virtual void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_s_e_t_I_n_t_e_n_s_i_t_y │ │ │ │ -void setIntensity(float intensity) │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_4_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_i_n_t_e_n_s_i_t_y__ │ │ │ │ -float intensity_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_2_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_s_e_t_P_o_s_i_t_i_o_n │ │ │ │ -void setPosition(const Vector3 &position) │ │ │ │ -Set position. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_0_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_L_i_g_h_t_S_o_u_r_c_e │ │ │ │ -LightSource() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_g_e_t_A_t_t_e_n_u_a_t_i_o_n │ │ │ │ -const Vector3 & getAttenuation() const │ │ │ │ -Get the attenuation parameters of the light. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_1_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_s_e_t_A_t_t_e_n_u_a_t_i_o_n │ │ │ │ -void setAttenuation(const Vector3 &attenuation) │ │ │ │ -Set the attenuation parameters of the light. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_1_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_a_n_g_l_e__ │ │ │ │ -Angle angle_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_1_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_~_L_i_g_h_t_S_o_u_r_c_e │ │ │ │ -virtual ~LightSource() │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_9_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_r_e_l_a_t_i_v_e__ │ │ │ │ -bool relative_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_2_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_T_y_p_e_s │ │ │ │ -Types │ │ │ │ -Enumeration of different types of lights. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_5_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_P_O_S_I_T_I_O_N_A_L │ │ │ │ -@ POSITIONAL │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_7_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_i_s_R_e_l_a_t_i_v_e_T_o_C_a_m_e_r_a │ │ │ │ -bool isRelativeToCamera() const │ │ │ │ -Test if a LightSource will move with the Camera. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_1_7_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_a_t_t_e_n_u_a_t_i_o_n__ │ │ │ │ -Vector3 attenuation_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_0_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_d_i_r_e_c_t_i_o_n__ │ │ │ │ -Vector3 direction_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_0_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_p_o_s_i_t_i_o_n__ │ │ │ │ -Vector3 position_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_0_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_t_y_p_e__ │ │ │ │ -Index type_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_2_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_o_u_r_c_e_:_:_r___p_o_s_i_t_i_o_n__ │ │ │ │ -Vector3 r_position_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_1_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_3_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_e_t_F_o_g_I_n_t_e_n_s_i_t_y │ │ │ │ -void setFogIntensity(float value) │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_1_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_c_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m_E_n_a_b_l_e_d │ │ │ │ -bool coordinateSystemEnabled() const │ │ │ │ -Shows coordinate system. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_8_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_e_t_S_w_a_p_S_i_d_e_B_y_S_i_d_e_S_t_e_r_e_o │ │ │ │ -void setSwapSideBySideStereo(bool state) │ │ │ │ -Settings for side by side stereo side swapping. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_0_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_M_a_t_e_r_i_a_l │ │ │ │ -Material & getMaterial() │ │ │ │ -Gives access to the default material parameters. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_4_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_w_a_p_S_i_d_e_B_y_S_i_d_e_S_t_e_r_e_o │ │ │ │ -bool swapSideBySideStereo() const │ │ │ │ -Get settings for side by side stereo side swapping. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_0_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_F_o_c_a_l_D_i_s_t_a_n_c_e │ │ │ │ -float getFocalDistance() const │ │ │ │ -Get the focal distance for the stereo view. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_9_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_e_y_e___d_i_s_t_a_n_c_e__ │ │ │ │ -float eye_distance_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_7_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_C_a_m_e_r_a │ │ │ │ -virtual Camera & getCamera() │ │ │ │ -Get the camera. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_4_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_M_a_t_e_r_i_a_l │ │ │ │ -const Material & getMaterial() const │ │ │ │ -Gives access to the default material parameters, const version. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_5_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_S_t_a_g_e │ │ │ │ -Stage(const Stage &stage) │ │ │ │ -Copy constructor. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_e_t_F_o_c_a_l_D_i_s_t_a_n_c_e │ │ │ │ -void setFocalDistance(float value) │ │ │ │ -Set the focal distance for the stereo view. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_9_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_L_i_g_h_t_S_o_u_r_c_e │ │ │ │ -virtual LightSource & getLightSource(Position i) │ │ │ │ -Get a reference to the i-th light source. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_1_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_m_a_t_e_r_i_a_l__ │ │ │ │ -Material material_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_8_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_C_a_m_e_r_a │ │ │ │ -virtual const Camera & getCamera() const │ │ │ │ -Get the camera (const) │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_5_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_b_a_c_k_g_r_o_u_n_d___c_o_l_o_r__ │ │ │ │ -ColorRGBA background_color_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_5_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_B_a_c_k_g_r_o_u_n_d_C_o_l_o_r │ │ │ │ -virtual const ColorRGBA & getBackgroundColor() const │ │ │ │ -Get the background color. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_6_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_h_o_w___c_o_o_r_d_i_n_a_t_e___s_y_s_t_e_m__ │ │ │ │ -bool show_coordinate_system_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_6_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_e_t_I_n_f_o_C_o_l_o_r │ │ │ │ -virtual void setInfoColor(const ColorRGBA &color) │ │ │ │ -Set the background color. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_7_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_c_l_e_a_r │ │ │ │ -virtual void clear() │ │ │ │ -Explicit default initialization. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_i_n_f_o___c_o_l_o_r__ │ │ │ │ -ColorRGBA info_color_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_5_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_c_a_m_e_r_a__ │ │ │ │ -Camera camera_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_6_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_e_t_C_a_m_e_r_a │ │ │ │ -virtual void setCamera(const Camera &camera) │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_5_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_f_o_c_a_l___d_i_s_t_a_n_c_e__ │ │ │ │ -float focal_distance_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_7_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_I_n_f_o_C_o_l_o_r │ │ │ │ -virtual const ColorRGBA & getInfoColor() const │ │ │ │ -Get the background color. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_6_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_f_o_g___i_n_t_e_n_s_i_t_y__ │ │ │ │ -float fog_intensity_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_7_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_c_a_l_c_u_l_a_t_e_A_b_s_o_l_u_t_e_C_o_o_r_d_i_n_a_t_e_s │ │ │ │ -Vector3 calculateAbsoluteCoordinates(Vector3 pos) const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_e_t_B_a_c_k_g_r_o_u_n_d_C_o_l_o_r │ │ │ │ -virtual void setBackgroundColor(const ColorRGBA &color) │ │ │ │ -Set the background color. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_6_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_F_o_g_I_n_t_e_n_s_i_t_y │ │ │ │ -float getFogIntensity() const │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_0_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_c_a_l_c_u_l_a_t_e_R_e_l_a_t_i_v_e_C_o_o_r_d_i_n_a_t_e_s │ │ │ │ -Vector3 calculateRelativeCoordinates(Vector3 pos) const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_r_e_m_o_v_e_L_i_g_h_t_S_o_u_r_c_e │ │ │ │ -virtual void removeLightSource(const LightSource &light_source) │ │ │ │ -Remove a light source. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_L_i_g_h_t_S_o_u_r_c_e_s │ │ │ │ -virtual const std::list< LightSource > & getLightSources() const │ │ │ │ -Get the light sources (const) │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_1_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_d_u_m_p │ │ │ │ -virtual void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_S_t_a_g_e │ │ │ │ -Stage() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_~_S_t_a_g_e │ │ │ │ -virtual ~Stage() │ │ │ │ -Destructor. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_0_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_g_e_t_E_y_e_D_i_s_t_a_n_c_e │ │ │ │ -float getEyeDistance() const │ │ │ │ -Get the eye distance for the stereo view. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_8_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_a_d_d_L_i_g_h_t_S_o_u_r_c_e │ │ │ │ -virtual void addLightSource(const LightSource &light_source) │ │ │ │ -Add a light source. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_e_t_E_y_e_D_i_s_t_a_n_c_e │ │ │ │ -void setEyeDistance(float value) │ │ │ │ -Set the eye distance for the stereo view. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_8_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_h_o_w_C_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m │ │ │ │ -void showCoordinateSystem(bool state) │ │ │ │ -Show coordinate system. │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_3_7_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_s_w_a_p___s_i_d_e___b_y___s_i_d_e___s_t_e_r_e_o__ │ │ │ │ -bool swap_side_by_side_stereo_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_8_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_c_l_e_a_r_L_i_g_h_t_S_o_u_r_c_e_s │ │ │ │ -void clearLightSources() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_l_i_g_h_t___s_o_u_r_c_e_s__ │ │ │ │ -std::list< LightSource > light_sources_ │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_4_6_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_M_a_t_e_r_i_a_l │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_4_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_R_a_y_t_r_a_c_i_n_g_M_a_t_e_r_i_a_l │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_8_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_C_a_m_e_r_a │ │ │ │ -DDeeffiinniittiioonn _c_a_m_e_r_a_._h_:_2_4 │ │ │ │ -_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ -#define BALL_VIEW_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ -_e_x_c_e_p_t_i_o_n_._h │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_F_a_k_e_D_r_i_v_e_r │ │ │ │ +DDeeffiinniittiioonn _f_a_k_e_D_r_i_v_e_r_._h_:_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_F_a_k_e_D_r_i_v_e_r_:_:_s_e_t_U_p │ │ │ │ +bool setUp() │ │ │ │ +DDeeffiinniittiioonn _f_a_k_e_D_r_i_v_e_r_._h_:_1_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_F_a_k_e_D_r_i_v_e_r_:_:_F_a_k_e_D_r_i_v_e_r │ │ │ │ +FakeDriver(Scene *receiver) │ │ │ │ +DDeeffiinniittiioonn _f_a_k_e_D_r_i_v_e_r_._h_:_1_0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_F_a_k_e_D_r_i_v_e_r_:_:_t_e_a_r_D_o_w_n │ │ │ │ +bool tearDown() │ │ │ │ +DDeeffiinniittiioonn _f_a_k_e_D_r_i_v_e_r_._h_:_1_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_F_a_k_e_D_r_i_v_e_r_:_:_s_e_t_E_n_a_b_l_e_d │ │ │ │ +void setEnabled(bool enabled) │ │ │ │ +DDeeffiinniittiioonn _f_a_k_e_D_r_i_v_e_r_._h_:_1_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_I_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r │ │ │ │ +DDeeffiinniittiioonn _i_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r_._h_:_1_9 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_I_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r_:_:_e_m_i_t_P_o_s_i_t_i_o_n_C_h_a_n_g_e │ │ │ │ +void emitPositionChange(double x, double y, double z, double a, double b, │ │ │ │ +double c) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_I_n_p_u_t_D_e_v_i_c_e_D_r_i_v_e_r_:_:_s_e_t_E_n_a_b_l_e_d │ │ │ │ +void setEnabled(bool enabled) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e │ │ │ │ +DDeeffiinniittiioonn _s_c_e_n_e_._h_:_1_4_1 │ │ │ │ +_Q_T_h_r_e_a_d │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d61/a01130.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: logitModel.h File Reference │ │ │ +BALL: molecularSurfaceGrid.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,39 +65,52 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -Classes | │ │ │ -Namespaces
    │ │ │ -
    logitModel.h File Reference
    │ │ │ +Namespaces | │ │ │ +Functions | │ │ │ +Variables
    │ │ │ +
    molecularSurfaceGrid.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/QSAR/classificationModel.h>
    │ │ │ +
    #include <BALL/common.h>
    │ │ │ +#include <BALL/MATHS/vector3.h>
    │ │ │ +#include <BALL/KERNEL/system.h>
    │ │ │ +#include <BALL/DATATYPE/regularData3D.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -

    │ │ │ -Classes

    class  BALL::QSAR::LogitModel
     
    │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ +

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::QSAR
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +

    │ │ │ +Functions

    BALL_EXPORT TRegularData3D< char > * BALL::calculateSESGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
     
    BALL_EXPORT TRegularData3D< char > * BALL::calculateSASGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ +Variables

    BALL_EXPORT const char BALL::CCONN__INSIDE
     
    BALL_EXPORT const char BALL::CCONN__OUTSIDE
     
    BALL_EXPORT const char BALL::CCONN__INSIDE_PROBE
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,21 +1,37 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -logitModel.h File Reference │ │ │ │ -#include <_B_A_L_L_/_Q_S_A_R_/_c_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l_._h> │ │ │ │ + * _S_O_L_V_A_T_I_O_N │ │ │ │ +_N_a_m_e_s_p_a_c_e_s | _F_u_n_c_t_i_o_n_s | _V_a_r_i_a_b_l_e_s │ │ │ │ +molecularSurfaceGrid.h File Reference │ │ │ │ +#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_r_e_g_u_l_a_r_D_a_t_a_3_D_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_Q_S_A_R_:_:_L_o_g_i_t_M_o_d_e_l │ │ │ │ -  │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_Q_S_A_R │ │ │ │ +FFuunnccttiioonnss │ │ │ │ +_B_A_L_L___E_X_P_O_R_T _T_R_e_g_u_l_a_r_D_a_t_a_3_D< char > *  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_S_E_S_G_r_i_d (const _V_e_c_t_o_r_3 │ │ │ │ + &lower, const _V_e_c_t_o_r_3 &upper, _f_l_o_a_t │ │ │ │ + spacing, const _S_y_s_t_e_m &system, _f_l_o_a_t │ │ │ │ + probe_radius) │ │ │ │ +  │ │ │ │ +_B_A_L_L___E_X_P_O_R_T _T_R_e_g_u_l_a_r_D_a_t_a_3_D< char > *  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_S_A_S_G_r_i_d (const _V_e_c_t_o_r_3 │ │ │ │ + &lower, const _V_e_c_t_o_r_3 &upper, _f_l_o_a_t │ │ │ │ + spacing, const _S_y_s_t_e_m &system, _f_l_o_a_t │ │ │ │ + probe_radius) │ │ │ │ +  │ │ │ │ +VVaarriiaabblleess │ │ │ │ +_B_A_L_L___E_X_P_O_R_T const char  _B_A_L_L_:_:_C_C_O_N_N_____I_N_S_I_D_E │ │ │ │ +  │ │ │ │ +_B_A_L_L___E_X_P_O_R_T const char  _B_A_L_L_:_:_C_C_O_N_N_____O_U_T_S_I_D_E │ │ │ │ +  │ │ │ │ +_B_A_L_L___E_X_P_O_R_T const char  _B_A_L_L_:_:_C_C_O_N_N_____I_N_S_I_D_E___P_R_O_B_E │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d61/a01130_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: logitModel.h Source File │ │ │ +BALL: molecularSurfaceGrid.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,80 +70,80 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    logitModel.h
    │ │ │ +
    molecularSurfaceGrid.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4//
    │ │ │ -
    5
    │ │ │ -
    6#ifndef LOGITMODEL
    │ │ │ -
    7#define LOGITMODEL
    │ │ │ -
    8
    │ │ │ -
    9#ifndef CLASSIFICATION
    │ │ │ -
    10#include <BALL/QSAR/classificationModel.h>
    │ │ │ -
    11#endif
    │ │ │ -
    12
    │ │ │ +
    4// $Id: molecularSurfaceGrid.h,v 1.15 2005/12/23 17:01:59 amoll Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_SOLVATION_MOLECULARSURFACEGRID_H
    │ │ │ +
    8#define BALL_SOLVATION_MOLECULARSURFACEGRID_H
    │ │ │ +
    9
    │ │ │ +
    10#ifndef BALL_COMMON_H
    │ │ │ +
    11# include <BALL/common.h>
    │ │ │ +
    12#endif
    │ │ │
    13
    │ │ │ -
    14
    │ │ │ -
    15namespace BALL{
    │ │ │ -
    16 namespace QSAR {
    │ │ │ +
    14#ifndef BALL_MATHS_VECTOR3_H
    │ │ │ +
    15# include <BALL/MATHS/vector3.h>
    │ │ │ +
    16#endif
    │ │ │
    17
    │ │ │ -
    │ │ │ -
    19 class BALL_EXPORT LogitModel : public ClassificationModel
    │ │ │ -
    20 {
    │ │ │ -
    21 public:
    │ │ │ -
    25 LogitModel(const QSARData& q);
    │ │ │ -
    26
    │ │ │ -
    27 ~LogitModel();
    │ │ │ +
    18#ifndef BALL_KERNEL_SYSTEM_H
    │ │ │ +
    19# include <BALL/KERNEL/system.h>
    │ │ │ +
    20#endif
    │ │ │ +
    21
    │ │ │ +
    22#ifndef BALL_DATATYPE_REGULARDATA3D_H
    │ │ │ +
    23# include <BALL/DATATYPE/regularData3D.h>
    │ │ │ +
    24#endif
    │ │ │ +
    25
    │ │ │ +
    26namespace BALL
    │ │ │ +
    27{
    │ │ │
    28
    │ │ │ -
    29 EIGEN_MAKE_ALIGNED_OPERATOR_NEW
    │ │ │ -
    31
    │ │ │ -
    32
    │ │ │ -
    36 void train();
    │ │ │ -
    37
    │ │ │ -
    38 Eigen::VectorXd predict(const vector<double>& substance, bool transform);
    │ │ │ -
    39
    │ │ │ -
    40 void saveToFile(string filename);
    │ │ │ -
    41
    │ │ │ -
    42 void readFromFile(string filename);
    │ │ │ -
    44
    │ │ │ -
    45
    │ │ │ -
    46 protected:
    │ │ │ -
    50 Eigen::MatrixXd training_result_;
    │ │ │ -
    52
    │ │ │ -
    53 };
    │ │ │ -
    │ │ │ -
    54 }
    │ │ │ -
    55}
    │ │ │ -
    56
    │ │ │ -
    57#endif // LOGITMODEL
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::QSAR::LogitModel::LogitModel
    LogitModel(const QSARData &q)
    │ │ │ -
    BALL::QSAR::LogitModel::predict
    Eigen::VectorXd predict(const vector< double > &substance, bool transform)
    │ │ │ - │ │ │ -
    BALL::QSAR::LogitModel::readFromFile
    void readFromFile(string filename)
    │ │ │ -
    BALL::QSAR::LogitModel::training_result_
    Eigen::MatrixXd training_result_
    Definition logitModel.h:50
    │ │ │ -
    BALL::QSAR::LogitModel::saveToFile
    void saveToFile(string filename)
    │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    29 // Define the entry values for an SES or SAS grid
    │ │ │ +
    30 BALL_EXPORT extern const char CCONN__INSIDE;
    │ │ │ +
    31 BALL_EXPORT extern const char CCONN__OUTSIDE;
    │ │ │ +
    32 BALL_EXPORT extern const char CCONN__INSIDE_PROBE;
    │ │ │ +
    33
    │ │ │ +
    37 BALL_EXPORT TRegularData3D<char>* calculateSESGrid
    │ │ │ +
    38 (const Vector3& lower, const Vector3& upper,
    │ │ │ +
    39 float spacing, const System& system, float probe_radius);
    │ │ │ +
    40
    │ │ │ +
    44 BALL_EXPORT TRegularData3D<char>* calculateSASGrid
    │ │ │ +
    45 (const Vector3& lower, const Vector3& upper,
    │ │ │ +
    46 float spacing, const System& system, float probe_radius);
    │ │ │ +
    47
    │ │ │ +
    48
    │ │ │ +
    49} // namespace BALL
    │ │ │ +
    50
    │ │ │ +
    51#endif // BALL_SOLVATION_MOLECULARSURFACEGRID_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::calculateSESGrid
    BALL_EXPORT TRegularData3D< char > * calculateSESGrid(const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
    │ │ │ +
    BALL::calculateSASGrid
    BALL_EXPORT TRegularData3D< char > * calculateSASGrid(const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
    │ │ │ + │ │ │ +
    BALL::CCONN__OUTSIDE
    BALL_EXPORT const char CCONN__OUTSIDE
    │ │ │ +
    BALL::CCONN__INSIDE
    BALL_EXPORT const char CCONN__INSIDE
    │ │ │ +
    BALL::CCONN__INSIDE_PROBE
    BALL_EXPORT const char CCONN__INSIDE_PROBE
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ + │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,82 +1,82 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ -logitModel.h │ │ │ │ + * _S_O_L_V_A_T_I_O_N │ │ │ │ +molecularSurfaceGrid.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// │ │ │ │ -5 │ │ │ │ -6#ifndef LOGITMODEL │ │ │ │ -7#define LOGITMODEL │ │ │ │ -8 │ │ │ │ -9#ifndef CLASSIFICATION │ │ │ │ -10#include <_B_A_L_L_/_Q_S_A_R_/_c_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l_._h> │ │ │ │ -11#endif │ │ │ │ -12 │ │ │ │ +4// $Id: molecularSurfaceGrid.h,v 1.15 2005/12/23 17:01:59 amoll Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_SOLVATION_MOLECULARSURFACEGRID_H │ │ │ │ +8#define BALL_SOLVATION_MOLECULARSURFACEGRID_H │ │ │ │ +9 │ │ │ │ +10#ifndef BALL_COMMON_H │ │ │ │ +11# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +12#endif │ │ │ │ 13 │ │ │ │ -14 │ │ │ │ -15namespace _B_A_L_L{ │ │ │ │ -16 namespace QSAR { │ │ │ │ +14#ifndef BALL_MATHS_VECTOR3_H │ │ │ │ +15# include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +16#endif │ │ │ │ 17 │ │ │ │ -_1_9 class _B_A_L_L___E_X_P_O_R_T _L_o_g_i_t_M_o_d_e_l : public _C_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l │ │ │ │ -20 { │ │ │ │ -21 public: │ │ │ │ -_2_5 _L_o_g_i_t_M_o_d_e_l(const _Q_S_A_R_D_a_t_a& q); │ │ │ │ -26 │ │ │ │ -_2_7 _~_L_o_g_i_t_M_o_d_e_l(); │ │ │ │ +18#ifndef BALL_KERNEL_SYSTEM_H │ │ │ │ +19# include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ +20#endif │ │ │ │ +21 │ │ │ │ +22#ifndef BALL_DATATYPE_REGULARDATA3D_H │ │ │ │ +23# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_r_e_g_u_l_a_r_D_a_t_a_3_D_._h> │ │ │ │ +24#endif │ │ │ │ +25 │ │ │ │ +26namespace _B_A_L_L │ │ │ │ +27{ │ │ │ │ 28 │ │ │ │ -29 EIGEN_MAKE_ALIGNED_OPERATOR_NEW │ │ │ │ -31 │ │ │ │ -32 │ │ │ │ -_3_6 void _t_r_a_i_n(); │ │ │ │ -37 │ │ │ │ -_3_8 Eigen::VectorXd _p_r_e_d_i_c_t(const vector& substance, bool transform); │ │ │ │ -39 │ │ │ │ -_4_0 void _s_a_v_e_T_o_F_i_l_e(string filename); │ │ │ │ -41 │ │ │ │ -_4_2 void _r_e_a_d_F_r_o_m_F_i_l_e(string filename); │ │ │ │ -44 │ │ │ │ -45 │ │ │ │ -46 protected: │ │ │ │ -_5_0 Eigen::MatrixXd _t_r_a_i_n_i_n_g___r_e_s_u_l_t__; │ │ │ │ -52 │ │ │ │ -53 }; │ │ │ │ -54 } │ │ │ │ -55} │ │ │ │ -56 │ │ │ │ -57#endif // LOGITMODEL │ │ │ │ -_c_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l_._h │ │ │ │ +29 // Define the entry values for an SES or SAS grid │ │ │ │ +30 _B_A_L_L___E_X_P_O_R_T extern const char _C_C_O_N_N_____I_N_S_I_D_E; │ │ │ │ +31 _B_A_L_L___E_X_P_O_R_T extern const char _C_C_O_N_N_____O_U_T_S_I_D_E; │ │ │ │ +32 _B_A_L_L___E_X_P_O_R_T extern const char _C_C_O_N_N_____I_N_S_I_D_E___P_R_O_B_E; │ │ │ │ +33 │ │ │ │ +_3_7 _B_A_L_L___E_X_P_O_R_T _T_R_e_g_u_l_a_r_D_a_t_a_3_D_<_c_h_a_r_>* _c_a_l_c_u_l_a_t_e_S_E_S_G_r_i_d │ │ │ │ +38 (const _V_e_c_t_o_r_3& lower, const _V_e_c_t_o_r_3& upper, │ │ │ │ +39 float spacing, const _S_y_s_t_e_m& system, float probe_radius); │ │ │ │ +40 │ │ │ │ +_4_4 _B_A_L_L___E_X_P_O_R_T _T_R_e_g_u_l_a_r_D_a_t_a_3_D_<_c_h_a_r_>* _c_a_l_c_u_l_a_t_e_S_A_S_G_r_i_d │ │ │ │ +45 (const _V_e_c_t_o_r_3& lower, const _V_e_c_t_o_r_3& upper, │ │ │ │ +46 float spacing, const _S_y_s_t_e_m& system, float probe_radius); │ │ │ │ +47 │ │ │ │ +48 │ │ │ │ +49} // namespace BALL │ │ │ │ +50 │ │ │ │ +51#endif // BALL_SOLVATION_MOLECULARSURFACEGRID_H │ │ │ │ +_c_o_m_m_o_n_._h │ │ │ │ +_v_e_c_t_o_r_3_._h │ │ │ │ +_r_e_g_u_l_a_r_D_a_t_a_3_D_._h │ │ │ │ +_B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_S_E_S_G_r_i_d │ │ │ │ +BALL_EXPORT TRegularData3D< char > * calculateSESGrid(const Vector3 &lower, │ │ │ │ +const Vector3 &upper, float spacing, const System &system, float probe_radius) │ │ │ │ +_B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_S_A_S_G_r_i_d │ │ │ │ +BALL_EXPORT TRegularData3D< char > * calculateSASGrid(const Vector3 &lower, │ │ │ │ +const Vector3 &upper, float spacing, const System &system, float probe_radius) │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_C_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l │ │ │ │ -DDeeffiinniittiioonn _c_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l_._h_:_2_8 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_L_o_g_i_t_M_o_d_e_l │ │ │ │ -DDeeffiinniittiioonn _l_o_g_i_t_M_o_d_e_l_._h_:_2_0 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_L_o_g_i_t_M_o_d_e_l_:_:_L_o_g_i_t_M_o_d_e_l │ │ │ │ -LogitModel(const QSARData &q) │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_L_o_g_i_t_M_o_d_e_l_:_:_p_r_e_d_i_c_t │ │ │ │ -Eigen::VectorXd predict(const vector< double > &substance, bool transform) │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_L_o_g_i_t_M_o_d_e_l_:_:_~_L_o_g_i_t_M_o_d_e_l │ │ │ │ -~LogitModel() │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_L_o_g_i_t_M_o_d_e_l_:_:_r_e_a_d_F_r_o_m_F_i_l_e │ │ │ │ -void readFromFile(string filename) │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_L_o_g_i_t_M_o_d_e_l_:_:_t_r_a_i_n_i_n_g___r_e_s_u_l_t__ │ │ │ │ -Eigen::MatrixXd training_result_ │ │ │ │ -DDeeffiinniittiioonn _l_o_g_i_t_M_o_d_e_l_._h_:_5_0 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_L_o_g_i_t_M_o_d_e_l_:_:_s_a_v_e_T_o_F_i_l_e │ │ │ │ -void saveToFile(string filename) │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_L_o_g_i_t_M_o_d_e_l_:_:_t_r_a_i_n │ │ │ │ -void train() │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_Q_S_A_R_D_a_t_a │ │ │ │ -DDeeffiinniittiioonn _Q_S_A_R_D_a_t_a_._h_:_5_6 │ │ │ │ +_B_A_L_L_:_:_C_C_O_N_N_____O_U_T_S_I_D_E │ │ │ │ +BALL_EXPORT const char CCONN__OUTSIDE │ │ │ │ +_B_A_L_L_:_:_C_C_O_N_N_____I_N_S_I_D_E │ │ │ │ +BALL_EXPORT const char CCONN__INSIDE │ │ │ │ +_B_A_L_L_:_:_C_C_O_N_N_____I_N_S_I_D_E___P_R_O_B_E │ │ │ │ +BALL_EXPORT const char CCONN__INSIDE_PROBE │ │ │ │ +_B_A_L_L_:_:_T_R_e_g_u_l_a_r_D_a_t_a_3_D │ │ │ │ +DDeeffiinniittiioonn _r_e_g_u_l_a_r_D_a_t_a_3_D_._h_:_4_6 │ │ │ │ +_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ +DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_s_y_s_t_e_m_._h │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d61/a03858.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Public Attributes | │ │ │ List of all members │ │ │
    BALL::CIFFile::SaveFrame Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/FORMAT/CIFFile.h>

    │ │ │ +

    #include <BALL/FORMAT/CIFFile.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -122,15 +122,15 @@ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    void clear ()
     
    void start (String name)
     
     
    Item dummy_data_item_
     
    │ │ │

    Detailed Description

    │ │ │

    Nested class for the saveframes of the CIFFile

    │ │ │ │ │ │ -

    Definition at line 76 of file CIFFile.h.

    │ │ │ +

    Definition at line 76 of file CIFFile.h.

    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ addDataItem()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -182,15 +182,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 86 of file CIFFile.h.

    │ │ │ +

    Definition at line 86 of file CIFFile.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getDataItem() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -337,15 +337,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 83 of file CIFFile.h.

    │ │ │ +

    Definition at line 83 of file CIFFile.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ start()

    │ │ │ │ │ │
    │ │ │ @@ -372,15 +372,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    String BALL::CIFFile::SaveFrame::category
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 105 of file CIFFile.h.

    │ │ │ +

    Definition at line 105 of file CIFFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ dummy_data_item_

    │ │ │ │ │ │
    │ │ │ @@ -388,15 +388,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Item BALL::CIFFile::SaveFrame::dummy_data_item_
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 111 of file CIFFile.h.

    │ │ │ +

    Definition at line 111 of file CIFFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ framename

    │ │ │ │ │ │
    │ │ │ @@ -405,15 +405,15 @@ │ │ │ │ │ │ String BALL::CIFFile::SaveFrame::framename │ │ │ │ │ │ │ │ │
    │ │ │

    The name of this saveframe

    │ │ │ │ │ │ -

    Definition at line 104 of file CIFFile.h.

    │ │ │ +

    Definition at line 104 of file CIFFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ items

    │ │ │ │ │ │
    │ │ │ @@ -423,15 +423,15 @@ │ │ │ std::vector<Item> BALL::CIFFile::SaveFrame::items │ │ │ │ │ │ │ │ │
    │ │ │

    Stores all dataitems of the saveframe
    │ │ │

    │ │ │ │ │ │ -

    Definition at line 108 of file CIFFile.h.

    │ │ │ +

    Definition at line 108 of file CIFFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ pair_items

    │ │ │ │ │ │
    │ │ │ @@ -439,15 +439,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    StringHashMap<Index> BALL::CIFFile::SaveFrame::pair_items
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 109 of file CIFFile.h.

    │ │ │ +

    Definition at line 109 of file CIFFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d64/a06166.html │ │ │ @@ -83,15 +83,15 @@ │ │ │ Protected Attributes | │ │ │ Friends | │ │ │ List of all members │ │ │
    BALL::ScoringFunction Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SCORING/COMMON/scoringFunction.h>

    │ │ │ +

    #include <BALL/SCORING/COMMON/scoringFunction.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::ScoringFunction:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::DifferentiableScoringFunction │ │ │ @@ -426,15 +426,15 @@ │ │ │ class PharmacophoreConstraint │ │ │   │ │ │ class SideChainOptimizer │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 28 of file scoringFunction.h.

    │ │ │ +

    Definition at line 28 of file scoringFunction.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ScoringFunction() [1/6]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -2763,15 +2763,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ friend
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 31 of file scoringFunction.h.

    │ │ │ +

    Definition at line 31 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ SideChainOptimizer

    │ │ │ │ │ │
    │ │ │ @@ -2787,15 +2787,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 32 of file scoringFunction.h.

    │ │ │ +

    Definition at line 32 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ all_ligand_nonbonded_

    │ │ │ │ │ │ @@ -2813,15 +2813,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    All nonbonded pairs of the current ligand. Calculated without cutoff by createAllLigandNonBondedPairs().

    │ │ │ │ │ │ -

    Definition at line 770 of file scoringFunction.h.

    │ │ │ +

    Definition at line 770 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ all_residues_hashgrid_

    │ │ │ │ │ │
    │ │ │ @@ -2837,15 +2837,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 669 of file scoringFunction.h.

    │ │ │ +

    Definition at line 669 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ allowed_intermolecular_overlap_

    │ │ │ │ │ │
    │ │ │ @@ -2862,15 +2862,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Allowed overlap in Angstroem for two atoms of two different molecules (used since even in many crystal structures, some atoms overlap minimally).

    │ │ │ │ │ │ -

    Definition at line 735 of file scoringFunction.h.

    │ │ │ +

    Definition at line 735 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ allowed_intramolecular_overlap_

    │ │ │ │ │ │
    │ │ │ @@ -2887,15 +2887,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Allowed overlap in Angstroem for two atoms of the same molecule (used since even in many crystal structures, some atoms overlap minimally).

    │ │ │ │ │ │ -

    Definition at line 741 of file scoringFunction.h.

    │ │ │ +

    Definition at line 741 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ atoms_to_fragments_

    │ │ │ │ │ │
    │ │ │ @@ -2912,15 +2912,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Maps each ligand atom to its StaticLigandFragments (if StaticLigandFragments have been calculated).

    │ │ │ │ │ │ -

    Definition at line 681 of file scoringFunction.h.

    │ │ │ +

    Definition at line 681 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ base_function_

    │ │ │ │ │ │
    │ │ │ @@ -2937,15 +2937,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    The base funcion for scoring simple terms

    │ │ │ │ │ │ -

    Definition at line 626 of file scoringFunction.h.

    │ │ │ +

    Definition at line 626 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ burial_depth_scale_

    │ │ │ │ │ │
    │ │ │ @@ -2961,15 +2961,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 787 of file scoringFunction.h.

    │ │ │ +

    Definition at line 787 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ conformation_scale_

    │ │ │ │ │ │
    │ │ │ @@ -2986,15 +2986,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Allows scaling down the contribution of the conformational energy of the ligand to the overall score.

    │ │ │ │ │ │ -

    Definition at line 775 of file scoringFunction.h.

    │ │ │ +

    Definition at line 775 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ constraints

    │ │ │ │ │ │
    │ │ │ @@ -3004,15 +3004,15 @@ │ │ │ list<Constraint*> BALL::ScoringFunction::constraints {} │ │ │ │ │ │ │ │ │
    │ │ │

    List holding all ReferenceAreas of the ScoringFunction.
    │ │ │ ReferenceAreas can be added/deleted/modified directly by the user and will be used during all future calls of updateScore().

    │ │ │ │ │ │ -

    Definition at line 460 of file scoringFunction.h.

    │ │ │ +

    Definition at line 460 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ exp_energy_mean_

    │ │ │ │ │ │
    │ │ │ @@ -3029,15 +3029,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Mean of the experimentally determined binding free energy of the used training data set.

    │ │ │ │ │ │ -

    Definition at line 797 of file scoringFunction.h.

    │ │ │ +

    Definition at line 797 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ exp_energy_stddev_

    │ │ │ │ │ │
    │ │ │ @@ -3054,15 +3054,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Standard deviation of the experimentally determined binding free energy of the used training data set.

    │ │ │ │ │ │ -

    Definition at line 792 of file scoringFunction.h.

    │ │ │ +

    Definition at line 792 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ flexible_residues_

    │ │ │ │ │ │
    │ │ │ @@ -3078,15 +3078,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 799 of file scoringFunction.h.

    │ │ │ +

    Definition at line 799 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ flexible_residues_hashgrid_

    │ │ │ │ │ │
    │ │ │ @@ -3102,15 +3102,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 671 of file scoringFunction.h.

    │ │ │ +

    Definition at line 671 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ flexres_org_positions_

    │ │ │ │ │ │
    │ │ │ @@ -3127,15 +3127,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Original positions of all atoms of all flexible residues, i.e. as they appear in the input receptor object.

    │ │ │ │ │ │ -

    Definition at line 821 of file scoringFunction.h.

    │ │ │ +

    Definition at line 821 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ hashgrid_

    │ │ │ │ │ │
    │ │ │ @@ -3152,15 +3152,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    HashGrid used to find potential interaction partners for a ligand atom.

    │ │ │ │ │ │ -

    Definition at line 667 of file scoringFunction.h.

    │ │ │ +

    Definition at line 667 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ hashgrid_search_radius_

    │ │ │ │ │ │
    │ │ │ @@ -3177,15 +3177,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Number of boxes around a ligand atom that are to be searched.

    │ │ │ │ │ │ -

    Definition at line 704 of file scoringFunction.h.

    │ │ │ +

    Definition at line 704 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ignore_h_clashes_

    │ │ │ │ │ │
    │ │ │ @@ -3202,15 +3202,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Determines whether an overlap between two Hydrogen atoms should be considered a sterical clash.

    │ │ │ │ │ │ -

    Definition at line 719 of file scoringFunction.h.

    │ │ │ +

    Definition at line 719 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ intercept_

    │ │ │ │ │ │
    │ │ │ @@ -3227,15 +3227,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    The intercept necessary for calculating the score

    │ │ │ │ │ │ -

    Definition at line 621 of file scoringFunction.h.

    │ │ │ +

    Definition at line 621 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ligand_

    │ │ │ │ │ │
    │ │ │ @@ -3252,15 +3252,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Ligand to dock

    │ │ │ │ │ │ -

    Definition at line 611 of file scoringFunction.h.

    │ │ │ +

    Definition at line 611 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ligand_atoms_

    │ │ │ │ │ │
    │ │ │ @@ -3277,15 +3277,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Number of atoms of the current ligand candidate. Value is set by each call of calculateGeometricalCenter()

    │ │ │ │ │ │ -

    Definition at line 657 of file scoringFunction.h.

    │ │ │ +

    Definition at line 657 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ligand_center_

    │ │ │ │ │ │
    │ │ │ @@ -3302,15 +3302,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Geometrical center of the current ligand

    │ │ │ │ │ │ -

    Definition at line 662 of file scoringFunction.h.

    │ │ │ +

    Definition at line 662 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ligand_intramol_overlaps_

    │ │ │ │ │ │
    │ │ │ @@ -3327,15 +3327,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Number of overlapping ligand atom pairs as determined by the last call of update().

    │ │ │ │ │ │ -

    Definition at line 729 of file scoringFunction.h.

    │ │ │ +

    Definition at line 729 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ligand_radius_

    │ │ │ │ │ │
    │ │ │ @@ -3352,15 +3352,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Radius of the current ligand, i.e. the maximal distance from its geometrical center

    │ │ │ │ │ │ -

    Definition at line 651 of file scoringFunction.h.

    │ │ │ +

    Definition at line 651 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ max_number_of_errors_

    │ │ │ │ │ │
    │ │ │ @@ -3377,15 +3377,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Max number of unassigned atoms

    │ │ │ │ │ │ -

    Definition at line 641 of file scoringFunction.h.

    │ │ │ +

    Definition at line 641 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ misplaced_ligand_atoms_

    │ │ │ │ │ │
    │ │ │ @@ -3402,15 +3402,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Number of ligand atoms that were found to be lying outside of hash_grid_, as determined by the last call of createNonBondedPairList().

    │ │ │ │ │ │ -

    Definition at line 699 of file scoringFunction.h.

    │ │ │ +

    Definition at line 699 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ name_

    │ │ │ │ │ │
    │ │ │ @@ -3427,15 +3427,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Name of the scoring function

    │ │ │ │ │ │ -

    Definition at line 596 of file scoringFunction.h.

    │ │ │ +

    Definition at line 596 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ neighbor_cutoff_2_

    │ │ │ │ │ │
    │ │ │ @@ -3452,15 +3452,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Number of target atoms within this squared distance of ligand atoms are used to approximate the depth of burial of the ligand.

    │ │ │ │ │ │ -

    Definition at line 747 of file scoringFunction.h.

    │ │ │ +

    Definition at line 747 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ neighboring_target_atoms_

    │ │ │ │ │ │
    │ │ │ @@ -3478,15 +3478,15 @@ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Average number of target atoms within a distance of 'neighbor_cutoff' Angstroem of a ligand atom.
    │ │ │ the value is calculated during each call of createNonBondedPairList().

    │ │ │ │ │ │ -

    Definition at line 693 of file scoringFunction.h.

    │ │ │ +

    Definition at line 693 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ nonbonded_cutoff_

    │ │ │ │ │ │
    │ │ │ @@ -3503,15 +3503,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Cutoff value for nonbonded energy.

    │ │ │ │ │ │ -

    Definition at line 709 of file scoringFunction.h.

    │ │ │ +

    Definition at line 709 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ nonbonded_cutoff_2_

    │ │ │ │ │ │
    │ │ │ @@ -3528,15 +3528,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Squared cutoff value for nonbonded energy.

    │ │ │ │ │ │ -

    Definition at line 714 of file scoringFunction.h.

    │ │ │ +

    Definition at line 714 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ number_of_errors_

    │ │ │ │ │ │
    │ │ │ @@ -3553,15 +3553,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Actual number of counted errors

    │ │ │ │ │ │ -

    Definition at line 646 of file scoringFunction.h.

    │ │ │ +

    Definition at line 646 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ options_

    │ │ │ │ │ │
    │ │ │ @@ -3578,15 +3578,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Scoring function options

    │ │ │ │ │ │ -

    Definition at line 601 of file scoringFunction.h.

    │ │ │ +

    Definition at line 601 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ overlaps_

    │ │ │ │ │ │
    │ │ │ @@ -3603,15 +3603,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Number of overlapping receptor-ligand atom pairs as determined by the last call of update().

    │ │ │ │ │ │ -

    Definition at line 724 of file scoringFunction.h.

    │ │ │ +

    Definition at line 724 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ receptor_

    │ │ │ │ │ │
    │ │ │ @@ -3628,15 +3628,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Receptor to dock in

    │ │ │ │ │ │ -

    Definition at line 606 of file scoringFunction.h.

    │ │ │ +

    Definition at line 606 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ reference_neighbors_

    │ │ │ │ │ │
    │ │ │ @@ -3653,15 +3653,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Average number of interactions per atom of a reference ligand within a small radius. This is used to estimate the depth of burial of the ligand (candidate).

    │ │ │ │ │ │ -

    Definition at line 687 of file scoringFunction.h.

    │ │ │ +

    Definition at line 687 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ resolution_

    │ │ │ │ │ │
    │ │ │ @@ -3678,15 +3678,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Resolution that was specified by use of the Options object in the constructor.

    │ │ │ │ │ │ -

    Definition at line 676 of file scoringFunction.h.

    │ │ │ +

    Definition at line 676 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ result_

    │ │ │ │ │ │
    │ │ │ @@ -3703,15 +3703,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Saves the final and all intermediate results of the last call of updateScore().

    │ │ │ │ │ │ -

    Definition at line 804 of file scoringFunction.h.

    │ │ │ +

    Definition at line 804 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ rotatable_ligand_bonds_

    │ │ │ │ │ │
    │ │ │ @@ -3728,15 +3728,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Rotatable bonds of the current ligand molecule. They are calculated by the function createStaticLigandFragments().

    │ │ │ │ │ │ -

    Definition at line 815 of file scoringFunction.h.

    │ │ │ +

    Definition at line 815 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ score_

    │ │ │ │ │ │
    │ │ │ @@ -3753,15 +3753,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Overall score of the scoring function

    │ │ │ │ │ │ -

    Definition at line 616 of file scoringFunction.h.

    │ │ │ +

    Definition at line 616 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ scoring_components_

    │ │ │ │ │ │
    │ │ │ @@ -3778,15 +3778,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    The scoring components used by a particular scoring function (e.g. HBonds, VDW, etc.)

    │ │ │ │ │ │ -

    Definition at line 631 of file scoringFunction.h.

    │ │ │ +

    Definition at line 631 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ static_ligand_energy_

    │ │ │ │ │ │
    │ │ │ @@ -3803,15 +3803,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Energy of the StaticLigandFragments. Is calculated once for each ligand candidate by createStaticLigandFragments().

    │ │ │ │ │ │ -

    Definition at line 809 of file scoringFunction.h.

    │ │ │ +

    Definition at line 809 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ static_ligand_fragments_

    │ │ │ │ │ │
    │ │ │ @@ -3830,15 +3830,15 @@ │ │ │ │ │ │ │ │ │
    │ │ │

    contains the static fragments of the current ligand candidate.
    │ │ │ The conformation of each ligand is not changed during docking; only the position of fragments in relation to each other is modified.
    │ │ │ Thus, if static_ligand_fragments_ is not empty, createNonBondedPairList() will automatically search only for inter-fragment atom-pairs and ligand-receptor pairs, but not for intra-fragment pairs.

    │ │ │ │ │ │ -

    Definition at line 756 of file scoringFunction.h.

    │ │ │ +

    Definition at line 756 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ static_residues_hashgrid_

    │ │ │ │ │ │
    │ │ │ @@ -3854,15 +3854,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 670 of file scoringFunction.h.

    │ │ │ +

    Definition at line 670 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ store_interactions_

    │ │ │ │ │ │
    │ │ │ @@ -3880,15 +3880,15 @@ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Determines whether interactions calculated by this ScoringFunction should be saved to each ligand atom a in a->interactions.
    │ │ │ By default this is disabled for new ScoringFunctions.

    │ │ │ │ │ │ -

    Definition at line 763 of file scoringFunction.h.

    │ │ │ +

    Definition at line 763 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ store_interactions_phC_only_

    │ │ │ │ │ │
    │ │ │ @@ -3904,15 +3904,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 765 of file scoringFunction.h.

    │ │ │ +

    Definition at line 765 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ SUBCATEGORY_NAME

    │ │ │ │ │ │
    │ │ │ @@ -3928,15 +3928,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 36 of file scoringFunction.h.

    │ │ │ +

    Definition at line 36 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ unassigned_atoms_

    │ │ │ │ │ │
    │ │ │ @@ -3953,15 +3953,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    Atoms, for which the setup of the force field fails

    │ │ │ │ │ │ -

    Definition at line 636 of file scoringFunction.h.

    │ │ │ +

    Definition at line 636 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ use_all_lig_nonb_

    │ │ │ │ │ │
    │ │ │ @@ -3978,15 +3978,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    see Default::ALL_LIG_NONB_PAIRS

    │ │ │ │ │ │ -

    Definition at line 780 of file scoringFunction.h.

    │ │ │ +

    Definition at line 780 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ use_static_lig_fragments_

    │ │ │ │ │ │
    │ │ │ @@ -4003,15 +4003,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    see Default::USE_STATIC_LIG_FRAGMENTS

    │ │ │ │ │ │ -

    Definition at line 785 of file scoringFunction.h.

    │ │ │ +

    Definition at line 785 of file scoringFunction.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d67/a01232.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: pyConstant.h File Reference │ │ │ +BALL: atom.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,38 +65,230 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces
    │ │ │ -
    pyConstant.h File Reference
    │ │ │ +Namespaces | │ │ │ +Macros
    │ │ │ +
    atom.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/COMMON/global.h>
    │ │ │ +
    #include <BALL/CONCEPT/composite.h>
    │ │ │ +#include <BALL/CONCEPT/property.h>
    │ │ │ +#include <BALL/CONCEPT/randomAccessIterator.h>
    │ │ │ +#include <BALL/MATHS/vector3.h>
    │ │ │ +#include <BALL/KERNEL/atom.iC>
    │ │ │ +#include <BALL/KERNEL/bondIterator.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::Constant
    class  BALL::Atom
     
    class  BALL::Atom::BondIteratorTraits
     
    │ │ │ │ │ │ │ │ │ │ │ │ +

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ +Macros

    #define BALL_ATOM_DEFAULT_ELEMENT   &Element::UNKNOWN
     
    #define BALL_ATOM_DEFAULT_CHARGE   0
     
    #define BALL_ATOM_DEFAULT_FORMAL_CHARGE   0
     
    #define BALL_ATOM_DEFAULT_NAME   ""
     
    #define BALL_ATOM_DEFAULT_TYPE_NAME   "?"
     
    #define BALL_ATOM_DEFAULT_POSITION   0,0,0
     
    #define BALL_ATOM_DEFAULT_RADIUS   0
     
    #define BALL_ATOM_DEFAULT_TYPE   Atom::UNKNOWN_TYPE
     
    #define BALL_ATOM_DEFAULT_VELOCITY   0,0,0
     
    #define BALL_ATOM_DEFAULT_FORCE   0,0,0
     
    │ │ │ +

    Macro Definition Documentation

    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_CHARGE

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_CHARGE   0
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 26 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_ELEMENT

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_ELEMENT   &Element::UNKNOWN
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 25 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_FORCE

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_FORCE   0,0,0
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 34 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_FORMAL_CHARGE

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_FORMAL_CHARGE   0
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 27 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_NAME

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_NAME   ""
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 28 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_POSITION

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_POSITION   0,0,0
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 30 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_RADIUS

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_RADIUS   0
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 31 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_TYPE

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_TYPE   Atom::UNKNOWN_TYPE
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 32 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_TYPE_NAME

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_TYPE_NAME   "?"
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 29 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_ATOM_DEFAULT_VELOCITY

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_ATOM_DEFAULT_VELOCITY   0,0,0
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 33 of file atom.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,20 +1,78 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _P_Y_T_H_O_N │ │ │ │ - * _E_X_T_E_N_S_I_O_N_S │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -pyConstant.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s │ │ │ │ +atom.h File Reference │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_c_o_m_p_o_s_i_t_e_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_p_e_r_t_y_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_r_a_n_d_o_m_A_c_c_e_s_s_I_t_e_r_a_t_o_r_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +#include │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_b_o_n_d_I_t_e_r_a_t_o_r_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_C_o_n_s_t_a_n_t │ │ │ │ +class   _B_A_L_L_:_:_A_t_o_m │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +MMaaccrrooss │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___E_L_E_M_E_N_T   &_E_l_e_m_e_n_t_:_:_U_N_K_N_O_W_N │ │ │ │ +  │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___C_H_A_R_G_E   0 │ │ │ │ +  │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___F_O_R_M_A_L___C_H_A_R_G_E   0 │ │ │ │ +  │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___N_A_M_E   "" │ │ │ │ +  │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___T_Y_P_E___N_A_M_E   "?" │ │ │ │ +  │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___P_O_S_I_T_I_O_N   0,0,0 │ │ │ │ +  │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___R_A_D_I_U_S   0 │ │ │ │ +  │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___T_Y_P_E   Atom::UNKNOWN_TYPE │ │ │ │ +  │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___V_E_L_O_C_I_T_Y   0,0,0 │ │ │ │ +  │ │ │ │ +#define  _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___F_O_R_C_E   0,0,0 │ │ │ │ +  │ │ │ │ +********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__CCHHAARRGGEE ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_CHARGE   0 │ │ │ │ +Definition at line _2_6 of file _a_t_o_m_._h. │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__EELLEEMMEENNTT ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_ELEMENT   &_E_l_e_m_e_n_t_:_:_U_N_K_N_O_W_N │ │ │ │ +Definition at line _2_5 of file _a_t_o_m_._h. │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__FFOORRCCEE ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_FORCE   0,0,0 │ │ │ │ +Definition at line _3_4 of file _a_t_o_m_._h. │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__FFOORRMMAALL__CCHHAARRGGEE ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_FORMAL_CHARGE   0 │ │ │ │ +Definition at line _2_7 of file _a_t_o_m_._h. │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__NNAAMMEE ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_NAME   "" │ │ │ │ +Definition at line _2_8 of file _a_t_o_m_._h. │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__PPOOSSIITTIIOONN ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_POSITION   0,0,0 │ │ │ │ +Definition at line _3_0 of file _a_t_o_m_._h. │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__RRAADDIIUUSS ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_RADIUS   0 │ │ │ │ +Definition at line _3_1 of file _a_t_o_m_._h. │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__TTYYPPEE ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_TYPE   Atom::UNKNOWN_TYPE │ │ │ │ +Definition at line _3_2 of file _a_t_o_m_._h. │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__TTYYPPEE__NNAAMMEE ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_TYPE_NAME   "?" │ │ │ │ +Definition at line _2_9 of file _a_t_o_m_._h. │ │ │ │ +********** _?◆_? BBAALLLL__AATTOOMM__DDEEFFAAUULLTT__VVEELLOOCCIITTYY ********** │ │ │ │ +#define BALL_ATOM_DEFAULT_VELOCITY   0,0,0 │ │ │ │ +Definition at line _3_3 of file _a_t_o_m_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d67/a01232_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: pyConstant.h Source File │ │ │ +BALL: atom.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,152 +70,785 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    pyConstant.h
    │ │ │ +
    atom.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4// $Id: pyConstant.h,v 1.12 2005/12/23 17:01:57 amoll Exp $
    │ │ │ -
    5//
    │ │ │ -
    6
    │ │ │ -
    7#ifndef BALL_PYTHON_PYCONSTANT_H
    │ │ │ -
    8#define BALL_PYTHON_PYCONSTANT_H
    │ │ │ -
    9
    │ │ │ -
    10#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ -
    11# include <BALL/COMMON/global.h>
    │ │ │ -
    12#endif
    │ │ │ -
    13
    │ │ │ -
    14namespace BALL
    │ │ │ -
    15{
    │ │ │ -
    16
    │ │ │ -
    │ │ │ -
    21 class Constant
    │ │ │ -
    22 {
    │ │ │ -
    23 public:
    │ │ │ -
    24
    │ │ │ -
    25 // PI
    │ │ │ -
    26 static double PI;
    │ │ │ -
    27
    │ │ │ -
    29 static double E;
    │ │ │ -
    30
    │ │ │ -
    34 static double EPSILON;
    │ │ │ -
    38 static double ELEMENTARY_CHARGE; // C
    │ │ │ -
    39
    │ │ │ -
    41 static double e0;
    │ │ │ -
    42
    │ │ │ -
    46 static double ELECTRON_MASS ; // kg
    │ │ │ -
    47
    │ │ │ -
    51 static double PROTON_MASS ; // kg
    │ │ │ -
    52
    │ │ │ -
    56 static double NEUTRON_MASS ; // kg
    │ │ │ -
    57
    │ │ │ -
    61 static double AVOGADRO;
    │ │ │ -
    62
    │ │ │ -
    65 static double NA;
    │ │ │ -
    66
    │ │ │ -
    69 static double MOL;
    │ │ │ -
    70
    │ │ │ -
    74 static double BOLTZMANN;
    │ │ │ -
    75
    │ │ │ -
    78 static double k;
    │ │ │ -
    79
    │ │ │ -
    83 static double PLANCK;
    │ │ │ -
    84
    │ │ │ -
    87 static double h;
    │ │ │ -
    88
    │ │ │ -
    91 static double GAS_CONSTANT;
    │ │ │ +
    4
    │ │ │ +
    5#ifndef BALL_KERNEL_ATOM_H
    │ │ │ +
    6#define BALL_KERNEL_ATOM_H
    │ │ │ +
    7
    │ │ │ +
    8#ifndef BALL_CONCEPT_COMPOSITE_H
    │ │ │ +
    9# include <BALL/CONCEPT/composite.h>
    │ │ │ +
    10#endif
    │ │ │ +
    11
    │ │ │ +
    12#ifndef BALL_CONCEPT_PROPERTY_H
    │ │ │ +
    13# include <BALL/CONCEPT/property.h>
    │ │ │ +
    14#endif
    │ │ │ +
    15
    │ │ │ +
    16#ifndef BALL_CONCEPT_RANDOMACCESSITERATOR_H
    │ │ │ +
    17# include <BALL/CONCEPT/randomAccessIterator.h>
    │ │ │ +
    18#endif
    │ │ │ +
    19
    │ │ │ +
    20#ifndef BALL_MATHS_VECTOR3_H
    │ │ │ +
    21# include <BALL/MATHS/vector3.h>
    │ │ │ +
    22#endif
    │ │ │ +
    23
    │ │ │ +
    24// Defines for default values for an atom
    │ │ │ +
    25#define BALL_ATOM_DEFAULT_ELEMENT &Element::UNKNOWN
    │ │ │ +
    26#define BALL_ATOM_DEFAULT_CHARGE 0
    │ │ │ +
    27#define BALL_ATOM_DEFAULT_FORMAL_CHARGE 0
    │ │ │ +
    28#define BALL_ATOM_DEFAULT_NAME ""
    │ │ │ +
    29#define BALL_ATOM_DEFAULT_TYPE_NAME "?"
    │ │ │ +
    30#define BALL_ATOM_DEFAULT_POSITION 0,0,0
    │ │ │ +
    31#define BALL_ATOM_DEFAULT_RADIUS 0
    │ │ │ +
    32#define BALL_ATOM_DEFAULT_TYPE Atom::UNKNOWN_TYPE
    │ │ │ +
    33#define BALL_ATOM_DEFAULT_VELOCITY 0,0,0
    │ │ │ +
    34#define BALL_ATOM_DEFAULT_FORCE 0,0,0
    │ │ │ +
    35
    │ │ │ +
    36namespace BALL
    │ │ │ +
    37{
    │ │ │ +
    38 class Bond;
    │ │ │ +
    39 class Element;
    │ │ │ +
    40 class Fragment;
    │ │ │ +
    41 class Residue;
    │ │ │ +
    42 class Chain;
    │ │ │ +
    43 class SecondaryStructure;
    │ │ │ +
    44 class Molecule;
    │ │ │ +
    45 class MolecularInteractions;
    │ │ │ +
    46
    │ │ │ +
    │ │ │ +
    87 class BALL_EXPORT Atom
    │ │ │ +
    88 : public Composite,
    │ │ │ +
    89 public PropertyManager
    │ │ │ +
    90 {
    │ │ │ +
    91 public:
    │ │ │
    92
    │ │ │ -
    95 static double R;
    │ │ │ -
    96
    │ │ │ -
    99 static double FARADAY;
    │ │ │ +
    97 friend class Bond;
    │ │ │ +
    98
    │ │ │ +
    99 BALL_CREATE_DEEP(Atom)
    │ │ │
    100
    │ │ │ -
    103 static double F;
    │ │ │ +
    101
    │ │ │ +
    103 typedef short Type;
    │ │ │
    104
    │ │ │ -
    108 static double BOHR_RADIUS;
    │ │ │ -
    109
    │ │ │ -
    112 static double a0;
    │ │ │ -
    113
    │ │ │ -
    114 // the following values from:
    │ │ │ -
    115 // P.W.Atkins: Physical Chemistry, 5th ed., Oxford University Press, 1995
    │ │ │ -
    116
    │ │ │ -
    120 static double VACUUM_PERMITTIVITY;
    │ │ │ -
    121
    │ │ │ -
    125 static double VACUUM_PERMEABILITY;
    │ │ │ +
    108
    │ │ │ +
    111 enum
    │ │ │ +
    112 {
    │ │ │ +
    116 UNKNOWN_TYPE = -1,
    │ │ │ +
    117
    │ │ │ +
    121 ANY_TYPE = 0,
    │ │ │ +
    122
    │ │ │ +
    124 MAX_NUMBER_OF_BONDS = 12
    │ │ │ +
    125 };
    │ │ │
    126
    │ │ │ -
    130 static double SPEED_OF_LIGHT;
    │ │ │ -
    131
    │ │ │ -
    134 static double c;
    │ │ │ -
    135
    │ │ │ -
    139 static double GRAVITATIONAL_CONSTANT;
    │ │ │ -
    140
    │ │ │ -
    144 static double FINE_STRUCTURE_CONSTANT;
    │ │ │ -
    145
    │ │ │ -
    149 static double DEG_PER_RAD;
    │ │ │ -
    150
    │ │ │ -
    154 static double RAD_PER_DEG;
    │ │ │ -
    155
    │ │ │ -
    159 static double MM_PER_INCH ;
    │ │ │ -
    160
    │ │ │ -
    164 static double M_PER_FOOT ;
    │ │ │ -
    165
    │ │ │ -
    169 static double JOULE_PER_CAL;
    │ │ │ -
    170
    │ │ │ -
    174 static double CAL_PER_JOULE;
    │ │ │ -
    175 };
    │ │ │ +
    │ │ │ +
    130 enum Property
    │ │ │ +
    131 {
    │ │ │ +
    132 NUMBER_OF_PROPERTIES = 0
    │ │ │ +
    133 };
    │ │ │ +
    │ │ │ +
    134
    │ │ │ +
    │ │ │ +
    138 enum FullNameType
    │ │ │ +
    139 {
    │ │ │ +
    140 // Do not add extensions
    │ │ │ +
    141 NO_VARIANT_EXTENSIONS,
    │ │ │ +
    142 // Add the residue extensions
    │ │ │ +
    143 ADD_VARIANT_EXTENSIONS,
    │ │ │ +
    144 // Add the residue ID
    │ │ │ +
    145 ADD_RESIDUE_ID,
    │ │ │ +
    146 // Add the residue ID and the residue extension
    │ │ │ +
    147 ADD_VARIANT_EXTENSIONS_AND_ID,
    │ │ │ +
    148 // Add the chain ID and the residue ID
    │ │ │ +
    149 ADD_CHAIN_RESIDUE_ID,
    │ │ │ +
    150 // Add the chain ID and the residue ID
    │ │ │ +
    151 ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID
    │ │ │ +
    152 };
    │ │ │
    │ │ │ -
    176
    │ │ │ -
    177} // namespace BALL
    │ │ │ +
    153
    │ │ │ +
    155
    │ │ │ +
    159
    │ │ │ +
    177 Atom();
    │ │ │
    178
    │ │ │ -
    179#endif // BALL_PYTHON_PYCONSTANT_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Constant::GRAVITATIONAL_CONSTANT
    static double GRAVITATIONAL_CONSTANT
    Definition pyConstant.h:139
    │ │ │ -
    BALL::Constant::AVOGADRO
    static double AVOGADRO
    Definition pyConstant.h:61
    │ │ │ -
    BALL::Constant::MOL
    static double MOL
    Definition pyConstant.h:69
    │ │ │ -
    BALL::Constant::CAL_PER_JOULE
    static double CAL_PER_JOULE
    Definition pyConstant.h:174
    │ │ │ -
    BALL::Constant::FINE_STRUCTURE_CONSTANT
    static double FINE_STRUCTURE_CONSTANT
    Definition pyConstant.h:144
    │ │ │ -
    BALL::Constant::GAS_CONSTANT
    static double GAS_CONSTANT
    Definition pyConstant.h:91
    │ │ │ -
    BALL::Constant::DEG_PER_RAD
    static double DEG_PER_RAD
    Definition pyConstant.h:149
    │ │ │ -
    BALL::Constant::MM_PER_INCH
    static double MM_PER_INCH
    Definition pyConstant.h:159
    │ │ │ -
    BALL::Constant::E
    static double E
    Euler's number - base of the natural logarithm.
    Definition pyConstant.h:29
    │ │ │ -
    BALL::Constant::FARADAY
    static double FARADAY
    Definition pyConstant.h:99
    │ │ │ -
    BALL::Constant::R
    static double R
    Definition pyConstant.h:95
    │ │ │ -
    BALL::Constant::BOLTZMANN
    static double BOLTZMANN
    Definition pyConstant.h:74
    │ │ │ -
    BALL::Constant::VACUUM_PERMEABILITY
    static double VACUUM_PERMEABILITY
    Definition pyConstant.h:125
    │ │ │ -
    BALL::Constant::e0
    static double e0
    Elementary charge (alias)
    Definition pyConstant.h:41
    │ │ │ -
    BALL::Constant::PLANCK
    static double PLANCK
    Definition pyConstant.h:83
    │ │ │ -
    BALL::Constant::VACUUM_PERMITTIVITY
    static double VACUUM_PERMITTIVITY
    Definition pyConstant.h:120
    │ │ │ -
    BALL::Constant::SPEED_OF_LIGHT
    static double SPEED_OF_LIGHT
    Definition pyConstant.h:130
    │ │ │ -
    BALL::Constant::ELEMENTARY_CHARGE
    static double ELEMENTARY_CHARGE
    Definition pyConstant.h:38
    │ │ │ -
    BALL::Constant::F
    static double F
    Definition pyConstant.h:103
    │ │ │ -
    BALL::Constant::k
    static double k
    Definition pyConstant.h:78
    │ │ │ -
    BALL::Constant::ELECTRON_MASS
    static double ELECTRON_MASS
    Definition pyConstant.h:46
    │ │ │ -
    BALL::Constant::M_PER_FOOT
    static double M_PER_FOOT
    Definition pyConstant.h:164
    │ │ │ -
    BALL::Constant::PI
    static double PI
    Definition pyConstant.h:26
    │ │ │ -
    BALL::Constant::NA
    static double NA
    Definition pyConstant.h:65
    │ │ │ -
    BALL::Constant::JOULE_PER_CAL
    static double JOULE_PER_CAL
    Definition pyConstant.h:169
    │ │ │ -
    BALL::Constant::c
    static double c
    Definition pyConstant.h:134
    │ │ │ -
    BALL::Constant::EPSILON
    static double EPSILON
    Definition pyConstant.h:34
    │ │ │ -
    BALL::Constant::NEUTRON_MASS
    static double NEUTRON_MASS
    Definition pyConstant.h:56
    │ │ │ -
    BALL::Constant::h
    static double h
    Definition pyConstant.h:87
    │ │ │ -
    BALL::Constant::RAD_PER_DEG
    static double RAD_PER_DEG
    Definition pyConstant.h:154
    │ │ │ -
    BALL::Constant::a0
    static double a0
    Definition pyConstant.h:112
    │ │ │ -
    BALL::Constant::BOHR_RADIUS
    static double BOHR_RADIUS
    Definition pyConstant.h:108
    │ │ │ -
    BALL::Constant::PROTON_MASS
    static double PROTON_MASS
    Definition pyConstant.h:51
    │ │ │ - │ │ │ +
    189 Atom(const Atom& atom, bool deep = true);
    │ │ │ +
    190
    │ │ │ +
    207 Atom(Element& element,
    │ │ │ +
    208 const String& name, const String& type_name = BALL_ATOM_DEFAULT_TYPE_NAME,
    │ │ │ +
    209 Type atom_type = BALL_ATOM_DEFAULT_TYPE,
    │ │ │ +
    210 const Vector3& position = Vector3(BALL_ATOM_DEFAULT_POSITION),
    │ │ │ +
    211 const Vector3& velocity = Vector3(BALL_ATOM_DEFAULT_VELOCITY),
    │ │ │ +
    212 const Vector3& force = Vector3(BALL_ATOM_DEFAULT_FORCE),
    │ │ │ +
    213 float charge = BALL_ATOM_DEFAULT_CHARGE,
    │ │ │ +
    214 float radius = BALL_ATOM_DEFAULT_RADIUS,
    │ │ │ +
    215 Index formal_charge = BALL_ATOM_DEFAULT_FORMAL_CHARGE);
    │ │ │ +
    216
    │ │ │ +
    218
    │ │ │ +
    222
    │ │ │ +
    229 virtual ~Atom();
    │ │ │ +
    230
    │ │ │ +
    240 virtual void clear();
    │ │ │ +
    241
    │ │ │ +
    247 virtual void destroy();
    │ │ │ +
    248
    │ │ │ +
    250
    │ │ │ +
    253
    │ │ │ +
    257 virtual void persistentWrite(PersistenceManager& pm, const char* name = 0) const;
    │ │ │ +
    258
    │ │ │ +
    262 virtual void persistentRead(PersistenceManager& pm);
    │ │ │ +
    263
    │ │ │ +
    265
    │ │ │ +
    268
    │ │ │ +
    278 void set(const Atom& atom, bool deep = true);
    │ │ │ +
    279
    │ │ │ +
    285 void get(Atom& atom, bool deep = true) const;
    │ │ │ +
    286
    │ │ │ +
    295 Atom& operator = (const Atom& atom);
    │ │ │ +
    296
    │ │ │ +
    301 void swap(Atom& atom);
    │ │ │ +
    302
    │ │ │ +
    304
    │ │ │ +
    307
    │ │ │ +
    312 bool operator == (const Atom& atom) const;
    │ │ │ +
    313
    │ │ │ +
    317 bool operator != (const Atom& atom) const;
    │ │ │ +
    318
    │ │ │ +
    320
    │ │ │ +
    323
    │ │ │ +
    325 void setElement(const Element& element);
    │ │ │ +
    326
    │ │ │ +
    328 const Element& getElement() const;
    │ │ │ +
    329
    │ │ │ +
    334 void setCharge(float charge);
    │ │ │ +
    335
    │ │ │ +
    340 float getCharge() const;
    │ │ │ +
    341
    │ │ │ +
    343 void setFormalCharge(Index formal_charge);
    │ │ │ +
    344
    │ │ │ +
    346 Index getFormalCharge() const;
    │ │ │ +
    347
    │ │ │ +
    355 const Molecule* getMolecule() const;
    │ │ │ +
    357 Molecule* getMolecule();
    │ │ │ +
    358
    │ │ │ +
    359
    │ │ │ +
    367 const Fragment* getFragment() const;
    │ │ │ +
    369 Fragment* getFragment();
    │ │ │ +
    370
    │ │ │ +
    378 const Residue* getResidue() const;
    │ │ │ +
    380 Residue* getResidue();
    │ │ │ +
    381
    │ │ │ +
    387 const SecondaryStructure* getSecondaryStructure() const;
    │ │ │ +
    389 SecondaryStructure* getSecondaryStructure();
    │ │ │ +
    390
    │ │ │ +
    396 const Chain* getChain() const;
    │ │ │ +
    398 Chain* getChain();
    │ │ │ +
    399
    │ │ │ +
    401 void setName(const String& name);
    │ │ │ +
    402
    │ │ │ +
    404 const String& getName() const;
    │ │ │ +
    405
    │ │ │ +
    435 String getFullName(FullNameType type = ADD_VARIANT_EXTENSIONS) const;
    │ │ │ +
    436
    │ │ │ +
    440 void setPosition(const Vector3& position);
    │ │ │ +
    441
    │ │ │ +
    443 Vector3& getPosition();
    │ │ │ +
    444
    │ │ │ +
    446 const Vector3& getPosition() const;
    │ │ │ +
    447
    │ │ │ +
    451 void setRadius(float radius);
    │ │ │ +
    452
    │ │ │ +
    454 float getRadius() const;
    │ │ │ +
    455
    │ │ │ +
    457 void setType(Type atom_type);
    │ │ │ +
    458
    │ │ │ +
    460 Type getType() const;
    │ │ │ +
    461
    │ │ │ +
    463 String getTypeName() const;
    │ │ │ +
    464
    │ │ │ +
    466 void setTypeName(const String& name);
    │ │ │ +
    467
    │ │ │ +
    471 void setVelocity(const Vector3& velocity);
    │ │ │ +
    472
    │ │ │ +
    476 Vector3& getVelocity();
    │ │ │ +
    477
    │ │ │ +
    481 const Vector3& getVelocity() const;
    │ │ │ +
    482
    │ │ │ +
    486 void setForce(const Vector3& force);
    │ │ │ +
    488 const Vector3& getForce() const;
    │ │ │ +
    490 Vector3& getForce();
    │ │ │ +
    491
    │ │ │ +
    492
    │ │ │ +
    494 Size countBonds() const;
    │ │ │ +
    495
    │ │ │ +
    508 Bond* getBond(Position index);
    │ │ │ +
    509
    │ │ │ +
    513 const Bond* getBond(Position index) const;
    │ │ │ +
    514
    │ │ │ +
    522 Bond* getBond(const Atom& atom);
    │ │ │ +
    523
    │ │ │ +
    531 const Bond* getBond(const Atom& atom) const;
    │ │ │ +
    533
    │ │ │ +
    534
    │ │ │ +
    538
    │ │ │ +
    548 Bond* createBond(Atom& atom);
    │ │ │ +
    549
    │ │ │ +
    561 Bond* createBond(Bond& bond, Atom& atom);
    │ │ │ +
    562
    │ │ │ +
    567 Bond* cloneBond(Bond& bond, Atom& atom);
    │ │ │ +
    568
    │ │ │ +
    580 bool destroyBond(const Atom& atom);
    │ │ │ +
    581
    │ │ │ +
    593 void destroyBonds();
    │ │ │ +
    594
    │ │ │ +
    603 Atom* getPartnerAtom(Position i);
    │ │ │ +
    604
    │ │ │ +
    613 const Atom* getPartnerAtom(Position i) const;
    │ │ │ +
    614
    │ │ │ +
    621 float getDistance(const Atom& a) const;
    │ │ │ +
    622
    │ │ │ +
    623 MolecularInteractions* interactions;
    │ │ │ +
    624
    │ │ │ +
    625 void addInteraction(const Atom* atom, String interaction_type, double energy);
    │ │ │ +
    626
    │ │ │ +
    627 void addInteraction(String interaction_type, double energy);
    │ │ │ +
    628
    │ │ │ +
    629 void disableStoreInteractions();
    │ │ │ +
    630
    │ │ │ +
    631 void enableStoreInteractions();
    │ │ │ +
    632
    │ │ │ +
    633 bool store_interactions_disabled_;
    │ │ │ +
    634
    │ │ │ +
    636
    │ │ │ +
    640
    │ │ │ +
    647 bool hasBond(const Bond& bond) const;
    │ │ │ +
    648
    │ │ │ +
    657 bool isBoundTo(const Atom& atom) const;
    │ │ │ +
    658
    │ │ │ +
    664 bool isBound() const;
    │ │ │ +
    665
    │ │ │ +
    673 bool isGeminal(const Atom& atom) const;
    │ │ │ +
    674
    │ │ │ +
    681 bool isVicinal(const Atom& atom) const;
    │ │ │ +
    683
    │ │ │ +
    687 virtual bool isAtom() const { return true; }
    │ │ │ +
    689
    │ │ │ +
    693
    │ │ │ +
    698 virtual bool isValid() const;
    │ │ │ +
    699
    │ │ │ +
    707 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ +
    709
    │ │ │ +
    713
    │ │ │ +
    719 bool applyBonds(UnaryProcessor<Bond>& processor);
    │ │ │ +
    720
    │ │ │ +
    722
    │ │ │ +
    725
    │ │ │ +
    726 typedef Index BondIteratorPosition;
    │ │ │ +
    727
    │ │ │ +
    │ │ │ +
    728 class BALL_EXPORT BondIteratorTraits
    │ │ │ +
    729 {
    │ │ │ +
    730 public:
    │ │ │ +
    731
    │ │ │ +
    732 BALL_CREATE_DEEP(BondIteratorTraits)
    │ │ │ +
    733
    │ │ │ +
    734 virtual ~BondIteratorTraits() {}
    │ │ │ +
    735
    │ │ │ +
    │ │ │ +
    736 BondIteratorTraits()
    │ │ │ +
    737 : bound_(0),
    │ │ │ +
    738 position_(0)
    │ │ │ +
    739 {
    │ │ │ +
    740 }
    │ │ │ +
    │ │ │ +
    741
    │ │ │ +
    │ │ │ +
    742 BondIteratorTraits(const Atom& atom)
    │ │ │ +
    743 : bound_((Atom*)&atom),
    │ │ │ +
    744 position_(0)
    │ │ │ +
    745 {
    │ │ │ +
    746 }
    │ │ │ +
    │ │ │ +
    747
    │ │ │ +
    │ │ │ +
    748 BondIteratorTraits(const BondIteratorTraits& traits, bool /* deep */ = true)
    │ │ │ +
    749 : bound_(traits.bound_),
    │ │ │ +
    750 position_(traits.position_)
    │ │ │ +
    751 {
    │ │ │ +
    752 }
    │ │ │ +
    │ │ │ +
    753
    │ │ │ +
    │ │ │ +
    754 BondIteratorTraits& operator = (const BondIteratorTraits& traits)
    │ │ │ +
    755 {
    │ │ │ +
    756 bound_ = traits.bound_;
    │ │ │ +
    757 position_ = traits.position_;
    │ │ │ +
    758 return *this;
    │ │ │ +
    759 }
    │ │ │ +
    │ │ │ +
    760
    │ │ │ +
    761 Atom* getContainer() { return bound_; }
    │ │ │ +
    762
    │ │ │ +
    763 const Atom* getContainer() const { return bound_; }
    │ │ │ +
    764
    │ │ │ +
    765 bool isSingular() const { return (bound_ == 0); }
    │ │ │ +
    766
    │ │ │ +
    767 BondIteratorPosition& getPosition() { return position_; }
    │ │ │ +
    768
    │ │ │ +
    769 const BondIteratorPosition& getPosition() const { return position_; }
    │ │ │ +
    770
    │ │ │ +
    771 // Comparison: We do net check whether these traits are bound to
    │ │ │ +
    772 // the same container here for efficiency reasons.
    │ │ │ +
    773
    │ │ │ +
    │ │ │ +
    774 bool operator == (const BondIteratorTraits& traits) const
    │ │ │ +
    775 {
    │ │ │ +
    776 return (position_ == traits.position_);
    │ │ │ +
    777 }
    │ │ │ +
    │ │ │ +
    778
    │ │ │ +
    │ │ │ +
    779 bool operator != (const BondIteratorTraits& traits) const
    │ │ │ +
    780 {
    │ │ │ +
    781 return !(position_ == traits.position_);
    │ │ │ +
    782 }
    │ │ │ +
    │ │ │ +
    783
    │ │ │ +
    │ │ │ +
    784 bool operator < (const BondIteratorTraits& traits) const
    │ │ │ +
    785 {
    │ │ │ +
    786 return (position_ < traits.position_);
    │ │ │ +
    787 }
    │ │ │ +
    │ │ │ +
    788
    │ │ │ +
    │ │ │ +
    789 Distance getDistance(const BondIteratorTraits& traits) const
    │ │ │ +
    790 {
    │ │ │ +
    791 return (Distance)(position_ - traits.position_);
    │ │ │ +
    792 }
    │ │ │ +
    │ │ │ +
    793
    │ │ │ +
    │ │ │ +
    794 bool isValid() const
    │ │ │ +
    795 {
    │ │ │ +
    796 return (bound_ != 0 && position_ >= 0 && position_ < bound_->number_of_bonds_);
    │ │ │ +
    797 }
    │ │ │ +
    │ │ │ +
    798
    │ │ │ +
    │ │ │ +
    799 void invalidate()
    │ │ │ +
    800 {
    │ │ │ +
    801 bound_ = 0;
    │ │ │ +
    802 position_ = 0;
    │ │ │ +
    803 }
    │ │ │ +
    │ │ │ +
    804
    │ │ │ +
    805 void toBegin() { position_ = 0; }
    │ │ │ +
    806
    │ │ │ +
    807 bool isBegin() const { return (position_ == 0); }
    │ │ │ +
    808
    │ │ │ +
    809 void toEnd() { position_ = bound_->number_of_bonds_; }
    │ │ │ +
    810
    │ │ │ +
    811 bool isEnd() const { return (position_ >= bound_->number_of_bonds_);}
    │ │ │ +
    812
    │ │ │ +
    813 Bond& getData() { return *(bound_->bond_[position_]); }
    │ │ │ +
    814
    │ │ │ +
    815 const Bond& getData() const { return *(bound_->bond_[position_]); }
    │ │ │ +
    816
    │ │ │ +
    817 void forward() { ++position_; }
    │ │ │ +
    818
    │ │ │ +
    │ │ │ +
    819 friend std::ostream& operator << (std::ostream& s, const BondIteratorTraits& traits)
    │ │ │ +
    820 {
    │ │ │ +
    821 return (s << traits.position_ << ' ');
    │ │ │ +
    822 }
    │ │ │ +
    │ │ │ +
    823
    │ │ │ +
    │ │ │ +
    824 void dump(std::ostream& s) const
    │ │ │ +
    825 {
    │ │ │ +
    826 s << position_ << std::endl;
    │ │ │ +
    827 }
    │ │ │ +
    │ │ │ +
    828
    │ │ │ +
    │ │ │ +
    829 void toRBegin()
    │ │ │ +
    830 {
    │ │ │ +
    831 position_ = bound_->number_of_bonds_ - 1;
    │ │ │ +
    832 }
    │ │ │ +
    │ │ │ +
    833
    │ │ │ +
    │ │ │ +
    834 bool isRBegin() const
    │ │ │ +
    835 {
    │ │ │ +
    836 return (position_ == bound_->number_of_bonds_ - 1);
    │ │ │ +
    837 }
    │ │ │ +
    │ │ │ +
    838
    │ │ │ +
    │ │ │ +
    839 void toREnd()
    │ │ │ +
    840 {
    │ │ │ +
    841 position_ = -1;
    │ │ │ +
    842 }
    │ │ │ +
    │ │ │ +
    843
    │ │ │ +
    │ │ │ +
    844 bool isREnd() const
    │ │ │ +
    845 {
    │ │ │ +
    846 return (position_ <= -1);
    │ │ │ +
    847 }
    │ │ │ +
    │ │ │ +
    848
    │ │ │ +
    │ │ │ +
    849 void backward()
    │ │ │ +
    850 {
    │ │ │ +
    851 --position_;
    │ │ │ +
    852 }
    │ │ │ +
    │ │ │ +
    853
    │ │ │ +
    │ │ │ +
    854 void backward(Distance distance)
    │ │ │ +
    855 {
    │ │ │ +
    856 position_ -= distance;
    │ │ │ +
    857 }
    │ │ │ +
    │ │ │ +
    858
    │ │ │ +
    │ │ │ +
    859 void forward(Distance distance)
    │ │ │ +
    860 {
    │ │ │ +
    861 position_ += distance;
    │ │ │ +
    862 }
    │ │ │ +
    │ │ │ +
    863
    │ │ │ +
    │ │ │ +
    864 Bond& getData(Index index)
    │ │ │ +
    865 {
    │ │ │ +
    866 return *(bound_->bond_[index]);
    │ │ │ +
    867 }
    │ │ │ +
    │ │ │ +
    868
    │ │ │ +
    │ │ │ +
    869 const Bond& getData(Index index) const
    │ │ │ +
    870 {
    │ │ │ +
    871 return *(bound_->bond_[index]);
    │ │ │ +
    872 }
    │ │ │ +
    │ │ │ +
    873
    │ │ │ +
    874 private:
    │ │ │ +
    875
    │ │ │ +
    876 Atom* bound_;
    │ │ │ +
    877 BondIteratorPosition position_;
    │ │ │ +
    878
    │ │ │ +
    879 };
    │ │ │ +
    │ │ │ +
    880
    │ │ │ +
    881 friend class BondIteratorTraits;
    │ │ │ +
    882
    │ │ │ +
    885 typedef RandomAccessIterator
    │ │ │ +
    886 <Atom, Bond, BondIteratorPosition, BondIteratorTraits>
    │ │ │ +
    887 BondIterator;
    │ │ │ +
    888
    │ │ │ +
    │ │ │ +
    890 BondIterator beginBond()
    │ │ │ +
    891 {
    │ │ │ +
    892 return BondIterator::begin(*this);
    │ │ │ +
    893 }
    │ │ │ +
    │ │ │ +
    894
    │ │ │ +
    │ │ │ +
    896 BondIterator endBond()
    │ │ │ +
    897 {
    │ │ │ +
    898 return BondIterator::end(*this);
    │ │ │ +
    899 }
    │ │ │ +
    │ │ │ +
    900
    │ │ │ +
    902 typedef ConstRandomAccessIterator
    │ │ │ +
    903 <Atom, Bond, BondIteratorPosition, BondIteratorTraits>
    │ │ │ +
    904 BondConstIterator;
    │ │ │ +
    905
    │ │ │ +
    │ │ │ +
    907 BondConstIterator beginBond() const
    │ │ │ +
    908 {
    │ │ │ +
    909 return BondConstIterator::begin(*this);
    │ │ │ +
    910 }
    │ │ │ +
    │ │ │ +
    911
    │ │ │ +
    │ │ │ +
    913 BondConstIterator endBond() const
    │ │ │ +
    914 {
    │ │ │ +
    915 return BondConstIterator::end(*this);
    │ │ │ +
    916 }
    │ │ │ +
    │ │ │ +
    917
    │ │ │ +
    919 typedef std::reverse_iterator<BondIterator> BondReverseIterator;
    │ │ │ +
    920
    │ │ │ +
    │ │ │ +
    922 BondReverseIterator rbeginBond()
    │ │ │ +
    923 {
    │ │ │ +
    924 return BondReverseIterator(endBond());
    │ │ │ +
    925 }
    │ │ │ +
    │ │ │ +
    926
    │ │ │ +
    │ │ │ +
    928 BondReverseIterator rendBond()
    │ │ │ +
    929 {
    │ │ │ +
    930 return BondReverseIterator(beginBond());
    │ │ │ +
    931 }
    │ │ │ +
    │ │ │ +
    932
    │ │ │ +
    934 typedef std::reverse_iterator<BondConstIterator> BondConstReverseIterator;
    │ │ │ +
    935
    │ │ │ +
    │ │ │ +
    937 BondConstReverseIterator rbeginBond() const
    │ │ │ +
    938 {
    │ │ │ +
    939 return BondConstReverseIterator(endBond());
    │ │ │ +
    940 }
    │ │ │ +
    │ │ │ +
    941
    │ │ │ +
    │ │ │ +
    943 BondConstReverseIterator rendBond() const
    │ │ │ +
    944 {
    │ │ │ +
    945 return BondConstReverseIterator(beginBond());
    │ │ │ +
    946 }
    │ │ │ +
    │ │ │ +
    947
    │ │ │ +
    949
    │ │ │ +
    952
    │ │ │ +
    954 typedef std::list<Atom*> AtomPtrList;
    │ │ │ +
    955
    │ │ │ +
    957 typedef std::list<Position> AtomIndexList;
    │ │ │ +
    958
    │ │ │ +
    959 protected:
    │ │ │ +
    960
    │ │ │ +
    962
    │ │ │ +
    965
    │ │ │ +
    967 static AtomIndexList free_list_;
    │ │ │ +
    968
    │ │ │ +
    970 String name_;
    │ │ │ +
    972 String type_name_;
    │ │ │ +
    974 const Element* element_;
    │ │ │ +
    976 float radius_;
    │ │ │ +
    978 Type type_;
    │ │ │ +
    980 unsigned char number_of_bonds_;
    │ │ │ +
    982 Bond* bond_[MAX_NUMBER_OF_BONDS];
    │ │ │ +
    984 Index formal_charge_;
    │ │ │ +
    986 Vector3 position_;
    │ │ │ +
    988 float charge_;
    │ │ │ +
    990 Vector3 velocity_;
    │ │ │ +
    992 Vector3 force_;
    │ │ │ +
    994
    │ │ │ +
    995
    │ │ │ +
    996
    │ │ │ +
    997 private:
    │ │ │ +
    998
    │ │ │ +
    1000 void clear_();
    │ │ │ +
    1001
    │ │ │ +
    1003 void swapLastBond_(const Atom* atom);
    │ │ │ +
    1004
    │ │ │ +
    1005 };
    │ │ │ +
    │ │ │ +
    1006
    │ │ │ +
    1007// required for visual studio
    │ │ │ +
    1008#ifdef BALL_COMPILER_MSVC
    │ │ │ +
    1009#include <vector>
    │ │ │ +
    1010template class BALL_EXPORT std::vector<Atom*>;
    │ │ │ +
    1011#endif
    │ │ │ +
    1012
    │ │ │ +
    1013# ifndef BALL_NO_INLINE_FUNCTIONS
    │ │ │ +
    1014# include <BALL/KERNEL/atom.iC>
    │ │ │ +
    1015# endif
    │ │ │ +
    1016} // namespace BALL
    │ │ │ +
    1017
    │ │ │ +
    1018#ifndef BALL_KERNEL_BONDITERATOR_H
    │ │ │ +
    1019# include <BALL/KERNEL/bondIterator.h>
    │ │ │ +
    1020#endif
    │ │ │ +
    1021
    │ │ │ +
    1022
    │ │ │ +
    1023#endif // BALL_KERNEL_ATOM_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_ATOM_DEFAULT_FORCE
    #define BALL_ATOM_DEFAULT_FORCE
    Definition atom.h:34
    │ │ │ +
    BALL_ATOM_DEFAULT_FORMAL_CHARGE
    #define BALL_ATOM_DEFAULT_FORMAL_CHARGE
    Definition atom.h:27
    │ │ │ +
    BALL_ATOM_DEFAULT_TYPE_NAME
    #define BALL_ATOM_DEFAULT_TYPE_NAME
    Definition atom.h:29
    │ │ │ +
    BALL_ATOM_DEFAULT_RADIUS
    #define BALL_ATOM_DEFAULT_RADIUS
    Definition atom.h:31
    │ │ │ +
    BALL_ATOM_DEFAULT_POSITION
    #define BALL_ATOM_DEFAULT_POSITION
    Definition atom.h:30
    │ │ │ +
    BALL_ATOM_DEFAULT_VELOCITY
    #define BALL_ATOM_DEFAULT_VELOCITY
    Definition atom.h:33
    │ │ │ +
    BALL_ATOM_DEFAULT_TYPE
    #define BALL_ATOM_DEFAULT_TYPE
    Definition atom.h:32
    │ │ │ +
    BALL_ATOM_DEFAULT_CHARGE
    #define BALL_ATOM_DEFAULT_CHARGE
    Definition atom.h:26
    │ │ │ + │ │ │ +
    BALL_CREATE_DEEP
    #define BALL_CREATE_DEEP(name)
    Definition create.h:26
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Atom::getPosition
    Vector3 & getPosition()
    Return the atom coordinates (mutable)
    │ │ │ +
    BALL::Atom::getMolecule
    Molecule * getMolecule()
    Return the molecule the atom is contained in (mutable)
    │ │ │ +
    BALL::Atom::store_interactions_disabled_
    bool store_interactions_disabled_
    Definition atom.h:633
    │ │ │ +
    BALL::Atom::isVicinal
    bool isVicinal(const Atom &atom) const
    │ │ │ +
    BALL::Atom::persistentWrite
    virtual void persistentWrite(PersistenceManager &pm, const char *name=0) const
    │ │ │ +
    BALL::Atom::isAtom
    virtual bool isAtom() const
    Definition atom.h:687
    │ │ │ +
    BALL::Atom::number_of_bonds_
    unsigned char number_of_bonds_
    Definition atom.h:980
    │ │ │ +
    BALL::Atom::isBoundTo
    bool isBoundTo(const Atom &atom) const
    │ │ │ +
    BALL::Atom::getBond
    Bond * getBond(const Atom &atom)
    │ │ │ +
    BALL::Atom::get
    void get(Atom &atom, bool deep=true) const
    │ │ │ +
    BALL::Atom::force_
    Vector3 force_
    Definition atom.h:992
    │ │ │ +
    BALL::Atom::isBound
    bool isBound() const
    │ │ │ +
    BALL::Atom::getBond
    Bond * getBond(Position index)
    │ │ │ +
    BALL::Atom::getRadius
    float getRadius() const
    Return the atom radius.
    │ │ │ +
    BALL::Atom::setForce
    void setForce(const Vector3 &force)
    │ │ │ +
    BALL::Atom::getDistance
    float getDistance(const Atom &a) const
    │ │ │ +
    BALL::Atom::element_
    const Element * element_
    Definition atom.h:974
    │ │ │ +
    BALL::Atom::persistentRead
    virtual void persistentRead(PersistenceManager &pm)
    │ │ │ +
    BALL::Atom::getResidue
    const Residue * getResidue() const
    │ │ │ +
    BALL::Atom::radius_
    float radius_
    Definition atom.h:976
    │ │ │ +
    BALL::Atom::destroy
    virtual void destroy()
    │ │ │ +
    BALL::Atom::getFormalCharge
    Index getFormalCharge() const
    Return the atom's formal charge.
    │ │ │ +
    BALL::Atom::setRadius
    void setRadius(float radius)
    │ │ │ +
    BALL::Atom::getFullName
    String getFullName(FullNameType type=ADD_VARIANT_EXTENSIONS) const
    │ │ │ +
    BALL::Atom::rbeginBond
    BondReverseIterator rbeginBond()
    Return a reverse bond iterator pointing to the last bond.
    Definition atom.h:922
    │ │ │ +
    BALL::Atom::set
    void set(const Atom &atom, bool deep=true)
    │ │ │ +
    BALL::Atom::getForce
    const Vector3 & getForce() const
    Return the atom's force vector (const)
    │ │ │ +
    BALL::Atom::enableStoreInteractions
    void enableStoreInteractions()
    │ │ │ +
    BALL::Atom::FullNameType
    FullNameType
    Definition atom.h:139
    │ │ │ +
    BALL::Atom::ADD_VARIANT_EXTENSIONS
    @ ADD_VARIANT_EXTENSIONS
    Definition atom.h:143
    │ │ │ +
    BALL::Atom::ADD_VARIANT_EXTENSIONS_AND_ID
    @ ADD_VARIANT_EXTENSIONS_AND_ID
    Definition atom.h:147
    │ │ │ +
    BALL::Atom::NO_VARIANT_EXTENSIONS
    @ NO_VARIANT_EXTENSIONS
    Definition atom.h:141
    │ │ │ +
    BALL::Atom::ADD_CHAIN_RESIDUE_ID
    @ ADD_CHAIN_RESIDUE_ID
    Definition atom.h:149
    │ │ │ +
    BALL::Atom::ADD_RESIDUE_ID
    @ ADD_RESIDUE_ID
    Definition atom.h:145
    │ │ │ +
    BALL::Atom::isGeminal
    bool isGeminal(const Atom &atom) const
    │ │ │ +
    BALL::Atom::endBond
    BondIterator endBond()
    Return a past-the-end bond iterator.
    Definition atom.h:896
    │ │ │ +
    BALL::Atom::getResidue
    Residue * getResidue()
    Return the residue the atom is contained in (mutable)
    │ │ │ + │ │ │ +
    BALL::Atom::setVelocity
    void setVelocity(const Vector3 &velocity)
    │ │ │ +
    BALL::Atom::setElement
    void setElement(const Element &element)
    Assign the atom's element.
    │ │ │ +
    BALL::Atom::setType
    void setType(Type atom_type)
    Assign the numerical atom type.
    │ │ │ +
    BALL::Atom::getBond
    const Bond * getBond(const Atom &atom) const
    │ │ │ +
    BALL::Atom::velocity_
    Vector3 velocity_
    Definition atom.h:990
    │ │ │ +
    BALL::Atom::beginBond
    BondIterator beginBond()
    Return a bond iterator pointing to the first bond of the atom.
    Definition atom.h:890
    │ │ │ +
    BALL::Atom::addInteraction
    void addInteraction(const Atom *atom, String interaction_type, double energy)
    │ │ │ +
    BALL::Atom::createBond
    Bond * createBond(Atom &atom)
    │ │ │ +
    BALL::Atom::getChain
    Chain * getChain()
    Return the chain the atom is contained in (mutable)
    │ │ │ +
    BALL::Atom::cloneBond
    Bond * cloneBond(Bond &bond, Atom &atom)
    │ │ │ +
    BALL::Atom::BondIterator
    RandomAccessIterator< Atom, Bond, BondIteratorPosition, BondIteratorTraits > BondIterator
    Definition atom.h:887
    │ │ │ +
    BALL::Atom::endBond
    BondConstIterator endBond() const
    Return a constant past-the-end bond iterator.
    Definition atom.h:913
    │ │ │ +
    BALL::Atom::AtomPtrList
    std::list< Atom * > AtomPtrList
    Definition atom.h:954
    │ │ │ +
    BALL::Atom::getName
    const String & getName() const
    Return the atom name.
    │ │ │ +
    BALL::Atom::getBond
    const Bond * getBond(Position index) const
    │ │ │ +
    BALL::Atom::getPartnerAtom
    Atom * getPartnerAtom(Position i)
    │ │ │ +
    BALL::Atom::getFragment
    const Fragment * getFragment() const
    │ │ │ +
    BALL::Atom::type_
    Type type_
    Definition atom.h:978
    │ │ │ +
    BALL::Atom::Atom
    Atom(Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, Index formal_charge=BALL_ATOM_DEFAULT_FORMAL_CHARGE)
    │ │ │ +
    BALL::Atom::Type
    short Type
    Definition atom.h:103
    │ │ │ +
    BALL::Atom::free_list_
    static AtomIndexList free_list_
    Definition atom.h:967
    │ │ │ +
    BALL::Atom::clear
    virtual void clear()
    │ │ │ +
    BALL::Atom::setName
    void setName(const String &name)
    Set the atom name.
    │ │ │ +
    BALL::Atom::countBonds
    Size countBonds() const
    Return the number of bonds.
    │ │ │ + │ │ │ +
    BALL::Atom::getPartnerAtom
    const Atom * getPartnerAtom(Position i) const
    │ │ │ +
    BALL::Atom::getMolecule
    const Molecule * getMolecule() const
    │ │ │ +
    BALL::Atom::rendBond
    BondConstReverseIterator rendBond() const
    Return a constant past-the-end bond iterator for reverse traversal.
    Definition atom.h:943
    │ │ │ +
    BALL::Atom::getSecondaryStructure
    SecondaryStructure * getSecondaryStructure()
    Return the secondary structure the atom is contained in (mutable)
    │ │ │ +
    BALL::Atom::setCharge
    void setCharge(float charge)
    │ │ │ +
    BALL::Atom::swap
    void swap(Atom &atom)
    │ │ │ +
    BALL::Atom::isValid
    virtual bool isValid() const
    │ │ │ +
    BALL::Atom::getPosition
    const Vector3 & getPosition() const
    Return the atom coordinates (const)
    │ │ │ +
    BALL::Atom::getForce
    Vector3 & getForce()
    Return the atom's force vector (mutable)
    │ │ │ +
    BALL::Atom::getSecondaryStructure
    const SecondaryStructure * getSecondaryStructure() const
    │ │ │ +
    BALL::Atom::getVelocity
    Vector3 & getVelocity()
    │ │ │ +
    BALL::Atom::setFormalCharge
    void setFormalCharge(Index formal_charge)
    Set the atom's formal charge.
    │ │ │ +
    BALL::Atom::BondReverseIterator
    std::reverse_iterator< BondIterator > BondReverseIterator
    Reverse random access iterator for bonds.
    Definition atom.h:919
    │ │ │ +
    BALL::Atom::dump
    virtual void dump(std::ostream &s=std::cout, Size depth=0) const
    │ │ │ +
    BALL::Atom::BondConstIterator
    ConstRandomAccessIterator< Atom, Bond, BondIteratorPosition, BondIteratorTraits > BondConstIterator
    Constant random access iterator for bonds.
    Definition atom.h:904
    │ │ │ +
    BALL::Atom::createBond
    Bond * createBond(Bond &bond, Atom &atom)
    │ │ │ +
    BALL::Atom::applyBonds
    bool applyBonds(UnaryProcessor< Bond > &processor)
    │ │ │ +
    BALL::Atom::BondConstReverseIterator
    std::reverse_iterator< BondConstIterator > BondConstReverseIterator
    Constant reverse random access iterator for bonds.
    Definition atom.h:934
    │ │ │ +
    BALL::Atom::setTypeName
    void setTypeName(const String &name)
    Assign the atom type name.
    │ │ │ +
    BALL::Atom::getChain
    const Chain * getChain() const
    │ │ │ +
    BALL::Atom::getFragment
    Fragment * getFragment()
    Return the fragment the atom is contained in (mutable)
    │ │ │ +
    BALL::Atom::position_
    Vector3 position_
    Definition atom.h:986
    │ │ │ +
    BALL::Atom::setPosition
    void setPosition(const Vector3 &position)
    │ │ │ +
    BALL::Atom::hasBond
    bool hasBond(const Bond &bond) const
    │ │ │ +
    BALL::Atom::disableStoreInteractions
    void disableStoreInteractions()
    │ │ │ +
    BALL::Atom::getCharge
    float getCharge() const
    │ │ │ +
    BALL::Atom::rendBond
    BondReverseIterator rendBond()
    Return a past-the-end bond iterator for reverse traversal.
    Definition atom.h:928
    │ │ │ +
    BALL::Atom::destroyBond
    bool destroyBond(const Atom &atom)
    │ │ │ +
    BALL::Atom::getType
    Type getType() const
    Return the (numerical) atom type.
    │ │ │ +
    BALL::Atom::formal_charge_
    Index formal_charge_
    Definition atom.h:984
    │ │ │ +
    BALL::Atom::rbeginBond
    BondConstReverseIterator rbeginBond() const
    Return a constant reverse bond iterator pointing to the first atom.
    Definition atom.h:937
    │ │ │ +
    BALL::Atom::getVelocity
    const Vector3 & getVelocity() const
    │ │ │ +
    BALL::Atom::AtomIndexList
    std::list< Position > AtomIndexList
    Definition atom.h:957
    │ │ │ +
    BALL::Atom::getTypeName
    String getTypeName() const
    Return the atom type name.
    │ │ │ +
    BALL::Atom::getElement
    const Element & getElement() const
    Return the atom's element.
    │ │ │ +
    BALL::Atom::BondIteratorPosition
    Index BondIteratorPosition
    Definition atom.h:726
    │ │ │ +
    BALL::Atom::beginBond
    BondConstIterator beginBond() const
    Return a constant bond iterator pointing to the first bond.
    Definition atom.h:907
    │ │ │ +
    BALL::Atom::addInteraction
    void addInteraction(String interaction_type, double energy)
    │ │ │ +
    BALL::Atom::type_name_
    String type_name_
    Definition atom.h:972
    │ │ │ +
    BALL::Atom::name_
    String name_
    Definition atom.h:970
    │ │ │ +
    BALL::Atom::Atom
    Atom(const Atom &atom, bool deep=true)
    │ │ │ +
    BALL::Atom::charge_
    float charge_
    Definition atom.h:988
    │ │ │ +
    BALL::Atom::destroyBonds
    void destroyBonds()
    │ │ │ +
    BALL::Atom::interactions
    MolecularInteractions * interactions
    Definition atom.h:623
    │ │ │ +
    BALL::Atom::~Atom
    virtual ~Atom()
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Atom::BondIteratorTraits::dump
    void dump(std::ostream &s) const
    Definition atom.h:824
    │ │ │ +
    BALL::Atom::BondIteratorTraits::getDistance
    Distance getDistance(const BondIteratorTraits &traits) const
    Definition atom.h:789
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Atom::BondIteratorTraits::getPosition
    BondIteratorPosition & getPosition()
    Definition atom.h:767
    │ │ │ +
    BALL::Atom::BondIteratorTraits::BondIteratorTraits
    BondIteratorTraits(const Atom &atom)
    Definition atom.h:742
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Atom::BondIteratorTraits::getData
    Bond & getData(Index index)
    Definition atom.h:864
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Atom::BondIteratorTraits::getData
    const Bond & getData(Index index) const
    Definition atom.h:869
    │ │ │ +
    BALL::Atom::BondIteratorTraits::backward
    void backward(Distance distance)
    Definition atom.h:854
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Atom::BondIteratorTraits::getData
    const Bond & getData() const
    Definition atom.h:815
    │ │ │ +
    BALL::Atom::BondIteratorTraits::getContainer
    const Atom * getContainer() const
    Definition atom.h:763
    │ │ │ + │ │ │ +
    BALL::Atom::BondIteratorTraits::forward
    void forward(Distance distance)
    Definition atom.h:859
    │ │ │ + │ │ │ +
    BALL::Atom::BondIteratorTraits::BondIteratorTraits
    BondIteratorTraits(const BondIteratorTraits &traits, bool=true)
    Definition atom.h:748
    │ │ │ +
    BALL::Atom::BondIteratorTraits::getPosition
    const BondIteratorPosition & getPosition() const
    Definition atom.h:769
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,211 +1,994 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _P_Y_T_H_O_N │ │ │ │ - * _E_X_T_E_N_S_I_O_N_S │ │ │ │ -pyConstant.h │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ +atom.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: pyConstant.h,v 1.12 2005/12/23 17:01:57 amoll Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_PYTHON_PYCONSTANT_H │ │ │ │ -8#define BALL_PYTHON_PYCONSTANT_H │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ -11# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -12#endif │ │ │ │ -13 │ │ │ │ -14namespace _B_A_L_L │ │ │ │ -15{ │ │ │ │ -16 │ │ │ │ -_2_1 class _C_o_n_s_t_a_n_t │ │ │ │ -22 { │ │ │ │ -23 public: │ │ │ │ -24 │ │ │ │ -25 // PI │ │ │ │ -_2_6 static double _P_I; │ │ │ │ -27 │ │ │ │ -_2_9 static double _E; │ │ │ │ -30 │ │ │ │ -_3_4 static double _E_P_S_I_L_O_N; │ │ │ │ -_3_8 static double _E_L_E_M_E_N_T_A_R_Y___C_H_A_R_G_E; // C │ │ │ │ -39 │ │ │ │ -_4_1 static double _e_0; │ │ │ │ -42 │ │ │ │ -_4_6 static double _E_L_E_C_T_R_O_N___M_A_S_S ; // kg │ │ │ │ -47 │ │ │ │ -_5_1 static double _P_R_O_T_O_N___M_A_S_S ; // kg │ │ │ │ -52 │ │ │ │ -_5_6 static double _N_E_U_T_R_O_N___M_A_S_S ; // kg │ │ │ │ -57 │ │ │ │ -_6_1 static double _A_V_O_G_A_D_R_O; │ │ │ │ -62 │ │ │ │ -_6_5 static double _N_A; │ │ │ │ -66 │ │ │ │ -_6_9 static double _M_O_L; │ │ │ │ -70 │ │ │ │ -_7_4 static double _B_O_L_T_Z_M_A_N_N; │ │ │ │ -75 │ │ │ │ -_7_8 static double _k; │ │ │ │ -79 │ │ │ │ -_8_3 static double _P_L_A_N_C_K; │ │ │ │ -84 │ │ │ │ -_8_7 static double _h; │ │ │ │ -88 │ │ │ │ -_9_1 static double _G_A_S___C_O_N_S_T_A_N_T; │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_KERNEL_ATOM_H │ │ │ │ +6#define BALL_KERNEL_ATOM_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_CONCEPT_COMPOSITE_H │ │ │ │ +9# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_c_o_m_p_o_s_i_t_e_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12#ifndef BALL_CONCEPT_PROPERTY_H │ │ │ │ +13# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_p_e_r_t_y_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifndef BALL_CONCEPT_RANDOMACCESSITERATOR_H │ │ │ │ +17# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_r_a_n_d_o_m_A_c_c_e_s_s_I_t_e_r_a_t_o_r_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20#ifndef BALL_MATHS_VECTOR3_H │ │ │ │ +21# include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +22#endif │ │ │ │ +23 │ │ │ │ +24// Defines for default values for an atom │ │ │ │ +_2_5#define BALL_ATOM_DEFAULT_ELEMENT &Element::UNKNOWN │ │ │ │ +_2_6#define BALL_ATOM_DEFAULT_CHARGE 0 │ │ │ │ +_2_7#define BALL_ATOM_DEFAULT_FORMAL_CHARGE 0 │ │ │ │ +_2_8#define BALL_ATOM_DEFAULT_NAME "" │ │ │ │ +_2_9#define BALL_ATOM_DEFAULT_TYPE_NAME "?" │ │ │ │ +_3_0#define BALL_ATOM_DEFAULT_POSITION 0,0,0 │ │ │ │ +_3_1#define BALL_ATOM_DEFAULT_RADIUS 0 │ │ │ │ +_3_2#define BALL_ATOM_DEFAULT_TYPE Atom::UNKNOWN_TYPE │ │ │ │ +_3_3#define BALL_ATOM_DEFAULT_VELOCITY 0,0,0 │ │ │ │ +_3_4#define BALL_ATOM_DEFAULT_FORCE 0,0,0 │ │ │ │ +35 │ │ │ │ +36namespace _B_A_L_L │ │ │ │ +37{ │ │ │ │ +38 class Bond; │ │ │ │ +39 class Element; │ │ │ │ +40 class Fragment; │ │ │ │ +41 class Residue; │ │ │ │ +42 class Chain; │ │ │ │ +43 class SecondaryStructure; │ │ │ │ +44 class Molecule; │ │ │ │ +45 class MolecularInteractions; │ │ │ │ +46 │ │ │ │ +_8_7 class _B_A_L_L___E_X_P_O_R_T _A_t_o_m │ │ │ │ +88 : public _C_o_m_p_o_s_i_t_e, │ │ │ │ +89 public _P_r_o_p_e_r_t_y_M_a_n_a_g_e_r │ │ │ │ +90 { │ │ │ │ +91 public: │ │ │ │ 92 │ │ │ │ -_9_5 static double _R; │ │ │ │ -96 │ │ │ │ -_9_9 static double _F_A_R_A_D_A_Y; │ │ │ │ +_9_7 friend class _B_o_n_d; │ │ │ │ +98 │ │ │ │ +99 _B_A_L_L___C_R_E_A_T_E___D_E_E_P(_A_t_o_m) │ │ │ │ 100 │ │ │ │ -_1_0_3 static double _F; │ │ │ │ +101 │ │ │ │ +_1_0_3 typedef short _T_y_p_e; │ │ │ │ 104 │ │ │ │ -_1_0_8 static double _B_O_H_R___R_A_D_I_U_S; │ │ │ │ -109 │ │ │ │ -_1_1_2 static double _a_0; │ │ │ │ -113 │ │ │ │ -114 // the following values from: │ │ │ │ -115 // P.W.Atkins: Physical Chemistry, 5th ed., Oxford University Press, 1995 │ │ │ │ -116 │ │ │ │ -_1_2_0 static double _V_A_C_U_U_M___P_E_R_M_I_T_T_I_V_I_T_Y; │ │ │ │ -121 │ │ │ │ -_1_2_5 static double _V_A_C_U_U_M___P_E_R_M_E_A_B_I_L_I_T_Y; │ │ │ │ +108 │ │ │ │ +111 enum │ │ │ │ +112 { │ │ │ │ +_1_1_6 UNKNOWN_TYPE = -1, │ │ │ │ +117 │ │ │ │ +_1_2_1 ANY_TYPE = 0, │ │ │ │ +122 │ │ │ │ +124 MAX_NUMBER_OF_BONDS = 12 │ │ │ │ +_1_2_5 }; │ │ │ │ 126 │ │ │ │ -_1_3_0 static double _S_P_E_E_D___O_F___L_I_G_H_T; │ │ │ │ -131 │ │ │ │ -_1_3_4 static double _c; │ │ │ │ -135 │ │ │ │ -_1_3_9 static double _G_R_A_V_I_T_A_T_I_O_N_A_L___C_O_N_S_T_A_N_T; │ │ │ │ -140 │ │ │ │ -_1_4_4 static double _F_I_N_E___S_T_R_U_C_T_U_R_E___C_O_N_S_T_A_N_T; │ │ │ │ -145 │ │ │ │ -_1_4_9 static double _D_E_G___P_E_R___R_A_D; │ │ │ │ -150 │ │ │ │ -_1_5_4 static double _R_A_D___P_E_R___D_E_G; │ │ │ │ +_1_3_0 enum _P_r_o_p_e_r_t_y │ │ │ │ +131 { │ │ │ │ +132 NUMBER_OF_PROPERTIES = 0 │ │ │ │ +_1_3_3 }; │ │ │ │ +134 │ │ │ │ +_1_3_8 enum _F_u_l_l_N_a_m_e_T_y_p_e │ │ │ │ +139 { │ │ │ │ +140 // Do not add extensions │ │ │ │ +_1_4_1 _N_O___V_A_R_I_A_N_T___E_X_T_E_N_S_I_O_N_S, │ │ │ │ +142 // Add the residue extensions │ │ │ │ +_1_4_3 _A_D_D___V_A_R_I_A_N_T___E_X_T_E_N_S_I_O_N_S, │ │ │ │ +144 // Add the residue ID │ │ │ │ +_1_4_5 _A_D_D___R_E_S_I_D_U_E___I_D, │ │ │ │ +146 // Add the residue ID and the residue extension │ │ │ │ +_1_4_7 _A_D_D___V_A_R_I_A_N_T___E_X_T_E_N_S_I_O_N_S___A_N_D___I_D, │ │ │ │ +148 // Add the chain ID and the residue ID │ │ │ │ +_1_4_9 _A_D_D___C_H_A_I_N___R_E_S_I_D_U_E___I_D, │ │ │ │ +150 // Add the chain ID and the residue ID │ │ │ │ +151 ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID │ │ │ │ +_1_5_2 }; │ │ │ │ +153 │ │ │ │ 155 │ │ │ │ -_1_5_9 static double _M_M___P_E_R___I_N_C_H ; │ │ │ │ -160 │ │ │ │ -_1_6_4 static double _M___P_E_R___F_O_O_T ; │ │ │ │ -165 │ │ │ │ -_1_6_9 static double _J_O_U_L_E___P_E_R___C_A_L; │ │ │ │ -170 │ │ │ │ -_1_7_4 static double _C_A_L___P_E_R___J_O_U_L_E; │ │ │ │ -175 }; │ │ │ │ -176 │ │ │ │ -177} // namespace BALL │ │ │ │ +159 │ │ │ │ +_1_7_7 _A_t_o_m(); │ │ │ │ 178 │ │ │ │ -179#endif // BALL_PYTHON_PYCONSTANT_H │ │ │ │ +_1_8_9 _A_t_o_m(const _A_t_o_m& atom, bool deep = true); │ │ │ │ +190 │ │ │ │ +_2_0_7 _A_t_o_m(_E_l_e_m_e_n_t& element, │ │ │ │ +208 const _S_t_r_i_n_g& name, const _S_t_r_i_n_g& type_name = _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___T_Y_P_E___N_A_M_E, │ │ │ │ +209 _T_y_p_e atom_type = _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___T_Y_P_E, │ │ │ │ +210 const _V_e_c_t_o_r_3& position = _V_e_c_t_o_r_3(_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___P_O_S_I_T_I_O_N), │ │ │ │ +211 const _V_e_c_t_o_r_3& velocity = _V_e_c_t_o_r_3(_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___V_E_L_O_C_I_T_Y), │ │ │ │ +212 const _V_e_c_t_o_r_3& force = _V_e_c_t_o_r_3(_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___F_O_R_C_E), │ │ │ │ +213 float charge = _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___C_H_A_R_G_E, │ │ │ │ +214 float radius = _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___R_A_D_I_U_S, │ │ │ │ +215 _I_n_d_e_x formal_charge = _B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___F_O_R_M_A_L___C_H_A_R_G_E); │ │ │ │ +216 │ │ │ │ +218 │ │ │ │ +222 │ │ │ │ +_2_2_9 virtual _~_A_t_o_m(); │ │ │ │ +230 │ │ │ │ +_2_4_0 virtual void _c_l_e_a_r(); │ │ │ │ +241 │ │ │ │ +_2_4_7 virtual void _d_e_s_t_r_o_y(); │ │ │ │ +248 │ │ │ │ +250 │ │ │ │ +253 │ │ │ │ +_2_5_7 virtual void _p_e_r_s_i_s_t_e_n_t_W_r_i_t_e(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm, const char* name = 0) │ │ │ │ +const; │ │ │ │ +258 │ │ │ │ +_2_6_2 virtual void _p_e_r_s_i_s_t_e_n_t_R_e_a_d(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm); │ │ │ │ +263 │ │ │ │ +265 │ │ │ │ +268 │ │ │ │ +_2_7_8 void _s_e_t(const _A_t_o_m& atom, bool deep = true); │ │ │ │ +279 │ │ │ │ +_2_8_5 void _g_e_t(_A_t_o_m& atom, bool deep = true) const; │ │ │ │ +286 │ │ │ │ +_2_9_5 _A_t_o_m& operator = (const _A_t_o_m& atom); │ │ │ │ +296 │ │ │ │ +_3_0_1 void _s_w_a_p(_A_t_o_m& atom); │ │ │ │ +302 │ │ │ │ +304 │ │ │ │ +307 │ │ │ │ +_3_1_2 bool operator == (const _A_t_o_m& atom) const; │ │ │ │ +313 │ │ │ │ +_3_1_7 bool operator != (const _A_t_o_m& atom) const; │ │ │ │ +318 │ │ │ │ +320 │ │ │ │ +323 │ │ │ │ +_3_2_5 void _s_e_t_E_l_e_m_e_n_t(const _E_l_e_m_e_n_t& element); │ │ │ │ +326 │ │ │ │ +_3_2_8 const _E_l_e_m_e_n_t& _g_e_t_E_l_e_m_e_n_t() const; │ │ │ │ +329 │ │ │ │ +_3_3_4 void _s_e_t_C_h_a_r_g_e(float charge); │ │ │ │ +335 │ │ │ │ +_3_4_0 float _g_e_t_C_h_a_r_g_e() const; │ │ │ │ +341 │ │ │ │ +_3_4_3 void _s_e_t_F_o_r_m_a_l_C_h_a_r_g_e(_I_n_d_e_x formal_charge); │ │ │ │ +344 │ │ │ │ +_3_4_6 _I_n_d_e_x _g_e_t_F_o_r_m_a_l_C_h_a_r_g_e() const; │ │ │ │ +347 │ │ │ │ +_3_5_5 const _M_o_l_e_c_u_l_e* _g_e_t_M_o_l_e_c_u_l_e() const; │ │ │ │ +_3_5_7 _M_o_l_e_c_u_l_e* _g_e_t_M_o_l_e_c_u_l_e(); │ │ │ │ +358 │ │ │ │ +359 │ │ │ │ +_3_6_7 const _F_r_a_g_m_e_n_t* _g_e_t_F_r_a_g_m_e_n_t() const; │ │ │ │ +_3_6_9 _F_r_a_g_m_e_n_t* _g_e_t_F_r_a_g_m_e_n_t(); │ │ │ │ +370 │ │ │ │ +_3_7_8 const _R_e_s_i_d_u_e* _g_e_t_R_e_s_i_d_u_e() const; │ │ │ │ +_3_8_0 _R_e_s_i_d_u_e* _g_e_t_R_e_s_i_d_u_e(); │ │ │ │ +381 │ │ │ │ +_3_8_7 const _S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e* _g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e() const; │ │ │ │ +_3_8_9 _S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e* _g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e(); │ │ │ │ +390 │ │ │ │ +_3_9_6 const _C_h_a_i_n* _g_e_t_C_h_a_i_n() const; │ │ │ │ +_3_9_8 _C_h_a_i_n* _g_e_t_C_h_a_i_n(); │ │ │ │ +399 │ │ │ │ +_4_0_1 void _s_e_t_N_a_m_e(const _S_t_r_i_n_g& name); │ │ │ │ +402 │ │ │ │ +_4_0_4 const _S_t_r_i_n_g& _g_e_t_N_a_m_e() const; │ │ │ │ +405 │ │ │ │ +_4_3_5 _S_t_r_i_n_g _g_e_t_F_u_l_l_N_a_m_e(_F_u_l_l_N_a_m_e_T_y_p_e type = ADD_VARIANT_EXTENSIONS) const; │ │ │ │ +436 │ │ │ │ +_4_4_0 void _s_e_t_P_o_s_i_t_i_o_n(const _V_e_c_t_o_r_3& position); │ │ │ │ +441 │ │ │ │ +_4_4_3 _V_e_c_t_o_r_3& _g_e_t_P_o_s_i_t_i_o_n(); │ │ │ │ +444 │ │ │ │ +_4_4_6 const _V_e_c_t_o_r_3& _g_e_t_P_o_s_i_t_i_o_n() const; │ │ │ │ +447 │ │ │ │ +_4_5_1 void _s_e_t_R_a_d_i_u_s(float radius); │ │ │ │ +452 │ │ │ │ +_4_5_4 float _g_e_t_R_a_d_i_u_s() const; │ │ │ │ +455 │ │ │ │ +_4_5_7 void _s_e_t_T_y_p_e(_T_y_p_e atom_type); │ │ │ │ +458 │ │ │ │ +_4_6_0 _T_y_p_e _g_e_t_T_y_p_e() const; │ │ │ │ +461 │ │ │ │ +_4_6_3 _S_t_r_i_n_g _g_e_t_T_y_p_e_N_a_m_e() const; │ │ │ │ +464 │ │ │ │ +_4_6_6 void _s_e_t_T_y_p_e_N_a_m_e(const _S_t_r_i_n_g& name); │ │ │ │ +467 │ │ │ │ +_4_7_1 void _s_e_t_V_e_l_o_c_i_t_y(const _V_e_c_t_o_r_3& velocity); │ │ │ │ +472 │ │ │ │ +_4_7_6 _V_e_c_t_o_r_3& _g_e_t_V_e_l_o_c_i_t_y(); │ │ │ │ +477 │ │ │ │ +_4_8_1 const _V_e_c_t_o_r_3& _g_e_t_V_e_l_o_c_i_t_y() const; │ │ │ │ +482 │ │ │ │ +_4_8_6 void _s_e_t_F_o_r_c_e(const _V_e_c_t_o_r_3& force); │ │ │ │ +_4_8_8 const _V_e_c_t_o_r_3& _g_e_t_F_o_r_c_e() const; │ │ │ │ +_4_9_0 _V_e_c_t_o_r_3& _g_e_t_F_o_r_c_e(); │ │ │ │ +491 │ │ │ │ +492 │ │ │ │ +_4_9_4 _S_i_z_e _c_o_u_n_t_B_o_n_d_s() const; │ │ │ │ +495 │ │ │ │ +_5_0_8 _B_o_n_d* _g_e_t_B_o_n_d(_P_o_s_i_t_i_o_n index); │ │ │ │ +509 │ │ │ │ +_5_1_3 const _B_o_n_d* _g_e_t_B_o_n_d(_P_o_s_i_t_i_o_n index) const; │ │ │ │ +514 │ │ │ │ +_5_2_2 _B_o_n_d* _g_e_t_B_o_n_d(const _A_t_o_m& atom); │ │ │ │ +523 │ │ │ │ +_5_3_1 const _B_o_n_d* _g_e_t_B_o_n_d(const _A_t_o_m& atom) const; │ │ │ │ +533 │ │ │ │ +534 │ │ │ │ +538 │ │ │ │ +_5_4_8 _B_o_n_d* _c_r_e_a_t_e_B_o_n_d(_A_t_o_m& atom); │ │ │ │ +549 │ │ │ │ +_5_6_1 _B_o_n_d* _c_r_e_a_t_e_B_o_n_d(_B_o_n_d& bond, _A_t_o_m& atom); │ │ │ │ +562 │ │ │ │ +_5_6_7 _B_o_n_d* _c_l_o_n_e_B_o_n_d(_B_o_n_d& bond, _A_t_o_m& atom); │ │ │ │ +568 │ │ │ │ +_5_8_0 bool _d_e_s_t_r_o_y_B_o_n_d(const _A_t_o_m& atom); │ │ │ │ +581 │ │ │ │ +_5_9_3 void _d_e_s_t_r_o_y_B_o_n_d_s(); │ │ │ │ +594 │ │ │ │ +_6_0_3 _A_t_o_m* _g_e_t_P_a_r_t_n_e_r_A_t_o_m(_P_o_s_i_t_i_o_n i); │ │ │ │ +604 │ │ │ │ +_6_1_3 const _A_t_o_m* _g_e_t_P_a_r_t_n_e_r_A_t_o_m(_P_o_s_i_t_i_o_n i) const; │ │ │ │ +614 │ │ │ │ +_6_2_1 float _g_e_t_D_i_s_t_a_n_c_e(const _A_t_o_m& a) const; │ │ │ │ +622 │ │ │ │ +_6_2_3 _M_o_l_e_c_u_l_a_r_I_n_t_e_r_a_c_t_i_o_n_s* _i_n_t_e_r_a_c_t_i_o_n_s; │ │ │ │ +624 │ │ │ │ +_6_2_5 void _a_d_d_I_n_t_e_r_a_c_t_i_o_n(const _A_t_o_m* atom, _S_t_r_i_n_g interaction_type, double │ │ │ │ +energy); │ │ │ │ +626 │ │ │ │ +_6_2_7 void _a_d_d_I_n_t_e_r_a_c_t_i_o_n(_S_t_r_i_n_g interaction_type, double energy); │ │ │ │ +628 │ │ │ │ +_6_2_9 void _d_i_s_a_b_l_e_S_t_o_r_e_I_n_t_e_r_a_c_t_i_o_n_s(); │ │ │ │ +630 │ │ │ │ +_6_3_1 void _e_n_a_b_l_e_S_t_o_r_e_I_n_t_e_r_a_c_t_i_o_n_s(); │ │ │ │ +632 │ │ │ │ +_6_3_3 bool _s_t_o_r_e___i_n_t_e_r_a_c_t_i_o_n_s___d_i_s_a_b_l_e_d__; │ │ │ │ +634 │ │ │ │ +636 │ │ │ │ +640 │ │ │ │ +_6_4_7 bool _h_a_s_B_o_n_d(const _B_o_n_d& bond) const; │ │ │ │ +648 │ │ │ │ +_6_5_7 bool _i_s_B_o_u_n_d_T_o(const _A_t_o_m& atom) const; │ │ │ │ +658 │ │ │ │ +_6_6_4 bool _i_s_B_o_u_n_d() const; │ │ │ │ +665 │ │ │ │ +_6_7_3 bool _i_s_G_e_m_i_n_a_l(const _A_t_o_m& atom) const; │ │ │ │ +674 │ │ │ │ +_6_8_1 bool _i_s_V_i_c_i_n_a_l(const _A_t_o_m& atom) const; │ │ │ │ +683 │ │ │ │ +_6_8_7 virtual bool _i_s_A_t_o_m() const { return true; } │ │ │ │ +689 │ │ │ │ +693 │ │ │ │ +_6_9_8 virtual bool _i_s_V_a_l_i_d() const; │ │ │ │ +699 │ │ │ │ +_7_0_7 virtual void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const; │ │ │ │ +709 │ │ │ │ +713 │ │ │ │ +_7_1_9 bool _a_p_p_l_y_B_o_n_d_s(_U_n_a_r_y_P_r_o_c_e_s_s_o_r_<_B_o_n_d_>& processor); │ │ │ │ +720 │ │ │ │ +722 │ │ │ │ +725 │ │ │ │ +_7_2_6 typedef _I_n_d_e_x _B_o_n_d_I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n; │ │ │ │ +727 │ │ │ │ +_7_2_8 class _B_A_L_L___E_X_P_O_R_T _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +729 { │ │ │ │ +730 public: │ │ │ │ +731 │ │ │ │ +732 _B_A_L_L___C_R_E_A_T_E___D_E_E_P(_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s) │ │ │ │ +733 │ │ │ │ +_7_3_4 virtual ~_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s() {} │ │ │ │ +735 │ │ │ │ +_7_3_6 _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s() │ │ │ │ +737 : bound_(0), │ │ │ │ +738 position_(0) │ │ │ │ +739 { │ │ │ │ +740 } │ │ │ │ +741 │ │ │ │ +_7_4_2 _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s(const _A_t_o_m& atom) │ │ │ │ +743 : bound_((_A_t_o_m*)&atom), │ │ │ │ +744 position_(0) │ │ │ │ +745 { │ │ │ │ +746 } │ │ │ │ +747 │ │ │ │ +_7_4_8 _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s(const _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits, bool /* deep */ = │ │ │ │ +true) │ │ │ │ +749 : bound_(traits.bound_), │ │ │ │ +750 position_(traits.position_) │ │ │ │ +751 { │ │ │ │ +752 } │ │ │ │ +753 │ │ │ │ +_7_5_4 _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& operator = (const _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) │ │ │ │ +755 { │ │ │ │ +756 bound_ = traits.bound_; │ │ │ │ +757 position_ = traits.position_; │ │ │ │ +758 return *this; │ │ │ │ +759 } │ │ │ │ +760 │ │ │ │ +_7_6_1 _A_t_o_m* _g_e_t_C_o_n_t_a_i_n_e_r() { return bound_; } │ │ │ │ +762 │ │ │ │ +_7_6_3 const _A_t_o_m* _g_e_t_C_o_n_t_a_i_n_e_r() const { return bound_; } │ │ │ │ +764 │ │ │ │ +_7_6_5 bool _i_s_S_i_n_g_u_l_a_r() const { return (bound_ == 0); } │ │ │ │ +766 │ │ │ │ +_7_6_7 _B_o_n_d_I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n& _g_e_t_P_o_s_i_t_i_o_n() { return position_; } │ │ │ │ +768 │ │ │ │ +_7_6_9 const _B_o_n_d_I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n& _g_e_t_P_o_s_i_t_i_o_n() const { return position_; } │ │ │ │ +770 │ │ │ │ +771 // Comparison: We do net check whether these traits are bound to │ │ │ │ +772 // the same container here for efficiency reasons. │ │ │ │ +773 │ │ │ │ +_7_7_4 bool operator == (const _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) const │ │ │ │ +775 { │ │ │ │ +776 return (position_ == traits.position_); │ │ │ │ +777 } │ │ │ │ +778 │ │ │ │ +_7_7_9 bool operator != (const _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) const │ │ │ │ +780 { │ │ │ │ +781 return !(position_ == traits.position_); │ │ │ │ +782 } │ │ │ │ +783 │ │ │ │ +_7_8_4 bool operator < (const _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) const │ │ │ │ +785 { │ │ │ │ +786 return (position_ < traits.position_); │ │ │ │ +787 } │ │ │ │ +788 │ │ │ │ +_7_8_9 _D_i_s_t_a_n_c_e _g_e_t_D_i_s_t_a_n_c_e(const _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) const │ │ │ │ +790 { │ │ │ │ +791 return (_D_i_s_t_a_n_c_e)(position_ - traits.position_); │ │ │ │ +792 } │ │ │ │ +793 │ │ │ │ +_7_9_4 bool _i_s_V_a_l_i_d() const │ │ │ │ +795 { │ │ │ │ +796 return (bound_ != 0 && position_ >= 0 && position_ < bound_- │ │ │ │ +>number_of_bonds_); │ │ │ │ +797 } │ │ │ │ +798 │ │ │ │ +_7_9_9 void _i_n_v_a_l_i_d_a_t_e() │ │ │ │ +800 { │ │ │ │ +801 bound_ = 0; │ │ │ │ +802 position_ = 0; │ │ │ │ +803 } │ │ │ │ +804 │ │ │ │ +_8_0_5 void _t_o_B_e_g_i_n() { position_ = 0; } │ │ │ │ +806 │ │ │ │ +_8_0_7 bool _i_s_B_e_g_i_n() const { return (position_ == 0); } │ │ │ │ +808 │ │ │ │ +_8_0_9 void _t_o_E_n_d() { position_ = bound_->number_of_bonds_; } │ │ │ │ +810 │ │ │ │ +_8_1_1 bool _i_s_E_n_d() const { return (position_ >= bound_->number_of_bonds_);} │ │ │ │ +812 │ │ │ │ +_8_1_3 _B_o_n_d& _g_e_t_D_a_t_a() { return *(bound_->bond_[position_]); } │ │ │ │ +814 │ │ │ │ +_8_1_5 const _B_o_n_d& _g_e_t_D_a_t_a() const { return *(bound_->bond_[position_]); } │ │ │ │ +816 │ │ │ │ +_8_1_7 void _f_o_r_w_a_r_d() { ++position_; } │ │ │ │ +818 │ │ │ │ +_8_1_9 friend std::ostream& operator << (std::ostream& s, const │ │ │ │ +_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) │ │ │ │ +820 { │ │ │ │ +821 return (s << traits.position_ << ' '); │ │ │ │ +822 } │ │ │ │ +823 │ │ │ │ +_8_2_4 void _d_u_m_p(std::ostream& s) const │ │ │ │ +825 { │ │ │ │ +826 s << position_ << std::endl; │ │ │ │ +827 } │ │ │ │ +828 │ │ │ │ +_8_2_9 void _t_o_R_B_e_g_i_n() │ │ │ │ +830 { │ │ │ │ +831 position_ = bound_->number_of_bonds_ - 1; │ │ │ │ +832 } │ │ │ │ +833 │ │ │ │ +_8_3_4 bool _i_s_R_B_e_g_i_n() const │ │ │ │ +835 { │ │ │ │ +836 return (position_ == bound_->number_of_bonds_ - 1); │ │ │ │ +837 } │ │ │ │ +838 │ │ │ │ +_8_3_9 void _t_o_R_E_n_d() │ │ │ │ +840 { │ │ │ │ +841 position_ = -1; │ │ │ │ +842 } │ │ │ │ +843 │ │ │ │ +_8_4_4 bool _i_s_R_E_n_d() const │ │ │ │ +845 { │ │ │ │ +846 return (position_ <= -1); │ │ │ │ +847 } │ │ │ │ +848 │ │ │ │ +_8_4_9 void _b_a_c_k_w_a_r_d() │ │ │ │ +850 { │ │ │ │ +851 --position_; │ │ │ │ +852 } │ │ │ │ +853 │ │ │ │ +_8_5_4 void _b_a_c_k_w_a_r_d(_D_i_s_t_a_n_c_e distance) │ │ │ │ +855 { │ │ │ │ +856 position_ -= distance; │ │ │ │ +857 } │ │ │ │ +858 │ │ │ │ +_8_5_9 void _f_o_r_w_a_r_d(_D_i_s_t_a_n_c_e distance) │ │ │ │ +860 { │ │ │ │ +861 position_ += distance; │ │ │ │ +862 } │ │ │ │ +863 │ │ │ │ +_8_6_4 _B_o_n_d& _g_e_t_D_a_t_a(_I_n_d_e_x index) │ │ │ │ +865 { │ │ │ │ +866 return *(bound_->bond_[index]); │ │ │ │ +867 } │ │ │ │ +868 │ │ │ │ +_8_6_9 const _B_o_n_d& _g_e_t_D_a_t_a(_I_n_d_e_x index) const │ │ │ │ +870 { │ │ │ │ +871 return *(bound_->bond_[index]); │ │ │ │ +872 } │ │ │ │ +873 │ │ │ │ +874 private: │ │ │ │ +875 │ │ │ │ +876 _A_t_o_m* bound_; │ │ │ │ +877 _B_o_n_d_I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n position_; │ │ │ │ +878 │ │ │ │ +879 }; │ │ │ │ +880 │ │ │ │ +_8_8_1 friend class _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s; │ │ │ │ +882 │ │ │ │ +885 typedef _R_a_n_d_o_m_A_c_c_e_s_s_I_t_e_r_a_t_o_r │ │ │ │ +886 <_A_t_o_m, _B_o_n_d, _B_o_n_d_I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n, _B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s> │ │ │ │ +_8_8_7 _B_o_n_d_I_t_e_r_a_t_o_r; │ │ │ │ +888 │ │ │ │ +_8_9_0 _B_o_n_d_I_t_e_r_a_t_o_r _b_e_g_i_n_B_o_n_d() │ │ │ │ +891 { │ │ │ │ +892 return BondIterator::begin(*this); │ │ │ │ +893 } │ │ │ │ +894 │ │ │ │ +_8_9_6 _B_o_n_d_I_t_e_r_a_t_o_r _e_n_d_B_o_n_d() │ │ │ │ +897 { │ │ │ │ +898 return BondIterator::end(*this); │ │ │ │ +899 } │ │ │ │ +900 │ │ │ │ +902 typedef _C_o_n_s_t_R_a_n_d_o_m_A_c_c_e_s_s_I_t_e_r_a_t_o_r │ │ │ │ +903 <_A_t_o_m, _B_o_n_d, BondIteratorPosition, BondIteratorTraits> │ │ │ │ +_9_0_4 _B_o_n_d_C_o_n_s_t_I_t_e_r_a_t_o_r; │ │ │ │ +905 │ │ │ │ +_9_0_7 _B_o_n_d_C_o_n_s_t_I_t_e_r_a_t_o_r _b_e_g_i_n_B_o_n_d() const │ │ │ │ +908 { │ │ │ │ +909 return BondConstIterator::begin(*this); │ │ │ │ +910 } │ │ │ │ +911 │ │ │ │ +_9_1_3 _B_o_n_d_C_o_n_s_t_I_t_e_r_a_t_o_r _e_n_d_B_o_n_d() const │ │ │ │ +914 { │ │ │ │ +915 return BondConstIterator::end(*this); │ │ │ │ +916 } │ │ │ │ +917 │ │ │ │ +_9_1_9 typedef std::reverse_iterator _B_o_n_d_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r; │ │ │ │ +920 │ │ │ │ +_9_2_2 _B_o_n_d_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r _r_b_e_g_i_n_B_o_n_d() │ │ │ │ +923 { │ │ │ │ +924 return _B_o_n_d_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r(endBond()); │ │ │ │ +925 } │ │ │ │ +926 │ │ │ │ +_9_2_8 _B_o_n_d_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r _r_e_n_d_B_o_n_d() │ │ │ │ +929 { │ │ │ │ +930 return _B_o_n_d_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r(beginBond()); │ │ │ │ +931 } │ │ │ │ +932 │ │ │ │ +_9_3_4 typedef std::reverse_iterator _B_o_n_d_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r; │ │ │ │ +935 │ │ │ │ +_9_3_7 _B_o_n_d_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r _r_b_e_g_i_n_B_o_n_d() const │ │ │ │ +938 { │ │ │ │ +939 return _B_o_n_d_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r(endBond()); │ │ │ │ +940 } │ │ │ │ +941 │ │ │ │ +_9_4_3 _B_o_n_d_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r _r_e_n_d_B_o_n_d() const │ │ │ │ +944 { │ │ │ │ +945 return _B_o_n_d_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r(beginBond()); │ │ │ │ +946 } │ │ │ │ +947 │ │ │ │ +949 │ │ │ │ +952 │ │ │ │ +_9_5_4 typedef std::list _A_t_o_m_P_t_r_L_i_s_t; │ │ │ │ +955 │ │ │ │ +_9_5_7 typedef std::list _A_t_o_m_I_n_d_e_x_L_i_s_t; │ │ │ │ +958 │ │ │ │ +959 protected: │ │ │ │ +960 │ │ │ │ +962 │ │ │ │ +965 │ │ │ │ +_9_6_7 static _A_t_o_m_I_n_d_e_x_L_i_s_t _f_r_e_e___l_i_s_t__; │ │ │ │ +968 │ │ │ │ +_9_7_0 _S_t_r_i_n_g _n_a_m_e__; │ │ │ │ +_9_7_2 _S_t_r_i_n_g _t_y_p_e___n_a_m_e__; │ │ │ │ +_9_7_4 const _E_l_e_m_e_n_t* _e_l_e_m_e_n_t__; │ │ │ │ +_9_7_6 float _r_a_d_i_u_s__; │ │ │ │ +_9_7_8 _T_y_p_e _t_y_p_e__; │ │ │ │ +_9_8_0 unsigned char _n_u_m_b_e_r___o_f___b_o_n_d_s__; │ │ │ │ +_9_8_2 _B_o_n_d* bond_[MAX_NUMBER_OF_BONDS]; │ │ │ │ +_9_8_4 _I_n_d_e_x _f_o_r_m_a_l___c_h_a_r_g_e__; │ │ │ │ +_9_8_6 _V_e_c_t_o_r_3 _p_o_s_i_t_i_o_n__; │ │ │ │ +_9_8_8 float _c_h_a_r_g_e__; │ │ │ │ +_9_9_0 _V_e_c_t_o_r_3 _v_e_l_o_c_i_t_y__; │ │ │ │ +_9_9_2 _V_e_c_t_o_r_3 _f_o_r_c_e__; │ │ │ │ +994 │ │ │ │ +995 │ │ │ │ +996 │ │ │ │ +997 private: │ │ │ │ +998 │ │ │ │ +1000 void clear_(); │ │ │ │ +1001 │ │ │ │ +1003 void swapLastBond_(const _A_t_o_m* atom); │ │ │ │ +1004 │ │ │ │ +1005 }; │ │ │ │ +1006 │ │ │ │ +1007// required for visual studio │ │ │ │ +1008#ifdef BALL_COMPILER_MSVC │ │ │ │ +1009#include │ │ │ │ +1010template class _B_A_L_L___E_X_P_O_R_T std::vector; │ │ │ │ +1011#endif │ │ │ │ +1012 │ │ │ │ +1013# ifndef BALL_NO_INLINE_FUNCTIONS │ │ │ │ +1014# include │ │ │ │ +1015# endif │ │ │ │ +1016} // namespace BALL │ │ │ │ +1017 │ │ │ │ +1018#ifndef BALL_KERNEL_BONDITERATOR_H │ │ │ │ +1019# include <_B_A_L_L_/_K_E_R_N_E_L_/_b_o_n_d_I_t_e_r_a_t_o_r_._h> │ │ │ │ +1020#endif │ │ │ │ +1021 │ │ │ │ +1022 │ │ │ │ +1023#endif // BALL_KERNEL_ATOM_H │ │ │ │ +_p_r_o_p_e_r_t_y_._h │ │ │ │ +_r_a_n_d_o_m_A_c_c_e_s_s_I_t_e_r_a_t_o_r_._h │ │ │ │ +_c_o_m_p_o_s_i_t_e_._h │ │ │ │ +_b_o_n_d_I_t_e_r_a_t_o_r_._h │ │ │ │ +_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___F_O_R_C_E │ │ │ │ +#define BALL_ATOM_DEFAULT_FORCE │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_3_4 │ │ │ │ +_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___F_O_R_M_A_L___C_H_A_R_G_E │ │ │ │ +#define BALL_ATOM_DEFAULT_FORMAL_CHARGE │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_2_7 │ │ │ │ +_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___T_Y_P_E___N_A_M_E │ │ │ │ +#define BALL_ATOM_DEFAULT_TYPE_NAME │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_2_9 │ │ │ │ +_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___R_A_D_I_U_S │ │ │ │ +#define BALL_ATOM_DEFAULT_RADIUS │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_3_1 │ │ │ │ +_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___P_O_S_I_T_I_O_N │ │ │ │ +#define BALL_ATOM_DEFAULT_POSITION │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_3_0 │ │ │ │ +_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___V_E_L_O_C_I_T_Y │ │ │ │ +#define BALL_ATOM_DEFAULT_VELOCITY │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_3_3 │ │ │ │ +_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___T_Y_P_E │ │ │ │ +#define BALL_ATOM_DEFAULT_TYPE │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_3_2 │ │ │ │ +_B_A_L_L___A_T_O_M___D_E_F_A_U_L_T___C_H_A_R_G_E │ │ │ │ +#define BALL_ATOM_DEFAULT_CHARGE │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_2_6 │ │ │ │ +_v_e_c_t_o_r_3_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E___D_E_E_P │ │ │ │ +#define BALL_CREATE_DEEP(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_2_6 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_2_2 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_G_R_A_V_I_T_A_T_I_O_N_A_L___C_O_N_S_T_A_N_T │ │ │ │ -static double GRAVITATIONAL_CONSTANT │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_3_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_A_V_O_G_A_D_R_O │ │ │ │ -static double AVOGADRO │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_6_1 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_M_O_L │ │ │ │ -static double MOL │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_6_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_C_A_L___P_E_R___J_O_U_L_E │ │ │ │ -static double CAL_PER_JOULE │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_7_4 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_F_I_N_E___S_T_R_U_C_T_U_R_E___C_O_N_S_T_A_N_T │ │ │ │ -static double FINE_STRUCTURE_CONSTANT │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_4_4 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_G_A_S___C_O_N_S_T_A_N_T │ │ │ │ -static double GAS_CONSTANT │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_9_1 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_D_E_G___P_E_R___R_A_D │ │ │ │ -static double DEG_PER_RAD │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_4_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_M_M___P_E_R___I_N_C_H │ │ │ │ -static double MM_PER_INCH │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_5_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_E │ │ │ │ -static double E │ │ │ │ -Euler's number - base of the natural logarithm. │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_2_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_F_A_R_A_D_A_Y │ │ │ │ -static double FARADAY │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_R │ │ │ │ -static double R │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_9_5 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_B_O_L_T_Z_M_A_N_N │ │ │ │ -static double BOLTZMANN │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_V_A_C_U_U_M___P_E_R_M_E_A_B_I_L_I_T_Y │ │ │ │ -static double VACUUM_PERMEABILITY │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_2_5 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_e_0 │ │ │ │ -static double e0 │ │ │ │ -Elementary charge (alias) │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_4_1 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_P_L_A_N_C_K │ │ │ │ -static double PLANCK │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_8_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_V_A_C_U_U_M___P_E_R_M_I_T_T_I_V_I_T_Y │ │ │ │ -static double VACUUM_PERMITTIVITY │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_2_0 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_S_P_E_E_D___O_F___L_I_G_H_T │ │ │ │ -static double SPEED_OF_LIGHT │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_3_0 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_E_L_E_M_E_N_T_A_R_Y___C_H_A_R_G_E │ │ │ │ -static double ELEMENTARY_CHARGE │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_3_8 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_F │ │ │ │ -static double F │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_0_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_k │ │ │ │ -static double k │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_7_8 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_E_L_E_C_T_R_O_N___M_A_S_S │ │ │ │ -static double ELECTRON_MASS │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_M___P_E_R___F_O_O_T │ │ │ │ -static double M_PER_FOOT │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_6_4 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_P_I │ │ │ │ -static double PI │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_2_6 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_N_A │ │ │ │ -static double NA │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_6_5 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_J_O_U_L_E___P_E_R___C_A_L │ │ │ │ -static double JOULE_PER_CAL │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_6_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_c │ │ │ │ -static double c │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_3_4 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_E_P_S_I_L_O_N │ │ │ │ -static double EPSILON │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_3_4 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_N_E_U_T_R_O_N___M_A_S_S │ │ │ │ -static double NEUTRON_MASS │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_5_6 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_h │ │ │ │ -static double h │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_8_7 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_R_A_D___P_E_R___D_E_G │ │ │ │ -static double RAD_PER_DEG │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_5_4 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_a_0 │ │ │ │ -static double a0 │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_1_2 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_B_O_H_R___R_A_D_I_U_S │ │ │ │ -static double BOHR_RADIUS │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_1_0_8 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_:_:_P_R_O_T_O_N___M_A_S_S │ │ │ │ -static double PROTON_MASS │ │ │ │ -DDeeffiinniittiioonn _p_y_C_o_n_s_t_a_n_t_._h_:_5_1 │ │ │ │ -_g_l_o_b_a_l_._h │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r │ │ │ │ +DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_6_0 │ │ │ │ +_B_A_L_L_:_:_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r │ │ │ │ +DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_._h_:_3_4_4 │ │ │ │ +_B_A_L_L_:_:_C_o_n_s_t_R_a_n_d_o_m_A_c_c_e_s_s_I_t_e_r_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _r_a_n_d_o_m_A_c_c_e_s_s_I_t_e_r_a_t_o_r_._h_:_2_6 │ │ │ │ +_B_A_L_L_:_:_R_a_n_d_o_m_A_c_c_e_s_s_I_t_e_r_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _r_a_n_d_o_m_A_c_c_e_s_s_I_t_e_r_a_t_o_r_._h_:_4_1_5 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_P_o_s_i_t_i_o_n │ │ │ │ +Vector3 & getPosition() │ │ │ │ +Return the atom coordinates (mutable) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_M_o_l_e_c_u_l_e │ │ │ │ +Molecule * getMolecule() │ │ │ │ +Return the molecule the atom is contained in (mutable) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_t_o_r_e___i_n_t_e_r_a_c_t_i_o_n_s___d_i_s_a_b_l_e_d__ │ │ │ │ +bool store_interactions_disabled_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_6_3_3 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_i_s_V_i_c_i_n_a_l │ │ │ │ +bool isVicinal(const Atom &atom) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_p_e_r_s_i_s_t_e_n_t_W_r_i_t_e │ │ │ │ +virtual void persistentWrite(PersistenceManager &pm, const char *name=0) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_i_s_A_t_o_m │ │ │ │ +virtual bool isAtom() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_6_8_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_n_u_m_b_e_r___o_f___b_o_n_d_s__ │ │ │ │ +unsigned char number_of_bonds_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_8_0 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_i_s_B_o_u_n_d_T_o │ │ │ │ +bool isBoundTo(const Atom &atom) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_B_o_n_d │ │ │ │ +Bond * getBond(const Atom &atom) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t │ │ │ │ +void get(Atom &atom, bool deep=true) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_f_o_r_c_e__ │ │ │ │ +Vector3 force_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_9_2 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_i_s_B_o_u_n_d │ │ │ │ +bool isBound() const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_B_o_n_d │ │ │ │ +Bond * getBond(Position index) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_R_a_d_i_u_s │ │ │ │ +float getRadius() const │ │ │ │ +Return the atom radius. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_F_o_r_c_e │ │ │ │ +void setForce(const Vector3 &force) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_D_i_s_t_a_n_c_e │ │ │ │ +float getDistance(const Atom &a) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_e_l_e_m_e_n_t__ │ │ │ │ +const Element * element_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_7_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_p_e_r_s_i_s_t_e_n_t_R_e_a_d │ │ │ │ +virtual void persistentRead(PersistenceManager &pm) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_R_e_s_i_d_u_e │ │ │ │ +const Residue * getResidue() const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_r_a_d_i_u_s__ │ │ │ │ +float radius_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_7_6 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_d_e_s_t_r_o_y │ │ │ │ +virtual void destroy() │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_F_o_r_m_a_l_C_h_a_r_g_e │ │ │ │ +Index getFormalCharge() const │ │ │ │ +Return the atom's formal charge. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_R_a_d_i_u_s │ │ │ │ +void setRadius(float radius) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_F_u_l_l_N_a_m_e │ │ │ │ +String getFullName(FullNameType type=ADD_VARIANT_EXTENSIONS) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_r_b_e_g_i_n_B_o_n_d │ │ │ │ +BondReverseIterator rbeginBond() │ │ │ │ +Return a reverse bond iterator pointing to the last bond. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_2_2 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t │ │ │ │ +void set(const Atom &atom, bool deep=true) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_F_o_r_c_e │ │ │ │ +const Vector3 & getForce() const │ │ │ │ +Return the atom's force vector (const) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_e_n_a_b_l_e_S_t_o_r_e_I_n_t_e_r_a_c_t_i_o_n_s │ │ │ │ +void enableStoreInteractions() │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_F_u_l_l_N_a_m_e_T_y_p_e │ │ │ │ +FullNameType │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_1_3_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_A_D_D___V_A_R_I_A_N_T___E_X_T_E_N_S_I_O_N_S │ │ │ │ +@ ADD_VARIANT_EXTENSIONS │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_1_4_3 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_A_D_D___V_A_R_I_A_N_T___E_X_T_E_N_S_I_O_N_S___A_N_D___I_D │ │ │ │ +@ ADD_VARIANT_EXTENSIONS_AND_ID │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_1_4_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_N_O___V_A_R_I_A_N_T___E_X_T_E_N_S_I_O_N_S │ │ │ │ +@ NO_VARIANT_EXTENSIONS │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_1_4_1 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_A_D_D___C_H_A_I_N___R_E_S_I_D_U_E___I_D │ │ │ │ +@ ADD_CHAIN_RESIDUE_ID │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_1_4_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_A_D_D___R_E_S_I_D_U_E___I_D │ │ │ │ +@ ADD_RESIDUE_ID │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_1_4_5 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_i_s_G_e_m_i_n_a_l │ │ │ │ +bool isGeminal(const Atom &atom) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_e_n_d_B_o_n_d │ │ │ │ +BondIterator endBond() │ │ │ │ +Return a past-the-end bond iterator. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_9_6 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_R_e_s_i_d_u_e │ │ │ │ +Residue * getResidue() │ │ │ │ +Return the residue the atom is contained in (mutable) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_A_t_o_m │ │ │ │ +Atom() │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_V_e_l_o_c_i_t_y │ │ │ │ +void setVelocity(const Vector3 &velocity) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_E_l_e_m_e_n_t │ │ │ │ +void setElement(const Element &element) │ │ │ │ +Assign the atom's element. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_T_y_p_e │ │ │ │ +void setType(Type atom_type) │ │ │ │ +Assign the numerical atom type. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_B_o_n_d │ │ │ │ +const Bond * getBond(const Atom &atom) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_v_e_l_o_c_i_t_y__ │ │ │ │ +Vector3 velocity_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_9_0 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_b_e_g_i_n_B_o_n_d │ │ │ │ +BondIterator beginBond() │ │ │ │ +Return a bond iterator pointing to the first bond of the atom. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_9_0 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_a_d_d_I_n_t_e_r_a_c_t_i_o_n │ │ │ │ +void addInteraction(const Atom *atom, String interaction_type, double energy) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_c_r_e_a_t_e_B_o_n_d │ │ │ │ +Bond * createBond(Atom &atom) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_C_h_a_i_n │ │ │ │ +Chain * getChain() │ │ │ │ +Return the chain the atom is contained in (mutable) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_c_l_o_n_e_B_o_n_d │ │ │ │ +Bond * cloneBond(Bond &bond, Atom &atom) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r │ │ │ │ +RandomAccessIterator< Atom, Bond, BondIteratorPosition, BondIteratorTraits > │ │ │ │ +BondIterator │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_8_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_e_n_d_B_o_n_d │ │ │ │ +BondConstIterator endBond() const │ │ │ │ +Return a constant past-the-end bond iterator. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_1_3 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_A_t_o_m_P_t_r_L_i_s_t │ │ │ │ +std::list< Atom * > AtomPtrList │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_5_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_N_a_m_e │ │ │ │ +const String & getName() const │ │ │ │ +Return the atom name. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_B_o_n_d │ │ │ │ +const Bond * getBond(Position index) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_P_a_r_t_n_e_r_A_t_o_m │ │ │ │ +Atom * getPartnerAtom(Position i) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_F_r_a_g_m_e_n_t │ │ │ │ +const Fragment * getFragment() const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_t_y_p_e__ │ │ │ │ +Type type_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_7_8 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_A_t_o_m │ │ │ │ +Atom(Element &element, const String &name, const String │ │ │ │ +&type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Type atom_type=BALL_ATOM_DEFAULT_TYPE, │ │ │ │ +const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 │ │ │ │ +&velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3 │ │ │ │ +(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float │ │ │ │ +radius=BALL_ATOM_DEFAULT_RADIUS, Index │ │ │ │ +formal_charge=BALL_ATOM_DEFAULT_FORMAL_CHARGE) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_T_y_p_e │ │ │ │ +short Type │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_1_0_3 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_f_r_e_e___l_i_s_t__ │ │ │ │ +static AtomIndexList free_list_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_6_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_c_l_e_a_r │ │ │ │ +virtual void clear() │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_N_a_m_e │ │ │ │ +void setName(const String &name) │ │ │ │ +Set the atom name. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_c_o_u_n_t_B_o_n_d_s │ │ │ │ +Size countBonds() const │ │ │ │ +Return the number of bonds. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_P_r_o_p_e_r_t_y │ │ │ │ +Property │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_1_3_1 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_P_a_r_t_n_e_r_A_t_o_m │ │ │ │ +const Atom * getPartnerAtom(Position i) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_M_o_l_e_c_u_l_e │ │ │ │ +const Molecule * getMolecule() const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_r_e_n_d_B_o_n_d │ │ │ │ +BondConstReverseIterator rendBond() const │ │ │ │ +Return a constant past-the-end bond iterator for reverse traversal. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_4_3 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e │ │ │ │ +SecondaryStructure * getSecondaryStructure() │ │ │ │ +Return the secondary structure the atom is contained in (mutable) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_C_h_a_r_g_e │ │ │ │ +void setCharge(float charge) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_w_a_p │ │ │ │ +void swap(Atom &atom) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_i_s_V_a_l_i_d │ │ │ │ +virtual bool isValid() const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_P_o_s_i_t_i_o_n │ │ │ │ +const Vector3 & getPosition() const │ │ │ │ +Return the atom coordinates (const) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_F_o_r_c_e │ │ │ │ +Vector3 & getForce() │ │ │ │ +Return the atom's force vector (mutable) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e │ │ │ │ +const SecondaryStructure * getSecondaryStructure() const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_V_e_l_o_c_i_t_y │ │ │ │ +Vector3 & getVelocity() │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_F_o_r_m_a_l_C_h_a_r_g_e │ │ │ │ +void setFormalCharge(Index formal_charge) │ │ │ │ +Set the atom's formal charge. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ +std::reverse_iterator< BondIterator > BondReverseIterator │ │ │ │ +Reverse random access iterator for bonds. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_1_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_d_u_m_p │ │ │ │ +virtual void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ +ConstRandomAccessIterator< Atom, Bond, BondIteratorPosition, BondIteratorTraits │ │ │ │ +> BondConstIterator │ │ │ │ +Constant random access iterator for bonds. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_c_r_e_a_t_e_B_o_n_d │ │ │ │ +Bond * createBond(Bond &bond, Atom &atom) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_a_p_p_l_y_B_o_n_d_s │ │ │ │ +bool applyBonds(UnaryProcessor< Bond > &processor) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ +std::reverse_iterator< BondConstIterator > BondConstReverseIterator │ │ │ │ +Constant reverse random access iterator for bonds. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_3_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_T_y_p_e_N_a_m_e │ │ │ │ +void setTypeName(const String &name) │ │ │ │ +Assign the atom type name. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_C_h_a_i_n │ │ │ │ +const Chain * getChain() const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_F_r_a_g_m_e_n_t │ │ │ │ +Fragment * getFragment() │ │ │ │ +Return the fragment the atom is contained in (mutable) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_p_o_s_i_t_i_o_n__ │ │ │ │ +Vector3 position_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_8_6 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_s_e_t_P_o_s_i_t_i_o_n │ │ │ │ +void setPosition(const Vector3 &position) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_h_a_s_B_o_n_d │ │ │ │ +bool hasBond(const Bond &bond) const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_d_i_s_a_b_l_e_S_t_o_r_e_I_n_t_e_r_a_c_t_i_o_n_s │ │ │ │ +void disableStoreInteractions() │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_C_h_a_r_g_e │ │ │ │ +float getCharge() const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_r_e_n_d_B_o_n_d │ │ │ │ +BondReverseIterator rendBond() │ │ │ │ +Return a past-the-end bond iterator for reverse traversal. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_2_8 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_d_e_s_t_r_o_y_B_o_n_d │ │ │ │ +bool destroyBond(const Atom &atom) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_T_y_p_e │ │ │ │ +Type getType() const │ │ │ │ +Return the (numerical) atom type. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_f_o_r_m_a_l___c_h_a_r_g_e__ │ │ │ │ +Index formal_charge_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_8_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_r_b_e_g_i_n_B_o_n_d │ │ │ │ +BondConstReverseIterator rbeginBond() const │ │ │ │ +Return a constant reverse bond iterator pointing to the first atom. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_3_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_V_e_l_o_c_i_t_y │ │ │ │ +const Vector3 & getVelocity() const │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_A_t_o_m_I_n_d_e_x_L_i_s_t │ │ │ │ +std::list< Position > AtomIndexList │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_5_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_T_y_p_e_N_a_m_e │ │ │ │ +String getTypeName() const │ │ │ │ +Return the atom type name. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_g_e_t_E_l_e_m_e_n_t │ │ │ │ +const Element & getElement() const │ │ │ │ +Return the atom's element. │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_P_o_s_i_t_i_o_n │ │ │ │ +Index BondIteratorPosition │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_2_6 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_b_e_g_i_n_B_o_n_d │ │ │ │ +BondConstIterator beginBond() const │ │ │ │ +Return a constant bond iterator pointing to the first bond. │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_a_d_d_I_n_t_e_r_a_c_t_i_o_n │ │ │ │ +void addInteraction(String interaction_type, double energy) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_t_y_p_e___n_a_m_e__ │ │ │ │ +String type_name_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_7_2 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_n_a_m_e__ │ │ │ │ +String name_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_7_0 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_A_t_o_m │ │ │ │ +Atom(const Atom &atom, bool deep=true) │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_c_h_a_r_g_e__ │ │ │ │ +float charge_ │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_8_8 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_d_e_s_t_r_o_y_B_o_n_d_s │ │ │ │ +void destroyBonds() │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_i_n_t_e_r_a_c_t_i_o_n_s │ │ │ │ +MolecularInteractions * interactions │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_6_2_3 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_~_A_t_o_m │ │ │ │ +virtual ~Atom() │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_2_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_n_v_a_l_i_d_a_t_e │ │ │ │ +void invalidate() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_9_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_d_u_m_p │ │ │ │ +void dump(std::ostream &s) const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_2_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_D_i_s_t_a_n_c_e │ │ │ │ +Distance getDistance(const BondIteratorTraits &traits) const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_8_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +BondIteratorTraits() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_3_6 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_t_o_E_n_d │ │ │ │ +void toEnd() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_0_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_P_o_s_i_t_i_o_n │ │ │ │ +BondIteratorPosition & getPosition() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_6_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +BondIteratorTraits(const Atom &atom) │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_4_2 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_t_o_B_e_g_i_n │ │ │ │ +void toBegin() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_0_5 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_b_a_c_k_w_a_r_d │ │ │ │ +void backward() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_4_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_f_o_r_w_a_r_d │ │ │ │ +void forward() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_1_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_D_a_t_a │ │ │ │ +Bond & getData(Index index) │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_6_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_B_e_g_i_n │ │ │ │ +bool isBegin() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_0_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_t_o_R_E_n_d │ │ │ │ +void toREnd() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_3_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_C_o_n_t_a_i_n_e_r │ │ │ │ +Atom * getContainer() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_6_1 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_R_E_n_d │ │ │ │ +bool isREnd() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_4_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_E_n_d │ │ │ │ +bool isEnd() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_1_1 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_D_a_t_a │ │ │ │ +const Bond & getData(Index index) const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_6_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_b_a_c_k_w_a_r_d │ │ │ │ +void backward(Distance distance) │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_5_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_S_i_n_g_u_l_a_r │ │ │ │ +bool isSingular() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_6_5 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_t_o_R_B_e_g_i_n │ │ │ │ +void toRBegin() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_2_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_R_B_e_g_i_n │ │ │ │ +bool isRBegin() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_3_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_D_a_t_a │ │ │ │ +const Bond & getData() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_1_5 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_C_o_n_t_a_i_n_e_r │ │ │ │ +const Atom * getContainer() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_6_3 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_i_s_V_a_l_i_d │ │ │ │ +bool isValid() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_9_4 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_f_o_r_w_a_r_d │ │ │ │ +void forward(Distance distance) │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_5_9 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_D_a_t_a │ │ │ │ +Bond & getData() │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_8_1_3 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +BondIteratorTraits(const BondIteratorTraits &traits, bool=true) │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_4_8 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_:_:_B_o_n_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_g_e_t_P_o_s_i_t_i_o_n │ │ │ │ +const BondIteratorPosition & getPosition() const │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_7_6_9 │ │ │ │ +_B_A_L_L_:_:_B_o_n_d │ │ │ │ +DDeeffiinniittiioonn _b_o_n_d_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n │ │ │ │ +DDeeffiinniittiioonn _c_h_a_i_n_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_F_r_a_g_m_e_n_t │ │ │ │ +DDeeffiinniittiioonn _f_r_a_g_m_e_n_t_._h_:_2_2 │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_a_r_I_n_t_e_r_a_c_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _m_o_l_e_c_u_l_a_r_I_n_t_e_r_a_c_t_i_o_n_s_._h_:_1_2 │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e │ │ │ │ +DDeeffiinniittiioonn _m_o_l_e_c_u_l_e_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_E_l_e_m_e_n_t │ │ │ │ +DDeeffiinniittiioonn _P_T_E_._h_:_5_5 │ │ │ │ +_B_A_L_L_:_:_R_e_s_i_d_u_e │ │ │ │ +DDeeffiinniittiioonn _r_e_s_i_d_u_e_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e │ │ │ │ +DDeeffiinniittiioonn _s_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d67/a06282.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Static Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::HydrogenBond::Option Struct Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SCORING/COMPONENTS/hydrogenBond.h>

    │ │ │ +

    #include <BALL/SCORING/COMPONENTS/hydrogenBond.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -97,15 +97,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Static Public Attributes

    static const char * HB_IDEAL_LENGTH
     
    static const char * HB_IDEAL_ANGLE
     
    static const char * HB_ANG_UPPER
     
    static const char * VERBOSITY
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 20 of file hydrogenBond.h.

    │ │ │ +

    Definition at line 20 of file hydrogenBond.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ HB_ANG_LOWER

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -119,15 +119,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ static
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 40 of file hydrogenBond.h.

    │ │ │ +

    Definition at line 40 of file hydrogenBond.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ HB_ANG_UPPER

    │ │ │ │ │ │
    │ │ │ @@ -143,15 +143,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 44 of file hydrogenBond.h.

    │ │ │ +

    Definition at line 44 of file hydrogenBond.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ HB_DIST_LOWER

    │ │ │ │ │ │
    │ │ │ @@ -167,15 +167,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 32 of file hydrogenBond.h.

    │ │ │ +

    Definition at line 32 of file hydrogenBond.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ HB_DIST_UPPER

    │ │ │ │ │ │
    │ │ │ @@ -191,15 +191,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 36 of file hydrogenBond.h.

    │ │ │ +

    Definition at line 36 of file hydrogenBond.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ HB_IDEAL_ANGLE

    │ │ │ │ │ │
    │ │ │ @@ -215,15 +215,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 28 of file hydrogenBond.h.

    │ │ │ +

    Definition at line 28 of file hydrogenBond.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ HB_IDEAL_LENGTH

    │ │ │ │ │ │
    │ │ │ @@ -239,15 +239,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 24 of file hydrogenBond.h.

    │ │ │ +

    Definition at line 24 of file hydrogenBond.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ VERBOSITY

    │ │ │ │ │ │
    │ │ │ @@ -263,15 +263,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 48 of file hydrogenBond.h.

    │ │ │ +

    Definition at line 48 of file hydrogenBond.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d6a/a06014.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::SizeOfSSSR Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/QSAR/simpleDescriptors.h>

    │ │ │ +

    #include <BALL/QSAR/simpleDescriptors.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::SizeOfSSSR:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::SimpleBase │ │ │ @@ -104,23 +104,23 @@ │ │ │   │ │ │
    Assignment
    │ │ │ SizeOfSSSR & operator= (const SizeOfSSSR &sssr) │ │ │   │ │ │ - Public Member Functions inherited from BALL::SimpleBase │ │ │  SimpleBase () │ │ │   │ │ │ - SimpleBase (const SimpleBase &sb) │ │ │ + SimpleBase (const SimpleBase &sb) │ │ │   │ │ │  SimpleBase (const String &name) │ │ │   │ │ │  SimpleBase (const String &name, const String &unit) │ │ │   │ │ │ virtual ~SimpleBase () │ │ │   │ │ │ -virtual SimpleBase & operator= (const SimpleBase &sb) │ │ │ +virtual SimpleBase & operator= (const SimpleBase &sb) │ │ │   │ │ │ void computeAllDescriptors (AtomContainer &ac) │ │ │   │ │ │ void setDataFolder (const char *folder) │ │ │   │ │ │ - Public Member Functions inherited from BALL::Descriptor │ │ │  Descriptor () │ │ │ @@ -180,15 +180,15 @@ │ │ │ void calculate_ (AtomContainer &ac) │ │ │   │ │ │ - Protected Member Functions inherited from BALL::Descriptor │ │ │ │ │ │

    Detailed Description

    │ │ │

    This descriptor returns the number of rings in the SSSR

    │ │ │ │ │ │ -

    Definition at line 1359 of file simpleDescriptors.h.

    │ │ │ +

    Definition at line 1359 of file simpleDescriptors.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ SizeOfSSSR() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d6e/a07794.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::VIEW::CompositeManager Class Reference
    Visualisation » Kernel » Other classes
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/compositeManager.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/compositeManager.h>

    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -144,29 +144,29 @@ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Types

    Typedefs for STL compliance
    typedef Composite * value_type
     
    typedef Composite *& reference
     
    virtual void dump (std::ostream &s=std::cout, Size depth=0) const
     
    │ │ │

    Detailed Description

    │ │ │

    CompositeManager class. Management of Composites. This class is a container for all Composite objects, which are used in an application. When the CompositeManager is destroyed, all inserted Composites are deleted.

    │ │ │ │ │ │ -

    Definition at line 26 of file compositeManager.h.

    │ │ │ +

    Definition at line 26 of file compositeManager.h.

    │ │ │

    Member Typedef Documentation

    │ │ │ │ │ │

    ◆ CompositeConstIterator

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef HashSet<Composite*>::ConstIterator BALL::VIEW::CompositeManager::CompositeConstIterator
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 45 of file compositeManager.h.

    │ │ │ +

    Definition at line 45 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ CompositeIterator

    │ │ │ │ │ │
    │ │ │ @@ -174,15 +174,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef HashSet<Composite*>::Iterator BALL::VIEW::CompositeManager::CompositeIterator
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 42 of file compositeManager.h.

    │ │ │ +

    Definition at line 42 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ const_pointer

    │ │ │ │ │ │
    │ │ │ @@ -190,15 +190,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef const Composite** BALL::VIEW::CompositeManager::const_pointer
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 36 of file compositeManager.h.

    │ │ │ +

    Definition at line 36 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ const_reference

    │ │ │ │ │ │
    │ │ │ @@ -206,15 +206,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef const Composite*& BALL::VIEW::CompositeManager::const_reference
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 35 of file compositeManager.h.

    │ │ │ +

    Definition at line 35 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ difference_type

    │ │ │ │ │ │
    │ │ │ @@ -222,15 +222,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Index BALL::VIEW::CompositeManager::difference_type
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 37 of file compositeManager.h.

    │ │ │ +

    Definition at line 37 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ iterator

    │ │ │ │ │ │
    │ │ │ @@ -238,15 +238,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef HashSet<Composite*>::Iterator BALL::VIEW::CompositeManager::iterator
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 39 of file compositeManager.h.

    │ │ │ +

    Definition at line 39 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ pointer

    │ │ │ │ │ │
    │ │ │ @@ -254,15 +254,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Composite** BALL::VIEW::CompositeManager::pointer
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 34 of file compositeManager.h.

    │ │ │ +

    Definition at line 34 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ reference

    │ │ │ │ │ │
    │ │ │ @@ -270,15 +270,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Composite*& BALL::VIEW::CompositeManager::reference
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 33 of file compositeManager.h.

    │ │ │ +

    Definition at line 33 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ size_type

    │ │ │ │ │ │
    │ │ │ @@ -286,15 +286,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Size BALL::VIEW::CompositeManager::size_type
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 38 of file compositeManager.h.

    │ │ │ +

    Definition at line 38 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ value_type

    │ │ │ │ │ │
    │ │ │ @@ -302,15 +302,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Composite* BALL::VIEW::CompositeManager::value_type
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 32 of file compositeManager.h.

    │ │ │ +

    Definition at line 32 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ CompositeManager() [1/2]

    │ │ │ │ │ │ @@ -394,15 +394,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 110 of file compositeManager.h.

    │ │ │ +

    Definition at line 110 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ begin() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -421,15 +421,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 118 of file compositeManager.h.

    │ │ │ +

    Definition at line 118 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ clear()

    │ │ │ │ │ │
    │ │ │ @@ -517,15 +517,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 114 of file compositeManager.h.

    │ │ │ +

    Definition at line 114 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ end() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -544,15 +544,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 122 of file compositeManager.h.

    │ │ │ +

    Definition at line 122 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getComposites() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -571,15 +571,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 126 of file compositeManager.h.

    │ │ │ +

    Definition at line 126 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getComposites() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -598,15 +598,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 130 of file compositeManager.h.

    │ │ │ +

    Definition at line 130 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNumberOfComposites()

    │ │ │ │ │ │
    │ │ │ @@ -626,15 +626,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Return the number of inserted Composites

    │ │ │ │ │ │ -

    Definition at line 101 of file compositeManager.h.

    │ │ │ +

    Definition at line 101 of file compositeManager.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ has()

    │ │ │ │ │ │
    │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d70/a04658.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::AtomTypePredicate Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/KERNEL/standardPredicates.h>

    │ │ │ +

    #include <BALL/KERNEL/standardPredicates.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::AtomTypePredicate:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::ExpressionPredicate │ │ │ @@ -126,15 +126,15 @@ │ │ │ - Protected Attributes inherited from BALL::ExpressionPredicate │ │ │ String argument_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Predicate for matching atom types. Returns true, if the type name of the atom matches exactly the argument of this predicate.

    │ │ │ │ │ │ -

    Definition at line 121 of file standardPredicates.h.

    │ │ │ +

    Definition at line 121 of file standardPredicates.h.

    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ operator()()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d76/a03694.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Public Attributes | │ │ │ List of all members │ │ │
    BALL::PoseClustering::ClusterProperties Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/DOCKING/COMMON/poseClustering.h>

    │ │ │ +

    #include <BALL/DOCKING/COMMON/poseClustering.h>

    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -108,15 +108,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

     ClusterProperties ()
     
     ClusterProperties (const ClusterProperties &)
     
    boost::variant< Eigen::VectorXf, RigidTransformation > center
     
    float merged_at
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 228 of file poseClustering.h.

    │ │ │ +

    Definition at line 228 of file poseClustering.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ClusterProperties() [1/3]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -245,15 +245,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    boost::variant<Eigen::VectorXf, RigidTransformation> BALL::PoseClustering::ClusterProperties::center
    │ │ │
    │ │ │

    The center of the cluster. Depending on the type of transformations we allow, this is either stored as a rigid transformation or as the 3N-dimensional vector given by the atom coordinates. The special case of using only the center of mass is achieved by setting the rotation matrix to identity.

    │ │ │ │ │ │ -

    Definition at line 260 of file poseClustering.h.

    │ │ │ +

    Definition at line 260 of file poseClustering.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ merged_at

    │ │ │ │ │ │
    │ │ │ @@ -262,15 +262,15 @@ │ │ │ │ │ │ float BALL::PoseClustering::ClusterProperties::merged_at │ │ │ │ │ │ │ │ │
    │ │ │

    The value at which this cluster is merged with its sibling.

    │ │ │ │ │ │ -

    Definition at line 264 of file poseClustering.h.

    │ │ │ +

    Definition at line 264 of file poseClustering.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ poses

    │ │ │ │ │ │
    │ │ │ @@ -279,15 +279,15 @@ │ │ │ │ │ │ std::set<Index> BALL::PoseClustering::ClusterProperties::poses │ │ │ │ │ │ │ │ │
    │ │ │

    The poses contained in this cluster.

    │ │ │ │ │ │ -

    Definition at line 246 of file poseClustering.h.

    │ │ │ +

    Definition at line 246 of file poseClustering.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ size

    │ │ │ │ │ │
    │ │ │ @@ -296,15 +296,15 @@ │ │ │ │ │ │ Size BALL::PoseClustering::ClusterProperties::size │ │ │ │ │ │ │ │ │
    │ │ │

    The number of poses contained in this cluster.

    │ │ │ │ │ │ -

    Definition at line 250 of file poseClustering.h.

    │ │ │ +

    Definition at line 250 of file poseClustering.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d78/a01745.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: antechamberFile.h File Reference │ │ │ +BALL: shiftedLVMM.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,31 +65,36 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    antechamberFile.h File Reference
    │ │ │ +
    shiftedLVMM.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/FORMAT/genericMolFile.h>
    │ │ │ +
    #include <BALL/MOLMEC/MINIMIZATION/energyMinimizer.h>
    │ │ │ +#include <BALL/MOLMEC/MINIMIZATION/lineSearch.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::AntechamberFile
    class  BALL::ShiftedLVMMMinimizer
     
    struct  BALL::ShiftedLVMMMinimizer::Option
     
    struct  BALL::ShiftedLVMMMinimizer::Default
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ ├── html2text {} │ │ │ │ @@ -1,19 +1,25 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _F_O_R_M_A_T │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _M_I_N_I_M_I_Z_A_T_I_O_N │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -antechamberFile.h File Reference │ │ │ │ -#include <_B_A_L_L_/_F_O_R_M_A_T_/_g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h> │ │ │ │ +shiftedLVMM.h File Reference │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h> │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_l_i_n_e_S_e_a_r_c_h_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ + class   _B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d78/a01745_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: antechamberFile.h Source File │ │ │ +BALL: shiftedLVMM.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,89 +70,237 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    antechamberFile.h
    │ │ │ +
    shiftedLVMM.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_FORMAT_ANTECHAMBERFILE_H
    │ │ │ -
    6#define BALL_FORMAT_ANTECHAMBERFILE_H
    │ │ │ -
    7
    │ │ │ -
    8#ifndef BALL_FORMAT_GENERICMOLFILE_H
    │ │ │ -
    9# include <BALL/FORMAT/genericMolFile.h>
    │ │ │ -
    10#endif
    │ │ │ -
    11
    │ │ │ -
    12namespace BALL
    │ │ │ -
    13{
    │ │ │ -
    14 class Atom;
    │ │ │ -
    15 class AtomContainer;
    │ │ │ -
    16 class System;
    │ │ │ +
    4// $Id: shiftedLVMM.h,v 1.1.4.6 2007/08/07 09:12:35 aleru Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H
    │ │ │ +
    8#define BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H
    │ │ │ +
    9
    │ │ │ +
    10#ifndef BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H
    │ │ │ +
    11# include <BALL/MOLMEC/MINIMIZATION/energyMinimizer.h>
    │ │ │ +
    12#endif
    │ │ │ +
    13
    │ │ │ +
    14#ifndef BALL_MOLMEC_MINIMIZATION_LINESEARCH_H
    │ │ │ +
    15# include <BALL/MOLMEC/MINIMIZATION/lineSearch.h>
    │ │ │ +
    16#endif
    │ │ │
    17
    │ │ │ -
    │ │ │ -
    25 class BALL_EXPORT AntechamberFile
    │ │ │ -
    26 : public GenericMolFile
    │ │ │ -
    27 {
    │ │ │ -
    28 public:
    │ │ │ -
    29
    │ │ │ -
    33
    │ │ │ -
    36 AntechamberFile();
    │ │ │ -
    37
    │ │ │ -
    41 AntechamberFile(const String& filename, File::OpenMode open_mode = std::ios::in);
    │ │ │ -
    42
    │ │ │ -
    44 virtual ~AntechamberFile();
    │ │ │ -
    46
    │ │ │ -
    50
    │ │ │ -
    54 virtual bool write(const AtomContainer& ac);
    │ │ │ -
    55
    │ │ │ -
    59 virtual bool write(const System& system);
    │ │ │ -
    60
    │ │ │ -
    64 virtual bool read(System& system);
    │ │ │ -
    65
    │ │ │ -
    69 virtual Molecule* read();
    │ │ │ -
    70
    │ │ │ -
    74 virtual bool write(const Molecule& molecule);
    │ │ │ -
    75
    │ │ │ -
    77
    │ │ │ -
    78 protected:
    │ │ │ -
    79 void ac_split_(const String& line, std::vector<String>& split);
    │ │ │ -
    80 };
    │ │ │ -
    │ │ │ -
    81}
    │ │ │ -
    82#endif
    │ │ │ - │ │ │ - │ │ │ -
    BALL::PDB::Atom
    char Atom[5]
    Definition PDBdefs.h:257
    │ │ │ - │ │ │ - │ │ │ -
    BALL::AntechamberFile::AntechamberFile
    AntechamberFile(const String &filename, File::OpenMode open_mode=std::ios::in)
    │ │ │ -
    BALL::AntechamberFile::~AntechamberFile
    virtual ~AntechamberFile()
    Destructor.
    │ │ │ -
    BALL::AntechamberFile::read
    virtual Molecule * read()
    │ │ │ -
    BALL::AntechamberFile::write
    virtual bool write(const AtomContainer &ac)
    │ │ │ -
    BALL::AntechamberFile::read
    virtual bool read(System &system)
    │ │ │ -
    BALL::AntechamberFile::ac_split_
    void ac_split_(const String &line, std::vector< String > &split)
    │ │ │ - │ │ │ -
    BALL::AntechamberFile::write
    virtual bool write(const System &system)
    │ │ │ -
    BALL::AntechamberFile::write
    virtual bool write(const Molecule &molecule)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::File::OpenMode
    std::ios::openmode OpenMode
    Definition file.h:165
    │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    18namespace BALL
    │ │ │ +
    19{
    │ │ │ +
    │ │ │ +
    36 class BALL_EXPORT ShiftedLVMMMinimizer
    │ │ │ +
    37 : public EnergyMinimizer
    │ │ │ +
    38 {
    │ │ │ +
    39 public:
    │ │ │ +
    40
    │ │ │ +
    41 BALL_CREATE(ShiftedLVMMMinimizer)
    │ │ │ +
    42
    │ │ │ +
    43
    │ │ │ +
    46
    │ │ │ +
    47
    │ │ │ +
    │ │ │ +
    52 struct Option
    │ │ │ +
    53 {
    │ │ │ +
    56 static const char* UPDATE_METHOD;
    │ │ │ +
    57
    │ │ │ +
    60 static const char* CORRECTION_PARAMETER;
    │ │ │ +
    61
    │ │ │ +
    65 static const char* NUM_OF_COLUMNS;
    │ │ │ +
    66 };
    │ │ │ +
    │ │ │ +
    67
    │ │ │ +
    │ │ │ +
    68 struct BALL_EXPORT Default
    │ │ │ +
    69 {
    │ │ │ +
    73 static const Size UPDATE_METHOD;
    │ │ │ +
    74
    │ │ │ +
    78 static const Size CORRECTION_PARAMETER;
    │ │ │ +
    79
    │ │ │ +
    83 static const Size NUM_OF_COLUMNS;
    │ │ │ +
    84 };
    │ │ │ +
    │ │ │ +
    85
    │ │ │ +
    87
    │ │ │ +
    90
    │ │ │ +
    │ │ │ +
    93 enum UpdateMethod
    │ │ │ +
    94 {
    │ │ │ +
    97 RANK_1 = 1,
    │ │ │ +
    98
    │ │ │ +
    101 RANK_2 = 2
    │ │ │ +
    102 };
    │ │ │ +
    │ │ │ +
    103
    │ │ │ +
    │ │ │ +
    106 enum CorrectionParameter
    │ │ │ +
    107 {
    │ │ │ +
    110 UNIT_VALUE = 1,
    │ │ │ +
    111
    │ │ │ +
    114 BALANCING_VALUE = 2,
    │ │ │ +
    115
    │ │ │ +
    118 SQUARE_ROOT = 3,
    │ │ │ +
    119
    │ │ │ +
    122 GEOMETRIC_MEAN = 4,
    │ │ │ +
    123
    │ │ │ +
    126 RATIO_OF_SHIFT_PARAMS = 5
    │ │ │ +
    127 };
    │ │ │ +
    │ │ │ +
    128
    │ │ │ +
    130
    │ │ │ +
    133
    │ │ │ +
    136 ShiftedLVMMMinimizer();
    │ │ │ +
    137
    │ │ │ +
    140 ShiftedLVMMMinimizer(ForceField& force_field);
    │ │ │ +
    141
    │ │ │ +
    144 ShiftedLVMMMinimizer(ForceField& force_field, SnapShotManager *ssm);
    │ │ │ +
    145
    │ │ │ +
    148 ShiftedLVMMMinimizer(ForceField& force_field, SnapShotManager* ssm, const Options& options);
    │ │ │ +
    149
    │ │ │ +
    152 ShiftedLVMMMinimizer(ForceField& force_field, const Options& options);
    │ │ │ +
    153
    │ │ │ +
    156 ShiftedLVMMMinimizer(const ShiftedLVMMMinimizer& rhs);
    │ │ │ +
    157
    │ │ │ +
    160 virtual ~ShiftedLVMMMinimizer();
    │ │ │ +
    161
    │ │ │ +
    163
    │ │ │ +
    166
    │ │ │ +
    169 const ShiftedLVMMMinimizer& operator = (const ShiftedLVMMMinimizer& rhs);
    │ │ │ +
    170
    │ │ │ +
    172
    │ │ │ +
    175
    │ │ │ +
    178 virtual bool specificSetup();
    │ │ │ +
    179
    │ │ │ +
    181
    │ │ │ +
    184
    │ │ │ +
    187 void setUpdateMethod(UpdateMethod updt);
    │ │ │ +
    188
    │ │ │ +
    191 UpdateMethod getUpdateMethod() const;
    │ │ │ +
    192
    │ │ │ +
    195 void setCorrectionParameter(CorrectionParameter corr);
    │ │ │ +
    196
    │ │ │ +
    199 CorrectionParameter getCorrectionParameter() const;
    │ │ │ +
    200
    │ │ │ +
    204 void setMaxNumOfColumns(Size num);
    │ │ │ +
    205
    │ │ │ +
    209 Size getMaxNumOfColumns() const;
    │ │ │ +
    210
    │ │ │ +
    217 virtual double findStep();
    │ │ │ +
    218
    │ │ │ +
    222 virtual void updateDirection();
    │ │ │ +
    223
    │ │ │ +
    232 virtual bool minimize(Size iterations = 0, bool resume = false);
    │ │ │ +
    233
    │ │ │ +
    234 protected:
    │ │ │ +
    235
    │ │ │ +
    237
    │ │ │ +
    240
    │ │ │ +
    243 LineSearch line_search_;
    │ │ │ +
    244
    │ │ │ +
    247 bool first_iter_;
    │ │ │ +
    248
    │ │ │ +
    251 Size number_of_atoms_;
    │ │ │ +
    252
    │ │ │ +
    256 Size max_number_of_cols_;
    │ │ │ +
    257
    │ │ │ +
    261 Size curr_number_of_cols_;
    │ │ │ +
    262
    │ │ │ +
    265 Size updt_method_;
    │ │ │ +
    266
    │ │ │ +
    269 Size corr_par_;
    │ │ │ +
    270
    │ │ │ +
    273 double prev_shift_val_;
    │ │ │ +
    274
    │ │ │ +
    277 vector<Vector3> shift_s_;
    │ │ │ +
    278
    │ │ │ +
    281 vector<Vector3> grad_diff_;
    │ │ │ +
    282
    │ │ │ +
    285 vector<float> updt_u_;
    │ │ │ +
    286
    │ │ │ +
    289 vector<float> updt_v_;
    │ │ │ +
    290
    │ │ │ +
    293 vector<Vector3> shifted_direction_;
    │ │ │ +
    294
    │ │ │ +
    298 vector<Vector3> hess_factor_;
    │ │ │ +
    299
    │ │ │ +
    303 vector<Vector3> initial_atoms_;
    │ │ │ +
    304
    │ │ │ +
    306
    │ │ │ +
    307 };
    │ │ │ +
    │ │ │ +
    308} // end of namespace BALL
    │ │ │ +
    309
    │ │ │ +
    310#endif // BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H
    │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(ForceField &force_field)
    │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::findStep
    virtual double findStep()
    │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(ForceField &force_field, SnapShotManager *ssm)
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::setCorrectionParameter
    void setCorrectionParameter(CorrectionParameter corr)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::initial_atoms_
    vector< Vector3 > initial_atoms_
    Definition shiftedLVMM.h:303
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::getCorrectionParameter
    CorrectionParameter getCorrectionParameter() const
    │ │ │ + │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::setUpdateMethod
    void setUpdateMethod(UpdateMethod updt)
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::specificSetup
    virtual bool specificSetup()
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(const ShiftedLVMMMinimizer &rhs)
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::setMaxNumOfColumns
    void setMaxNumOfColumns(Size num)
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::hess_factor_
    vector< Vector3 > hess_factor_
    Definition shiftedLVMM.h:298
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(ForceField &force_field, const Options &options)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::updateDirection
    virtual void updateDirection()
    │ │ │ + │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::grad_diff_
    vector< Vector3 > grad_diff_
    Definition shiftedLVMM.h:281
    │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::minimize
    virtual bool minimize(Size iterations=0, bool resume=false)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(ForceField &force_field, SnapShotManager *ssm, const Options &options)
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::shifted_direction_
    vector< Vector3 > shifted_direction_
    Definition shiftedLVMM.h:293
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::shift_s_
    vector< Vector3 > shift_s_
    Definition shiftedLVMM.h:277
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::getUpdateMethod
    UpdateMethod getUpdateMethod() const
    │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::getMaxNumOfColumns
    Size getMaxNumOfColumns() const
    │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::Option::CORRECTION_PARAMETER
    static const char * CORRECTION_PARAMETER
    Definition shiftedLVMM.h:60
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::Option::UPDATE_METHOD
    static const char * UPDATE_METHOD
    Definition shiftedLVMM.h:56
    │ │ │ +
    BALL::ShiftedLVMMMinimizer::Option::NUM_OF_COLUMNS
    static const char * NUM_OF_COLUMNS
    Definition shiftedLVMM.h:65
    │ │ │ + │ │ │ +
    BALL::ShiftedLVMMMinimizer::Default::CORRECTION_PARAMETER
    static const Size CORRECTION_PARAMETER
    Definition shiftedLVMM.h:78
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,101 +1,296 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _F_O_R_M_A_T │ │ │ │ -antechamberFile.h │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _M_I_N_I_M_I_Z_A_T_I_O_N │ │ │ │ +shiftedLVMM.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_FORMAT_ANTECHAMBERFILE_H │ │ │ │ -6#define BALL_FORMAT_ANTECHAMBERFILE_H │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_FORMAT_GENERICMOLFILE_H │ │ │ │ -9# include <_B_A_L_L_/_F_O_R_M_A_T_/_g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12namespace _B_A_L_L │ │ │ │ -13{ │ │ │ │ -14 class _A_t_o_m; │ │ │ │ -15 class AtomContainer; │ │ │ │ -16 class System; │ │ │ │ +4// $Id: shiftedLVMM.h,v 1.1.4.6 2007/08/07 09:12:35 aleru Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H │ │ │ │ +8#define BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H │ │ │ │ +9 │ │ │ │ +10#ifndef BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H │ │ │ │ +11# include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h> │ │ │ │ +12#endif │ │ │ │ +13 │ │ │ │ +14#ifndef BALL_MOLMEC_MINIMIZATION_LINESEARCH_H │ │ │ │ +15# include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_l_i_n_e_S_e_a_r_c_h_._h> │ │ │ │ +16#endif │ │ │ │ 17 │ │ │ │ -_2_5 class _B_A_L_L___E_X_P_O_R_T _A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ -26 : public _G_e_n_e_r_i_c_M_o_l_F_i_l_e │ │ │ │ -27 { │ │ │ │ -28 public: │ │ │ │ -29 │ │ │ │ -33 │ │ │ │ -_3_6 _A_n_t_e_c_h_a_m_b_e_r_F_i_l_e(); │ │ │ │ -37 │ │ │ │ -_4_1 _A_n_t_e_c_h_a_m_b_e_r_F_i_l_e(const _S_t_r_i_n_g& filename, _F_i_l_e_:_:_O_p_e_n_M_o_d_e open_mode = std:: │ │ │ │ -ios::in); │ │ │ │ +18namespace _B_A_L_L │ │ │ │ +19{ │ │ │ │ +_3_6 class _B_A_L_L___E_X_P_O_R_T _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +37 : public _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r │ │ │ │ +38 { │ │ │ │ +39 public: │ │ │ │ +40 │ │ │ │ +41 _B_A_L_L___C_R_E_A_T_E(_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r) │ │ │ │ 42 │ │ │ │ -_4_4 virtual _~_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e(); │ │ │ │ +43 │ │ │ │ 46 │ │ │ │ -50 │ │ │ │ -_5_4 virtual bool _w_r_i_t_e(const _A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ -55 │ │ │ │ -_5_9 virtual bool _w_r_i_t_e(const _S_y_s_t_e_m& system); │ │ │ │ -60 │ │ │ │ -_6_4 virtual bool _r_e_a_d(_S_y_s_t_e_m& system); │ │ │ │ -65 │ │ │ │ -_6_9 virtual _M_o_l_e_c_u_l_e* _r_e_a_d(); │ │ │ │ -70 │ │ │ │ -_7_4 virtual bool _w_r_i_t_e(const _M_o_l_e_c_u_l_e& molecule); │ │ │ │ -75 │ │ │ │ -77 │ │ │ │ -78 protected: │ │ │ │ -_7_9 void _a_c___s_p_l_i_t__(const _S_t_r_i_n_g& line, std::vector& split); │ │ │ │ -80 }; │ │ │ │ -81} │ │ │ │ -82#endif │ │ │ │ -_g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h │ │ │ │ +47 │ │ │ │ +_5_2 struct _O_p_t_i_o_n │ │ │ │ +53 { │ │ │ │ +_5_6 static const char* _U_P_D_A_T_E___M_E_T_H_O_D; │ │ │ │ +57 │ │ │ │ +_6_0 static const char* _C_O_R_R_E_C_T_I_O_N___P_A_R_A_M_E_T_E_R; │ │ │ │ +61 │ │ │ │ +_6_5 static const char* _N_U_M___O_F___C_O_L_U_M_N_S; │ │ │ │ +66 }; │ │ │ │ +67 │ │ │ │ +_6_8 struct _B_A_L_L___E_X_P_O_R_T _D_e_f_a_u_l_t │ │ │ │ +69 { │ │ │ │ +_7_3 static const _S_i_z_e _U_P_D_A_T_E___M_E_T_H_O_D; │ │ │ │ +74 │ │ │ │ +_7_8 static const _S_i_z_e _C_O_R_R_E_C_T_I_O_N___P_A_R_A_M_E_T_E_R; │ │ │ │ +79 │ │ │ │ +_8_3 static const _S_i_z_e _N_U_M___O_F___C_O_L_U_M_N_S; │ │ │ │ +84 }; │ │ │ │ +85 │ │ │ │ +87 │ │ │ │ +90 │ │ │ │ +_9_3 enum _U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ +94 { │ │ │ │ +_9_7 RANK_1 = 1, │ │ │ │ +98 │ │ │ │ +101 RANK_2 = 2 │ │ │ │ +_1_0_2 }; │ │ │ │ +103 │ │ │ │ +_1_0_6 enum _C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r │ │ │ │ +107 { │ │ │ │ +_1_1_0 UNIT_VALUE = 1, │ │ │ │ +111 │ │ │ │ +_1_1_4 BALANCING_VALUE = 2, │ │ │ │ +115 │ │ │ │ +_1_1_8 SQUARE_ROOT = 3, │ │ │ │ +119 │ │ │ │ +_1_2_2 GEOMETRIC_MEAN = 4, │ │ │ │ +123 │ │ │ │ +126 RATIO_OF_SHIFT_PARAMS = 5 │ │ │ │ +_1_2_7 }; │ │ │ │ +128 │ │ │ │ +130 │ │ │ │ +133 │ │ │ │ +_1_3_6 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(); │ │ │ │ +137 │ │ │ │ +_1_4_0 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ +141 │ │ │ │ +_1_4_4 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field, _S_n_a_p_S_h_o_t_M_a_n_a_g_e_r *ssm); │ │ │ │ +145 │ │ │ │ +_1_4_8 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field, _S_n_a_p_S_h_o_t_M_a_n_a_g_e_r* ssm, const │ │ │ │ +_O_p_t_i_o_n_s& options); │ │ │ │ +149 │ │ │ │ +_1_5_2 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field, const _O_p_t_i_o_n_s& options); │ │ │ │ +153 │ │ │ │ +_1_5_6 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(const _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r& rhs); │ │ │ │ +157 │ │ │ │ +_1_6_0 virtual _~_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(); │ │ │ │ +161 │ │ │ │ +163 │ │ │ │ +166 │ │ │ │ +_1_6_9 const _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r& operator = (const _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r& rhs); │ │ │ │ +170 │ │ │ │ +172 │ │ │ │ +175 │ │ │ │ +_1_7_8 virtual bool _s_p_e_c_i_f_i_c_S_e_t_u_p(); │ │ │ │ +179 │ │ │ │ +181 │ │ │ │ +184 │ │ │ │ +_1_8_7 void _s_e_t_U_p_d_a_t_e_M_e_t_h_o_d(_U_p_d_a_t_e_M_e_t_h_o_d updt); │ │ │ │ +188 │ │ │ │ +_1_9_1 _U_p_d_a_t_e_M_e_t_h_o_d _g_e_t_U_p_d_a_t_e_M_e_t_h_o_d() const; │ │ │ │ +192 │ │ │ │ +_1_9_5 void _s_e_t_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r(_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r corr); │ │ │ │ +196 │ │ │ │ +_1_9_9 _C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r _g_e_t_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r() const; │ │ │ │ +200 │ │ │ │ +_2_0_4 void _s_e_t_M_a_x_N_u_m_O_f_C_o_l_u_m_n_s(_S_i_z_e num); │ │ │ │ +205 │ │ │ │ +_2_0_9 _S_i_z_e _g_e_t_M_a_x_N_u_m_O_f_C_o_l_u_m_n_s() const; │ │ │ │ +210 │ │ │ │ +_2_1_7 virtual double _f_i_n_d_S_t_e_p(); │ │ │ │ +218 │ │ │ │ +_2_2_2 virtual void _u_p_d_a_t_e_D_i_r_e_c_t_i_o_n(); │ │ │ │ +223 │ │ │ │ +_2_3_2 virtual bool _m_i_n_i_m_i_z_e(_S_i_z_e iterations = 0, bool resume = false); │ │ │ │ +233 │ │ │ │ +234 protected: │ │ │ │ +235 │ │ │ │ +237 │ │ │ │ +240 │ │ │ │ +_2_4_3 _L_i_n_e_S_e_a_r_c_h _l_i_n_e___s_e_a_r_c_h__; │ │ │ │ +244 │ │ │ │ +_2_4_7 bool _f_i_r_s_t___i_t_e_r__; │ │ │ │ +248 │ │ │ │ +_2_5_1 _S_i_z_e _n_u_m_b_e_r___o_f___a_t_o_m_s__; │ │ │ │ +252 │ │ │ │ +_2_5_6 _S_i_z_e _m_a_x___n_u_m_b_e_r___o_f___c_o_l_s__; │ │ │ │ +257 │ │ │ │ +_2_6_1 _S_i_z_e _c_u_r_r___n_u_m_b_e_r___o_f___c_o_l_s__; │ │ │ │ +262 │ │ │ │ +_2_6_5 _S_i_z_e _u_p_d_t___m_e_t_h_o_d__; │ │ │ │ +266 │ │ │ │ +_2_6_9 _S_i_z_e _c_o_r_r___p_a_r__; │ │ │ │ +270 │ │ │ │ +_2_7_3 double _p_r_e_v___s_h_i_f_t___v_a_l__; │ │ │ │ +274 │ │ │ │ +_2_7_7 vector _s_h_i_f_t___s__; │ │ │ │ +278 │ │ │ │ +_2_8_1 vector _g_r_a_d___d_i_f_f__; │ │ │ │ +282 │ │ │ │ +_2_8_5 vector _u_p_d_t___u__; │ │ │ │ +286 │ │ │ │ +_2_8_9 vector _u_p_d_t___v__; │ │ │ │ +290 │ │ │ │ +_2_9_3 vector _s_h_i_f_t_e_d___d_i_r_e_c_t_i_o_n__; │ │ │ │ +294 │ │ │ │ +_2_9_8 vector _h_e_s_s___f_a_c_t_o_r__; │ │ │ │ +299 │ │ │ │ +_3_0_3 vector _i_n_i_t_i_a_l___a_t_o_m_s__; │ │ │ │ +304 │ │ │ │ +306 │ │ │ │ +307 }; │ │ │ │ +308} // end of namespace BALL │ │ │ │ +309 │ │ │ │ +310#endif // BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H │ │ │ │ +_l_i_n_e_S_e_a_r_c_h_._h │ │ │ │ +_e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_:_:_A_t_o_m │ │ │ │ -char Atom[5] │ │ │ │ -DDeeffiinniittiioonn _P_D_B_d_e_f_s_._h_:_2_5_7 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _a_n_t_e_c_h_a_m_b_e_r_F_i_l_e_._h_:_2_7 │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ -AntechamberFile(const String &filename, File::OpenMode open_mode=std::ios::in) │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_~_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ -virtual ~AntechamberFile() │ │ │ │ -Destructor. │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_r_e_a_d │ │ │ │ -virtual Molecule * read() │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_w_r_i_t_e │ │ │ │ -virtual bool write(const AtomContainer &ac) │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_r_e_a_d │ │ │ │ -virtual bool read(System &system) │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_a_c___s_p_l_i_t__ │ │ │ │ -void ac_split_(const String &line, std::vector< String > &split) │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e │ │ │ │ -AntechamberFile() │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_w_r_i_t_e │ │ │ │ -virtual bool write(const System &system) │ │ │ │ -_B_A_L_L_:_:_A_n_t_e_c_h_a_m_b_e_r_F_i_l_e_:_:_w_r_i_t_e │ │ │ │ -virtual bool write(const Molecule &molecule) │ │ │ │ -_B_A_L_L_:_:_G_e_n_e_r_i_c_M_o_l_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h_:_5_8 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e │ │ │ │ -DDeeffiinniittiioonn _m_o_l_e_c_u_l_e_._h_:_3_1 │ │ │ │ -_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ -DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_F_i_l_e_:_:_O_p_e_n_M_o_d_e │ │ │ │ -std::ios::openmode OpenMode │ │ │ │ -DDeeffiinniittiioonn _f_i_l_e_._h_:_1_6_5 │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ +_B_A_L_L_:_:_S_n_a_p_S_h_o_t_M_a_n_a_g_e_r │ │ │ │ +DDeeffiinniittiioonn _s_n_a_p_S_h_o_t_M_a_n_a_g_e_r_._h_:_3_4 │ │ │ │ +_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r │ │ │ │ +DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_3_0 │ │ │ │ +_B_A_L_L_:_:_L_i_n_e_S_e_a_r_c_h │ │ │ │ +DDeeffiinniittiioonn _l_i_n_e_S_e_a_r_c_h_._h_:_3_3 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +ShiftedLVMMMinimizer(ForceField &force_field) │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_~_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +virtual ~ShiftedLVMMMinimizer() │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_f_i_n_d_S_t_e_p │ │ │ │ +virtual double findStep() │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_u_p_d_t___m_e_t_h_o_d__ │ │ │ │ +Size updt_method_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_6_5 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +ShiftedLVMMMinimizer(ForceField &force_field, SnapShotManager *ssm) │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_e_t_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r │ │ │ │ +void setCorrectionParameter(CorrectionParameter corr) │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_c_o_r_r___p_a_r__ │ │ │ │ +Size corr_par_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_6_9 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_c_u_r_r___n_u_m_b_e_r___o_f___c_o_l_s__ │ │ │ │ +Size curr_number_of_cols_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_6_1 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_i_n_i_t_i_a_l___a_t_o_m_s__ │ │ │ │ +vector< Vector3 > initial_atoms_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_3_0_3 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_g_e_t_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r │ │ │ │ +CorrectionParameter getCorrectionParameter() const │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +ShiftedLVMMMinimizer() │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_u_p_d_t___v__ │ │ │ │ +vector< float > updt_v_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_8_9 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_e_t_U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ +void setUpdateMethod(UpdateMethod updt) │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_p_e_c_i_f_i_c_S_e_t_u_p │ │ │ │ +virtual bool specificSetup() │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +ShiftedLVMMMinimizer(const ShiftedLVMMMinimizer &rhs) │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_e_t_M_a_x_N_u_m_O_f_C_o_l_u_m_n_s │ │ │ │ +void setMaxNumOfColumns(Size num) │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_h_e_s_s___f_a_c_t_o_r__ │ │ │ │ +vector< Vector3 > hess_factor_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_9_8 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +ShiftedLVMMMinimizer(ForceField &force_field, const Options &options) │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_n_u_m_b_e_r___o_f___a_t_o_m_s__ │ │ │ │ +Size number_of_atoms_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_5_1 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r │ │ │ │ +CorrectionParameter │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_1_0_7 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_u_p_d_a_t_e_D_i_r_e_c_t_i_o_n │ │ │ │ +virtual void updateDirection() │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_p_r_e_v___s_h_i_f_t___v_a_l__ │ │ │ │ +double prev_shift_val_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_7_3 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_u_p_d_t___u__ │ │ │ │ +vector< float > updt_u_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_8_5 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_g_r_a_d___d_i_f_f__ │ │ │ │ +vector< Vector3 > grad_diff_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_8_1 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ +UpdateMethod │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_9_4 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_m_i_n_i_m_i_z_e │ │ │ │ +virtual bool minimize(Size iterations=0, bool resume=false) │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_l_i_n_e___s_e_a_r_c_h__ │ │ │ │ +LineSearch line_search_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_4_3 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_f_i_r_s_t___i_t_e_r__ │ │ │ │ +bool first_iter_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_4_7 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ +ShiftedLVMMMinimizer(ForceField &force_field, SnapShotManager *ssm, const │ │ │ │ +Options &options) │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_h_i_f_t_e_d___d_i_r_e_c_t_i_o_n__ │ │ │ │ +vector< Vector3 > shifted_direction_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_9_3 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_h_i_f_t___s__ │ │ │ │ +vector< Vector3 > shift_s_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_7_7 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_g_e_t_U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ +UpdateMethod getUpdateMethod() const │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_m_a_x___n_u_m_b_e_r___o_f___c_o_l_s__ │ │ │ │ +Size max_number_of_cols_ │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_5_6 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_g_e_t_M_a_x_N_u_m_O_f_C_o_l_u_m_n_s │ │ │ │ +Size getMaxNumOfColumns() const │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_5_3 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_C_O_R_R_E_C_T_I_O_N___P_A_R_A_M_E_T_E_R │ │ │ │ +static const char * CORRECTION_PARAMETER │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_6_0 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_U_P_D_A_T_E___M_E_T_H_O_D │ │ │ │ +static const char * UPDATE_METHOD │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_5_6 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_N_U_M___O_F___C_O_L_U_M_N_S │ │ │ │ +static const char * NUM_OF_COLUMNS │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_6_5 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_6_9 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_C_O_R_R_E_C_T_I_O_N___P_A_R_A_M_E_T_E_R │ │ │ │ +static const Size CORRECTION_PARAMETER │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_7_8 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_N_U_M___O_F___C_O_L_U_M_N_S │ │ │ │ +static const Size NUM_OF_COLUMNS │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_8_3 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_U_P_D_A_T_E___M_E_T_H_O_D │ │ │ │ +static const Size UPDATE_METHOD │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_7_3 │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d79/a01766.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: PDBRecords.h File Reference │ │ │ +BALL: MMFF94Parameters.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,41 +65,102 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces
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    PDBRecords.h File Reference
    │ │ │ +Namespaces | │ │ │ +Macros | │ │ │ +Functions | │ │ │ +Variables
    │ │ │ +
    MMFF94Parameters.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <vector>
    │ │ │ -#include <stdexcept>
    │ │ │ -#include <BALL/DATATYPE/hashMap.h>
    │ │ │ -#include <BALL/CONCEPT/persistenceManager.h>
    │ │ │ +
    #include <BALL/common.h>
    │ │ │ +#include <BALL/DATATYPE/hashMap.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::PDBRecords
    class  BALL::MMFF94ParametersBase
     
    class  BALL::MMFF94AtomTypeEquivalences
     
    struct  BALL::MMFF94AtomType
     Class to store the values of an atom type from MMFFPROP.PAR. More...
     
    class  BALL::MMFF94AtomTypes
     
    class  BALL::MMFF94StretchParameters
     
    struct  BALL::MMFF94StretchParameters::BondData
     
    struct  BALL::MMFF94StretchParameters::EmpiricalBondData
     
    class  BALL::MMFF94BendParameters
     
    class  BALL::MMFF94StretchBendParameters
     
    class  BALL::MMFF94TorsionParameters
     
    class  BALL::MMFF94PlaneParameters
     
    class  BALL::MMFF94VDWParameters
     
    struct  BALL::MMFF94VDWParameters::VDWEntry
     
    class  BALL::MMFF94ESParameters
     
    │ │ │ │ │ │ │ │ │ │ │ │ +

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +

    │ │ │ +Macros

    #define MMFF94_INVALID_VALUE   99.0
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +

    │ │ │ +Functions

    Position BALL::getMMFF94Index (Position atom_type1, Position atom_type2)
     
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    │ │ │ +Variables

    Size BALL::MMFF94_number_atom_types
     hold the maximum number of MMFF94 atom types + 1 (wildcard)
     
    │ │ │ +

    Macro Definition Documentation

    │ │ │ + │ │ │ +

    ◆ MMFF94_INVALID_VALUE

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    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define MMFF94_INVALID_VALUE   99.0
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    Definition at line 33 of file MMFF94Parameters.h.

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    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,22 +1,62 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _F_O_R_M_A_T │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -PDBRecords.h File Reference │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _M_M_F_F_9_4 │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s | _F_u_n_c_t_i_o_n_s | _V_a_r_i_a_b_l_e_s │ │ │ │ +MMFF94Parameters.h File Reference │ │ │ │ +#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ #include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e │ │ │ │ +  Class to store the values of an atom type from MMFFPROP.PAR. _M_o_r_e_._._. │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_E_m_p_i_r_i_c_a_l_B_o_n_d_D_a_t_a │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_T_o_r_s_i_o_n_P_a_r_a_m_e_t_e_r_s │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_P_l_a_n_e_P_a_r_a_m_e_t_e_r_s │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s_:_:_V_D_W_E_n_t_r_y │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_E_S_P_a_r_a_m_e_t_e_r_s │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +MMaaccrrooss │ │ │ │ +#define  _M_M_F_F_9_4___I_N_V_A_L_I_D___V_A_L_U_E   99.0 │ │ │ │ +  │ │ │ │ +FFuunnccttiioonnss │ │ │ │ +_P_o_s_i_t_i_o_n  _B_A_L_L_:_:_g_e_t_M_M_F_F_9_4_I_n_d_e_x (_P_o_s_i_t_i_o_n atom_type1, _P_o_s_i_t_i_o_n atom_type2) │ │ │ │ +  │ │ │ │ +VVaarriiaabblleess │ │ │ │ +_S_i_z_e  _B_A_L_L_:_:_M_M_F_F_9_4___n_u_m_b_e_r___a_t_o_m___t_y_p_e_s │ │ │ │ +  hold the maximum number of _M_M_F_F_9_4 atom types + 1 (wildcard) │ │ │ │ +  │ │ │ │ +********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ +********** _?◆_? MMMMFFFF9944__IINNVVAALLIIDD__VVAALLUUEE ********** │ │ │ │ +#define MMFF94_INVALID_VALUE   99.0 │ │ │ │ +Definition at line _3_3 of file _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d79/a01766_source.html │ │ │ @@ -21,3625 +21,7689 @@ │ │ │ 00000140: 2267 656e 6572 6174 6f72 2220 636f 6e74 "generator" cont │ │ │ 00000150: 656e 743d 2244 6f78 7967 656e 2031 2e39 ent="Doxygen 1.9 │ │ │ 00000160: 2e38 222f 3e0a 3c6d 6574 6120 6e61 6d65 .8"/>..BALL: PDBReco │ │ │ -000001c0: 7264 732e 6820 536f 7572 6365 2046 696c rds.h Source Fil │ │ │ -000001d0: 653c 2f74 6974 6c65 3e0a 3c6c 696e 6b20 e........< │ │ │ -000003c0: 626f 6479 3e0a 3c64 6976 2069 643d 2274 body>.
    ... . . . < │ │ │ -000004e0: 2f74 723e 0a20 3c2f 7462 6f64 793e 0a3c /tr>. .< │ │ │ -000004f0: 2f74 6162 6c65 3e0a 3c2f 6469 763e 0a3c /table>..< │ │ │ -00000500: 212d 2d20 656e 6420 6865 6164 6572 2070 !-- end header p │ │ │ -00000510: 6172 7420 2d2d 3e0a 3c21 2d2d 2047 656e art -->.../* @ │ │ │ -00000560: 6c69 6365 6e73 6520 6d61 676e 6574 3a3f license magnet:? │ │ │ -00000570: 7874 3d75 726e 3a62 7469 683a 6433 6439 xt=urn:btih:d3d9 │ │ │ -00000580: 6139 6136 3539 3535 3231 6639 3636 3661 a9a6595521f9666a │ │ │ -00000590: 3565 3934 6363 3833 3064 6162 3833 6236 5e94cc830dab83b6 │ │ │ -000005a0: 3536 3939 2661 6d70 3b64 6e3d 6578 7061 5699&dn=expa │ │ │ -000005b0: 742e 7478 7420 4d49 5420 2a2f 0a76 6172 t.txt MIT */.var │ │ │ -000005c0: 2073 6561 7263 6842 6f78 203d 206e 6577 searchBox = new │ │ │ -000005d0: 2053 6561 7263 6842 6f78 2822 7365 6172 SearchBox("sear │ │ │ -000005e0: 6368 426f 7822 2c20 222e 2e2f 2e2e 2f73 chBox", "../../s │ │ │ -000005f0: 6561 7263 682f 222c 272e 6874 6d6c 2729 earch/",'.html') │ │ │ -00000600: 3b0a 2f2a 2040 6c69 6365 6e73 652d 656e ;./* @license-en │ │ │ -00000610: 6420 2a2f 0a3c 2f73 6372 6970 743e 0a3c d */..< │ │ │ -00000620: 7363 7269 7074 2074 7970 653d 2274 6578 script type="tex │ │ │ -00000630: 742f 6a61 7661 7363 7269 7074 2220 7372 t/javascript" sr │ │ │ -00000640: 633d 222e 2e2f 2e2e 2f6d 656e 7564 6174 c="../../menudat │ │ │ -00000650: 612e 6a73 223e 3c2f 7363 7269 7074 3e0a a.js">. │ │ │ -00000660: 3c73 6372 6970 7420 7479 7065 3d22 7465 ../* │ │ │ -000006c0: 406c 6963 656e 7365 206d 6167 6e65 743a @license magnet: │ │ │ -000006d0: 3f78 743d 7572 6e3a 6274 6968 3a64 3364 ?xt=urn:btih:d3d │ │ │ -000006e0: 3961 3961 3635 3935 3532 3166 3936 3636 9a9a6595521f9666 │ │ │ -000006f0: 6135 6539 3463 6338 3330 6461 6238 3362 a5e94cc830dab83b │ │ │ -00000700: 3635 3639 3926 616d 703b 646e 3d65 7870 65699&dn=exp │ │ │ -00000710: 6174 2e74 7874 204d 4954 202a 2f0a 2428 at.txt MIT */.$( │ │ │ -00000720: 6675 6e63 7469 6f6e 2829 207b 0a20 2069 function() {. i │ │ │ -00000730: 6e69 744d 656e 7528 272e 2e2f 2e2e 2f27 nitMenu('../../' │ │ │ -00000740: 2c74 7275 652c 6661 6c73 652c 2773 6561 ,true,false,'sea │ │ │ -00000750: 7263 682e 7068 7027 2c27 5365 6172 6368 rch.php','Search │ │ │ -00000760: 2729 3b0a 2020 2428 646f 6375 6d65 6e74 ');. $(document │ │ │ -00000770: 292e 7265 6164 7928 6675 6e63 7469 6f6e ).ready(function │ │ │ -00000780: 2829 207b 2069 6e69 745f 7365 6172 6368 () { init_search │ │ │ -00000790: 2829 3b20 7d29 3b0a 7d29 3b0a 2f2a 2040 (); });.});./* @ │ │ │ -000007a0: 6c69 6365 6e73 652d 656e 6420 2a2f 0a3c license-end */.< │ │ │ -000007b0: 2f73 6372 6970 743e 0a3c 6469 7620 6964 /script>.
    .........
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    BALL │ │ │ -000004a0: 3c73 7061 6e20 6964 3d22 7072 6f6a 6563  1 │ │ │ -000004c0: 2e35 2e30 3c2f 7370 616e 3e0a 2020 203c .5.0. < │ │ │ -000004d0: 2f64 6976 3e0a 2020 3c2f 7464 3e0a 203c /div>.
    │ │ │ +00000450: 0a20 3c74 626f 6479 3e0a 203c 7472 2069 . . . │ │ │ +00000470: 2020 3c74 6420 6964 3d22 7072 6f6a 6563 . .
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    BALL& │ │ │ +000004c0: 2331 3630 3b31 2e35 2e30 3c2f 7370 616e #160;1.5.0.
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    MMFF94Parame │ │ │ +00000d60: 7465 7273 2e68 3c2f 6469 763e 3c2f 6469 ters.h
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    3 │ │ │ +00000f70: 3c2f 7370 616e 3e3c 7370 616e 2063 6c61 //< │ │ │ +00000f90: 2f73 7061 6e3e 3c2f 6469 763e 0a3c 6469 /span>
    .< │ │ │ +00000fb0: 6120 6964 3d22 6c30 3030 3034 2220 6e61 a id="l00004" na │ │ │ +00000fc0: 6d65 3d22 6c30 3030 3034 223e 3c2f 613e me="l00004"> │ │ │ +00000fd0: 3c73 7061 6e20 636c 6173 733d 226c 696e 4// $Id: M │ │ │ +00001010: 4d46 4639 3450 6172 616d 6574 6572 732e MFF94Parameters. │ │ │ +00001020: 682c 7620 312e 312e 382e 3120 3230 3037 h,v 1.1.8.1 2007 │ │ │ +00001030: 2f30 332f 3235 2032 313a 3235 3a31 3720 /03/25 21:25:17 │ │ │ +00001040: 6f6c 6976 6572 2045 7870 2024 203c 2f73 oliver Exp $
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    │ │ │ +00001130: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +00001160: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 7// Mo │ │ │ +000011a0: 6c65 6375 6c61 7220 4d65 6368 616e 6963 lecular Mechanic │ │ │ +000011b0: 733a 204d 4d46 4639 3420 666f 7263 6520 s: MMFF94 force │ │ │ +000011c0: 6669 656c 6420 636c 6173 733c 2f73 7061 field class
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    8 .
    │ │ │ +00001280: 2039 3c2f 7370 616e 3e3c 7370 616e 2063 9#ifndef BALL │ │ │ +000012b0: 5f4d 4f4c 4d45 435f 4d4d 4646 3934 5f4d _MOLMEC_MMFF94_M │ │ │ +000012c0: 4d46 4639 3450 4152 414d 4554 4552 535f MFF94PARAMETERS_ │ │ │ +000012d0: 483c 2f73 7061 6e3e 3c2f 6469 763e 0a3c H
    .< │ │ │ +000012e0: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +000012f0: 3e3c 6120 6964 3d22 6c30 3030 3130 2220 > 10#d │ │ │ +00001350: 6566 696e 6520 4241 4c4c 5f4d 4f4c 4d45 efine BALL_MOLME │ │ │ +00001360: 435f 4d4d 4646 3934 5f4d 4d46 4639 3450 C_MMFF94_MMFF94P │ │ │ +00001370: 4152 414d 4554 4552 535f 483c 2f73 7061 ARAMETERS_H
    .
    11 .
    │ │ │ +00001430: 3132 3c2f 7370 616e 3e3c 7370 616e 2063 12#ifndef BALL │ │ │ +00001460: 5f43 4f4d 4d4f 4e5f 483c 2f73 7061 6e3e _COMMON_H │ │ │ +00001470: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
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    .
    │ │ │ +00001590: 2020 3134 3c2f 7370 616e 3e3c 7370 616e 14#endif
    .
    15 < │ │ │ +00001620: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00001670: 2031 363c 2f73 7061 6e3e 3c73 7061 6e20 16#ifndef BAL │ │ │ +000016a0: 4c5f 4441 5441 5459 5045 5f48 4153 484d L_DATATYPE_HASHM │ │ │ +000016b0: 4150 5f48 3c2f 7370 616e 3e3c 2f64 6976 AP_H
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    17< │ │ │ +00001710: 2f73 7061 6e3e 3c73 7061 6e20 636c 6173 /span># include << │ │ │ +00001740: 6120 636c 6173 733d 2263 6f64 6522 2068 a class="code" h │ │ │ +00001750: 7265 663d 222e 2e2f 2e2e 2f64 342f 6439 ref="../../d4/d9 │ │ │ +00001760: 622f 6130 3230 3339 2e68 746d 6c22 3e42 b/a02039.html">B │ │ │ +00001770: 414c 4c2f 4441 5441 5459 5045 2f68 6173 ALL/DATATYPE/has │ │ │ +00001780: 684d 6170 2e68 3c2f 613e 2667 743b 3c2f hMap.h>
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    .
    < │ │ │ +000018b0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +000018c0: 6e6f 223e 2020 2032 303c 2f73 7061 6e3e no"> 20 │ │ │ +000018d0: 3c73 7061 6e20 636c 6173 733d 226b 6579 namespace │ │ │ +000018f0: 3c2f 7370 616e 3e3c 6120 636c 6173 733d BALL .
    2 │ │ │ +00001990: 313c 2f73 7061 6e3e 7b3c 2f64 6976 3e0a 1{
    . │ │ │ +000019a0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +000019d0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 22
    .
    < │ │ │ +00001a30: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00001a40: 6e6f 223e 2020 2032 333c 2f73 7061 6e3e no"> 23 │ │ │ +00001a50: 2020 3c73 7061 6e20 636c 6173 733d 226b class Atom;
    .
    24< │ │ │ +00001b30: 2f73 7061 6e3e 2020 3c73 7061 6e20 636c /span> cl │ │ │ +00001b50: 6173 7320 3c2f 7370 616e 3e50 6172 616d ass Param │ │ │ +00001b60: 6574 6572 733b 3c2f 6469 763e 0a3c 6469 eters;
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    │ │ │ +00001e20: 2020 3237 3c2f 7370 616e 3e20 3c2f 6469 27 .
    29 │ │ │ +00001e80: 3c2f 7370 616e 3e20 203c 7370 616e 2063 e │ │ │ +00001ea0: 7874 6572 6e3c 2f73 7061 6e3e 203c 6120 xtern Size < │ │ │ +00001ef0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +00001f00: 5f76 6172 6961 626c 6522 2068 7265 663d _variable" href= │ │ │ +00001f10: 222e 2e2f 2e2e 2f64 612f 6461 322f 6130 "../../da/da2/a0 │ │ │ +00001f20: 3232 3137 2e68 746d 6c23 6137 3637 6439 2217.html#a767d9 │ │ │ +00001f30: 6261 3731 3239 6132 3638 6265 3863 3561 ba7129a268be8c5a │ │ │ +00001f40: 3931 3965 3564 3335 3135 3922 3e4d 4d46 919e5d35159">MMF │ │ │ +00001f50: 4639 345f 6e75 6d62 6572 5f61 746f 6d5f F94_number_atom_ │ │ │ +00001f60: 7479 7065 733c 2f61 3e3b 3c2f 6469 763e types;
    │ │ │ +00001f70: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +00001fa0: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 30
    . │ │ │ +00001fe0: 3c61 2069 643d 226c 3030 3033 3122 206e 31 class │ │ │ +00002040: 3c2f 7370 616e 3e3c 6120 636c 6173 733d │ │ │ +00002080: 4d4d 4646 3934 4174 6f6d 5479 7065 4571 MMFF94AtomTypeEq │ │ │ +00002090: 7569 7661 6c65 6e63 6573 3c2f 613e 3b3c uivalences;< │ │ │ +000020a0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
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    3 │ │ │ +000021a0: 333c 2f61 3e3c 2f73 7061 6e3e 3c73 7061 3#define M │ │ │ +000021d0: 4d46 4639 345f 494e 5641 4c49 445f 5641 MFF94_INVALID_VA │ │ │ +000021e0: 4c55 4520 3939 2e30 3c2f 7370 616e 3e3c LUE 99.0< │ │ │ +000021f0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00002240: 2033 343c 2f73 7061 6e3e 203c 2f64 6976 34
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    │ │ │ +00002370: 3339 3c2f 613e 3c2f 7370 616e 3e20 203c 39 < │ │ │ +00002380: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +00002390: 6f72 6422 3e63 6c61 7373 203c 2f73 7061 ord">class BA │ │ │ +00002400: 4c4c 5f45 5850 4f52 543c 2f61 3e20 3c61 LL_EXPORT MMFF94Par │ │ │ +00002450: 616d 6574 6572 7342 6173 653c 2f61 3e3c ametersBase< │ │ │ +00002460: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +000024b0: 2034 303c 2f73 7061 6e3e 2020 7b3c 2f64 40 {.
    4 │ │ │ +00002510: 313c 2f73 7061 6e3e 2020 2020 3c73 7061 1 public: │ │ │ +00002540: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +00002590: 2020 3432 3c2f 7370 616e 3e20 3c2f 6469 42 .
    43 │ │ │ +000025f0: 3c2f 7370 616e 3e20 2020 203c 6120 636c BALL_CREA │ │ │ +00002660: 5445 3c2f 613e 283c 6120 636c 6173 733d TE( │ │ │ +000026a0: 4d4d 4646 3934 5061 7261 6d65 7465 7273 MMFF94Parameters │ │ │ +000026b0: 4261 7365 3c2f 613e 293c 2f64 6976 3e0a Base)
    . │ │ │ +000026c0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +000026f0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 44
    .
    < │ │ │ +00002750: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00002760: 6e6f 223e 2020 2034 353c 2f73 7061 6e3e no"> 45 │ │ │ +00002770: 2020 2020 3c2f 6469 763e 0a3c 6469 7620
    .
    46 MMFF94Paramete │ │ │ +00002870: 7273 4261 7365 3c2f 613e 2829 3b3c 2f64 rsBase();.
    4 │ │ │ +000028d0: 373c 2f73 7061 6e3e 203c 2f64 6976 3e0a 7
    . │ │ │ +000028e0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +00002910: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 49< │ │ │ +00002980: 2f61 3e3c 2f73 7061 6e3e 2020 2020 7669 /a> vi │ │ │ +00002990: 7274 7561 6c20 7e3c 6120 636c 6173 733d rtual ~ │ │ │ +000029d0: 4d4d 4646 3934 5061 7261 6d65 7465 7273 MMFF94Parameters │ │ │ +000029e0: 4261 7365 3c2f 613e 2829 207b 7d3b 3c2f Base() {};.
    │ │ │ +00002a40: 3530 3c2f 7370 616e 3e20 3c2f 6469 763e 50
    │ │ │ +00002a50: 0a3c 6469 7620 636c 6173 733d 2266 6f6c .
    .
    < │ │ │ +00002ae0: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ +00002af0: 7265 663d 222e 2e2f 2e2e 2f64 382f 6465 ref="../../d8/de │ │ │ +00002b00: 372f 6130 3532 3530 2e68 746d 6c23 6139 7/a05250.html#a9 │ │ │ +00002b10: 6463 3430 3131 3063 3036 3733 3662 3732 dc40110c06736b72 │ │ │ +00002b20: 6166 6265 6435 3363 6632 6636 6337 6322 afbed53cf2f6c7c" │ │ │ +00002b30: 3e20 2020 3532 3c2f 613e 3c2f 7370 616e > 52 const │ │ │ +00002b60: 3c2f 7370 616e 3e20 3c61 2063 6c61 7373 MMFF94Parameter │ │ │ +00002bb0: 7342 6173 653c 2f61 3e26 616d 703b 206f sBase& o │ │ │ +00002bc0: 7065 7261 746f 7220 3d20 283c 7370 616e perator = (const MMFF94Par │ │ │ +00002c30: 616d 6574 6572 7342 6173 653c 2f61 3e26 ametersBase& │ │ │ +00002c40: 616d 703b 293c 2f64 6976 3e0a 3c64 6976 amp;)
    .
    < │ │ │ +00002c80: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00002c90: 6e6f 223e 2020 2035 333c 2f73 7061 6e3e no"> 53 │ │ │ +00002ca0: 2020 2020 2020 207b 3c73 7061 6e20 636c {return │ │ │ +00002cd0: 2a3c 7370 616e 2063 6c61 7373 3d22 6b65 *this;};
    ..
    54 │ │ │ +00002d50: 3c2f 7370 616e 3e20 3c2f 6469 763e 0a3c
    .< │ │ │ +00002d60: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00002d70: 3e3c 6120 6964 3d22 6c30 3030 3536 2220 > 56 virtual void │ │ │ +00002e50: 3c2f 7370 616e 3e20 3c61 2063 6c61 7373 clear( │ │ │ +00002ec0: 293c 2f64 6976 3e0a 3c64 6976 2063 6c61 )
    .
    │ │ │ +00002f10: 2020 2035 373c 2f73 7061 6e3e 2020 2020 57 │ │ │ +00002f20: 2020 3b3c 2f64 6976 3e0a 3c64 6976 2063 ;
    .
    58 < │ │ │ +00002f80: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00003020: 2020 2036 303c 2f61 3e3c 2f73 7061 6e3e 60 │ │ │ +00003030: 2020 2020 3c73 7061 6e20 636c 6173 733d bo │ │ │ +00003050: 6f6c 3c2f 7370 616e 3e20 3c61 2063 6c61 ol isInitia │ │ │ +000030c0: 6c69 7a65 643c 2f61 3e28 2920 7b20 3c73 lized() { return is_initial │ │ │ +00003100: 697a 6564 5f3b 7d3c 2f64 6976 3e0a 3c64 ized_;}
    . │ │ │ +00003120: 3c61 2069 643d 226c 3030 3036 3122 206e 61
    .
    63 bool read │ │ │ +000032a0: 5061 7261 6d65 7465 7273 3c2f 613e 283c Parameters(< │ │ │ +000032b0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +000032c0: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +000032d0: 2f2e 2e2f 6437 2f64 3334 2f61 3034 3037 /../d7/d34/a0407 │ │ │ +000032e0: 382e 6874 6d6c 223e 5061 7261 6d65 7465 8.html">Paramete │ │ │ +000032f0: 7273 3c2f 613e 2661 6d70 3b20 702c 203c rs& p, < │ │ │ +00003300: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +00003310: 6f72 6422 3e63 6f6e 7374 3c2f 7370 616e ord">const Strin │ │ │ +00003360: 673c 2f61 3e26 616d 703b 2073 6563 7469 g& secti │ │ │ +00003370: 6f6e 293b 3c2f 6469 763e 0a3c 6469 7620 on);
    .
    64 │ │ │ +000033d0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ +00003420: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ +00003430: 7265 663d 222e 2e2f 2e2e 2f64 382f 6465 ref="../../d8/de │ │ │ +00003440: 372f 6130 3532 3530 2e68 746d 6c23 6166 7/a05250.html#af │ │ │ +00003450: 3965 3063 6636 3563 6530 3130 6537 6536 9e0cf65ce010e7e6 │ │ │ +00003460: 6664 3933 3864 3762 3536 6466 3661 6322 fd938d7b56df6ac" │ │ │ +00003470: 3e20 2020 3636 3c2f 613e 3c2f 7370 616e > 66 v │ │ │ +000034a0: 6f69 643c 2f73 7061 6e3e 203c 6120 636c oid setEqui │ │ │ +00003510: 7661 6c65 6e63 6573 3c2f 613e 283c 7370 valences(const │ │ │ +00003540: 3c61 2063 6c61 7373 3d22 636f 6465 2068 MMFF94A │ │ │ +00003580: 746f 6d54 7970 6545 7175 6976 616c 656e tomTypeEquivalen │ │ │ +00003590: 6365 733c 2f61 3e26 616d 703b 2065 7175 ces& equ │ │ │ +000035a0: 6929 207b 2065 7175 6976 5f20 3d20 2661 i) { equiv_ = &a │ │ │ +000035b0: 6d70 3b65 7175 693b 7d3c 2f64 6976 3e0a mp;equi;}
    . │ │ │ +000035c0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +000035f0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 67
    .< │ │ │ +00003620: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00003630: 3e3c 6120 6964 3d22 6c30 3030 3638 2220 > 68 pro │ │ │ +00003690: 7465 6374 6564 3c2f 7370 616e 3e3a 3c2f tected:.
    │ │ │ +000036f0: 3639 3c2f 7370 616e 3e20 3c2f 6469 763e 69
    │ │ │ +00003700: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +00003730: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 70 │ │ │ +000037a0: 3c2f 613e 3c2f 7370 616e 3e20 2020 203c < │ │ │ +000037b0: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +000037c0: 6f72 6422 3e76 6972 7475 616c 3c2f 7370 ord">virtual bo │ │ │ +000037f0: 6f6c 3c2f 7370 616e 3e20 3c61 2063 6c61 ol setup_(const std::vecto │ │ │ +00003890: 7226 6c74 3b73 7464 3a3a 7665 6374 6f72 r<std::vector │ │ │ +000038a0: 266c 743b 5374 7269 6e67 2667 743b 2026 <String> & │ │ │ +000038b0: 6774 3b26 616d 703b 2920 7b20 3c73 7061 gt;&) { return true;};
    .< │ │ │ +00003910: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00003920: 3e3c 6120 6964 3d22 6c30 3030 3731 2220 > 71
    .
    72 bool < │ │ │ +00003a40: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +00003a50: 5f76 6172 6961 626c 6522 2068 7265 663d _variable" href= │ │ │ +00003a60: 222e 2e2f 2e2e 2f64 382f 6465 372f 6130 "../../d8/de7/a0 │ │ │ +00003a70: 3532 3530 2e68 746d 6c23 6133 3131 6239 5250.html#a311b9 │ │ │ +00003a80: 3134 3366 3234 3132 3038 6530 3562 6232 143f241208e05bb2 │ │ │ +00003a90: 6263 6436 6530 6238 6561 6522 3e69 735f bcd6e0b8eae">is_ │ │ │ +00003aa0: 696e 6974 6961 6c69 7a65 645f 3c2f 613e initialized_ │ │ │ +00003ab0: 3b3c 2f64 6976 3e0a 3c64 6976 2063 6c61 ;
    .
    │ │ │ +00003b00: 2020 2037 333c 2f73 7061 6e3e 203c 2f64 73 .
    7 │ │ │ +00003b60: 343c 2f73 7061 6e3e 2020 2020 3c73 7061 4 // nr of neede │ │ │ +00003b90: 6420 6669 656c 6473 2069 6e20 7061 7261 d fields in para │ │ │ +00003ba0: 6d65 7465 7220 6669 6c65 733c 2f73 7061 meter files
    ..
    76 co │ │ │ +00003df0: 6e73 743c 2f73 7061 6e3e 203c 6120 636c nst MMFF94AtomTy │ │ │ +00003e40: 7065 4571 7569 7661 6c65 6e63 6573 3c2f peEquivalences* equiv_;.
    7 │ │ │ +00003f10: 373c 2f73 7061 6e3e 2020 7d3b 3c2f 6469 7 };.
    .
    78 < │ │ │ +00003f80: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00003fd0: 2037 393c 2f73 7061 6e3e 203c 2f64 6976 79
    .
    . │ │ │ +000041a0: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +000041d0: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 84 p │ │ │ +00004210: 7562 6c69 633c 2f73 7061 6e3e 203c 6120 ublic MMFF94Para │ │ │ +00004260: 6d65 7465 7273 4261 7365 3c2f 613e 3c2f metersBase.
    │ │ │ +000042c0: 3835 3c2f 7370 616e 3e20 207b 3c2f 6469 85 {.
    86 │ │ │ +00004320: 3c2f 7370 616e 3e20 2020 203c 7370 616e public: │ │ │ +00004350: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +000043a0: 2020 3837 3c2f 7370 616e 3e20 3c2f 6469 87 .
    │ │ │ +00004450: 3839 3c2f 613e 3c2f 7370 616e 3e20 2020 89 │ │ │ +00004460: 203c 6120 636c 6173 733d 2263 6f64 6520 M │ │ │ +000044c0: 4d46 4639 3441 746f 6d54 7970 6545 7175 MFF94AtomTypeEqu │ │ │ +000044d0: 6976 616c 656e 6365 733c 2f61 3e28 293b ivalences(); │ │ │ +000044e0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +00004530: 2020 3930 3c2f 7370 616e 3e20 3c2f 6469 90 .
    │ │ │ +000045e0: 3932 3c2f 613e 3c2f 7370 616e 3e20 2020 92 │ │ │ +000045f0: 203c 6120 636c 6173 733d 2263 6f64 6520 M │ │ │ +00004650: 4d46 4639 3441 746f 6d54 7970 6545 7175 MFF94AtomTypeEqu │ │ │ +00004660: 6976 616c 656e 6365 733c 2f61 3e28 3c73 ivalences(const │ │ │ +00004690: 203c 6120 636c 6173 733d 2263 6f64 6520 MMFF94 │ │ │ +000046d0: 4174 6f6d 5479 7065 4571 7569 7661 6c65 AtomTypeEquivale │ │ │ +000046e0: 6e63 6573 3c2f 613e 2661 6d70 3b20 746f nces& to │ │ │ +000046f0: 5f63 6f70 7929 3b3c 2f64 6976 3e0a 3c64 _copy);
    . │ │ │ +00004710: 3c61 2069 643d 226c 3030 3039 3322 206e 93
    ..< │ │ │ +00004890: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +000048a0: 3e3c 6120 6964 3d22 6c30 3030 3936 2220 > 96
    . │ │ │ +00004900: 3c61 2069 643d 226c 3030 3039 3822 206e 98 void │ │ │ +00004a20: 636c 6561 723c 2f61 3e28 293c 2f64 6976 clear()
    .
    99< │ │ │ +00004a80: 2f73 7061 6e3e 2020 2020 2020 3b3c 2f64 /span> ;.
    10 │ │ │ +00004ae0: 303c 2f73 7061 6e3e 203c 2f64 6976 3e0a 0
    . │ │ │ +00004af0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +00004b20: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 105< │ │ │ +00004b90: 2f61 3e3c 2f73 7061 6e3e 2020 2020 3c61 /a> Index │ │ │ +00004be0: 203c 6120 636c 6173 733d 2263 6f64 6520 g │ │ │ +00004c40: 6574 4571 7569 7661 6c65 6e63 653c 2f61 etEquivalence(Posit │ │ │ +00004c90: 696f 6e3c 2f61 3e20 6f72 6967 696e 616c ion original │ │ │ +00004ca0: 2c20 3c61 2063 6c61 7373 3d22 636f 6465 , Posit │ │ │ +00004ce0: 696f 6e3c 2f61 3e20 6e75 6d62 6572 2920 ion number) │ │ │ +00004cf0: 3c73 7061 6e20 636c 6173 733d 226b 6579 const;
    .
    106 < │ │ │ +00004d70: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00004dc0: 3130 373c 2f73 7061 6e3e 2020 2020 3c73 107 protected:
    .
    < │ │ │ +00004e30: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00004e40: 6e6f 223e 2020 3130 383c 2f73 7061 6e3e no"> 108 │ │ │ +00004e50: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +00004ea0: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 109 virt │ │ │ +00004f20: 7561 6c3c 2f73 7061 6e3e 203c 7370 616e ual bool │ │ │ +00004f50: 203c 6120 636c 6173 733d 2263 6f64 6520 s │ │ │ +00004fb0: 6574 7570 5f3c 2f61 3e28 3c73 7061 6e20 etup_( │ │ │ +00004fd0: 636f 6e73 743c 2f73 7061 6e3e 2073 7464 const std │ │ │ +00004fe0: 3a3a 7665 6374 6f72 266c 743b 7374 643a ::vector<std: │ │ │ +00004ff0: 3a76 6563 746f 7226 6c74 3b53 7472 696e :vector<Strin │ │ │ +00005000: 6726 6774 3b20 2667 743b 2661 6d70 3b29 g> >&) │ │ │ +00005010: 3b3c 2f64 6976 3e0a 3c64 6976 2063 6c61 ;
    .
    │ │ │ +00005060: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 110 std::vecto │ │ │ +000050d0: 7226 6c74 3b73 7464 3a3a 7665 6374 6f72 r<std::vector │ │ │ +000050e0: 266c 743b 506f 7369 7469 6f6e 2667 743b <Position> │ │ │ +000050f0: 2026 6774 3b20 3c61 2063 6c61 7373 3d22 > equivalences │ │ │ +00005160: 5f3c 2f61 3e3b 3c2f 6469 763e 0a3c 6469 _;
    .< │ │ │ +00005180: 6120 6964 3d22 6c30 3031 3131 2220 6e61 a id="l00111" na │ │ │ +00005190: 6d65 3d22 6c30 3031 3131 223e 3c2f 613e me="l00111"> │ │ │ +000051a0: 3c73 7061 6e20 636c 6173 733d 226c 696e 111 │ │ │ +00005210: 3c2f 7370 616e 3e20 2020 2073 7464 3a3a std:: │ │ │ +00005220: 7665 6374 6f72 266c 743b 5374 7269 6e67 vector<String │ │ │ +00005230: 2667 743b 2020 2020 3c61 2063 6c61 7373 > names_ │ │ │ +000052a0: 3b3c 2f64 6976 3e0a 3c64 6976 2063 6c61 ;
    .
    │ │ │ +000052f0: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 112 std::vecto │ │ │ +00005360: 7226 6c74 3b62 6f6f 6c26 6774 3b20 2020 r<bool> │ │ │ +00005370: 2020 203c 6120 636c 6173 733d 2263 6f64 exists_;.
    11 │ │ │ +00005430: 333c 2f73 7061 6e3e 2020 7d3b 3c2f 6469 3 };.
    .
    114 │ │ │ +000054a0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +000054f0: 2031 3135 3c2f 7370 616e 3e20 3c2f 6469 115 .
    .
    117 struct │ │ │ +000055f0: 203c 2f73 7061 6e3e 3c61 2063 6c61 7373 BALL_EXPORT< │ │ │ +00005660: 2f61 3e20 3c61 2063 6c61 7373 3d22 636f /a> MM │ │ │ +000056a0: 4646 3934 4174 6f6d 5479 7065 3c2f 613e FF94AtomType │ │ │ +000056b0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    ...
    < │ │ │ +00005a10: 2069 643d 226c 3030 3132 3422 206e 616d id="l00124" nam │ │ │ +00005a20: 653d 226c 3030 3132 3422 3e3c 2f61 3e3c e="l00124">< │ │ │ 00005a30: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ -00005a40: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 109< │ │ │ -00005aa0: 2f73 7061 6e3e 2020 2020 3c61 2063 6c61 /span> Reference │ │ │ -00005af0: 203c 6120 636c 6173 733d 2263 6f64 6520 f │ │ │ -00005b50: 726f 6e74 3c2f 613e 2829 207b 203c 7370 ront() { return records_.fron │ │ │ -00005bf0: 743c 2f61 3e28 293b 207d 3c2f 6469 763e t(); }
    │ │ │ -00005c00: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ -00005c30: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 111 │ │ │ -00005ca0: 3c2f 613e 3c2f 7370 616e 3e20 2020 203c < │ │ │ -00005cb0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ -00005cc0: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ -00005cd0: 2f2e 2e2f 6465 2f64 6335 2f61 3033 3630 /../de/dc5/a0360 │ │ │ -00005ce0: 322e 6874 6d6c 223e 436f 6e73 7452 6566 2.html">ConstRef │ │ │ -00005cf0: 6572 656e 6365 3c2f 613e 203c 6120 636c erence front() const │ │ │ -00005d80: 203c 2f73 7061 6e3e 7b20 3c73 7061 6e20 { return records_.front(); }
    . │ │ │ -00005e40: 3c61 2069 643d 226c 3030 3131 3322 206e 113 Reference back() { return records_.< │ │ │ -00005fc0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ -00005fd0: 5f66 756e 6374 696f 6e22 2068 7265 663d _function" href= │ │ │ -00005fe0: 222e 2e2f 2e2e 2f64 652f 6463 352f 6130 "../../de/dc5/a0 │ │ │ -00005ff0: 3336 3032 2e68 746d 6c23 6134 3962 3931 3602.html#a49b91 │ │ │ -00006000: 3635 3232 3037 3236 3031 3031 3131 3834 6522072601011184 │ │ │ -00006010: 3561 3836 3963 6333 6533 3922 3e62 6163 5a869cc3e39">bac │ │ │ -00006020: 6b3c 2f61 3e28 293b 207d 3c2f 6469 763e k(); }
    │ │ │ -00006030: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ -00006060: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 115 │ │ │ -000060d0: 3c2f 613e 3c2f 7370 616e 3e20 2020 203c < │ │ │ -000060e0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ -000060f0: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ -00006100: 2f2e 2e2f 6465 2f64 6335 2f61 3033 3630 /../de/dc5/a0360 │ │ │ -00006110: 322e 6874 6d6c 223e 436f 6e73 7452 6566 2.html">ConstRef │ │ │ -00006120: 6572 656e 6365 3c2f 613e 203c 6120 636c erence back() const │ │ │ -000061b0: 3c2f 7370 616e 3e7b 203c 7370 616e 2063 { return │ │ │ -000061e0: 2072 6563 6f72 6473 5f2e 3c61 2063 6c61 records_.back │ │ │ -00006250: 2829 3b20 7d3c 2f64 6976 3e0a 3c64 6976 (); }
    .
    < │ │ │ -00006290: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ -000062a0: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 117< │ │ │ -00006300: 2f73 7061 6e3e 2020 2020 3c73 7061 6e20 /span> void │ │ │ -00006330: 3c61 2063 6c61 7373 3d22 636f 6465 2068 pu │ │ │ -00006390: 7368 5f62 6163 6b3c 2f61 3e28 3c61 2063 sh_back(ConstRefere │ │ │ -000063e0: 6e63 653c 2f61 3e20 7829 207b 2072 6563 nce x) { rec │ │ │ -000063f0: 6f72 6473 5f2e 7075 7368 5f62 6163 6b28 ords_.push_back( │ │ │ -00006400: 7829 3b20 7d3c 2f64 6976 3e0a 3c64 6976 x); }
    .
    < │ │ │ -00006440: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ -00006450: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 119< │ │ │ -000064b0: 2f73 7061 6e3e 2020 2020 3c73 7061 6e20 /span> void │ │ │ -000064e0: 3c61 2063 6c61 7373 3d22 636f 6465 2068 in │ │ │ -00006540: 7365 7274 3c2f 613e 283c 6120 636c 6173 sert(Iterator pos, ConstReference< │ │ │ -00006600: 2f61 3e20 7661 6c75 6529 207b 2072 6563 /a> value) { rec │ │ │ -00006610: 6f72 6473 5f2e 696e 7365 7274 2870 6f73 ords_.insert(pos │ │ │ -00006620: 2c20 7661 6c75 6529 3b20 7d3c 2f64 6976 , value); }
    .
    12 │ │ │ -000066d0: 313c 2f61 3e3c 2f73 7061 6e3e 2020 2020 1 │ │ │ -000066e0: 3c73 7061 6e20 636c 6173 733d 226b 6579 void insert(< │ │ │ -00006770: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ -00006780: 5f74 7970 6564 6566 2220 6872 6566 3d22 _typedef" href=" │ │ │ -00006790: 2e2e 2f2e 2e2f 6433 2f64 3734 2f61 3034 ../../d3/d74/a04 │ │ │ -000067a0: 3431 382e 6874 6d6c 2361 3861 3737 3439 418.html#a8a7749 │ │ │ -000067b0: 6363 3561 3133 6236 3136 3839 3138 3934 cc5a13b616891894 │ │ │ -000067c0: 3032 3665 3862 3362 6137 223e 4974 6572 026e8b3ba7">Iter │ │ │ -000067d0: 6174 6f72 3c2f 613e 2070 6f73 2c20 3c61 ator pos, SizeT │ │ │ -00006840: 7970 653c 2f61 3e20 6e2c 203c 6120 636c ype n, ConstReferen │ │ │ -00006890: 6365 3c2f 613e 2076 616c 7565 2920 7b20 ce value) { │ │ │ -000068a0: 7265 636f 7264 735f 2e69 6e73 6572 7428 records_.insert( │ │ │ -000068b0: 706f 732c 206e 2c20 7661 6c75 6529 3b20 pos, n, value); │ │ │ -000068c0: 7d3c 2f64 6976 3e0a 3c64 6976 2063 6c61 }
    .
    │ │ │ -00006910: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 123 │ │ │ -00006990: 766f 6964 3c2f 7370 616e 3e20 3c61 2063 void pop_ba │ │ │ -00006a00: 636b 3c2f 613e 2829 207b 2072 6563 6f72 ck() { recor │ │ │ -00006a10: 6473 5f2e 706f 705f 6261 636b 2829 3b20 ds_.pop_back(); │ │ │ -00006a20: 7d3c 2f64 6976 3e0a 3c64 6976 2063 6c61 }
    .
    │ │ │ -00006a70: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 125 Iterator │ │ │ -00006b40: 3c61 2063 6c61 7373 3d22 636f 6465 2068 er │ │ │ -00006ba0: 6173 653c 2f61 3e28 3c61 2063 6c61 7373 ase(Iterator pos) { return │ │ │ -00006c40: 2072 6563 6f72 6473 5f2e 6572 6173 6528 records_.erase( │ │ │ -00006c50: 706f 7329 3b20 7d3c 2f64 6976 3e0a 3c64 pos); }
    . │ │ │ -00006c70: 3c61 2069 643d 226c 3030 3132 3722 206e 127 Iterato │ │ │ -00006d70: 723c 2f61 3e20 3c61 2063 6c61 7373 3d22 r erase(Itera │ │ │ -00006e40: 746f 723c 2f61 3e20 6669 7273 742c 203c tor first, < │ │ │ -00006e50: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ -00006e60: 5f74 7970 6564 6566 2220 6872 6566 3d22 _typedef" href=" │ │ │ -00006e70: 2e2e 2f2e 2e2f 6433 2f64 3734 2f61 3034 ../../d3/d74/a04 │ │ │ -00006e80: 3431 382e 6874 6d6c 2361 3861 3737 3439 418.html#a8a7749 │ │ │ -00006e90: 6363 3561 3133 6236 3136 3839 3138 3934 cc5a13b616891894 │ │ │ -00006ea0: 3032 3665 3862 3362 6137 223e 4974 6572 026e8b3ba7">Iter │ │ │ -00006eb0: 6174 6f72 3c2f 613e 206c 6173 7429 207b ator last) { │ │ │ -00006ec0: 203c 7370 616e 2063 6c61 7373 3d22 6b65 retur │ │ │ -00006ee0: 6e3c 2f73 7061 6e3e 2072 6563 6f72 6473 n records │ │ │ -00006ef0: 5f2e 6572 6173 6528 6669 7273 742c 206c _.erase(first, l │ │ │ -00006f00: 6173 7429 3b20 7d3c 2f64 6976 3e0a 3c64 ast); }
    . │ │ │ -00006f20: 3c61 2069 643d 226c 3030 3132 3922 206e 129 bool operator == (< │ │ │ -00006ff0: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ -00007000: 6f72 6422 3e63 6f6e 7374 3c2f 7370 616e ord">const PDBRe │ │ │ -00007050: 636f 7264 733c 2f61 3e26 616d 703b 2072 cords& r │ │ │ -00007060: 6873 293c 7370 616e 2063 6c61 7373 3d22 hs) const │ │ │ -00007080: 3c2f 7370 616e 3e7b 203c 7370 616e 2063 { return │ │ │ -000070b0: 2072 6563 6f72 6473 5f20 3d3d 2072 6873 records_ == rhs │ │ │ -000070c0: 2e3c 6120 636c 6173 733d 2263 6f64 6520 .r │ │ │ -00007120: 6563 6f72 6473 5f3c 2f61 3e3b 207d 3c2f ecords_; }.
    │ │ │ -000071d0: 2031 3331 3c2f 613e 3c2f 7370 616e 3e20 131 │ │ │ -000071e0: 2020 203c 7370 616e 2063 6c61 7373 3d22 boo │ │ │ -00007200: 6c3c 2f73 7061 6e3e 206f 7065 7261 746f l operato │ │ │ -00007210: 7220 213d 2028 3c73 7061 6e20 636c 6173 r != (cons │ │ │ -00007230: 743c 2f73 7061 6e3e 203c 6120 636c 6173 t PDBRecords │ │ │ -00007280: 2661 6d70 3b20 7268 7329 3c73 7061 6e20 & rhs) │ │ │ -000072a0: 2063 6f6e 7374 203c 2f73 7061 6e3e 7b20 const { │ │ │ -000072b0: 3c73 7061 6e20 636c 6173 733d 226b 6579 return │ │ │ -000072d0: 3c2f 7370 616e 3e20 7265 636f 7264 735f records_ │ │ │ -000072e0: 2021 3d20 7268 732e 3c61 2063 6c61 7373 != rhs.records_; }
    .
    124 │ │ │ +00005a50: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +00005aa0: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 126 P │ │ │ +00005b40: 6f73 6974 696f 6e3c 2f61 3e20 3c61 2063 osition crd;
    .
    127 .
    │ │ │ +00005cb0: 2031 3239 3c2f 613e 3c2f 7370 616e 3e20 129 │ │ │ +00005cc0: 2020 203c 6120 636c 6173 733d 2263 6f64 Posi │ │ │ +00005d00: 7469 6f6e 3c2f 613e 203c 6120 636c 6173 tion val;< │ │ │ +00005d70: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00005dc0: 3133 303c 2f73 7061 6e3e 203c 2f64 6976 130
    .
    13 │ │ │ +00005e70: 323c 2f61 3e3c 2f73 7061 6e3e 2020 2020 2 │ │ │ +00005e80: 3c73 7061 6e20 636c 6173 733d 226b 6579 bool pilp;.
    13 │ │ │ +00005f60: 333c 2f73 7061 6e3e 203c 2f64 6976 3e0a 3
    . │ │ │ +00005f70: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +00005fa0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 137< │ │ │ +00006010: 2f61 3e3c 2f73 7061 6e3e 2020 2020 3c61 /a> Position< │ │ │ +00006060: 2f61 3e20 3c61 2063 6c61 7373 3d22 636f /a> mltb;
    .
    138< │ │ │ +00006120: 2f73 7061 6e3e 203c 2f64 6976 3e0a 3c64 /span>
    . │ │ │ +00006140: 3c61 2069 643d 226c 3030 3134 3022 206e 140 bool     │ │ │ +00006260: 6172 6f6d 3c2f 613e 3b3c 2f64 6976 3e0a arom;
    . │ │ │ +00006270: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +000062a0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 141
    .
    < │ │ │ +00006300: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00006310: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 143< │ │ │ +00006370: 2f73 7061 6e3e 2020 2020 3c73 7061 6e20 /span> bool │ │ │ +000063a0: 3c61 2063 6c61 7373 3d22 636f 6465 2068 li │ │ │ +00006400: 6e3c 2f61 3e3b 3c2f 6469 763e 0a3c 6469 n;
    .< │ │ │ +00006420: 6120 6964 3d22 6c30 3031 3434 2220 6e61 a id="l00144" na │ │ │ +00006430: 6d65 3d22 6c30 3031 3434 223e 3c2f 613e me="l00144"> │ │ │ +00006440: 3c73 7061 6e20 636c 6173 733d 226c 696e 144
    ..
    147 │ │ │ +00006600: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ +00006650: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ +00006660: 7265 663d 222e 2e2f 2e2e 2f64 382f 6434 ref="../../d8/d4 │ │ │ +00006670: 342f 6130 3532 3538 2e68 746d 6c23 6137 4/a05258.html#a7 │ │ │ +00006680: 3833 6434 6165 3365 3433 6639 3036 6439 83d4ae3e43f906d9 │ │ │ +00006690: 3833 3732 3633 3032 3933 3136 6437 3122 837263029316d71" │ │ │ +000066a0: 3e20 2031 3439 3c2f 613e 3c2f 7370 616e > 149 b │ │ │ +000066d0: 6f6f 6c3c 2f73 7061 6e3e 203c 6120 636c ool valid;
    .
    150 │ │ │ +000067a0: 7d3b 3c2f 6469 763e 0a3c 2f64 6976 3e0a };
    .
    . │ │ │ +000067b0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +000067e0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 151
    .
    < │ │ │ +00006840: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00006850: 6e6f 223e 2020 3135 323c 2f73 7061 6e3e no"> 152 │ │ │ +00006860: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +000068b0: 2020 3135 343c 2f73 7061 6e3e 203c 2f64 154 .
    .
    157 class │ │ │ +000069b0: 203c 2f73 7061 6e3e 3c61 2063 6c61 7373 BALL_EXPORT< │ │ │ +00006a20: 2f61 3e20 3c61 2063 6c61 7373 3d22 636f /a> MMF │ │ │ +00006a60: 4639 3441 746f 6d54 7970 6573 3c2f 613e F94AtomTypes │ │ │ +00006a70: 3a3c 2f64 6976 3e0a 3c64 6976 2063 6c61 :
    .
    │ │ │ +00006ac0: 2020 3135 383c 2f73 7061 6e3e 2020 2020 158 │ │ │ +00006ad0: 3c73 7061 6e20 636c 6173 733d 226b 6579 public MMF │ │ │ +00006b30: 4639 3450 6172 616d 6574 6572 7342 6173 F94ParametersBas │ │ │ +00006b40: 653c 2f61 3e3c 2f64 6976 3e0a 3c64 6976 e
    .
    < │ │ │ +00006b80: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00006b90: 6e6f 223e 2020 3135 393c 2f73 7061 6e3e no"> 159 │ │ │ +00006ba0: 2020 7b3c 2f64 6976 3e0a 3c64 6976 2063 {
    .
    160 │ │ │ +00006c00: 2020 3c73 7061 6e20 636c 6173 733d 226b public:
    .< │ │ │ +00006c40: 6120 6964 3d22 6c30 3031 3631 2220 6e61 a id="l00161" na │ │ │ +00006c50: 6d65 3d22 6c30 3031 3631 223e 3c2f 613e me="l00161"> │ │ │ +00006c60: 3c73 7061 6e20 636c 6173 733d 226c 696e 161
    ..
    164< │ │ │ +00006e00: 2f73 7061 6e3e 203c 2f64 6976 3e0a 3c64 /span>
    . │ │ │ +00006e20: 3c61 2069 643d 226c 3030 3136 3622 206e 166 MMFF94 │ │ │ +00006f20: 4174 6f6d 5479 7065 733c 2f61 3e28 3c73 AtomTypes(const │ │ │ +00006f50: 203c 6120 636c 6173 733d 2263 6f64 6520 MMFF94 │ │ │ +00006f90: 4174 6f6d 5479 7065 733c 2f61 3e26 616d AtomTypes&am │ │ │ +00006fa0: 703b 2074 6f5f 636f 7079 293b 3c2f 6469 p; to_copy);.
    167 │ │ │ +00007000: 3c2f 7370 616e 3e20 3c2f 6469 763e 0a3c
    .< │ │ │ +00007010: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00007020: 3e3c 6120 6964 3d22 6c30 3031 3639 2220 > 169 ~MMFF │ │ │ +00007120: 3934 4174 6f6d 5479 7065 733c 2f61 3e28 94AtomTypes( │ │ │ +00007130: 2920 7b7d 3b3c 2f64 6976 3e0a 3c64 6976 ) {};
    .
    < │ │ │ +00007170: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00007180: 6e6f 223e 2020 3137 303c 2f73 7061 6e3e no"> 170 │ │ │ +00007190: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +000071e0: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 172 cons │ │ │ +00007260: 743c 2f73 7061 6e3e 2073 7464 3a3a 7665 t std::ve │ │ │ +00007270: 6374 6f72 266c 743b 4d4d 4646 3934 4174 ctor<MMFF94At │ │ │ +00007280: 6f6d 5479 7065 2667 743b 2661 6d70 3b20 omType>& │ │ │ +00007290: 3c61 2063 6c61 7373 3d22 636f 6465 2068 ge │ │ │ +000072f0: 7441 746f 6d54 7970 6573 3c2f 613e 2829 tAtomTypes() │ │ │ +00007300: 3c73 7061 6e20 636c 6173 733d 226b 6579 const { │ │ │ +00007340: 7265 7475 726e 3c2f 7370 616e 3e20 6461 return da │ │ │ +00007350: 7461 5f3b 7d3c 2f64 6976 3e0a 3c64 6976 ta_;}
    .
    < │ │ │ +00007370: 2069 643d 226c 3030 3137 3322 206e 616d id="l00173" nam │ │ │ +00007380: 653d 226c 3030 3137 3322 3e3c 2f61 3e3c e="l00173">< │ │ │ 00007390: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ -000073a0: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 133< │ │ │ -00007400: 2f73 7061 6e3e 2020 2020 3c73 7061 6e20 /span> bool │ │ │ -00007430: 6f70 6572 6174 6f72 2026 6c74 3b20 283c operator < (< │ │ │ -00007440: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ -00007450: 6f72 6422 3e63 6f6e 7374 3c2f 7370 616e ord">const PDBRe │ │ │ -000074a0: 636f 7264 733c 2f61 3e26 616d 703b 2072 cords& r │ │ │ -000074b0: 6873 293c 7370 616e 2063 6c61 7373 3d22 hs) const │ │ │ -000074d0: 3c2f 7370 616e 3e7b 203c 7370 616e 2063 { return │ │ │ -00007500: 2072 6563 6f72 6473 5f20 266c 743b 2072 records_ < r │ │ │ -00007510: 6873 2e3c 6120 636c 6173 733d 2263 6f64 hs.records_; } │ │ │ -00007580: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ -000075d0: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ -000075e0: 7265 663d 222e 2e2f 2e2e 2f64 332f 6437 ref="../../d3/d7 │ │ │ -000075f0: 342f 6130 3434 3138 2e68 746d 6c23 6161 4/a04418.html#aa │ │ │ -00007600: 6331 3739 3834 3537 3332 6261 3733 3961 c179845732ba739a │ │ │ -00007610: 6461 6534 6164 6430 6365 6538 6438 6522 dae4add0cee8d8e" │ │ │ -00007620: 3e20 2031 3335 3c2f 613e 3c2f 7370 616e > 135 b │ │ │ -00007650: 6f6f 6c3c 2f73 7061 6e3e 206f 7065 7261 ool opera │ │ │ -00007660: 746f 7220 2667 743b 2028 3c73 7061 6e20 tor > ( │ │ │ -00007680: 636f 6e73 743c 2f73 7061 6e3e 203c 6120 const PDBRecords │ │ │ -000076d0: 3c2f 613e 2661 6d70 3b20 7268 7329 3c73 & rhs) const { re │ │ │ -00007720: 7475 726e 3c2f 7370 616e 3e20 7265 636f turn reco │ │ │ -00007730: 7264 735f 2026 6774 3b20 7268 732e 3c61 rds_ > rhs.reco │ │ │ -000077a0: 7264 735f 3c2f 613e 3b20 7d3c 2f64 6976 rds_; }
    .
    13 │ │ │ -00007850: 373c 2f61 3e3c 2f73 7061 6e3e 2020 2020 7 │ │ │ -00007860: 3c73 7061 6e20 636c 6173 733d 226b 6579 bool operator & │ │ │ -00007890: 6c74 3b3d 2028 3c73 7061 6e20 636c 6173 lt;= (cons │ │ │ -000078b0: 743c 2f73 7061 6e3e 203c 6120 636c 6173 t PDBRecords │ │ │ -00007900: 2661 6d70 3b20 7268 7329 3c73 7061 6e20 & rhs) │ │ │ -00007920: 2063 6f6e 7374 203c 2f73 7061 6e3e 7b20 const { │ │ │ -00007930: 3c73 7061 6e20 636c 6173 733d 226b 6579 return │ │ │ -00007950: 3c2f 7370 616e 3e20 7265 636f 7264 735f records_ │ │ │ -00007960: 2026 6c74 3b3d 2072 6873 2e3c 6120 636c <= rhs.records │ │ │ -000079d0: 5f3c 2f61 3e3b 207d 3c2f 6469 763e 0a3c _; }
    .< │ │ │ -000079e0: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ -000079f0: 3e3c 6120 6964 3d22 6c30 3031 3339 2220 > 139 bool operator > │ │ │ -00007ac0: 3d20 283c 7370 616e 2063 6c61 7373 3d22 = (const P │ │ │ -00007b20: 4442 5265 636f 7264 733c 2f61 3e26 616d DBRecords&am │ │ │ -00007b30: 703b 2072 6873 293c 7370 616e 2063 6c61 p; rhs) co │ │ │ -00007b50: 6e73 7420 3c2f 7370 616e 3e7b 203c 7370 nst { return     records_ &g │ │ │ -00007b90: 743b 3d20 7268 732e 3c61 2063 6c61 7373 t;= rhs.records_; }
    .
    < │ │ │ -00007c40: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ -00007c50: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 141< │ │ │ -00007cb0: 2f73 7061 6e3e 2020 2020 3c73 7061 6e20 /span> void │ │ │ -00007ce0: 3c61 2063 6c61 7373 3d22 636f 6465 2068 sw │ │ │ -00007d40: 6170 3c2f 613e 283c 6120 636c 6173 733d ap( │ │ │ -00007d80: 5044 4252 6563 6f72 6473 3c2f 613e 2661 PDBRecords&a │ │ │ -00007d90: 6d70 3b20 7268 7329 207b 2072 6563 6f72 mp; rhs) { recor │ │ │ -00007da0: 6473 5f2e 7377 6170 2872 6873 2e3c 6120 ds_.swap(rhs.recor │ │ │ -00007e10: 6473 5f3c 2f61 3e29 3b20 7d3c 2f64 6976 ds_); }
    .
    14 │ │ │ -00007ec0: 333c 2f61 3e3c 2f73 7061 6e3e 2020 2020 3 │ │ │ -00007ed0: 3c61 2063 6c61 7373 3d22 636f 6465 2068 ConstRe │ │ │ -00007f10: 6665 7265 6e63 653c 2f61 3e20 6f70 6572 ference oper │ │ │ -00007f20: 6174 6f72 205b 5d20 283c 6120 636c 6173 ator [] (SizeType n) cons │ │ │ -00007fb0: 7420 3c2f 7370 616e 3e7b 203c 7370 616e t { return records_[n]; │ │ │ -00007ff0: 7d3c 2f64 6976 3e0a 3c64 6976 2063 6c61 }
    .
    │ │ │ -00008040: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 145 R │ │ │ -000080e0: 6566 6572 656e 6365 3c2f 613e 206f 7065 eference ope │ │ │ -000080f0: 7261 746f 7220 5b5d 2028 3c61 2063 6c61 rator [] (SizeType< │ │ │ -00008160: 2f61 3e20 6e29 207b 203c 7370 616e 2063 /a> n) { return │ │ │ -00008190: 2072 6563 6f72 6473 5f5b 6e5d 3b20 7d3c records_[n]; }< │ │ │ -000081a0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ -00008240: 2020 3134 393c 2f61 3e3c 2f73 7061 6e3e 149 │ │ │ -00008250: 2020 2020 3c61 2063 6c61 7373 3d22 636f Con │ │ │ -00008290: 7374 5265 6665 7265 6e63 653c 2f61 3e20 stReference │ │ │ -000082a0: 3c61 2063 6c61 7373 3d22 636f 6465 2068 at │ │ │ -00008300: 3c2f 613e 283c 6120 636c 6173 733d 2263 (SizeType n │ │ │ -00008370: 293c 7370 616e 2063 6c61 7373 3d22 6b65 ) const { return r │ │ │ -000083c0: 6563 6f72 6473 5f2e 3c61 2063 6c61 7373 ecords_.at(n); │ │ │ -00008430: 207d 3c2f 6469 763e 0a3c 6469 7620 636c }
    .
    153 │ │ │ -00008520: 5265 6665 7265 6e63 653c 2f61 3e20 3c61 Reference at( │ │ │ -000085f0: 5369 7a65 5479 7065 3c2f 613e 206e 2920 SizeType n) │ │ │ -00008600: 7b20 3c73 7061 6e20 636c 6173 733d 226b { retu │ │ │ -00008620: 726e 3c2f 7370 616e 3e20 7265 636f 7264 rn record │ │ │ -00008630: 735f 2e3c 6120 636c 6173 733d 2263 6f64 s_.at(n); }.
    15 │ │ │ -000086f0: 353c 2f73 7061 6e3e 203c 2f64 6976 3e0a 5
    . │ │ │ -00008700: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ -00008730: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 159
    .
    < │ │ │ -00008790: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ -000087a0: 6e6f 223e 2020 3136 323c 2f73 7061 6e3e no"> 162 │ │ │ -000087b0: 2020 2020 3c73 7061 6e20 636c 6173 733d //void │ │ │ -000087d0: 2077 7269 7465 2850 6572 7369 7374 656e write(Persisten │ │ │ -000087e0: 6365 4d61 6e61 6765 7226 616d 703b 2070 ceManager& p │ │ │ -000087f0: 6d29 2063 6f6e 7374 3b3c 2f73 7061 6e3e m) const; │ │ │ -00008800: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ -00008850: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ -00008860: 7265 663d 222e 2e2f 2e2e 2f64 332f 6437 ref="../../d3/d7 │ │ │ -00008870: 342f 6130 3434 3138 2e68 746d 6c23 6135 4/a04418.html#a5 │ │ │ -00008880: 6237 3834 6231 3633 6439 6432 3463 3838 b784b163d9d24c88 │ │ │ -00008890: 3035 6162 3163 6135 3332 3262 6534 3522 05ab1ca5322be45" │ │ │ -000088a0: 3e20 2031 3633 3c2f 613e 3c2f 7370 616e > 163 v │ │ │ -000088d0: 6f69 643c 2f73 7061 6e3e 203c 6120 636c oid persist │ │ │ -00008940: 656e 7457 7269 7465 3c2f 613e 283c 6120 entWrite(Persistenc │ │ │ -00008990: 654d 616e 6167 6572 3c2f 613e 2661 6d70 eManager& │ │ │ -000089a0: 3b20 706d 2c20 3c73 7061 6e20 636c 6173 ; pm, cons │ │ │ -000089c0: 743c 2f73 7061 6e3e 203c 7370 616e 2063 t char* │ │ │ -000089f0: 6e61 6d65 2920 3c73 7061 6e20 636c 6173 name) cons │ │ │ -00008a10: 743c 2f73 7061 6e3e 3b3c 2f64 6976 3e0a t;
    . │ │ │ -00008a20: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ -00008a50: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 164
    .
    < │ │ │ -00008ab0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ -00008ac0: 6e6f 223e 2020 3136 373c 2f73 7061 6e3e no"> 167 │ │ │ -00008ad0: 2020 2020 3c73 7061 6e20 636c 6173 733d //bool │ │ │ -00008af0: 2072 6561 6428 5065 7273 6973 7465 6e63 read(Persistenc │ │ │ -00008b00: 654d 616e 6167 6572 2661 6d70 3b20 706d eManager& pm │ │ │ -00008b10: 293b 3c2f 7370 616e 3e3c 2f64 6976 3e0a );
    . │ │ │ -00008b20: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ -00008b50: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 168< │ │ │ -00008bc0: 2f61 3e3c 2f73 7061 6e3e 2020 2020 3c73 /a> void persistentRead │ │ │ -00008c60: 3c2f 613e 283c 6120 636c 6173 733d 2263 (Pe │ │ │ -00008ca0: 7273 6973 7465 6e63 654d 616e 6167 6572 rsistenceManager │ │ │ -00008cb0: 3c2f 613e 2661 6d70 3b20 706d 293b 3c2f & pm);.
    1 │ │ │ -00008d10: 3639 3c2f 7370 616e 3e20 3c2f 6469 763e 69
    │ │ │ -00008d20: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ -00008d50: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 171
    .< │ │ │ -00008d90: 6120 6964 3d22 6c30 3031 3732 2220 6e61 a id="l00172" na │ │ │ -00008da0: 6d65 3d22 6c30 3031 3732 223e 3c2f 613e me="l00172"> │ │ │ -00008db0: 3c73 7061 6e20 636c 6173 733d 226c 696e 172 prote │ │ │ -00008df0: 6374 6564 3c2f 7370 616e 3e3a 3c2f 6469 cted:.
    1 │ │ │ -00008ea0: 3734 3c2f 613e 3c2f 7370 616e 3e20 2020 74 │ │ │ -00008eb0: 2073 7464 3a3a 7665 6374 6f72 266c 743b std::vector< │ │ │ -00008ec0: 5374 7269 6e67 2667 743b 203c 6120 636c String> records │ │ │ -00008f30: 5f3c 2f61 3e3b 3c2f 6469 763e 0a3c 6469 _;
    .< │ │ │ -00008f50: 6120 6964 3d22 6c30 3031 3735 2220 6e61 a id="l00175" na │ │ │ -00008f60: 6d65 3d22 6c30 3031 3735 223e 3c2f 613e me="l00175"> │ │ │ -00008f70: 3c73 7061 6e20 636c 6173 733d 226c 696e 175 };
    ..
    176 │ │ │ -00008ff0: 3c2f 7370 616e 3e20 203c 2f64 6976 3e0a
    . │ │ │ -00009000: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ -00009030: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 177} // n │ │ │ -00009070: 616d 6573 7061 6365 2042 414c 4c3c 2f73 amespace BALL
    .
    178 │ │ │ -000090e0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ -00009130: 2031 3739 3c2f 7370 616e 3e3c 7370 616e 179#endif // BAL │ │ │ -00009180: 4c5f 464f 524d 4154 5f50 4442 5245 434f L_FORMAT_PDBRECO │ │ │ -00009190: 5244 535f 483c 2f73 7061 6e3e 3c2f 6469 RDS_H.
    │ │ │ -00009210: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ -00009290: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    < │ │ │ -000092f0: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6437 a href="../../d7 │ │ │ -00009300: 2f64 6562 2f61 3032 3039 302e 6874 6d6c /deb/a02090.html │ │ │ -00009310: 2361 3834 3939 3866 3734 6664 3761 3538 #a84998f74fd7a58 │ │ │ -00009320: 6365 6366 6362 6238 3164 3438 6234 3332 cecfcbb81d48b432 │ │ │ -00009330: 3362 223e 4241 4c4c 5f43 5245 4154 453c 3b">BALL_CREATE< │ │ │ -00009340: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    #de │ │ │ -00009360: 6669 6e65 2042 414c 4c5f 4352 4541 5445 fine BALL_CREATE │ │ │ -00009370: 286e 616d 6529 3c2f 6469 763e 3c64 6976 (name)
    < │ │ │ -00009390: 623e 4465 6669 6e69 7469 6f6e 3c2f 623e b>Definition │ │ │ -000093a0: 203c 6120 6872 6566 3d22 2e2e 2f2e 2e2f create.h:62
    .
    BALL │ │ │ -00009450: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    Defi │ │ │ -00009470: 6e69 7469 6f6e 3c2f 623e 203c 6120 6872 nition cons │ │ │ -000094b0: 7461 6e74 732e 683a 3133 3c2f 613e 3c2f tants.h:13
    .
    BALL::Persi │ │ │ -00009530: 7374 656e 6365 4d61 6e61 6765 723c 2f61 stenceManager
    .
    < │ │ │ -00009640: 6469 7620 636c 6173 733d 2274 7464 6566 div class="ttdef │ │ │ -00009650: 223e 3c62 3e44 6566 696e 6974 696f 6e3c ">Definition< │ │ │ -00009660: 2f62 3e20 3c61 2068 7265 663d 222e 2e2f /b> persistentO │ │ │ -000096a0: 626a 6563 742e 683a 3239 3c2f 613e 3c2f bject.h:29
    .
    BALL::Strin │ │ │ -00009720: 673c 2f61 3e3c 2f64 6976 3e3c 6469 7620 g
    Definition │ │ │ -00009750: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 string.h:57 │ │ │ -00009790: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ -00009840: 3a53 7472 696e 673a 3a61 743c 2f61 3e3c :String::at< │ │ │ -00009850: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    char &a │ │ │ -00009870: 6d70 3b20 6174 2873 697a 655f 7420 706f mp; at(size_t po │ │ │ -00009880: 7329 3c2f 6469 763e 3c2f 6469 763e 0a3c s)
    .< │ │ │ -00009890: 6469 7620 636c 6173 733d 2274 7463 2220 div class="ttc" │ │ │ -000098a0: 6964 3d22 6161 3033 3630 325f 6874 6d6c id="aa03602_html │ │ │ -000098b0: 5f61 3439 6239 3136 3532 3230 3732 3630 _a49b91652207260 │ │ │ -000098c0: 3130 3131 3138 3435 6138 3639 6363 3365 10111845a869cc3e │ │ │ -000098d0: 3339 223e 3c64 6976 2063 6c61 7373 3d22 39">
    BAL │ │ │ -00009930: 4c3a 3a53 7472 696e 673a 3a62 6163 6b3c L::String::back< │ │ │ -00009940: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    .
    │ │ │ -000099c0: 3c64 6976 2063 6c61 7373 3d22 7474 6e61
    BALL::S │ │ │ -00009a20: 7472 696e 673a 3a66 726f 6e74 3c2f 613e tring::front │ │ │ -00009a30: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    char & │ │ │ -00009a50: 616d 703b 2066 726f 6e74 2829 3c2f 6469 amp; front()
    .
    │ │ │ -00009aa0: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 BALL::PDBReco │ │ │ -00009ad0: 7264 733c 2f61 3e3c 2f64 6976 3e3c 6469 rds
    │ │ │ -00009af0: 3c62 3e44 6566 696e 6974 696f 6e3c 2f62 Definition PDBRecords.h: │ │ │ -00009b40: 3333 3c2f 613e 3c2f 6469 763e 3c2f 6469 33
    .
    < │ │ │ -00009c10: 6469 7620 636c 6173 733d 2274 7464 6563 div class="ttdec │ │ │ -00009c20: 6922 3e43 6f6e 7374 5265 6665 7265 6e63 i">ConstReferenc │ │ │ -00009c30: 6520 6174 2853 697a 6554 7970 6520 6e29 e at(SizeType n) │ │ │ -00009c40: 2063 6f6e 7374 3c2f 6469 763e 3c64 6976 const
    < │ │ │ -00009c60: 623e 4465 6669 6e69 7469 6f6e 3c2f 623e b>Definition │ │ │ -00009c70: 203c 6120 6872 6566 3d22 2e2e 2f2e 2e2f PDBRecords.h:1 │ │ │ -00009cb0: 3439 3c2f 613e 3c2f 6469 763e 3c2f 6469 49
    .
    BALL::PDBRecord │ │ │ -00009d70: 733a 3a62 6567 696e 3c2f 613e 3c2f 6469 s::begin
    ConstItera │ │ │ -00009da0: 746f 7220 6265 6769 6e28 2920 636f 6e73 tor begin() cons │ │ │ -00009db0: 743c 2f64 6976 3e3c 6469 7620 636c 6173 t
    Def │ │ │ -00009dd0: 696e 6974 696f 6e3c 2f62 3e20 3c61 2068 inition PDB │ │ │ -00009e10: 5265 636f 7264 732e 683a 3831 3c2f 613e Records.h:81 │ │ │ -00009e20: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ -00009ed0: 3a50 4442 5265 636f 7264 733a 3a63 6c65 :PDBRecords::cle │ │ │ -00009ee0: 6172 3c2f 613e 3c2f 6469 763e 3c64 6976 ar
    │ │ │ -00009f00: 766f 6964 2063 6c65 6172 2829 3c2f 6469 void clear()
    Clear funct │ │ │ -00009f30: 696f 6e20 6f66 2074 6865 204f 4349 2c20 ion of the OCI, │ │ │ -00009f40: 646f 696e 6720 6e6f 7468 696e 6720 6865 doing nothing he │ │ │ -00009f50: 7265 2e3c 2f64 6976 3e3c 6469 7620 636c re.
    . │ │ │ -00009fd0: 3c64 6976 2063 6c61 7373 3d22 7474 6322
    BA │ │ │ -0000a070: 4c4c 3a3a 5044 4252 6563 6f72 6473 3a3a LL::PDBRecords:: │ │ │ -0000a080: 6361 7061 6369 7479 3c2f 613e 3c2f 6469 capacity
    SizeType c │ │ │ -0000a0b0: 6170 6163 6974 7928 2920 636f 6e73 743c apacity() const< │ │ │ -0000a0c0: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    Defin │ │ │ -0000a0e0: 6974 696f 6e3c 2f62 3e20 3c61 2068 7265 ition PDBRe │ │ │ -0000a120: 636f 7264 732e 683a 3130 313c 2f61 3e3c cords.h:101< │ │ │ -0000a130: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    .
    BALL:: │ │ │ -0000a1e0: 5044 4252 6563 6f72 6473 3a3a 7265 636f PDBRecords::reco │ │ │ -0000a1f0: 7264 735f 3c2f 613e 3c2f 6469 763e 3c64 rds_
    std::vector< │ │ │ -0000a220: 3b20 5374 7269 6e67 2026 6774 3b20 7265 ; String > re │ │ │ -0000a230: 636f 7264 735f 3c2f 6469 763e 3c64 6976 cords_
    T │ │ │ -0000a250: 6865 2050 4442 2072 6563 6f72 6420 6275 he PDB record bu │ │ │ -0000a260: 6666 6572 2e3c 2f64 6976 3e3c 6469 7620 ffer.
    Definition │ │ │ -0000a290: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 PDBRecords.h:17 │ │ │ -0000a2d0: 343c 2f61 3e3c 2f64 6976 3e3c 2f64 6976 4
    .
    │ │ │ -0000a380: 4241 4c4c 3a3a 5044 4252 6563 6f72 6473 BALL::PDBRecords │ │ │ -0000a390: 3a3a 5265 6665 7265 6e63 653c 2f61 3e3c ::Reference< │ │ │ -0000a3a0: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    String │ │ │ -0000a3c0: 2661 6d70 3b20 5265 6665 7265 6e63 653c & Reference< │ │ │ -0000a3d0: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    Defin │ │ │ -0000a3f0: 6974 696f 6e3c 2f62 3e20 3c61 2068 7265 ition PDBRe │ │ │ -0000a430: 636f 7264 732e 683a 3438 3c2f 613e 3c2f cords.h:48
    .
    │ │ │ -0000a490: 3c64 6976 2063 6c61 7373 3d22 7474 6e61
    BALL::P │ │ │ -0000a4f0: 4442 5265 636f 7264 733a 3a70 6f70 5f62 DBRecords::pop_b │ │ │ -0000a500: 6163 6b3c 2f61 3e3c 2f64 6976 3e3c 6469 ack
    void pop_back() │ │ │ -0000a530: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    Defi │ │ │ -0000a550: 6e69 7469 6f6e 3c2f 623e 203c 6120 6872 nition PDBR │ │ │ -0000a590: 6563 6f72 6473 2e68 3a31 3233 3c2f 613e ecords.h:123 │ │ │ -0000a5a0: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ -0000a650: 3a50 4442 5265 636f 7264 733a 3a62 6163 :PDBRecords::bac │ │ │ -0000a660: 6b3c 2f61 3e3c 2f64 6976 3e3c 6469 7620 k
    C │ │ │ -0000a680: 6f6e 7374 5265 6665 7265 6e63 6520 6261 onstReference ba │ │ │ -0000a690: 636b 2829 2063 6f6e 7374 3c2f 6469 763e ck() const
    │ │ │ -0000a6a0: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    Definition │ │ │ -0000a6c0: 3c2f 623e 203c 6120 6872 6566 3d22 2e2e PDBRecords │ │ │ -0000a700: 2e68 3a31 3135 3c2f 613e 3c2f 6469 763e .h:115
    │ │ │ -0000a710: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ -0000a770: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 BALL::PDBRe │ │ │ -0000a7c0: 636f 7264 733a 3a63 6f6e 7374 5f69 7465 cords::const_ite │ │ │ -0000a7d0: 7261 746f 723c 2f61 3e3c 2f64 6976 3e3c rator
    < │ │ │ -0000a7e0: 6469 7620 636c 6173 733d 2274 7464 6563 div class="ttdec │ │ │ -0000a7f0: 6922 3e73 7464 3a3a 7665 6374 6f72 266c i">std::vector&l │ │ │ -0000a800: 743b 2053 7472 696e 6720 2667 743b 3a3a t; String >:: │ │ │ -0000a810: 636f 6e73 745f 6974 6572 6174 6f72 2063 const_iterator c │ │ │ -0000a820: 6f6e 7374 5f69 7465 7261 746f 723c 2f64 onst_iterator
    Definit │ │ │ -0000a850: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion PDBReco │ │ │ -0000a890: 7264 732e 683a 3430 3c2f 613e 3c2f 6469 rds.h:40
    .
    BALL::PDB │ │ │ -0000a950: 5265 636f 7264 733a 3a43 6f6e 7374 4974 Records::ConstIt │ │ │ -0000a960: 6572 6174 6f72 3c2f 613e 3c2f 6469 763e erator
    │ │ │ -0000a970: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    std::vector& │ │ │ -0000a990: 6c74 3b20 5374 7269 6e67 2026 6774 3b3a lt; String >: │ │ │ -0000a9a0: 3a63 6f6e 7374 5f69 7465 7261 746f 7220 :const_iterator │ │ │ -0000a9b0: 436f 6e73 7449 7465 7261 746f 723c 2f64 ConstIterator
    Definit │ │ │ -0000a9e0: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion PDBReco │ │ │ -0000aa20: 7264 732e 683a 3339 3c2f 613e 3c2f 6469 rds.h:39
    .
    BALL::PDB │ │ │ -0000aae0: 5265 636f 7264 733a 3a73 697a 655f 7479 Records::size_ty │ │ │ -0000aaf0: 7065 3c2f 613e 3c2f 6469 763e 3c64 6976 pe
    │ │ │ -0000ab10: 7374 643a 3a76 6563 746f 7226 6c74 3b20 std::vector< │ │ │ -0000ab20: 5374 7269 6e67 2026 6774 3b3a 3a73 697a String >::siz │ │ │ -0000ab30: 655f 7479 7065 2073 697a 655f 7479 7065 e_type size_type │ │ │ -0000ab40: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    Defi │ │ │ -0000ab60: 6e69 7469 6f6e 3c2f 623e 203c 6120 6872 nition PDBR │ │ │ -0000aba0: 6563 6f72 6473 2e68 3a35 333c 2f61 3e3c ecords.h:53< │ │ │ -0000abb0: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    .
    BALL:: │ │ │ -0000ac60: 5044 4252 6563 6f72 6473 3a3a 696e 7365 PDBRecords::inse │ │ │ -0000ac70: 7274 3c2f 613e 3c2f 6469 763e 3c64 6976 rt
    │ │ │ -0000ac90: 766f 6964 2069 6e73 6572 7428 4974 6572 void insert(Iter │ │ │ -0000aca0: 6174 6f72 2070 6f73 2c20 5369 7a65 5479 ator pos, SizeTy │ │ │ -0000acb0: 7065 206e 2c20 436f 6e73 7452 6566 6572 pe n, ConstRefer │ │ │ -0000acc0: 656e 6365 2076 616c 7565 293c 2f64 6976 ence value)
    Definitio │ │ │ -0000acf0: 6e3c 2f62 3e20 3c61 2068 7265 663d 222e n PDBRecord │ │ │ -0000ad30: 732e 683a 3132 313c 2f61 3e3c 2f64 6976 s.h:121
    .
    BALL::PDBR │ │ │ -0000adf0: 6563 6f72 6473 3a3a 7065 7273 6973 7465 ecords::persiste │ │ │ -0000ae00: 6e74 5772 6974 653c 2f61 3e3c 2f64 6976 ntWrite
    void persis │ │ │ -0000ae30: 7465 6e74 5772 6974 6528 5065 7273 6973 tentWrite(Persis │ │ │ -0000ae40: 7465 6e63 654d 616e 6167 6572 2026 616d tenceManager &am │ │ │ -0000ae50: 703b 706d 2c20 636f 6e73 7420 6368 6172 p;pm, const char │ │ │ -0000ae60: 202a 6e61 6d65 2920 636f 6e73 743c 2f64 *name) const
    .
    < │ │ │ -0000aec0: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ -0000aed0: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::PD │ │ │ -0000af20: 4252 6563 6f72 6473 3a3a 7265 7369 7a65 BRecords::resize │ │ │ -0000af30: 3c2f 613e 3c2f 6469 763e 3c64 6976 2063
    vo │ │ │ -0000af50: 6964 2072 6573 697a 6528 5369 7a65 5479 id resize(SizeTy │ │ │ -0000af60: 7065 2073 7a2c 2056 616c 7565 5479 7065 pe sz, ValueType │ │ │ -0000af70: 2063 3d56 616c 7565 5479 7065 2829 293c c=ValueType())< │ │ │ -0000af80: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    Defin │ │ │ -0000afa0: 6974 696f 6e3c 2f62 3e20 3c61 2068 7265 ition PDBRe │ │ │ -0000afe0: 636f 7264 732e 683a 3130 373c 2f61 3e3c cords.h:107< │ │ │ -0000aff0: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    . │ │ │ -0000b160: 0a3c 6469 7620 636c 6173 733d 2274 7463 .
    B │ │ │ -0000b200: 414c 4c3a 3a50 4442 5265 636f 7264 733a ALL::PDBRecords: │ │ │ -0000b210: 3a72 6566 6572 656e 6365 3c2f 613e 3c2f :reference
    String & │ │ │ -0000b240: 616d 703b 2072 6566 6572 656e 6365 3c2f amp; reference
    Defini │ │ │ -0000b270: 7469 6f6e 3c2f 623e 203c 6120 6872 6566 tion PDBRec │ │ │ -0000b2b0: 6f72 6473 2e68 3a34 373c 2f61 3e3c 2f64 ords.h:47
    .
    < │ │ │ -0000b310: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ -0000b320: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::PD │ │ │ -0000b370: 4252 6563 6f72 6473 3a3a 656d 7074 793c BRecords::empty< │ │ │ -0000b380: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    boo │ │ │ -0000b3a0: 6c20 656d 7074 7928 2920 636f 6e73 743c l empty() const< │ │ │ -0000b3b0: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    Defin │ │ │ -0000b3d0: 6974 696f 6e3c 2f62 3e20 3c61 2068 7265 ition PDBRe │ │ │ -0000b410: 636f 7264 732e 683a 3130 333c 2f61 3e3c cords.h:103< │ │ │ -0000b420: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    .
    BALL:: │ │ │ -0000b4d0: 5044 4252 6563 6f72 6473 3a3a 636f 6e73 PDBRecords::cons │ │ │ -0000b4e0: 745f 7265 7665 7273 655f 6974 6572 6174 t_reverse_iterat │ │ │ -0000b4f0: 6f72 3c2f 613e 3c2f 6469 763e 3c64 6976 or
    │ │ │ -0000b510: 7374 643a 3a76 6563 746f 7226 6c74 3b20 std::vector< │ │ │ -0000b520: 5374 7269 6e67 2026 6774 3b3a 3a63 6f6e String >::con │ │ │ -0000b530: 7374 5f72 6576 6572 7365 5f69 7465 7261 st_reverse_itera │ │ │ -0000b540: 746f 7220 636f 6e73 745f 7265 7665 7273 tor const_revers │ │ │ -0000b550: 655f 6974 6572 6174 6f72 3c2f 6469 763e e_iterator
    │ │ │ -0000b560: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    Definition │ │ │ -0000b580: 3c2f 623e 203c 6120 6872 6566 3d22 2e2e PDBRecords │ │ │ -0000b5c0: 2e68 3a34 343c 2f61 3e3c 2f64 6976 3e3c .h:44
    < │ │ │ -0000b5d0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    < │ │ │ -0000b630: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6433 a href="../../d3 │ │ │ -0000b640: 2f64 3734 2f61 3034 3431 382e 6874 6d6c /d74/a04418.html │ │ │ -0000b650: 2361 3763 6438 3266 3162 3662 3065 6266 #a7cd82f1b6b0ebf │ │ │ -0000b660: 6138 3138 6533 3162 3231 6330 6333 3465 a818e31b21c0c34e │ │ │ -0000b670: 6239 223e 4241 4c4c 3a3a 5044 4252 6563 b9">BALL::PDBRec │ │ │ -0000b680: 6f72 6473 3a3a 656e 643c 2f61 3e3c 2f64 ords::end
    ConstIter │ │ │ -0000b6b0: 6174 6f72 2065 6e64 2829 2063 6f6e 7374 ator end() const │ │ │ -0000b6c0: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    Defi │ │ │ -0000b6e0: 6e69 7469 6f6e 3c2f 623e 203c 6120 6872 nition PDBR │ │ │ -0000b720: 6563 6f72 6473 2e68 3a38 353c 2f61 3e3c ecords.h:85< │ │ │ -0000b730: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    .
    BALL:: │ │ │ -0000b7e0: 5044 4252 6563 6f72 6473 3a3a 5265 7665 PDBRecords::Reve │ │ │ -0000b7f0: 7273 6549 7465 7261 746f 723c 2f61 3e3c rseIterator< │ │ │ -0000b800: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    std::ve │ │ │ -0000b820: 6374 6f72 266c 743b 2053 7472 696e 6720 ctor< String │ │ │ -0000b830: 2667 743b 3a3a 7265 7665 7273 655f 6974 >::reverse_it │ │ │ -0000b840: 6572 6174 6f72 2052 6576 6572 7365 4974 erator ReverseIt │ │ │ -0000b850: 6572 6174 6f72 3c2f 6469 763e 3c64 6976 erator
    < │ │ │ -0000b870: 623e 4465 6669 6e69 7469 6f6e 3c2f 623e b>Definition │ │ │ -0000b880: 203c 6120 6872 6566 3d22 2e2e 2f2e 2e2f PDBRecords.h:4 │ │ │ -0000b8c0: 313c 2f61 3e3c 2f64 6976 3e3c 2f64 6976 1
    .
    │ │ │ -0000b9b0: 7374 643a 3a76 6563 746f 7226 6c74 3b20 std::vector< │ │ │ -0000b9c0: 5374 7269 6e67 2026 6774 3b3a 3a72 6576 String >::rev │ │ │ -0000b9d0: 6572 7365 5f69 7465 7261 746f 7220 7265 erse_iterator re │ │ │ -0000b9e0: 7665 7273 655f 6974 6572 6174 6f72 3c2f verse_iterator
    Defini │ │ │ -0000ba10: 7469 6f6e 3c2f 623e 203c 6120 6872 6566 tion PDBRec │ │ │ -0000ba50: 6f72 6473 2e68 3a34 323c 2f61 3e3c 2f64 ords.h:42
    .
    < │ │ │ -0000bab0: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ -0000bac0: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::PD │ │ │ -0000bb10: 4252 6563 6f72 6473 3a3a 5369 7a65 5479 BRecords::SizeTy │ │ │ -0000bb20: 7065 3c2f 613e 3c2f 6469 763e 3c64 6976 pe
    │ │ │ -0000bb40: 7374 643a 3a76 6563 746f 7226 6c74 3b20 std::vector< │ │ │ -0000bb50: 5374 7269 6e67 2026 6774 3b3a 3a73 697a String >::siz │ │ │ -0000bb60: 655f 7479 7065 2053 697a 6554 7970 653c e_type SizeType< │ │ │ -0000bb70: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    Defin │ │ │ -0000bb90: 6974 696f 6e3c 2f62 3e20 3c61 2068 7265 ition PDBRe │ │ │ -0000bbd0: 636f 7264 732e 683a 3534 3c2f 613e 3c2f cords.h:54
    .
    │ │ │ -0000bc30: 3c64 6976 2063 6c61 7373 3d22 7474 6e61
    BALL::P │ │ │ -0000bc90: 4442 5265 636f 7264 733a 3a69 6e73 6572 DBRecords::inser │ │ │ -0000bca0: 743c 2f61 3e3c 2f64 6976 3e3c 6469 7620 t
    v │ │ │ -0000bcc0: 6f69 6420 696e 7365 7274 2849 7465 7261 oid insert(Itera │ │ │ -0000bcd0: 746f 7220 706f 732c 2043 6f6e 7374 5265 tor pos, ConstRe │ │ │ -0000bce0: 6665 7265 6e63 6520 7661 6c75 6529 3c2f ference value)
    Defini │ │ │ -0000bd10: 7469 6f6e 3c2f 623e 203c 6120 6872 6566 tion PDBRec │ │ │ -0000bd50: 6f72 6473 2e68 3a31 3139 3c2f 613e 3c2f ords.h:119
    .
    │ │ │ -0000bdb0: 3c64 6976 2063 6c61 7373 3d22 7474 6e61
    BALL::P │ │ │ -0000be10: 4442 5265 636f 7264 733a 3a56 616c 7565 DBRecords::Value │ │ │ -0000be20: 5479 7065 3c2f 613e 3c2f 6469 763e 3c64 Type
    String ValueTy │ │ │ -0000be50: 7065 3c2f 6469 763e 3c64 6976 2063 6c61 pe
    De │ │ │ -0000be70: 6669 6e69 7469 6f6e 3c2f 623e 203c 6120 finition PD │ │ │ -0000beb0: 4252 6563 6f72 6473 2e68 3a34 363c 2f61 BRecords.h:46
    .
    BALL │ │ │ -0000bf70: 3a3a 5044 4252 6563 6f72 6473 3a3a 4974 ::PDBRecords::It │ │ │ -0000bf80: 6572 6174 6f72 3c2f 613e 3c2f 6469 763e erator
    │ │ │ -0000bf90: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    std::vector& │ │ │ -0000bfb0: 6c74 3b20 5374 7269 6e67 2026 6774 3b3a lt; String >: │ │ │ -0000bfc0: 3a69 7465 7261 746f 7220 4974 6572 6174 :iterator Iterat │ │ │ -0000bfd0: 6f72 3c2f 6469 763e 3c64 6976 2063 6c61 or
    De │ │ │ -0000bff0: 6669 6e69 7469 6f6e 3c2f 623e 203c 6120 finition PD │ │ │ -0000c030: 4252 6563 6f72 6473 2e68 3a33 373c 2f61 BRecords.h:37
    .
    BALL │ │ │ -0000c0f0: 3a3a 5044 4252 6563 6f72 6473 3a3a 4469 ::PDBRecords::Di │ │ │ -0000c100: 6666 6572 656e 6365 5479 7065 3c2f 613e fferenceType │ │ │ -0000c110: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    std::v │ │ │ -0000c130: 6563 746f 7226 6c74 3b20 5374 7269 6e67 ector< String │ │ │ -0000c140: 2026 6774 3b3a 3a64 6966 6665 7265 6e63 >::differenc │ │ │ -0000c150: 655f 7479 7065 2044 6966 6665 7265 6e63 e_type Differenc │ │ │ -0000c160: 6554 7970 653c 2f64 6976 3e3c 6469 7620 eType
    Definition │ │ │ -0000c190: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 PDBRecords.h:52 │ │ │ -0000c1d0: 3c2f 613e 3c2f 6469 763e 3c2f 6469 763e
    │ │ │ -0000c1e0: 0a3c 6469 7620 636c 6173 733d 2274 7463 .
    │ │ │ -0000c2a0: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    ConstReferen │ │ │ -0000c2c0: 6365 2066 726f 6e74 2829 2063 6f6e 7374 ce front() const │ │ │ -0000c2d0: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    Defi │ │ │ -0000c2f0: 6e69 7469 6f6e 3c2f 623e 203c 6120 6872 nition PDBR │ │ │ -0000c330: 6563 6f72 6473 2e68 3a31 3131 3c2f 613e ecords.h:111 │ │ │ -0000c340: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ -0000c3f0: 3a50 4442 5265 636f 7264 733a 3a72 656e :PDBRecords::ren │ │ │ -0000c400: 643c 2f61 3e3c 2f64 6976 3e3c 6469 7620 d
    R │ │ │ -0000c420: 6576 6572 7365 4974 6572 6174 6f72 2072 everseIterator r │ │ │ -0000c430: 656e 6428 293c 2f64 6976 3e3c 6469 7620 end()
    Definition │ │ │ -0000c460: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 PDBRecords.h:95 │ │ │ -0000c4a0: 3c2f 613e 3c2f 6469 763e 3c2f 6469 763e
    │ │ │ -0000c4b0: 0a3c 6469 7620 636c 6173 733d 2274 7463 .
    B │ │ │ -0000c550: 414c 4c3a 3a50 4442 5265 636f 7264 733a ALL::PDBRecords: │ │ │ -0000c560: 3a69 7465 7261 746f 723c 2f61 3e3c 2f64 :iterator
    std::vect │ │ │ -0000c590: 6f72 266c 743b 2053 7472 696e 6720 2667 or< String &g │ │ │ -0000c5a0: 743b 3a3a 6974 6572 6174 6f72 2069 7465 t;::iterator ite │ │ │ -0000c5b0: 7261 746f 723c 2f64 6976 3e3c 6469 7620 rator
    Definition │ │ │ -0000c5e0: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 PDBRecords.h:38 │ │ │ -0000c620: 3c2f 613e 3c2f 6469 763e 3c2f 6469 763e
    │ │ │ -0000c630: 0a3c 6469 7620 636c 6173 733d 2274 7463 .
    < │ │ │ -0000c6f0: 6469 7620 636c 6173 733d 2274 7464 6563 div class="ttdec │ │ │ -0000c700: 6922 3e52 6566 6572 656e 6365 2062 6163 i">Reference bac │ │ │ -0000c710: 6b28 293c 2f64 6976 3e3c 6469 7620 636c k()
    . │ │ │ -0000c790: 3c64 6976 2063 6c61 7373 3d22 7474 6322
    BA │ │ │ -0000c830: 4c4c 3a3a 5044 4252 6563 6f72 6473 3a3a LL::PDBRecords:: │ │ │ -0000c840: 436f 6e73 7452 6576 6572 7365 4974 6572 ConstReverseIter │ │ │ -0000c850: 6174 6f72 3c2f 613e 3c2f 6469 763e 3c64 ator
    std::vector< │ │ │ -0000c880: 3b20 5374 7269 6e67 2026 6774 3b3a 3a63 ; String >::c │ │ │ -0000c890: 6f6e 7374 5f72 6576 6572 7365 5f69 7465 onst_reverse_ite │ │ │ -0000c8a0: 7261 746f 7220 436f 6e73 7452 6576 6572 rator ConstRever │ │ │ -0000c8b0: 7365 4974 6572 6174 6f72 3c2f 6469 763e seIterator
    │ │ │ -0000c8c0: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    Definition │ │ │ -0000c8e0: 3c2f 623e 203c 6120 6872 6566 3d22 2e2e PDBRecords │ │ │ -0000c920: 2e68 3a34 333c 2f61 3e3c 2f64 6976 3e3c .h:43
    < │ │ │ -0000c930: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    < │ │ │ -0000c990: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6433 a href="../../d3 │ │ │ -0000c9a0: 2f64 3734 2f61 3034 3431 382e 6874 6d6c /d74/a04418.html │ │ │ -0000c9b0: 2361 6231 3936 6462 3632 3838 3266 6635 #ab196db62882ff5 │ │ │ -0000c9c0: 6264 3631 6264 3736 3932 6337 6633 3131 bd61bd7692c7f311 │ │ │ -0000c9d0: 3831 223e 4241 4c4c 3a3a 5044 4252 6563 81">BALL::PDBRec │ │ │ -0000c9e0: 6f72 6473 3a3a 7377 6170 3c2f 613e 3c2f ords::swap
    void swa │ │ │ -0000ca10: 7028 5044 4252 6563 6f72 6473 2026 616d p(PDBRecords &am │ │ │ -0000ca20: 703b 7268 7329 3c2f 6469 763e 3c64 6976 p;rhs)
    < │ │ │ -0000ca40: 623e 4465 6669 6e69 7469 6f6e 3c2f 623e b>Definition │ │ │ -0000ca50: 203c 6120 6872 6566 3d22 2e2e 2f2e 2e2f PDBRecords.h:1 │ │ │ -0000ca90: 3431 3c2f 613e 3c2f 6469 763e 3c2f 6469 41
    .
    c │ │ │ -0000cb80: 6f6e 7374 2053 7472 696e 6720 2661 6d70 onst String & │ │ │ -0000cb90: 3b20 436f 6e73 7452 6566 6572 656e 6365 ; ConstReference │ │ │ -0000cba0: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    Defi │ │ │ -0000cbc0: 6e69 7469 6f6e 3c2f 623e 203c 6120 6872 nition PDBR │ │ │ -0000cc00: 6563 6f72 6473 2e68 3a35 303c 2f61 3e3c ecords.h:50< │ │ │ -0000cc10: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    .
    BALL:: │ │ │ -0000ccc0: 5044 4252 6563 6f72 6473 3a3a 7661 6c75 PDBRecords::valu │ │ │ -0000ccd0: 655f 7479 7065 3c2f 613e 3c2f 6469 763e e_type
    │ │ │ -0000cce0: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    String value │ │ │ -0000cd00: 5f74 7970 653c 2f64 6976 3e3c 6469 7620 _type
    Definition │ │ │ -0000cd30: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 PDBRecords.h:45 │ │ │ -0000cd70: 3c2f 613e 3c2f 6469 763e 3c2f 6469 763e
    │ │ │ -0000cd80: 0a3c 6469 7620 636c 6173 733d 2274 7463 .
    ReverseIter │ │ │ -0000ce60: 6174 6f72 2072 6265 6769 6e28 293c 2f64 ator rbegin()
    Definit │ │ │ -0000ce90: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion PDBReco │ │ │ -0000ced0: 7264 732e 683a 3931 3c2f 613e 3c2f 6469 rds.h:91
    .
    BALL::PDB │ │ │ -0000cf90: 5265 636f 7264 733a 3a72 656e 643c 2f61 Records::rend
    Const │ │ │ -0000cfc0: 5265 7665 7273 6549 7465 7261 746f 7220 ReverseIterator │ │ │ -0000cfd0: 7265 6e64 2829 2063 6f6e 7374 3c2f 6469 rend() const
    Definiti │ │ │ -0000d000: 6f6e 3c2f 623e 203c 6120 6872 6566 3d22 on PDBRecor │ │ │ -0000d040: 6473 2e68 3a39 333c 2f61 3e3c 2f64 6976 ds.h:93
    .
    BALL::PDBR │ │ │ -0000d100: 6563 6f72 6473 3a3a 7075 7368 5f62 6163 ecords::push_bac │ │ │ -0000d110: 6b3c 2f61 3e3c 2f64 6976 3e3c 6469 7620 k
    v │ │ │ -0000d130: 6f69 6420 7075 7368 5f62 6163 6b28 436f oid push_back(Co │ │ │ -0000d140: 6e73 7452 6566 6572 656e 6365 2078 293c nstReference x)< │ │ │ -0000d150: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    Defin │ │ │ -0000d170: 6974 696f 6e3c 2f62 3e20 3c61 2068 7265 ition PDBRe │ │ │ -0000d1b0: 636f 7264 732e 683a 3131 373c 2f61 3e3c cords.h:117< │ │ │ -0000d1c0: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    .
    BALL:: │ │ │ -0000d270: 5044 4252 6563 6f72 6473 3a3a 636f 6e73 PDBRecords::cons │ │ │ -0000d280: 745f 7265 6665 7265 6e63 653c 2f61 3e3c t_reference< │ │ │ -0000d290: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    const S │ │ │ -0000d2b0: 7472 696e 6720 2661 6d70 3b20 636f 6e73 tring & cons │ │ │ -0000d2c0: 745f 7265 6665 7265 6e63 653c 2f64 6976 t_reference
    Definitio │ │ │ -0000d2f0: 6e3c 2f62 3e20 3c61 2068 7265 663d 222e n PDBRecord │ │ │ -0000d330: 732e 683a 3439 3c2f 613e 3c2f 6469 763e s.h:49
    │ │ │ -0000d340: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ -0000d3a0: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 BALL::PDBRe │ │ │ -0000d3f0: 636f 7264 733a 3a6d 6178 5f73 697a 653c cords::max_size< │ │ │ -0000d400: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    < │ │ │ -0000d450: 623e 4465 6669 6e69 7469 6f6e 3c2f 623e b>Definition │ │ │ -0000d460: 203c 6120 6872 6566 3d22 2e2e 2f2e 2e2f PDBRecords.h:9 │ │ │ -0000d4a0: 393c 2f61 3e3c 2f64 6976 3e3c 2f64 6976 9
    .
    │ │ │ -0000d570: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    SizeType siz │ │ │ -0000d590: 6528 2920 636f 6e73 743c 2f64 6976 3e3c e() const
    < │ │ │ -0000d5a0: 6469 7620 636c 6173 733d 2274 7464 6566 div class="ttdef │ │ │ -0000d5b0: 223e 3c62 3e44 6566 696e 6974 696f 6e3c ">Definition< │ │ │ -0000d5c0: 2f62 3e20 3c61 2068 7265 663d 222e 2e2f /b> PDBRecords. │ │ │ -0000d600: 683a 3937 3c2f 613e 3c2f 6469 763e 3c2f h:97
    .
    .
    │ │ │ -0000d850: 766f 6964 2070 6572 7369 7374 656e 7452 void persistentR │ │ │ -0000d860: 6561 6428 5065 7273 6973 7465 6e63 654d ead(PersistenceM │ │ │ -0000d870: 616e 6167 6572 2026 616d 703b 706d 293c anager &pm)< │ │ │ -0000d880: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    .
    BALL:: │ │ │ -0000d930: 5044 4252 6563 6f72 6473 3a3a 6572 6173 PDBRecords::eras │ │ │ -0000d940: 653c 2f61 3e3c 2f64 6976 3e3c 6469 7620 e
    I │ │ │ -0000d960: 7465 7261 746f 7220 6572 6173 6528 4974 terator erase(It │ │ │ -0000d970: 6572 6174 6f72 2070 6f73 293c 2f64 6976 erator pos)
    Definitio │ │ │ -0000d9a0: 6e3c 2f62 3e20 3c61 2068 7265 663d 222e n PDBRecord │ │ │ -0000d9e0: 732e 683a 3132 353c 2f61 3e3c 2f64 6976 s.h:125
    .
    BALL::PDBR │ │ │ -0000daa0: 6563 6f72 6473 3a3a 6469 6666 6572 656e ecords::differen │ │ │ -0000dab0: 6365 5f74 7970 653c 2f61 3e3c 2f64 6976 ce_type
    std::vector │ │ │ -0000dae0: 266c 743b 2053 7472 696e 6720 2667 743b < String > │ │ │ -0000daf0: 3a3a 6469 6666 6572 656e 6365 5f74 7970 ::difference_typ │ │ │ -0000db00: 6520 6469 6666 6572 656e 6365 5f74 7970 e difference_typ │ │ │ -0000db10: 653c 2f64 6976 3e3c 6469 7620 636c 6173 e
    Def │ │ │ -0000db30: 696e 6974 696f 6e3c 2f62 3e20 3c61 2068 inition PDB │ │ │ -0000db70: 5265 636f 7264 732e 683a 3531 3c2f 613e Records.h:51 │ │ │ -0000db80: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ -0000dc30: 3a50 4442 5265 636f 7264 733a 3a65 7261 :PDBRecords::era │ │ │ -0000dc40: 7365 3c2f 613e 3c2f 6469 763e 3c64 6976 se
    │ │ │ -0000dc60: 4974 6572 6174 6f72 2065 7261 7365 2849 Iterator erase(I │ │ │ -0000dc70: 7465 7261 746f 7220 6669 7273 742c 2049 terator first, I │ │ │ -0000dc80: 7465 7261 746f 7220 6c61 7374 293c 2f64 terator last)
    Definit │ │ │ -0000dcb0: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion PDBReco │ │ │ -0000dcf0: 7264 732e 683a 3132 373c 2f61 3e3c 2f64 rds.h:127
    .
    < │ │ │ -0000dd50: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ -0000dd60: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::PD │ │ │ -0000ddb0: 4252 6563 6f72 6473 3a3a 6672 6f6e 743c BRecords::front< │ │ │ -0000ddc0: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    Ref │ │ │ -0000dde0: 6572 656e 6365 2066 726f 6e74 2829 3c2f erence front()
    Defini │ │ │ -0000de10: 7469 6f6e 3c2f 623e 203c 6120 6872 6566 tion PDBRec │ │ │ -0000de50: 6f72 6473 2e68 3a31 3039 3c2f 613e 3c2f ords.h:109
    .
    │ │ │ -0000deb0: 3c64 6976 2063 6c61 7373 3d22 7474 6e61
    BALL::P │ │ │ -0000df10: 4442 5265 636f 7264 733a 3a72 6265 6769 DBRecords::rbegi │ │ │ -0000df20: 6e3c 2f61 3e3c 2f64 6976 3e3c 6469 7620 n
    C │ │ │ -0000df40: 6f6e 7374 5265 7665 7273 6549 7465 7261 onstReverseItera │ │ │ -0000df50: 746f 7220 7262 6567 696e 2829 2063 6f6e tor rbegin() con │ │ │ -0000df60: 7374 3c2f 6469 763e 3c64 6976 2063 6c61 st
    De │ │ │ -0000df80: 6669 6e69 7469 6f6e 3c2f 623e 203c 6120 finition PD │ │ │ -0000dfc0: 4252 6563 6f72 6473 2e68 3a38 393c 2f61 BRecords.h:89
    .
    BALL │ │ │ -0000e080: 3a3a 5044 4252 6563 6f72 6473 3a3a 656e ::PDBRecords::en │ │ │ -0000e090: 643c 2f61 3e3c 2f64 6976 3e3c 6469 7620 d
    I │ │ │ -0000e0b0: 7465 7261 746f 7220 656e 6428 293c 2f64 terator end()
    Definit │ │ │ -0000e0e0: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion PDBReco │ │ │ -0000e120: 7264 732e 683a 3837 3c2f 613e 3c2f 6469 rds.h:87
    .
    BALL_EXPO │ │ │ -0000e1e0: 5254 3c2f 613e 3c2f 6469 763e 3c64 6976 RT
    │ │ │ -0000e200: 2364 6566 696e 6520 4241 4c4c 5f45 5850 #define BALL_EXP │ │ │ -0000e210: 4f52 543c 2f64 6976 3e3c 6469 7620 636c ORT
    .
    < │ │ │ -0000e2b0: 212d 2d20 636f 6e74 656e 7473 202d 2d3e !-- contents --> │ │ │ -0000e2c0: 0a3c 212d 2d20 7374 6172 7420 666f 6f74 ..
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    176 vi │ │ │ +00007560: 7274 7561 6c3c 2f73 7061 6e3e 203c 7370 rtual bool setup_(const s │ │ │ +00007620: 7464 3a3a 7665 6374 6f72 266c 743b 7374 td::vector<st │ │ │ +00007630: 643a 3a76 6563 746f 7226 6c74 3b53 7472 d::vector<Str │ │ │ +00007640: 696e 6726 6774 3b20 2667 743b 2661 6d70 ing> >& │ │ │ +00007650: 3b29 3b3c 2f64 6976 3e0a 3c64 6976 2063 ;);
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    177 std::vec │ │ │ +00007710: 746f 7226 6c74 3b4d 4d46 4639 3441 746f tor<MMFF94Ato │ │ │ +00007720: 6d54 7970 6526 6774 3b20 3c61 2063 6c61 mType> data_;
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    .< │ │ │ +00007900: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00007910: 3e3c 6120 6964 3d22 6c30 3031 3835 2220 > 185 │ │ │ +00007980: 3c2f 7370 616e 3e20 203c 7370 616e 2063 c │ │ │ +000079a0: 6c61 7373 203c 2f73 7061 6e3e 3c61 2063 lass BALL_EXP │ │ │ +00007a10: 4f52 543c 2f61 3e20 3c61 2063 6c61 7373 ORT MMFF94StretchPa │ │ │ +00007a60: 7261 6d65 7465 7273 3c2f 613e 3a3c 2f64 rameters:.
    18 │ │ │ +00007ac0: 363c 2f73 7061 6e3e 2020 2020 3c73 7061 6 public │ │ │ +00007af0: 3c61 2063 6c61 7373 3d22 636f 6465 2068 MMFF94P │ │ │ +00007b30: 6172 616d 6574 6572 7342 6173 653c 2f61 arametersBase
    .
    │ │ │ +00007b90: 2020 3138 373c 2f73 7061 6e3e 2020 7b3c 187 {< │ │ │ +00007ba0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
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    192 │ │ │ +00007e20: 207b 3c2f 6469 763e 0a3c 6469 7620 636c {
    ..< │ │ │ +00007f60: 6120 6964 3d22 6c30 3031 3934 2220 6e61 a id="l00194" na │ │ │ +00007f70: 6d65 3d22 6c30 3031 3934 223e 3c2f 613e me="l00194"> │ │ │ +00007f80: 3c73 7061 6e20 636c 6173 733d 226c 696e 194
    .
    195 double │ │ │ +00008080: 203c 6120 636c 6173 733d 2263 6f64 6520 k │ │ │ +000080e0: 625f 6e6f 726d 616c 3c2f 613e 3b3c 2f64 b_normal;.
    │ │ │ +00008190: 3139 363c 2f61 3e3c 2f73 7061 6e3e 2020 196 │ │ │ +000081a0: 2020 2020 3c73 7061 6e20 636c 6173 733d do │ │ │ +000081c0: 7562 6c65 3c2f 7370 616e 3e20 3c61 2063 uble r0_nor │ │ │ +00008230: 6d61 6c3c 2f61 3e3b 3c2f 6469 763e 0a3c mal;
    .< │ │ │ +00008240: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00008250: 3e3c 6120 6964 3d22 6c30 3031 3937 2220 > 197 < │ │ │ +000082f0: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +00008300: 6f72 6474 7970 6522 3e62 6f6f 6c3c 2f73 ordtype">bool     standard_bon │ │ │ +00008380: 645f 6578 6973 7473 3c2f 613e 3b3c 2f64 d_exists;.
    19 │ │ │ +000083e0: 383c 2f73 7061 6e3e 2020 2020 2020 3c2f 8 .
    │ │ │ +00008490: 2032 3030 3c2f 613e 3c2f 7370 616e 3e20 200 │ │ │ +000084a0: 2020 2020 203c 7370 616e 2063 6c61 7373 d │ │ │ +000084c0: 6f75 626c 653c 2f73 7061 6e3e 203c 6120 ouble kb_sb │ │ │ +00008530: 6d62 3c2f 613e 3b3c 2f64 6976 3e0a 3c64 mb;
    . │ │ │ +00008550: 3c61 2069 643d 226c 3030 3230 3122 206e 201 double r0_sbmb; │ │ │ +00008680: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ +000086d0: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ +000086e0: 7265 663d 222e 2e2f 2e2e 2f64 652f 6434 ref="../../de/d4 │ │ │ +000086f0: 662f 6130 3532 3730 2e68 746d 6c23 6132 f/a05270.html#a2 │ │ │ +00008700: 6361 6638 6163 6137 6530 3561 3638 3033 caf8aca7e05a6803 │ │ │ +00008710: 3033 6634 6663 3061 3166 6530 6666 3922 03f4fc0a1fe0ff9" │ │ │ +00008720: 3e20 2032 3032 3c2f 613e 3c2f 7370 616e > 202 bool sbmb │ │ │ +000087c0: 5f65 7869 7374 733c 2f61 3e3b 3c2f 6469 _exists;.
    2 │ │ │ +00008870: 3033 3c2f 613e 3c2f 7370 616e 3e20 2020 03 │ │ │ +00008880: 2020 203c 7370 616e 2063 6c61 7373 3d22 boo │ │ │ +000088a0: 6c3c 2f73 7061 6e3e 2020 3c61 2063 6c61 l empirica │ │ │ +00008910: 6c3c 2f61 3e3b 3c2f 6469 763e 0a3c 6469 l;
    .< │ │ │ +00008930: 6120 6964 3d22 6c30 3032 3034 2220 6e61 a id="l00204" na │ │ │ +00008940: 6d65 3d22 6c30 3032 3034 223e 3c2f 613e me="l00204"> │ │ │ +00008950: 3c73 7061 6e20 636c 6173 733d 226c 696e 204 };
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    2 │ │ │ +000089d0: 3035 3c2f 7370 616e 3e20 3c2f 6469 763e 05
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    │ │ │ +00008a70: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 │ │ │ +00008aa0: 2020 3230 373c 2f61 3e3c 2f73 7061 6e3e 207 │ │ │ +00008ab0: 2020 2020 3c73 7061 6e20 636c 6173 733d struct │ │ │ +00008ad0: 203c 2f73 7061 6e3e 3c61 2063 6c61 7373 EmpiricalBondD │ │ │ +00008b20: 6174 613c 2f61 3e3c 2f64 6976 3e0a 3c64 ata
    . │ │ │ +00008b40: 3c61 2069 643d 226c 3030 3230 3822 206e 208 {
    . │ │ │ +00008ba0: 3c61 2069 643d 226c 3030 3230 3922 206e 209 double kb;
    .
    21 │ │ │ +00008d70: 303c 2f61 3e3c 2f73 7061 6e3e 2020 2020 0 │ │ │ +00008d80: 2020 3c73 7061 6e20 636c 6173 733d 226b doub │ │ │ +00008da0: 6c65 3c2f 7370 616e 3e20 3c61 2063 6c61 le r0;< │ │ │ +00008e10: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00008e60: 3231 313c 2f73 7061 6e3e 2020 2020 7d3b 211 }; │ │ │ +00008e70: 3c2f 6469 763e 0a3c 2f64 6976 3e0a 3c64
    .
    . │ │ │ +00008e90: 3c61 2069 643d 226c 3030 3231 3222 206e 212
    .
    214 t │ │ │ +00008fa0: 7970 6564 6566 3c2f 7370 616e 3e20 3c61 ypedef HashMap&l │ │ │ +00008ff0: 743b 506f 7369 7469 6f6e 2c20 426f 6e64 t;Position, Bond │ │ │ +00009000: 4461 7461 2667 743b 3c2f 613e 203c 6120 Data> Stretc │ │ │ +00009070: 684d 6170 3c2f 613e 3b3c 2f64 6976 3e0a hMap;
    . │ │ │ +00009080: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +000090b0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 215< │ │ │ +00009120: 2f61 3e3c 2f73 7061 6e3e 2020 2020 3c73 /a> typedef Hash │ │ │ +00009190: 4d61 7026 6c74 3b50 6f73 6974 696f 6e2c Map<Position, │ │ │ +000091a0: 2045 6d70 6972 6963 616c 426f 6e64 4461 EmpiricalBondDa │ │ │ +000091b0: 7461 2667 743b 3c2f 613e 203c 6120 636c ta> Empirica │ │ │ +00009220: 6c53 7472 6574 6368 4d61 703c 2f61 3e3b lStretchMap; │ │ │ +00009230: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +00009280: 2032 3136 3c2f 7370 616e 3e20 3c2f 6469 216 .
    217 │ │ │ +000092e0: 3c2f 7370 616e 3e20 2020 203c 6120 636c BALL_CREA │ │ │ +00009350: 5445 3c2f 613e 283c 6120 636c 6173 733d TE( │ │ │ +00009390: 4d4d 4646 3934 5374 7265 7463 6850 6172 MMFF94StretchPar │ │ │ +000093a0: 616d 6574 6572 733c 2f61 3e29 3c2f 6469 ameters).
    218 │ │ │ +00009400: 3c2f 7370 616e 3e20 3c2f 6469 763e 0a3c
    .< │ │ │ +00009410: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00009420: 3e3c 6120 6964 3d22 6c30 3032 3139 2220 > 219
    . │ │ │ +00009480: 3c61 2069 643d 226c 3030 3232 3022 206e 220 MMFF94Stret │ │ │ +00009560: 6368 5061 7261 6d65 7465 7273 3c2f 613e chParameters │ │ │ +00009570: 2829 3b3c 2f64 6976 3e0a 3c64 6976 2063 ();
    .
    221 < │ │ │ +000095d0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>..
    224 │ │ │ +00009740: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ +00009790: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ +000097a0: 7265 663d 222e 2e2f 2e2e 2f64 372f 6463 ref="../../d7/dc │ │ │ +000097b0: 372f 6130 3532 3636 2e68 746d 6c23 6139 7/a05266.html#a9 │ │ │ +000097c0: 6565 6439 6564 6563 3936 3035 6531 3164 eed9edec9605e11d │ │ │ +000097d0: 6566 6137 3261 6163 3232 3337 6132 6222 efa72aac2237a2b" │ │ │ +000097e0: 3e20 2032 3236 3c2f 613e 3c2f 7370 616e > 226 const MMFF94Stretc │ │ │ +00009840: 6850 6172 616d 6574 6572 733c 2f61 3e26 hParameters& │ │ │ +00009850: 616d 703b 206f 7065 7261 746f 7220 3d20 amp; operator = │ │ │ +00009860: 2863 6f6e 7374 203c 6120 636c 6173 733d (const │ │ │ +000098a0: 4d4d 4646 3934 5374 7265 7463 6850 6172 MMFF94StretchPar │ │ │ +000098b0: 616d 6574 6572 733c 2f61 3e26 616d 703b ameters& │ │ │ +000098c0: 2070 6172 616d 293c 2f64 6976 3e0a 3c64 param)
    . │ │ │ +000098e0: 3c61 2069 643d 226c 3030 3232 3722 206e 227 ;
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    .
    < │ │ │ +000099c0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +000099d0: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 230< │ │ │ +00009a30: 2f73 7061 6e3e 2020 2020 7669 7274 7561 /span> virtua │ │ │ +00009a40: 6c20 3c73 7061 6e20 636c 6173 733d 226b l void │ │ │ +00009a60: 3c2f 7370 616e 3e20 636c 6561 7228 293c clear()< │ │ │ +00009a70: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00009ac0: 3233 313c 2f73 7061 6e3e 2020 2020 2020 231 │ │ │ +00009ad0: 3b3c 2f64 6976 3e0a 3c64 6976 2063 6c61 ;
    .
    │ │ │ +00009b20: 2020 3233 323c 2f73 7061 6e3e 203c 2f64 232 .
    │ │ │ +00009bd0: 3233 343c 2f61 3e3c 2f73 7061 6e3e 2020 234 │ │ │ +00009be0: 2020 3c73 7061 6e20 636c 6173 733d 226b bool │ │ │ +00009c00: 3c2f 7370 616e 3e20 6173 7369 676e 5061 assignPa │ │ │ +00009c10: 7261 6d65 7465 7273 283c 6120 636c 6173 rameters(Position t │ │ │ +00009c60: 7970 6531 2c20 3c61 2063 6c61 7373 3d22 ype1, P │ │ │ +00009ca0: 6f73 6974 696f 6e3c 2f61 3e20 7479 7065 osition type │ │ │ +00009cb0: 322c 203c 6120 636c 6173 733d 2263 6f64 2, Bon │ │ │ +00009cf0: 6444 6174 613c 2f61 3e26 616d 703b 2064 dData& d │ │ │ +00009d00: 6174 6129 2063 6f6e 7374 3b3c 2f64 6976 ata) const;
    .
    235< │ │ │ +00009d60: 2f73 7061 6e3e 203c 2f64 6976 3e0a 3c64 /span>
    . │ │ │ +00009d80: 3c61 2069 643d 226c 3030 3233 3722 206e 237 bool readEmpiricalP │ │ │ +00009e50: 6172 616d 6574 6572 7328 3c61 2063 6c61 arameters(Parameters& p, const │ │ │ +00009eb0: 3c61 2063 6c61 7373 3d22 636f 6465 2068 String< │ │ │ +00009ef0: 2f61 3e26 616d 703b 2073 6563 7469 6f6e /a>& section │ │ │ +00009f00: 293b 3c2f 6469 763e 0a3c 6469 7620 636c );
    .
    238 .
    │ │ │ +0000a000: 2032 3430 3c2f 613e 3c2f 7370 616e 3e20 240 │ │ │ +0000a010: 2020 2063 6f6e 7374 203c 6120 636c 6173 const StretchMap │ │ │ +0000a060: 2661 6d70 3b20 6765 7442 6f6e 6450 6172 & getBondPar │ │ │ +0000a070: 616d 6574 6572 7328 293c 7370 616e 2063 ameters() │ │ │ +0000a090: 636f 6e73 7420 3c2f 7370 616e 3e7b 203c const { < │ │ │ +0000a0a0: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +0000a0b0: 6f72 6466 6c6f 7722 3e72 6574 7572 6e3c ordflow">return< │ │ │ +0000a0c0: 2f73 7061 6e3e 2070 6172 616d 6574 6572 /span> parameter │ │ │ +0000a0d0: 735f 3b7d 3c2f 6469 763e 0a3c 6469 7620 s_;}
    .
    241 │ │ │ +0000a130: 2020 203c 2f64 6976 3e0a 3c64 6976 2063
    .
    243 co │ │ │ +0000a200: 6e73 743c 2f73 7061 6e3e 203c 6120 636c nst EmpiricalStr │ │ │ +0000a250: 6574 6368 4d61 703c 2f61 3e26 616d 703b etchMap& │ │ │ +0000a260: 203c 6120 636c 6173 733d 2263 6f64 6520 g │ │ │ +0000a2c0: 6574 456d 7069 7269 6361 6c50 6172 616d etEmpiricalParam │ │ │ +0000a2d0: 6574 6572 733c 2f61 3e28 293c 7370 616e eters() const { │ │ │ +0000a300: 203c 7370 616e 2063 6c61 7373 3d22 6b65 retur │ │ │ +0000a320: 6e3c 2f73 7061 6e3e 2065 6d70 6972 6963 n empiric │ │ │ +0000a330: 616c 5f70 6172 616d 6574 6572 735f 3b7d al_parameters_;} │ │ │ +0000a340: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +0000a390: 2032 3434 3c2f 7370 616e 3e20 3c2f 6469 244 .
    2 │ │ │ +0000a440: 3435 3c2f 613e 3c2f 7370 616e 3e20 2020 45 │ │ │ +0000a450: 203c 7370 616e 2063 6c61 7373 3d22 6b65 static d │ │ │ +0000a490: 6f75 626c 653c 2f73 7061 6e3e 2072 6164 ouble rad │ │ │ +0000a4a0: 6969 5b5d 3b3c 2f64 6976 3e0a 3c64 6976 ii[];
    .
    < │ │ │ +0000a4e0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000a4f0: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 246< │ │ │ +0000a550: 2f73 7061 6e3e 2020 2020 3c73 7061 6e20 /span> │ │ │ +0000a570: 7374 6174 6963 3c2f 7370 616e 3e20 3c73 static double electroneg │ │ │ +0000a5b0: 6174 6976 6573 5b5d 3b3c 2f64 6976 3e0a atives[];
    . │ │ │ +0000a5c0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +0000a5f0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 247
    .
    < │ │ │ +0000a650: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000a660: 6e6f 223e 2020 3234 383c 2f73 7061 6e3e no"> 248 │ │ │ +0000a670: 2020 2020 3c73 7061 6e20 636c 6173 733d protec │ │ │ +0000a690: 7465 643c 2f73 7061 6e3e 3a3c 2f64 6976 ted:
    .
    249< │ │ │ +0000a6f0: 2f73 7061 6e3e 203c 2f64 6976 3e0a 3c64 /span>
    . │ │ │ +0000a710: 3c61 2069 643d 226c 3030 3235 3022 206e 250 virtual │ │ │ +0000a7d0: 203c 7370 616e 2063 6c61 7373 3d22 6b65 bool< │ │ │ +0000a7f0: 2f73 7061 6e3e 203c 6120 636c 6173 733d /span> setup_( │ │ │ +0000a860: 3c73 7061 6e20 636c 6173 733d 226b 6579 const std::vector&l │ │ │ +0000a890: 743b 7374 643a 3a76 6563 746f 7226 6c74 t;std::vector< │ │ │ +0000a8a0: 3b53 7472 696e 6726 6774 3b20 2667 743b ;String> > │ │ │ +0000a8b0: 2661 6d70 3b29 3b3c 2f64 6976 3e0a 3c64 &);
    . │ │ │ +0000a8d0: 3c61 2069 643d 226c 3030 3235 3122 206e 251
    .
    253 StretchMap │ │ │ +0000aa10: 3c61 2063 6c61 7373 3d22 636f 6465 2068 pa │ │ │ +0000aa70: 7261 6d65 7465 7273 5f3c 2f61 3e3b 3c2f rameters_;.
    │ │ │ +0000ab20: 2032 3534 3c2f 613e 3c2f 7370 616e 3e20 254 │ │ │ +0000ab30: 2020 203c 7370 616e 2063 6c61 7373 3d22 mutable │ │ │ +0000ab50: 3c2f 7370 616e 3e20 3c61 2063 6c61 7373 StretchMap │ │ │ +0000aba0: 3c61 2063 6c61 7373 3d22 636f 6465 2068 bu │ │ │ +0000ac00: 6666 6572 6564 5f70 6172 616d 6574 6572 ffered_parameter │ │ │ +0000ac10: 735f 3c2f 613e 3b3c 2f64 6976 3e0a 3c64 s_;
    . │ │ │ +0000ac30: 3c61 2069 643d 226c 3030 3235 3522 206e 255 EmpiricalSt │ │ │ +0000ad10: 7265 7463 684d 6170 3c2f 613e 203c 6120 retchMap empir │ │ │ +0000ad80: 6963 616c 5f70 6172 616d 6574 6572 735f ical_parameters_ │ │ │ +0000ad90: 3c2f 613e 3b3c 2f64 6976 3e0a 3c64 6976 ;
    .
    < │ │ │ +0000add0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000ade0: 6e6f 223e 2020 3235 363c 2f73 7061 6e3e no"> 256 │ │ │ +0000adf0: 2020 7d3b 3c2f 6469 763e 0a3c 2f64 6976 };
    .
    .
    257< │ │ │ +0000ae50: 2f73 7061 6e3e 203c 2f64 6976 3e0a 3c64 /span>
    . │ │ │ +0000ae70: 3c61 2069 643d 226c 3030 3235 3922 206e 259
    .
    │ │ │ +0000af00: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +0000af30: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 263 class BALL_E │ │ │ +0000b010: 5850 4f52 543c 2f61 3e20 3c61 2063 6c61 XPORT MMFF94BendPar │ │ │ +0000b060: 616d 6574 6572 733c 2f61 3e3c 2f64 6976 ameters
    .
    264< │ │ │ +0000b0c0: 2f73 7061 6e3e 2020 2020 3a20 3c73 7061 /span> : public │ │ │ +0000b0f0: 3c61 2063 6c61 7373 3d22 636f 6465 2068 MMFF94P │ │ │ +0000b130: 6172 616d 6574 6572 7342 6173 653c 2f61 arametersBase
    .
    │ │ │ +0000b190: 2020 3236 353c 2f73 7061 6e3e 2020 7b3c 265 {< │ │ │ +0000b1a0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +0000b1f0: 3236 363c 2f73 7061 6e3e 2020 2020 3c73 266 public:
    .
    267 .
    │ │ │ +0000b320: 2032 3639 3c2f 613e 3c2f 7370 616e 3e20 269 │ │ │ +0000b330: 2020 203c 7370 616e 2063 6c61 7373 3d22 typedef │ │ │ +0000b350: 3c2f 7370 616e 3e20 3c61 2063 6c61 7373 HashMap<Posi │ │ │ +0000b3a0: 7469 6f6e 2c20 7374 643a 3a70 6169 7226 tion, std::pair& │ │ │ +0000b3b0: 6c74 3b64 6f75 626c 652c 2064 6f75 626c lt;double, doubl │ │ │ +0000b3c0: 6526 6774 3b3c 2f61 3e20 2667 743b 203c e> > < │ │ │ +0000b3d0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +0000b3e0: 5f74 7970 6564 6566 2220 6872 6566 3d22 _typedef" href=" │ │ │ +0000b3f0: 2e2e 2f2e 2e2f 6436 2f64 3965 2f61 3035 ../../d6/d9e/a05 │ │ │ +0000b400: 3237 382e 6874 6d6c 2361 6562 6131 3365 278.html#aeba13e │ │ │ +0000b410: 3465 3264 3661 3430 6434 6234 6237 6539 4e2d6a40d4b4b7e9 │ │ │ +0000b420: 3135 6361 6638 6661 3331 223e 4265 6e64 15caf8fa31">Bend │ │ │ +0000b430: 4d61 703c 2f61 3e3b 3c2f 6469 763e 0a3c Map;
    .< │ │ │ +0000b440: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +0000b450: 3e3c 6120 6964 3d22 6c30 3032 3730 2220 > 270
    .
    271 │ │ │ +0000b4f0: 2020 203c 6120 636c 6173 733d 2263 6f64 B │ │ │ +0000b550: 414c 4c5f 4352 4541 5445 3c2f 613e 283c ALL_CREATE(< │ │ │ +0000b560: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +0000b570: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +0000b580: 2f2e 2e2f 6436 2f64 3965 2f61 3035 3237 /../d6/d9e/a0527 │ │ │ +0000b590: 382e 6874 6d6c 223e 4d4d 4646 3934 4265 8.html">MMFF94Be │ │ │ +0000b5a0: 6e64 5061 7261 6d65 7465 7273 3c2f 613e ndParameters │ │ │ +0000b5b0: 293c 2f64 6976 3e0a 3c64 6976 2063 6c61 )
    .
    │ │ │ +0000b600: 2020 3237 323c 2f73 7061 6e3e 203c 2f64 272 .
    27 │ │ │ +0000b660: 333c 2f73 7061 6e3e 2020 2020 3c2f 6469 3 .
    2 │ │ │ +0000b710: 3734 3c2f 613e 3c2f 7370 616e 3e20 2020 74 │ │ │ +0000b720: 203c 6120 636c 6173 733d 2263 6f64 6520 MMFF94 │ │ │ +0000b760: 4265 6e64 5061 7261 6d65 7465 7273 3c2f BendParameters();
    .
    < │ │ │ +0000b7b0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000b7c0: 6e6f 223e 2020 3237 353c 2f73 7061 6e3e no"> 275 │ │ │ +0000b7d0: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +0000b820: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 277 virtual ~< │ │ │ +0000b890: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +0000b8a0: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +0000b8b0: 2f2e 2e2f 6436 2f64 3965 2f61 3035 3237 /../d6/d9e/a0527 │ │ │ +0000b8c0: 382e 6874 6d6c 223e 4d4d 4646 3934 4265 8.html">MMFF94Be │ │ │ +0000b8d0: 6e64 5061 7261 6d65 7465 7273 3c2f 613e ndParameters │ │ │ +0000b8e0: 2829 3b3c 2f64 6976 3e0a 3c64 6976 2063 ();
    .
    278 < │ │ │ +0000b940: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +0000b9e0: 2020 3238 303c 2f61 3e3c 2f73 7061 6e3e 280 │ │ │ +0000b9f0: 2020 2020 636f 6e73 7420 3c61 2063 6c61 const MMFF94BendPar │ │ │ +0000ba40: 616d 6574 6572 733c 2f61 3e26 616d 703b ameters& │ │ │ +0000ba50: 206f 7065 7261 746f 7220 3d20 2863 6f6e operator = (con │ │ │ +0000ba60: 7374 203c 6120 636c 6173 733d 2263 6f64 st MMFF │ │ │ +0000baa0: 3934 4265 6e64 5061 7261 6d65 7465 7273 94BendParameters │ │ │ +0000bab0: 3c2f 613e 2661 6d70 3b20 7061 7261 6d29 & param) │ │ │ +0000bac0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +0000bb10: 2032 3831 3c2f 7370 616e 3e20 2020 2020 281 │ │ │ +0000bb20: 203b 3c2f 6469 763e 0a3c 6469 7620 636c ;
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    282 .
    │ │ │ +0000bc20: 2032 3834 3c2f 613e 3c2f 7370 616e 3e20 284 │ │ │ +0000bc30: 2020 2076 6972 7475 616c 203c 7370 616e virtual void │ │ │ +0000bc60: 2063 6c65 6172 2829 3c2f 6469 763e 0a3c clear()
    .< │ │ │ +0000bc70: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +0000bc80: 3e3c 6120 6964 3d22 6c30 3032 3835 2220 > 285 ;
    │ │ │ +0000bcd0: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +0000bd00: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 286
    .< │ │ │ +0000bd40: 6120 6964 3d22 6c30 3032 3838 2220 6e61 a id="l00288" na │ │ │ +0000bd50: 6d65 3d22 6c30 3032 3838 223e 3c2f 613e me="l00288"> │ │ │ +0000bd60: 3c73 7061 6e20 636c 6173 733d 226c 696e 288 │ │ │ +0000bdd0: 3c2f 7370 616e 3e20 2020 203c 7370 616e bool │ │ │ +0000be00: 2061 7373 6967 6e50 6172 616d 6574 6572 assignParameter │ │ │ +0000be10: 7328 3c61 2063 6c61 7373 3d22 636f 6465 s(Posit │ │ │ +0000be50: 696f 6e3c 2f61 3e20 6265 6e64 5f74 7970 ion bend_typ │ │ │ +0000be60: 652c 3c2f 6469 763e 0a3c 6469 7620 636c e,
    .
    289 │ │ │ +0000bec0: 2020 2020 2020 2020 2020 2020 2020 2020 │ │ │ +0000bed0: 2020 2020 3c61 2063 6c61 7373 3d22 636f Pos │ │ │ +0000bf10: 6974 696f 6e3c 2f61 3e20 6174 6f6d 5f74 ition atom_t │ │ │ +0000bf20: 7970 6531 2c20 3c61 2063 6c61 7373 3d22 ype1, P │ │ │ +0000bf60: 6f73 6974 696f 6e3c 2f61 3e20 6174 6f6d osition atom │ │ │ +0000bf70: 5f74 7970 6532 2c20 3c61 2063 6c61 7373 _type2, Position at │ │ │ +0000bfc0: 6f6d 5f74 7970 6533 2c20 3c2f 6469 763e om_type3,
    │ │ │ +0000bfd0: 0a3c 6469 7620 636c 6173 733d 226c 696e .
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    . │ │ │ +0000c0c0: 3c61 2069 643d 226c 3030 3239 3122 206e 291
    .
    292 │ │ │ +0000c160: 2020 7072 6f74 6563 7465 643a 3c2f 6469 protected:.
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    .
    295< │ │ │ +0000c400: 2f73 7061 6e3e 203c 2f64 6976 3e0a 3c64 /span>
    . │ │ │ +0000c420: 3c61 2069 643d 226c 3030 3239 3622 206e 296 Position getIndex_(Position bend_type, Position atom_type1, < │ │ │ +0000c5b0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +0000c5c0: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +0000c5d0: 2f2e 2e2f 6431 2f64 3832 2f61 3038 3937 /../d1/d82/a0897 │ │ │ +0000c5e0: 342e 6874 6d6c 223e 506f 7369 7469 6f6e 4.html">Position │ │ │ +0000c5f0: 3c2f 613e 2061 746f 6d5f 7479 7065 322c atom_type2, │ │ │ +0000c600: 203c 6120 636c 6173 733d 2263 6f64 6520 Positi │ │ │ +0000c640: 6f6e 3c2f 613e 2061 746f 6d5f 7479 7065 on atom_type │ │ │ +0000c650: 3329 2063 6f6e 7374 3b3c 2f64 6976 3e0a 3) const;
    . │ │ │ +0000c660: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +0000c690: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 297
    .
    < │ │ │ +0000c6f0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000c700: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 299< │ │ │ +0000c760: 2f73 7061 6e3e 2020 2020 3c61 2063 6c61 /span> BendMap p │ │ │ +0000c7b0: 6172 616d 6574 6572 735f 3b3c 2f64 6976 arameters_;
    .
    30 │ │ │ +0000c860: 303c 2f61 3e3c 2f73 7061 6e3e 2020 2020 0 │ │ │ +0000c870: 6d75 7461 626c 6520 3c61 2063 6c61 7373 mutable BendMap buf │ │ │ +0000c8c0: 6665 7265 645f 7061 7261 6d65 7465 7273 fered_parameters │ │ │ +0000c8d0: 5f3b 3c2f 6469 763e 0a3c 6469 7620 636c _;
    .
    301 } │ │ │ +0000c930: 3b3c 2f64 6976 3e0a 3c2f 6469 763e 0a3c ;
    .
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    .
    303 │ │ │ +0000c9f0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +0000ca40: 2033 3036 3c2f 7370 616e 3e20 3c2f 6469 306 .
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    .
    316 t │ │ │ +0000ceb0: 7970 6564 6566 3c2f 7370 616e 3e20 3c61 ypedef HashMap&l │ │ │ +0000cf00: 743b 506f 7369 7469 6f6e 2c20 7374 643a t;Position, std: │ │ │ +0000cf10: 3a70 6169 7226 6c74 3b64 6f75 626c 652c :pair<double, │ │ │ +0000cf20: 2064 6f75 626c 6526 6774 3b3c 2f61 3e20 double> │ │ │ +0000cf30: 2667 743b 203c 6120 636c 6173 733d 2263 > StretchBendMap │ │ │ +0000cfa0: 3c2f 613e 3b3c 2f64 6976 3e0a 3c64 6976 ;
    .
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    ..
    < │ │ │ +0000d160: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000d170: 6e6f 223e 2020 3331 393c 2f73 7061 6e3e no"> 319 │ │ │ +0000d180: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
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    .
    < │ │ │ +0000d230: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ +0000d240: 7265 663d 222e 2e2f 2e2e 2f64 362f 6434 ref="../../d6/d4 │ │ │ +0000d250: 352f 6130 3532 3832 2e68 746d 6c23 6139 5/a05282.html#a9 │ │ │ +0000d260: 6534 3165 3262 6438 6366 3564 6436 3961 e41e2bd8cf5dd69a │ │ │ +0000d270: 6162 3639 3533 3538 6330 3933 3830 3722 ab695358c093807" │ │ │ +0000d280: 3e20 2033 3231 3c2f 613e 3c2f 7370 616e > 321 MM │ │ │ +0000d2d0: 4646 3934 5374 7265 7463 6842 656e 6450 FF94StretchBendP │ │ │ +0000d2e0: 6172 616d 6574 6572 733c 2f61 3e28 293b arameters(); │ │ │ +0000d2f0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +0000d340: 2033 3232 3c2f 7370 616e 3e20 3c2f 6469 322 .
    3 │ │ │ +0000d3f0: 3234 3c2f 613e 3c2f 7370 616e 3e20 2020 24 │ │ │ +0000d400: 2076 6972 7475 616c 207e 3c61 2063 6c61 virtual ~MMFF94Stretch │ │ │ +0000d450: 4265 6e64 5061 7261 6d65 7465 7273 3c2f BendParameters();
    .
    < │ │ │ +0000d4a0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000d4b0: 6e6f 223e 2020 3332 353c 2f73 7061 6e3e no"> 325 │ │ │ +0000d4c0: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +0000d510: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 327 const MMFF94Stret │ │ │ +0000d5c0: 6368 4265 6e64 5061 7261 6d65 7465 7273 chBendParameters │ │ │ +0000d5d0: 3c2f 613e 2661 6d70 3b20 6f70 6572 6174 & operat │ │ │ +0000d5e0: 6f72 203d 2028 636f 6e73 7420 3c61 2063 or = (const MMFF94Stret │ │ │ +0000d630: 6368 4265 6e64 5061 7261 6d65 7465 7273 chBendParameters │ │ │ +0000d640: 3c2f 613e 2661 6d70 3b20 7061 7261 6d29 & param) │ │ │ +0000d650: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +0000d6a0: 2033 3238 3c2f 7370 616e 3e20 2020 2020 328 │ │ │ +0000d6b0: 203b 3c2f 6469 763e 0a3c 6469 7620 636c ;
    .
    329 .
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    .< │ │ │ +0000d800: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +0000d810: 3e3c 6120 6964 3d22 6c30 3033 3332 2220 > 332 ;
    │ │ │ +0000d860: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +0000d890: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 333
    .< │ │ │ +0000d8d0: 6120 6964 3d22 6c30 3033 3335 2220 6e61 a id="l00335" na │ │ │ +0000d8e0: 6d65 3d22 6c30 3033 3335 223e 3c2f 613e me="l00335"> │ │ │ +0000d8f0: 3c73 7061 6e20 636c 6173 733d 226c 696e 335 │ │ │ +0000d960: 3c2f 7370 616e 3e20 2020 203c 7370 616e bool │ │ │ +0000d990: 2061 7373 6967 6e50 6172 616d 6574 6572 assignParameter │ │ │ +0000d9a0: 7328 3c61 2063 6c61 7373 3d22 636f 6465 s(Posit │ │ │ +0000d9e0: 696f 6e3c 2f61 3e20 7374 7265 7463 685f ion stretch_ │ │ │ +0000d9f0: 6265 6e64 5f74 7970 652c 2063 6f6e 7374 bend_type, const │ │ │ +0000da00: 203c 6120 636c 6173 733d 2263 6f64 6520 Atom& atom1, c │ │ │ +0000da50: 6f6e 7374 203c 6120 636c 6173 733d 2263 onst At │ │ │ +0000da90: 6f6d 3c2f 613e 2661 6d70 3b20 6174 6f6d om& atom │ │ │ +0000daa0: 322c 2063 6f6e 7374 203c 6120 636c 6173 2, const Atom& │ │ │ +0000daf0: 6174 6f6d 332c 203c 2f64 6976 3e0a 3c64 atom3,
    . │ │ │ +0000db10: 3c61 2069 643d 226c 3030 3333 3622 206e 336 │ │ │ +0000db60: 2020 2020 2020 2020 203c 7370 616e 2063 double │ │ │ +0000db90: 2661 6d70 3b20 6b62 615f 696a 6b2c 203c & kba_ijk, < │ │ │ +0000dba0: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +0000dbb0: 6f72 6474 7970 6522 3e64 6f75 626c 653c ordtype">double< │ │ │ +0000dbc0: 2f73 7061 6e3e 2661 6d70 3b20 6b62 615f /span>& kba_ │ │ │ +0000dbd0: 6b6a 6929 2063 6f6e 7374 3b3c 2f64 6976 kji) const;
    .
    337< │ │ │ +0000dc30: 2f73 7061 6e3e 203c 2f64 6976 3e0a 3c64 /span>
    . │ │ │ +0000dc50: 3c61 2069 643d 226c 3030 3334 3122 206e 341 bool readEmpiricalP │ │ │ +0000dd20: 6172 616d 6574 6572 7328 3c61 2063 6c61 arameters(Parameters& p, const │ │ │ +0000dd80: 3c61 2063 6c61 7373 3d22 636f 6465 2068 String< │ │ │ +0000ddc0: 2f61 3e26 616d 703b 2073 6563 7469 6f6e /a>& section │ │ │ +0000ddd0: 293b 3c2f 6469 763e 0a3c 6469 7620 636c );
    .
    342 │ │ │ +0000de30: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +0000de80: 2020 3334 343c 2f73 7061 6e3e 203c 2f64 344 .
    34 │ │ │ +0000dee0: 353c 2f73 7061 6e3e 2020 2020 7072 6f74 5 prot │ │ │ +0000def0: 6563 7465 643a 3c2f 6469 763e 0a3c 6469 ected:
    .< │ │ │ +0000df10: 6120 6964 3d22 6c30 3033 3436 2220 6e61 a id="l00346" na │ │ │ +0000df20: 6d65 3d22 6c30 3033 3436 223e 3c2f 613e me="l00346"> │ │ │ +0000df30: 3c73 7061 6e20 636c 6173 733d 226c 696e 346
    .
    347 virtual < │ │ │ +0000e010: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +0000e020: 6f72 6474 7970 6522 3e62 6f6f 6c3c 2f73 ordtype">bool setup_(cons │ │ │ +0000e040: 7420 3c61 2063 6c61 7373 3d22 636f 6465 t s │ │ │ +0000e080: 7464 3c2f 613e 3a3a 7665 6374 6f72 266c td::vector&l │ │ │ +0000e090: 743b 3c61 2063 6c61 7373 3d22 636f 6465 t;s │ │ │ +0000e0d0: 7464 3c2f 613e 3a3a 7665 6374 6f72 266c td::vector&l │ │ │ +0000e0e0: 743b 3c61 2063 6c61 7373 3d22 636f 6465 t;Strin │ │ │ +0000e120: 673c 2f61 3e26 6774 3b20 2667 743b 2661 g> >&a │ │ │ +0000e130: 6d70 3b29 3b3c 2f64 6976 3e0a 3c64 6976 mp;);
    .
    < │ │ │ +0000e170: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000e180: 6e6f 223e 2020 3334 383c 2f73 7061 6e3e no"> 348 │ │ │ +0000e190: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +0000e1e0: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 349 P │ │ │ +0000e280: 6f73 6974 696f 6e3c 2f61 3e20 6765 7449 osition getI │ │ │ +0000e290: 6e64 6578 5f28 3c61 2063 6c61 7373 3d22 ndex_(P │ │ │ +0000e2d0: 6f73 6974 696f 6e3c 2f61 3e20 7374 7265 osition stre │ │ │ +0000e2e0: 7463 685f 6265 6e64 5f74 7970 652c 3c2f tch_bend_type,.
    3 │ │ │ +0000e340: 3530 3c2f 7370 616e 3e20 2020 2020 2020 50 │ │ │ +0000e350: 2020 2020 2020 2020 2020 2020 2020 2020 │ │ │ +0000e360: 3c61 2063 6c61 7373 3d22 636f 6465 2068 Positio │ │ │ +0000e3a0: 6e3c 2f61 3e20 6174 6f6d 5f74 7970 6531 n atom_type1 │ │ │ +0000e3b0: 2c20 3c61 2063 6c61 7373 3d22 636f 6465 , Posit │ │ │ +0000e3f0: 696f 6e3c 2f61 3e20 6174 6f6d 5f74 7970 ion atom_typ │ │ │ +0000e400: 6532 2c20 3c61 2063 6c61 7373 3d22 636f e2, Pos │ │ │ +0000e440: 6974 696f 6e3c 2f61 3e20 6174 6f6d 5f74 ition atom_t │ │ │ +0000e450: 7970 6533 2920 636f 6e73 743b 203c 2f64 ype3) const; .
    35 │ │ │ +0000e4b0: 313c 2f73 7061 6e3e 203c 2f64 6976 3e0a 1
    . │ │ │ +0000e4c0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +0000e4f0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 352< │ │ │ +0000e560: 2f61 3e3c 2f73 7061 6e3e 2020 2020 3c61 /a> Position< │ │ │ +0000e5b0: 2f61 3e20 6765 7449 6e64 6578 4279 526f /a> getIndexByRo │ │ │ +0000e5c0: 775f 283c 6120 636c 6173 733d 2263 6f64 w_(Posi │ │ │ +0000e600: 7469 6f6e 3c2f 613e 2072 312c 203c 6120 tion r1, Position r2, │ │ │ +0000e690: 506f 7369 7469 6f6e 3c2f 613e 2072 3329 Position r3) │ │ │ +0000e6a0: 2063 6f6e 7374 3b3c 2f64 6976 3e0a 3c64 const;
    . │ │ │ +0000e6c0: 3c61 2069 643d 226c 3030 3335 3322 206e 353
    .    .
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    │ │ │ +0000e9d0: 2033 3537 3c2f 613e 3c2f 7370 616e 3e20 357 │ │ │ +0000e9e0: 2020 203c 6120 636c 6173 733d 2263 6f64 Stre │ │ │ +0000ea20: 7463 6842 656e 644d 6170 3c2f 613e 2070 tchBendMap p │ │ │ +0000ea30: 6172 616d 6574 6572 735f 6279 5f72 6f77 arameters_by_row │ │ │ +0000ea40: 5f3b 3c2f 6469 763e 0a3c 6469 7620 636c _;
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    .
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    .< │ │ │ +0000edc0: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +0000edd0: 3e3c 6120 6964 3d22 6c30 3033 3638 2220 > 368 {
    .< │ │ │ +0000ee30: 6120 6964 3d22 6c30 3033 3639 2220 6e61 a id="l00369" na │ │ │ +0000ee40: 6d65 3d22 6c30 3033 3639 223e 3c2f 613e me="l00369"> │ │ │ +0000ee50: 3c73 7061 6e20 636c 6173 733d 226c 696e 369 publi │ │ │ +0000ee90: 633c 2f73 7061 6e3e 3a3c 2f64 6976 3e0a c:
    . │ │ │ +0000eea0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
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    < │ │ │ +0000ef30: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000ef40: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 372< │ │ │ +0000efa0: 2f73 7061 6e3e 2020 2020 3c73 7061 6e20 /span> │ │ │ +0000efc0: 7479 7065 6465 663c 2f73 7061 6e3e 203c typedef < │ │ │ +0000efd0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +0000efe0: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +0000eff0: 2f2e 2e2f 6430 2f64 6539 2f61 3033 3533 /../d0/de9/a0353 │ │ │ +0000f000: 302e 6874 6d6c 223e 4861 7368 4d61 7026 0.html">HashMap& │ │ │ +0000f010: 6c74 3b53 7472 696e 672c 2073 7464 3a3a lt;String, std:: │ │ │ +0000f020: 7665 6374 6f72 266c 743b 646f 7562 6c65 vector<double │ │ │ +0000f030: 2667 743b 3c2f 613e 2026 6774 3b20 3c61 > > Torsi │ │ │ +0000f0a0: 6f6e 734d 6170 3c2f 613e 3b3c 2f64 6976 onsMap;
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    376 │ │ │ +0000f2e0: 2020 3c2f 6469 763e 0a3c 6469 7620 636c
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    377 │ │ │ +0000f3d0: 4d4d 4646 3934 546f 7273 696f 6e50 6172 MMFF94TorsionPar │ │ │ +0000f3e0: 616d 6574 6572 733c 2f61 3e28 293b 3c2f ameters();.
    3 │ │ │ +0000f440: 3738 3c2f 7370 616e 3e20 3c2f 6469 763e 78
    │ │ │ +0000f450: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +0000f480: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 380 │ │ │ +0000f4f0: 3c2f 613e 3c2f 7370 616e 3e20 2020 2076 v │ │ │ +0000f500: 6972 7475 616c 207e 3c61 2063 6c61 7373 irtual ~MMFF94TorsionPa │ │ │ +0000f550: 7261 6d65 7465 7273 3c2f 613e 2829 3b3c rameters();< │ │ │ +0000f560: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
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    .
    38 │ │ │ +0000f660: 333c 2f61 3e3c 2f73 7061 6e3e 2020 2020 3 │ │ │ +0000f670: 636f 6e73 7420 3c61 2063 6c61 7373 3d22 const M │ │ │ +0000f6b0: 4d46 4639 3454 6f72 7369 6f6e 5061 7261 MFF94TorsionPara │ │ │ +0000f6c0: 6d65 7465 7273 3c2f 613e 2661 6d70 3b20 meters& │ │ │ +0000f6d0: 6f70 6572 6174 6f72 203d 2028 636f 6e73 operator = (cons │ │ │ +0000f6e0: 7420 3c61 2063 6c61 7373 3d22 636f 6465 t MMFF9 │ │ │ +0000f720: 3454 6f72 7369 6f6e 5061 7261 6d65 7465 4TorsionParamete │ │ │ +0000f730: 7273 3c2f 613e 2661 6d70 3b20 7061 7261 rs& para │ │ │ +0000f740: 6d29 3c2f 6469 763e 0a3c 6469 7620 636c m)
    .
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    .
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    │ │ │ +0000f8f0: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +0000f920: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 388 ;.
    389 │ │ │ +0000f9a0: 3c2f 7370 616e 3e20 3c2f 6469 763e 0a3c
    .< │ │ │ +0000f9b0: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +0000f9c0: 3e3c 6120 6964 3d22 6c30 3033 3931 2220 > 391     bool assignParamet │ │ │ +0000fa90: 6572 7328 3c61 2063 6c61 7373 3d22 636f ers(Pos │ │ │ +0000fad0: 6974 696f 6e3c 2f61 3e20 7479 7065 5f69 ition type_i │ │ │ +0000fae0: 6e64 6578 2c3c 2f64 6976 3e0a 3c64 6976 ndex,
    .
    < │ │ │ +0000fb20: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +0000fb30: 6e6f 223e 2020 3339 323c 2f73 7061 6e3e no"> 392 │ │ │ +0000fb40: 2020 2020 2020 2020 2020 2020 2020 2020 │ │ │ +0000fb50: 2020 2020 2020 203c 6120 636c 6173 733d │ │ │ +0000fb90: 496e 6465 783c 2f61 3e20 6174 312c 203c Index at1, < │ │ │ +0000fba0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +0000fbb0: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +0000fbc0: 2f2e 2e2f 6464 2f64 3963 2f61 3038 3934 /../dd/d9c/a0894 │ │ │ +0000fbd0: 362e 6874 6d6c 223e 496e 6465 783c 2f61 6.html">Index at2, │ │ │ +0000fc20: 496e 6465 783c 2f61 3e20 6174 332c 203c Index at3, < │ │ │ +0000fc30: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +0000fc40: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +0000fc50: 2f2e 2e2f 6464 2f64 3963 2f61 3038 3934 /../dd/d9c/a0894 │ │ │ +0000fc60: 362e 6874 6d6c 223e 496e 6465 783c 2f61 6.html">Index at4,
    .< │ │ │ +0000fc90: 6120 6964 3d22 6c30 3033 3933 2220 6e61 a id="l00393" na │ │ │ +0000fca0: 6d65 3d22 6c30 3033 3933 223e 3c2f 613e me="l00393"> │ │ │ +0000fcb0: 3c73 7061 6e20 636c 6173 733d 226c 696e 393 │ │ │ +0000fce0: 2020 2020 2020 2020 3c73 7061 6e20 636c double& │ │ │ +0000fd10: 616d 703b 2076 312c 203c 7370 616e 2063 amp; v1, double │ │ │ +0000fd40: 2661 6d70 3b20 7632 2c20 3c73 7061 6e20 & v2, double& v3) const │ │ │ +0000fd80: 3b3c 2f64 6976 3e0a 3c64 6976 2063 6c61 ;
    .
    │ │ │ +0000fdd0: 2020 3339 343c 2f73 7061 6e3e 203c 2f64 394 .
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    .
    397 virtual < │ │ │ +0000ff60: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +0000ff70: 6f72 6474 7970 6522 3e62 6f6f 6c3c 2f73 ordtype">bool setup_(cons │ │ │ +0000ff90: 7420 3c61 2063 6c61 7373 3d22 636f 6465 t s │ │ │ +0000ffd0: 7464 3c2f 613e 3a3a 7665 6374 6f72 266c td::vector&l │ │ │ +0000ffe0: 743b 3c61 2063 6c61 7373 3d22 636f 6465 t;s │ │ │ +00010020: 7464 3c2f 613e 3a3a 7665 6374 6f72 266c td::vector&l │ │ │ +00010030: 743b 3c61 2063 6c61 7373 3d22 636f 6465 t;Strin │ │ │ +00010070: 673c 2f61 3e26 6774 3b20 2667 743b 2661 g> >&a │ │ │ +00010080: 6d70 3b29 3b3c 2f64 6976 3e0a 3c64 6976 mp;);
    .
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    .
    │ │ │ +00010130: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 399 S │ │ │ +000101d0: 7472 696e 673c 2f61 3e20 6765 7449 6e64 tring getInd │ │ │ +000101e0: 6578 5f28 3c61 2063 6c61 7373 3d22 636f ex_(Pos │ │ │ +00010220: 6974 696f 6e3c 2f61 3e20 7479 7065 2c20 ition type, │ │ │ +00010230: 3c61 2063 6c61 7373 3d22 636f 6465 2068 Positio │ │ │ +00010270: 6e3c 2f61 3e20 6174 6f6d 5f74 7970 6531 n atom_type1 │ │ │ +00010280: 2c20 3c61 2063 6c61 7373 3d22 636f 6465 , Posit │ │ │ +000102c0: 696f 6e3c 2f61 3e20 6174 6f6d 5f74 7970 ion atom_typ │ │ │ +000102d0: 6532 2c20 3c61 2063 6c61 7373 3d22 636f e2, Pos │ │ │ +00010310: 6974 696f 6e3c 2f61 3e20 6174 6f6d 5f74 ition atom_t │ │ │ +00010320: 7970 6533 2c20 3c61 2063 6c61 7373 3d22 ype3, P │ │ │ +00010360: 6f73 6974 696f 6e3c 2f61 3e20 6174 6f6d osition atom │ │ │ +00010370: 5f74 7970 6534 2920 636f 6e73 743b 3c2f _type4) const;.
    4 │ │ │ +000103d0: 3030 3c2f 7370 616e 3e20 3c2f 6469 763e 00
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    .
    403 mutable │ │ │ +000105a0: 203c 6120 636c 6173 733d 2263 6f64 6520 Torsio │ │ │ +000105e0: 6e73 4d61 703c 2f61 3e20 6275 6666 6572 nsMap buffer │ │ │ +000105f0: 6564 5f70 6172 616d 6574 6572 735f 3b3c ed_parameters_;< │ │ │ +00010600: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +000106a0: 2020 3430 343c 2f61 3e3c 2f73 7061 6e3e 404 │ │ │ +000106b0: 2020 2020 7374 6174 6963 203c 6120 636c static Position │ │ │ +00010700: 2069 635f 5b35 5d3b 3c2f 6469 763e 0a3c ic_[5];
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    .
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    .
    415< │ │ │ +00010b20: 2f73 7061 6e3e 2020 2020 3a20 7075 626c /span> : publ │ │ │ +00010b30: 6963 203c 6120 636c 6173 733d 2263 6f64 ic MMFF │ │ │ +00010b70: 3934 5061 7261 6d65 7465 7273 4261 7365 94ParametersBase │ │ │ +00010b80: 3c2f 613e 3c2f 6469 763e 0a3c 6469 7620
    .
    416 │ │ │ +00010be0: 207b 3c2f 6469 763e 0a3c 6469 7620 636c {
    .
    417 │ │ │ +00010c40: 203c 7370 616e 2063 6c61 7373 3d22 6b65 public:
    .
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    .
    │ │ │ +00010d10: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 420 type │ │ │ +00010d90: 6465 663c 2f73 7061 6e3e 203c 6120 636c def HashMap<S │ │ │ +00010de0: 7472 696e 672c 2064 6f75 626c 6526 6774 tring, double> │ │ │ +00010df0: 3b3c 2f61 3e20 3c61 2063 6c61 7373 3d22 ; PlaneMap; │ │ │ +00010e60: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +00010eb0: 2034 3231 3c2f 7370 616e 3e20 3c2f 6469 421 .
    422 │ │ │ +00010f10: 3c2f 7370 616e 3e20 2020 203c 6120 636c BALL_CREA │ │ │ +00010f80: 5445 3c2f 613e 283c 6120 636c 6173 733d TE( │ │ │ +00010fc0: 4d4d 4646 3934 506c 616e 6550 6172 616d MMFF94PlaneParam │ │ │ +00010fd0: 6574 6572 733c 2f61 3e29 3c2f 6469 763e eters)
    │ │ │ +00010fe0: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +00011010: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 423
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    .
    < │ │ │ +000110d0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +000110e0: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 425< │ │ │ +00011140: 2f73 7061 6e3e 2020 2020 3c61 2063 6c61 /span> MMFF94PlanePa │ │ │ +00011190: 7261 6d65 7465 7273 3c2f 613e 2829 3b3c rameters();< │ │ │ +000111a0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
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    .
    42 │ │ │ +000112a0: 383c 2f61 3e3c 2f73 7061 6e3e 2020 2020 8 │ │ │ +000112b0: 7669 7274 7561 6c20 7e3c 6120 636c 6173 virtual ~MMFF94PlanePar │ │ │ +00011300: 616d 6574 6572 733c 2f61 3e28 293b 3c2f ameters();.
    4 │ │ │ +00011360: 3239 3c2f 7370 616e 3e20 3c2f 6469 763e 29
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    43 │ │ │ +00011540: 323c 2f73 7061 6e3e 2020 2020 2020 3b3c 2 ;< │ │ │ +00011550: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
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    .
    43 │ │ │ +00011650: 353c 2f61 3e3c 2f73 7061 6e3e 2020 2020 5 │ │ │ +00011660: 7669 7274 7561 6c20 3c73 7061 6e20 636c virtual void cl │ │ │ +00011690: 6561 7228 293c 2f64 6976 3e0a 3c64 6976 ear()
    .
    < │ │ │ +000116d0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +000116e0: 6e6f 223e 2020 3433 363c 2f73 7061 6e3e no"> 436 │ │ │ +000116f0: 2020 2020 2020 3b3c 2f64 6976 3e0a 3c64 ;
    . │ │ │ +00011710: 3c61 2069 643d 226c 3030 3433 3722 206e 437
    .
    439 bool as │ │ │ +00011830: 7369 676e 5061 7261 6d65 7465 7273 283c signParameters(< │ │ │ +00011840: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +00011850: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +00011860: 2f2e 2e2f 6464 2f64 3963 2f61 3038 3934 /../dd/d9c/a0894 │ │ │ +00011870: 362e 6874 6d6c 223e 496e 6465 783c 2f61 6.html">Index at1, │ │ │ +000118c0: 496e 6465 783c 2f61 3e20 6174 322c 203c Index at2, < │ │ │ +000118d0: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +000118e0: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +000118f0: 2f2e 2e2f 6464 2f64 3963 2f61 3038 3934 /../dd/d9c/a0894 │ │ │ +00011900: 362e 6874 6d6c 223e 496e 6465 783c 2f61 6.html">Index at3, │ │ │ +00011950: 496e 6465 783c 2f61 3e20 6174 342c 203c Index at4, < │ │ │ +00011960: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +00011970: 6f72 6474 7970 6522 3e64 6f75 626c 653c ordtype">double< │ │ │ +00011980: 2f73 7061 6e3e 2661 6d70 3b20 7629 2063 /span>& v) c │ │ │ +00011990: 6f6e 7374 3b3c 2f64 6976 3e0a 3c64 6976 onst;
    .
    < │ │ │ +000119d0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +000119e0: 6e6f 223e 2020 3434 303c 2f73 7061 6e3e no"> 440 │ │ │ +000119f0: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +00011a40: 2020 3434 313c 2f73 7061 6e3e 2020 2020 441 │ │ │ +00011a50: 7072 6f74 6563 7465 643a 3c2f 6469 763e protected:
    │ │ │ +00011a60: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +00011a90: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 442
    .< │ │ │ +00011ad0: 6120 6964 3d22 6c30 3034 3433 2220 6e61 a id="l00443" na │ │ │ +00011ae0: 6d65 3d22 6c30 3034 3433 223e 3c2f 613e me="l00443"> │ │ │ +00011af0: 3c73 7061 6e20 636c 6173 733d 226c 696e 443 │ │ │ +00011b60: 3c2f 7370 616e 3e20 2020 2076 6972 7475 virtu │ │ │ +00011b70: 616c 203c 7370 616e 2063 6c61 7373 3d22 al boo │ │ │ +00011b90: 6c3c 2f73 7061 6e3e 2073 6574 7570 5f28 l setup_( │ │ │ +00011ba0: 636f 6e73 7420 3c61 2063 6c61 7373 3d22 const std::vect │ │ │ +00011bf0: 6f72 266c 743b 3c61 2063 6c61 7373 3d22 or<std::vect │ │ │ +00011c40: 6f72 266c 743b 3c61 2063 6c61 7373 3d22 or<S │ │ │ +00011c80: 7472 696e 673c 2f61 3e26 6774 3b20 2667 tring> &g │ │ │ +00011c90: 743b 2661 6d70 3b29 3b3c 2f64 6976 3e0a t;&);
    . │ │ │ +00011ca0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +00011cd0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 444
    .
    < │ │ │ +00011d30: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00011d40: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 445< │ │ │ +00011da0: 2f73 7061 6e3e 2020 2020 3c61 2063 6c61 /span> String ge │ │ │ +00011df0: 7449 6e64 6578 5f28 3c61 2063 6c61 7373 tIndex_(Position at │ │ │ +00011e40: 6f6d 5f74 7970 6531 2c20 3c61 2063 6c61 om_type1, Position │ │ │ +00011e90: 6174 6f6d 5f74 7970 6532 2c20 3c61 2063 atom_type2, Position atom_type3, Position< │ │ │ +00011f30: 2f61 3e20 6174 6f6d 5f74 7970 6534 2920 /a> atom_type4) │ │ │ +00011f40: 636f 6e73 743b 3c2f 6469 763e 0a3c 6469 const;
    .< │ │ │ +00011f60: 6120 6964 3d22 6c30 3034 3436 2220 6e61 a id="l00446" na │ │ │ +00011f70: 6d65 3d22 6c30 3034 3436 223e 3c2f 613e me="l00446"> │ │ │ +00011f80: 3c73 7061 6e20 636c 6173 733d 226c 696e 446
    .
    448 │ │ │ +00012090: 506c 616e 654d 6170 3c2f 613e 2070 6172 PlaneMap par │ │ │ +000120a0: 616d 6574 6572 735f 3b3c 2f64 6976 3e0a ameters_;
    . │ │ │ +000120b0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +000120e0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 449< │ │ │ +00012150: 2f61 3e3c 2f73 7061 6e3e 2020 2020 6d75 /a> mu │ │ │ +00012160: 7461 626c 6520 3c61 2063 6c61 7373 3d22 table P │ │ │ +000121a0: 6c61 6e65 4d61 703c 2f61 3e20 6275 6666 laneMap buff │ │ │ +000121b0: 6572 6564 5f70 6172 616d 6574 6572 735f ered_parameters_ │ │ │ +000121c0: 3b3c 2f64 6976 3e0a 3c64 6976 2063 6c61 ;
    .
    │ │ │ +00012210: 2020 3435 303c 2f73 7061 6e3e 2020 7d3b 450 }; │ │ │ +00012220: 3c2f 6469 763e 0a3c 2f64 6976 3e0a 3c64
    .
    . │ │ │ +00012240: 3c61 2069 643d 226c 3030 3435 3122 206e 451
    .
    454 < │ │ │ +000122e0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    .< │ │ │ +00012340: 6120 6964 3d22 6c30 3034 3538 2220 6e61 a id="l00458" na │ │ │ +00012350: 6d65 3d22 6c30 3034 3538 223e 3c2f 613e me="l00458"> │ │ │ +00012360: 3c73 7061 6e20 636c 6173 733d 226c 696e 458 class BALL_EX │ │ │ +00012420: 504f 5254 3c2f 613e 203c 6120 636c 6173 PORT MMFF94VDWParam │ │ │ +00012470: 6574 6572 733c 2f61 3e3c 2f64 6976 3e0a eters
    . │ │ │ +00012480: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +000124b0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 459 : public │ │ │ +000124e0: 203c 6120 636c 6173 733d 2263 6f64 6520 MMFF94 │ │ │ +00012520: 5061 7261 6d65 7465 7273 4261 7365 3c2f ParametersBase
    .
    460 { │ │ │ +00012590: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +000125e0: 2034 3631 3c2f 7370 616e 3e20 2020 203c 461 < │ │ │ +000125f0: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +00012600: 6f72 6422 3e70 7562 6c69 633c 2f73 7061 ord">public:
    .
    462 < │ │ │ +00012670: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    .< │ │ │ +000126d0: 6120 6964 3d22 6c30 3034 3633 2220 6e61 a id="l00463" na │ │ │ +000126e0: 6d65 3d22 6c30 3034 3633 223e 3c2f 613e me="l00463"> │ │ │ +000126f0: 3c73 7061 6e20 636c 6173 733d 226c 696e 463 s │ │ │ +00012760: 7472 7563 7420 3c2f 7370 616e 3e3c 6120 truct VDWEntry< │ │ │ +000127b0: 2f61 3e3c 2f64 6976 3e0a 3c64 6976 2063 /a>
    .
    464 │ │ │ +00012810: 2020 7b3c 2f64 6976 3e0a 3c64 6976 2063 {
    .
    465 double │ │ │ +00012950: 616c 7068 615f 693c 2f61 3e3b 3c2f 6469 alpha_i;.
    4 │ │ │ +00012a00: 3636 3c2f 613e 3c2f 7370 616e 3e20 2020 66 │ │ │ +00012a10: 2020 203c 7370 616e 2063 6c61 7373 3d22 dou │ │ │ +00012a30: 626c 653c 2f73 7061 6e3e 203c 6120 636c ble ni; │ │ │ +00012aa0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ +00012af0: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ +00012b00: 7265 663d 222e 2e2f 2e2e 2f64 652f 6464 ref="../../de/dd │ │ │ +00012b10: 362f 6130 3532 3938 2e68 746d 6c23 6136 6/a05298.html#a6 │ │ │ +00012b20: 3164 3264 3164 6536 6135 3863 3136 6564 1d2d1de6a58c16ed │ │ │ +00012b30: 6164 3335 3761 3062 3661 3238 3261 3822 ad357a0b6a282a8" │ │ │ +00012b40: 3e20 2034 3637 3c2f 613e 3c2f 7370 616e > 467 double < │ │ │ +00012b80: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +00012b90: 5f76 6172 6961 626c 6522 2068 7265 663d _variable" href= │ │ │ +00012ba0: 222e 2e2f 2e2e 2f64 652f 6464 362f 6130 "../../de/dd6/a0 │ │ │ +00012bb0: 3532 3938 2e68 746d 6c23 6136 3164 3264 5298.html#a61d2d │ │ │ +00012bc0: 3164 6536 6135 3863 3136 6564 6164 3335 1de6a58c16edad35 │ │ │ +00012bd0: 3761 3062 3661 3238 3261 3822 3e61 693c 7a0b6a282a8">ai< │ │ │ +00012be0: 2f61 3e3b 3c2f 6469 763e 0a3c 6469 7620 /a>;
    .
    468 double gi;
    .< │ │ │ +00012d30: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00012d40: 3e3c 6120 6964 3d22 6c30 3034 3639 2220 > 469 < │ │ │ +00012de0: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +00012df0: 6f72 6474 7970 6522 3e73 686f 7274 3c2f ordtype">short donor_accep │ │ │ +00012e70: 746f 723c 2f61 3e3b 3c2f 6469 763e 0a3c tor;
    .< │ │ │ +00012e80: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00012e90: 3e3c 6120 6964 3d22 6c30 3034 3730 2220 > 470 < │ │ │ +00012f30: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +00012f40: 6f72 6474 7970 6522 3e62 6f6f 6c3c 2f73 ordtype">bool valid;< │ │ │ +00012fc0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00013010: 3437 313c 2f73 7061 6e3e 2020 2020 7d3b 471 }; │ │ │ +00013020: 3c2f 6469 763e 0a3c 2f64 6976 3e0a 3c64
    .
    . │ │ │ +00013040: 3c61 2069 643d 226c 3030 3437 3222 206e 472
    .
    473 │ │ │ +000130e0: 2020 3c61 2063 6c61 7373 3d22 636f 6465 BA │ │ │ +00013140: 4c4c 5f43 5245 4154 453c 2f61 3e28 3c61 LL_CREATE(MMFF94VDW │ │ │ +00013190: 5061 7261 6d65 7465 7273 3c2f 613e 293c Parameters)< │ │ │ +000131a0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +000131f0: 3437 343c 2f73 7061 6e3e 203c 2f64 6976 474
    .
    475< │ │ │ +00013250: 2f73 7061 6e3e 2020 2020 3c2f 6469 763e /span>
    │ │ │ +00013260: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +00013290: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 476 │ │ │ +00013300: 3c2f 613e 3c2f 7370 616e 3e20 2020 203c < │ │ │ +00013310: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +00013320: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +00013330: 2f2e 2e2f 6436 2f64 6633 2f61 3035 3239 /../d6/df3/a0529 │ │ │ +00013340: 342e 6874 6d6c 223e 4d4d 4646 3934 5644 4.html">MMFF94VD │ │ │ +00013350: 5750 6172 616d 6574 6572 733c 2f61 3e28 WParameters( │ │ │ +00013360: 293b 3c2f 6469 763e 0a3c 6469 7620 636c );
    .
    477 .
    │ │ │ +00013460: 2034 3739 3c2f 613e 3c2f 7370 616e 3e20 479 │ │ │ +00013470: 2020 2076 6972 7475 616c 207e 3c61 2063 virtual ~MMFF94VDWPa │ │ │ +000134c0: 7261 6d65 7465 7273 3c2f 613e 2829 3b3c rameters();< │ │ │ +000134d0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00013520: 3438 303c 2f73 7061 6e3e 203c 2f64 6976 480
    .
    48 │ │ │ +000135d0: 323c 2f61 3e3c 2f73 7061 6e3e 2020 2020 2 │ │ │ +000135e0: 636f 6e73 7420 3c61 2063 6c61 7373 3d22 const M │ │ │ +00013620: 4d46 4639 3456 4457 5061 7261 6d65 7465 MFF94VDWParamete │ │ │ +00013630: 7273 3c2f 613e 2661 6d70 3b20 6f70 6572 rs& oper │ │ │ +00013640: 6174 6f72 203d 2028 636f 6e73 7420 3c61 ator = (const MMFF94VDW │ │ │ +00013690: 5061 7261 6d65 7465 7273 3c2f 613e 2661 Parameters&a │ │ │ +000136a0: 6d70 3b20 7061 7261 6d29 3c2f 6469 763e mp; param)
    │ │ │ +000136b0: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +000136e0: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 483 ;.
    484 │ │ │ +00013760: 3c2f 7370 616e 3e20 3c2f 6469 763e 0a3c
    .< │ │ │ +00013770: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00013780: 3e3c 6120 6964 3d22 6c30 3034 3836 2220 > 486     vir │ │ │ +00013820: 7475 616c 203c 7370 616e 2063 6c61 7373 tual v │ │ │ +00013840: 6f69 643c 2f73 7061 6e3e 2063 6c65 6172 oid clear │ │ │ +00013850: 2829 3c2f 6469 763e 0a3c 6469 7620 636c ()
    .
    487 │ │ │ +000138b0: 2020 203b 3c2f 6469 763e 0a3c 6469 7620 ;
    .
    488 │ │ │ +00013910: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ +00013960: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ +00013970: 7265 663d 222e 2e2f 2e2e 2f64 362f 6466 ref="../../d6/df │ │ │ +00013980: 332f 6130 3532 3934 2e68 746d 6c23 6130 3/a05294.html#a0 │ │ │ +00013990: 3264 6331 3761 6437 6139 6366 3238 3037 2dc17ad7a9cf2807 │ │ │ +000139a0: 6666 3062 6230 6333 3839 3731 3635 3622 ff0bb0c38971656" │ │ │ +000139b0: 3e20 2034 3930 3c2f 613e 3c2f 7370 616e > 490 d │ │ │ +000139e0: 6f75 626c 653c 2f73 7061 6e3e 2067 6574 ouble get │ │ │ +000139f0: 5228 3c61 2063 6c61 7373 3d22 636f 6465 R(Posit │ │ │ +00013a30: 696f 6e3c 2f61 3e20 6174 6f6d 5f74 7970 ion atom_typ │ │ │ +00013a40: 6529 2063 6f6e 7374 3b3c 2f64 6976 3e0a e) const;
    . │ │ │ +00013a50: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +00013a80: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 491
    .
    < │ │ │ +00013ae0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00013af0: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 493< │ │ │ +00013b50: 2f73 7061 6e3e 2020 2020 636f 6e73 7420 /span> const │ │ │ +00013b60: 3c61 2063 6c61 7373 3d22 636f 6465 2068 VDWEnt │ │ │ +00013ba0: 7279 3c2f 613e 2661 6d70 3b20 6765 7450 ry& getP │ │ │ +00013bb0: 6172 616d 6574 6572 7328 3c61 2063 6c61 arameters(Index at) │ │ │ +00013c00: 2063 6f6e 7374 3b3c 2f64 6976 3e0a 3c64 const;
    . │ │ │ +00013c20: 3c61 2069 643d 226c 3030 3439 3422 206e 494
    .
    496 bool as │ │ │ +00013d40: 7369 676e 5061 7261 6d65 7465 7273 283c signParameters(< │ │ │ +00013d50: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +00013d60: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +00013d70: 2f2e 2e2f 6431 2f64 3832 2f61 3038 3937 /../d1/d82/a0897 │ │ │ +00013d80: 342e 6874 6d6c 223e 506f 7369 7469 6f6e 4.html">Position │ │ │ +00013d90: 3c2f 613e 2061 7431 2c20 3c61 2063 6c61 at1, Position │ │ │ +00013de0: 6174 322c 203c 7370 616e 2063 6c61 7373 at2, d │ │ │ +00013e00: 6f75 626c 653c 2f73 7061 6e3e 2661 6d70 ouble& │ │ │ +00013e10: 3b20 7269 6a2c 203c 7370 616e 2063 6c61 ; rij, double&a │ │ │ +00013e40: 6d70 3b20 7269 6a5f 375f 2c20 3c73 7061 mp; rij_7_, double& eij) co │ │ │ +00013e80: 6e73 743b 3c2f 6469 763e 0a3c 6469 7620 nst;
    .
    497 │ │ │ +00013ee0: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +00013f30: 2034 3938 3c2f 7370 616e 3e20 2020 2070 498 p │ │ │ +00013f40: 726f 7465 6374 6564 3a3c 2f64 6976 3e0a rotected:
    . │ │ │ +00013f50: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +00013f80: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 499
    .
    < │ │ │ +00013fe0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00013ff0: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 500< │ │ │ +00014050: 2f73 7061 6e3e 2020 2020 7669 7274 7561 /span> virtua │ │ │ +00014060: 6c20 3c73 7061 6e20 636c 6173 733d 226b l bool │ │ │ +00014080: 3c2f 7370 616e 3e20 7365 7475 705f 2863 setup_(c │ │ │ +00014090: 6f6e 7374 203c 6120 636c 6173 733d 2263 onst std::vecto │ │ │ +000140e0: 7226 6c74 3b3c 6120 636c 6173 733d 2263 r<std::vecto │ │ │ +00014130: 7226 6c74 3b3c 6120 636c 6173 733d 2263 r<St │ │ │ +00014170: 7269 6e67 3c2f 613e 2667 743b 2026 6774 ring> > │ │ │ +00014180: 3b26 616d 703b 293b 3c2f 6469 763e 0a3c ;&);
    .< │ │ │ +00014190: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +000141a0: 3e3c 6120 6964 3d22 6c30 3035 3031 2220 > 501
    .
    503 std::v │ │ │ +000142e0: 6563 746f 7226 6c74 3b3c 6120 636c 6173 ector<VDWEntry& │ │ │ +00014330: 6774 3b20 7061 7261 6d65 7465 7273 5f3b gt; parameters_; │ │ │ +00014340: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +00014390: 2035 3034 3c2f 7370 616e 3e20 3c2f 6469 504 .
    505 │ │ │ +000143f0: 3c2f 7370 616e 3e20 2020 203c 7370 616e // R star ii fo │ │ │ +00014420: 7220 616c 6c20 696e 6469 7669 6475 616c r all individual │ │ │ +00014430: 2061 746f 6d20 7479 7065 733c 2f73 7061 atom types
    .
    506 mutable < │ │ │ +00014500: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +00014510: 5f6e 616d 6573 7061 6365 2220 6872 6566 _namespace" href │ │ │ +00014520: 3d22 2e2e 2f2e 2e2f 6438 2f64 3566 2f61 ="../../d8/d5f/a │ │ │ +00014530: 3032 3231 362e 6874 6d6c 223e 7374 643c 02216.html">std< │ │ │ +00014540: 2f61 3e3a 3a76 6563 746f 7226 6c74 3b3c /a>::vector<< │ │ │ +00014550: 7370 616e 2063 6c61 7373 3d22 6b65 7977 span class="keyw │ │ │ +00014560: 6f72 6474 7970 6522 3e64 6f75 626c 653c ordtype">double< │ │ │ +00014570: 2f73 7061 6e3e 2667 743b 2072 735f 3b3c /span>> rs_;< │ │ │ +00014580: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +000145d0: 3530 373c 2f73 7061 6e3e 203c 2f64 6976 507
    .
    508< │ │ │ +00014630: 2f73 7061 6e3e 2020 2020 3c73 7061 6e20 /span> │ │ │ +00014650: 2f2f 2052 2073 7461 7220 696a 2066 6f72 // R star ij for │ │ │ +00014660: 2070 6169 7273 206f 6620 6174 6f6d 2074 pairs of atom t │ │ │ +00014670: 7970 6573 3c2f 7370 616e 3e3c 2f64 6976 ypes
    .
    50 │ │ │ +00014720: 393c 2f61 3e3c 2f73 7061 6e3e 2020 2020 9 │ │ │ +00014730: 6d75 7461 626c 6520 3c61 2063 6c61 7373 mutable std::ve │ │ │ +00014780: 6374 6f72 266c 743b 3c73 7061 6e20 636c ctor<double& │ │ │ +000147b0: 6774 3b20 7269 6a5f 3b3c 2f64 6976 3e0a gt; rij_;
    . │ │ │ +000147c0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +000147f0: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 510 // │ │ │ +00014830: 2052 2073 7461 7220 696a 205e 2037 2066 R star ij ^ 7 f │ │ │ +00014840: 6f72 2070 6169 7273 206f 6620 6174 6f6d or pairs of atom │ │ │ +00014850: 2074 7970 6573 3c2f 7370 616e 3e3c 2f64 types.
    │ │ │ +00014900: 3531 313c 2f61 3e3c 2f73 7061 6e3e 2020 511 │ │ │ +00014910: 2020 6d75 7461 626c 6520 3c61 2063 6c61 mutable std:: │ │ │ +00014960: 7665 6374 6f72 266c 743b 3c73 7061 6e20 vector<double> rij_7_;.
    51 │ │ │ +000149f0: 323c 2f73 7061 6e3e 2020 2020 3c73 7061 2 // R star ij a │ │ │ +00014a20: 6e64 2066 6f72 2070 6169 7273 206f 6620 nd for pairs of │ │ │ +00014a30: 6174 6f6d 2074 7970 6573 3c2f 7370 616e atom types
    .
    │ │ │ +00014a90: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 513 mutable std::vector<double> eij_;< │ │ │ +00014b80: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00014bd0: 3531 343c 2f73 7061 6e3e 2020 2020 3c73 514 // bools if │ │ │ +00014c00: 696e 6469 7675 616c 2076 616c 7565 2077 indivual value w │ │ │ +00014c10: 6173 2061 6c72 6561 6479 2063 616c 6375 as already calcu │ │ │ +00014c20: 6c61 7465 643c 2f73 7061 6e3e 3c2f 6469 lated.
    5 │ │ │ +00014cd0: 3135 3c2f 613e 3c2f 7370 616e 3e20 2020 15 │ │ │ +00014ce0: 206d 7574 6162 6c65 203c 6120 636c 6173 mutable std::v │ │ │ +00014d30: 6563 746f 7226 6c74 3b3c 7370 616e 2063 ector<bool&g │ │ │ +00014d60: 743b 2020 2020 6361 6c63 756c 6174 6564 t; calculated │ │ │ +00014d70: 5f3b 3c2f 6469 763e 0a3c 6469 7620 636c _;
    .
    516 } │ │ │ +00014dd0: 3b3c 2f64 6976 3e0a 3c2f 6469 763e 0a3c ;
    .
    .< │ │ │ +00014de0: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00014df0: 3e3c 6120 6964 3d22 6c30 3035 3137 2220 > 517
    .
    518 │ │ │ +00014e90: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +00014ee0: 2035 3231 3c2f 7370 616e 3e20 3c2f 6469 521 .
    ..
    < │ │ │ +000150c0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +000150d0: 6e6f 223e 2020 3532 363c 2f73 7061 6e3e no"> 526 │ │ │ +000150e0: 2020 2020 3a20 7075 626c 6963 203c 6120 : public MMFF94Para │ │ │ +00015130: 6d65 7465 7273 4261 7365 3c2f 613e 3c2f metersBase.
    5 │ │ │ +00015190: 3237 3c2f 7370 616e 3e20 207b 3c2f 6469 27 {.
    528 │ │ │ +000151f0: 3c2f 7370 616e 3e20 2020 203c 7370 616e public:< │ │ │ +00015220: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00015270: 3532 393c 2f73 7061 6e3e 203c 2f64 6976 529
    .
    530< │ │ │ +000152d0: 2f73 7061 6e3e 2020 2020 3c61 2063 6c61 /span> BALL_CREAT │ │ │ +00015340: 453c 2f61 3e28 3c61 2063 6c61 7373 3d22 E(M │ │ │ +00015380: 4d46 4639 3445 5350 6172 616d 6574 6572 MFF94ESParameter │ │ │ +00015390: 733c 2f61 3e29 3c2f 6469 763e 0a3c 6469 s)
    .< │ │ │ +000153b0: 6120 6964 3d22 6c30 3035 3331 2220 6e61 a id="l00531" na │ │ │ +000153c0: 6d65 3d22 6c30 3035 3331 223e 3c2f 613e me="l00531"> │ │ │ +000153d0: 3c73 7061 6e20 636c 6173 733d 226c 696e 531
    .
    532 │ │ │ +00015450: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    ..< │ │ │ +00015560: 6469 7620 636c 6173 733d 226c 696e 6522 div class="line" │ │ │ +00015570: 3e3c 6120 6964 3d22 6c30 3035 3334 2220 > 534
    .
    536 virtual │ │ │ +00015670: 207e 3c61 2063 6c61 7373 3d22 636f 6465 ~MMFF9 │ │ │ +000156b0: 3445 5350 6172 616d 6574 6572 733c 2f61 4ESParameters();
    .
    537 │ │ │ +00015720: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    < │ │ │ +00015770: 6120 636c 6173 733d 226c 696e 6522 2068 a class="line" h │ │ │ +00015780: 7265 663d 222e 2e2f 2e2e 2f64 622f 6464 ref="../../db/dd │ │ │ +00015790: 372f 6130 3533 3032 2e68 746d 6c23 6137 7/a05302.html#a7 │ │ │ +000157a0: 3836 3637 6633 3466 3163 6633 6563 3265 8667f34f1cf3ec2e │ │ │ +000157b0: 6466 6261 3833 3532 6330 3663 6230 6522 dfba8352c06cb0e" │ │ │ +000157c0: 3e20 2035 3339 3c2f 613e 3c2f 7370 616e > 539 const MMFF94ESPara │ │ │ +00015820: 6d65 7465 7273 3c2f 613e 2661 6d70 3b20 meters& │ │ │ +00015830: 6f70 6572 6174 6f72 203d 2028 636f 6e73 operator = (cons │ │ │ +00015840: 7420 3c61 2063 6c61 7373 3d22 636f 6465 t MMFF9 │ │ │ +00015880: 3445 5350 6172 616d 6574 6572 733c 2f61 4ESParameters& param).
    54 │ │ │ +000158f0: 303c 2f73 7061 6e3e 2020 2020 2020 3b3c 0 ;< │ │ │ +00015900: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00015950: 3534 313c 2f73 7061 6e3e 203c 2f64 6976 541
    .
    54 │ │ │ +00015a00: 333c 2f61 3e3c 2f73 7061 6e3e 2020 2020 3 │ │ │ +00015a10: 7669 7274 7561 6c20 3c73 7061 6e20 636c virtual void cl │ │ │ +00015a40: 6561 7228 293c 2f64 6976 3e0a 3c64 6976 ear()
    .
    < │ │ │ +00015a80: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00015a90: 6e6f 223e 2020 3534 343c 2f73 7061 6e3e no"> 544 │ │ │ +00015aa0: 2020 2020 2020 3b3c 2f64 6976 3e0a 3c64 ;
    . │ │ │ +00015ac0: 3c61 2069 643d 226c 3030 3534 3522 206e 545
    .
    550 double │ │ │ +00015be0: 6765 7450 6172 7469 616c 4368 6172 6765 getPartialCharge │ │ │ +00015bf0: 283c 6120 636c 6173 733d 2263 6f64 6520 (Positi │ │ │ +00015c30: 6f6e 3c2f 613e 2061 7431 2c20 3c61 2063 on at1, Position at2, │ │ │ +00015cc0: 506f 7369 7469 6f6e 3c2f 613e 2062 7429 Position bt) │ │ │ +00015cd0: 2063 6f6e 7374 3b3c 2f64 6976 3e0a 3c64 const;
    . │ │ │ +00015cf0: 3c61 2069 643d 226c 3030 3535 3122 206e 551
    .< │ │ │ +00015d50: 6120 6964 3d22 6c30 3035 3533 2220 6e61 a id="l00553" na │ │ │ +00015d60: 6d65 3d22 6c30 3035 3533 223e 3c2f 613e me="l00553"> │ │ │ +00015d70: 3c73 7061 6e20 636c 6173 733d 226c 696e 553 │ │ │ +00015de0: 3c2f 7370 616e 3e20 2020 203c 7370 616e bool │ │ │ +00015e10: 2072 6561 6445 6d70 6972 6963 616c 5061 readEmpiricalPa │ │ │ +00015e20: 7261 6d65 7465 7273 283c 6120 636c 6173 rameters(Parameters │ │ │ +00015e70: 2661 6d70 3b20 702c 2063 6f6e 7374 203c & p, const < │ │ │ +00015e80: 6120 636c 6173 733d 2263 6f64 6520 686c a class="code hl │ │ │ +00015e90: 5f63 6c61 7373 2220 6872 6566 3d22 2e2e _class" href=".. │ │ │ +00015ea0: 2f2e 2e2f 6465 2f64 6335 2f61 3033 3630 /../de/dc5/a0360 │ │ │ +00015eb0: 322e 6874 6d6c 223e 5374 7269 6e67 3c2f 2.html">String& section) │ │ │ +00015ed0: 3b3c 2f64 6976 3e0a 3c64 6976 2063 6c61 ;
    .
    │ │ │ +00015f20: 2020 3535 343c 2f73 7061 6e3e 203c 2f64 554 .
    │ │ │ +00015fd0: 3535 363c 2f61 3e3c 2f73 7061 6e3e 2020 556 │ │ │ +00015fe0: 2020 3c73 7061 6e20 636c 6173 733d 226b doub │ │ │ +00016000: 6c65 3c2f 7370 616e 3e20 6765 7450 6869 le getPhi │ │ │ +00016010: 283c 6120 636c 6173 733d 2263 6f64 6520 (Index< │ │ │ +00016050: 2f61 3e20 6174 6f6d 5f74 7970 6529 2063 /a> atom_type) c │ │ │ +00016060: 6f6e 7374 3b3c 2f64 6976 3e0a 3c64 6976 onst;
    .
    < │ │ │ +000160a0: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +000160b0: 6e6f 223e 2020 3535 373c 2f73 7061 6e3e no"> 557 │ │ │ +000160c0: 203c 2f64 6976 3e0a 3c64 6976 2063 6c61
    .
    │ │ │ +00016110: 3c61 2063 6c61 7373 3d22 6c69 6e65 2220 559 │ │ │ +00016190: 646f 7562 6c65 3c2f 7370 616e 3e20 6765 double ge │ │ │ +000161a0: 7450 4243 4928 3c61 2063 6c61 7373 3d22 tPBCI(I │ │ │ +000161e0: 6e64 6578 3c2f 613e 2061 746f 6d5f 7479 ndex atom_ty │ │ │ +000161f0: 7065 2920 636f 6e73 743b 3c2f 6469 763e pe) const;
    │ │ │ +00016200: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +00016230: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 560
    .< │ │ │ +00016270: 6120 6964 3d22 6c30 3035 3631 2220 6e61 a id="l00561" na │ │ │ +00016280: 6d65 3d22 6c30 3035 3631 223e 3c2f 613e me="l00561"> │ │ │ +00016290: 3c73 7061 6e20 636c 6173 733d 226c 696e 561 protected:< │ │ │ +000162c0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00016310: 3536 323c 2f73 7061 6e3e 203c 2f64 6976 562
    .
    56 │ │ │ +000163c0: 333c 2f61 3e3c 2f73 7061 6e3e 2020 2020 3 │ │ │ +000163d0: 7669 7274 7561 6c20 3c73 7061 6e20 636c virtual bool se │ │ │ +00016400: 7475 705f 2863 6f6e 7374 203c 6120 636c tup_(const std: │ │ │ +00016450: 3a76 6563 746f 7226 6c74 3b3c 6120 636c :vector<std: │ │ │ +000164a0: 3a76 6563 746f 7226 6c74 3b3c 6120 636c :vector<String&g │ │ │ +000164f0: 743b 2026 6774 3b26 616d 703b 293b 3c2f t; >&);.
    │ │ │ +000165a0: 2035 3634 3c2f 613e 3c2f 7370 616e 3e20 564 │ │ │ +000165b0: 2020 203c 6120 636c 6173 733d 2263 6f64 Posi │ │ │ +000165f0: 7469 6f6e 3c2f 613e 2067 6574 496e 6465 tion getInde │ │ │ +00016600: 785f 283c 6120 636c 6173 733d 2263 6f64 x_(Posi │ │ │ +00016640: 7469 6f6e 3c2f 613e 2061 7431 2c20 3c61 tion at1, Position< │ │ │ +00016690: 2f61 3e20 6174 322c 203c 6120 636c 6173 /a> at2, Position b │ │ │ +000166e0: 7429 2063 6f6e 7374 3b3c 2f64 6976 3e0a t) const;
    . │ │ │ +000166f0: 3c64 6976 2063 6c61 7373 3d22 6c69 6e65
    < │ │ │ +00016720: 2f61 3e3c 7370 616e 2063 6c61 7373 3d22 /a> 565
    .
    < │ │ │ +00016780: 7370 616e 2063 6c61 7373 3d22 6c69 6e65 span class="line │ │ │ +00016790: 6e6f 223e 3c61 2063 6c61 7373 3d22 6c69 no"> 567< │ │ │ +000167f0: 2f73 7061 6e3e 2020 2020 3c61 2063 6c61 /span> std:: │ │ │ +00016840: 7665 6374 6f72 266c 743b 3c73 7061 6e20 vector<double> parameters │ │ │ +00016880: 5f2c 2070 6869 735f 2c20 7062 6369 735f _, phis_, pbcis_ │ │ │ +00016890: 3b3c 2f64 6976 3e0a 3c64 6976 2063 6c61 ;
    .
    │ │ │ +000168e0: 2020 3536 383c 2f73 7061 6e3e 2020 7d3b 568 }; │ │ │ +000168f0: 3c2f 6469 763e 0a3c 2f64 6976 3e0a 3c64
    .
    . │ │ │ +00016910: 3c61 2069 643d 226c 3030 3536 3922 206e 569
    .
    570 < │ │ │ +000169b0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    │ │ │ +00016a00: 3537 313c 2f73 7061 6e3e 7d20 3c73 7061 571} // namespace B │ │ │ +00016a30: 414c 4c3c 2f73 7061 6e3e 3c2f 6469 763e ALL
    │ │ │ +00016a40: 0a3c 6469 7620 636c 6173 733d 226c 696e .
    │ │ │ +00016a70: 3c2f 613e 3c73 7061 6e20 636c 6173 733d 572
    .< │ │ │ +00016ab0: 6120 6964 3d22 6c30 3035 3733 2220 6e61 a id="l00573" na │ │ │ +00016ac0: 6d65 3d22 6c30 3035 3733 223e 3c2f 613e me="l00573"> │ │ │ +00016ad0: 3c73 7061 6e20 636c 6173 733d 226c 696e 573#end │ │ │ +00016b10: 6966 203c 2f73 7061 6e3e 3c73 7061 6e20 if │ │ │ +00016b30: 2f2f 2042 414c 4c5f 4d4f 4c4d 4543 5f4d // BALL_MOLMEC_M │ │ │ +00016b40: 4d46 4639 345f 4d4d 4646 3934 5041 5241 MFF94_MMFF94PARA │ │ │ +00016b50: 4d45 5445 5253 5f48 3c2f 7370 616e 3e3c METERS_H< │ │ │ +00016b60: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    .
    │ │ │ +00016c10: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 hashMap.h │ │ │ +00016c40: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL_ │ │ │ +00016cf0: 4352 4541 5445 3c2f 613e 3c2f 6469 763e CREATE
    │ │ │ +00016d00: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    #define BALL │ │ │ +00016d20: 5f43 5245 4154 4528 6e61 6d65 293c 2f64 _CREATE(name)
    Definit │ │ │ +00016d50: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion create. │ │ │ +00016d90: 683a 3632 3c2f 613e 3c2f 6469 763e 3c2f h:62
    .
    S │ │ │ +00016e20: 544c 206e 616d 6573 7061 6365 2e3c 2f64 TL namespace.
    .
    BALL
    Definiti │ │ │ +00016ec0: 6f6e 3c2f 623e 203c 6120 6872 6566 3d22 on constant │ │ │ +00016f00: 732e 683a 3133 3c2f 613e 3c2f 6469 763e s.h:13
    │ │ │ +00016f10: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +00016f70: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 BALL::MMFF9 │ │ │ +00016fc0: 345f 6e75 6d62 6572 5f61 746f 6d5f 7479 4_number_atom_ty │ │ │ +00016fd0: 7065 733c 2f61 3e3c 2f64 6976 3e3c 6469 pes
    Size MMFF94_num │ │ │ +00017000: 6265 725f 6174 6f6d 5f74 7970 6573 3c2f ber_atom_types
    hold the │ │ │ +00017030: 6d61 7869 6d75 6d20 6e75 6d62 6572 206f maximum number o │ │ │ +00017040: 6620 4d4d 4646 3934 2061 746f 6d20 7479 f MMFF94 atom ty │ │ │ +00017050: 7065 7320 2b20 3120 2877 696c 6463 6172 pes + 1 (wildcar │ │ │ +00017060: 6429 3c2f 6469 763e 3c2f 6469 763e 0a3c d)
    .< │ │ │ +00017070: 6469 7620 636c 6173 733d 2274 7463 2220 div class="ttc" │ │ │ +00017080: 6964 3d22 6161 3032 3231 375f 6874 6d6c id="aa02217_html │ │ │ +00017090: 5f61 6533 3935 6532 6463 6134 6133 3265 _ae395e2dca4a32e │ │ │ +000170a0: 3866 6365 3139 6438 6462 3832 6139 3533 8fce19d8db82a953 │ │ │ +000170b0: 3839 223e 3c64 6976 2063 6c61 7373 3d22 89">
    BAL │ │ │ +00017110: 4c3a 3a67 6574 4d4d 4646 3934 496e 6465 L::getMMFF94Inde │ │ │ +00017120: 783c 2f61 3e3c 2f64 6976 3e3c 6469 7620 x
    P │ │ │ +00017140: 6f73 6974 696f 6e20 6765 744d 4d46 4639 osition getMMFF9 │ │ │ +00017150: 3449 6e64 6578 2850 6f73 6974 696f 6e20 4Index(Position │ │ │ +00017160: 6174 6f6d 5f74 7970 6531 2c20 506f 7369 atom_type1, Posi │ │ │ +00017170: 7469 6f6e 2061 746f 6d5f 7479 7065 3229 tion atom_type2) │ │ │ +00017180: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ +00017230: 3a50 4442 3a3a 4174 6f6d 3c2f 613e 3c2f :PDB::Atom
    char Ato │ │ │ +00017260: 6d5b 355d 3c2f 6469 763e 3c64 6976 2063 m[5]
    │ │ │ +00017280: 4465 6669 6e69 7469 6f6e 3c2f 623e 203c Definition < │ │ │ +00017290: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6463 a href="../../dc │ │ │ +000172a0: 2f64 6439 2f61 3031 3332 385f 736f 7572 /dd9/a01328_sour │ │ │ +000172b0: 6365 2e68 746d 6c23 6c30 3032 3537 223e ce.html#l00257"> │ │ │ +000172c0: 5044 4264 6566 732e 683a 3235 373c 2f61 PDBdefs.h:257
    .
    BALL::Ha │ │ │ +00017340: 7368 4d61 703c 2f61 3e3c 2f64 6976 3e3c shMap
    < │ │ │ +00017350: 6469 7620 636c 6173 733d 2274 7464 6f63 div class="ttdoc │ │ │ +00017360: 223e 4861 7368 4d61 7020 636c 6173 7320 ">HashMap class │ │ │ +00017370: 6261 7365 6420 6f6e 2074 6865 2053 544c based on the STL │ │ │ +00017380: 206d 6170 2028 636f 6e74 6169 6e69 6e67 map (containing │ │ │ +00017390: 2073 6572 7665 7261 6c20 636f 6e76 656e serveral conven │ │ │ +000173a0: 6965 6e63 6520 6675 6e63 7469 6f6e 7329 ience functions) │ │ │ +000173b0: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    Defi │ │ │ +000173d0: 6e69 7469 6f6e 3c2f 623e 203c 6120 6872 nition hash │ │ │ +00017410: 4d61 702e 683a 3734 3c2f 613e 3c2f 6469 Map.h:74
    .
    │ │ │ +00017460: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 BALL::String< │ │ │ +00017490: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    .
    BALL::Param │ │ │ +00017570: 6574 6572 733c 2f61 3e3c 2f64 6976 3e3c eters
    < │ │ │ +00017580: 6469 7620 636c 6173 733d 2274 7464 6566 div class="ttdef │ │ │ +00017590: 223e 3c62 3e44 6566 696e 6974 696f 6e3c ">Definition< │ │ │ +000175a0: 2f62 3e20 3c61 2068 7265 663d 222e 2e2f /b> parameters. │ │ │ +000175e0: 683a 3235 3c2f 613e 3c2f 6469 763e 3c2f h:25
    .
    B │ │ │ +00017650: 414c 4c3a 3a41 746f 6d3c 2f61 3e3c 2f64 ALL::Atom
    Definit │ │ │ +00017680: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion atom.h: │ │ │ +000176c0: 3930 3c2f 613e 3c2f 6469 763e 3c2f 6469 90
    .
    Definitio │ │ │ +00017770: 6e3c 2f62 3e20 3c61 2068 7265 663d 222e n MMFF94Par │ │ │ +000177b0: 616d 6574 6572 732e 683a 3430 3c2f 613e ameters.h:40 │ │ │ +000177c0: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ +00017870: 3a4d 4d46 4639 3450 6172 616d 6574 6572 :MMFF94Parameter │ │ │ +00017880: 7342 6173 653a 3a69 735f 696e 6974 6961 sBase::is_initia │ │ │ +00017890: 6c69 7a65 645f 3c2f 613e 3c2f 6469 763e lized_
    │ │ │ +000178a0: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    bool is_init │ │ │ +000178c0: 6961 6c69 7a65 645f 3c2f 6469 763e 3c64 ialized_
    Definition MMFF94Parame │ │ │ +00017930: 7465 7273 2e68 3a37 323c 2f61 3e3c 2f64 ters.h:72
    .
    < │ │ │ +00017990: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ +000179a0: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::MM │ │ │ +000179f0: 4646 3934 5061 7261 6d65 7465 7273 4261 FF94ParametersBa │ │ │ +00017a00: 7365 3a3a 7265 6164 5061 7261 6d65 7465 se::readParamete │ │ │ +00017a10: 7273 3c2f 613e 3c2f 6469 763e 3c64 6976 rs
    │ │ │ +00017a30: 626f 6f6c 2072 6561 6450 6172 616d 6574 bool readParamet │ │ │ +00017a40: 6572 7328 5061 7261 6d65 7465 7273 2026 ers(Parameters & │ │ │ +00017a50: 616d 703b 702c 2063 6f6e 7374 2053 7472 amp;p, const Str │ │ │ +00017a60: 696e 6720 2661 6d70 3b73 6563 7469 6f6e ing &section │ │ │ +00017a70: 293c 2f64 6976 3e3c 2f64 6976 3e0a 3c64 )
    .
    BALL │ │ │ +00017b20: 3a3a 4d4d 4646 3934 5061 7261 6d65 7465 ::MMFF94Paramete │ │ │ +00017b30: 7273 4261 7365 3a3a 7365 7475 705f 3c2f rsBase::setup_
    .< │ │ │ +00017c30: 6469 7620 636c 6173 733d 2274 7463 2220 div class="ttc" │ │ │ +00017c40: 6964 3d22 6161 3035 3235 305f 6874 6d6c id="aa05250_html │ │ │ +00017c50: 5f61 3761 6330 6264 3366 3964 3263 6132 _a7ac0bd3f9d2ca2 │ │ │ +00017c60: 6265 3364 3231 6439 3265 6138 3435 6131 be3d21d92ea845a1 │ │ │ +00017c70: 6535 223e 3c64 6976 2063 6c61 7373 3d22 e5">
    BAL │ │ │ +00017cd0: 4c3a 3a4d 4d46 4639 3450 6172 616d 6574 L::MMFF94Paramet │ │ │ +00017ce0: 6572 7342 6173 653a 3a65 7175 6976 5f3c ersBase::equiv_< │ │ │ +00017cf0: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    < │ │ │ +00017d50: 623e 4465 6669 6e69 7469 6f6e 3c2f 623e b>Definition │ │ │ +00017d60: 203c 6120 6872 6566 3d22 2e2e 2f2e 2e2f MMFF94Paramete │ │ │ +00017da0: 7273 2e68 3a37 363c 2f61 3e3c 2f64 6976 rs.h:76
    .
    BALL::MMFF │ │ │ +00017e60: 3934 5061 7261 6d65 7465 7273 4261 7365 94ParametersBase │ │ │ +00017e70: 3a3a 6e75 6d62 6572 5f65 7870 6563 7465 ::number_expecte │ │ │ +00017e80: 645f 6669 656c 6473 5f3c 2f61 3e3c 2f64 d_fields_
    Size numb │ │ │ +00017eb0: 6572 5f65 7870 6563 7465 645f 6669 656c er_expected_fiel │ │ │ +00017ec0: 6473 5f3c 2f64 6976 3e3c 6469 7620 636c ds_
    .
    virtual void c │ │ │ +00018030: 6c65 6172 2829 3c2f 6469 763e 3c64 6976 lear()
    C │ │ │ +00018050: 6c65 6172 206d 6574 686f 642e 3c2f 6469 lear method.
    .
    BALL::MMF │ │ │ +00018110: 4639 3450 6172 616d 6574 6572 7342 6173 F94ParametersBas │ │ │ +00018120: 653a 3a69 7349 6e69 7469 616c 697a 6564 e::isInitialized │ │ │ +00018130: 3c2f 613e 3c2f 6469 763e 3c64 6976 2063
    bo │ │ │ +00018150: 6f6c 2069 7349 6e69 7469 616c 697a 6564 ol isInitialized │ │ │ +00018160: 2829 3c2f 6469 763e 3c64 6976 2063 6c61 ()
    .
    void │ │ │ +000182d0: 7365 7445 7175 6976 616c 656e 6365 7328 setEquivalences( │ │ │ +000182e0: 636f 6e73 7420 4d4d 4646 3934 4174 6f6d const MMFF94Atom │ │ │ +000182f0: 5479 7065 4571 7569 7661 6c65 6e63 6573 TypeEquivalences │ │ │ +00018300: 2026 616d 703b 6571 7569 293c 2f64 6976 &equi)
    Definitio │ │ │ +00018330: 6e3c 2f62 3e20 3c61 2068 7265 663d 222e n MMFF94Par │ │ │ +00018370: 616d 6574 6572 732e 683a 3636 3c2f 613e ameters.h:66 │ │ │ +00018380: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    . │ │ │ +000183b0: 3c64 6976 2063 6c61 7373 3d22 7474 6e61
    BALL::MMF │ │ │ +000183f0: 4639 3441 746f 6d54 7970 6545 7175 6976 F94AtomTypeEquiv │ │ │ +00018400: 616c 656e 6365 733c 2f61 3e3c 2f64 6976 alences
    Definitio │ │ │ +00018430: 6e3c 2f62 3e20 3c61 2068 7265 663d 222e n MMFF94Par │ │ │ +00018470: 616d 6574 6572 732e 683a 3835 3c2f 613e ameters.h:85 │ │ │ +00018480: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ +00018530: 3a4d 4d46 4639 3441 746f 6d54 7970 6545 :MMFF94AtomTypeE │ │ │ +00018540: 7175 6976 616c 656e 6365 733a 3a6e 616d quivalences::nam │ │ │ +00018550: 6573 5f3c 2f61 3e3c 2f64 6976 3e3c 6469 es_
    std::vector< │ │ │ +00018580: 2053 7472 696e 6720 2667 743b 206e 616d String > nam │ │ │ +00018590: 6573 5f3c 2f64 6976 3e3c 6469 7620 636c es_
    < │ │ │ +00018610: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    < │ │ │ +00018670: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6432 a href="../../d2 │ │ │ +00018680: 2f64 6264 2f61 3035 3235 342e 6874 6d6c /dbd/a05254.html │ │ │ +00018690: 2361 3362 6433 3361 3338 3833 3339 3930 #a3bd33a38833990 │ │ │ +000186a0: 3938 6261 3666 6539 3665 3631 3831 6435 98ba6fe96e6181d5 │ │ │ +000186b0: 6635 223e 4241 4c4c 3a3a 4d4d 4646 3934 f5">BALL::MMFF94 │ │ │ +000186c0: 4174 6f6d 5479 7065 4571 7569 7661 6c65 AtomTypeEquivale │ │ │ +000186d0: 6e63 6573 3a3a 636c 6561 723c 2f61 3e3c nces::clear< │ │ │ +000186e0: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    void cl │ │ │ +00018700: 6561 7228 293c 2f64 6976 3e3c 6469 7620 ear()
    Cl │ │ │ +00018720: 6561 7220 6d65 7468 6f64 2e3c 2f64 6976 ear method.
    .
    BALL::MMFF │ │ │ +000187e0: 3934 4174 6f6d 5479 7065 4571 7569 7661 94AtomTypeEquiva │ │ │ +000187f0: 6c65 6e63 6573 3a3a 4d4d 4646 3934 4174 lences::MMFF94At │ │ │ +00018800: 6f6d 5479 7065 4571 7569 7661 6c65 6e63 omTypeEquivalenc │ │ │ +00018810: 6573 3c2f 613e 3c2f 6469 763e 3c64 6976 es
    │ │ │ +00018830: 4d4d 4646 3934 4174 6f6d 5479 7065 4571 MMFF94AtomTypeEq │ │ │ +00018840: 7569 7661 6c65 6e63 6573 2863 6f6e 7374 uivalences(const │ │ │ +00018850: 204d 4d46 4639 3441 746f 6d54 7970 6545 MMFF94AtomTypeE │ │ │ +00018860: 7175 6976 616c 656e 6365 7320 2661 6d70 quivalences & │ │ │ +00018870: 3b74 6f5f 636f 7079 293c 2f64 6976 3e3c ;to_copy)
    < │ │ │ +00018880: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    < │ │ │ +000188e0: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6432 a href="../../d2 │ │ │ +000188f0: 2f64 6264 2f61 3035 3235 342e 6874 6d6c /dbd/a05254.html │ │ │ +00018900: 2361 3661 3435 6138 6435 3263 3564 3366 #a6a45a8d52c5d3f │ │ │ +00018910: 6235 3138 3839 6337 3831 6663 3963 6561 b51889c781fc9cea │ │ │ +00018920: 3530 223e 4241 4c4c 3a3a 4d4d 4646 3934 50">BALL::MMFF94 │ │ │ +00018930: 4174 6f6d 5479 7065 4571 7569 7661 6c65 AtomTypeEquivale │ │ │ +00018940: 6e63 6573 3a3a 6578 6973 7473 5f3c 2f61 nces::exists_
    std:: │ │ │ +00018970: 7665 6374 6f72 266c 743b 2062 6f6f 6c20 vector< bool │ │ │ +00018980: 2667 743b 2065 7869 7374 735f 3c2f 6469 > exists_
    Definiti │ │ │ +000189b0: 6f6e 3c2f 623e 203c 6120 6872 6566 3d22 on MMFF94Pa │ │ │ +000189f0: 7261 6d65 7465 7273 2e68 3a31 3132 3c2f rameters.h:112
    .< │ │ │ +00018a10: 6469 7620 636c 6173 733d 2274 7463 2220 div class="ttc" │ │ │ +00018a20: 6964 3d22 6161 3035 3235 345f 6874 6d6c id="aa05254_html │ │ │ +00018a30: 5f61 6136 6137 6138 6561 3766 3561 6539 _aa6a7a8ea7f5ae9 │ │ │ +00018a40: 6663 3334 3633 3936 3163 3836 3834 3765 fc3463961c86847e │ │ │ +00018a50: 3334 223e 3c64 6976 2063 6c61 7373 3d22 34">
    BAL │ │ │ +00018ab0: 4c3a 3a4d 4d46 4639 3441 746f 6d54 7970 L::MMFF94AtomTyp │ │ │ +00018ac0: 6545 7175 6976 616c 656e 6365 733a 3a7e eEquivalences::~ │ │ │ +00018ad0: 4d4d 4646 3934 4174 6f6d 5479 7065 4571 MMFF94AtomTypeEq │ │ │ +00018ae0: 7569 7661 6c65 6e63 6573 3c2f 613e 3c2f uivalences
    ~MMFF94A │ │ │ +00018b10: 746f 6d54 7970 6545 7175 6976 616c 656e tomTypeEquivalen │ │ │ +00018b20: 6365 7328 293c 2f64 6976 3e3c 2f64 6976 ces()
    .
    . │ │ │ +00018ce0: 3c64 6976 2063 6c61 7373 3d22 7474 6322
    BA │ │ │ +00018d80: 4c4c 3a3a 4d4d 4646 3934 4174 6f6d 5479 LL::MMFF94AtomTy │ │ │ +00018d90: 7065 4571 7569 7661 6c65 6e63 6573 3a3a peEquivalences:: │ │ │ +00018da0: 7365 7475 705f 3c2f 613e 3c2f 6469 763e setup_
    │ │ │ +00018db0: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    virtual bool │ │ │ +00018dd0: 2073 6574 7570 5f28 636f 6e73 7420 7374 setup_(const st │ │ │ +00018de0: 643a 3a76 6563 746f 7226 6c74 3b20 7374 d::vector< st │ │ │ +00018df0: 643a 3a76 6563 746f 7226 6c74 3b20 5374 d::vector< St │ │ │ +00018e00: 7269 6e67 2026 6774 3b20 2667 743b 2026 ring > > & │ │ │ +00018e10: 616d 703b 293c 2f64 6976 3e3c 2f64 6976 amp;)
    .
    MMFF94 │ │ │ +00018f20: 4174 6f6d 5479 7065 4571 7569 7661 6c65 AtomTypeEquivale │ │ │ +00018f30: 6e63 6573 2829 3c2f 6469 763e 3c2f 6469 nces()
    .
    I │ │ │ +00019030: 6e64 6578 2067 6574 4571 7569 7661 6c65 ndex getEquivale │ │ │ +00019040: 6e63 6528 506f 7369 7469 6f6e 206f 7269 nce(Position ori │ │ │ +00019050: 6769 6e61 6c2c 2050 6f73 6974 696f 6e20 ginal, Position │ │ │ +00019060: 6e75 6d62 6572 2920 636f 6e73 743c 2f64 number) const
    .
    BALL::MMFF94 │ │ │ +000190e0: 4174 6f6d 5479 7065 3c2f 613e 3c2f 6469 AtomType
    Class to st │ │ │ +00019110: 6f72 6520 7468 6520 7661 6c75 6573 206f ore the values o │ │ │ +00019120: 6620 616e 2061 746f 6d20 7479 7065 2066 f an atom type f │ │ │ +00019130: 726f 6d20 4d4d 4646 5052 4f50 2e50 4152 rom MMFFPROP.PAR │ │ │ +00019140: 2e3c 2f64 6976 3e3c 6469 7620 636c 6173 .
    .
    BALL::MMFF94At │ │ │ +00019270: 6f6d 5479 7065 3a3a 6d6c 7462 3c2f 613e omType::mltb │ │ │ +00019280: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    Positi │ │ │ +000192a0: 6f6e 206d 6c74 623c 2f64 6976 3e3c 6469 on mltb
    │ │ │ +000192c0: 3c62 3e44 6566 696e 6974 696f 6e3c 2f62 Definition MMFF94Paramet │ │ │ +00019310: 6572 732e 683a 3133 373c 2f61 3e3c 2f64 ers.h:137
    .
    < │ │ │ +00019370: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ +00019380: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::MM │ │ │ +000193d0: 4646 3934 4174 6f6d 5479 7065 3a3a 6172 FF94AtomType::ar │ │ │ +000193e0: 6f6d 3c2f 613e 3c2f 6469 763e 3c64 6976 om
    │ │ │ +00019400: 626f 6f6c 2061 726f 6d3c 2f64 6976 3e3c bool arom
    < │ │ │ +00019410: 6469 7620 636c 6173 733d 2274 7464 6f63 div class="ttdoc │ │ │ +00019420: 223e 6973 2061 726f 6d61 7469 633c 2f64 ">is aromatic
    Definit │ │ │ +00019450: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion MMFF94P │ │ │ +00019490: 6172 616d 6574 6572 732e 683a 3134 303c arameters.h:140< │ │ │ +000194a0: 2f61 3e3c 2f64 6976 3e3c 2f64 6976 3e0a /a>
    . │ │ │ +000194b0: 3c64 6976 2063 6c61 7373 3d22 7474 6322
    BA │ │ │ +00019550: 4c4c 3a3a 4d4d 4646 3934 4174 6f6d 5479 LL::MMFF94AtomTy │ │ │ +00019560: 7065 3a3a 7661 6c69 643c 2f61 3e3c 2f64 pe::valid
    bool vali │ │ │ +00019590: 643c 2f64 6976 3e3c 6469 7620 636c 6173 d
    Is thi │ │ │ +000195b0: 7320 6120 7661 6c69 6420 4d4d 4646 3934 s a valid MMFF94 │ │ │ +000195c0: 2061 746f 6d20 7479 7065 3f3c 2f64 6976 atom type?
    Definitio │ │ │ +000195f0: 6e3c 2f62 3e20 3c61 2068 7265 663d 222e n MMFF94Par │ │ │ +00019630: 616d 6574 6572 732e 683a 3134 393c 2f61 ameters.h:149
    .
    BALL │ │ │ +000196f0: 3a3a 4d4d 4646 3934 4174 6f6d 5479 7065 ::MMFF94AtomType │ │ │ +00019700: 3a3a 6c69 6e3c 2f61 3e3c 2f64 6976 3e3c ::lin
    < │ │ │ +00019710: 6469 7620 636c 6173 733d 2274 7464 6563 div class="ttdec │ │ │ +00019720: 6922 3e62 6f6f 6c20 6c69 6e3c 2f64 6976 i">bool lin
    has linear b │ │ │ +00019750: 6f6e 643c 2f64 6976 3e3c 6469 7620 636c ond
    < │ │ │ +000197d0: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    < │ │ │ +00019830: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6438 a href="../../d8 │ │ │ +00019840: 2f64 3434 2f61 3035 3235 382e 6874 6d6c /d44/a05258.html │ │ │ +00019850: 2361 3936 6463 3132 3238 3166 6161 6639 #a96dc12281faaf9 │ │ │ +00019860: 6333 3433 3565 3937 3237 3930 6639 3861 c3435e972790f98a │ │ │ +00019870: 3739 223e 4241 4c4c 3a3a 4d4d 4646 3934 79">BALL::MMFF94 │ │ │ +00019880: 4174 6f6d 5479 7065 3a3a 6173 7065 633c AtomType::aspec< │ │ │ +00019890: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    Pos │ │ │ +000198b0: 6974 696f 6e20 6173 7065 633c 2f64 6976 ition aspec
    atomic numbe │ │ │ +000198e0: 723b 3c2f 6469 763e 3c64 6976 2063 6c61 r;
    .
    BALL::MMFF94A │ │ │ +00019a10: 746f 6d54 7970 653a 3a76 616c 3c2f 613e tomType::val │ │ │ +00019a20: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    Positi │ │ │ +00019a40: 6f6e 2076 616c 3c2f 6469 763e 3c64 6976 on val
    n │ │ │ +00019a60: 756d 6265 7220 6f66 2062 6f6e 6473 206d umber of bonds m │ │ │ +00019a70: 6164 6520 746f 2074 6869 7320 6174 6f6d ade to this atom │ │ │ +00019a80: 2074 7970 653c 2f64 6976 3e3c 6469 7620 type
    Definition │ │ │ +00019ab0: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 MMFF94Parameter │ │ │ +00019af0: 732e 683a 3132 393c 2f61 3e3c 2f64 6976 s.h:129
    .
    BALL::MMFF │ │ │ +00019bb0: 3934 4174 6f6d 5479 7065 3a3a 4d4d 4646 94AtomType::MMFF │ │ │ +00019bc0: 3934 4174 6f6d 5479 7065 3c2f 613e 3c2f 94AtomType
    MMFF94At │ │ │ +00019bf0: 6f6d 5479 7065 2829 3c2f 6469 763e 3c2f omType()
    .
    bool │ │ │ +00019ce0: 7362 6d62 3c2f 6469 763e 3c64 6976 2063 sbmb
    can │ │ │ +00019d00: 2068 6176 6520 6120 6465 6c6f 6361 6c69 have a delocali │ │ │ +00019d10: 7a65 6420 7369 6e67 6c65 2062 6f6e 643c zed single bond< │ │ │ +00019d20: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    Defin │ │ │ +00019d40: 6974 696f 6e3c 2f62 3e20 3c61 2068 7265 ition MMFF9 │ │ │ +00019d80: 3450 6172 616d 6574 6572 732e 683a 3134 4Parameters.h:14 │ │ │ +00019d90: 363c 2f61 3e3c 2f64 6976 3e3c 2f64 6976 6
    .
    │ │ │ +00019e40: 4241 4c4c 3a3a 4d4d 4646 3934 4174 6f6d BALL::MMFF94Atom │ │ │ +00019e50: 5479 7065 3a3a 7069 6c70 3c2f 613e 3c2f Type::pilp
    bool pil │ │ │ +00019e80: 703c 2f64 6976 3e3c 6469 7620 636c 6173 p
    has pi │ │ │ +00019ea0: 206c 6f6e 6520 7061 6972 2065 6c65 6374 lone pair elect │ │ │ +00019eb0: 726f 6e73 3c2f 6469 763e 3c64 6976 2063 rons
    │ │ │ +00019ed0: 4465 6669 6e69 7469 6f6e 3c2f 623e 203c Definition < │ │ │ +00019ee0: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6430 a href="../../d0 │ │ │ +00019ef0: 2f64 3739 2f61 3031 3736 365f 736f 7572 /d79/a01766_sour │ │ │ +00019f00: 6365 2e68 746d 6c23 6c30 3031 3332 223e ce.html#l00132"> │ │ │ +00019f10: 4d4d 4646 3934 5061 7261 6d65 7465 7273 MMFF94Parameters │ │ │ +00019f20: 2e68 3a31 3332 3c2f 613e 3c2f 6469 763e .h:132
    │ │ │ +00019f30: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +00019f90: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 BALL::MMFF9 │ │ │ +00019fe0: 3441 746f 6d54 7970 653a 3a63 7264 3c2f 4AtomType::crd
    necessary numbe │ │ │ +0001a040: 7220 6f66 2062 6f6e 6465 6420 6e65 6967 r of bonded neig │ │ │ +0001a050: 6862 6f75 7273 3c2f 6469 763e 3c64 6976 hbours
    < │ │ │ +0001a070: 623e 4465 6669 6e69 7469 6f6e 3c2f 623e b>Definition │ │ │ +0001a080: 203c 6120 6872 6566 3d22 2e2e 2f2e 2e2f MMFF94Paramete │ │ │ +0001a0c0: 7273 2e68 3a31 3236 3c2f 613e 3c2f 6469 rs.h:126
    .
    │ │ │ +0001a110: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 BALL::MMFF94A │ │ │ +0001a140: 746f 6d54 7970 6573 3c2f 613e 3c2f 6469 tomTypes
    Definiti │ │ │ +0001a170: 6f6e 3c2f 623e 203c 6120 6872 6566 3d22 on MMFF94Pa │ │ │ +0001a1b0: 7261 6d65 7465 7273 2e68 3a31 3539 3c2f rameters.h:159
    .< │ │ │ +0001a1d0: 6469 7620 636c 6173 733d 2274 7463 2220 div class="ttc" │ │ │ +0001a1e0: 6964 3d22 6161 3035 3236 325f 6874 6d6c id="aa05262_html │ │ │ +0001a1f0: 5f61 3036 6138 3366 3565 3538 3538 6632 _a06a83f5e5858f2 │ │ │ +0001a200: 6561 3730 3838 6535 3164 6562 6232 6630 ea7088e51debb2f0 │ │ │ +0001a210: 3030 223e 3c64 6976 2063 6c61 7373 3d22 00">
    BAL │ │ │ +0001a270: 4c3a 3a4d 4d46 4639 3441 746f 6d54 7970 L::MMFF94AtomTyp │ │ │ +0001a280: 6573 3a3a 7365 7475 705f 3c2f 613e 3c2f es::setup_
    virtual │ │ │ +0001a2b0: 626f 6f6c 2073 6574 7570 5f28 636f 6e73 bool setup_(cons │ │ │ +0001a2c0: 7420 7374 643a 3a76 6563 746f 7226 6c74 t std::vector< │ │ │ +0001a2d0: 3b20 7374 643a 3a76 6563 746f 7226 6c74 ; std::vector< │ │ │ +0001a2e0: 3b20 5374 7269 6e67 2026 6774 3b20 2667 ; String > &g │ │ │ +0001a2f0: 743b 2026 616d 703b 293c 2f64 6976 3e3c t; &)
    < │ │ │ +0001a300: 2f64 6976 3e0a 3c64 6976 2063 6c61 7373 /div>.
    < │ │ │ +0001a360: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6464 a href="../../dd │ │ │ +0001a370: 2f64 6630 2f61 3035 3236 322e 6874 6d6c /df0/a05262.html │ │ │ +0001a380: 2361 3335 3639 6134 6637 3065 3163 6336 #a3569a4f70e1cc6 │ │ │ +0001a390: 3434 6539 3161 3235 6236 3163 6633 3964 44e91a25b61cf39d │ │ │ +0001a3a0: 3338 223e 4241 4c4c 3a3a 4d4d 4646 3934 38">BALL::MMFF94 │ │ │ +0001a3b0: 4174 6f6d 5479 7065 733a 3a64 6174 615f AtomTypes::data_ │ │ │ +0001a3c0: 3c2f 613e 3c2f 6469 763e 3c64 6976 2063
    st │ │ │ +0001a3e0: 643a 3a76 6563 746f 7226 6c74 3b20 4d4d d::vector< MM │ │ │ +0001a3f0: 4646 3934 4174 6f6d 5479 7065 2026 6774 FF94AtomType > │ │ │ +0001a400: 3b20 6461 7461 5f3c 2f64 6976 3e3c 6469 ; data_
    │ │ │ +0001a420: 3c62 3e44 6566 696e 6974 696f 6e3c 2f62 Definition MMFF94Paramet │ │ │ +0001a470: 6572 732e 683a 3137 373c 2f61 3e3c 2f64 ers.h:177
    .
    < │ │ │ +0001a4d0: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ +0001a4e0: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::MM │ │ │ +0001a530: 4646 3934 4174 6f6d 5479 7065 733a 3a4d FF94AtomTypes::M │ │ │ +0001a540: 4d46 4639 3441 746f 6d54 7970 6573 3c2f MFF94AtomTypes
    .
    BALL:: │ │ │ +0001a650: 4d4d 4646 3934 4174 6f6d 5479 7065 733a MMFF94AtomTypes: │ │ │ +0001a660: 3a7e 4d4d 4646 3934 4174 6f6d 5479 7065 :~MMFF94AtomType │ │ │ +0001a670: 733c 2f61 3e3c 2f64 6976 3e3c 6469 7620 s
    ~ │ │ │ +0001a690: 4d4d 4646 3934 4174 6f6d 5479 7065 7328 MMFF94AtomTypes( │ │ │ +0001a6a0: 293c 2f64 6976 3e3c 6469 7620 636c 6173 )
    .
    BALL::MMFF94At │ │ │ +0001a7d0: 6f6d 5479 7065 733a 3a4d 4d46 4639 3441 omTypes::MMFF94A │ │ │ +0001a7e0: 746f 6d54 7970 6573 3c2f 613e 3c2f 6469 tomTypes
    MMFF94Atom │ │ │ +0001a810: 5479 7065 7328 293c 2f64 6976 3e3c 2f64 Types()
    .
    < │ │ │ +0001a8f0: 6469 7620 636c 6173 733d 2274 7464 6563 div class="ttdec │ │ │ +0001a900: 6922 3e63 6f6e 7374 2073 7464 3a3a 7665 i">const std::ve │ │ │ +0001a910: 6374 6f72 266c 743b 204d 4d46 4639 3441 ctor< MMFF94A │ │ │ +0001a920: 746f 6d54 7970 6520 2667 743b 2026 616d tomType > &am │ │ │ +0001a930: 703b 2067 6574 4174 6f6d 5479 7065 7328 p; getAtomTypes( │ │ │ +0001a940: 2920 636f 6e73 743c 2f64 6976 3e3c 6469 ) const
    │ │ │ +0001a960: 3c62 3e44 6566 696e 6974 696f 6e3c 2f62 Definition MMFF94Paramet │ │ │ +0001a9b0: 6572 732e 683a 3137 323c 2f61 3e3c 2f64 ers.h:172
    .
    BALL::MMFF94 │ │ │ +0001aa30: 5374 7265 7463 6850 6172 616d 6574 6572 StretchParameter │ │ │ +0001aa40: 733c 2f61 3e3c 2f64 6976 3e3c 6469 7620 s
    Definition │ │ │ +0001aa70: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 MMFF94Parameter │ │ │ +0001aab0: 732e 683a 3138 373c 2f61 3e3c 2f64 6976 s.h:187
    .
    BALL::MMFF │ │ │ +0001ab70: 3934 5374 7265 7463 6850 6172 616d 6574 94StretchParamet │ │ │ +0001ab80: 6572 733a 3a62 7566 6665 7265 645f 7061 ers::buffered_pa │ │ │ +0001ab90: 7261 6d65 7465 7273 5f3c 2f61 3e3c 2f64 rameters_
    StretchMa │ │ │ +0001abc0: 7020 6275 6666 6572 6564 5f70 6172 616d p buffered_param │ │ │ +0001abd0: 6574 6572 735f 3c2f 6469 763e 3c64 6976 eters_
    < │ │ │ +0001abf0: 623e 4465 6669 6e69 7469 6f6e 3c2f 623e b>Definition │ │ │ +0001ac00: 203c 6120 6872 6566 3d22 2e2e 2f2e 2e2f MMFF94Paramete │ │ │ +0001ac40: 7273 2e68 3a32 3534 3c2f 613e 3c2f 6469 rs.h:254
    .
    BALL::MMF │ │ │ +0001ad00: 4639 3453 7472 6574 6368 5061 7261 6d65 F94StretchParame │ │ │ +0001ad10: 7465 7273 3a3a 656d 7069 7269 6361 6c5f ters::empirical_ │ │ │ +0001ad20: 7061 7261 6d65 7465 7273 5f3c 2f61 3e3c parameters_< │ │ │ +0001ad30: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    Empiric │ │ │ +0001ad50: 616c 5374 7265 7463 684d 6170 2065 6d70 alStretchMap emp │ │ │ +0001ad60: 6972 6963 616c 5f70 6172 616d 6574 6572 irical_parameter │ │ │ +0001ad70: 735f 3c2f 6469 763e 3c64 6976 2063 6c61 s_
    .
    HashMa │ │ │ +0001aee0: 7026 6c74 3b20 506f 7369 7469 6f6e 2c20 p< Position, │ │ │ +0001aef0: 426f 6e64 4461 7461 2026 6774 3b20 5374 BondData > St │ │ │ +0001af00: 7265 7463 684d 6170 3c2f 6469 763e 3c64 retchMap
    Definition MMFF94Parame │ │ │ +0001af70: 7465 7273 2e68 3a32 3134 3c2f 613e 3c2f ters.h:214
    .
    │ │ │ +0001afd0: 3c64 6976 2063 6c61 7373 3d22 7474 6e61
    BALL::M │ │ │ +0001b030: 4d46 4639 3453 7472 6574 6368 5061 7261 MFF94StretchPara │ │ │ +0001b040: 6d65 7465 7273 3a3a 7365 7475 705f 3c2f meters::setup_
    .
    < │ │ │ +0001b110: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ +0001b120: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::MM │ │ │ +0001b170: 4646 3934 5374 7265 7463 6850 6172 616d FF94StretchParam │ │ │ +0001b180: 6574 6572 733a 3a67 6574 456d 7069 7269 eters::getEmpiri │ │ │ +0001b190: 6361 6c50 6172 616d 6574 6572 733c 2f61 calParameters
    const │ │ │ +0001b1c0: 2045 6d70 6972 6963 616c 5374 7265 7463 EmpiricalStretc │ │ │ +0001b1d0: 684d 6170 2026 616d 703b 2067 6574 456d hMap & getEm │ │ │ +0001b1e0: 7069 7269 6361 6c50 6172 616d 6574 6572 piricalParameter │ │ │ +0001b1f0: 7328 2920 636f 6e73 743c 2f64 6976 3e3c s() const
    < │ │ │ +0001b200: 6469 7620 636c 6173 733d 2274 7464 6566 div class="ttdef │ │ │ +0001b210: 223e 3c62 3e44 6566 696e 6974 696f 6e3c ">Definition< │ │ │ +0001b220: 2f62 3e20 3c61 2068 7265 663d 222e 2e2f /b> MMFF94Param │ │ │ +0001b260: 6574 6572 732e 683a 3234 333c 2f61 3e3c eters.h:243< │ │ │ +0001b270: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    .
    BALL:: │ │ │ +0001b320: 4d4d 4646 3934 5374 7265 7463 6850 6172 MMFF94StretchPar │ │ │ +0001b330: 616d 6574 6572 733a 3a45 6d70 6972 6963 ameters::Empiric │ │ │ +0001b340: 616c 5374 7265 7463 684d 6170 3c2f 613e alStretchMap │ │ │ +0001b350: 3c2f 6469 763e 3c64 6976 2063 6c61 7373
    HashMa │ │ │ +0001b370: 7026 6c74 3b20 506f 7369 7469 6f6e 2c20 p< Position, │ │ │ +0001b380: 456d 7069 7269 6361 6c42 6f6e 6444 6174 EmpiricalBondDat │ │ │ +0001b390: 6120 2667 743b 2045 6d70 6972 6963 616c a > Empirical │ │ │ +0001b3a0: 5374 7265 7463 684d 6170 3c2f 6469 763e StretchMap
    │ │ │ +0001b3b0: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    Definition │ │ │ +0001b3d0: 3c2f 623e 203c 6120 6872 6566 3d22 2e2e MMFF94Para │ │ │ +0001b410: 6d65 7465 7273 2e68 3a32 3135 3c2f 613e meters.h:215 │ │ │ +0001b420: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ +0001b4d0: 3a4d 4d46 4639 3453 7472 6574 6368 5061 :MMFF94StretchPa │ │ │ +0001b4e0: 7261 6d65 7465 7273 3a3a 7061 7261 6d65 rameters::parame │ │ │ +0001b4f0: 7465 7273 5f3c 2f61 3e3c 2f64 6976 3e3c ters_
    < │ │ │ +0001b500: 6469 7620 636c 6173 733d 2274 7464 6563 div class="ttdec │ │ │ +0001b510: 6922 3e53 7472 6574 6368 4d61 7020 7061 i">StretchMap pa │ │ │ +0001b520: 7261 6d65 7465 7273 5f3c 2f64 6976 3e3c rameters_
    < │ │ │ +0001b530: 6469 7620 636c 6173 733d 2274 7464 6f63 div class="ttdoc │ │ │ +0001b540: 223e 7374 616e 6461 7264 2070 6172 616d ">standard param │ │ │ +0001b550: 6574 6572 733c 2f64 6976 3e3c 6469 7620 eters
    Definition │ │ │ +0001b580: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 MMFF94Parameter │ │ │ +0001b5c0: 732e 683a 3235 333c 2f61 3e3c 2f64 6976 s.h:253
    .
    < │ │ │ +0001b610: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6465 a href="../../de │ │ │ +0001b620: 2f64 3466 2f61 3035 3237 302e 6874 6d6c /d4f/a05270.html │ │ │ +0001b630: 223e 4241 4c4c 3a3a 4d4d 4646 3934 5374 ">BALL::MMFF94St │ │ │ +0001b640: 7265 7463 6850 6172 616d 6574 6572 733a retchParameters: │ │ │ +0001b650: 3a42 6f6e 6444 6174 613c 2f61 3e3c 2f64 :BondData
    Definit │ │ │ +0001b680: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion MMFF94P │ │ │ +0001b6c0: 6172 616d 6574 6572 732e 683a 3139 323c arameters.h:192< │ │ │ +0001b6d0: 2f61 3e3c 2f64 6976 3e3c 2f64 6976 3e0a /a>
    . │ │ │ +0001b6e0: 3c64 6976 2063 6c61 7373 3d22 7474 6322
    BA │ │ │ +0001b780: 4c4c 3a3a 4d4d 4646 3934 5374 7265 7463 LL::MMFF94Stretc │ │ │ +0001b790: 6850 6172 616d 6574 6572 733a 3a42 6f6e hParameters::Bon │ │ │ +0001b7a0: 6444 6174 613a 3a42 6f6e 6444 6174 613c dData::BondData< │ │ │ +0001b7b0: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    .
    double r0_norm │ │ │ +0001b8e0: 616c 3c2f 6469 763e 3c64 6976 2063 6c61 al
    .
    bool sbmb_e │ │ │ +0001ba60: 7869 7374 733c 2f64 6976 3e3c 6469 7620 xists
    Definition │ │ │ +0001ba90: 3c61 2068 7265 663d 222e 2e2f 2e2e 2f64 MMFF94Parameter │ │ │ +0001bad0: 732e 683a 3230 323c 2f61 3e3c 2f64 6976 s.h:202
    .
    BALL::MMFF │ │ │ +0001bb90: 3934 5374 7265 7463 6850 6172 616d 6574 94StretchParamet │ │ │ +0001bba0: 6572 733a 3a42 6f6e 6444 6174 613a 3a73 ers::BondData::s │ │ │ +0001bbb0: 7461 6e64 6172 645f 626f 6e64 5f65 7869 tandard_bond_exi │ │ │ +0001bbc0: 7374 733c 2f61 3e3c 2f64 6976 3e3c 6469 sts
    bool standard_b │ │ │ +0001bbf0: 6f6e 645f 6578 6973 7473 3c2f 6469 763e ond_exists
    │ │ │ +0001bc00: 3c64 6976 2063 6c61 7373 3d22 7474 6465
    Definition │ │ │ +0001bc20: 3c2f 623e 203c 6120 6872 6566 3d22 2e2e MMFF94Para │ │ │ +0001bc60: 6d65 7465 7273 2e68 3a31 3937 3c2f 613e meters.h:197 │ │ │ +0001bc70: 3c2f 6469 763e 3c2f 6469 763e 0a3c 6469
    .
    BALL: │ │ │ +0001bd20: 3a4d 4d46 4639 3453 7472 6574 6368 5061 :MMFF94StretchPa │ │ │ +0001bd30: 7261 6d65 7465 7273 3a3a 426f 6e64 4461 rameters::BondDa │ │ │ +0001bd40: 7461 3a3a 7230 5f73 626d 623c 2f61 3e3c ta::r0_sbmb< │ │ │ +0001bd50: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    double │ │ │ +0001bd70: 7230 5f73 626d 623c 2f64 6976 3e3c 6469 r0_sbmb
    │ │ │ +0001bd90: 3c62 3e44 6566 696e 6974 696f 6e3c 2f62 Definition MMFF94Paramet │ │ │ +0001bde0: 6572 732e 683a 3230 313c 2f61 3e3c 2f64 ers.h:201
    .
    < │ │ │ +0001be40: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ +0001be50: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::MM │ │ │ +0001bea0: 4646 3934 5374 7265 7463 6850 6172 616d FF94StretchParam │ │ │ +0001beb0: 6574 6572 733a 3a42 6f6e 6444 6174 613a eters::BondData: │ │ │ +0001bec0: 3a6b 625f 6e6f 726d 616c 3c2f 613e 3c2f :kb_normal
    double k │ │ │ +0001bef0: 625f 6e6f 726d 616c 3c2f 6469 763e 3c64 b_normal
    Definition MMFF94Parame │ │ │ +0001bf60: 7465 7273 2e68 3a31 3935 3c2f 613e 3c2f ters.h:195
    .
    │ │ │ +0001bfc0: 3c64 6976 2063 6c61 7373 3d22 7474 6e61
    BALL::M │ │ │ +0001c020: 4d46 4639 3453 7472 6574 6368 5061 7261 MFF94StretchPara │ │ │ +0001c030: 6d65 7465 7273 3a3a 426f 6e64 4461 7461 meters::BondData │ │ │ +0001c040: 3a3a 656d 7069 7269 6361 6c3c 2f61 3e3c ::empirical< │ │ │ +0001c050: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    bool em │ │ │ +0001c070: 7069 7269 6361 6c3c 2f64 6976 3e3c 6469 pirical
    │ │ │ +0001c090: 3c62 3e44 6566 696e 6974 696f 6e3c 2f62 Definition MMFF94Paramet │ │ │ +0001c0e0: 6572 732e 683a 3230 333c 2f61 3e3c 2f64 ers.h:203
    .
    < │ │ │ +0001c140: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ +0001c150: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::MM │ │ │ +0001c1a0: 4646 3934 5374 7265 7463 6850 6172 616d FF94StretchParam │ │ │ +0001c1b0: 6574 6572 733a 3a42 6f6e 6444 6174 613a eters::BondData: │ │ │ +0001c1c0: 3a6b 625f 7362 6d62 3c2f 613e 3c2f 6469 :kb_sbmb
    double kb_ │ │ │ +0001c1f0: 7362 6d62 3c2f 6469 763e 3c64 6976 2063 sbmb
    par │ │ │ +0001c210: 616d 6574 6572 7320 666f 7220 6f70 7469 ameters for opti │ │ │ +0001c220: 6e61 6c20 7369 6e67 6c65 2d62 6f6e 64e2 nal single-bond. │ │ │ +0001c230: 8093 6d75 6c74 6970 6c65 2062 6f6e 6420 ..multiple bond │ │ │ +0001c240: 6361 7365 7320 2873 6565 204d 4d46 4650 cases (see MMFFP │ │ │ +0001c250: 524f 502e 5041 5229 3c2f 6469 763e 3c64 ROP.PAR)
    Definition MMFF94Parame │ │ │ +0001c2c0: 7465 7273 2e68 3a32 3030 3c2f 613e 3c2f ters.h:200
    .
    BALL::MMFF9 │ │ │ +0001c340: 3453 7472 6574 6368 5061 7261 6d65 7465 4StretchParamete │ │ │ +0001c350: 7273 3a3a 456d 7069 7269 6361 6c42 6f6e rs::EmpiricalBon │ │ │ +0001c360: 6444 6174 613c 2f61 3e3c 2f64 6976 3e3c dData
    < │ │ │ +0001c370: 6469 7620 636c 6173 733d 2274 7464 6566 div class="ttdef │ │ │ +0001c380: 223e 3c62 3e44 6566 696e 6974 696f 6e3c ">Definition< │ │ │ +0001c390: 2f62 3e20 3c61 2068 7265 663d 222e 2e2f /b> MMFF94Param │ │ │ +0001c3d0: 6574 6572 732e 683a 3230 383c 2f61 3e3c eters.h:208< │ │ │ +0001c3e0: 2f64 6976 3e3c 2f64 6976 3e0a 3c64 6976 /div>
    ..
    BALL::MMFF │ │ │ +0001c610: 3934 5374 7265 7463 6850 6172 616d 6574 94StretchParamet │ │ │ +0001c620: 6572 733a 3a45 6d70 6972 6963 616c 426f ers::EmpiricalBo │ │ │ +0001c630: 6e64 4461 7461 3a3a 7230 3c2f 613e 3c2f ndData::r0
    double r │ │ │ +0001c660: 303c 2f64 6976 3e3c 6469 7620 636c 6173 0
    .
    .< │ │ │ +0001c7e0: 6469 7620 636c 6173 733d 2274 7463 2220 div class="ttc" │ │ │ +0001c7f0: 6964 3d22 6161 3035 3237 385f 6874 6d6c id="aa05278_html │ │ │ +0001c800: 5f61 6562 6131 3365 3465 3264 3661 3430 _aeba13e4e2d6a40 │ │ │ +0001c810: 6434 6234 6237 6539 3135 6361 6638 6661 d4b4b7e915caf8fa │ │ │ +0001c820: 3331 223e 3c64 6976 2063 6c61 7373 3d22 31">
    BAL │ │ │ +0001c880: 4c3a 3a4d 4d46 4639 3442 656e 6450 6172 L::MMFF94BendPar │ │ │ +0001c890: 616d 6574 6572 733a 3a42 656e 644d 6170 ameters::BendMap │ │ │ +0001c8a0: 3c2f 613e 3c2f 6469 763e 3c64 6976 2063
    Ha │ │ │ +0001c8c0: 7368 4d61 7026 6c74 3b20 506f 7369 7469 shMap< Positi │ │ │ +0001c8d0: 6f6e 2c20 7374 643a 3a70 6169 7226 6c74 on, std::pair< │ │ │ +0001c8e0: 3b20 646f 7562 6c65 2c20 646f 7562 6c65 ; double, double │ │ │ +0001c8f0: 2026 6774 3b20 2667 743b 2042 656e 644d > > BendM │ │ │ +0001c900: 6170 3c2f 6469 763e 3c64 6976 2063 6c61 ap
    Map w │ │ │ +0001c920: 6974 6820 7468 6520 666f 7263 6520 636f ith the force co │ │ │ +0001c930: 6e73 7461 6e74 2061 6e64 2072 6566 6572 nstant and refer │ │ │ +0001c940: 656e 6365 2061 6e67 6c65 2e3c 2f64 6976 ence angle.
    Definitio │ │ │ +0001c970: 6e3c 2f62 3e20 3c61 2068 7265 663d 222e n MMFF94Par │ │ │ +0001c9b0: 616d 6574 6572 732e 683a 3236 393c 2f61 ameters.h:269
    .
    BALL::MM │ │ │ +0001ca30: 4646 3934 5374 7265 7463 6842 656e 6450 FF94StretchBendP │ │ │ +0001ca40: 6172 616d 6574 6572 733c 2f61 3e3c 2f64 arameters
    Definit │ │ │ +0001ca70: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion MMFF94P │ │ │ +0001cab0: 6172 616d 6574 6572 732e 683a 3331 323c arameters.h:312< │ │ │ +0001cac0: 2f61 3e3c 2f64 6976 3e3c 2f64 6976 3e0a /a>
    . │ │ │ +0001cad0: 3c64 6976 2063 6c61 7373 3d22 7474 6322
    BA │ │ │ +0001cb70: 4c4c 3a3a 4d4d 4646 3934 5374 7265 7463 LL::MMFF94Stretc │ │ │ +0001cb80: 6842 656e 6450 6172 616d 6574 6572 733a hBendParameters: │ │ │ +0001cb90: 3a53 7472 6574 6368 4265 6e64 4d61 703c :StretchBendMap< │ │ │ +0001cba0: 2f61 3e3c 2f64 6976 3e3c 6469 7620 636c /a>
    Map with the fo │ │ │ +0001cc30: 7263 6520 636f 6e73 7461 6e74 2061 6e64 rce constant and │ │ │ +0001cc40: 2072 6566 6572 656e 6365 2061 6e67 6c65 reference angle │ │ │ +0001cc50: 2e3c 2f64 6976 3e3c 6469 7620 636c 6173 .
    .
    .
    │ │ │ +0001ce70: 4241 4c4c 3a3a 4d4d 4646 3934 546f 7273 BALL::MMFF94Tors │ │ │ +0001ce80: 696f 6e50 6172 616d 6574 6572 733a 3a54 ionParameters::T │ │ │ +0001ce90: 6f72 7369 6f6e 734d 6170 3c2f 613e 3c2f orsionsMap
    HashMap& │ │ │ +0001cec0: 6c74 3b20 5374 7269 6e67 2c20 7374 643a lt; String, std: │ │ │ +0001ced0: 3a76 6563 746f 7226 6c74 3b20 646f 7562 :vector< doub │ │ │ +0001cee0: 6c65 2026 6774 3b20 2667 743b 2054 6f72 le > > Tor │ │ │ +0001cef0: 7369 6f6e 734d 6170 3c2f 6469 763e 3c64 sionsMap
    Map with the fo │ │ │ +0001cf20: 7263 6520 636f 6e73 7461 6e74 2061 6e64 rce constant and │ │ │ +0001cf30: 2072 6566 6572 656e 6365 2061 6e67 6c65 reference angle │ │ │ +0001cf40: 2e3c 2f64 6976 3e3c 6469 7620 636c 6173 .
    .
    . │ │ │ +0001d0c0: 3c64 6976 2063 6c61 7373 3d22 7474 6322
    BA │ │ │ +0001d160: 4c4c 3a3a 4d4d 4646 3934 506c 616e 6550 LL::MMFF94PlaneP │ │ │ +0001d170: 6172 616d 6574 6572 733a 3a50 6c61 6e65 arameters::Plane │ │ │ +0001d180: 4d61 703c 2f61 3e3c 2f64 6976 3e3c 6469 Map
    HashMap< Str │ │ │ +0001d1b0: 696e 672c 2064 6f75 626c 6520 2667 743b ing, double > │ │ │ +0001d1c0: 2050 6c61 6e65 4d61 703c 2f64 6976 3e3c PlaneMap
    < │ │ │ +0001d1d0: 6469 7620 636c 6173 733d 2274 7464 6f63 div class="ttdoc │ │ │ +0001d1e0: 223e 4d61 7020 7769 7468 2074 6865 2066 ">Map with the f │ │ │ +0001d1f0: 6f72 6365 2063 6f6e 7374 616e 742e 3c2f orce constant.
    Defini │ │ │ +0001d220: 7469 6f6e 3c2f 623e 203c 6120 6872 6566 tion MMFF94 │ │ │ +0001d260: 5061 7261 6d65 7465 7273 2e68 3a34 3230 Parameters.h:420 │ │ │ +0001d270: 3c2f 613e 3c2f 6469 763e 3c2f 6469 763e
    │ │ │ +0001d280: 0a3c 6469 7620 636c 6173 733d 2274 7463 .
    BALL: │ │ │ +0001d2e0: 3a4d 4d46 4639 3456 4457 5061 7261 6d65 :MMFF94VDWParame │ │ │ +0001d2f0: 7465 7273 3c2f 613e 3c2f 6469 763e 3c64 ters
    Definition MMFF94Parame │ │ │ +0001d360: 7465 7273 2e68 3a34 3630 3c2f 613e 3c2f ters.h:460
    .
    BALL::MMFF9 │ │ │ +0001d3e0: 3456 4457 5061 7261 6d65 7465 7273 3a3a 4VDWParameters:: │ │ │ +0001d3f0: 5644 5745 6e74 7279 3c2f 613e 3c2f 6469 VDWEntry
    Definiti │ │ │ +0001d420: 6f6e 3c2f 623e 203c 6120 6872 6566 3d22 on MMFF94Pa │ │ │ +0001d460: 7261 6d65 7465 7273 2e68 3a34 3634 3c2f rameters.h:464
    .< │ │ │ +0001d480: 6469 7620 636c 6173 733d 2274 7463 2220 div class="ttc" │ │ │ +0001d490: 6964 3d22 6161 3035 3239 385f 6874 6d6c id="aa05298_html │ │ │ +0001d4a0: 5f61 3066 6134 3132 3865 3561 3730 6233 _a0fa4128e5a70b3 │ │ │ +0001d4b0: 3039 3364 3934 3862 3234 6163 6436 3362 093d948b24acd63b │ │ │ +0001d4c0: 6664 223e 3c64 6976 2063 6c61 7373 3d22 fd">
    BAL │ │ │ +0001d520: 4c3a 3a4d 4d46 4639 3456 4457 5061 7261 L::MMFF94VDWPara │ │ │ +0001d530: 6d65 7465 7273 3a3a 5644 5745 6e74 7279 meters::VDWEntry │ │ │ +0001d540: 3a3a 7661 6c69 643c 2f61 3e3c 2f64 6976 ::valid
    bool valid< │ │ │ +0001d570: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    Defin │ │ │ +0001d590: 6974 696f 6e3c 2f62 3e20 3c61 2068 7265 ition MMFF9 │ │ │ +0001d5d0: 3450 6172 616d 6574 6572 732e 683a 3437 4Parameters.h:47 │ │ │ +0001d5e0: 303c 2f61 3e3c 2f64 6976 3e3c 2f64 6976 0
    .
    double │ │ │ +0001d6e0: 2061 6c70 6861 5f69 3c2f 6469 763e 3c64 alpha_i
    Definition MMFF94Parame │ │ │ +0001d750: 7465 7273 2e68 3a34 3635 3c2f 613e 3c2f ters.h:465
    .
    │ │ │ +0001d7b0: 3c64 6976 2063 6c61 7373 3d22 7474 6e61
    BALL::M │ │ │ +0001d810: 4d46 4639 3456 4457 5061 7261 6d65 7465 MFF94VDWParamete │ │ │ +0001d820: 7273 3a3a 5644 5745 6e74 7279 3a3a 6169 rs::VDWEntry::ai │ │ │ +0001d830: 3c2f 613e 3c2f 6469 763e 3c64 6976 2063
    do │ │ │ +0001d850: 7562 6c65 2061 693c 2f64 6976 3e3c 6469 uble ai
    │ │ │ +0001d870: 3c62 3e44 6566 696e 6974 696f 6e3c 2f62 Definition MMFF94Paramet │ │ │ +0001d8c0: 6572 732e 683a 3436 373c 2f61 3e3c 2f64 ers.h:467
    .
    < │ │ │ +0001d920: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ +0001d930: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL::MM │ │ │ +0001d980: 4646 3934 5644 5750 6172 616d 6574 6572 FF94VDWParameter │ │ │ +0001d990: 733a 3a56 4457 456e 7472 793a 3a64 6f6e s::VDWEntry::don │ │ │ +0001d9a0: 6f72 5f61 6363 6570 746f 723c 2f61 3e3c or_acceptor< │ │ │ +0001d9b0: 2f64 6976 3e3c 6469 7620 636c 6173 733d /div>
    short d │ │ │ +0001d9d0: 6f6e 6f72 5f61 6363 6570 746f 723c 2f64 onor_acceptor
    Definit │ │ │ +0001da00: 696f 6e3c 2f62 3e20 3c61 2068 7265 663d ion MMFF94P │ │ │ +0001da40: 6172 616d 6574 6572 732e 683a 3436 393c arameters.h:469< │ │ │ +0001da50: 2f61 3e3c 2f64 6976 3e3c 2f64 6976 3e0a /a>
    . │ │ │ +0001da60: 3c64 6976 2063 6c61 7373 3d22 7474 6322
    BA │ │ │ +0001db00: 4c4c 3a3a 4d4d 4646 3934 5644 5750 6172 LL::MMFF94VDWPar │ │ │ +0001db10: 616d 6574 6572 733a 3a56 4457 456e 7472 ameters::VDWEntr │ │ │ +0001db20: 793a 3a67 693c 2f61 3e3c 2f64 6976 3e3c y::gi
    < │ │ │ +0001db30: 6469 7620 636c 6173 733d 2274 7464 6563 div class="ttdec │ │ │ +0001db40: 6922 3e64 6f75 626c 6520 6769 3c2f 6469 i">double gi
    Definiti │ │ │ +0001db70: 6f6e 3c2f 623e 203c 6120 6872 6566 3d22 on MMFF94Pa │ │ │ +0001dbb0: 7261 6d65 7465 7273 2e68 3a34 3638 3c2f rameters.h:468
    .< │ │ │ +0001dbd0: 6469 7620 636c 6173 733d 2274 7463 2220 div class="ttc" │ │ │ +0001dbe0: 6964 3d22 6161 3035 3239 385f 6874 6d6c id="aa05298_html │ │ │ +0001dbf0: 5f61 6632 6137 3466 3733 6661 3032 3137 _af2a74f73fa0217 │ │ │ +0001dc00: 3662 6130 3866 6261 6339 3765 6265 6365 6ba08fbac97ebece │ │ │ +0001dc10: 3132 223e 3c64 6976 2063 6c61 7373 3d22 12">
    BAL │ │ │ +0001dc70: 4c3a 3a4d 4d46 4639 3456 4457 5061 7261 L::MMFF94VDWPara │ │ │ +0001dc80: 6d65 7465 7273 3a3a 5644 5745 6e74 7279 meters::VDWEntry │ │ │ +0001dc90: 3a3a 6e69 3c2f 613e 3c2f 6469 763e 3c64 ::ni
    double ni
    Definitio │ │ │ +0001dce0: 6e3c 2f62 3e20 3c61 2068 7265 663d 222e n MMFF94Par │ │ │ +0001dd20: 616d 6574 6572 732e 683a 3436 363c 2f61 ameters.h:466
    .
    BALL::MM │ │ │ +0001dda0: 4646 3934 4553 5061 7261 6d65 7465 7273 FF94ESParameters │ │ │ +0001ddb0: 3c2f 613e 3c2f 6469 763e 3c64 6976 2063
    │ │ │ +0001ddd0: 4465 6669 6e69 7469 6f6e 3c2f 623e 203c Definition < │ │ │ +0001dde0: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6430 a href="../../d0 │ │ │ +0001ddf0: 2f64 3739 2f61 3031 3736 365f 736f 7572 /d79/a01766_sour │ │ │ +0001de00: 6365 2e68 746d 6c23 6c30 3035 3235 223e ce.html#l00525"> │ │ │ +0001de10: 4d4d 4646 3934 5061 7261 6d65 7465 7273 MMFF94Parameters │ │ │ +0001de20: 2e68 3a35 3237 3c2f 613e 3c2f 6469 763e .h:527
    │ │ │ +0001de30: 3c2f 6469 763e 0a3c 6469 7620 636c 6173
    .
    │ │ │ +0001deb0: 0a3c 6469 7620 636c 6173 733d 2274 7463 .
    BALL_ │ │ │ +0001df10: 5349 5a45 5f54 5950 453c 2f61 3e3c 2f64 SIZE_TYPE
    .
    < │ │ │ +0001df70: 6469 7620 636c 6173 733d 2274 746e 616d div class="ttnam │ │ │ +0001df80: 6522 3e3c 6120 6872 6566 3d22 2e2e 2f2e e">BALL_EXP │ │ │ +0001dfd0: 4f52 543c 2f61 3e3c 2f64 6976 3e3c 6469 ORT
    #define BALL_EX │ │ │ +0001e000: 504f 5254 3c2f 6469 763e 3c64 6976 2063 PORT
    │ │ │ +0001e020: 4465 6669 6e69 7469 6f6e 3c2f 623e 203c Definition < │ │ │ +0001e030: 6120 6872 6566 3d22 2e2e 2f2e 2e2f 6465 a href="../../de │ │ │ +0001e040: 2f64 3334 2f61 3230 3334 345f 736f 7572 /d34/a20344_sour │ │ │ +0001e050: 6365 2e68 746d 6c23 6c30 3030 3530 223e ce.html#l00050"> │ │ │ +0001e060: 434f 4d4d 4f4e 2f67 6c6f 6261 6c2e 683a COMMON/global.h: │ │ │ +0001e070: 3530 3c2f 613e 3c2f 6469 763e 3c2f 6469 50
    .
    │ │ │ +0001e0a0: 3c21 2d2d 2063 6f6e 7465 6e74 7320 2d2d .
    │ │ │ +0001e100: 0a47 656e 6572 6174 6564 2062 7926 2331 .Generated by │ │ │ +0001e110: 3630 3b3c 6120 6872 6566 3d22 6874 7470 60; │ │ │ +0001e140: 3c69 6d67 2063 6c61 7373 3d22 666f 6f74 doxygen │ │ │ +0001e190: 222f 3e3c 2f61 3e20 312e 392e 380a 3c2f 1.9.8.
    │ │ │ +0001e1b0: 0a3c 2f62 6f64 793e 0a3c 2f68 746d 6c3e .. │ │ │ +0001e1c0: 0a . │ │ │ ├── html2text {} │ │ │ │ @@ -1,295 +1,709 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _F_O_R_M_A_T │ │ │ │ -PDBRecords.h │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _M_M_F_F_9_4 │ │ │ │ +MMFF94Parameters.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_FORMAT_PDBRECORDS_H │ │ │ │ -6#define BALL_FORMAT_PDBRECORDS_H │ │ │ │ -7 │ │ │ │ -8#include │ │ │ │ -9#include │ │ │ │ -10 │ │ │ │ -11#ifndef BALL_DATATYPE_HASHMAP_H │ │ │ │ -12# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ -13#endif │ │ │ │ -14 │ │ │ │ -15#ifndef BALL_CONCEPT_PERSISTENCEMANAGER_H │ │ │ │ -16# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h> │ │ │ │ -17#endif │ │ │ │ -18 │ │ │ │ -19namespace _B_A_L_L │ │ │ │ -20{ │ │ │ │ -21 │ │ │ │ -_3_1 class _B_A_L_L___E_X_P_O_R_T _P_D_B_R_e_c_o_r_d_s │ │ │ │ -32 : public _P_e_r_s_i_s_t_e_n_t_O_b_j_e_c_t │ │ │ │ -33 { │ │ │ │ -34 public: │ │ │ │ -35 │ │ │ │ -36 /* STL compatibility typedefs */ │ │ │ │ -_3_7 typedef std::vector::iterator _I_t_e_r_a_t_o_r; │ │ │ │ -_3_8 typedef std::vector::iterator _i_t_e_r_a_t_o_r; │ │ │ │ -_3_9 typedef std::vector::const_iterator _C_o_n_s_t_I_t_e_r_a_t_o_r; │ │ │ │ -_4_0 typedef std::vector::const_iterator _c_o_n_s_t___i_t_e_r_a_t_o_r; │ │ │ │ -_4_1 typedef std::vector::reverse_iterator _R_e_v_e_r_s_e_I_t_e_r_a_t_o_r; │ │ │ │ -_4_2 typedef std::vector::reverse_iterator _r_e_v_e_r_s_e___i_t_e_r_a_t_o_r; │ │ │ │ -_4_3 typedef std::vector::const_reverse_iterator _C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r; │ │ │ │ -_4_4 typedef std::vector::const_reverse_iterator _c_o_n_s_t___r_e_v_e_r_s_e___i_t_e_r_a_t_o_r; │ │ │ │ -_4_5 typedef _S_t_r_i_n_g _v_a_l_u_e___t_y_p_e; │ │ │ │ -_4_6 typedef _S_t_r_i_n_g _V_a_l_u_e_T_y_p_e; │ │ │ │ -_4_7 typedef _S_t_r_i_n_g& _r_e_f_e_r_e_n_c_e; │ │ │ │ -_4_8 typedef _S_t_r_i_n_g& _R_e_f_e_r_e_n_c_e; │ │ │ │ -_4_9 typedef const _S_t_r_i_n_g& _c_o_n_s_t___r_e_f_e_r_e_n_c_e; │ │ │ │ -_5_0 typedef const _S_t_r_i_n_g& _C_o_n_s_t_R_e_f_e_r_e_n_c_e; │ │ │ │ -_5_1 typedef std::vector::difference_type _d_i_f_f_e_r_e_n_c_e___t_y_p_e; │ │ │ │ -_5_2 typedef std::vector::difference_type _D_i_f_f_e_r_e_n_c_e_T_y_p_e; │ │ │ │ -_5_3 typedef std::vector::size_type _s_i_z_e___t_y_p_e; │ │ │ │ -_5_4 typedef std::vector::size_type _S_i_z_e_T_y_p_e; │ │ │ │ -55 │ │ │ │ -56 _B_A_L_L___C_R_E_A_T_E(_P_D_B_R_e_c_o_r_d_s) │ │ │ │ -57 │ │ │ │ +4// $Id: MMFF94Parameters.h,v 1.1.8.1 2007/03/25 21:25:17 oliver Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7// Molecular Mechanics: MMFF94 force field class │ │ │ │ +8 │ │ │ │ +9#ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H │ │ │ │ +10#define BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H │ │ │ │ +11 │ │ │ │ +12#ifndef BALL_COMMON_H │ │ │ │ +13# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifndef BALL_DATATYPE_HASHMAP_H │ │ │ │ +17# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20namespace _B_A_L_L │ │ │ │ +21{ │ │ │ │ +22 │ │ │ │ +23 class _A_t_o_m; │ │ │ │ +24 class Parameters; │ │ │ │ +25 │ │ │ │ +_2_6 _P_o_s_i_t_i_o_n _g_e_t_M_M_F_F_9_4_I_n_d_e_x(_P_o_s_i_t_i_o_n atom_type1, _P_o_s_i_t_i_o_n atom_type2); │ │ │ │ +27 │ │ │ │ +29 extern _S_i_z_e _M_M_F_F_9_4___n_u_m_b_e_r___a_t_o_m___t_y_p_e_s; │ │ │ │ +30 │ │ │ │ +31 class _M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s; │ │ │ │ +32 │ │ │ │ +_3_3#define MMFF94_INVALID_VALUE 99.0 │ │ │ │ +34 │ │ │ │ +36 │ │ │ │ +_3_9 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +40 { │ │ │ │ +41 public: │ │ │ │ +42 │ │ │ │ +43 _B_A_L_L___C_R_E_A_T_E(_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e) │ │ │ │ +44 │ │ │ │ +45 │ │ │ │ +_4_6 _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e(); │ │ │ │ +47 │ │ │ │ +_4_9 virtual ~_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e() {}; │ │ │ │ +50 │ │ │ │ +_5_2 const _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e& operator = (const _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e&) │ │ │ │ +53 {return *this;}; │ │ │ │ +54 │ │ │ │ +_5_6 virtual void _c_l_e_a_r() │ │ │ │ +57 ; │ │ │ │ 58 │ │ │ │ -_6_1 _P_D_B_R_e_c_o_r_d_s() ; │ │ │ │ -_6_3 _P_D_B_R_e_c_o_r_d_s(const _P_D_B_R_e_c_o_r_d_s& pdbi) ; │ │ │ │ -_6_5 virtual ~_P_D_B_R_e_c_o_r_d_s() ; │ │ │ │ +_6_0 bool _i_s_I_n_i_t_i_a_l_i_z_e_d() { return is_initialized_;} │ │ │ │ +61 │ │ │ │ +_6_3 bool _r_e_a_d_P_a_r_a_m_e_t_e_r_s(_P_a_r_a_m_e_t_e_r_s& p, const _S_t_r_i_n_g& section); │ │ │ │ +64 │ │ │ │ +_6_6 void _s_e_t_E_q_u_i_v_a_l_e_n_c_e_s(const _M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s& equi) { equiv_ = │ │ │ │ +&equi;} │ │ │ │ 67 │ │ │ │ -_7_2 _P_D_B_R_e_c_o_r_d_s& operator = (const _P_D_B_R_e_c_o_r_d_s& rhs); │ │ │ │ -74 │ │ │ │ -_8_1 _C_o_n_s_t_I_t_e_r_a_t_o_r begin() const { return records_._b_e_g_i_n(); } │ │ │ │ -_8_3 _I_t_e_r_a_t_o_r _b_e_g_i_n() { return records_.begin(); } │ │ │ │ -_8_5 _C_o_n_s_t_I_t_e_r_a_t_o_r _e_n_d() const { return records_.end(); } │ │ │ │ -_8_7 _I_t_e_r_a_t_o_r _e_n_d() { return records_.end(); } │ │ │ │ -_8_9 _C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r _r_b_e_g_i_n() const { return records_.rbegin(); } │ │ │ │ -_9_1 _R_e_v_e_r_s_e_I_t_e_r_a_t_o_r _r_b_e_g_i_n() { return records_.rbegin(); } │ │ │ │ -_9_3 _C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r _r_e_n_d() const { return records_.rend(); } │ │ │ │ -_9_5 _R_e_v_e_r_s_e_I_t_e_r_a_t_o_r _r_e_n_d() { return records_.rend(); } │ │ │ │ -_9_7 _S_i_z_e_T_y_p_e _s_i_z_e() const { return records_.size(); } │ │ │ │ -_9_9 _S_i_z_e_T_y_p_e _m_a_x___s_i_z_e() const { return records_.max_size(); } │ │ │ │ -_1_0_1 _S_i_z_e_T_y_p_e _c_a_p_a_c_i_t_y() const { return records_.capacity(); } │ │ │ │ -_1_0_3 bool _e_m_p_t_y() const { return records_.empty(); } │ │ │ │ -_1_0_5 void _c_l_e_a_r() { records_.clear(); } │ │ │ │ -_1_0_7 void _r_e_s_i_z_e(_S_i_z_e_T_y_p_e sz, _V_a_l_u_e_T_y_p_e c = _V_a_l_u_e_T_y_p_e()) { records_.resize(sz, │ │ │ │ -c); } │ │ │ │ -_1_0_9 _R_e_f_e_r_e_n_c_e _f_r_o_n_t() { return records_._f_r_o_n_t(); } │ │ │ │ -_1_1_1 _C_o_n_s_t_R_e_f_e_r_e_n_c_e _f_r_o_n_t() const { return records_._f_r_o_n_t(); } │ │ │ │ -_1_1_3 _R_e_f_e_r_e_n_c_e _b_a_c_k() { return records_._b_a_c_k(); } │ │ │ │ -_1_1_5 _C_o_n_s_t_R_e_f_e_r_e_n_c_e _b_a_c_k() const { return records_._b_a_c_k(); } │ │ │ │ -_1_1_7 void _p_u_s_h___b_a_c_k(_C_o_n_s_t_R_e_f_e_r_e_n_c_e x) { records_.push_back(x); } │ │ │ │ -_1_1_9 void _i_n_s_e_r_t(_I_t_e_r_a_t_o_r pos, _C_o_n_s_t_R_e_f_e_r_e_n_c_e value) { records_.insert(pos, │ │ │ │ -value); } │ │ │ │ -_1_2_1 void _i_n_s_e_r_t(_I_t_e_r_a_t_o_r pos, _S_i_z_e_T_y_p_e n, _C_o_n_s_t_R_e_f_e_r_e_n_c_e value) │ │ │ │ -{ records_.insert(pos, n, value); } │ │ │ │ -_1_2_3 void _p_o_p___b_a_c_k() { records_.pop_back(); } │ │ │ │ -_1_2_5 _I_t_e_r_a_t_o_r _e_r_a_s_e(_I_t_e_r_a_t_o_r pos) { return records_.erase(pos); } │ │ │ │ -_1_2_7 _I_t_e_r_a_t_o_r _e_r_a_s_e(_I_t_e_r_a_t_o_r first, _I_t_e_r_a_t_o_r last) { return records_.erase │ │ │ │ -(first, last); } │ │ │ │ -_1_2_9 bool operator == (const _P_D_B_R_e_c_o_r_d_s& rhs) const { return records_ == │ │ │ │ -rhs._r_e_c_o_r_d_s__; } │ │ │ │ -_1_3_1 bool operator != (const _P_D_B_R_e_c_o_r_d_s& rhs) const { return records_ != │ │ │ │ -rhs._r_e_c_o_r_d_s__; } │ │ │ │ -_1_3_3 bool operator < (const _P_D_B_R_e_c_o_r_d_s& rhs) const { return records_ < │ │ │ │ -rhs._r_e_c_o_r_d_s__; } │ │ │ │ -_1_3_5 bool operator > (const _P_D_B_R_e_c_o_r_d_s& rhs) const { return records_ > │ │ │ │ -rhs._r_e_c_o_r_d_s__; } │ │ │ │ -_1_3_7 bool operator <= (const _P_D_B_R_e_c_o_r_d_s& rhs) const { return records_ <= │ │ │ │ -rhs._r_e_c_o_r_d_s__; } │ │ │ │ -_1_3_9 bool operator >= (const _P_D_B_R_e_c_o_r_d_s& rhs) const { return records_ >= │ │ │ │ -rhs._r_e_c_o_r_d_s__; } │ │ │ │ -_1_4_1 void _s_w_a_p(_P_D_B_R_e_c_o_r_d_s& rhs) { records_.swap(rhs._r_e_c_o_r_d_s__); } │ │ │ │ -_1_4_3 _C_o_n_s_t_R_e_f_e_r_e_n_c_e operator [] (_S_i_z_e_T_y_p_e n) const { return records_[n]; } │ │ │ │ -_1_4_5 _R_e_f_e_r_e_n_c_e operator [] (_S_i_z_e_T_y_p_e n) { return records_[n]; } │ │ │ │ -_1_4_9 _C_o_n_s_t_R_e_f_e_r_e_n_c_e _a_t(_S_i_z_e_T_y_p_e n) const { return records_._a_t(n); } │ │ │ │ -_1_5_3 _R_e_f_e_r_e_n_c_e _a_t(_S_i_z_e_T_y_p_e n) { return records_._a_t(n); } │ │ │ │ -155 │ │ │ │ -159 │ │ │ │ -162 //void write(PersistenceManager& pm) const; │ │ │ │ -_1_6_3 void _p_e_r_s_i_s_t_e_n_t_W_r_i_t_e(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm, const char* name) const; │ │ │ │ +68 protected: │ │ │ │ +69 │ │ │ │ +_7_0 virtual bool _s_e_t_u_p__(const std::vector >&) { return │ │ │ │ +true;}; │ │ │ │ +71 │ │ │ │ +_7_2 bool _i_s___i_n_i_t_i_a_l_i_z_e_d__; │ │ │ │ +73 │ │ │ │ +74 // nr of needed fields in parameter files │ │ │ │ +_7_5 _S_i_z_e _n_u_m_b_e_r___e_x_p_e_c_t_e_d___f_i_e_l_d_s__; │ │ │ │ +_7_6 const _M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s* _e_q_u_i_v__; │ │ │ │ +77 }; │ │ │ │ +78 │ │ │ │ +79 │ │ │ │ +_8_3 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s: │ │ │ │ +84 public _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +85 { │ │ │ │ +86 public: │ │ │ │ +87 │ │ │ │ +_8_9 _M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s(); │ │ │ │ +90 │ │ │ │ +_9_2 _M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s(const _M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s& to_copy); │ │ │ │ +93 │ │ │ │ +_9_5 _~_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s(); │ │ │ │ +96 │ │ │ │ +_9_8 void _c_l_e_a_r() │ │ │ │ +99 ; │ │ │ │ +100 │ │ │ │ +_1_0_5 _I_n_d_e_x _g_e_t_E_q_u_i_v_a_l_e_n_c_e(_P_o_s_i_t_i_o_n original, _P_o_s_i_t_i_o_n number) const; │ │ │ │ +106 │ │ │ │ +107 protected: │ │ │ │ +108 │ │ │ │ +_1_0_9 virtual bool _s_e_t_u_p__(const std::vector >&); │ │ │ │ +_1_1_0 std::vector > _e_q_u_i_v_a_l_e_n_c_e_s__; │ │ │ │ +_1_1_1 std::vector _n_a_m_e_s__; │ │ │ │ +_1_1_2 std::vector _e_x_i_s_t_s__; │ │ │ │ +113 }; │ │ │ │ +114 │ │ │ │ +115 │ │ │ │ +_1_1_7 struct _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_A_t_o_m_T_y_p_e │ │ │ │ +118 { │ │ │ │ +_1_2_0 _M_M_F_F_9_4_A_t_o_m_T_y_p_e(); │ │ │ │ +121 │ │ │ │ +_1_2_3 _P_o_s_i_t_i_o_n _a_s_p_e_c; │ │ │ │ +124 │ │ │ │ +_1_2_6 _P_o_s_i_t_i_o_n _c_r_d; │ │ │ │ +127 │ │ │ │ +_1_2_9 _P_o_s_i_t_i_o_n _v_a_l; │ │ │ │ +130 │ │ │ │ +_1_3_2 bool _p_i_l_p; │ │ │ │ +133 │ │ │ │ +_1_3_7 _P_o_s_i_t_i_o_n _m_l_t_b; │ │ │ │ +138 │ │ │ │ +_1_4_0 bool _a_r_o_m; │ │ │ │ +141 │ │ │ │ +_1_4_3 bool _l_i_n; │ │ │ │ +144 │ │ │ │ +_1_4_6 bool _s_b_m_b; │ │ │ │ +147 │ │ │ │ +_1_4_9 bool _v_a_l_i_d; │ │ │ │ +150 }; │ │ │ │ +151 │ │ │ │ +152 │ │ │ │ +154 │ │ │ │ +_1_5_7 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_A_t_o_m_T_y_p_e_s: │ │ │ │ +158 public _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +159 { │ │ │ │ +160 public: │ │ │ │ +161 │ │ │ │ +_1_6_3 _M_M_F_F_9_4_A_t_o_m_T_y_p_e_s(); │ │ │ │ 164 │ │ │ │ -167 //bool read(PersistenceManager& pm); │ │ │ │ -_1_6_8 void _p_e_r_s_i_s_t_e_n_t_R_e_a_d(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm); │ │ │ │ -169 │ │ │ │ -171 │ │ │ │ -172 protected: │ │ │ │ -_1_7_4 std::vector _r_e_c_o_r_d_s__; │ │ │ │ -175 }; │ │ │ │ -176 │ │ │ │ -177} // namespace BALL │ │ │ │ -178 │ │ │ │ -179#endif // BALL_FORMAT_PDBRECORDS_H │ │ │ │ +_1_6_6 _M_M_F_F_9_4_A_t_o_m_T_y_p_e_s(const _M_M_F_F_9_4_A_t_o_m_T_y_p_e_s& to_copy); │ │ │ │ +167 │ │ │ │ +_1_6_9 _~_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s() {}; │ │ │ │ +170 │ │ │ │ +_1_7_2 const std::vector& _g_e_t_A_t_o_m_T_y_p_e_s() const { return data_;} │ │ │ │ +173 │ │ │ │ +174 protected: │ │ │ │ +175 │ │ │ │ +_1_7_6 virtual bool _s_e_t_u_p__(const std::vector >&); │ │ │ │ +_1_7_7 std::vector _d_a_t_a__; │ │ │ │ +178 }; │ │ │ │ +179 │ │ │ │ +181 │ │ │ │ +_1_8_5 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s: │ │ │ │ +186 public _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +187 { │ │ │ │ +188 public: │ │ │ │ +189 │ │ │ │ +_1_9_1 struct _B_o_n_d_D_a_t_a │ │ │ │ +192 { │ │ │ │ +_1_9_3 _B_o_n_d_D_a_t_a(); │ │ │ │ +194 │ │ │ │ +_1_9_5 double _k_b___n_o_r_m_a_l; │ │ │ │ +_1_9_6 double _r_0___n_o_r_m_a_l; │ │ │ │ +_1_9_7 bool _s_t_a_n_d_a_r_d___b_o_n_d___e_x_i_s_t_s; │ │ │ │ +198 │ │ │ │ +_2_0_0 double _k_b___s_b_m_b; │ │ │ │ +_2_0_1 double _r_0___s_b_m_b; │ │ │ │ +_2_0_2 bool _s_b_m_b___e_x_i_s_t_s; │ │ │ │ +_2_0_3 bool _e_m_p_i_r_i_c_a_l; │ │ │ │ +204 }; │ │ │ │ +205 │ │ │ │ +_2_0_7 struct _E_m_p_i_r_i_c_a_l_B_o_n_d_D_a_t_a │ │ │ │ +208 { │ │ │ │ +_2_0_9 double _k_b; │ │ │ │ +_2_1_0 double _r_0; │ │ │ │ +211 }; │ │ │ │ +212 │ │ │ │ +_2_1_4 typedef _H_a_s_h_M_a_p_<_P_o_s_i_t_i_o_n_,_ _B_o_n_d_D_a_t_a_> _S_t_r_e_t_c_h_M_a_p; │ │ │ │ +_2_1_5 typedef _H_a_s_h_M_a_p_<_P_o_s_i_t_i_o_n_,_ _E_m_p_i_r_i_c_a_l_B_o_n_d_D_a_t_a_> _E_m_p_i_r_i_c_a_l_S_t_r_e_t_c_h_M_a_p; │ │ │ │ +216 │ │ │ │ +217 _B_A_L_L___C_R_E_A_T_E(_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s) │ │ │ │ +218 │ │ │ │ +219 │ │ │ │ +_2_2_0 _M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +221 │ │ │ │ +_2_2_3 virtual ~_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +224 │ │ │ │ +_2_2_6 const _M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s& operator = (const _M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s& │ │ │ │ +param) │ │ │ │ +227 ; │ │ │ │ +228 │ │ │ │ +_2_3_0 virtual void clear() │ │ │ │ +231 ; │ │ │ │ +232 │ │ │ │ +_2_3_4 bool assignParameters(_P_o_s_i_t_i_o_n type1, _P_o_s_i_t_i_o_n type2, _B_o_n_d_D_a_t_a& data) │ │ │ │ +const; │ │ │ │ +235 │ │ │ │ +_2_3_7 bool readEmpiricalParameters(_P_a_r_a_m_e_t_e_r_s& p, const _S_t_r_i_n_g& section); │ │ │ │ +238 │ │ │ │ +_2_4_0 const _S_t_r_e_t_c_h_M_a_p& getBondParameters() const { return parameters_;} │ │ │ │ +241 │ │ │ │ +_2_4_3 const _E_m_p_i_r_i_c_a_l_S_t_r_e_t_c_h_M_a_p& _g_e_t_E_m_p_i_r_i_c_a_l_P_a_r_a_m_e_t_e_r_s() const { return │ │ │ │ +empirical_parameters_;} │ │ │ │ +244 │ │ │ │ +_2_4_5 static double radii[]; │ │ │ │ +_2_4_6 static double electronegatives[]; │ │ │ │ +247 │ │ │ │ +248 protected: │ │ │ │ +249 │ │ │ │ +_2_5_0 virtual bool _s_e_t_u_p__(const std::vector >&); │ │ │ │ +251 │ │ │ │ +_2_5_3 _S_t_r_e_t_c_h_M_a_p _p_a_r_a_m_e_t_e_r_s__; │ │ │ │ +_2_5_4 mutable _S_t_r_e_t_c_h_M_a_p _b_u_f_f_e_r_e_d___p_a_r_a_m_e_t_e_r_s__; │ │ │ │ +_2_5_5 _E_m_p_i_r_i_c_a_l_S_t_r_e_t_c_h_M_a_p _e_m_p_i_r_i_c_a_l___p_a_r_a_m_e_t_e_r_s__; │ │ │ │ +256 }; │ │ │ │ +257 │ │ │ │ +259 │ │ │ │ +_2_6_3 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +264 : public _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +265 { │ │ │ │ +266 public: │ │ │ │ +267 │ │ │ │ +_2_6_9 typedef _H_a_s_h_M_a_p_<_P_o_s_i_t_i_o_n_,_ _s_t_d_:_:_p_a_i_r_<_d_o_u_b_l_e_,_ _d_o_u_b_l_e_> > _B_e_n_d_M_a_p; │ │ │ │ +270 │ │ │ │ +271 _B_A_L_L___C_R_E_A_T_E(_M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s) │ │ │ │ +272 │ │ │ │ +273 │ │ │ │ +_2_7_4 _M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +275 │ │ │ │ +_2_7_7 virtual ~_M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +278 │ │ │ │ +_2_8_0 const _M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s& operator = (const _M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s& param) │ │ │ │ +281 ; │ │ │ │ +282 │ │ │ │ +_2_8_4 virtual void clear() │ │ │ │ +285 ; │ │ │ │ +286 │ │ │ │ +_2_8_8 bool assignParameters(_P_o_s_i_t_i_o_n bend_type, │ │ │ │ +289 _P_o_s_i_t_i_o_n atom_type1, _P_o_s_i_t_i_o_n atom_type2, _P_o_s_i_t_i_o_n atom_type3, │ │ │ │ +290 double& ka, double& angle) const; │ │ │ │ +291 │ │ │ │ +292 protected: │ │ │ │ +293 │ │ │ │ +_2_9_4 virtual bool setup_(const _s_t_d::vector<_s_t_d::vector<_S_t_r_i_n_g> >&); │ │ │ │ +295 │ │ │ │ +_2_9_6 _P_o_s_i_t_i_o_n getIndex_(_P_o_s_i_t_i_o_n bend_type, _P_o_s_i_t_i_o_n atom_type1, _P_o_s_i_t_i_o_n │ │ │ │ +atom_type2, _P_o_s_i_t_i_o_n atom_type3) const; │ │ │ │ +297 │ │ │ │ +_2_9_9 _B_e_n_d_M_a_p parameters_; │ │ │ │ +_3_0_0 mutable _B_e_n_d_M_a_p buffered_parameters_; │ │ │ │ +301 }; │ │ │ │ +302 │ │ │ │ +303 │ │ │ │ +306 │ │ │ │ +_3_1_0 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +311 : public _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +312 { │ │ │ │ +313 public: │ │ │ │ +314 │ │ │ │ +_3_1_6 typedef _H_a_s_h_M_a_p_<_P_o_s_i_t_i_o_n_,_ _s_t_d_:_:_p_a_i_r_<_d_o_u_b_l_e_,_ _d_o_u_b_l_e_> > _S_t_r_e_t_c_h_B_e_n_d_M_a_p; │ │ │ │ +317 │ │ │ │ +318 _B_A_L_L___C_R_E_A_T_E(_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s) │ │ │ │ +319 │ │ │ │ +320 │ │ │ │ +_3_2_1 _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +322 │ │ │ │ +_3_2_4 virtual ~_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +325 │ │ │ │ +_3_2_7 const _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s& operator = (const │ │ │ │ +_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s& param) │ │ │ │ +328 ; │ │ │ │ +329 │ │ │ │ +_3_3_1 virtual void clear() │ │ │ │ +332 ; │ │ │ │ +333 │ │ │ │ +_3_3_5 bool assignParameters(_P_o_s_i_t_i_o_n stretch_bend_type, const _A_t_o_m& atom1, const │ │ │ │ +_A_t_o_m& atom2, const _A_t_o_m& atom3, │ │ │ │ +336 double& kba_ijk, double& kba_kji) const; │ │ │ │ +337 │ │ │ │ +_3_4_1 bool readEmpiricalParameters(_P_a_r_a_m_e_t_e_r_s& p, const _S_t_r_i_n_g& section); │ │ │ │ +342 │ │ │ │ +344 │ │ │ │ +345 protected: │ │ │ │ +346 │ │ │ │ +_3_4_7 virtual bool setup_(const _s_t_d::vector<_s_t_d::vector<_S_t_r_i_n_g> >&); │ │ │ │ +348 │ │ │ │ +_3_4_9 _P_o_s_i_t_i_o_n getIndex_(_P_o_s_i_t_i_o_n stretch_bend_type, │ │ │ │ +350 _P_o_s_i_t_i_o_n atom_type1, _P_o_s_i_t_i_o_n atom_type2, _P_o_s_i_t_i_o_n atom_type3) const; │ │ │ │ +351 │ │ │ │ +_3_5_2 _P_o_s_i_t_i_o_n getIndexByRow_(_P_o_s_i_t_i_o_n r1, _P_o_s_i_t_i_o_n r2, _P_o_s_i_t_i_o_n r3) const; │ │ │ │ +353 │ │ │ │ +_3_5_5 _S_t_r_e_t_c_h_B_e_n_d_M_a_p parameters_; │ │ │ │ +_3_5_6 mutable _S_t_r_e_t_c_h_B_e_n_d_M_a_p buffered_parameters_; │ │ │ │ +_3_5_7 _S_t_r_e_t_c_h_B_e_n_d_M_a_p parameters_by_row_; │ │ │ │ +358 }; │ │ │ │ +359 │ │ │ │ +362 │ │ │ │ +_3_6_6 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_T_o_r_s_i_o_n_P_a_r_a_m_e_t_e_r_s │ │ │ │ +367 : public _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +368 { │ │ │ │ +369 public: │ │ │ │ +370 │ │ │ │ +_3_7_2 typedef _H_a_s_h_M_a_p_<_S_t_r_i_n_g_,_ _s_t_d_:_:_v_e_c_t_o_r_<_d_o_u_b_l_e_> > _T_o_r_s_i_o_n_s_M_a_p; │ │ │ │ +373 │ │ │ │ +374 _B_A_L_L___C_R_E_A_T_E(_M_M_F_F_9_4_T_o_r_s_i_o_n_P_a_r_a_m_e_t_e_r_s) │ │ │ │ +375 │ │ │ │ +376 │ │ │ │ +_3_7_7 _M_M_F_F_9_4_T_o_r_s_i_o_n_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +378 │ │ │ │ +_3_8_0 virtual ~_M_M_F_F_9_4_T_o_r_s_i_o_n_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +381 │ │ │ │ +_3_8_3 const _M_M_F_F_9_4_T_o_r_s_i_o_n_P_a_r_a_m_e_t_e_r_s& operator = (const _M_M_F_F_9_4_T_o_r_s_i_o_n_P_a_r_a_m_e_t_e_r_s& │ │ │ │ +param) │ │ │ │ +384 ; │ │ │ │ +385 │ │ │ │ +_3_8_7 virtual void clear() │ │ │ │ +388 ; │ │ │ │ +389 │ │ │ │ +_3_9_1 bool assignParameters(_P_o_s_i_t_i_o_n type_index, │ │ │ │ +392 _I_n_d_e_x at1, _I_n_d_e_x at2, _I_n_d_e_x at3, _I_n_d_e_x at4, │ │ │ │ +393 double& v1, double& v2, double& v3) const; │ │ │ │ +394 │ │ │ │ +395 protected: │ │ │ │ +396 │ │ │ │ +_3_9_7 virtual bool setup_(const _s_t_d::vector<_s_t_d::vector<_S_t_r_i_n_g> >&); │ │ │ │ +398 │ │ │ │ +_3_9_9 _S_t_r_i_n_g getIndex_(_P_o_s_i_t_i_o_n type, _P_o_s_i_t_i_o_n atom_type1, _P_o_s_i_t_i_o_n atom_type2, │ │ │ │ +_P_o_s_i_t_i_o_n atom_type3, _P_o_s_i_t_i_o_n atom_type4) const; │ │ │ │ +400 │ │ │ │ +_4_0_2 _T_o_r_s_i_o_n_s_M_a_p parameters_; │ │ │ │ +_4_0_3 mutable _T_o_r_s_i_o_n_s_M_a_p buffered_parameters_; │ │ │ │ +_4_0_4 static _P_o_s_i_t_i_o_n ic_[5]; │ │ │ │ +_4_0_5 static _P_o_s_i_t_i_o_n lc_[5]; │ │ │ │ +406 }; │ │ │ │ +407 │ │ │ │ +410 │ │ │ │ +_4_1_4 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_P_l_a_n_e_P_a_r_a_m_e_t_e_r_s │ │ │ │ +415 : public _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +416 { │ │ │ │ +417 public: │ │ │ │ +418 │ │ │ │ +_4_2_0 typedef _H_a_s_h_M_a_p_<_S_t_r_i_n_g_,_ _d_o_u_b_l_e_> _P_l_a_n_e_M_a_p; │ │ │ │ +421 │ │ │ │ +422 _B_A_L_L___C_R_E_A_T_E(_M_M_F_F_9_4_P_l_a_n_e_P_a_r_a_m_e_t_e_r_s) │ │ │ │ +423 │ │ │ │ +424 │ │ │ │ +_4_2_5 _M_M_F_F_9_4_P_l_a_n_e_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +426 │ │ │ │ +_4_2_8 virtual ~_M_M_F_F_9_4_P_l_a_n_e_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +429 │ │ │ │ +_4_3_1 const _M_M_F_F_9_4_P_l_a_n_e_P_a_r_a_m_e_t_e_r_s& operator = (const _M_M_F_F_9_4_P_l_a_n_e_P_a_r_a_m_e_t_e_r_s& │ │ │ │ +param) │ │ │ │ +432 ; │ │ │ │ +433 │ │ │ │ +_4_3_5 virtual void clear() │ │ │ │ +436 ; │ │ │ │ +437 │ │ │ │ +_4_3_9 bool assignParameters(_I_n_d_e_x at1, _I_n_d_e_x at2, _I_n_d_e_x at3, _I_n_d_e_x at4, double& │ │ │ │ +v) const; │ │ │ │ +440 │ │ │ │ +441 protected: │ │ │ │ +442 │ │ │ │ +_4_4_3 virtual bool setup_(const _s_t_d::vector<_s_t_d::vector<_S_t_r_i_n_g> >&); │ │ │ │ +444 │ │ │ │ +_4_4_5 _S_t_r_i_n_g getIndex_(_P_o_s_i_t_i_o_n atom_type1, _P_o_s_i_t_i_o_n atom_type2, _P_o_s_i_t_i_o_n │ │ │ │ +atom_type3, _P_o_s_i_t_i_o_n atom_type4) const; │ │ │ │ +446 │ │ │ │ +_4_4_8 _P_l_a_n_e_M_a_p parameters_; │ │ │ │ +_4_4_9 mutable _P_l_a_n_e_M_a_p buffered_parameters_; │ │ │ │ +450 }; │ │ │ │ +451 │ │ │ │ +454 │ │ │ │ +_4_5_8 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s │ │ │ │ +459 : public _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +460 { │ │ │ │ +461 public: │ │ │ │ +462 │ │ │ │ +_4_6_3 struct _V_D_W_E_n_t_r_y │ │ │ │ +464 { │ │ │ │ +_4_6_5 double _a_l_p_h_a___i; │ │ │ │ +_4_6_6 double _n_i; │ │ │ │ +_4_6_7 double _a_i; │ │ │ │ +_4_6_8 double _g_i; │ │ │ │ +_4_6_9 short _d_o_n_o_r___a_c_c_e_p_t_o_r; │ │ │ │ +_4_7_0 bool _v_a_l_i_d; │ │ │ │ +471 }; │ │ │ │ +472 │ │ │ │ +473 _B_A_L_L___C_R_E_A_T_E(_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s) │ │ │ │ +474 │ │ │ │ +475 │ │ │ │ +_4_7_6 _M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +477 │ │ │ │ +_4_7_9 virtual ~_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +480 │ │ │ │ +_4_8_2 const _M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s& operator = (const _M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s& param) │ │ │ │ +483 ; │ │ │ │ +484 │ │ │ │ +_4_8_6 virtual void clear() │ │ │ │ +487 ; │ │ │ │ +488 │ │ │ │ +_4_9_0 double getR(_P_o_s_i_t_i_o_n atom_type) const; │ │ │ │ +491 │ │ │ │ +_4_9_3 const _V_D_W_E_n_t_r_y& getParameters(_I_n_d_e_x at) const; │ │ │ │ +494 │ │ │ │ +_4_9_6 bool assignParameters(_P_o_s_i_t_i_o_n at1, _P_o_s_i_t_i_o_n at2, double& rij, double& │ │ │ │ +rij_7_, double& eij) const; │ │ │ │ +497 │ │ │ │ +498 protected: │ │ │ │ +499 │ │ │ │ +_5_0_0 virtual bool setup_(const _s_t_d::vector<_s_t_d::vector<_S_t_r_i_n_g> >&); │ │ │ │ +501 │ │ │ │ +_5_0_3 _s_t_d::vector<_V_D_W_E_n_t_r_y> parameters_; │ │ │ │ +504 │ │ │ │ +505 // R star ii for all individual atom types │ │ │ │ +_5_0_6 mutable _s_t_d::vector rs_; │ │ │ │ +507 │ │ │ │ +508 // R star ij for pairs of atom types │ │ │ │ +_5_0_9 mutable _s_t_d::vector rij_; │ │ │ │ +510 // R star ij ^ 7 for pairs of atom types │ │ │ │ +_5_1_1 mutable _s_t_d::vector rij_7_; │ │ │ │ +512 // R star ij and for pairs of atom types │ │ │ │ +_5_1_3 mutable _s_t_d::vector eij_; │ │ │ │ +514 // bools if indivual value was already calculated │ │ │ │ +_5_1_5 mutable _s_t_d::vector calculated_; │ │ │ │ +516 }; │ │ │ │ +517 │ │ │ │ +518 │ │ │ │ +521 │ │ │ │ +_5_2_5 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_E_S_P_a_r_a_m_e_t_e_r_s │ │ │ │ +526 : public _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +527 { │ │ │ │ +528 public: │ │ │ │ +529 │ │ │ │ +530 _B_A_L_L___C_R_E_A_T_E(_M_M_F_F_9_4_E_S_P_a_r_a_m_e_t_e_r_s) │ │ │ │ +531 │ │ │ │ +532 │ │ │ │ +_5_3_3 _M_M_F_F_9_4_E_S_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +534 │ │ │ │ +_5_3_6 virtual ~_M_M_F_F_9_4_E_S_P_a_r_a_m_e_t_e_r_s(); │ │ │ │ +537 │ │ │ │ +_5_3_9 const _M_M_F_F_9_4_E_S_P_a_r_a_m_e_t_e_r_s& operator = (const _M_M_F_F_9_4_E_S_P_a_r_a_m_e_t_e_r_s& param) │ │ │ │ +540 ; │ │ │ │ +541 │ │ │ │ +_5_4_3 virtual void clear() │ │ │ │ +544 ; │ │ │ │ +545 │ │ │ │ +_5_5_0 double getPartialCharge(_P_o_s_i_t_i_o_n at1, _P_o_s_i_t_i_o_n at2, _P_o_s_i_t_i_o_n bt) const; │ │ │ │ +551 │ │ │ │ +_5_5_3 bool readEmpiricalParameters(_P_a_r_a_m_e_t_e_r_s& p, const _S_t_r_i_n_g& section); │ │ │ │ +554 │ │ │ │ +_5_5_6 double getPhi(_I_n_d_e_x atom_type) const; │ │ │ │ +557 │ │ │ │ +_5_5_9 double getPBCI(_I_n_d_e_x atom_type) const; │ │ │ │ +560 │ │ │ │ +561 protected: │ │ │ │ +562 │ │ │ │ +_5_6_3 virtual bool setup_(const _s_t_d::vector<_s_t_d::vector<_S_t_r_i_n_g> >&); │ │ │ │ +_5_6_4 _P_o_s_i_t_i_o_n getIndex_(_P_o_s_i_t_i_o_n at1, _P_o_s_i_t_i_o_n at2, _P_o_s_i_t_i_o_n bt) const; │ │ │ │ +565 │ │ │ │ +_5_6_7 _s_t_d::vector parameters_, phis_, pbcis_; │ │ │ │ +568 }; │ │ │ │ +569 │ │ │ │ +570 │ │ │ │ +571} // namespace BALL │ │ │ │ +572 │ │ │ │ +573#endif // BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H │ │ │ │ +_c_o_m_m_o_n_._h │ │ │ │ _h_a_s_h_M_a_p_._h │ │ │ │ -_p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h │ │ │ │ _B_A_L_L___C_R_E_A_T_E │ │ │ │ #define BALL_CREATE(name) │ │ │ │ DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_s_t_d │ │ │ │ +STL namespace. │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h_:_7_3 │ │ │ │ -_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_t_O_b_j_e_c_t │ │ │ │ -DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_t_O_b_j_e_c_t_._h_:_2_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4___n_u_m_b_e_r___a_t_o_m___t_y_p_e_s │ │ │ │ +Size MMFF94_number_atom_types │ │ │ │ +hold the maximum number of MMFF94 atom types + 1 (wildcard) │ │ │ │ +_B_A_L_L_:_:_g_e_t_M_M_F_F_9_4_I_n_d_e_x │ │ │ │ +Position getMMFF94Index(Position atom_type1, Position atom_type2) │ │ │ │ +_B_A_L_L_:_:_P_D_B_:_:_A_t_o_m │ │ │ │ +char Atom[5] │ │ │ │ +DDeeffiinniittiioonn _P_D_B_d_e_f_s_._h_:_2_5_7 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_M_a_p │ │ │ │ +HashMap class based on the STL map (containing serveral convenience functions) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_M_a_p_._h_:_7_4 │ │ │ │ _B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g_:_:_a_t │ │ │ │ -char & at(size_t pos) │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g_:_:_b_a_c_k │ │ │ │ -char & back() │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g_:_:_f_r_o_n_t │ │ │ │ -char & front() │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_a_t │ │ │ │ -ConstReference at(SizeType n) const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_4_9 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_b_e_g_i_n │ │ │ │ -ConstIterator begin() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_8_1 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_c_l_e_a_r │ │ │ │ +_B_A_L_L_:_:_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _p_a_r_a_m_e_t_e_r_s_._h_:_2_5 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e_:_:_i_s___i_n_i_t_i_a_l_i_z_e_d__ │ │ │ │ +bool is_initialized_ │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_7_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e_:_:_r_e_a_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +bool readParameters(Parameters &p, const String §ion) │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e_:_:_s_e_t_u_p__ │ │ │ │ +virtual bool setup_(const std::vector< std::vector< String > > &) │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_7_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e_:_:_e_q_u_i_v__ │ │ │ │ +const MMFF94AtomTypeEquivalences * equiv_ │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_7_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e_:_:_n_u_m_b_e_r___e_x_p_e_c_t_e_d___f_i_e_l_d_s__ │ │ │ │ +Size number_expected_fields_ │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_7_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e_:_:_c_l_e_a_r │ │ │ │ +virtual void clear() │ │ │ │ +Clear method. │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e_:_:_i_s_I_n_i_t_i_a_l_i_z_e_d │ │ │ │ +bool isInitialized() │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_6_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_B_a_s_e_:_:_s_e_t_E_q_u_i_v_a_l_e_n_c_e_s │ │ │ │ +void setEquivalences(const MMFF94AtomTypeEquivalences &equi) │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_6_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_8_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s_:_:_n_a_m_e_s__ │ │ │ │ +std::vector< String > names_ │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_1_1 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s_:_:_c_l_e_a_r │ │ │ │ void clear() │ │ │ │ -Clear function of the OCI, doing nothing here. │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_0_5 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_c_a_p_a_c_i_t_y │ │ │ │ -SizeType capacity() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_0_1 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_r_e_c_o_r_d_s__ │ │ │ │ -std::vector< String > records_ │ │ │ │ -The PDB record buffer. │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_7_4 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_R_e_f_e_r_e_n_c_e │ │ │ │ -String & Reference │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_p_o_p___b_a_c_k │ │ │ │ -void pop_back() │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_2_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_b_a_c_k │ │ │ │ -ConstReference back() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_1_5 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_c_o_n_s_t___i_t_e_r_a_t_o_r │ │ │ │ -std::vector< String >::const_iterator const_iterator │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ -std::vector< String >::const_iterator ConstIterator │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_3_9 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_s_i_z_e___t_y_p_e │ │ │ │ -std::vector< String >::size_type size_type │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_i_n_s_e_r_t │ │ │ │ -void insert(Iterator pos, SizeType n, ConstReference value) │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_2_1 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_p_e_r_s_i_s_t_e_n_t_W_r_i_t_e │ │ │ │ -void persistentWrite(PersistenceManager &pm, const char *name) const │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_r_e_s_i_z_e │ │ │ │ -void resize(SizeType sz, ValueType c=ValueType()) │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_0_7 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_a_t │ │ │ │ -Reference at(SizeType n) │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_5_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_r_e_f_e_r_e_n_c_e │ │ │ │ -String & reference │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_7 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_e_m_p_t_y │ │ │ │ -bool empty() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_0_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_c_o_n_s_t___r_e_v_e_r_s_e___i_t_e_r_a_t_o_r │ │ │ │ -std::vector< String >::const_reverse_iterator const_reverse_iterator │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_4 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_e_n_d │ │ │ │ -ConstIterator end() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_8_5 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ -std::vector< String >::reverse_iterator ReverseIterator │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_1 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_r_e_v_e_r_s_e___i_t_e_r_a_t_o_r │ │ │ │ -std::vector< String >::reverse_iterator reverse_iterator │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_2 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_S_i_z_e_T_y_p_e │ │ │ │ -std::vector< String >::size_type SizeType │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_5_4 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_i_n_s_e_r_t │ │ │ │ -void insert(Iterator pos, ConstReference value) │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_1_9 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_V_a_l_u_e_T_y_p_e │ │ │ │ -String ValueType │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_I_t_e_r_a_t_o_r │ │ │ │ -std::vector< String >::iterator Iterator │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_3_7 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_D_i_f_f_e_r_e_n_c_e_T_y_p_e │ │ │ │ -std::vector< String >::difference_type DifferenceType │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_5_2 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_f_r_o_n_t │ │ │ │ -ConstReference front() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_1_1 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_r_e_n_d │ │ │ │ -ReverseIterator rend() │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_9_5 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_i_t_e_r_a_t_o_r │ │ │ │ -std::vector< String >::iterator iterator │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_3_8 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_b_a_c_k │ │ │ │ -Reference back() │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_1_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ -std::vector< String >::const_reverse_iterator ConstReverseIterator │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_s_w_a_p │ │ │ │ -void swap(PDBRecords &rhs) │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_4_1 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_C_o_n_s_t_R_e_f_e_r_e_n_c_e │ │ │ │ -const String & ConstReference │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_5_0 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_v_a_l_u_e___t_y_p_e │ │ │ │ -String value_type │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_5 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_r_b_e_g_i_n │ │ │ │ -ReverseIterator rbegin() │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_9_1 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_r_e_n_d │ │ │ │ -ConstReverseIterator rend() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_9_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_p_u_s_h___b_a_c_k │ │ │ │ -void push_back(ConstReference x) │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_1_7 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_c_o_n_s_t___r_e_f_e_r_e_n_c_e │ │ │ │ -const String & const_reference │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_4_9 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_m_a_x___s_i_z_e │ │ │ │ -SizeType max_size() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_s_i_z_e │ │ │ │ -SizeType size() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_9_7 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_b_e_g_i_n │ │ │ │ -Iterator begin() │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_8_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_p_e_r_s_i_s_t_e_n_t_R_e_a_d │ │ │ │ -void persistentRead(PersistenceManager &pm) │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_e_r_a_s_e │ │ │ │ -Iterator erase(Iterator pos) │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_2_5 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_d_i_f_f_e_r_e_n_c_e___t_y_p_e │ │ │ │ -std::vector< String >::difference_type difference_type │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_5_1 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_e_r_a_s_e │ │ │ │ -Iterator erase(Iterator first, Iterator last) │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_2_7 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_f_r_o_n_t │ │ │ │ -Reference front() │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_1_0_9 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_r_b_e_g_i_n │ │ │ │ -ConstReverseIterator rbegin() const │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_8_9 │ │ │ │ -_B_A_L_L_:_:_P_D_B_R_e_c_o_r_d_s_:_:_e_n_d │ │ │ │ -Iterator end() │ │ │ │ -DDeeffiinniittiioonn _P_D_B_R_e_c_o_r_d_s_._h_:_8_7 │ │ │ │ +Clear method. │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s │ │ │ │ +MMFF94AtomTypeEquivalences(const MMFF94AtomTypeEquivalences &to_copy) │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s_:_:_e_x_i_s_t_s__ │ │ │ │ +std::vector< bool > exists_ │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_1_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s_:_:_~_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s │ │ │ │ +~MMFF94AtomTypeEquivalences() │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s_:_:_e_q_u_i_v_a_l_e_n_c_e_s__ │ │ │ │ +std::vector< std::vector< Position > > equivalences_ │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_1_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s_:_:_s_e_t_u_p__ │ │ │ │ +virtual bool setup_(const std::vector< std::vector< String > > &) │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s │ │ │ │ +MMFF94AtomTypeEquivalences() │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_E_q_u_i_v_a_l_e_n_c_e_s_:_:_g_e_t_E_q_u_i_v_a_l_e_n_c_e │ │ │ │ +Index getEquivalence(Position original, Position number) const │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e │ │ │ │ +Class to store the values of an atom type from MMFFPROP.PAR. │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_1_8 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_m_l_t_b │ │ │ │ +Position mltb │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_3_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_a_r_o_m │ │ │ │ +bool arom │ │ │ │ +is aromatic │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_4_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_v_a_l_i_d │ │ │ │ +bool valid │ │ │ │ +Is this a valid MMFF94 atom type? │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_4_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_l_i_n │ │ │ │ +bool lin │ │ │ │ +has linear bond │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_4_3 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_a_s_p_e_c │ │ │ │ +Position aspec │ │ │ │ +atomic number; │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_2_3 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_v_a_l │ │ │ │ +Position val │ │ │ │ +number of bonds made to this atom type │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_2_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e │ │ │ │ +MMFF94AtomType() │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_s_b_m_b │ │ │ │ +bool sbmb │ │ │ │ +can have a delocalized single bond │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_4_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_p_i_l_p │ │ │ │ +bool pilp │ │ │ │ +has pi lone pair electrons │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_3_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_:_:_c_r_d │ │ │ │ +Position crd │ │ │ │ +necessary number of bonded neighbours │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_2_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_5_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s_:_:_s_e_t_u_p__ │ │ │ │ +virtual bool setup_(const std::vector< std::vector< String > > &) │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s_:_:_d_a_t_a__ │ │ │ │ +std::vector< MMFF94AtomType > data_ │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_7_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s │ │ │ │ +MMFF94AtomTypes(const MMFF94AtomTypes &to_copy) │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s_:_:_~_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s │ │ │ │ +~MMFF94AtomTypes() │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_6_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s │ │ │ │ +MMFF94AtomTypes() │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_A_t_o_m_T_y_p_e_s_:_:_g_e_t_A_t_o_m_T_y_p_e_s │ │ │ │ +const std::vector< MMFF94AtomType > & getAtomTypes() const │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_7_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_8_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_b_u_f_f_e_r_e_d___p_a_r_a_m_e_t_e_r_s__ │ │ │ │ +StretchMap buffered_parameters_ │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_5_4 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_e_m_p_i_r_i_c_a_l___p_a_r_a_m_e_t_e_r_s__ │ │ │ │ +EmpiricalStretchMap empirical_parameters_ │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_5_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_S_t_r_e_t_c_h_M_a_p │ │ │ │ +HashMap< Position, BondData > StretchMap │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_1_4 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_s_e_t_u_p__ │ │ │ │ +virtual bool setup_(const std::vector< std::vector< String > > &) │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_g_e_t_E_m_p_i_r_i_c_a_l_P_a_r_a_m_e_t_e_r_s │ │ │ │ +const EmpiricalStretchMap & getEmpiricalParameters() const │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_4_3 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_E_m_p_i_r_i_c_a_l_S_t_r_e_t_c_h_M_a_p │ │ │ │ +HashMap< Position, EmpiricalBondData > EmpiricalStretchMap │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_1_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_p_a_r_a_m_e_t_e_r_s__ │ │ │ │ +StretchMap parameters_ │ │ │ │ +standard parameters │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_5_3 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_9_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a_:_:_B_o_n_d_D_a_t_a │ │ │ │ +BondData() │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a_:_:_r_0___n_o_r_m_a_l │ │ │ │ +double r0_normal │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_9_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a_:_:_s_b_m_b___e_x_i_s_t_s │ │ │ │ +bool sbmb_exists │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_0_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a_:_:_s_t_a_n_d_a_r_d___b_o_n_d___e_x_i_s_t_s │ │ │ │ +bool standard_bond_exists │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_9_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a_:_:_r_0___s_b_m_b │ │ │ │ +double r0_sbmb │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_0_1 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a_:_:_k_b___n_o_r_m_a_l │ │ │ │ +double kb_normal │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_9_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a_:_:_e_m_p_i_r_i_c_a_l │ │ │ │ +bool empirical │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_0_3 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_B_o_n_d_D_a_t_a_:_:_k_b___s_b_m_b │ │ │ │ +double kb_sbmb │ │ │ │ +parameters for optinal single-bond–multiple bond cases (see MMFFPROP.PAR) │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_0_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_E_m_p_i_r_i_c_a_l_B_o_n_d_D_a_t_a │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_0_8 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_E_m_p_i_r_i_c_a_l_B_o_n_d_D_a_t_a_:_:_k_b │ │ │ │ +double kb │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_0_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s_:_:_E_m_p_i_r_i_c_a_l_B_o_n_d_D_a_t_a_:_:_r_0 │ │ │ │ +double r0 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_1_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_6_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s_:_:_B_e_n_d_M_a_p │ │ │ │ +HashMap< Position, std::pair< double, double > > BendMap │ │ │ │ +Map with the force constant and reference angle. │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_6_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_3_1_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s_:_:_S_t_r_e_t_c_h_B_e_n_d_M_a_p │ │ │ │ +HashMap< Position, std::pair< double, double > > StretchBendMap │ │ │ │ +Map with the force constant and reference angle. │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_3_1_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_T_o_r_s_i_o_n_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_3_6_8 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_T_o_r_s_i_o_n_P_a_r_a_m_e_t_e_r_s_:_:_T_o_r_s_i_o_n_s_M_a_p │ │ │ │ +HashMap< String, std::vector< double > > TorsionsMap │ │ │ │ +Map with the force constant and reference angle. │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_3_7_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_l_a_n_e_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_1_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_P_l_a_n_e_P_a_r_a_m_e_t_e_r_s_:_:_P_l_a_n_e_M_a_p │ │ │ │ +HashMap< String, double > PlaneMap │ │ │ │ +Map with the force constant. │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_2_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_6_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s_:_:_V_D_W_E_n_t_r_y │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_6_4 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s_:_:_V_D_W_E_n_t_r_y_:_:_v_a_l_i_d │ │ │ │ +bool valid │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_7_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s_:_:_V_D_W_E_n_t_r_y_:_:_a_l_p_h_a___i │ │ │ │ +double alpha_i │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_6_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s_:_:_V_D_W_E_n_t_r_y_:_:_a_i │ │ │ │ +double ai │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_6_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s_:_:_V_D_W_E_n_t_r_y_:_:_d_o_n_o_r___a_c_c_e_p_t_o_r │ │ │ │ +short donor_acceptor │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_6_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s_:_:_V_D_W_E_n_t_r_y_:_:_g_i │ │ │ │ +double gi │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_6_8 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s_:_:_V_D_W_E_n_t_r_y_:_:_n_i │ │ │ │ +double ni │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_6_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_E_S_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_5_2_7 │ │ │ │ +_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d7a/a08030.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::VIEW::AddBallAndStickModel Class Reference
    Visualisation » Model Processors
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/MODELS/ballAndStickModel.h>

    │ │ │ +

    #include <BALL/VIEW/MODELS/ballAndStickModel.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::AddBallAndStickModel:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::AtomBondModelBaseProcessor │ │ │ @@ -181,18 +181,18 @@ │ │ │ virtual ~UnaryProcessor () │ │ │   │ │ │ virtual bool start () │ │ │   │ │ │ virtual bool finish () │ │ │   │ │ │ - Public Member Functions inherited from BALL::PropertyManager │ │ │ -BALL_INLINE PropertyManager () │ │ │ +BALL_INLINE PropertyManager () │ │ │  Default constructor.
    │ │ │   │ │ │ -BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │ +BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │  Copy constructor.
    │ │ │   │ │ │ virtual ~PropertyManager () │ │ │  Destructor.
    │ │ │   │ │ │ virtual void destroy () │ │ │  Clears all properties.
    │ │ │ @@ -331,15 +331,15 @@ │ │ │   │ │ │ float surface_drawing_precision_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    AddBallAndStickModel class. The class AddBallAndStickModel is a model processor that is responsible for creating either a ball and stick model or a stick model. In a ball and stick model the graphical representation of the Atom objects (Sphere objects) have a different radius than the representation of the Bond objects (Tube objects). Otherwise in the stick model the radi of the ball and the stick components are equal. For information about the processor concept see Processor in the BALL documentation.

    │ │ │ │ │ │ -

    Definition at line 35 of file ballAndStickModel.h.

    │ │ │ +

    Definition at line 35 of file ballAndStickModel.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ AddBallAndStickModel() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -509,15 +509,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 162 of file ballAndStickModel.h.

    │ │ │ +

    Definition at line 162 of file ballAndStickModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ dump()

    │ │ │ │ │ │
    │ │ │ @@ -600,15 +600,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 166 of file ballAndStickModel.h.

    │ │ │ +

    Definition at line 166 of file ballAndStickModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ enableStickModel()

    │ │ │ │ │ │
    │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d7c/a03318.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::UnaryPredicate< T > Class Template Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/CONCEPT/predicate.h>

    │ │ │ +

    #include <BALL/CONCEPT/predicate.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::UnaryPredicate< T >:
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ │ │ │ @@ -96,15 +96,15 @@ │ │ │ │ │ │ │ │ │
    virtual bool operator() (const T &) const
     
    │ │ │

    Detailed Description

    │ │ │
    template<typename T>
    │ │ │ class BALL::UnaryPredicate< T >

    Generic Unary Predicate Class

    │ │ │ │ │ │ -

    Definition at line 28 of file CONCEPT/predicate.h.

    │ │ │ +

    Definition at line 28 of file CONCEPT/predicate.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ~UnaryPredicate()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ @@ -123,15 +123,15 @@ │ │ │ │ │ │ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 33 of file CONCEPT/predicate.h.

    │ │ │ +

    Definition at line 33 of file CONCEPT/predicate.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ operator()()

    │ │ │ │ │ │ @@ -154,15 +154,15 @@ │ │ │ │ │ │ │ │ │ virtual │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 57 of file CONCEPT/predicate.h.

    │ │ │ +

    Definition at line 57 of file CONCEPT/predicate.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d7e/a00770.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: buildBondsProcessor.h File Reference │ │ │ +BALL: glRenderWindow.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,47 +65,44 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    buildBondsProcessor.h File Reference
    │ │ │ +
    glRenderWindow.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/CONCEPT/processor.h>
    │ │ │ -#include <BALL/KERNEL/atomContainer.h>
    │ │ │ -#include <BALL/DATATYPE/hashMap.h>
    │ │ │ -#include <BALL/KERNEL/bond.h>
    │ │ │ -#include <BALL/DATATYPE/options.h>
    │ │ │ +
    #include <BALL/COMMON/global.h>
    │ │ │ +#include <BALL/DATATYPE/string.h>
    │ │ │ +#include <BALL/VIEW/RENDERING/renderWindow.h>
    │ │ │ +#include <BALL/VIEW/DATATYPE/colorRGBA.h>
    │ │ │ +#include <BALL/SYSTEM/mutex.h>
    │ │ │ +#include <QtOpenGL/qgl.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::BuildBondsProcessor
     
    struct  BALL::BuildBondsProcessor::Option
     Option names. More...
     
    struct  BALL::BuildBondsProcessor::Default
     Default values for options. More...
    class  BALL::VIEW::GLRenderWindow
     
    │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ + │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,29 +1,27 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ + * _V_I_E_W │ │ │ │ + * _R_E_N_D_E_R_I_N_G │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -buildBondsProcessor.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_b_o_n_d_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +glRenderWindow.h File Reference │ │ │ │ +#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_r_e_n_d_e_r_W_i_n_d_o_w_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_c_o_l_o_r_R_G_B_A_._h> │ │ │ │ +#include <_B_A_L_L_/_S_Y_S_T_E_M_/_m_u_t_e_x_._h> │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ - class   _B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ -  _O_p_t_i_o_n names. _M_o_r_e_._._. │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ -  _D_e_f_a_u_l_t values for options. _M_o_r_e_._._. │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │ +  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d7e/a00770_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: buildBondsProcessor.h Source File │ │ │ +BALL: glRenderWindow.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,209 +70,192 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    buildBondsProcessor.h
    │ │ │ +
    glRenderWindow.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5#ifndef BALL_STRUCTURE_BUILDBONDSPROCESSOR_H
    │ │ │ -
    6#define BALL_STRUCTURE_BUILDBONDSPROCESSOR_H
    │ │ │ +
    5#ifndef BALL_VIEW_RENDERING_GLRENDERWINDOW_H
    │ │ │ +
    6#define BALL_VIEW_RENDERING_GLRENDERWINDOW_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_CONCEPT_PROCESSOR_H
    │ │ │ -
    9 #include <BALL/CONCEPT/processor.h>
    │ │ │ +
    8#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ +
    9# include <BALL/COMMON/global.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_KERNEL_ATOMCONTAINER_H
    │ │ │ -
    13 #include <BALL/KERNEL/atomContainer.h>
    │ │ │ +
    12#ifndef BALL_DATATYPE_STRING_H
    │ │ │ +
    13# include <BALL/DATATYPE/string.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │ -
    16#ifndef BALL_DATATYPE_HASHMAP_H
    │ │ │ -
    17 #include <BALL/DATATYPE/hashMap.h>
    │ │ │ +
    16#ifndef BALL_VIEW_RENDERING_RENDERWINDOW_H
    │ │ │ +
    17# include <BALL/VIEW/RENDERING/renderWindow.h>
    │ │ │
    18#endif
    │ │ │
    19
    │ │ │ -
    20#ifndef BALL_KERNEL_BOND_H
    │ │ │ -
    21 #include <BALL/KERNEL/bond.h>
    │ │ │ +
    20#ifndef BALL_VIEW_DATATYPE_COLORRGBA_H
    │ │ │ +
    21# include <BALL/VIEW/DATATYPE/colorRGBA.h>
    │ │ │
    22#endif
    │ │ │
    23
    │ │ │ -
    24#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ -
    25 #include <BALL/DATATYPE/options.h>
    │ │ │ +
    24#ifndef BALL_SYSTEM_MUTEX_H
    │ │ │ +
    25# include <BALL/SYSTEM/mutex.h>
    │ │ │
    26#endif
    │ │ │
    27
    │ │ │ -
    28namespace BALL
    │ │ │ -
    29{
    │ │ │ -
    30
    │ │ │ -
    │ │ │ -
    34 class BALL_EXPORT BuildBondsProcessor
    │ │ │ -
    35 : public UnaryProcessor<AtomContainer>
    │ │ │ -
    36 {
    │ │ │ -
    37
    │ │ │ -
    38 public:
    │ │ │ -
    39
    │ │ │ -
    │ │ │ -
    44 struct BALL_EXPORT Option
    │ │ │ -
    45 {
    │ │ │ -
    49 static const char* BONDLENGTHS_FILENAME;
    │ │ │ -
    50
    │ │ │ -
    57 static const char* DELETE_EXISTING_BONDS;
    │ │ │ +
    28#include <QtOpenGL/qgl.h>
    │ │ │ +
    29
    │ │ │ +
    30namespace BALL
    │ │ │ +
    31{
    │ │ │ +
    32 namespace VIEW
    │ │ │ +
    33 {
    │ │ │ +
    │ │ │ +
    37 class BALL_VIEW_EXPORT GLRenderWindow
    │ │ │ +
    38 : public RenderWindow,
    │ │ │ +
    39 public QGLWidget
    │ │ │ +
    40 {
    │ │ │ +
    41
    │ │ │ +
    42 public:
    │ │ │ +
    43 GLRenderWindow();
    │ │ │ +
    44 GLRenderWindow(QWidget* parent_widget, const char* name = NULL, Qt::WindowFlags w_flags = 0);
    │ │ │ +
    45 GLRenderWindow(const GLRenderWindow& window, QWidget* parent_widget, const char* name = NULL, Qt::WindowFlags w_flags = 0);
    │ │ │ +
    46
    │ │ │ +
    47 virtual ~GLRenderWindow();
    │ │ │ +
    48
    │ │ │ +
    49 /* RenderWindow methods */
    │ │ │ +
    50 virtual bool init();
    │ │ │ +
    51 virtual bool resize(const unsigned int width, const unsigned int height);
    │ │ │ +
    52 virtual void refresh();
    │ │ │ +
    53
    │ │ │ +
    54 // render the given text in the given color and size at window coordinates (x, y)
    │ │ │ +
    55 virtual void renderText(int x, int y, const String& text, const ColorRGBA& color, Size size = 16);
    │ │ │ +
    56 // render the given text in the given color and size at world coordinates (x, y, z)
    │ │ │ +
    57 virtual void renderText(float x, float y, float z, const String& text, const ColorRGBA& color, Size size = 16);
    │ │ │
    58
    │ │ │ -
    64 static const char* REESTIMATE_BONDORDERS_RINGS;
    │ │ │ -
    65
    │ │ │ -
    71 static const char* DELETE_OVERESTIMATED_BONDS;
    │ │ │ -
    72 };
    │ │ │ -
    │ │ │ -
    73
    │ │ │ -
    │ │ │ -
    75 struct BALL_EXPORT Default
    │ │ │ -
    76 {
    │ │ │ -
    78 static const char* BONDLENGTHS_FILENAME;
    │ │ │ -
    79
    │ │ │ -
    81 static const bool DELETE_EXISTING_BONDS;
    │ │ │ -
    82
    │ │ │ -
    84 static const bool REESTIMATE_BONDORDERS_RINGS;
    │ │ │ -
    85
    │ │ │ -
    87 static const bool DELETE_OVERESTIMATED_BONDS;
    │ │ │ -
    88 };
    │ │ │ +
    60 void lockGLContext();
    │ │ │ +
    61
    │ │ │ +
    63 void unlockGLContext();
    │ │ │ +
    64
    │ │ │ +
    66 void ignoreEvents(bool ignore) {ignore_events_ = ignore;}
    │ │ │ +
    67
    │ │ │ +
    │ │ │ +
    69 void setDownsamplingFactor(float dsfactor)
    │ │ │ +
    70 {down_sampling_factor_ = dsfactor;}
    │ │ │
    │ │ │ -
    90
    │ │ │ -
    91
    │ │ │ +
    71
    │ │ │ +
    │ │ │ +
    73 void setStereoDelta(float delta)
    │ │ │ +
    74 {stereo_delta_ = delta;}
    │ │ │ +
    │ │ │ +
    75
    │ │ │ +
    76 void setupStereo(float eye_separation, float focal_length);
    │ │ │ +
    77
    │ │ │ +
    79 void safeBufferSwap();
    │ │ │ +
    80
    │ │ │ +
    │ │ │ +
    82 float getDownsamplingFactor() const
    │ │ │ +
    83 {return down_sampling_factor_;}
    │ │ │ +
    │ │ │ +
    84
    │ │ │ +
    85 float stereo_delta_;
    │ │ │ +
    86
    │ │ │ +
    87 protected:
    │ │ │ +
    88
    │ │ │ +
    94 virtual void customEvent(QEvent* evt);
    │ │ │
    95
    │ │ │ -
    96 BALL_CREATE(BuildBondsProcessor);
    │ │ │ -
    97
    │ │ │ -
    99 BuildBondsProcessor();
    │ │ │ -
    100
    │ │ │ -
    102 BuildBondsProcessor(const BuildBondsProcessor& bbp);
    │ │ │ -
    103
    │ │ │ -
    107 BuildBondsProcessor(const String& file_name);
    │ │ │ -
    108
    │ │ │ -
    110 virtual ~BuildBondsProcessor();
    │ │ │ +
    96 void paintEvent(QPaintEvent* e);
    │ │ │ +
    97 static QGLFormat gl_format_;
    │ │ │ +
    98
    │ │ │ +
    99 // ID of the fullscreen texture used to paste image into GPU framebuffer
    │ │ │ +
    100 GLuint m_screenTexID;
    │ │ │ +
    101 // type of the texture used
    │ │ │ +
    102 GLenum FB_TEXTURE_TARGET;
    │ │ │ +
    103 // format of the GL texture (GL_RGB, GL_RGBA, etc.)
    │ │ │ +
    104 GLenum FB_TEXTURE_FORMAT;
    │ │ │ +
    105 // internal format specified when creating the textures
    │ │ │ +
    106 GLenum FB_INTERNAL_TEXTURE_FORMAT;
    │ │ │ +
    107 // data type of the GL texture (GL_FLOAT, GL_UNSIGNED_INT, etc.)
    │ │ │ +
    108 GLenum FB_TEXTURE_DATATYPE;
    │ │ │ +
    109
    │ │ │ +
    110 void createTexture(const unsigned int winWidth, const unsigned int winHeight);
    │ │ │ +
    111 void deleteTexture();
    │ │ │
    112
    │ │ │ -
    116
    │ │ │ -
    118 virtual bool start();
    │ │ │ -
    119
    │ │ │ -
    121 virtual Processor::Result operator () (AtomContainer& ac);
    │ │ │ +
    113 void checkGL();
    │ │ │ +
    114
    │ │ │ +
    115 bool errorInGL(GLenum& error);
    │ │ │ +
    116 String getGLErrorString(GLenum error);
    │ │ │ +
    117
    │ │ │ +
    118 mutable Mutex contex_mutex_;
    │ │ │ +
    119 bool ignore_events_;
    │ │ │ +
    120 float down_sampling_factor_;
    │ │ │ +
    121 //float stereo_delta_;
    │ │ │ +
    122 };
    │ │ │ +
    │ │ │
    123
    │ │ │ -
    128 Size getNumberOfBondsBuilt();
    │ │ │ -
    129
    │ │ │ -
    133 void setBondLengths(const String& file_name);
    │ │ │ -
    134
    │ │ │ -
    136 HashMap<Size, HashMap<Size, HashMap<int, float> > > getBondMap() { return bond_lengths_;};
    │ │ │ -
    137
    │ │ │ -
    139
    │ │ │ -
    144 BuildBondsProcessor& operator = (const BuildBondsProcessor& bbp);
    │ │ │ -
    146
    │ │ │ -
    151 Options options;
    │ │ │ -
    152
    │ │ │ -
    155 void setDefaultOptions();
    │ │ │ -
    157
    │ │ │ -
    158 protected:
    │ │ │ -
    159
    │ │ │ -
    161 Size buildBondsHashGrid3_(AtomContainer& ac);
    │ │ │ -
    162
    │ │ │ -
    164 void estimateBondOrders_(AtomContainer& ac);
    │ │ │ -
    165
    │ │ │ -
    167 void reestimateBondOrdersRings_(AtomContainer& ac);
    │ │ │ -
    168
    │ │ │ -
    170 void deleteOverestimatedBonds_(AtomContainer& ac);
    │ │ │ -
    171
    │ │ │ -
    175 void readBondLengthsFromFile_(const String& file_name = "");
    │ │ │ -
    176
    │ │ │ -
    178 Size num_bonds_;
    │ │ │ -
    179
    │ │ │ -
    181 HashMap<Size, HashMap<Size, HashMap<int, float> > > bond_lengths_;
    │ │ │ -
    182
    │ │ │ -
    184 HashMap<Size, HashMap<Size, float> > max_bond_lengths_;
    │ │ │ -
    185
    │ │ │ -
    187 HashMap<Size, HashMap<Size, float> > min_bond_lengths_;
    │ │ │ -
    188
    │ │ │ -
    189 /*_ returns the best fitting bond order of a bond between atoms of
    │ │ │ -
    190 element e1 and element e2 with a distance of length
    │ │ │ -
    191 */
    │ │ │ -
    192 Bond::BondOrder getNearestBondOrder_(float length, Size e1, Size e2);
    │ │ │ -
    193
    │ │ │ -
    194 /*_ Returns true if the atom with atomic number an1 and atom with
    │ │ │ -
    195 atomic number an2 can share a bond. If, the parameter length
    │ │ │ -
    196 holds the maximal length of such a bond.
    │ │ │ -
    197 */
    │ │ │ -
    198 bool getMaxBondLength_(float& length, Size an1, Size an2);
    │ │ │ -
    199
    │ │ │ -
    200 /*_ Returns true if the atom with atomic number an1 and atom with
    │ │ │ -
    201 atomic number an2 can share a bond. If, the parameter length
    │ │ │ -
    202 holds the minimal length of such a bond.
    │ │ │ -
    203 */
    │ │ │ -
    204 bool getMinBondLength_(float& length, Size an1, Size an2);
    │ │ │ -
    205
    │ │ │ -
    207 float max_length_;
    │ │ │ -
    208 };
    │ │ │ -
    │ │ │ -
    209
    │ │ │ -
    210} // namespace BALL
    │ │ │ -
    211
    │ │ │ -
    212
    │ │ │ -
    213#endif // BALL_STRUCTURE_BUILDBONDSPROCESSOR_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::HashMap
    HashMap class based on the STL map (containing serveral convenience functions)
    Definition hashMap.h:74
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Bond::BondOrder
    BondOrder
    Definition bond.h:97
    │ │ │ - │ │ │ -
    BALL::BuildBondsProcessor::BuildBondsProcessor
    BuildBondsProcessor()
    default constructor
    │ │ │ -
    BALL::BuildBondsProcessor::getNumberOfBondsBuilt
    Size getNumberOfBondsBuilt()
    Return the number of bonds built during the last application.
    │ │ │ -
    BALL::BuildBondsProcessor::max_bond_lengths_
    HashMap< Size, HashMap< Size, float > > max_bond_lengths_
    structure were the bond maxima stored in (used in buildBonds_)
    Definition buildBondsProcessor.h:184
    │ │ │ -
    BALL::BuildBondsProcessor::buildBondsHashGrid3_
    Size buildBondsHashGrid3_(AtomContainer &ac)
    builds bonds, based on atom distances read from parameter file using a 3D hash grid
    │ │ │ -
    BALL::BuildBondsProcessor::num_bonds_
    Size num_bonds_
    number of bonds, which are created during the processor call
    Definition buildBondsProcessor.h:178
    │ │ │ -
    BALL::BuildBondsProcessor::start
    virtual bool start()
    processor method which is called before the operator () call
    │ │ │ -
    BALL::BuildBondsProcessor::bond_lengths_
    HashMap< Size, HashMap< Size, HashMap< int, float > > > bond_lengths_
    structure where bond order distances are stored in
    Definition buildBondsProcessor.h:181
    │ │ │ -
    BALL::BuildBondsProcessor::setBondLengths
    void setBondLengths(const String &file_name)
    │ │ │ -
    BALL::BuildBondsProcessor::getMaxBondLength_
    bool getMaxBondLength_(float &length, Size an1, Size an2)
    │ │ │ -
    BALL::BuildBondsProcessor::max_length_
    float max_length_
    parameter which holds the longest possible bond
    Definition buildBondsProcessor.h:207
    │ │ │ -
    BALL::BuildBondsProcessor::getBondMap
    HashMap< Size, HashMap< Size, HashMap< int, float > > > getBondMap()
    Return the bond length Hashmap.
    Definition buildBondsProcessor.h:136
    │ │ │ -
    BALL::BuildBondsProcessor::BuildBondsProcessor
    BuildBondsProcessor(const BuildBondsProcessor &bbp)
    copy construcor
    │ │ │ -
    BALL::BuildBondsProcessor::getNearestBondOrder_
    Bond::BondOrder getNearestBondOrder_(float length, Size e1, Size e2)
    │ │ │ -
    BALL::BuildBondsProcessor::getMinBondLength_
    bool getMinBondLength_(float &length, Size an1, Size an2)
    │ │ │ -
    BALL::BuildBondsProcessor::reestimateBondOrdersRings_
    void reestimateBondOrdersRings_(AtomContainer &ac)
    reestimate the bond orders of rings, as aromatic rings are often detected wrong
    │ │ │ -
    BALL::BuildBondsProcessor::estimateBondOrders_
    void estimateBondOrders_(AtomContainer &ac)
    after the bonds are built, the orders are estimated
    │ │ │ -
    BALL::BuildBondsProcessor::BALL_CREATE
    BALL_CREATE(BuildBondsProcessor)
    │ │ │ -
    BALL::BuildBondsProcessor::~BuildBondsProcessor
    virtual ~BuildBondsProcessor()
    destructor
    │ │ │ - │ │ │ - │ │ │ -
    BALL::BuildBondsProcessor::min_bond_lengths_
    HashMap< Size, HashMap< Size, float > > min_bond_lengths_
    structure were the bond minima stored in (used in buildBonds_)
    Definition buildBondsProcessor.h:187
    │ │ │ -
    BALL::BuildBondsProcessor::deleteOverestimatedBonds_
    void deleteOverestimatedBonds_(AtomContainer &ac)
    deletes bonds, like from multiple bonded hydrogens or halogens
    │ │ │ -
    BALL::BuildBondsProcessor::readBondLengthsFromFile_
    void readBondLengthsFromFile_(const String &file_name="")
    │ │ │ -
    BALL::BuildBondsProcessor::BuildBondsProcessor
    BuildBondsProcessor(const String &file_name)
    │ │ │ - │ │ │ -
    BALL::BuildBondsProcessor::Option::REESTIMATE_BONDORDERS_RINGS
    static const char * REESTIMATE_BONDORDERS_RINGS
    Definition buildBondsProcessor.h:64
    │ │ │ -
    BALL::BuildBondsProcessor::Option::DELETE_OVERESTIMATED_BONDS
    static const char * DELETE_OVERESTIMATED_BONDS
    Definition buildBondsProcessor.h:71
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::BuildBondsProcessor::Default::BONDLENGTHS_FILENAME
    static const char * BONDLENGTHS_FILENAME
    default file name for the bond lengths
    Definition buildBondsProcessor.h:78
    │ │ │ -
    BALL::BuildBondsProcessor::Default::DELETE_OVERESTIMATED_BONDS
    static const bool DELETE_OVERESTIMATED_BONDS
    this option is off by default
    Definition buildBondsProcessor.h:87
    │ │ │ -
    BALL::BuildBondsProcessor::Default::REESTIMATE_BONDORDERS_RINGS
    static const bool REESTIMATE_BONDORDERS_RINGS
    this option is off by default
    Definition buildBondsProcessor.h:84
    │ │ │ -
    BALL::BuildBondsProcessor::Default::DELETE_EXISTING_BONDS
    static const bool DELETE_EXISTING_BONDS
    this option is off by default
    Definition buildBondsProcessor.h:81
    │ │ │ +
    124 } // namespace VIEW
    │ │ │ +
    125
    │ │ │ +
    126} // namespace BALL
    │ │ │ +
    127
    │ │ │ +
    128#endif // BALL_VIEW_RENDERING_GLRENDERWINDOW_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::GLRenderWindow::GLRenderWindow
    GLRenderWindow(const GLRenderWindow &window, QWidget *parent_widget, const char *name=NULL, Qt::WindowFlags w_flags=0)
    │ │ │ +
    BALL::VIEW::GLRenderWindow::errorInGL
    bool errorInGL(GLenum &error)
    │ │ │ +
    BALL::VIEW::GLRenderWindow::createTexture
    void createTexture(const unsigned int winWidth, const unsigned int winHeight)
    │ │ │ +
    BALL::VIEW::GLRenderWindow::lockGLContext
    void lockGLContext()
    Lock the context for the current thread and make it active.
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::GLRenderWindow::paintEvent
    void paintEvent(QPaintEvent *e)
    │ │ │ + │ │ │ +
    BALL::VIEW::GLRenderWindow::renderText
    virtual void renderText(int x, int y, const String &text, const ColorRGBA &color, Size size=16)
    │ │ │ +
    BALL::VIEW::GLRenderWindow::setupStereo
    void setupStereo(float eye_separation, float focal_length)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::GLRenderWindow::setStereoDelta
    void setStereoDelta(float delta)
    Set the stereo delta for raytracing in pixels.
    Definition glRenderWindow.h:73
    │ │ │ +
    BALL::VIEW::GLRenderWindow::setDownsamplingFactor
    void setDownsamplingFactor(float dsfactor)
    Set the window's downsampling factor. This is a speed up factor.
    Definition glRenderWindow.h:69
    │ │ │ +
    BALL::VIEW::GLRenderWindow::customEvent
    virtual void customEvent(QEvent *evt)
    │ │ │ + │ │ │ +
    BALL::VIEW::GLRenderWindow::getGLErrorString
    String getGLErrorString(GLenum error)
    │ │ │ +
    BALL::VIEW::GLRenderWindow::ignoreEvents
    void ignoreEvents(bool ignore)
    Force the window to ignore paint events.
    Definition glRenderWindow.h:66
    │ │ │ +
    BALL::VIEW::GLRenderWindow::resize
    virtual bool resize(const unsigned int width, const unsigned int height)
    │ │ │ + │ │ │ +
    BALL::VIEW::GLRenderWindow::getDownsamplingFactor
    float getDownsamplingFactor() const
    Get the window's downsampling factor.
    Definition glRenderWindow.h:82
    │ │ │ +
    BALL::VIEW::GLRenderWindow::unlockGLContext
    void unlockGLContext()
    Unlock the context for the current thread and make it active.
    │ │ │ + │ │ │ +
    BALL::VIEW::GLRenderWindow::renderText
    virtual void renderText(float x, float y, float z, const String &text, const ColorRGBA &color, Size size=16)
    │ │ │ + │ │ │ +
    BALL::VIEW::GLRenderWindow::GLRenderWindow
    GLRenderWindow(QWidget *parent_widget, const char *name=NULL, Qt::WindowFlags w_flags=0)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::GLRenderWindow::gl_format_
    static QGLFormat gl_format_
    Definition glRenderWindow.h:97
    │ │ │ +
    BALL::VIEW::GLRenderWindow::safeBufferSwap
    void safeBufferSwap()
    Call swapBuffers() but first make sure the window is exposed.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,280 +1,248 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ -buildBondsProcessor.h │ │ │ │ + * _V_I_E_W │ │ │ │ + * _R_E_N_D_E_R_I_N_G │ │ │ │ +glRenderWindow.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_STRUCTURE_BUILDBONDSPROCESSOR_H │ │ │ │ -6#define BALL_STRUCTURE_BUILDBONDSPROCESSOR_H │ │ │ │ +5#ifndef BALL_VIEW_RENDERING_GLRENDERWINDOW_H │ │ │ │ +6#define BALL_VIEW_RENDERING_GLRENDERWINDOW_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_CONCEPT_PROCESSOR_H │ │ │ │ -9 #include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ +8#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ +9# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_KERNEL_ATOMCONTAINER_H │ │ │ │ -13 #include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ +12#ifndef BALL_DATATYPE_STRING_H │ │ │ │ +13# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#ifndef BALL_DATATYPE_HASHMAP_H │ │ │ │ -17 #include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ +16#ifndef BALL_VIEW_RENDERING_RENDERWINDOW_H │ │ │ │ +17# include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_r_e_n_d_e_r_W_i_n_d_o_w_._h> │ │ │ │ 18#endif │ │ │ │ 19 │ │ │ │ -20#ifndef BALL_KERNEL_BOND_H │ │ │ │ -21 #include <_B_A_L_L_/_K_E_R_N_E_L_/_b_o_n_d_._h> │ │ │ │ +20#ifndef BALL_VIEW_DATATYPE_COLORRGBA_H │ │ │ │ +21# include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_c_o_l_o_r_R_G_B_A_._h> │ │ │ │ 22#endif │ │ │ │ 23 │ │ │ │ -24#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ -25 #include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +24#ifndef BALL_SYSTEM_MUTEX_H │ │ │ │ +25# include <_B_A_L_L_/_S_Y_S_T_E_M_/_m_u_t_e_x_._h> │ │ │ │ 26#endif │ │ │ │ 27 │ │ │ │ -28namespace _B_A_L_L │ │ │ │ -29{ │ │ │ │ -30 │ │ │ │ -_3_4 class _B_A_L_L___E_X_P_O_R_T _B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r │ │ │ │ -35 : public _U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -36 { │ │ │ │ -37 │ │ │ │ -38 public: │ │ │ │ -39 │ │ │ │ -_4_4 struct _B_A_L_L___E_X_P_O_R_T _O_p_t_i_o_n │ │ │ │ -45 { │ │ │ │ -_4_9 static const char* _B_O_N_D_L_E_N_G_T_H_S___F_I_L_E_N_A_M_E; │ │ │ │ -50 │ │ │ │ -_5_7 static const char* _D_E_L_E_T_E___E_X_I_S_T_I_N_G___B_O_N_D_S; │ │ │ │ +28#include │ │ │ │ +29 │ │ │ │ +30namespace _B_A_L_L │ │ │ │ +31{ │ │ │ │ +32 namespace VIEW │ │ │ │ +33 { │ │ │ │ +_3_7 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _G_L_R_e_n_d_e_r_W_i_n_d_o_w │ │ │ │ +38 : public _R_e_n_d_e_r_W_i_n_d_o_w, │ │ │ │ +39 public _Q_G_L_W_i_d_g_e_t │ │ │ │ +40 { │ │ │ │ +41 │ │ │ │ +42 public: │ │ │ │ +_4_3 _G_L_R_e_n_d_e_r_W_i_n_d_o_w(); │ │ │ │ +_4_4 _G_L_R_e_n_d_e_r_W_i_n_d_o_w(_Q_W_i_d_g_e_t* parent_widget, const char* name = NULL, Qt:: │ │ │ │ +WindowFlags w_flags = 0); │ │ │ │ +_4_5 _G_L_R_e_n_d_e_r_W_i_n_d_o_w(const _G_L_R_e_n_d_e_r_W_i_n_d_o_w& window, _Q_W_i_d_g_e_t* parent_widget, const │ │ │ │ +char* name = NULL, Qt::WindowFlags w_flags = 0); │ │ │ │ +46 │ │ │ │ +_4_7 virtual _~_G_L_R_e_n_d_e_r_W_i_n_d_o_w(); │ │ │ │ +48 │ │ │ │ +49 /* RenderWindow methods */ │ │ │ │ +_5_0 virtual bool _i_n_i_t(); │ │ │ │ +_5_1 virtual bool _r_e_s_i_z_e(const unsigned int width, const unsigned int height); │ │ │ │ +_5_2 virtual void _r_e_f_r_e_s_h(); │ │ │ │ +53 │ │ │ │ +54 // render the given text in the given color and size at window coordinates │ │ │ │ +(x, y) │ │ │ │ +_5_5 virtual void _r_e_n_d_e_r_T_e_x_t(int x, int y, const _S_t_r_i_n_g& text, const _C_o_l_o_r_R_G_B_A& │ │ │ │ +color, _S_i_z_e size = 16); │ │ │ │ +56 // render the given text in the given color and size at world coordinates │ │ │ │ +(x, y, z) │ │ │ │ +_5_7 virtual void _r_e_n_d_e_r_T_e_x_t(float x, float y, float z, const _S_t_r_i_n_g& text, const │ │ │ │ +_C_o_l_o_r_R_G_B_A& color, _S_i_z_e size = 16); │ │ │ │ 58 │ │ │ │ -_6_4 static const char* _R_E_E_S_T_I_M_A_T_E___B_O_N_D_O_R_D_E_R_S___R_I_N_G_S; │ │ │ │ -65 │ │ │ │ -_7_1 static const char* _D_E_L_E_T_E___O_V_E_R_E_S_T_I_M_A_T_E_D___B_O_N_D_S; │ │ │ │ -72 }; │ │ │ │ -73 │ │ │ │ -_7_5 struct _B_A_L_L___E_X_P_O_R_T _D_e_f_a_u_l_t │ │ │ │ -76 { │ │ │ │ -_7_8 static const char* _B_O_N_D_L_E_N_G_T_H_S___F_I_L_E_N_A_M_E; │ │ │ │ -79 │ │ │ │ -_8_1 static const bool _D_E_L_E_T_E___E_X_I_S_T_I_N_G___B_O_N_D_S; │ │ │ │ -82 │ │ │ │ -_8_4 static const bool _R_E_E_S_T_I_M_A_T_E___B_O_N_D_O_R_D_E_R_S___R_I_N_G_S; │ │ │ │ -85 │ │ │ │ -_8_7 static const bool _D_E_L_E_T_E___O_V_E_R_E_S_T_I_M_A_T_E_D___B_O_N_D_S; │ │ │ │ -88 }; │ │ │ │ -90 │ │ │ │ -91 │ │ │ │ +_6_0 void _l_o_c_k_G_L_C_o_n_t_e_x_t(); │ │ │ │ +61 │ │ │ │ +_6_3 void _u_n_l_o_c_k_G_L_C_o_n_t_e_x_t(); │ │ │ │ +64 │ │ │ │ +_6_6 void _i_g_n_o_r_e_E_v_e_n_t_s(bool ignore) {ignore_events_ = ignore;} │ │ │ │ +67 │ │ │ │ +_6_9 void _s_e_t_D_o_w_n_s_a_m_p_l_i_n_g_F_a_c_t_o_r(float dsfactor) │ │ │ │ +70 {down_sampling_factor_ = dsfactor;} │ │ │ │ +71 │ │ │ │ +_7_3 void _s_e_t_S_t_e_r_e_o_D_e_l_t_a(float delta) │ │ │ │ +74 {stereo_delta_ = delta;} │ │ │ │ +75 │ │ │ │ +_7_6 void _s_e_t_u_p_S_t_e_r_e_o(float eye_separation, float focal_length); │ │ │ │ +77 │ │ │ │ +_7_9 void _s_a_f_e_B_u_f_f_e_r_S_w_a_p(); │ │ │ │ +80 │ │ │ │ +_8_2 float _g_e_t_D_o_w_n_s_a_m_p_l_i_n_g_F_a_c_t_o_r() const │ │ │ │ +83 {return down_sampling_factor_;} │ │ │ │ +84 │ │ │ │ +_8_5 float _s_t_e_r_e_o___d_e_l_t_a__; │ │ │ │ +86 │ │ │ │ +87 protected: │ │ │ │ +88 │ │ │ │ +_9_4 virtual void _c_u_s_t_o_m_E_v_e_n_t(_Q_E_v_e_n_t* evt); │ │ │ │ 95 │ │ │ │ -_9_6 _B_A_L_L___C_R_E_A_T_E(_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r); │ │ │ │ -97 │ │ │ │ -_9_9 _B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r(); │ │ │ │ -100 │ │ │ │ -_1_0_2 _B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r(const _B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r& bbp); │ │ │ │ -103 │ │ │ │ -_1_0_7 _B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r(const _S_t_r_i_n_g& file_name); │ │ │ │ -108 │ │ │ │ -_1_1_0 virtual _~_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r(); │ │ │ │ +_9_6 void _p_a_i_n_t_E_v_e_n_t(QPaintEvent* e); │ │ │ │ +_9_7 static QGLFormat _g_l___f_o_r_m_a_t__; │ │ │ │ +98 │ │ │ │ +99 // ID of the fullscreen texture used to paste image into GPU framebuffer │ │ │ │ +_1_0_0 GLuint _m___s_c_r_e_e_n_T_e_x_I_D; │ │ │ │ +101 // type of the texture used │ │ │ │ +_1_0_2 GLenum _F_B___T_E_X_T_U_R_E___T_A_R_G_E_T; │ │ │ │ +103 // format of the GL texture (GL_RGB, GL_RGBA, etc.) │ │ │ │ +_1_0_4 GLenum _F_B___T_E_X_T_U_R_E___F_O_R_M_A_T; │ │ │ │ +105 // internal format specified when creating the textures │ │ │ │ +_1_0_6 GLenum _F_B___I_N_T_E_R_N_A_L___T_E_X_T_U_R_E___F_O_R_M_A_T; │ │ │ │ +107 // data type of the GL texture (GL_FLOAT, GL_UNSIGNED_INT, etc.) │ │ │ │ +_1_0_8 GLenum _F_B___T_E_X_T_U_R_E___D_A_T_A_T_Y_P_E; │ │ │ │ +109 │ │ │ │ +_1_1_0 void _c_r_e_a_t_e_T_e_x_t_u_r_e(const unsigned int winWidth, const unsigned int │ │ │ │ +winHeight); │ │ │ │ +_1_1_1 void _d_e_l_e_t_e_T_e_x_t_u_r_e(); │ │ │ │ 112 │ │ │ │ -116 │ │ │ │ -_1_1_8 virtual bool _s_t_a_r_t(); │ │ │ │ -119 │ │ │ │ -_1_2_1 virtual _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t operator () (_A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ +_1_1_3 void _c_h_e_c_k_G_L(); │ │ │ │ +114 │ │ │ │ +_1_1_5 bool _e_r_r_o_r_I_n_G_L(GLenum& error); │ │ │ │ +_1_1_6 _S_t_r_i_n_g _g_e_t_G_L_E_r_r_o_r_S_t_r_i_n_g(GLenum error); │ │ │ │ +117 │ │ │ │ +_1_1_8 mutable _M_u_t_e_x _c_o_n_t_e_x___m_u_t_e_x__; │ │ │ │ +_1_1_9 bool _i_g_n_o_r_e___e_v_e_n_t_s__; │ │ │ │ +_1_2_0 float _d_o_w_n___s_a_m_p_l_i_n_g___f_a_c_t_o_r__; │ │ │ │ +121 //float stereo_delta_; │ │ │ │ +122 }; │ │ │ │ 123 │ │ │ │ -_1_2_8 _S_i_z_e _g_e_t_N_u_m_b_e_r_O_f_B_o_n_d_s_B_u_i_l_t(); │ │ │ │ -129 │ │ │ │ -_1_3_3 void _s_e_t_B_o_n_d_L_e_n_g_t_h_s(const _S_t_r_i_n_g& file_name); │ │ │ │ -134 │ │ │ │ -_1_3_6 _H_a_s_h_M_a_p_<_S_i_z_e_,_ _H_a_s_h_M_a_p_<_S_i_z_e_,_ _H_a_s_h_M_a_p_<_i_n_t_,_ _f_l_o_a_t_> > > _g_e_t_B_o_n_d_M_a_p() { return │ │ │ │ -bond_lengths_;}; │ │ │ │ -137 │ │ │ │ -139 │ │ │ │ -_1_4_4 _B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r& operator = (const _B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r& bbp); │ │ │ │ -146 │ │ │ │ -_1_5_1 _O_p_t_i_o_n_s _o_p_t_i_o_n_s; │ │ │ │ -152 │ │ │ │ -_1_5_5 void _s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s(); │ │ │ │ -157 │ │ │ │ -158 protected: │ │ │ │ -159 │ │ │ │ -_1_6_1 _S_i_z_e _b_u_i_l_d_B_o_n_d_s_H_a_s_h_G_r_i_d_3__(_A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ -162 │ │ │ │ -_1_6_4 void _e_s_t_i_m_a_t_e_B_o_n_d_O_r_d_e_r_s__(_A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ -165 │ │ │ │ -_1_6_7 void _r_e_e_s_t_i_m_a_t_e_B_o_n_d_O_r_d_e_r_s_R_i_n_g_s__(_A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ -168 │ │ │ │ -_1_7_0 void _d_e_l_e_t_e_O_v_e_r_e_s_t_i_m_a_t_e_d_B_o_n_d_s__(_A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ -171 │ │ │ │ -_1_7_5 void _r_e_a_d_B_o_n_d_L_e_n_g_t_h_s_F_r_o_m_F_i_l_e__(const _S_t_r_i_n_g& file_name = ""); │ │ │ │ -176 │ │ │ │ -_1_7_8 _S_i_z_e _n_u_m___b_o_n_d_s__; │ │ │ │ -179 │ │ │ │ -_1_8_1 _H_a_s_h_M_a_p_<_S_i_z_e_,_ _H_a_s_h_M_a_p_<_S_i_z_e_,_ _H_a_s_h_M_a_p_<_i_n_t_,_ _f_l_o_a_t_> > > _b_o_n_d___l_e_n_g_t_h_s__; │ │ │ │ -182 │ │ │ │ -_1_8_4 _H_a_s_h_M_a_p_<_S_i_z_e_,_ _H_a_s_h_M_a_p_<_S_i_z_e_,_ _f_l_o_a_t_> > _m_a_x___b_o_n_d___l_e_n_g_t_h_s__; │ │ │ │ -185 │ │ │ │ -_1_8_7 _H_a_s_h_M_a_p_<_S_i_z_e_,_ _H_a_s_h_M_a_p_<_S_i_z_e_,_ _f_l_o_a_t_> > _m_i_n___b_o_n_d___l_e_n_g_t_h_s__; │ │ │ │ -188 │ │ │ │ -189 /*_ returns the best fitting bond order of a bond between atoms of │ │ │ │ -190 element e1 and element e2 with a distance of length │ │ │ │ -191 */ │ │ │ │ -_1_9_2 _B_o_n_d_:_:_B_o_n_d_O_r_d_e_r _g_e_t_N_e_a_r_e_s_t_B_o_n_d_O_r_d_e_r__(float length, _S_i_z_e e1, _S_i_z_e e2); │ │ │ │ -193 │ │ │ │ -194 /*_ Returns true if the atom with atomic number an1 and atom with │ │ │ │ -195 atomic number an2 can share a bond. If, the parameter length │ │ │ │ -196 holds the maximal length of such a bond. │ │ │ │ -197 */ │ │ │ │ -_1_9_8 bool _g_e_t_M_a_x_B_o_n_d_L_e_n_g_t_h__(float& length, _S_i_z_e an1, _S_i_z_e an2); │ │ │ │ -199 │ │ │ │ -200 /*_ Returns true if the atom with atomic number an1 and atom with │ │ │ │ -201 atomic number an2 can share a bond. If, the parameter length │ │ │ │ -202 holds the minimal length of such a bond. │ │ │ │ -203 */ │ │ │ │ -_2_0_4 bool _g_e_t_M_i_n_B_o_n_d_L_e_n_g_t_h__(float& length, _S_i_z_e an1, _S_i_z_e an2); │ │ │ │ -205 │ │ │ │ -_2_0_7 float _m_a_x___l_e_n_g_t_h__; │ │ │ │ -208 }; │ │ │ │ -209 │ │ │ │ -210} // namespace BALL │ │ │ │ -211 │ │ │ │ -212 │ │ │ │ -213#endif // BALL_STRUCTURE_BUILDBONDSPROCESSOR_H │ │ │ │ -_b_o_n_d_._h │ │ │ │ -_a_t_o_m_C_o_n_t_a_i_n_e_r_._h │ │ │ │ -_o_p_t_i_o_n_s_._h │ │ │ │ -_h_a_s_h_M_a_p_._h │ │ │ │ -_p_r_o_c_e_s_s_o_r_._h │ │ │ │ +124 } // namespace VIEW │ │ │ │ +125 │ │ │ │ +126} // namespace BALL │ │ │ │ +127 │ │ │ │ +128#endif // BALL_VIEW_RENDERING_GLRENDERWINDOW_H │ │ │ │ +_c_o_l_o_r_R_G_B_A_._h │ │ │ │ +_r_e_n_d_e_r_W_i_n_d_o_w_._h │ │ │ │ +_m_u_t_e_x_._h │ │ │ │ +_s_t_r_i_n_g_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t │ │ │ │ -int Result │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_6_0 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_M_a_p │ │ │ │ -HashMap class based on the STL map (containing serveral convenience functions) │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_M_a_p_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ -DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ _B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_B_o_n_d_:_:_B_o_n_d_O_r_d_e_r │ │ │ │ -BondOrder │ │ │ │ -DDeeffiinniittiioonn _b_o_n_d_._h_:_9_7 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r │ │ │ │ -BuildBondsProcessor() │ │ │ │ -default constructor │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_g_e_t_N_u_m_b_e_r_O_f_B_o_n_d_s_B_u_i_l_t │ │ │ │ -Size getNumberOfBondsBuilt() │ │ │ │ -Return the number of bonds built during the last application. │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_m_a_x___b_o_n_d___l_e_n_g_t_h_s__ │ │ │ │ -HashMap< Size, HashMap< Size, float > > max_bond_lengths_ │ │ │ │ -structure were the bond maxima stored in (used in buildBonds_) │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_1_8_4 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_b_u_i_l_d_B_o_n_d_s_H_a_s_h_G_r_i_d_3__ │ │ │ │ -Size buildBondsHashGrid3_(AtomContainer &ac) │ │ │ │ -builds bonds, based on atom distances read from parameter file using a 3D hash │ │ │ │ -grid │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_n_u_m___b_o_n_d_s__ │ │ │ │ -Size num_bonds_ │ │ │ │ -number of bonds, which are created during the processor call │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_1_7_8 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_s_t_a_r_t │ │ │ │ -virtual bool start() │ │ │ │ -processor method which is called before the operator () call │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_b_o_n_d___l_e_n_g_t_h_s__ │ │ │ │ -HashMap< Size, HashMap< Size, HashMap< int, float > > > bond_lengths_ │ │ │ │ -structure where bond order distances are stored in │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_1_8_1 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_s_e_t_B_o_n_d_L_e_n_g_t_h_s │ │ │ │ -void setBondLengths(const String &file_name) │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_g_e_t_M_a_x_B_o_n_d_L_e_n_g_t_h__ │ │ │ │ -bool getMaxBondLength_(float &length, Size an1, Size an2) │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_m_a_x___l_e_n_g_t_h__ │ │ │ │ -float max_length_ │ │ │ │ -parameter which holds the longest possible bond │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_2_0_7 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_g_e_t_B_o_n_d_M_a_p │ │ │ │ -HashMap< Size, HashMap< Size, HashMap< int, float > > > getBondMap() │ │ │ │ -Return the bond length Hashmap. │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_1_3_6 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r │ │ │ │ -BuildBondsProcessor(const BuildBondsProcessor &bbp) │ │ │ │ -copy construcor │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_g_e_t_N_e_a_r_e_s_t_B_o_n_d_O_r_d_e_r__ │ │ │ │ -Bond::BondOrder getNearestBondOrder_(float length, Size e1, Size e2) │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_g_e_t_M_i_n_B_o_n_d_L_e_n_g_t_h__ │ │ │ │ -bool getMinBondLength_(float &length, Size an1, Size an2) │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_r_e_e_s_t_i_m_a_t_e_B_o_n_d_O_r_d_e_r_s_R_i_n_g_s__ │ │ │ │ -void reestimateBondOrdersRings_(AtomContainer &ac) │ │ │ │ -reestimate the bond orders of rings, as aromatic rings are often detected wrong │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_e_s_t_i_m_a_t_e_B_o_n_d_O_r_d_e_r_s__ │ │ │ │ -void estimateBondOrders_(AtomContainer &ac) │ │ │ │ -after the bonds are built, the orders are estimated │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_B_A_L_L___C_R_E_A_T_E │ │ │ │ -BALL_CREATE(BuildBondsProcessor) │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_~_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r │ │ │ │ -virtual ~BuildBondsProcessor() │ │ │ │ -destructor │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s │ │ │ │ -void setDefaultOptions() │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_o_p_t_i_o_n_s │ │ │ │ -Options options │ │ │ │ -options │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_1_5_1 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_m_i_n___b_o_n_d___l_e_n_g_t_h_s__ │ │ │ │ -HashMap< Size, HashMap< Size, float > > min_bond_lengths_ │ │ │ │ -structure were the bond minima stored in (used in buildBonds_) │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_1_8_7 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_d_e_l_e_t_e_O_v_e_r_e_s_t_i_m_a_t_e_d_B_o_n_d_s__ │ │ │ │ -void deleteOverestimatedBonds_(AtomContainer &ac) │ │ │ │ -deletes bonds, like from multiple bonded hydrogens or halogens │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_r_e_a_d_B_o_n_d_L_e_n_g_t_h_s_F_r_o_m_F_i_l_e__ │ │ │ │ -void readBondLengthsFromFile_(const String &file_name="") │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r │ │ │ │ -BuildBondsProcessor(const String &file_name) │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ -Option names. │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_4_5 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_R_E_E_S_T_I_M_A_T_E___B_O_N_D_O_R_D_E_R_S___R_I_N_G_S │ │ │ │ -static const char * REESTIMATE_BONDORDERS_RINGS │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_6_4 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_D_E_L_E_T_E___O_V_E_R_E_S_T_I_M_A_T_E_D___B_O_N_D_S │ │ │ │ -static const char * DELETE_OVERESTIMATED_BONDS │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_7_1 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_B_O_N_D_L_E_N_G_T_H_S___F_I_L_E_N_A_M_E │ │ │ │ -static const char * BONDLENGTHS_FILENAME │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_4_9 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_D_E_L_E_T_E___E_X_I_S_T_I_N_G___B_O_N_D_S │ │ │ │ -static const char * DELETE_EXISTING_BONDS │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ -Default values for options. │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_7_6 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_B_O_N_D_L_E_N_G_T_H_S___F_I_L_E_N_A_M_E │ │ │ │ -static const char * BONDLENGTHS_FILENAME │ │ │ │ -default file name for the bond lengths │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_7_8 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_D_E_L_E_T_E___O_V_E_R_E_S_T_I_M_A_T_E_D___B_O_N_D_S │ │ │ │ -static const bool DELETE_OVERESTIMATED_BONDS │ │ │ │ -this option is off by default │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_8_7 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_R_E_E_S_T_I_M_A_T_E___B_O_N_D_O_R_D_E_R_S___R_I_N_G_S │ │ │ │ -static const bool REESTIMATE_BONDORDERS_RINGS │ │ │ │ -this option is off by default │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_8_4 │ │ │ │ -_B_A_L_L_:_:_B_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_D_E_L_E_T_E___E_X_I_S_T_I_N_G___B_O_N_D_S │ │ │ │ -static const bool DELETE_EXISTING_BONDS │ │ │ │ -this option is off by default │ │ │ │ -DDeeffiinniittiioonn _b_u_i_l_d_B_o_n_d_s_P_r_o_c_e_s_s_o_r_._h_:_8_1 │ │ │ │ +_B_A_L_L_:_:_T_M_u_t_e_x_<_ _B_A_L_L___D_E_F_A_U_L_T___M_U_T_E_X___T_Y_P_E_ _> │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_C_o_l_o_r_R_G_B_A │ │ │ │ +DDeeffiinniittiioonn _c_o_l_o_r_R_G_B_A_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_4_0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w │ │ │ │ +GLRenderWindow(const GLRenderWindow &window, QWidget *parent_widget, const char │ │ │ │ +*name=NULL, Qt::WindowFlags w_flags=0) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_e_r_r_o_r_I_n_G_L │ │ │ │ +bool errorInGL(GLenum &error) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_c_r_e_a_t_e_T_e_x_t_u_r_e │ │ │ │ +void createTexture(const unsigned int winWidth, const unsigned int winHeight) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_l_o_c_k_G_L_C_o_n_t_e_x_t │ │ │ │ +void lockGLContext() │ │ │ │ +Lock the context for the current thread and make it active. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_i_n_i_t │ │ │ │ +virtual bool init() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_c_o_n_t_e_x___m_u_t_e_x__ │ │ │ │ +Mutex contex_mutex_ │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_1_1_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_p_a_i_n_t_E_v_e_n_t │ │ │ │ +void paintEvent(QPaintEvent *e) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_F_B___T_E_X_T_U_R_E___F_O_R_M_A_T │ │ │ │ +GLenum FB_TEXTURE_FORMAT │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_1_0_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_r_e_n_d_e_r_T_e_x_t │ │ │ │ +virtual void renderText(int x, int y, const String &text, const ColorRGBA │ │ │ │ +&color, Size size=16) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_s_e_t_u_p_S_t_e_r_e_o │ │ │ │ +void setupStereo(float eye_separation, float focal_length) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_F_B___T_E_X_T_U_R_E___T_A_R_G_E_T │ │ │ │ +GLenum FB_TEXTURE_TARGET │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_1_0_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_m___s_c_r_e_e_n_T_e_x_I_D │ │ │ │ +GLuint m_screenTexID │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_1_0_0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_s_e_t_S_t_e_r_e_o_D_e_l_t_a │ │ │ │ +void setStereoDelta(float delta) │ │ │ │ +Set the stereo delta for raytracing in pixels. │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_s_e_t_D_o_w_n_s_a_m_p_l_i_n_g_F_a_c_t_o_r │ │ │ │ +void setDownsamplingFactor(float dsfactor) │ │ │ │ +Set the window's downsampling factor. This is a speed up factor. │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_6_9 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_c_u_s_t_o_m_E_v_e_n_t │ │ │ │ +virtual void customEvent(QEvent *evt) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_~_G_L_R_e_n_d_e_r_W_i_n_d_o_w │ │ │ │ +virtual ~GLRenderWindow() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_g_e_t_G_L_E_r_r_o_r_S_t_r_i_n_g │ │ │ │ +String getGLErrorString(GLenum error) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_i_g_n_o_r_e_E_v_e_n_t_s │ │ │ │ +void ignoreEvents(bool ignore) │ │ │ │ +Force the window to ignore paint events. │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_6_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_r_e_s_i_z_e │ │ │ │ +virtual bool resize(const unsigned int width, const unsigned int height) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w │ │ │ │ +GLRenderWindow() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_g_e_t_D_o_w_n_s_a_m_p_l_i_n_g_F_a_c_t_o_r │ │ │ │ +float getDownsamplingFactor() const │ │ │ │ +Get the window's downsampling factor. │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_8_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_u_n_l_o_c_k_G_L_C_o_n_t_e_x_t │ │ │ │ +void unlockGLContext() │ │ │ │ +Unlock the context for the current thread and make it active. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_i_g_n_o_r_e___e_v_e_n_t_s__ │ │ │ │ +bool ignore_events_ │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_1_1_9 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_r_e_n_d_e_r_T_e_x_t │ │ │ │ +virtual void renderText(float x, float y, float z, const String &text, const │ │ │ │ +ColorRGBA &color, Size size=16) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_d_o_w_n___s_a_m_p_l_i_n_g___f_a_c_t_o_r__ │ │ │ │ +float down_sampling_factor_ │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_1_2_0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w │ │ │ │ +GLRenderWindow(QWidget *parent_widget, const char *name=NULL, Qt::WindowFlags │ │ │ │ +w_flags=0) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_F_B___I_N_T_E_R_N_A_L___T_E_X_T_U_R_E___F_O_R_M_A_T │ │ │ │ +GLenum FB_INTERNAL_TEXTURE_FORMAT │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_1_0_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_r_e_f_r_e_s_h │ │ │ │ +virtual void refresh() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_g_l___f_o_r_m_a_t__ │ │ │ │ +static QGLFormat gl_format_ │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_9_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_s_a_f_e_B_u_f_f_e_r_S_w_a_p │ │ │ │ +void safeBufferSwap() │ │ │ │ +Call swapBuffers() but first make sure the window is exposed. │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_F_B___T_E_X_T_U_R_E___D_A_T_A_T_Y_P_E │ │ │ │ +GLenum FB_TEXTURE_DATATYPE │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_1_0_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_s_t_e_r_e_o___d_e_l_t_a__ │ │ │ │ +float stereo_delta_ │ │ │ │ +DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_8_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_d_e_l_e_t_e_T_e_x_t_u_r_e │ │ │ │ +void deleteTexture() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w_:_:_c_h_e_c_k_G_L │ │ │ │ +void checkGL() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_T_R_e_n_d_e_r_W_i_n_d_o_w │ │ │ │ +DDeeffiinniittiioonn _r_e_n_d_e_r_W_i_n_d_o_w_._h_:_3_4 │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_Q_W_i_d_g_e_t │ │ │ │ +_Q_E_v_e_n_t │ │ │ │ +_Q_G_L_W_i_d_g_e_t │ │ │ │ +_g_l_o_b_a_l_._h │ │ │ │ +_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ +#define BALL_VIEW_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d7e/a03138.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::Exception::Precondition Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/COMMON/exception.h>

    │ │ │ +

    #include <BALL/COMMON/exception.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::Exception::Precondition:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::Exception::GeneralException │ │ │ @@ -138,15 +138,15 @@ │ │ │   │ │ │ std::string message_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Precondition failed. A precondition (as defined by BALL_PRECONDITION_EXCEPTION) has failed.

    │ │ │ │ │ │ -

    Definition at line 398 of file COMMON/exception.h.

    │ │ │ +

    Definition at line 398 of file COMMON/exception.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ Precondition()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d7e/a04594.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::KernelPredicate< Residue > Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/KERNEL/predicate.h>

    │ │ │ +

    #include <BALL/KERNEL/predicate.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::KernelPredicate< Residue >:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::UnaryPredicate< Composite > │ │ │ @@ -112,15 +112,15 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    virtual ~UnaryPredicate ()
     
    virtual bool operator() (const Composite &) const
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 119 of file KERNEL/predicate.h.

    │ │ │ +

    Definition at line 119 of file KERNEL/predicate.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ~KernelPredicate()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -137,15 +137,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inlinevirtual
    │ │ │
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    Definition at line 126 of file KERNEL/predicate.h.

    │ │ │ +

    Definition at line 126 of file KERNEL/predicate.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ operator()()

    │ │ │ │ │ │ @@ -168,15 +168,15 @@ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Constant virtual RTTI evaluation operator.

    │ │ │ │ │ │ -

    Definition at line 160 of file KERNEL/predicate.h.

    │ │ │ +

    Definition at line 160 of file KERNEL/predicate.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d82/a00857.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: ILPBondOrderStrategy.h File Reference │ │ │ +BALL: rescoring1D.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,62 +65,38 @@ │ │ │
    │ │ │
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    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces | │ │ │ -Typedefs
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    ILPBondOrderStrategy.h File Reference
    │ │ │ +Namespaces
    │ │ │ +
    rescoring1D.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/STRUCTURE/BONDORDERS/bondOrderAssignmentStrategy.h>
    │ │ │ -#include <BALL/STRUCTURE/BONDORDERS/bondOrderAssignment.h>
    │ │ │ +
    #include <BALL/SCORING/FUNCTIONS/rescoring.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::ILPBondOrderStrategy
    class  BALL::Rescoring1D
     
    │ │ │ │ │ │ │ │ │ │ │ │ -

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │

    │ │ │ -Typedefs

    typedef struct _lprec lprec
     
    │ │ │ -

    Typedef Documentation

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    ◆ lprec

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    typedef struct _lprec lprec
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    Definition at line 13 of file ILPBondOrderStrategy.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,28 +1,20 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ - * _B_O_N_D_O_R_D_E_R_S │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _T_y_p_e_d_e_f_s │ │ │ │ -ILPBondOrderStrategy.h File Reference │ │ │ │ -#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_B_O_N_D_O_R_D_E_R_S_/_b_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_S_t_r_a_t_e_g_y_._h> │ │ │ │ -#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_B_O_N_D_O_R_D_E_R_S_/_b_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h> │ │ │ │ + * _S_C_O_R_I_N_G │ │ │ │ + * _F_U_N_C_T_I_O_N_S │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ +rescoring1D.h File Reference │ │ │ │ +#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_F_U_N_C_T_I_O_N_S_/_r_e_s_c_o_r_i_n_g_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y │ │ │ │ +class   _B_A_L_L_:_:_R_e_s_c_o_r_i_n_g_1_D │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -TTyyppeeddeeffss │ │ │ │ -typedef struct _lprec  _l_p_r_e_c │ │ │ │ -  │ │ │ │ -********** TTyyppeeddeeff DDooccuummeennttaattiioonn ********** │ │ │ │ -********** _?◆_? llpprreecc ********** │ │ │ │ -typedef struct _lprec _l_p_r_e_c │ │ │ │ -Definition at line _1_3 of file _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d82/a00857_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: ILPBondOrderStrategy.h Source File │ │ │ +BALL: rescoring1D.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,97 +70,62 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
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    │ │ │ -
    ILPBondOrderStrategy.h
    │ │ │ +
    rescoring1D.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1#ifndef BALL_STRUCTURE_BONDORDERS_ILPBONDORDERSTRATEGY_H
    │ │ │ -
    2#define BALL_STRUCTURE_BONDORDERS_ILPBONDORDERSTRATEGY_H
    │ │ │ -
    3
    │ │ │ -
    4#ifndef BALL_STRUCTURE_BONDORDERS_BONDORDERASSIGNMENTSTRATEGY_H
    │ │ │ -
    5# include <BALL/STRUCTURE/BONDORDERS/bondOrderAssignmentStrategy.h>
    │ │ │ -
    6#endif
    │ │ │ -
    7
    │ │ │ -
    8#ifndef BALL_STRUCTURE_BONDORDERS_BONDORDERASSIGNMENT_H
    │ │ │ -
    9# include <BALL/STRUCTURE/BONDORDERS/bondOrderAssignment.h>
    │ │ │ -
    10#endif
    │ │ │ -
    11// forward declaration for lp_solve
    │ │ │ -
    12struct _lprec;
    │ │ │ -
    13typedef struct _lprec lprec;
    │ │ │ -
    14
    │ │ │ -
    15namespace BALL
    │ │ │ -
    16{
    │ │ │ -
    │ │ │ -
    23 class ILPBondOrderStrategy
    │ │ │ -
    24 : public BondOrderAssignmentStrategy
    │ │ │ -
    25 {
    │ │ │ -
    26 public:
    │ │ │ -
    27 ILPBondOrderStrategy(AssignBondOrderProcessor* parent);
    │ │ │ -
    28 virtual ~ILPBondOrderStrategy();
    │ │ │ -
    29
    │ │ │ -
    30 virtual void clear();
    │ │ │ -
    31 virtual void init();
    │ │ │ -
    32
    │ │ │ -
    33 virtual bool readOptions(const Options& options);
    │ │ │ -
    34 virtual void setDefaultOptions();
    │ │ │ -
    35
    │ │ │ -
    36 virtual boost::shared_ptr<BondOrderAssignment> computeNextSolution();
    │ │ │ -
    37
    │ │ │ -
    38 protected:
    │ │ │ -
    39 bool valid_;
    │ │ │ -
    40
    │ │ │ -
    41 // Vector for mapping from variable indices onto free bonds in the
    │ │ │ -
    42 // order used by the ILP
    │ │ │ -
    43 std::vector<Bond*> index_to_free_bond_;
    │ │ │ -
    44
    │ │ │ -
    45 // number of bond variables in the ILP
    │ │ │ -
    46 Position number_of_free_bonds_;
    │ │ │ -
    47
    │ │ │ -
    48 // Constant penalty (fixed bonds)
    │ │ │ -
    49 float const_penalty_;
    │ │ │ -
    50
    │ │ │ -
    51 // flag indicating whether constraints need to be added
    │ │ │ -
    52 bool first_solution_;
    │ │ │ -
    53
    │ │ │ -
    54 // the ilp
    │ │ │ -
    55 lprec* ilp_;
    │ │ │ -
    56 };
    │ │ │ -
    │ │ │ -
    57}
    │ │ │ -
    58#endif // BALL_STRUCTURE_BONDORDERS_ILPBONDORDERSTRATEGY_H
    │ │ │ - │ │ │ - │ │ │ -
    lprec
    struct _lprec lprec
    Definition ILPBondOrderStrategy.h:13
    │ │ │ - │ │ │ - │ │ │ -
    BALL::AssignBondOrderProcessor
    Assignment of bond orders from topology information.
    Definition assignBondOrderProcessor.h:90
    │ │ │ -
    BALL::BondOrderAssignmentStrategy
    Base class for bond order assignment algorithms.
    Definition bondOrderAssignmentStrategy.h:27
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::ILPBondOrderStrategy::index_to_free_bond_
    std::vector< Bond * > index_to_free_bond_
    Definition ILPBondOrderStrategy.h:43
    │ │ │ -
    BALL::ILPBondOrderStrategy::setDefaultOptions
    virtual void setDefaultOptions()
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::ILPBondOrderStrategy::ILPBondOrderStrategy
    ILPBondOrderStrategy(AssignBondOrderProcessor *parent)
    │ │ │ -
    BALL::ILPBondOrderStrategy::computeNextSolution
    virtual boost::shared_ptr< BondOrderAssignment > computeNextSolution()
    │ │ │ - │ │ │ -
    BALL::ILPBondOrderStrategy::readOptions
    virtual bool readOptions(const Options &options)
    │ │ │ - │ │ │ +Go to the documentation of this file.
    1// ----------------------------------------------------
    │ │ │ +
    2// $Maintainer: Marcel Schumann $
    │ │ │ +
    3// $Authors: Marcel Schumann $
    │ │ │ +
    4// ----------------------------------------------------
    │ │ │ +
    5
    │ │ │ +
    6#ifndef BALL_SCORING_FUNCTIONS_RESCORING1D_H
    │ │ │ +
    7#define BALL_SCORING_FUNCTIONS_RESCORING1D_H
    │ │ │ +
    8
    │ │ │ +
    9#include <BALL/SCORING/FUNCTIONS/rescoring.h>
    │ │ │ +
    10
    │ │ │ +
    11namespace BALL
    │ │ │ +
    12{
    │ │ │ +
    │ │ │ +
    13 class BALL_EXPORT Rescoring1D : public Rescoring
    │ │ │ +
    14 {
    │ │ │ +
    15 public:
    │ │ │ +
    16 Rescoring1D(AtomContainer& receptor, AtomContainer& reference_ligand, Options& options, String free_energy_label, ScoringFunction* sf);
    │ │ │ +
    17
    │ │ │ +
    18 protected:
    │ │ │ +
    19 void setup_();
    │ │ │ +
    20 const Protein* protein_;
    │ │ │ +
    21 void generateScoreContributions_(vector<vector<double> >* matrix, vector<double>* v);
    │ │ │ +
    22 };
    │ │ │ +
    │ │ │ +
    23}
    │ │ │ +
    24
    │ │ │ +
    25#endif
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Rescoring1D::protein_
    const Protein * protein_
    Definition rescoring1D.h:20
    │ │ │ +
    BALL::Rescoring1D::generateScoreContributions_
    void generateScoreContributions_(vector< vector< double > > *matrix, vector< double > *v)
    │ │ │ + │ │ │ +
    BALL::Rescoring1D::Rescoring1D
    Rescoring1D(AtomContainer &receptor, AtomContainer &reference_ligand, Options &options, String free_energy_label, ScoringFunction *sf)
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,114 +1,70 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ - * _B_O_N_D_O_R_D_E_R_S │ │ │ │ -ILPBondOrderStrategy.h │ │ │ │ + * _S_C_O_R_I_N_G │ │ │ │ + * _F_U_N_C_T_I_O_N_S │ │ │ │ +rescoring1D.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1#ifndef BALL_STRUCTURE_BONDORDERS_ILPBONDORDERSTRATEGY_H │ │ │ │ -2#define BALL_STRUCTURE_BONDORDERS_ILPBONDORDERSTRATEGY_H │ │ │ │ -3 │ │ │ │ -4#ifndef BALL_STRUCTURE_BONDORDERS_BONDORDERASSIGNMENTSTRATEGY_H │ │ │ │ -5# include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_B_O_N_D_O_R_D_E_R_S_/_b_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_S_t_r_a_t_e_g_y_._h> │ │ │ │ -6#endif │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_STRUCTURE_BONDORDERS_BONDORDERASSIGNMENT_H │ │ │ │ -9# include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_B_O_N_D_O_R_D_E_R_S_/_b_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h> │ │ │ │ -10#endif │ │ │ │ -11// forward declaration for lp_solve │ │ │ │ -12struct _lprec; │ │ │ │ -_1_3typedef struct _lprec _l_p_r_e_c; │ │ │ │ -14 │ │ │ │ -15namespace _B_A_L_L │ │ │ │ -16{ │ │ │ │ -_2_3 class _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y │ │ │ │ -24 : public _B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_S_t_r_a_t_e_g_y │ │ │ │ -25 { │ │ │ │ -26 public: │ │ │ │ -_2_7 _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y(_A_s_s_i_g_n_B_o_n_d_O_r_d_e_r_P_r_o_c_e_s_s_o_r* parent); │ │ │ │ -_2_8 virtual _~_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y(); │ │ │ │ -29 │ │ │ │ -_3_0 virtual void _c_l_e_a_r(); │ │ │ │ -_3_1 virtual void _i_n_i_t(); │ │ │ │ -32 │ │ │ │ -_3_3 virtual bool _r_e_a_d_O_p_t_i_o_n_s(const _O_p_t_i_o_n_s& options); │ │ │ │ -_3_4 virtual void _s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s(); │ │ │ │ -35 │ │ │ │ -_3_6 virtual boost::shared_ptr _c_o_m_p_u_t_e_N_e_x_t_S_o_l_u_t_i_o_n(); │ │ │ │ -37 │ │ │ │ -38 protected: │ │ │ │ -_3_9 bool _v_a_l_i_d__; │ │ │ │ -40 │ │ │ │ -41 // Vector for mapping from variable indices onto free bonds in the │ │ │ │ -42 // order used by the ILP │ │ │ │ -_4_3 std::vector _i_n_d_e_x___t_o___f_r_e_e___b_o_n_d__; │ │ │ │ -44 │ │ │ │ -45 // number of bond variables in the ILP │ │ │ │ -_4_6 _P_o_s_i_t_i_o_n _n_u_m_b_e_r___o_f___f_r_e_e___b_o_n_d_s__; │ │ │ │ -47 │ │ │ │ -48 // Constant penalty (fixed bonds) │ │ │ │ -_4_9 float _c_o_n_s_t___p_e_n_a_l_t_y__; │ │ │ │ -50 │ │ │ │ -51 // flag indicating whether constraints need to be added │ │ │ │ -_5_2 bool _f_i_r_s_t___s_o_l_u_t_i_o_n__; │ │ │ │ -53 │ │ │ │ -54 // the ilp │ │ │ │ -_5_5 _l_p_r_e_c* _i_l_p__; │ │ │ │ -56 }; │ │ │ │ -57} │ │ │ │ -58#endif // BALL_STRUCTURE_BONDORDERS_ILPBONDORDERSTRATEGY_H │ │ │ │ -_b_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_S_t_r_a_t_e_g_y_._h │ │ │ │ -_b_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_._h │ │ │ │ -_l_p_r_e_c │ │ │ │ -struct _lprec lprec │ │ │ │ -DDeeffiinniittiioonn _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_._h_:_1_3 │ │ │ │ +1// ---------------------------------------------------- │ │ │ │ +2// $Maintainer: Marcel Schumann $ │ │ │ │ +3// $Authors: Marcel Schumann $ │ │ │ │ +4// ---------------------------------------------------- │ │ │ │ +5 │ │ │ │ +6#ifndef BALL_SCORING_FUNCTIONS_RESCORING1D_H │ │ │ │ +7#define BALL_SCORING_FUNCTIONS_RESCORING1D_H │ │ │ │ +8 │ │ │ │ +9#include <_B_A_L_L_/_S_C_O_R_I_N_G_/_F_U_N_C_T_I_O_N_S_/_r_e_s_c_o_r_i_n_g_._h> │ │ │ │ +10 │ │ │ │ +11namespace _B_A_L_L │ │ │ │ +12{ │ │ │ │ +_1_3 class _B_A_L_L___E_X_P_O_R_T _R_e_s_c_o_r_i_n_g_1_D : public _R_e_s_c_o_r_i_n_g │ │ │ │ +14 { │ │ │ │ +15 public: │ │ │ │ +_1_6 _R_e_s_c_o_r_i_n_g_1_D(_A_t_o_m_C_o_n_t_a_i_n_e_r& receptor, _A_t_o_m_C_o_n_t_a_i_n_e_r& reference_ligand, │ │ │ │ +_O_p_t_i_o_n_s& options, _S_t_r_i_n_g free_energy_label, _S_c_o_r_i_n_g_F_u_n_c_t_i_o_n* sf); │ │ │ │ +17 │ │ │ │ +18 protected: │ │ │ │ +_1_9 void _s_e_t_u_p__(); │ │ │ │ +_2_0 const _P_r_o_t_e_i_n* _p_r_o_t_e_i_n__; │ │ │ │ +_2_1 void _g_e_n_e_r_a_t_e_S_c_o_r_e_C_o_n_t_r_i_b_u_t_i_o_n_s__(vector >* matrix, │ │ │ │ +vector* v); │ │ │ │ +22 }; │ │ │ │ +23} │ │ │ │ +24 │ │ │ │ +25#endif │ │ │ │ +_r_e_s_c_o_r_i_n_g_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ _B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_A_s_s_i_g_n_B_o_n_d_O_r_d_e_r_P_r_o_c_e_s_s_o_r │ │ │ │ -Assignment of bond orders from topology information. │ │ │ │ -DDeeffiinniittiioonn _a_s_s_i_g_n_B_o_n_d_O_r_d_e_r_P_r_o_c_e_s_s_o_r_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_B_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_S_t_r_a_t_e_g_y │ │ │ │ -Base class for bond order assignment algorithms. │ │ │ │ -DDeeffiinniittiioonn _b_o_n_d_O_r_d_e_r_A_s_s_i_g_n_m_e_n_t_S_t_r_a_t_e_g_y_._h_:_2_7 │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y │ │ │ │ -DDeeffiinniittiioonn _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_._h_:_2_5 │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_i_l_p__ │ │ │ │ -lprec * ilp_ │ │ │ │ -DDeeffiinniittiioonn _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_._h_:_5_5 │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_~_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y │ │ │ │ -virtual ~ILPBondOrderStrategy() │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_i_n_d_e_x___t_o___f_r_e_e___b_o_n_d__ │ │ │ │ -std::vector< Bond * > index_to_free_bond_ │ │ │ │ -DDeeffiinniittiioonn _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s │ │ │ │ -virtual void setDefaultOptions() │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_i_n_i_t │ │ │ │ -virtual void init() │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_v_a_l_i_d__ │ │ │ │ -bool valid_ │ │ │ │ -DDeeffiinniittiioonn _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_._h_:_3_9 │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_n_u_m_b_e_r___o_f___f_r_e_e___b_o_n_d_s__ │ │ │ │ -Position number_of_free_bonds_ │ │ │ │ -DDeeffiinniittiioonn _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_c_l_e_a_r │ │ │ │ -virtual void clear() │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_c_o_n_s_t___p_e_n_a_l_t_y__ │ │ │ │ -float const_penalty_ │ │ │ │ -DDeeffiinniittiioonn _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_._h_:_4_9 │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y │ │ │ │ -ILPBondOrderStrategy(AssignBondOrderProcessor *parent) │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_c_o_m_p_u_t_e_N_e_x_t_S_o_l_u_t_i_o_n │ │ │ │ -virtual boost::shared_ptr< BondOrderAssignment > computeNextSolution() │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_f_i_r_s_t___s_o_l_u_t_i_o_n__ │ │ │ │ -bool first_solution_ │ │ │ │ -DDeeffiinniittiioonn _I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_._h_:_5_2 │ │ │ │ -_B_A_L_L_:_:_I_L_P_B_o_n_d_O_r_d_e_r_S_t_r_a_t_e_g_y_:_:_r_e_a_d_O_p_t_i_o_n_s │ │ │ │ -virtual bool readOptions(const Options &options) │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_P_r_o_t_e_i_n │ │ │ │ +DDeeffiinniittiioonn _p_r_o_t_e_i_n_._h_:_3_0 │ │ │ │ +_B_A_L_L_:_:_S_c_o_r_i_n_g_F_u_n_c_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _s_c_o_r_i_n_g_F_u_n_c_t_i_o_n_._h_:_2_9 │ │ │ │ +_B_A_L_L_:_:_R_e_s_c_o_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _r_e_s_c_o_r_i_n_g_._h_:_1_8 │ │ │ │ +_B_A_L_L_:_:_R_e_s_c_o_r_i_n_g_1_D │ │ │ │ +DDeeffiinniittiioonn _r_e_s_c_o_r_i_n_g_1_D_._h_:_1_4 │ │ │ │ +_B_A_L_L_:_:_R_e_s_c_o_r_i_n_g_1_D_:_:_p_r_o_t_e_i_n__ │ │ │ │ +const Protein * protein_ │ │ │ │ +DDeeffiinniittiioonn _r_e_s_c_o_r_i_n_g_1_D_._h_:_2_0 │ │ │ │ +_B_A_L_L_:_:_R_e_s_c_o_r_i_n_g_1_D_:_:_g_e_n_e_r_a_t_e_S_c_o_r_e_C_o_n_t_r_i_b_u_t_i_o_n_s__ │ │ │ │ +void generateScoreContributions_(vector< vector< double > > *matrix, vector< │ │ │ │ +double > *v) │ │ │ │ +_B_A_L_L_:_:_R_e_s_c_o_r_i_n_g_1_D_:_:_s_e_t_u_p__ │ │ │ │ +void setup_() │ │ │ │ +_B_A_L_L_:_:_R_e_s_c_o_r_i_n_g_1_D_:_:_R_e_s_c_o_r_i_n_g_1_D │ │ │ │ +Rescoring1D(AtomContainer &receptor, AtomContainer &reference_ligand, Options │ │ │ │ +&options, String free_energy_label, ScoringFunction *sf) │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d85/a00908.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: electrostaticPotentialCalculator.h File Reference │ │ │ +BALL: PLP.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,44 +65,90 @@ │ │ │
    │ │ │
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    │ │ │ Classes | │ │ │ -Namespaces
    │ │ │ -
    electrostaticPotentialCalculator.h File Reference
    │ │ │ +Namespaces | │ │ │ +Macros
    │ │ │ +
    PLP.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/KERNEL/system.h>
    │ │ │ -#include <BALL/DATATYPE/options.h>
    │ │ │ -#include <BALL/STRUCTURE/defaultProcessors.h>
    │ │ │ +
    #include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
    │ │ │ +#include <BALL/MOLMEC/COMMON/forceField.h>
    │ │ │ +#include <BALL/MOLMEC/COMMON/support.h>
    │ │ │ +#include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
    │ │ │
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    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::ElectrostaticPotentialCalculator
    class  BALL::PLP
     
    struct  BALL::ElectrostaticPotentialCalculator::Option
     
    struct  BALL::ElectrostaticPotentialCalculator::Default
    struct  BALL::PLP::NonBondedPairData
     
    │ │ │ │ │ │ │ │ │ │ │ │ +

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ +Macros

    #define MMFF94_ES_ENABLED   "enable ES"
     flag to enable ES
     
    #define MMFF94_VDW_ENABLED   "enable VDW"
     flag to enable VDW
     
    │ │ │ +

    Macro Definition Documentation

    │ │ │ + │ │ │ +

    ◆ MMFF94_ES_ENABLED

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    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define MMFF94_ES_ENABLED   "enable ES"
    │ │ │ +
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    flag to enable ES

    │ │ │ + │ │ │ +

    Definition at line 49 of file PLP.h.

    │ │ │ + │ │ │ +
    │ │ │ +
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    ◆ MMFF94_VDW_ENABLED

    │ │ │ + │ │ │ +
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    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define MMFF94_VDW_ENABLED   "enable VDW"
    │ │ │ +
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    flag to enable VDW

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    Definition at line 52 of file PLP.h.

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    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,25 +1,41 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_O_L_V_A_T_I_O_N │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -electrostaticPotentialCalculator.h File Reference │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ -#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_d_e_f_a_u_l_t_P_r_o_c_e_s_s_o_r_s_._h> │ │ │ │ + * _S_C_O_R_I_N_G │ │ │ │ + * _C_O_M_P_O_N_E_N_T_S │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s │ │ │ │ +PLP.h File Reference │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_._h> │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_s_u_p_p_o_r_t_._h> │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_M_F_F_9_4_/_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ - class   _B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r │ │ │ │ + class   _B_A_L_L_:_:_P_L_P │ │ │ │   │ │ │ │ -struct   _B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_O_p_t_i_o_n │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ +struct   _B_A_L_L_:_:_P_L_P_:_:_N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +MMaaccrrooss │ │ │ │ +#define  _M_M_F_F_9_4___E_S___E_N_A_B_L_E_D   "enable ES" │ │ │ │ +  flag to enable ES │ │ │ │ +  │ │ │ │ +#define  _M_M_F_F_9_4___V_D_W___E_N_A_B_L_E_D   "enable VDW" │ │ │ │ +  flag to enable VDW │ │ │ │ +  │ │ │ │ +********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ +********** _?◆_? MMMMFFFF9944__EESS__EENNAABBLLEEDD ********** │ │ │ │ +#define MMFF94_ES_ENABLED   "enable ES" │ │ │ │ +flag to enable ES │ │ │ │ +Definition at line _4_9 of file _P_L_P_._h. │ │ │ │ +********** _?◆_? MMMMFFFF9944__VVDDWW__EENNAABBLLEEDD ********** │ │ │ │ +#define MMFF94_VDW_ENABLED   "enable VDW" │ │ │ │ +flag to enable VDW │ │ │ │ +Definition at line _5_2 of file _P_L_P_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d85/a00908_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: electrostaticPotentialCalculator.h Source File │ │ │ +BALL: PLP.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,143 +70,187 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    electrostaticPotentialCalculator.h
    │ │ │ +
    PLP.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ -
    2// vi: set ts=2:
    │ │ │ -
    3//
    │ │ │ -
    4// $Id: electrostaticPotentialCalculator.h,v 1.10 2005/12/23 17:01:59 amoll Exp $
    │ │ │ -
    5//
    │ │ │ -
    6
    │ │ │ -
    7#ifndef BALL_SOLVATION_ELECTROSTATICPOTENTIALCALCULATOR_H
    │ │ │ -
    8#define BALL_SOLVATION_ELECTROSTATICPOTENTIALCALCULATOR_H
    │ │ │ -
    9
    │ │ │ -
    10#ifndef BALL_KERNEL_SYSTEM_H
    │ │ │ -
    11 # include <BALL/KERNEL/system.h>
    │ │ │ -
    12#endif
    │ │ │ +Go to the documentation of this file.
    1// ----------------------------------------------------
    │ │ │ +
    2// $Maintainer: Marcel Schumann $
    │ │ │ +
    3// $Authors: Jan Fuhrmann, Marcel Schumann $
    │ │ │ +
    4// ----------------------------------------------------
    │ │ │ +
    5
    │ │ │ +
    6#ifndef BALL_SCORING_COMPONENTS_PLP_H
    │ │ │ +
    7#define BALL_SCORING_COMPONENTS_PLP_H
    │ │ │ +
    8
    │ │ │ +
    9#include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
    │ │ │ +
    10#include <BALL/MOLMEC/COMMON/forceField.h>
    │ │ │ +
    11#include <BALL/MOLMEC/COMMON/support.h>
    │ │ │ +
    12#include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
    │ │ │
    13
    │ │ │ -
    14#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ -
    15 # include <BALL/DATATYPE/options.h>
    │ │ │ -
    16#endif
    │ │ │ -
    17
    │ │ │ -
    18#ifndef BALL_STRUCTURE_DEFAULTPROCESSORS_H
    │ │ │ -
    19 # include <BALL/STRUCTURE/defaultProcessors.h>
    │ │ │ -
    20#endif
    │ │ │ -
    21
    │ │ │ -
    22namespace BALL
    │ │ │ -
    23{
    │ │ │ -
    24 class FragmentDB;
    │ │ │ -
    25
    │ │ │ -
    │ │ │ -
    33 class BALL_EXPORT ElectrostaticPotentialCalculator
    │ │ │ -
    34 {
    │ │ │ -
    35 BALL_CREATE(ElectrostaticPotentialCalculator)
    │ │ │ -
    36
    │ │ │ -
    37 public:
    │ │ │ -
    38
    │ │ │ -
    │ │ │ -
    43 struct Option
    │ │ │ -
    44 {
    │ │ │ -
    47 static const char* LOCALITY;
    │ │ │ -
    48 };
    │ │ │ -
    │ │ │ -
    49
    │ │ │ -
    │ │ │ -
    52 struct Default
    │ │ │ -
    53 {
    │ │ │ -
    57 static const bool LOCALITY;
    │ │ │ -
    58 };
    │ │ │ -
    │ │ │ -
    59
    │ │ │ -
    63
    │ │ │ -
    66 ElectrostaticPotentialCalculator()
    │ │ │ -
    67 ;
    │ │ │ -
    68
    │ │ │ -
    71 ElectrostaticPotentialCalculator(const ElectrostaticPotentialCalculator& epc)
    │ │ │ -
    72 ;
    │ │ │ -
    73
    │ │ │ -
    76 virtual ~ElectrostaticPotentialCalculator()
    │ │ │ -
    77 ;
    │ │ │ -
    78
    │ │ │ -
    80
    │ │ │ -
    83
    │ │ │ -
    88 void apply(System &S);
    │ │ │ -
    89
    │ │ │ -
    91 void setFragmentDB(const FragmentDB* db)
    │ │ │ -
    92 ;
    │ │ │ -
    93
    │ │ │ -
    95 const FragmentDB* getFragmentDB() const
    │ │ │ -
    96 ;
    │ │ │ +
    14
    │ │ │ +
    15namespace BALL
    │ │ │ +
    16{
    │ │ │ +
    │ │ │ +
    18 class BALL_EXPORT PLP : public ForceFieldComponent
    │ │ │ +
    19 {
    │ │ │ +
    20 public:
    │ │ │ +
    │ │ │ +
    21 struct NonBondedPairData
    │ │ │ +
    22 {
    │ │ │ +
    23 Size type;
    │ │ │ +
    24
    │ │ │ +
    │ │ │ +
    25 enum Type
    │ │ │ +
    26 {
    │ │ │ +
    27 steric = 0,
    │ │ │ +
    28 hydrogen_bond = 1,
    │ │ │ +
    29 // an atom pair of which both partners are taken from the same ligand molecule in order to evaluate the ligand nonbonded energy
    │ │ │ +
    30 conformation = 2
    │ │ │ +
    31 };
    │ │ │ +
    │ │ │ +
    32
    │ │ │ +
    33 /*
    │ │ │ +
    34 NonBondedPairData();
    │ │ │ +
    35
    │ │ │ +
    36 double eij;
    │ │ │ +
    37 double rij;
    │ │ │ +
    38 double rij_7;
    │ │ │ +
    39 double vdw_energy; // for debugging
    │ │ │ +
    40 // for electrostatics:
    │ │ │ +
    41 bool is_1_4;
    │ │ │ +
    42 double qi;
    │ │ │ +
    43 double qj;
    │ │ │ +
    44 double es_energy; // for debugging
    │ │ │ +
    45 */
    │ │ │ +
    46 };
    │ │ │ +
    │ │ │ +
    47
    │ │ │ +
    49 #define MMFF94_ES_ENABLED "enable ES"
    │ │ │ +
    50
    │ │ │ +
    52 #define MMFF94_VDW_ENABLED "enable VDW"
    │ │ │ +
    53
    │ │ │ +
    54 BALL_CREATE(PLP)
    │ │ │ +
    55
    │ │ │ +
    56
    │ │ │ +
    57 PLP() throw();
    │ │ │ +
    58
    │ │ │ +
    60 PLP(ForceField& force_field) throw();
    │ │ │ +
    61
    │ │ │ +
    63 PLP(const PLP& MMFF94_non_bonded) throw();
    │ │ │ +
    64
    │ │ │ +
    66 virtual ~PLP() throw();
    │ │ │ +
    67
    │ │ │ +
    69 const PLP& operator = (const PLP& anb) throw();
    │ │ │ +
    70
    │ │ │ +
    73 void setRotatableBonds(std::vector<Bond*>& bonds);
    │ │ │ +
    74
    │ │ │ +
    81 static Size getAtomType(const Atom* atom);
    │ │ │ +
    82
    │ │ │ +
    84 void update(const std::vector<std::pair<Atom*, Atom*> >& atom_vector);
    │ │ │ +
    85
    │ │ │ +
    87 virtual void clear() throw();
    │ │ │ +
    88
    │ │ │ +
    90 bool operator == (const PLP& anb) throw();
    │ │ │ +
    91
    │ │ │ +
    93 bool setup(Options& options);
    │ │ │ +
    94
    │ │ │ +
    96 virtual double updateEnergy() throw();
    │ │ │
    97
    │ │ │ -
    99
    │ │ │ -
    102
    │ │ │ -
    105 float operator() (const Vector3& pos)
    │ │ │ -
    106 ;
    │ │ │ -
    107
    │ │ │ -
    109
    │ │ │ +
    99 virtual void updateForces() throw();
    │ │ │ +
    100
    │ │ │ +
    107 virtual void update();
    │ │ │ +
    108
    │ │ │ +
    109 double getVDWEnergy() const;
    │ │ │ +
    110
    │ │ │ +
    111 double getESEnergy() const;
    │ │ │
    112
    │ │ │ -
    115 Options options;
    │ │ │ +
    113 protected:
    │ │ │ +
    114 //_ Value of the electrostatic energy
    │ │ │ +
    115 double es_energy_;
    │ │ │
    116
    │ │ │ -
    118
    │ │ │ -
    120 //_@{
    │ │ │ -
    121 protected:
    │ │ │ +
    117 //_ Value of the vdw energy
    │ │ │ +
    118 double vdw_energy_;
    │ │ │ +
    119
    │ │ │ +
    120 static bool isNSp3(const Atom* at);
    │ │ │ +
    121 static bool isSp3(const Atom* at);
    │ │ │
    122
    │ │ │ -
    123 System mySys_;
    │ │ │ -
    124
    │ │ │ -
    125 FragmentDB *frag_db_;
    │ │ │ -
    126
    │ │ │ -
    127 AssignRadiusProcessor radii_;
    │ │ │ -
    128
    │ │ │ -
    129 AssignChargeProcessor charges_;
    │ │ │ -
    130 //_@}
    │ │ │ -
    131 };
    │ │ │ -
    │ │ │ -
    132}
    │ │ │ -
    133
    │ │ │ -
    134
    │ │ │ -
    135#endif // BALL_SOLVATION_ELECTROSTATICPOTENTIALCALCULATOR_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::ElectrostaticPotentialCalculator::setFragmentDB
    void setFragmentDB(const FragmentDB *db)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ElectrostaticPotentialCalculator::getFragmentDB
    const FragmentDB * getFragmentDB() const
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ElectrostaticPotentialCalculator::ElectrostaticPotentialCalculator
    ElectrostaticPotentialCalculator(const ElectrostaticPotentialCalculator &epc)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ - │ │ │ +
    123 private:
    │ │ │ +
    124 struct GhTorsion
    │ │ │ +
    125 {
    │ │ │ +
    126 Atom* at1;
    │ │ │ +
    127 Atom* at2;
    │ │ │ +
    128 Atom* at3;
    │ │ │ +
    129 Atom* at4;
    │ │ │ +
    130 Size type;
    │ │ │ +
    131 };
    │ │ │ +
    132
    │ │ │ +
    133 void e1(double& d, double& e, double& delta);
    │ │ │ +
    134 void e2(double& d, double& e, double& delta);
    │ │ │ +
    135
    │ │ │ +
    136 std::vector<GhTorsion> ghtorsions_;
    │ │ │ +
    137
    │ │ │ +
    138 ForceField::PairVector atom_pair_vector_;
    │ │ │ +
    139
    │ │ │ +
    140 std::vector<NonBondedPairData> non_bonded_data_;
    │ │ │ +
    141
    │ │ │ +
    142 double cut_off_;
    │ │ │ +
    143 double vdw_cut_on_, vdw_cut_off_;
    │ │ │ +
    144 double es_cut_on_, es_cut_off_;
    │ │ │ +
    145 MMFF94VDWParameters vdw_parameters_;
    │ │ │ +
    146
    │ │ │ +
    147 // dielectric constant
    │ │ │ +
    148 double dc_;
    │ │ │ +
    149 // dielectric model exponent
    │ │ │ +
    150 double n_;
    │ │ │ +
    151 bool es_enabled_;
    │ │ │ +
    152 bool vdw_enabled_;
    │ │ │ +
    153 bool enable_es_switch_;
    │ │ │ +
    154 bool enable_vdw_switch_;
    │ │ │ +
    155 double es_d_on2_, es_d_off2_,
    │ │ │ +
    156 es_d_on_, es_d_off_,
    │ │ │ +
    157 es_ac_, es_bc_,
    │ │ │ +
    158 es_cc_, es_dc_, es_denom_, es_con_, es_cover3_, es_dover5_,
    │ │ │ +
    159 es_eadd_, es_eaddr_, es_const_, es_constr_;
    │ │ │ +
    160
    │ │ │ +
    161 std::vector<bool> dismiss_vector_;
    │ │ │ +
    162
    │ │ │ +
    163 std::vector<double> rotgrad_;
    │ │ │ +
    164 };
    │ │ │ +
    │ │ │ +
    165} //
    │ │ │ +
    166
    │ │ │ +
    167#endif // BALL_SCORING_COMPONENTS_PLP_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ +
    std
    STL namespace.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::ForceField::PairVector
    std::vector< std::pair< Atom *, Atom * > > PairVector
    Definition forceField.h:99
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,164 +1,193 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_O_L_V_A_T_I_O_N │ │ │ │ -electrostaticPotentialCalculator.h │ │ │ │ + * _S_C_O_R_I_N_G │ │ │ │ + * _C_O_M_P_O_N_E_N_T_S │ │ │ │ +PLP.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ -2// vi: set ts=2: │ │ │ │ -3// │ │ │ │ -4// $Id: electrostaticPotentialCalculator.h,v 1.10 2005/12/23 17:01:59 amoll │ │ │ │ -Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_SOLVATION_ELECTROSTATICPOTENTIALCALCULATOR_H │ │ │ │ -8#define BALL_SOLVATION_ELECTROSTATICPOTENTIALCALCULATOR_H │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_KERNEL_SYSTEM_H │ │ │ │ -11 # include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ -12#endif │ │ │ │ +1// ---------------------------------------------------- │ │ │ │ +2// $Maintainer: Marcel Schumann $ │ │ │ │ +3// $Authors: Jan Fuhrmann, Marcel Schumann $ │ │ │ │ +4// ---------------------------------------------------- │ │ │ │ +5 │ │ │ │ +6#ifndef BALL_SCORING_COMPONENTS_PLP_H │ │ │ │ +7#define BALL_SCORING_COMPONENTS_PLP_H │ │ │ │ +8 │ │ │ │ +9#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ +10#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_._h> │ │ │ │ +11#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_s_u_p_p_o_r_t_._h> │ │ │ │ +12#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_M_F_F_9_4_/_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ 13 │ │ │ │ -14#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ -15 # include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ -16#endif │ │ │ │ -17 │ │ │ │ -18#ifndef BALL_STRUCTURE_DEFAULTPROCESSORS_H │ │ │ │ -19 # include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_d_e_f_a_u_l_t_P_r_o_c_e_s_s_o_r_s_._h> │ │ │ │ -20#endif │ │ │ │ -21 │ │ │ │ -22namespace _B_A_L_L │ │ │ │ -23{ │ │ │ │ -24 class FragmentDB; │ │ │ │ -25 │ │ │ │ -_3_3 class _B_A_L_L___E_X_P_O_R_T _E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r │ │ │ │ -34 { │ │ │ │ -35 _B_A_L_L___C_R_E_A_T_E(_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r) │ │ │ │ -36 │ │ │ │ -37 public: │ │ │ │ -38 │ │ │ │ -_4_3 struct _O_p_t_i_o_n │ │ │ │ -44 { │ │ │ │ -_4_7 static const char* _L_O_C_A_L_I_T_Y; │ │ │ │ -48 }; │ │ │ │ -49 │ │ │ │ -_5_2 struct _D_e_f_a_u_l_t │ │ │ │ -53 { │ │ │ │ -_5_7 static const bool _L_O_C_A_L_I_T_Y; │ │ │ │ -58 }; │ │ │ │ -59 │ │ │ │ -63 │ │ │ │ -_6_6 _E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r() │ │ │ │ -67 ; │ │ │ │ -68 │ │ │ │ -_7_1 _E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r(const _E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r& │ │ │ │ -epc) │ │ │ │ -72 ; │ │ │ │ -73 │ │ │ │ -_7_6 virtual _~_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r() │ │ │ │ -77 ; │ │ │ │ -78 │ │ │ │ -80 │ │ │ │ -83 │ │ │ │ -_8_8 void _a_p_p_l_y(_S_y_s_t_e_m &S); │ │ │ │ -89 │ │ │ │ -_9_1 void _s_e_t_F_r_a_g_m_e_n_t_D_B(const _F_r_a_g_m_e_n_t_D_B* _d_b) │ │ │ │ -92 ; │ │ │ │ -93 │ │ │ │ -_9_5 const _F_r_a_g_m_e_n_t_D_B* _g_e_t_F_r_a_g_m_e_n_t_D_B() const │ │ │ │ -96 ; │ │ │ │ +14 │ │ │ │ +15namespace _B_A_L_L │ │ │ │ +16{ │ │ │ │ +_1_8 class _B_A_L_L___E_X_P_O_R_T _P_L_P : public _F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t │ │ │ │ +19 { │ │ │ │ +20 public: │ │ │ │ +_2_1 struct _N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a │ │ │ │ +22 { │ │ │ │ +_2_3 _S_i_z_e _t_y_p_e; │ │ │ │ +24 │ │ │ │ +_2_5 enum _T_y_p_e │ │ │ │ +26 { │ │ │ │ +_2_7 steric = 0, │ │ │ │ +_2_8 hydrogen_bond = 1, │ │ │ │ +29 // an atom pair of which both partners are taken from the same ligand │ │ │ │ +molecule in order to evaluate the ligand nonbonded energy │ │ │ │ +30 conformation = 2 │ │ │ │ +_3_1 }; │ │ │ │ +32 │ │ │ │ +33 /* │ │ │ │ +34 NonBondedPairData(); │ │ │ │ +35 │ │ │ │ +36 double eij; │ │ │ │ +37 double rij; │ │ │ │ +38 double rij_7; │ │ │ │ +39 double vdw_energy; // for debugging │ │ │ │ +40 // for electrostatics: │ │ │ │ +41 bool is_1_4; │ │ │ │ +42 double qi; │ │ │ │ +43 double qj; │ │ │ │ +44 double es_energy; // for debugging │ │ │ │ +45 */ │ │ │ │ +46 }; │ │ │ │ +47 │ │ │ │ +_4_9 #define MMFF94_ES_ENABLED "enable ES" │ │ │ │ +50 │ │ │ │ +_5_2 #define MMFF94_VDW_ENABLED "enable VDW" │ │ │ │ +53 │ │ │ │ +54 _B_A_L_L___C_R_E_A_T_E(PLP) │ │ │ │ +55 │ │ │ │ +56 │ │ │ │ +_5_7 _P_L_P() throw(); │ │ │ │ +58 │ │ │ │ +_6_0 _P_L_P(_F_o_r_c_e_F_i_e_l_d& force_field) throw(); │ │ │ │ +61 │ │ │ │ +_6_3 _P_L_P(const _P_L_P& MMFF94_non_bonded) throw(); │ │ │ │ +64 │ │ │ │ +_6_6 virtual ~_P_L_P() throw(); │ │ │ │ +67 │ │ │ │ +_6_9 const _P_L_P& operator = (const _P_L_P& anb) throw(); │ │ │ │ +70 │ │ │ │ +_7_3 void setRotatableBonds(_s_t_d::vector<_B_o_n_d*>& bonds); │ │ │ │ +74 │ │ │ │ +_8_1 static _S_i_z_e getAtomType(const _A_t_o_m* atom); │ │ │ │ +82 │ │ │ │ +_8_4 void update(const _s_t_d::vector<_s_t_d::pair<_A_t_o_m*, _A_t_o_m*> >& atom_vector); │ │ │ │ +85 │ │ │ │ +_8_7 virtual void clear() throw(); │ │ │ │ +88 │ │ │ │ +_9_0 bool operator == (const _P_L_P& anb) throw(); │ │ │ │ +91 │ │ │ │ +_9_3 bool setup(_O_p_t_i_o_n_s& options); │ │ │ │ +94 │ │ │ │ +_9_6 virtual double updateEnergy() throw(); │ │ │ │ 97 │ │ │ │ -99 │ │ │ │ -102 │ │ │ │ -_1_0_5 float operator() (const _V_e_c_t_o_r_3& pos) │ │ │ │ -106 ; │ │ │ │ -107 │ │ │ │ -109 │ │ │ │ +_9_9 virtual void updateForces() throw(); │ │ │ │ +100 │ │ │ │ +_1_0_7 virtual void update(); │ │ │ │ +108 │ │ │ │ +_1_0_9 double getVDWEnergy() const; │ │ │ │ +110 │ │ │ │ +_1_1_1 double getESEnergy() const; │ │ │ │ 112 │ │ │ │ -_1_1_5 _O_p_t_i_o_n_s _o_p_t_i_o_n_s; │ │ │ │ +113 protected: │ │ │ │ +114 //_ Value of the electrostatic energy │ │ │ │ +_1_1_5 double es_energy_; │ │ │ │ 116 │ │ │ │ -118 │ │ │ │ -120 //_@{ │ │ │ │ -121 protected: │ │ │ │ +117 //_ Value of the vdw energy │ │ │ │ +_1_1_8 double vdw_energy_; │ │ │ │ +119 │ │ │ │ +_1_2_0 static bool isNSp3(const _A_t_o_m* at); │ │ │ │ +_1_2_1 static bool isSp3(const _A_t_o_m* at); │ │ │ │ 122 │ │ │ │ -_1_2_3 _S_y_s_t_e_m _m_y_S_y_s__; │ │ │ │ -124 │ │ │ │ -_1_2_5 _F_r_a_g_m_e_n_t_D_B *_f_r_a_g___d_b__; │ │ │ │ -126 │ │ │ │ -_1_2_7 _A_s_s_i_g_n_R_a_d_i_u_s_P_r_o_c_e_s_s_o_r _r_a_d_i_i__; │ │ │ │ -128 │ │ │ │ -_1_2_9 _A_s_s_i_g_n_C_h_a_r_g_e_P_r_o_c_e_s_s_o_r _c_h_a_r_g_e_s__; │ │ │ │ -130 //_@} │ │ │ │ +123 private: │ │ │ │ +124 struct GhTorsion │ │ │ │ +125 { │ │ │ │ +126 _A_t_o_m* at1; │ │ │ │ +127 _A_t_o_m* at2; │ │ │ │ +128 _A_t_o_m* at3; │ │ │ │ +129 _A_t_o_m* at4; │ │ │ │ +130 _S_i_z_e type; │ │ │ │ 131 }; │ │ │ │ -132} │ │ │ │ -133 │ │ │ │ -134 │ │ │ │ -135#endif // BALL_SOLVATION_ELECTROSTATICPOTENTIALCALCULATOR_H │ │ │ │ -_d_e_f_a_u_l_t_P_r_o_c_e_s_s_o_r_s_._h │ │ │ │ -_d_b │ │ │ │ -db │ │ │ │ -DDeeffiinniittiioonn _G_A_F_F_T_y_p_e_P_r_o_c_e_s_s_o_r_._h_:_7_4 │ │ │ │ -_o_p_t_i_o_n_s_._h │ │ │ │ +132 │ │ │ │ +133 void e1(double& d, double& e, double& delta); │ │ │ │ +134 void e2(double& d, double& e, double& delta); │ │ │ │ +135 │ │ │ │ +136 std::vector ghtorsions_; │ │ │ │ +137 │ │ │ │ +138 _F_o_r_c_e_F_i_e_l_d_:_:_P_a_i_r_V_e_c_t_o_r atom_pair_vector_; │ │ │ │ +139 │ │ │ │ +140 std::vector non_bonded_data_; │ │ │ │ +141 │ │ │ │ +142 double cut_off_; │ │ │ │ +143 double vdw_cut_on_, vdw_cut_off_; │ │ │ │ +144 double es_cut_on_, es_cut_off_; │ │ │ │ +145 _M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s vdw_parameters_; │ │ │ │ +146 │ │ │ │ +147 // dielectric constant │ │ │ │ +148 double dc_; │ │ │ │ +149 // dielectric model exponent │ │ │ │ +150 double n_; │ │ │ │ +151 bool es_enabled_; │ │ │ │ +152 bool vdw_enabled_; │ │ │ │ +153 bool enable_es_switch_; │ │ │ │ +154 bool enable_vdw_switch_; │ │ │ │ +155 double es_d_on2_, es_d_off2_, │ │ │ │ +156 es_d_on_, es_d_off_, │ │ │ │ +157 es_ac_, es_bc_, │ │ │ │ +158 es_cc_, es_dc_, es_denom_, es_con_, es_cover3_, es_dover5_, │ │ │ │ +159 es_eadd_, es_eaddr_, es_const_, es_constr_; │ │ │ │ +160 │ │ │ │ +161 std::vector dismiss_vector_; │ │ │ │ +162 │ │ │ │ +163 std::vector rotgrad_; │ │ │ │ +164 }; │ │ │ │ +165} // │ │ │ │ +166 │ │ │ │ +167#endif // BALL_SCORING_COMPONENTS_PLP_H │ │ │ │ +_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h │ │ │ │ +_f_o_r_c_e_F_i_e_l_d_._h │ │ │ │ +_s_u_p_p_o_r_t_._h │ │ │ │ +_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h │ │ │ │ _B_A_L_L___C_R_E_A_T_E │ │ │ │ #define BALL_CREATE(name) │ │ │ │ DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_s_t_d │ │ │ │ +STL namespace. │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ _B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ -DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_3_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r │ │ │ │ -ElectrostaticPotentialCalculator() │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_m_y_S_y_s__ │ │ │ │ -System mySys_ │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_1_2_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_~_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r │ │ │ │ -virtual ~ElectrostaticPotentialCalculator() │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_f_r_a_g___d_b__ │ │ │ │ -FragmentDB * frag_db_ │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_1_2_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_s_e_t_F_r_a_g_m_e_n_t_D_B │ │ │ │ -void setFragmentDB(const FragmentDB *db) │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_a_p_p_l_y │ │ │ │ -void apply(System &S) │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_c_h_a_r_g_e_s__ │ │ │ │ -AssignChargeProcessor charges_ │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_1_2_9 │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_g_e_t_F_r_a_g_m_e_n_t_D_B │ │ │ │ -const FragmentDB * getFragmentDB() const │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_o_p_t_i_o_n_s │ │ │ │ -Options options │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_1_1_5 │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_r_a_d_i_i__ │ │ │ │ -AssignRadiusProcessor radii_ │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_1_2_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r │ │ │ │ -ElectrostaticPotentialCalculator(const ElectrostaticPotentialCalculator &epc) │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_O_p_t_i_o_n │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_4_4 │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_O_p_t_i_o_n_:_:_L_O_C_A_L_I_T_Y │ │ │ │ -static const char * LOCALITY │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_4_7 │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_E_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_:_:_D_e_f_a_u_l_t_:_:_L_O_C_A_L_I_T_Y │ │ │ │ -static const bool LOCALITY │ │ │ │ -DDeeffiinniittiioonn _e_l_e_c_t_r_o_s_t_a_t_i_c_P_o_t_e_n_t_i_a_l_C_a_l_c_u_l_a_t_o_r_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_A_s_s_i_g_n_R_a_d_i_u_s_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _d_e_f_a_u_l_t_P_r_o_c_e_s_s_o_r_s_._h_:_6_4 │ │ │ │ -_B_A_L_L_:_:_A_s_s_i_g_n_C_h_a_r_g_e_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _d_e_f_a_u_l_t_P_r_o_c_e_s_s_o_r_s_._h_:_1_4_6 │ │ │ │ -_B_A_L_L_:_:_F_r_a_g_m_e_n_t_D_B │ │ │ │ -DDeeffiinniittiioonn _f_r_a_g_m_e_n_t_D_B_._h_:_4_5 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ +_B_A_L_L_:_:_B_o_n_d │ │ │ │ +DDeeffiinniittiioonn _b_o_n_d_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_P_a_i_r_V_e_c_t_o_r │ │ │ │ +std::vector< std::pair< Atom *, Atom * > > PairVector │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_9_9 │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h_:_3_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_V_D_W_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_4_6_0 │ │ │ │ +_B_A_L_L_:_:_P_L_P │ │ │ │ +DDeeffiinniittiioonn _P_L_P_._h_:_1_9 │ │ │ │ +_B_A_L_L_:_:_P_L_P_:_:_N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a │ │ │ │ +DDeeffiinniittiioonn _P_L_P_._h_:_2_2 │ │ │ │ +_B_A_L_L_:_:_P_L_P_:_:_N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a_:_:_T_y_p_e │ │ │ │ +Type │ │ │ │ +DDeeffiinniittiioonn _P_L_P_._h_:_2_6 │ │ │ │ +_B_A_L_L_:_:_P_L_P_:_:_N_o_n_B_o_n_d_e_d_P_a_i_r_D_a_t_a_:_:_t_y_p_e │ │ │ │ +Size type │ │ │ │ +DDeeffiinniittiioonn _P_L_P_._h_:_2_3 │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ -_s_y_s_t_e_m_._h │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d85/a01352.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: MMFF94StretchBend.h File Reference │ │ │ +BALL: CCP4File.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,114 +65,39 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces | │ │ │ -Macros
    │ │ │ -
    MMFF94StretchBend.h File Reference
    │ │ │ +Namespaces
    │ │ │ +
    CCP4File.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
    │ │ │ -#include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
    │ │ │ +
    #include <BALL/SYSTEM/file.h>
    │ │ │ +#include <BALL/DATATYPE/regularData3D.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::MMFF94StretchBend
     
    struct  BALL::MMFF94StretchBend::StretchBend
     
    struct  BALL::MMFF94StretchBend::Bend
     see MMFFANG.PAR More...
     
    struct  BALL::MMFF94StretchBend::Stretch
    class  BALL::CCP4File
     
    │ │ │ │ │ │ │ │ │ │ │ │ -

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │

    │ │ │ -Macros

    #define MMFF94_BENDS_ENABLED   "enable Bends"
     flag to enable BENDS
     
    #define MMFF94_STRETCHES_ENABLED   "enable Stretches"
     flag to enable Stretches
     
    #define MMFF94_STRETCHBENDS_ENABLED   "enable StrechBends"
     flag to enable StretchBends
     
    │ │ │ -

    Macro Definition Documentation

    │ │ │ - │ │ │ -

    ◆ MMFF94_BENDS_ENABLED

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define MMFF94_BENDS_ENABLED   "enable Bends"
    │ │ │ -
    │ │ │ - │ │ │ -

    flag to enable BENDS

    │ │ │ - │ │ │ -

    Definition at line 84 of file MMFF94StretchBend.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ MMFF94_STRETCHBENDS_ENABLED

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define MMFF94_STRETCHBENDS_ENABLED   "enable StrechBends"
    │ │ │ -
    │ │ │ - │ │ │ -

    flag to enable StretchBends

    │ │ │ - │ │ │ -

    Definition at line 90 of file MMFF94StretchBend.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ MMFF94_STRETCHES_ENABLED

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    #define MMFF94_STRETCHES_ENABLED   "enable Stretches"
    │ │ │ -
    │ │ │ - │ │ │ -

    flag to enable Stretches

    │ │ │ - │ │ │ -

    Definition at line 87 of file MMFF94StretchBend.h.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,51 +1,20 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _M_O_L_M_E_C │ │ │ │ - * _M_M_F_F_9_4 │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s │ │ │ │ -MMFF94StretchBend.h File Reference │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_M_F_F_9_4_/_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ + * _F_O_R_M_A_T │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ +CCP4File.h File Reference │ │ │ │ +#include <_B_A_L_L_/_S_Y_S_T_E_M_/_f_i_l_e_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_r_e_g_u_l_a_r_D_a_t_a_3_D_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ - class   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d │ │ │ │ -  see MMFFANG.PAR _M_o_r_e_._._. │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h │ │ │ │ +class   _B_A_L_L_:_:_C_C_P_4_F_i_l_e │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -MMaaccrrooss │ │ │ │ -#define  _M_M_F_F_9_4___B_E_N_D_S___E_N_A_B_L_E_D   "enable Bends" │ │ │ │ -  flag to enable BENDS │ │ │ │ -  │ │ │ │ -#define  _M_M_F_F_9_4___S_T_R_E_T_C_H_E_S___E_N_A_B_L_E_D   "enable Stretches" │ │ │ │ -  flag to enable Stretches │ │ │ │ -  │ │ │ │ -#define  _M_M_F_F_9_4___S_T_R_E_T_C_H_B_E_N_D_S___E_N_A_B_L_E_D   "enable StrechBends" │ │ │ │ -  flag to enable StretchBends │ │ │ │ -  │ │ │ │ -********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ -********** _?◆_? MMMMFFFF9944__BBEENNDDSS__EENNAABBLLEEDD ********** │ │ │ │ -#define MMFF94_BENDS_ENABLED   "enable Bends" │ │ │ │ -flag to enable BENDS │ │ │ │ -Definition at line _8_4 of file _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h. │ │ │ │ -********** _?◆_? MMMMFFFF9944__SSTTRREETTCCHHBBEENNDDSS__EENNAABBLLEEDD ********** │ │ │ │ -#define MMFF94_STRETCHBENDS_ENABLED   "enable StrechBends" │ │ │ │ -flag to enable StretchBends │ │ │ │ -Definition at line _9_0 of file _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h. │ │ │ │ -********** _?◆_? MMMMFFFF9944__SSTTRREETTCCHHEESS__EENNAABBLLEEDD ********** │ │ │ │ -#define MMFF94_STRETCHES_ENABLED   "enable Stretches" │ │ │ │ -flag to enable Stretches │ │ │ │ -Definition at line _8_7 of file _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d85/a01352_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: MMFF94StretchBend.h Source File │ │ │ +BALL: CCP4File.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,260 +70,156 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    MMFF94StretchBend.h
    │ │ │ +
    CCP4File.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4// $Id: MMFF94StretchBend.h,v 1.1.8.1 2007/03/25 21:25:18 oliver Exp $
    │ │ │ -
    5//
    │ │ │ -
    6
    │ │ │ -
    7#ifndef BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H
    │ │ │ -
    8#define BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H
    │ │ │ -
    9
    │ │ │ -
    10#ifndef BALL_MOLMEC_COMMON_FORCEFIELDCOMPONENT_H
    │ │ │ -
    11# include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
    │ │ │ -
    12#endif
    │ │ │ -
    13
    │ │ │ -
    14#ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
    │ │ │ -
    15# include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
    │ │ │ -
    16#endif
    │ │ │ -
    17
    │ │ │ -
    18namespace BALL
    │ │ │ -
    19{
    │ │ │ -
    20 class MMFF94;
    │ │ │ -
    21
    │ │ │ -
    │ │ │ -
    25 class BALL_EXPORT MMFF94StretchBend
    │ │ │ -
    26 : public ForceFieldComponent
    │ │ │ -
    27 {
    │ │ │ -
    28 public:
    │ │ │ +
    4//
    │ │ │ +
    5
    │ │ │ +
    6#ifndef BALL_FORMAT_CCP4FILE_H
    │ │ │ +
    7#define BALL_FORMAT_CCP4FILE_H
    │ │ │ +
    8
    │ │ │ +
    9#ifndef BALL_SYSTEM_FILE_H
    │ │ │ +
    10# include <BALL/SYSTEM/file.h>
    │ │ │ +
    11#endif
    │ │ │ +
    12
    │ │ │ +
    13#ifndef BALL_DATATYPE_REGULARDATA3D_H
    │ │ │ +
    14# include <BALL/DATATYPE/regularData3D.h>
    │ │ │ +
    15#endif
    │ │ │ +
    16
    │ │ │ +
    17namespace BALL
    │ │ │ +
    18{
    │ │ │ +
    │ │ │ +
    26 class BALL_EXPORT CCP4File
    │ │ │ +
    27 : public File
    │ │ │ +
    28 {
    │ │ │
    29
    │ │ │ -
    │ │ │ -
    30 struct BALL_EXPORT StretchBend
    │ │ │ -
    31 {
    │ │ │ -
    32 double kba_ijk;
    │ │ │ -
    33 double kba_kji;
    │ │ │ -
    34 double energy; // debug
    │ │ │ -
    35 Index sbtijk;
    │ │ │ -
    36 Index stretch_i_j, stretch_j_k;
    │ │ │ -
    37 Index bend_index;
    │ │ │ -
    38 };
    │ │ │ -
    │ │ │ -
    39
    │ │ │ -
    │ │ │ -
    41 struct BALL_EXPORT Bend
    │ │ │ -
    42 {
    │ │ │ -
    43 Bend();
    │ │ │ -
    44
    │ │ │ -
    45 double theta0;
    │ │ │ -
    46 double delta_theta;
    │ │ │ -
    47 double theta;
    │ │ │ -
    48 double ka;
    │ │ │ -
    49 Atom* atom1;
    │ │ │ -
    50 Atom* atom2;
    │ │ │ -
    51 Atom* atom3;
    │ │ │ -
    52 bool is_linear;
    │ │ │ -
    53 Position ATIJK;
    │ │ │ -
    54 double energy; // debug
    │ │ │ -
    55 bool emperical; // debug
    │ │ │ -
    56 TVector3<double> n1, n2;
    │ │ │ -
    57 };
    │ │ │ -
    │ │ │ -
    58
    │ │ │ -
    │ │ │ -
    60 struct BALL_EXPORT Stretch
    │ │ │ -
    61 {
    │ │ │ -
    │ │ │ -
    62 Stretch()
    │ │ │ -
    63 : atom1(NULL),
    │ │ │ -
    64 atom2(NULL),
    │ │ │ -
    65 kb(0.0),
    │ │ │ -
    66 r0(0.0),
    │ │ │ -
    67 delta_r(0.0),
    │ │ │ -
    68 sbmb(false),
    │ │ │ -
    69 emperical(false)
    │ │ │ -
    70 {
    │ │ │ -
    71 }
    │ │ │ -
    │ │ │ -
    72
    │ │ │ -
    73 Atom* atom1;
    │ │ │ -
    74 Atom* atom2;
    │ │ │ -
    75 double kb;
    │ │ │ -
    76 double r0;
    │ │ │ -
    77 double delta_r;
    │ │ │ -
    78 bool sbmb;
    │ │ │ -
    79 bool emperical;
    │ │ │ -
    80 Vector3 n;
    │ │ │ -
    81 };
    │ │ │ -
    │ │ │ -
    82
    │ │ │ -
    84 #define MMFF94_BENDS_ENABLED "enable Bends"
    │ │ │ +
    30 public:
    │ │ │ +
    31
    │ │ │ +
    35
    │ │ │ +
    37 CCP4File();
    │ │ │ +
    38
    │ │ │ +
    42 CCP4File(const String& name, File::OpenMode open_mode = std::ios::in);
    │ │ │ +
    43
    │ │ │ +
    45 virtual ~CCP4File();
    │ │ │ +
    46
    │ │ │ +
    48
    │ │ │ +
    51
    │ │ │ +
    53 virtual void clear();
    │ │ │ +
    54
    │ │ │ +
    56
    │ │ │ +
    59
    │ │ │ +
    61 bool operator == (const CCP4File& file) const;
    │ │ │ +
    62
    │ │ │ +
    64
    │ │ │ +
    66
    │ │ │ +
    70 virtual bool open(const String& name, File::OpenMode open_mode = std::ios::in);
    │ │ │ +
    71
    │ │ │ +
    75 virtual bool readHeader();
    │ │ │ +
    76
    │ │ │ +
    80 virtual bool readSymmetryRecords();
    │ │ │ +
    81
    │ │ │ +
    84 virtual bool read(RegularData3D& map);
    │ │ │
    85
    │ │ │ -
    87 #define MMFF94_STRETCHES_ENABLED "enable Stretches"
    │ │ │ -
    88
    │ │ │ -
    90 #define MMFF94_STRETCHBENDS_ENABLED "enable StrechBends"
    │ │ │ -
    91
    │ │ │ -
    92 BALL_CREATE(MMFF94StretchBend)
    │ │ │ -
    93
    │ │ │ -
    94
    │ │ │ -
    96 MMFF94StretchBend();
    │ │ │ +
    89 virtual bool writeHeader();
    │ │ │ +
    90
    │ │ │ +
    94 virtual bool write(RegularData3D& map);
    │ │ │ +
    95
    │ │ │
    97
    │ │ │ -
    100 MMFF94StretchBend(ForceField& force_field);
    │ │ │ -
    101
    │ │ │ -
    104 MMFF94StretchBend(const MMFF94StretchBend& to_copy);
    │ │ │ +
    100
    │ │ │ +
    102
    │ │ │ +
    103 private:
    │ │ │ +
    104 const CCP4File& operator = (const CCP4File& file);
    │ │ │
    105
    │ │ │ -
    108 virtual ~MMFF94StretchBend();
    │ │ │ -
    109
    │ │ │ -
    113 virtual bool setup();
    │ │ │ -
    114
    │ │ │ -
    116 virtual double updateEnergy();
    │ │ │ -
    117
    │ │ │ -
    119 virtual double updateBendEnergy();
    │ │ │ -
    120
    │ │ │ -
    122 virtual double updateStretchEnergy();
    │ │ │ -
    123
    │ │ │ -
    125 virtual double updateStretchBendEnergy();
    │ │ │ -
    126
    │ │ │ -
    128 double getStretchEnergy() const;
    │ │ │ -
    129
    │ │ │ -
    131 double getBendEnergy() const;
    │ │ │ -
    132
    │ │ │ -
    134 double getStretchBendEnergy() const;
    │ │ │ -
    135
    │ │ │ -
    137 virtual void updateForces();
    │ │ │ -
    138
    │ │ │ -
    140 virtual void updateBendForces();
    │ │ │ -
    141
    │ │ │ -
    143 virtual void updateStretchForces();
    │ │ │ -
    144
    │ │ │ -
    146 virtual void updateStretchBendForces();
    │ │ │ -
    147
    │ │ │ -
    149 const vector<Bend>& getBends() const { return bends_;}
    │ │ │ -
    150
    │ │ │ -
    152 const vector<Stretch>& getStretches() const { return stretches_;}
    │ │ │ -
    153
    │ │ │ -
    155 const vector<StretchBend>& getStretchBends() const { return stretch_bends_;}
    │ │ │ -
    156
    │ │ │ -
    158 Index calculateSBTIJK(Position angle_type,
    │ │ │ -
    159 bool bond_type1,
    │ │ │ -
    160 bool bond_type2);
    │ │ │ -
    161
    │ │ │ -
    163 Position getBendType(const Bond& bond1, const Bond& bond2,
    │ │ │ -
    164 Atom& atom1, Atom& atom2, Atom& atom3) const;
    │ │ │ -
    165
    │ │ │ -
    167 double calculateBendEmpiricalReferenceAngle(Atom& atom1, Atom& atom2, Atom& atom3) const;
    │ │ │ -
    168
    │ │ │ -
    170 double calculateBendEmpiricalForceConstant(Atom& atom1, Atom& atom2, Atom& atom3, double angle_0) const;
    │ │ │ -
    171
    │ │ │ -
    173 double calculateStretchR0(const Bond& bond);
    │ │ │ -
    174
    │ │ │ -
    176 double calculateStretchConstant(const Bond& bond, double r0);
    │ │ │ -
    177
    │ │ │ -
    178 private:
    │ │ │ -
    179
    │ │ │ -
    180 inline void AddDV3_(Vector3& f3, const TVector3<double> d3);
    │ │ │ -
    181 void calculateDeltas_();
    │ │ │ -
    182 bool setupBends_();
    │ │ │ -
    183 bool setupStretches_();
    │ │ │ -
    184 bool setupStretchBends_();
    │ │ │ -
    185
    │ │ │ -
    186 void errorOccurred_(const String& string,
    │ │ │ -
    187 const Atom& a1, const Atom& a2, const Atom& a3);
    │ │ │ -
    188
    │ │ │ -
    189 vector<Bend> bends_;
    │ │ │ -
    190 vector<Stretch> stretches_;
    │ │ │ -
    191 vector<StretchBend> stretch_bends_;
    │ │ │ -
    192
    │ │ │ -
    193 const MMFF94StretchParameters* stretch_parameters_;
    │ │ │ -
    194 MMFF94BendParameters bend_parameters_;
    │ │ │ -
    195 MMFF94StretchBendParameters sb_parameters_;
    │ │ │ -
    196
    │ │ │ -
    197 static double bend_z_[];
    │ │ │ -
    198 static double bend_c_[];
    │ │ │ -
    199 static String bend_elements_[];
    │ │ │ -
    200
    │ │ │ -
    201 double stretch_energy_;
    │ │ │ -
    202 double bend_energy_;
    │ │ │ -
    203 double stretch_bend_energy_;
    │ │ │ -
    204
    │ │ │ -
    205 MMFF94* mmff94_;
    │ │ │ -
    206 bool stretch_enabled_, bend_enabled_, stretchbend_enabled_;
    │ │ │ -
    207 };
    │ │ │ -
    │ │ │ -
    208} // namespace BALL
    │ │ │ -
    209
    │ │ │ -
    210#endif // BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::MMFF94StretchBend::getStretches
    const vector< Stretch > & getStretches() const
    Definition MMFF94StretchBend.h:152
    │ │ │ -
    BALL::MMFF94StretchBend::getBendType
    Position getBendType(const Bond &bond1, const Bond &bond2, Atom &atom1, Atom &atom2, Atom &atom3) const
    │ │ │ -
    BALL::MMFF94StretchBend::getStretchBends
    const vector< StretchBend > & getStretchBends() const
    Definition MMFF94StretchBend.h:155
    │ │ │ -
    BALL::MMFF94StretchBend::calculateBendEmpiricalReferenceAngle
    double calculateBendEmpiricalReferenceAngle(Atom &atom1, Atom &atom2, Atom &atom3) const
    Bend emperical reference angle.
    │ │ │ -
    BALL::MMFF94StretchBend::calculateStretchConstant
    double calculateStretchConstant(const Bond &bond, double r0)
    │ │ │ -
    BALL::MMFF94StretchBend::calculateSBTIJK
    Index calculateSBTIJK(Position angle_type, bool bond_type1, bool bond_type2)
    │ │ │ -
    BALL::MMFF94StretchBend::calculateBendEmpiricalForceConstant
    double calculateBendEmpiricalForceConstant(Atom &atom1, Atom &atom2, Atom &atom3, double angle_0) const
    Bend emperical force constant.
    │ │ │ -
    BALL::MMFF94StretchBend::calculateStretchR0
    double calculateStretchR0(const Bond &bond)
    Calculate the radius value per Schomaker-Stevenson Rule.
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ +
    106 protected:
    │ │ │ +
    107
    │ │ │ +
    108 int readBinValueasInt_(char* header, Position pos);
    │ │ │ +
    109
    │ │ │ +
    110 float readBinValueasFloat_(char* header, Position pos);
    │ │ │ +
    111
    │ │ │ +
    113 bool swap_bytes_;
    │ │ │ +
    114
    │ │ │ +
    116 Distance offset_symops_;
    │ │ │ +
    117
    │ │ │ +
    119 Size col_axis_;
    │ │ │ +
    120 Size row_axis_;
    │ │ │ +
    121 Size sec_axis_;
    │ │ │ +
    122
    │ │ │ +
    124 Vector3 start_;
    │ │ │ +
    125
    │ │ │ +
    127 Vector3 extent_;
    │ │ │ +
    128
    │ │ │ +
    130 Vector3 sampling_rate_;
    │ │ │ +
    131
    │ │ │ +
    133 Vector3 cell_dimension_;
    │ │ │ +
    134
    │ │ │ +
    136 Angle alpha_, beta_, gamma_;
    │ │ │ +
    137
    │ │ │ +
    139 float mean_density_;
    │ │ │ +
    140
    │ │ │ +
    142 float deviation_sigma_;
    │ │ │ +
    143
    │ │ │ +
    145 Index space_group_;
    │ │ │ +
    146
    │ │ │ +
    148 Vector3 origin_, xaxis_, yaxis_, zaxis_;
    │ │ │ +
    149 };
    │ │ │ +
    │ │ │ +
    150} // namespace BALL
    │ │ │ +
    151
    │ │ │ +
    152#endif // BALL_FORMAT_DCDFILE_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::CCP4File::read
    virtual bool read(RegularData3D &map)
    │ │ │ +
    BALL::CCP4File::cell_dimension_
    Vector3 cell_dimension_
    dimension of the crystal unit cell in Angstrom/sample
    Definition CCP4File.h:133
    │ │ │ +
    BALL::CCP4File::sampling_rate_
    Vector3 sampling_rate_
    the sampling rates used for the map
    Definition CCP4File.h:130
    │ │ │ +
    BALL::CCP4File::open
    virtual bool open(const String &name, File::OpenMode open_mode=std::ios::in)
    │ │ │ +
    BALL::CCP4File::origin_
    Vector3 origin_
    geometry in cartesian coordinates
    Definition CCP4File.h:148
    │ │ │ +
    BALL::CCP4File::writeHeader
    virtual bool writeHeader()
    │ │ │ +
    BALL::CCP4File::offset_symops_
    Distance offset_symops_
    number of bytes used for storing symmetry operations
    Definition CCP4File.h:116
    │ │ │ +
    BALL::CCP4File::start_
    Vector3 start_
    the start coordinates in grid coordinates, i.e. indices
    Definition CCP4File.h:124
    │ │ │ +
    BALL::CCP4File::space_group_
    Index space_group_
    space group number
    Definition CCP4File.h:145
    │ │ │ +
    BALL::CCP4File::col_axis_
    Size col_axis_
    how do columns, rows and sections correspond to specific axes: 0=x, 1=y, 2=z
    Definition CCP4File.h:119
    │ │ │ +
    BALL::CCP4File::extent_
    Vector3 extent_
    the extent of the map
    Definition CCP4File.h:127
    │ │ │ +
    BALL::CCP4File::readBinValueasFloat_
    float readBinValueasFloat_(char *header, Position pos)
    │ │ │ +
    BALL::CCP4File::readHeader
    virtual bool readHeader()
    │ │ │ +
    BALL::CCP4File::readSymmetryRecords
    virtual bool readSymmetryRecords()
    │ │ │ +
    BALL::CCP4File::deviation_sigma_
    float deviation_sigma_
    rms deviation of whole map from mean density value
    Definition CCP4File.h:142
    │ │ │ +
    BALL::CCP4File::swap_bytes_
    bool swap_bytes_
    flag indicating that we have to swap bytes when reading header values
    Definition CCP4File.h:113
    │ │ │ + │ │ │ +
    BALL::CCP4File::readBinValueasInt_
    int readBinValueasInt_(char *header, Position pos)
    │ │ │ +
    BALL::CCP4File::~CCP4File
    virtual ~CCP4File()
    Destructor.
    │ │ │ +
    BALL::CCP4File::clear
    virtual void clear()
    Clear method.
    │ │ │ +
    BALL::CCP4File::write
    virtual bool write(RegularData3D &map)
    │ │ │ +
    BALL::CCP4File::CCP4File
    CCP4File()
    Default constructor.
    │ │ │ +
    BALL::CCP4File::alpha_
    Angle alpha_
    angles of the crystal unit cell
    Definition CCP4File.h:136
    │ │ │ +
    BALL::CCP4File::mean_density_
    float mean_density_
    mean density value
    Definition CCP4File.h:139
    │ │ │ +
    BALL::CCP4File::CCP4File
    CCP4File(const String &name, File::OpenMode open_mode=std::ios::in)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::File::OpenMode
    std::ios::openmode OpenMode
    Definition file.h:165
    │ │ │ │ │ │ │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,335 +1,208 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _M_O_L_M_E_C │ │ │ │ - * _M_M_F_F_9_4 │ │ │ │ -MMFF94StretchBend.h │ │ │ │ + * _F_O_R_M_A_T │ │ │ │ +CCP4File.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: MMFF94StretchBend.h,v 1.1.8.1 2007/03/25 21:25:18 oliver Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H │ │ │ │ -8#define BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_MOLMEC_COMMON_FORCEFIELDCOMPONENT_H │ │ │ │ -11# include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ -12#endif │ │ │ │ -13 │ │ │ │ -14#ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H │ │ │ │ -15# include <_B_A_L_L_/_M_O_L_M_E_C_/_M_M_F_F_9_4_/_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ -16#endif │ │ │ │ -17 │ │ │ │ -18namespace _B_A_L_L │ │ │ │ -19{ │ │ │ │ -20 class MMFF94; │ │ │ │ -21 │ │ │ │ -_2_5 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ -26 : public _F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t │ │ │ │ -27 { │ │ │ │ -28 public: │ │ │ │ +4// │ │ │ │ +5 │ │ │ │ +6#ifndef BALL_FORMAT_CCP4FILE_H │ │ │ │ +7#define BALL_FORMAT_CCP4FILE_H │ │ │ │ +8 │ │ │ │ +9#ifndef BALL_SYSTEM_FILE_H │ │ │ │ +10# include <_B_A_L_L_/_S_Y_S_T_E_M_/_f_i_l_e_._h> │ │ │ │ +11#endif │ │ │ │ +12 │ │ │ │ +13#ifndef BALL_DATATYPE_REGULARDATA3D_H │ │ │ │ +14# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_r_e_g_u_l_a_r_D_a_t_a_3_D_._h> │ │ │ │ +15#endif │ │ │ │ +16 │ │ │ │ +17namespace _B_A_L_L │ │ │ │ +18{ │ │ │ │ +_2_6 class _B_A_L_L___E_X_P_O_R_T _C_C_P_4_F_i_l_e │ │ │ │ +27 : public _F_i_l_e │ │ │ │ +28 { │ │ │ │ 29 │ │ │ │ -_3_0 struct _B_A_L_L___E_X_P_O_R_T _S_t_r_e_t_c_h_B_e_n_d │ │ │ │ -31 { │ │ │ │ -_3_2 double _k_b_a___i_j_k; │ │ │ │ -_3_3 double _k_b_a___k_j_i; │ │ │ │ -_3_4 double _e_n_e_r_g_y; // debug │ │ │ │ -_3_5 _I_n_d_e_x _s_b_t_i_j_k; │ │ │ │ -_3_6 _I_n_d_e_x _s_t_r_e_t_c_h___i___j, stretch_j_k; │ │ │ │ -_3_7 _I_n_d_e_x _b_e_n_d___i_n_d_e_x; │ │ │ │ -38 }; │ │ │ │ -39 │ │ │ │ -_4_1 struct _B_A_L_L___E_X_P_O_R_T _B_e_n_d │ │ │ │ -42 { │ │ │ │ -_4_3 _B_e_n_d(); │ │ │ │ -44 │ │ │ │ -_4_5 double _t_h_e_t_a_0; │ │ │ │ -_4_6 double _d_e_l_t_a___t_h_e_t_a; │ │ │ │ -_4_7 double _t_h_e_t_a; │ │ │ │ -_4_8 double _k_a; │ │ │ │ -_4_9 _A_t_o_m* _a_t_o_m_1; │ │ │ │ -_5_0 _A_t_o_m* _a_t_o_m_2; │ │ │ │ -_5_1 _A_t_o_m* _a_t_o_m_3; │ │ │ │ -_5_2 bool _i_s___l_i_n_e_a_r; │ │ │ │ -_5_3 _P_o_s_i_t_i_o_n _A_T_I_J_K; │ │ │ │ -_5_4 double _e_n_e_r_g_y; // debug │ │ │ │ -_5_5 bool _e_m_p_e_r_i_c_a_l; // debug │ │ │ │ -_5_6 _T_V_e_c_t_o_r_3_<_d_o_u_b_l_e_> _n_1, n2; │ │ │ │ -57 }; │ │ │ │ -58 │ │ │ │ -_6_0 struct _B_A_L_L___E_X_P_O_R_T _S_t_r_e_t_c_h │ │ │ │ -61 { │ │ │ │ -_6_2 _S_t_r_e_t_c_h() │ │ │ │ -63 : atom1(NULL), │ │ │ │ -64 atom2(NULL), │ │ │ │ -65 kb(0.0), │ │ │ │ -66 r0(0.0), │ │ │ │ -67 delta_r(0.0), │ │ │ │ -68 sbmb(false), │ │ │ │ -69 emperical(false) │ │ │ │ -70 { │ │ │ │ -71 } │ │ │ │ -72 │ │ │ │ -_7_3 _A_t_o_m* _a_t_o_m_1; │ │ │ │ -_7_4 _A_t_o_m* _a_t_o_m_2; │ │ │ │ -_7_5 double _k_b; │ │ │ │ -_7_6 double _r_0; │ │ │ │ -_7_7 double _d_e_l_t_a___r; │ │ │ │ -_7_8 bool _s_b_m_b; │ │ │ │ -_7_9 bool _e_m_p_e_r_i_c_a_l; │ │ │ │ -_8_0 _V_e_c_t_o_r_3 _n; │ │ │ │ -81 }; │ │ │ │ -82 │ │ │ │ -_8_4 #define MMFF94_BENDS_ENABLED "enable Bends" │ │ │ │ +30 public: │ │ │ │ +31 │ │ │ │ +35 │ │ │ │ +_3_7 _C_C_P_4_F_i_l_e(); │ │ │ │ +38 │ │ │ │ +_4_2 _C_C_P_4_F_i_l_e(const _S_t_r_i_n_g& name, _F_i_l_e_:_:_O_p_e_n_M_o_d_e open_mode = std::ios::in); │ │ │ │ +43 │ │ │ │ +_4_5 virtual _~_C_C_P_4_F_i_l_e(); │ │ │ │ +46 │ │ │ │ +48 │ │ │ │ +51 │ │ │ │ +_5_3 virtual void _c_l_e_a_r(); │ │ │ │ +54 │ │ │ │ +56 │ │ │ │ +59 │ │ │ │ +_6_1 bool operator == (const _C_C_P_4_F_i_l_e& file) const; │ │ │ │ +62 │ │ │ │ +64 │ │ │ │ +66 │ │ │ │ +_7_0 virtual bool _o_p_e_n(const _S_t_r_i_n_g& name, _F_i_l_e_:_:_O_p_e_n_M_o_d_e open_mode = std::ios:: │ │ │ │ +in); │ │ │ │ +71 │ │ │ │ +_7_5 virtual bool _r_e_a_d_H_e_a_d_e_r(); │ │ │ │ +76 │ │ │ │ +_8_0 virtual bool _r_e_a_d_S_y_m_m_e_t_r_y_R_e_c_o_r_d_s(); │ │ │ │ +81 │ │ │ │ +_8_4 virtual bool _r_e_a_d(_R_e_g_u_l_a_r_D_a_t_a_3_D& map); │ │ │ │ 85 │ │ │ │ -_8_7 #define MMFF94_STRETCHES_ENABLED "enable Stretches" │ │ │ │ -88 │ │ │ │ -_9_0 #define MMFF94_STRETCHBENDS_ENABLED "enable StrechBends" │ │ │ │ -91 │ │ │ │ -92 _B_A_L_L___C_R_E_A_T_E(MMFF94StretchBend) │ │ │ │ -93 │ │ │ │ -94 │ │ │ │ -_9_6 _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d(); │ │ │ │ +_8_9 virtual bool _w_r_i_t_e_H_e_a_d_e_r(); │ │ │ │ +90 │ │ │ │ +_9_4 virtual bool _w_r_i_t_e(_R_e_g_u_l_a_r_D_a_t_a_3_D& map); │ │ │ │ +95 │ │ │ │ 97 │ │ │ │ -_1_0_0 _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d(_F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ -101 │ │ │ │ -_1_0_4 _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d(const _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d& to_copy); │ │ │ │ +100 │ │ │ │ +102 │ │ │ │ +103 private: │ │ │ │ +104 const _C_C_P_4_F_i_l_e& operator = (const _C_C_P_4_F_i_l_e& file); │ │ │ │ 105 │ │ │ │ -_1_0_8 virtual ~_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d(); │ │ │ │ +106 protected: │ │ │ │ +107 │ │ │ │ +_1_0_8 int _r_e_a_d_B_i_n_V_a_l_u_e_a_s_I_n_t__(char* header, _P_o_s_i_t_i_o_n pos); │ │ │ │ 109 │ │ │ │ -_1_1_3 virtual bool setup(); │ │ │ │ +_1_1_0 float _r_e_a_d_B_i_n_V_a_l_u_e_a_s_F_l_o_a_t__(char* header, _P_o_s_i_t_i_o_n pos); │ │ │ │ +111 │ │ │ │ +_1_1_3 bool _s_w_a_p___b_y_t_e_s__; │ │ │ │ 114 │ │ │ │ -_1_1_6 virtual double updateEnergy(); │ │ │ │ +_1_1_6 _D_i_s_t_a_n_c_e _o_f_f_s_e_t___s_y_m_o_p_s__; │ │ │ │ 117 │ │ │ │ -_1_1_9 virtual double updateBendEnergy(); │ │ │ │ -120 │ │ │ │ -_1_2_2 virtual double updateStretchEnergy(); │ │ │ │ -123 │ │ │ │ -_1_2_5 virtual double updateStretchBendEnergy(); │ │ │ │ -126 │ │ │ │ -_1_2_8 double getStretchEnergy() const; │ │ │ │ -129 │ │ │ │ -_1_3_1 double getBendEnergy() const; │ │ │ │ -132 │ │ │ │ -_1_3_4 double getStretchBendEnergy() const; │ │ │ │ -135 │ │ │ │ -_1_3_7 virtual void updateForces(); │ │ │ │ -138 │ │ │ │ -_1_4_0 virtual void updateBendForces(); │ │ │ │ -141 │ │ │ │ -_1_4_3 virtual void updateStretchForces(); │ │ │ │ -144 │ │ │ │ -_1_4_6 virtual void updateStretchBendForces(); │ │ │ │ -147 │ │ │ │ -_1_4_9 const vector<_B_e_n_d>& getBends() const { return bends_;} │ │ │ │ -150 │ │ │ │ -_1_5_2 const vector& _g_e_t_S_t_r_e_t_c_h_e_s() const { return stretches_;} │ │ │ │ -153 │ │ │ │ -_1_5_5 const vector& _g_e_t_S_t_r_e_t_c_h_B_e_n_d_s() const { return │ │ │ │ -stretch_bends_;} │ │ │ │ -156 │ │ │ │ -_1_5_8 _I_n_d_e_x _c_a_l_c_u_l_a_t_e_S_B_T_I_J_K(_P_o_s_i_t_i_o_n angle_type, │ │ │ │ -159 bool bond_type1, │ │ │ │ -160 bool bond_type2); │ │ │ │ -161 │ │ │ │ -_1_6_3 _P_o_s_i_t_i_o_n _g_e_t_B_e_n_d_T_y_p_e(const _B_o_n_d& bond1, const _B_o_n_d& bond2, │ │ │ │ -164 _A_t_o_m& atom1, _A_t_o_m& atom2, _A_t_o_m& atom3) const; │ │ │ │ -165 │ │ │ │ -_1_6_7 double _c_a_l_c_u_l_a_t_e_B_e_n_d_E_m_p_i_r_i_c_a_l_R_e_f_e_r_e_n_c_e_A_n_g_l_e(_A_t_o_m& atom1, _A_t_o_m& atom2, _A_t_o_m& │ │ │ │ -atom3) const; │ │ │ │ -168 │ │ │ │ -_1_7_0 double _c_a_l_c_u_l_a_t_e_B_e_n_d_E_m_p_i_r_i_c_a_l_F_o_r_c_e_C_o_n_s_t_a_n_t(_A_t_o_m& atom1, _A_t_o_m& atom2, _A_t_o_m& │ │ │ │ -atom3, double angle_0) const; │ │ │ │ -171 │ │ │ │ -_1_7_3 double _c_a_l_c_u_l_a_t_e_S_t_r_e_t_c_h_R_0(const _B_o_n_d& bond); │ │ │ │ -174 │ │ │ │ -_1_7_6 double _c_a_l_c_u_l_a_t_e_S_t_r_e_t_c_h_C_o_n_s_t_a_n_t(const _B_o_n_d& bond, double r0); │ │ │ │ -177 │ │ │ │ -178 private: │ │ │ │ -179 │ │ │ │ -180 inline void AddDV3_(_V_e_c_t_o_r_3& f3, const _T_V_e_c_t_o_r_3_<_d_o_u_b_l_e_> d3); │ │ │ │ -181 void calculateDeltas_(); │ │ │ │ -182 bool setupBends_(); │ │ │ │ -183 bool setupStretches_(); │ │ │ │ -184 bool setupStretchBends_(); │ │ │ │ -185 │ │ │ │ -186 void errorOccurred_(const _S_t_r_i_n_g& string, │ │ │ │ -187 const _A_t_o_m& a1, const _A_t_o_m& a2, const _A_t_o_m& a3); │ │ │ │ -188 │ │ │ │ -189 vector bends_; │ │ │ │ -190 vector stretches_; │ │ │ │ -191 vector stretch_bends_; │ │ │ │ -192 │ │ │ │ -193 const _M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s* stretch_parameters_; │ │ │ │ -194 _M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s bend_parameters_; │ │ │ │ -195 _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s sb_parameters_; │ │ │ │ -196 │ │ │ │ -197 static double bend_z_[]; │ │ │ │ -198 static double bend_c_[]; │ │ │ │ -199 static _S_t_r_i_n_g bend_elements_[]; │ │ │ │ -200 │ │ │ │ -201 double stretch_energy_; │ │ │ │ -202 double bend_energy_; │ │ │ │ -203 double stretch_bend_energy_; │ │ │ │ -204 │ │ │ │ -205 _M_M_F_F_9_4* mmff94_; │ │ │ │ -206 bool stretch_enabled_, bend_enabled_, stretchbend_enabled_; │ │ │ │ -207 }; │ │ │ │ -208} // namespace BALL │ │ │ │ -209 │ │ │ │ -210#endif // BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H │ │ │ │ -_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h │ │ │ │ -_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_1_1_9 _S_i_z_e _c_o_l___a_x_i_s__; │ │ │ │ +_1_2_0 _S_i_z_e _r_o_w___a_x_i_s__; │ │ │ │ +_1_2_1 _S_i_z_e _s_e_c___a_x_i_s__; │ │ │ │ +122 │ │ │ │ +_1_2_4 _V_e_c_t_o_r_3 _s_t_a_r_t__; │ │ │ │ +125 │ │ │ │ +_1_2_7 _V_e_c_t_o_r_3 _e_x_t_e_n_t__; │ │ │ │ +128 │ │ │ │ +_1_3_0 _V_e_c_t_o_r_3 _s_a_m_p_l_i_n_g___r_a_t_e__; │ │ │ │ +131 │ │ │ │ +_1_3_3 _V_e_c_t_o_r_3 _c_e_l_l___d_i_m_e_n_s_i_o_n__; │ │ │ │ +134 │ │ │ │ +_1_3_6 _A_n_g_l_e _a_l_p_h_a__, beta_, gamma_; │ │ │ │ +137 │ │ │ │ +_1_3_9 float _m_e_a_n___d_e_n_s_i_t_y__; │ │ │ │ +140 │ │ │ │ +_1_4_2 float _d_e_v_i_a_t_i_o_n___s_i_g_m_a__; │ │ │ │ +143 │ │ │ │ +_1_4_5 _I_n_d_e_x _s_p_a_c_e___g_r_o_u_p__; │ │ │ │ +146 │ │ │ │ +_1_4_8 _V_e_c_t_o_r_3 _o_r_i_g_i_n__, xaxis_, yaxis_, zaxis_; │ │ │ │ +149 }; │ │ │ │ +150} // namespace BALL │ │ │ │ +151 │ │ │ │ +152#endif // BALL_FORMAT_DCDFILE_H │ │ │ │ +_f_i_l_e_._h │ │ │ │ +_r_e_g_u_l_a_r_D_a_t_a_3_D_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ +_B_A_L_L_:_:_T_R_e_g_u_l_a_r_D_a_t_a_3_D_<_ _f_l_o_a_t_ _> │ │ │ │ _B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_B_o_n_d │ │ │ │ -DDeeffiinniittiioonn _b_o_n_d_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_1 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4 │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_._h_:_5_1 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_8_7 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_6_5 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_3_1_2 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_2_7 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_g_e_t_S_t_r_e_t_c_h_e_s │ │ │ │ -const vector< Stretch > & getStretches() const │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_1_5_2 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_g_e_t_B_e_n_d_T_y_p_e │ │ │ │ -Position getBendType(const Bond &bond1, const Bond &bond2, Atom &atom1, Atom │ │ │ │ -&atom2, Atom &atom3) const │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_g_e_t_S_t_r_e_t_c_h_B_e_n_d_s │ │ │ │ -const vector< StretchBend > & getStretchBends() const │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_1_5_5 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_B_e_n_d_E_m_p_i_r_i_c_a_l_R_e_f_e_r_e_n_c_e_A_n_g_l_e │ │ │ │ -double calculateBendEmpiricalReferenceAngle(Atom &atom1, Atom &atom2, Atom │ │ │ │ -&atom3) const │ │ │ │ -Bend emperical reference angle. │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_S_t_r_e_t_c_h_C_o_n_s_t_a_n_t │ │ │ │ -double calculateStretchConstant(const Bond &bond, double r0) │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_S_B_T_I_J_K │ │ │ │ -Index calculateSBTIJK(Position angle_type, bool bond_type1, bool bond_type2) │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_B_e_n_d_E_m_p_i_r_i_c_a_l_F_o_r_c_e_C_o_n_s_t_a_n_t │ │ │ │ -double calculateBendEmpiricalForceConstant(Atom &atom1, Atom &atom2, Atom │ │ │ │ -&atom3, double angle_0) const │ │ │ │ -Bend emperical force constant. │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_S_t_r_e_t_c_h_R_0 │ │ │ │ -double calculateStretchR0(const Bond &bond) │ │ │ │ -Calculate the radius value per Schomaker-Stevenson Rule. │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_1 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_b_e_n_d___i_n_d_e_x │ │ │ │ -Index bend_index │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_7 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_s_t_r_e_t_c_h___i___j │ │ │ │ -Index stretch_i_j │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_k_b_a___i_j_k │ │ │ │ -double kba_ijk │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_s_b_t_i_j_k │ │ │ │ -Index sbtijk │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_e_n_e_r_g_y │ │ │ │ -double energy │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_4 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_k_b_a___k_j_i │ │ │ │ -double kba_kji │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d │ │ │ │ -see MMFFANG.PAR │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_2 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_t_h_e_t_a │ │ │ │ -double theta │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_7 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_n_1 │ │ │ │ -TVector3< double > n1 │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_6 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_A_T_I_J_K │ │ │ │ -Position ATIJK │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_i_s___l_i_n_e_a_r │ │ │ │ -bool is_linear │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_2 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_B_e_n_d │ │ │ │ -Bend() │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_t_h_e_t_a_0 │ │ │ │ -double theta0 │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_5 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_a_t_o_m_2 │ │ │ │ -Atom * atom2 │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_0 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_e_m_p_e_r_i_c_a_l │ │ │ │ -bool emperical │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_5 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_a_t_o_m_1 │ │ │ │ -Atom * atom1 │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_9 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_k_a │ │ │ │ -double ka │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_d_e_l_t_a___t_h_e_t_a │ │ │ │ -double delta_theta │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_e_n_e_r_g_y │ │ │ │ -double energy │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_4 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_a_t_o_m_3 │ │ │ │ -Atom * atom3 │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_1 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_6_1 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_d_e_l_t_a___r │ │ │ │ -double delta_r │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_7 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_k_b │ │ │ │ -double kb │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_5 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_n │ │ │ │ -Vector3 n │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_8_0 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_e_m_p_e_r_i_c_a_l │ │ │ │ -bool emperical │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_9 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_a_t_o_m_2 │ │ │ │ -Atom * atom2 │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_s_b_m_b │ │ │ │ -bool sbmb │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_8 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_S_t_r_e_t_c_h │ │ │ │ -Stretch() │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_6_2 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_r_0 │ │ │ │ -double r0 │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_6 │ │ │ │ -_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_a_t_o_m_1 │ │ │ │ -Atom * atom1 │ │ │ │ -DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_2_8 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_r_o_w___a_x_i_s__ │ │ │ │ +Size row_axis_ │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_2_0 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_r_e_a_d │ │ │ │ +virtual bool read(RegularData3D &map) │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_c_e_l_l___d_i_m_e_n_s_i_o_n__ │ │ │ │ +Vector3 cell_dimension_ │ │ │ │ +dimension of the crystal unit cell in Angstrom/sample │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_3_3 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_s_a_m_p_l_i_n_g___r_a_t_e__ │ │ │ │ +Vector3 sampling_rate_ │ │ │ │ +the sampling rates used for the map │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_3_0 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_o_p_e_n │ │ │ │ +virtual bool open(const String &name, File::OpenMode open_mode=std::ios::in) │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_o_r_i_g_i_n__ │ │ │ │ +Vector3 origin_ │ │ │ │ +geometry in cartesian coordinates │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_4_8 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_w_r_i_t_e_H_e_a_d_e_r │ │ │ │ +virtual bool writeHeader() │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_o_f_f_s_e_t___s_y_m_o_p_s__ │ │ │ │ +Distance offset_symops_ │ │ │ │ +number of bytes used for storing symmetry operations │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_1_6 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_s_t_a_r_t__ │ │ │ │ +Vector3 start_ │ │ │ │ +the start coordinates in grid coordinates, i.e. indices │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_2_4 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_s_p_a_c_e___g_r_o_u_p__ │ │ │ │ +Index space_group_ │ │ │ │ +space group number │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_4_5 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_c_o_l___a_x_i_s__ │ │ │ │ +Size col_axis_ │ │ │ │ +how do columns, rows and sections correspond to specific axes: 0=x, 1=y, 2=z │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_1_9 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_e_x_t_e_n_t__ │ │ │ │ +Vector3 extent_ │ │ │ │ +the extent of the map │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_2_7 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_r_e_a_d_B_i_n_V_a_l_u_e_a_s_F_l_o_a_t__ │ │ │ │ +float readBinValueasFloat_(char *header, Position pos) │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_r_e_a_d_H_e_a_d_e_r │ │ │ │ +virtual bool readHeader() │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_r_e_a_d_S_y_m_m_e_t_r_y_R_e_c_o_r_d_s │ │ │ │ +virtual bool readSymmetryRecords() │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_d_e_v_i_a_t_i_o_n___s_i_g_m_a__ │ │ │ │ +float deviation_sigma_ │ │ │ │ +rms deviation of whole map from mean density value │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_4_2 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_s_w_a_p___b_y_t_e_s__ │ │ │ │ +bool swap_bytes_ │ │ │ │ +flag indicating that we have to swap bytes when reading header values │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_1_3 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_s_e_c___a_x_i_s__ │ │ │ │ +Size sec_axis_ │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_2_1 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_r_e_a_d_B_i_n_V_a_l_u_e_a_s_I_n_t__ │ │ │ │ +int readBinValueasInt_(char *header, Position pos) │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_~_C_C_P_4_F_i_l_e │ │ │ │ +virtual ~CCP4File() │ │ │ │ +Destructor. │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_c_l_e_a_r │ │ │ │ +virtual void clear() │ │ │ │ +Clear method. │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_w_r_i_t_e │ │ │ │ +virtual bool write(RegularData3D &map) │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_C_C_P_4_F_i_l_e │ │ │ │ +CCP4File() │ │ │ │ +Default constructor. │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_a_l_p_h_a__ │ │ │ │ +Angle alpha_ │ │ │ │ +angles of the crystal unit cell │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_3_6 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_m_e_a_n___d_e_n_s_i_t_y__ │ │ │ │ +float mean_density_ │ │ │ │ +mean density value │ │ │ │ +DDeeffiinniittiioonn _C_C_P_4_F_i_l_e_._h_:_1_3_9 │ │ │ │ +_B_A_L_L_:_:_C_C_P_4_F_i_l_e_:_:_C_C_P_4_F_i_l_e │ │ │ │ +CCP4File(const String &name, File::OpenMode open_mode=std::ios::in) │ │ │ │ +_B_A_L_L_:_:_T_A_n_g_l_e_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_F_i_l_e │ │ │ │ +DDeeffiinniittiioonn _f_i_l_e_._h_:_1_3_6 │ │ │ │ +_B_A_L_L_:_:_F_i_l_e_:_:_O_p_e_n_M_o_d_e │ │ │ │ +std::ios::openmode OpenMode │ │ │ │ +DDeeffiinniittiioonn _f_i_l_e_._h_:_1_6_5 │ │ │ │ _B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d89/a00071.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: scene.h File Reference │ │ │ +BALL: RDFParameter.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,57 +65,40 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    scene.h File Reference
    │ │ │ +
    RDFParameter.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/VIEW/KERNEL/modularWidget.h>
    │ │ │ -#include <BALL/VIEW/RENDERING/RENDERERS/glRenderer.h>
    │ │ │ -#include <BALL/VIEW/KERNEL/common.h>
    │ │ │ -#include <BALL/VIEW/RENDERING/renderWindow.h>
    │ │ │ -#include <BALL/VIEW/RENDERING/glRenderWindow.h>
    │ │ │ -#include <BALL/VIEW/RENDERING/renderSetup.h>
    │ │ │ -#include <BALL/VIEW/DIALOGS/editSettings.h>
    │ │ │ -#include <BALL/VIEW/KERNEL/editOperation.h>
    │ │ │ -#include <BALL/VIEW/KERNEL/MODES/interactionModeManager.h>
    │ │ │ -#include <QtCore/QThread>
    │ │ │ -#include <QtCore/QTimer>
    │ │ │ -#include <QtGui/QDragEnterEvent>
    │ │ │ -#include <QtGui/QDropEvent>
    │ │ │ -#include <QtWidgets/QToolBar>
    │ │ │ -#include <QtGui/QFont>
    │ │ │ -#include <QtGui/QPicture>
    │ │ │ -#include <boost/shared_ptr.hpp>
    │ │ │ +
    #include <BALL/KERNEL/atom.h>
    │ │ │ +#include <BALL/STRUCTURE/radialDistributionFunction.h>
    │ │ │ +#include <BALL/FORMAT/parameterSection.h>
    │ │ │ +#include <BALL/MOLMEC/PARAMETER/forceFieldParameters.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::Scene
     
    class  BALL::VIEW::AnimationThread
    class  BALL::RDFParameter
     
    │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,40 +1,22 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _W_I_D_G_E_T_S │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -scene.h File Reference │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_R_E_N_D_E_R_E_R_S_/_g_l_R_e_n_d_e_r_e_r_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_r_e_n_d_e_r_W_i_n_d_o_w_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_r_e_n_d_e_r_S_e_t_u_p_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_D_I_A_L_O_G_S_/_e_d_i_t_S_e_t_t_i_n_g_s_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_e_d_i_t_O_p_e_r_a_t_i_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_M_O_D_E_S_/_i_n_t_e_r_a_c_t_i_o_n_M_o_d_e_M_a_n_a_g_e_r_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ +RDFParameter.h File Reference │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_._h> │ │ │ │ +#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_r_a_d_i_a_l_D_i_s_t_r_i_b_u_t_i_o_n_F_u_n_c_t_i_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_F_O_R_M_A_T_/_p_a_r_a_m_e_t_e_r_S_e_c_t_i_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_P_A_R_A_M_E_T_E_R_/_f_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_A_n_i_m_a_t_i_o_n_T_h_r_e_a_d │ │ │ │ +class   _B_A_L_L_:_:_R_D_F_P_a_r_a_m_e_t_e_r │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │ -  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d89/a00071_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: scene.h Source File │ │ │ +BALL: RDFParameter.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,1004 +70,130 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    scene.h
    │ │ │ +
    RDFParameter.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5#ifndef BALL_VIEW_WIDGETS_SCENE_H
    │ │ │ -
    6#define BALL_VIEW_WIDGETS_SCENE_H
    │ │ │ +
    5#ifndef BALL_STRUCTURE_RDFPARAMETER_H
    │ │ │ +
    6#define BALL_STRUCTURE_RDFPARAMETER_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H
    │ │ │ -
    9# include <BALL/VIEW/KERNEL/modularWidget.h>
    │ │ │ +
    8#ifndef BALL_KERNEL_ATOM_H
    │ │ │ +
    9# include <BALL/KERNEL/atom.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_VIEW_RENDERING_RENDERERSGLRENDERER_H
    │ │ │ -
    13# include <BALL/VIEW/RENDERING/RENDERERS/glRenderer.h>
    │ │ │ +
    12#ifndef BALL_STRUCTURE_RADIALDISTRIBUTIONFUNCTION_H
    │ │ │ +
    13# include <BALL/STRUCTURE/radialDistributionFunction.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │ -
    16#ifndef BALL_VIEW_KERNEL_COMMON_H
    │ │ │ -
    17# include <BALL/VIEW/KERNEL/common.h>
    │ │ │ +
    16#ifndef BALL_FORMAT_PARAMETERSECTION_H
    │ │ │ +
    17# include <BALL/FORMAT/parameterSection.h>
    │ │ │
    18#endif
    │ │ │
    19
    │ │ │ -
    20#ifndef BALL_VIEW_RENDERING_RENDERWINDOW_H
    │ │ │ -
    21# include <BALL/VIEW/RENDERING/renderWindow.h>
    │ │ │ +
    20#ifndef BALL_MOLMEC_PARAMETERS_FORCEFIELDPARAMETERS_H
    │ │ │ +
    21# include <BALL/MOLMEC/PARAMETER/forceFieldParameters.h>
    │ │ │
    22#endif
    │ │ │
    23
    │ │ │ -
    24#ifndef BALL_VIEW_RENDERING_GLRENDERWINDOW_H
    │ │ │ -
    25# include <BALL/VIEW/RENDERING/glRenderWindow.h>
    │ │ │ -
    26#endif
    │ │ │ -
    27
    │ │ │ -
    28#ifndef BALL_VIEW_RENDERING_RENDERSETUP_H
    │ │ │ -
    29# include <BALL/VIEW/RENDERING/renderSetup.h>
    │ │ │ -
    30#endif
    │ │ │ -
    31
    │ │ │ -
    32#ifndef BALL_VIEW_DIALOGS_EDITSETTINGS_H
    │ │ │ -
    33# include <BALL/VIEW/DIALOGS/editSettings.h>
    │ │ │ -
    34#endif
    │ │ │ +
    24namespace BALL
    │ │ │ +
    25{
    │ │ │ +
    │ │ │ +
    31 class BALL_EXPORT RDFParameter
    │ │ │ +
    32 : public ParameterSection
    │ │ │ +
    33 {
    │ │ │ +
    34 public:
    │ │ │
    35
    │ │ │ -
    36#ifndef BALL_VIEW_KERNEL_EDITOPERATION_H
    │ │ │ -
    37# include <BALL/VIEW/KERNEL/editOperation.h>
    │ │ │ -
    38#endif
    │ │ │ -
    39
    │ │ │ -
    40#ifndef BALL_VIEW_KERNEL_MODES_INTERACTIONMODEMANAGER_H
    │ │ │ -
    41# include <BALL/VIEW/KERNEL/MODES/interactionModeManager.h>
    │ │ │ -
    42#endif
    │ │ │ -
    43
    │ │ │ -
    44#include <QtCore/QThread>
    │ │ │ -
    45#include <QtCore/QTimer>
    │ │ │ -
    46#include <QtGui/QDragEnterEvent>
    │ │ │ -
    47#include <QtGui/QDropEvent>
    │ │ │ -
    48#include <QtWidgets/QToolBar>
    │ │ │ -
    49#include <QtGui/QFont>
    │ │ │ -
    50#include <QtGui/QPicture>
    │ │ │ -
    51
    │ │ │ -
    52#include <boost/shared_ptr.hpp>
    │ │ │ -
    53
    │ │ │ -
    54#ifdef BALL_HAS_RTFACT
    │ │ │ -
    55
    │ │ │ -
    56#ifndef BALL_VIEW_RENDERING_RAYTRACINGRENDERER_H
    │ │ │ -
    57# include <BALL/VIEW/RENDERING/RENDERERS/raytracingRenderer.h>
    │ │ │ -
    58#endif
    │ │ │ +
    36 BALL_CREATE(RDFParameter)
    │ │ │ +
    37
    │ │ │ +
    38
    │ │ │ +
    41
    │ │ │ +
    42
    │ │ │ +
    44 RDFParameter()
    │ │ │ +
    45 ;
    │ │ │ +
    46
    │ │ │ +
    50 RDFParameter(const RDFParameter& rdf_parameter)
    │ │ │ +
    51 ;
    │ │ │ +
    52
    │ │ │ +
    55 virtual ~RDFParameter()
    │ │ │ +
    56 ;
    │ │ │ +
    57
    │ │ │
    59
    │ │ │ -
    60#endif // BALL_HAS_RTFACT
    │ │ │ -
    61
    │ │ │ -
    62class QMouseEvent;
    │ │ │ -
    63class QRubberBand;
    │ │ │ -
    64class QMenu;
    │ │ │ -
    65class QImage;
    │ │ │ -
    66class QAction;
    │ │ │ -
    67class QWheelEvent;
    │ │ │ -
    68class QKeyEvent;
    │ │ │ +
    62
    │ │ │ +
    67 const RDFParameter& operator = (const RDFParameter& rdf_parameter)
    │ │ │ +
    68 ;
    │ │ │
    69
    │ │ │ -
    70namespace BALL
    │ │ │ -
    71{
    │ │ │ -
    72 class Bond;
    │ │ │ -
    73 class PDBAtom;
    │ │ │ -
    74 class AtomContainer;
    │ │ │ -
    75
    │ │ │ -
    76 namespace VIEW
    │ │ │ -
    77 {
    │ │ │ -
    78 class ColorMap;
    │ │ │ -
    79 class InteractionMode;
    │ │ │ -
    80 class Preferences;
    │ │ │ -
    81 class LightSettings;
    │ │ │ -
    82 class StageSettings;
    │ │ │ -
    83 class MaterialSettings;
    │ │ │ -
    84 class AnimationThread;
    │ │ │ -
    85 class ClippingPlane;
    │ │ │ -
    86 class CompositeMessage;
    │ │ │ -
    87 class ControlSelectionMessage;
    │ │ │ -
    88 class RepresentationMessage;
    │ │ │ -
    89 class DatasetMessage;
    │ │ │ -
    90 class SceneMessage;
    │ │ │ -
    91
    │ │ │ -
    92 class TransformationEvent6D;
    │ │ │ -
    93 class MotionTrackingEvent;
    │ │ │ -
    94 class ButtonEvent;
    │ │ │ -
    95 class RenderToBufferFinishedEvent;
    │ │ │ -
    96
    │ │ │ -
    │ │ │ -
    138 class BALL_VIEW_EXPORT Scene
    │ │ │ -
    139 : public QWidget,
    │ │ │ -
    140 public ModularWidget
    │ │ │ -
    141 {
    │ │ │ -
    142 friend class AnimationThread;
    │ │ │ -
    143 friend class RenderSetup;
    │ │ │ +
    72 virtual void clear()
    │ │ │ +
    73 ;
    │ │ │ +
    74
    │ │ │ +
    76
    │ │ │ +
    79
    │ │ │ +
    86 Position getIndex(Atom::Type type_i, Atom::Type type_j) const
    │ │ │ +
    87 ;
    │ │ │ +
    88
    │ │ │ +
    94 const RadialDistributionFunction& getRDF(Atom::Type type_i,
    │ │ │ +
    95 Atom::Type type_j) const
    │ │ │ +
    96 ;
    │ │ │ +
    97
    │ │ │ +
    103 const RadialDistributionFunction& getRDF(Position index) const
    │ │ │ +
    104 ;
    │ │ │ +
    105
    │ │ │ +
    107
    │ │ │ +
    113 virtual bool extractSection(ForceFieldParameters& parameters,
    │ │ │ +
    114 const String& section_name)
    │ │ │ +
    115 ;
    │ │ │ +
    116
    │ │ │ +
    120
    │ │ │ +
    128 bool hasRDF(Atom::Type solvent_atom_type, Atom::Type solute_atom_type)
    │ │ │ +
    129 const ;
    │ │ │ +
    130
    │ │ │ +
    134 bool hasParameters(Atom::Type solvent_atom_type,
    │ │ │ +
    135 Atom::Type solute_atom_type) const
    │ │ │ +
    136 ;
    │ │ │ +
    137
    │ │ │ +
    139
    │ │ │ +
    140 protected:
    │ │ │ +
    141
    │ │ │ +
    142 /*_ The vector containing all the read RDF representations */
    │ │ │ +
    143 std::vector<RadialDistributionFunction> rdf_list_;
    │ │ │
    144
    │ │ │ -
    145#ifdef BALL_HAS_RTFACT
    │ │ │ -
    146 typedef boost::shared_ptr<RaytracingRenderer> RaytracingRendererPtr;
    │ │ │ -
    147 typedef boost::shared_ptr<RenderWindow> RaytracingWindowPtr;
    │ │ │ -
    148#endif
    │ │ │ -
    149
    │ │ │ -
    150 Q_OBJECT
    │ │ │ -
    151
    │ │ │ -
    152 public:
    │ │ │ -
    153 BALL_EMBEDDABLE(Scene, ModularWidget)
    │ │ │ -
    154
    │ │ │ -
    155
    │ │ │ -
    158
    │ │ │ -
    159
    │ │ │ -
    │ │ │ -
    164 enum WindowType
    │ │ │ -
    165 {
    │ │ │ -
    167 CONTROL_WINDOW = 0,
    │ │ │ -
    168
    │ │ │ -
    170 LEFT_EYE_WINDOW,
    │ │ │ -
    171
    │ │ │ -
    173 RIGHT_EYE_WINDOW
    │ │ │ -
    174 };
    │ │ │ -
    │ │ │ -
    175
    │ │ │ -
    179
    │ │ │ -
    190 Scene(QWidget* parent_widget = 0, const char* name = NULL, Qt::WindowFlags w_flags = 0);
    │ │ │ -
    191
    │ │ │ -
    194 virtual ~Scene();
    │ │ │ -
    195
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    204 virtual void clear();
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    205
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    207
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    209
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    212
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    219 virtual void onNotify(Message *message);
    │ │ │ -
    220
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    223 virtual bool exportScene(Renderer &er) const;
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    224
    │ │ │ -
    225 String getBondOrderString_(Index order);
    │ │ │ -
    226
    │ │ │ -
    228
    │ │ │ -
    231
    │ │ │ -
    241 virtual void initializeWidget(MainControl& main_control);
    │ │ │ -
    242
    │ │ │ -
    244 virtual void fetchPreferences(INIFile& inifile);
    │ │ │ -
    245
    │ │ │ -
    247 virtual void writePreferences(INIFile& inifile);
    │ │ │ -
    248
    │ │ │ -
    259 virtual void checkMenu(MainControl& main_control);
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    260
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    262
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    265
    │ │ │ -
    269 virtual bool isValid() const;
    │ │ │ -
    270
    │ │ │ -
    277 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ -
    278
    │ │ │ -
    279 void setInfo(const QString& info_string);
    │ │ │ -
    280 bool isRecording() const;
    │ │ │ -
    281 void captureCamera();
    │ │ │ -
    282 Atom* getCurrentAtom() { return current_atom_; }
    │ │ │ -
    283 void setCurrentAtom(Atom* atom) { current_atom_ = atom; }
    │ │ │ -
    284 void notify(Message* msg) { notify_(msg); }
    │ │ │ -
    285 Vector2 map3DToViewport(const Vector3& coords);
    │ │ │ -
    286 Vector3 mapViewportTo3D(const Vector2& coords);
    │ │ │ -
    287 Vector3 mapViewportTo3D(int x, int y);
    │ │ │ -
    288 void setRubberBandGeometry(const QRect& rect);
    │ │ │ -
    289 void setRubberBandVisible(bool show);
    │ │ │ -
    290 void pickObjects(const QPoint& pos, list<GeometricObject*>& objects);
    │ │ │ -
    291 void pickObjects(const QPoint& pos1, const QPoint& pos2, list<GeometricObject*>& objects);
    │ │ │ -
    292 void merge(Composite* a1, Composite* a2);
    │ │ │ -
    293 std::list<AtomContainer*> getContainers();
    │ │ │ -
    294 void enterPickingMode();
    │ │ │ -
    295 void exitPickingMode();
    │ │ │ -
    296
    │ │ │ -
    297 void drawLine(const QPointF& a, const QPointF& b, QPainter* painter = 0);
    │ │ │ -
    298 void drawLine(const Vector2& a, const Vector2& b, QPainter* painter = 0);
    │ │ │ -
    299
    │ │ │ -
    300 Bond* getCurrentBond() { return current_bond_; }
    │ │ │ -
    301 void setCurrentBond(Bond* b) { current_bond_ = b; }
    │ │ │ -
    302
    │ │ │ -
    303 void changeBondOrder();
    │ │ │ -
    304 void changeBondOrder(Index delta);
    │ │ │ -
    305 void activatedOrderItem_(QAction* action);
    │ │ │ -
    306 void createMolecule_();
    │ │ │ -
    307 void setFormalCharge_();
    │ │ │ -
    308
    │ │ │ -
    309 void deselect(bool update=true);
    │ │ │ -
    310 void getClickedItems(const QPoint& p);
    │ │ │ -
    311
    │ │ │ -
    │ │ │ -
    313 Stage* getStage()
    │ │ │ -
    314 { return stage_;}
    │ │ │ -
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    315
    │ │ │ -
    │ │ │ -
    317 const Stage* getStage() const
    │ │ │ -
    318 { return stage_;}
    │ │ │ -
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    319
    │ │ │ -
    │ │ │ -
    321 StageSettings* getStageSettings()
    │ │ │ -
    322 { return stage_settings_; }
    │ │ │ -
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    323
    │ │ │ -
    │ │ │ -
    325 const StageSettings* getStageSettings() const
    │ │ │ -
    326 { return stage_settings_; }
    │ │ │ -
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    327
    │ │ │ -
    │ │ │ -
    329 MaterialSettings* getMaterialSettings()
    │ │ │ -
    330 { return material_settings_; }
    │ │ │ -
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    331
    │ │ │ -
    │ │ │ -
    333 const MaterialSettings* getMaterialSettings() const
    │ │ │ -
    334 { return material_settings_; }
    │ │ │ -
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    335
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    337 void setCamera(const Camera& camera);
    │ │ │ -
    338
    │ │ │ -
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    340 std::list<Camera>& getAnimationPoints()
    │ │ │ -
    341 { return animation_points_;}
    │ │ │ -
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    342
    │ │ │ -
    │ │ │ -
    344 static void setAnimationSmoothness(float value)
    │ │ │ -
    345 { animation_smoothness_ = value;}
    │ │ │ -
    │ │ │ -
    346
    │ │ │ -
    │ │ │ -
    348 static float getAnimationSmoothness()
    │ │ │ -
    349 { return animation_smoothness_;}
    │ │ │ -
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    350
    │ │ │ -
    │ │ │ -
    352 float getDownsamplingFactor() const
    │ │ │ -
    353 { return downsampling_factor_;}
    │ │ │ -
    │ │ │ -
    354
    │ │ │ -
    356 void setDownsamplingFactor(float ds_factor);
    │ │ │ -
    357
    │ │ │ -
    359 void setDefaultLighting(bool update_GL = true);
    │ │ │ -
    360
    │ │ │ -
    362 BALL_DEPRECATED static void setMouseSensitivity(float /* sensitivity */) {}
    │ │ │ -
    363
    │ │ │ -
    365 BALL_DEPRECATED static float getMouseSensitivity() { return 0; }
    │ │ │ -
    366
    │ │ │ -
    368 BALL_DEPRECATED static void setMouseWheelSensitivity(float /* sensitivity */) {}
    │ │ │ -
    369
    │ │ │ -
    371 BALL_DEPRECATED static float getMouseWheelSensitivity() { return 0; }
    │ │ │ -
    372
    │ │ │ -
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    374 static void setShowLightSources(bool state)
    │ │ │ -
    375 { show_light_sources_ = state;}
    │ │ │ -
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    376
    │ │ │ -
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    378 static bool showLightSourcesEnabled()
    │ │ │ -
    379 { return show_light_sources_;}
    │ │ │ -
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    380
    │ │ │ -
    │ │ │ -
    382 GLRenderer& getGLRenderer()
    │ │ │ -
    383 { return *gl_renderer_;}
    │ │ │ -
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    384
    │ │ │ -
    385#ifdef BALL_HAS_RTFACT
    │ │ │ -
    387 RaytracingRenderer& getRaytracingRenderer()
    │ │ │ -
    388 { return *rt_renderer_;}
    │ │ │ -
    389#endif
    │ │ │ -
    390
    │ │ │ -
    395 void setGLRenderer(GLRenderer& renderer);
    │ │ │ -
    396
    │ │ │ -
    398 static bool stereoBufferSupportTest();
    │ │ │ -
    399
    │ │ │ -
    401 bool inMoveMode() const;
    │ │ │ -
    402
    │ │ │ -
    404 bool exportPNG(const String& filename);
    │ │ │ -
    405
    │ │ │ -
    407 virtual void setWidgetVisible(bool state);
    │ │ │ -
    408
    │ │ │ -
    410 void setOffScreenRendering(bool enabled, Size factor);
    │ │ │ -
    411
    │ │ │ -
    413 virtual void paintEvent(QPaintEvent* e);
    │ │ │ -
    414
    │ │ │ -
    416 virtual bool eventFilter(QObject* object, QEvent* event);
    │ │ │ -
    417
    │ │ │ -
    419 virtual void projectionModeChanged();
    │ │ │ -
    420
    │ │ │ -
    422 static void setScreenShotNumber(Position pos) { screenshot_nr_ = pos;}
    │ │ │ -
    423
    │ │ │ -
    425 static void setPOVNumber(Position pos) { pov_nr_ = pos;}
    │ │ │ -
    426
    │ │ │ -
    428 static void setVRMLNumber(Position pos) {vrml_nr_ = pos;}
    │ │ │ -
    429
    │ │ │ -
    431 void rotate(float degree_right, float degree_up);
    │ │ │ -
    432
    │ │ │ -
    434 void rotateClockwise(float degree);
    │ │ │ -
    435
    │ │ │ -
    441 void move(Vector3 v);
    │ │ │ -
    442
    │ │ │ -
    443 // TODO: move this and the next function somewhere else...
    │ │ │ -
    449 void moveComposites(const std::list<Composite*>& composites, Vector3 v);
    │ │ │ -
    450
    │ │ │ -
    456 void rotateComposites(const std::list<Composite*>& composites, float degree_right, float degree_up, float degree_clockwise = 0);
    │ │ │ -
    457
    │ │ │ -
    459 bool isAnimationRunning() const;
    │ │ │ -
    460
    │ │ │ -
    462 void setTurnPoint(const Vector3& v) { system_origin_ = v;}
    │ │ │ -
    463
    │ │ │ -
    465 const Vector3& getTurnPoint() const { return system_origin_;}
    │ │ │ -
    466
    │ │ │ -
    468 void setFullScreen(bool state);
    │ │ │ -
    469
    │ │ │ -
    471 void setFPSEnabled(bool state) { show_fps_ = state; }
    │ │ │ -
    472
    │ │ │ -
    476 void showText(const String& text, Size font_size = 20);
    │ │ │ -
    477
    │ │ │ -
    479 bool isUpdateRunning() const { return update_running_;}
    │ │ │ -
    480
    │ │ │ -
    481 void resetTracking() {tracking_initialized_ = false;}
    │ │ │ -
    482
    │ │ │ -
    483 // TODO: this pretty hacky!
    │ │ │ -
    484 void updateAllMaterials();
    │ │ │ -
    485
    │ │ │ -
    486 void updateMaterialForRepresentation(Representation* rep, const Stage::Material& new_material);
    │ │ │ -
    487
    │ │ │ -
    488 void lightsUpdated(bool redraw = false);
    │ │ │ -
    489
    │ │ │ -
    491 void setupEnvironmentMap(const QImage& image);
    │ │ │ -
    492
    │ │ │ -
    493 Position prepareGridTextures(const RegularData3D& grid, const ColorMap& map);
    │ │ │ -
    494
    │ │ │ -
    495 void updateGL();
    │ │ │ -
    497 void initializePreferencesTab(Preferences &preferences);
    │ │ │ -
    498
    │ │ │ -
    500 void finalizePreferencesTab(Preferences &preferences);
    │ │ │ -
    501
    │ │ │ -
    503 virtual void applyPreferences();
    │ │ │ -
    504
    │ │ │ -
    506 void showContextMenu(QPoint pos);
    │ │ │ -
    507
    │ │ │ -
    508 // Allow to use the base class setCursor, too
    │ │ │ -
    509 using QWidget::setCursor;
    │ │ │ -
    510
    │ │ │ -
    512 void setCursor(String c);
    │ │ │ -
    513
    │ │ │ -
    515 void setElementCursor(int number);
    │ │ │ -
    516
    │ │ │ -
    518 virtual void addToolBarEntries(QToolBar* tb);
    │ │ │ -
    519
    │ │ │ -
    521 virtual void keyPressEvent(QKeyEvent* e);
    │ │ │ -
    522
    │ │ │ -
    524 public Q_SLOTS:
    │ │ │ -
    526 void createCoordinateSystem();
    │ │ │ -
    527
    │ │ │ -
    529 void createCoordinateSystemAtOrigin();
    │ │ │ -
    530
    │ │ │ -
    532 String exportPNG();
    │ │ │ -
    533
    │ │ │ -
    535 void exportPOVRay();
    │ │ │ -
    536
    │ │ │ -
    538 void exportNextPOVRay();
    │ │ │ -
    539
    │ │ │ -
    541 void printScene();
    │ │ │ -
    542
    │ │ │ -
    544 void showExportPNGDialog();
    │ │ │ -
    545
    │ │ │ -
    547 void showExportVRMLDialog();
    │ │ │ -
    548
    │ │ │ -
    550 void setPreview(bool state) { use_preview_ = state; }
    │ │ │ -
    551
    │ │ │ -
    553 bool usePreview() const { return use_preview_; }
    │ │ │ -
    554
    │ │ │ -
    555 bool useVertexBuffers() const { return want_to_use_vertex_buffer_; }
    │ │ │ -
    556
    │ │ │ -
    560 virtual void switchShowWidget();
    │ │ │ -
    561
    │ │ │ -
    563 void switchRenderer(RenderSetup::RendererType new_type);
    │ │ │ -
    564
    │ │ │ -
    566 void addGlWindow();
    │ │ │ -
    567
    │ │ │ -
    568#ifdef BALL_HAS_RTFACT
    │ │ │ -
    570 void addRTfactWindow();
    │ │ │ -
    571#endif
    │ │ │ -
    572
    │ │ │ -
    574 void exitStereo();
    │ │ │ -
    575
    │ │ │ -
    577 void enterStereo();
    │ │ │ -
    578
    │ │ │ -
    580 void enterActiveStereo();
    │ │ │ -
    581
    │ │ │ -
    583 void enterDualStereo();
    │ │ │ -
    584
    │ │ │ -
    586 void enterDualStereoDifferentDisplays();
    │ │ │ -
    587
    │ │ │ -
    589 void clearRecordedAnimation();
    │ │ │ -
    590
    │ │ │ -
    592 void startAnimation();
    │ │ │ -
    593
    │ │ │ -
    595 void stopAnimation();
    │ │ │ -
    596
    │ │ │ -
    598 void switchToLastMode();
    │ │ │ -
    599
    │ │ │ -
    601 void switchShowGrid();
    │ │ │ -
    602
    │ │ │ -
    604 void showInfos();
    │ │ │ -
    605
    │ │ │ -
    607 void setupViewVolume();
    │ │ │ -
    608
    │ │ │ -
    610 void storeViewPoint();
    │ │ │ -
    611
    │ │ │ -
    613 void restoreViewPoint();
    │ │ │ -
    614
    │ │ │ -
    616 void startContinuousLoop();
    │ │ │ -
    617
    │ │ │ -
    619 void stopContinuousLoop();
    │ │ │ -
    620
    │ │ │ -
    622 void toggleContinuousLoop();
    │ │ │ -
    623
    │ │ │ -
    625 void applyStereoDefaults();
    │ │ │ -
    626
    │ │ │ -
    627#ifdef BALL_HAS_RTFACT
    │ │ │ -
    628 RaytracingWindowPtr getWindow(WindowType aWindowType);
    │ │ │ -
    629#endif
    │ │ │ -
    630
    │ │ │ -
    631 void createNewMolecule();
    │ │ │ -
    632 void saturateWithHydrogens();
    │ │ │ -
    633 void optimizeStructure();
    │ │ │ -
    634 void computeBondOrders();
    │ │ │ -
    635
    │ │ │ -
    636 // slots for communication with PTEDialog
    │ │ │ -
    637 void setEditElementType(int element_number);
    │ │ │ -
    638 int getEditElementType();
    │ │ │ -
    639
    │ │ │ -
    641 InteractionModeManager& getInteractionModeManager() { return mode_manager_; }
    │ │ │ -
    642
    │ │ │ -
    644 protected Q_SLOTS:
    │ │ │ -
    645
    │ │ │ -
    649
    │ │ │ -
    653 virtual void showViewPoint_();
    │ │ │ -
    654
    │ │ │ -
    656 virtual void setViewPoint_();
    │ │ │ -
    657
    │ │ │ -
    659 virtual void resetCamera_();
    │ │ │ -
    660
    │ │ │ -
    664 virtual void resetRepresentationsForRenderer_(RenderSetup& rs);
    │ │ │ -
    665
    │ │ │ -
    667 virtual void dropEvent(QDropEvent* e);
    │ │ │ -
    668
    │ │ │ -
    670 virtual void dragEnterEvent(QDragEnterEvent* e);
    │ │ │ -
    671
    │ │ │ -
    672 // dummy slot for menu entries without immediate action (saves many lines code this way)
    │ │ │ -
    673 void dummySlot(){}
    │ │ │ -
    674
    │ │ │ -
    676
    │ │ │ -
    678 Q_SIGNALS:
    │ │ │ -
    679
    │ │ │ -
    680 // signal for communication with EditOperationDialog
    │ │ │ -
    681 void newEditOperation(EditOperation &eo);
    │ │ │ -
    682
    │ │ │ -
    684 protected:
    │ │ │ -
    685
    │ │ │ -
    688 void handleRepresentationMessage_(RepresentationMessage* rm);
    │ │ │ -
    689
    │ │ │ -
    692 void handleDatasetMessage_(DatasetMessage* dm);
    │ │ │ -
    693
    │ │ │ -
    696 void handleSceneMessage_(SceneMessage* sm);
    │ │ │ -
    697
    │ │ │ -
    700 void handleCompositeMessage_(CompositeMessage* cm);
    │ │ │ -
    701
    │ │ │ -
    704 void handleControlSelectionMessage_(ControlSelectionMessage* csm);
    │ │ │ -
    705
    │ │ │ -
    708 virtual void handleRenderToBufferFinishedEvent_(RenderToBufferFinishedEvent* evt);
    │ │ │ -
    709
    │ │ │ -
    714 void renderText_(QPointF const& point, QString const& text, QPaintDevice* current_dev);
    │ │ │ -
    715
    │ │ │ -
    721 void insert_(int x_, int y_, PDBAtom &atom_);
    │ │ │ -
    722
    │ │ │ -
    727 TVector2<float> getScreenPosition_(Vector3 vec);
    │ │ │ -
    728
    │ │ │ -
    729 void initializeMembers_();
    │ │ │ -
    730
    │ │ │ -
    731 void renderGrid_();
    │ │ │ -
    732
    │ │ │ -
    733 QAction *new_molecule_action_, *optimize_action_;
    │ │ │ -
    734 QAction *add_hydrogens_action_;
    │ │ │ -
    735 QAction *bondorders_action_;
    │ │ │ -
    736
    │ │ │ -
    737 Atom* current_atom_;
    │ │ │ -
    738 Bond* current_bond_;
    │ │ │ -
    739
    │ │ │ -
    740 // pick atoms/bonds only in highlighted AtomContainer?
    │ │ │ -
    741 static bool only_highlighted_;
    │ │ │ -
    742 // element for new atoms
    │ │ │ -
    743 int atomic_number_;
    │ │ │ -
    744
    │ │ │ -
    745 //undo stack
    │ │ │ -
    746 vector<EditOperation> undo_;
    │ │ │ -
    747 EditSettings* edit_settings_;
    │ │ │ -
    748 QList<QAction*> toolbar_actions_edit_controls_;
    │ │ │ -
    749
    │ │ │ -
    753
    │ │ │ -
    756 virtual void init();
    │ │ │ -
    757
    │ │ │ -
    764 virtual void paintGL();
    │ │ │ -
    765
    │ │ │ -
    772 virtual void resizeEvent(QResizeEvent* event);
    │ │ │ -
    773
    │ │ │ -
    779 virtual void customEvent(QEvent* evt);
    │ │ │ -
    780
    │ │ │ -
    784 virtual void transformationEvent6D(TransformationEvent6D* evt);
    │ │ │ -
    785
    │ │ │ -
    789 virtual void motionTrackingEvent(MotionTrackingEvent* evt);
    │ │ │ -
    790
    │ │ │ -
    794 virtual void buttonPressEvent(ButtonEvent* evt);
    │ │ │ -
    795
    │ │ │ -
    799 virtual void buttonReleaseEvent(ButtonEvent* evt);
    │ │ │ -
    800
    │ │ │ -
    805 virtual void mouseMoveEvent(QMouseEvent* qmouse_event);
    │ │ │ -
    806
    │ │ │ -
    811 virtual void mousePressEvent(QMouseEvent* qmouse_event);
    │ │ │ -
    812
    │ │ │ -
    817 virtual void mouseReleaseEvent(QMouseEvent* qmouse_event);
    │ │ │ -
    818
    │ │ │ -
    822 virtual void wheelEvent(QWheelEvent* qmouse_event);
    │ │ │ -
    823
    │ │ │ -
    824 virtual void mouseDoubleClickEvent(QMouseEvent* e);
    │ │ │ -
    825
    │ │ │ -
    826 //_
    │ │ │ -
    827 void animate_();
    │ │ │ -
    828
    │ │ │ -
    829 void rotateSystemClockwise_();
    │ │ │ -
    830 void zoomSystem_();
    │ │ │ -
    831
    │ │ │ -
    832 void selectionPressed_();
    │ │ │ -
    833 void selectionPressedMoved_();
    │ │ │ -
    834
    │ │ │ -
    835 void selectObjects_();
    │ │ │ -
    836 void pickParent_(QPoint p);
    │ │ │ -
    837
    │ │ │ -
    838 void writeLights_(INIFile& inifile) const;
    │ │ │ -
    839
    │ │ │ -
    840 void readLights_(const INIFile& inifile);
    │ │ │ -
    841
    │ │ │ -
    842 void createCoordinateSystem_(bool at_origin);
    │ │ │ -
    843
    │ │ │ -
    844 void registerRenderers_();
    │ │ │ -
    845
    │ │ │ -
    847 String createFPSInfo_(Renderer* renderer);
    │ │ │ -
    848
    │ │ │ -
    849 // Menu entry IDs
    │ │ │ -
    850 QAction *no_stereo_action_, *enter_stereo_action_, *active_stereo_action_, *dual_stereo_action_, *dual_stereo_different_display_action_;
    │ │ │ -
    851 QAction *record_animation_action_, *start_animation_action_, *clear_animation_action_, *cancel_animation_action_;
    │ │ │ -
    852 QAction *animation_export_POV_action_, *animation_export_VRML_action_, *animation_export_PNG_action_, *animation_repeat_action_;
    │ │ │ -
    853
    │ │ │ -
    854#ifdef BALL_HAS_RTFACT
    │ │ │ -
    855 QAction *toggle_continuous_loop_action_;
    │ │ │ -
    856#endif
    │ │ │ -
    857 QAction *switch_grid_;
    │ │ │ -
    858 QMenu* create_coordinate_system_;
    │ │ │ -
    859
    │ │ │ -
    860 Vector3 system_origin_;
    │ │ │ -
    861 Vector3 old_trackorigin_;
    │ │ │ -
    862 bool tracking_initialized_;
    │ │ │ -
    863 Quaternion old_trackrotation_;
    │ │ │ -
    864
    │ │ │ -
    865 bool update_running_;
    │ │ │ -
    866
    │ │ │ -
    867 QRubberBand* rb_;
    │ │ │ -
    868
    │ │ │ -
    869 Stage* stage_;
    │ │ │ -
    870 Camera stereo_camera_;
    │ │ │ -
    871 Camera stored_camera_;
    │ │ │ -
    872
    │ │ │ -
    873 std::vector<boost::shared_ptr<RenderSetup> > renderers_;
    │ │ │ -
    874 GLRenderer* gl_renderer_;
    │ │ │ -
    875
    │ │ │ -
    876#ifdef BALL_HAS_RTFACT
    │ │ │ -
    877 RaytracingRenderer* rt_renderer_;
    │ │ │ -
    878 RaytracingWindowPtr rt_window_;
    │ │ │ -
    879#endif
    │ │ │ -
    880
    │ │ │ -
    881 static bool show_light_sources_;
    │ │ │ -
    882 static float animation_smoothness_;
    │ │ │ -
    883 static float downsampling_factor_;
    │ │ │ -
    884
    │ │ │ -
    885 LightSettings* light_settings_;
    │ │ │ -
    886 StageSettings* stage_settings_;
    │ │ │ -
    887 MaterialSettings* material_settings_;
    │ │ │ -
    888
    │ │ │ -
    889 // nr of last png file export
    │ │ │ -
    890 static Position screenshot_nr_;
    │ │ │ -
    891 // nr of last pov file export
    │ │ │ -
    892 static Position pov_nr_;
    │ │ │ -
    893 //nr of last vrml or stl export
    │ │ │ -
    894 static Position vrml_nr_;
    │ │ │ -
    895
    │ │ │ -
    896 std::list<Camera> animation_points_;
    │ │ │ -
    897 AnimationThread* animation_thread_;
    │ │ │ -
    898 bool stop_animation_;
    │ │ │ -
    899#ifdef BALL_HAS_RTFACT
    │ │ │ -
    900 bool continuous_loop_;
    │ │ │ -
    901#endif
    │ │ │ -
    902 bool want_to_use_vertex_buffer_;
    │ │ │ -
    903 bool use_preview_;
    │ │ │ -
    904
    │ │ │ -
    905 PreciseTime time_;
    │ │ │ -
    906 QPoint info_point_;
    │ │ │ -
    907 QByteArray last_state_;
    │ │ │ -
    908 list<float> fps_;
    │ │ │ -
    909 bool show_fps_;
    │ │ │ -
    910 static bool offscreen_rendering_;
    │ │ │ -
    911 Size offscreen_factor_;
    │ │ │ -
    912 Size font_size_;
    │ │ │ -
    913 QToolBar* toolbar_view_controls_;
    │ │ │ -
    914 QToolBar* toolbar_edit_controls_;
    │ │ │ -
    915 QList<QAction*> toolbar_actions_view_controls_;
    │ │ │ -
    916
    │ │ │ -
    917 QString info_string_;
    │ │ │ -
    918
    │ │ │ -
    919 GLRenderWindow* main_display_;
    │ │ │ -
    921 Position main_renderer_;
    │ │ │ -
    922
    │ │ │ -
    923 Index stereo_left_eye_;
    │ │ │ -
    924 Index stereo_right_eye_;
    │ │ │ -
    925
    │ │ │ -
    926 QFont default_font_;
    │ │ │ -
    927
    │ │ │ -
    928 QPicture overlay_;
    │ │ │ -
    929 bool has_overlay_;
    │ │ │ -
    930 InteractionModeManager mode_manager_;
    │ │ │ -
    931 };
    │ │ │ -
    │ │ │ -
    932
    │ │ │ -
    933
    │ │ │ -
    │ │ │ -
    935 class BALL_VIEW_EXPORT AnimationThread
    │ │ │ -
    936 : public QThread
    │ │ │ -
    937 {
    │ │ │ -
    938 public:
    │ │ │ -
    939
    │ │ │ -
    941 AnimationThread(){};
    │ │ │ -
    942
    │ │ │ -
    944 virtual void run() {scene_->animate_();}
    │ │ │ -
    945
    │ │ │ -
    947 void mySleep(Size msec);
    │ │ │ -
    948
    │ │ │ -
    950 void setScene(Scene* scene) { scene_ = scene;}
    │ │ │ -
    951
    │ │ │ -
    953 Scene* getScene() { return scene_;}
    │ │ │ -
    954
    │ │ │ -
    955 protected:
    │ │ │ -
    956
    │ │ │ -
    957 Scene* scene_;
    │ │ │ -
    958 };
    │ │ │ -
    │ │ │ -
    959
    │ │ │ -
    960 } // namespace VIEW
    │ │ │ -
    961} // namespace BALL
    │ │ │ -
    962
    │ │ │ -
    963#endif // BALL_VIEW_WIDGETS_SCENE_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EMBEDDABLE
    #define BALL_EMBEDDABLE(TYPE, BASE)
    Definition embeddable.h:31
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::RepresentationMessage
    Base class for all messages concerning a Representation.
    Definition message.h:570
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::Scene::applyStereoDefaults
    void applyStereoDefaults()
    │ │ │ -
    BALL::VIEW::Scene::pov_nr_
    static Position pov_nr_
    Definition scene.h:892
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::Scene::registerRenderers_
    void registerRenderers_()
    │ │ │ -
    BALL::VIEW::Scene::add_hydrogens_action_
    QAction * add_hydrogens_action_
    Definition scene.h:734
    │ │ │ -
    BALL::VIEW::Scene::setPOVNumber
    static void setPOVNumber(Position pos)
    Definition scene.h:425
    │ │ │ -
    BALL::VIEW::Scene::dragEnterEvent
    virtual void dragEnterEvent(QDragEnterEvent *e)
    │ │ │ -
    BALL::VIEW::Scene::switchShowWidget
    virtual void switchShowWidget()
    │ │ │ -
    BALL::VIEW::Scene::setShowLightSources
    static void setShowLightSources(bool state)
    Definition scene.h:374
    │ │ │ -
    BALL::VIEW::Scene::rb_
    QRubberBand * rb_
    Definition scene.h:867
    │ │ │ -
    BALL::VIEW::Scene::changeBondOrder
    void changeBondOrder(Index delta)
    │ │ │ -
    BALL::VIEW::Scene::showText
    void showText(const String &text, Size font_size=20)
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::handleCompositeMessage_
    void handleCompositeMessage_(CompositeMessage *cm)
    │ │ │ -
    BALL::VIEW::Scene::setMouseSensitivity
    static BALL_DEPRECATED void setMouseSensitivity(float)
    Definition scene.h:362
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::setOffScreenRendering
    void setOffScreenRendering(bool enabled, Size factor)
    │ │ │ -
    BALL::VIEW::Scene::drawLine
    void drawLine(const Vector2 &a, const Vector2 &b, QPainter *painter=0)
    │ │ │ -
    BALL::VIEW::Scene::isUpdateRunning
    bool isUpdateRunning() const
    Definition scene.h:479
    │ │ │ -
    BALL::VIEW::Scene::setEditElementType
    void setEditElementType(int element_number)
    │ │ │ -
    BALL::VIEW::Scene::merge
    void merge(Composite *a1, Composite *a2)
    │ │ │ -
    BALL::VIEW::Scene::saturateWithHydrogens
    void saturateWithHydrogens()
    │ │ │ -
    BALL::VIEW::Scene::getGLRenderer
    GLRenderer & getGLRenderer()
    Definition scene.h:382
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::time_
    PreciseTime time_
    Definition scene.h:905
    │ │ │ -
    BALL::VIEW::Scene::setMouseWheelSensitivity
    static BALL_DEPRECATED void setMouseWheelSensitivity(float)
    Definition scene.h:368
    │ │ │ -
    BALL::VIEW::Scene::keyPressEvent
    virtual void keyPressEvent(QKeyEvent *e)
    Catch key events.
    │ │ │ -
    BALL::VIEW::Scene::buttonReleaseEvent
    virtual void buttonReleaseEvent(ButtonEvent *evt)
    │ │ │ -
    BALL::VIEW::Scene::handleControlSelectionMessage_
    void handleControlSelectionMessage_(ControlSelectionMessage *csm)
    │ │ │ -
    BALL::VIEW::Scene::getClickedItems
    void getClickedItems(const QPoint &p)
    │ │ │ -
    BALL::VIEW::Scene::stop_animation_
    bool stop_animation_
    Definition scene.h:898
    │ │ │ -
    BALL::VIEW::Scene::stage_settings_
    StageSettings * stage_settings_
    Definition scene.h:886
    │ │ │ -
    BALL::VIEW::Scene::setCurrentAtom
    void setCurrentAtom(Atom *atom)
    Definition scene.h:283
    │ │ │ -
    BALL::VIEW::Scene::info_string_
    QString info_string_
    Definition scene.h:917
    │ │ │ -
    BALL::VIEW::Scene::getCurrentBond
    Bond * getCurrentBond()
    Definition scene.h:300
    │ │ │ -
    BALL::VIEW::Scene::setTurnPoint
    void setTurnPoint(const Vector3 &v)
    Definition scene.h:462
    │ │ │ -
    BALL::VIEW::Scene::stored_camera_
    Camera stored_camera_
    Definition scene.h:871
    │ │ │ -
    BALL::VIEW::Scene::setRubberBandGeometry
    void setRubberBandGeometry(const QRect &rect)
    │ │ │ -
    BALL::VIEW::Scene::exportNextPOVRay
    void exportNextPOVRay()
    Export to POVRay whithout showing file dialog.
    │ │ │ -
    BALL::VIEW::Scene::mapViewportTo3D
    Vector3 mapViewportTo3D(const Vector2 &coords)
    │ │ │ -
    BALL::VIEW::Scene::stage_
    Stage * stage_
    Definition scene.h:869
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::stopContinuousLoop
    void stopContinuousLoop()
    │ │ │ -
    BALL::VIEW::Scene::setDefaultLighting
    void setDefaultLighting(bool update_GL=true)
    │ │ │ -
    BALL::VIEW::Scene::toolbar_actions_edit_controls_
    QList< QAction * > toolbar_actions_edit_controls_
    Definition scene.h:748
    │ │ │ -
    BALL::VIEW::Scene::current_atom_
    Atom * current_atom_
    Definition scene.h:737
    │ │ │ -
    BALL::VIEW::Scene::toolbar_actions_view_controls_
    QList< QAction * > toolbar_actions_view_controls_
    Definition scene.h:915
    │ │ │ -
    BALL::VIEW::Scene::offscreen_factor_
    Size offscreen_factor_
    Definition scene.h:911
    │ │ │ -
    BALL::VIEW::Scene::getMouseSensitivity
    static BALL_DEPRECATED float getMouseSensitivity()
    Definition scene.h:365
    │ │ │ -
    BALL::VIEW::Scene::only_highlighted_
    static bool only_highlighted_
    Definition scene.h:741
    │ │ │ -
    BALL::VIEW::Scene::readLights_
    void readLights_(const INIFile &inifile)
    │ │ │ -
    BALL::VIEW::Scene::use_preview_
    bool use_preview_
    Definition scene.h:903
    │ │ │ -
    BALL::VIEW::Scene::dummySlot
    void dummySlot()
    Definition scene.h:673
    │ │ │ -
    BALL::VIEW::Scene::setVRMLNumber
    static void setVRMLNumber(Position pos)
    Definition scene.h:428
    │ │ │ -
    BALL::VIEW::Scene::clearRecordedAnimation
    void clearRecordedAnimation()
    │ │ │ -
    BALL::VIEW::Scene::getStage
    const Stage * getStage() const
    Definition scene.h:317
    │ │ │ -
    BALL::VIEW::Scene::inMoveMode
    bool inMoveMode() const
    │ │ │ -
    BALL::VIEW::Scene::isAnimationRunning
    bool isAnimationRunning() const
    │ │ │ -
    BALL::VIEW::Scene::mouseReleaseEvent
    virtual void mouseReleaseEvent(QMouseEvent *qmouse_event)
    │ │ │ -
    BALL::VIEW::Scene::pickObjects
    void pickObjects(const QPoint &pos1, const QPoint &pos2, list< GeometricObject * > &objects)
    │ │ │ -
    BALL::VIEW::Scene::rotateComposites
    void rotateComposites(const std::list< Composite * > &composites, float degree_right, float degree_up, float degree_clockwise=0)
    │ │ │ -
    BALL::VIEW::Scene::show_light_sources_
    static bool show_light_sources_
    Definition scene.h:881
    │ │ │ -
    BALL::VIEW::Scene::animation_thread_
    AnimationThread * animation_thread_
    Definition scene.h:897
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::main_renderer_
    Position main_renderer_
    The index of the renderer responsible for the main display.
    Definition scene.h:921
    │ │ │ -
    BALL::VIEW::Scene::getMaterialSettings
    const MaterialSettings * getMaterialSettings() const
    Definition scene.h:333
    │ │ │ -
    BALL::VIEW::Scene::exportPNG
    String exportPNG()
    Export PNG image and return the filename.
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::getAnimationSmoothness
    static float getAnimationSmoothness()
    Definition scene.h:348
    │ │ │ -
    BALL::VIEW::Scene::createCoordinateSystem_
    void createCoordinateSystem_(bool at_origin)
    │ │ │ -
    BALL::VIEW::Scene::setPreview
    void setPreview(bool state)
    Enable or disable model previews e.g. while rotating.
    Definition scene.h:550
    │ │ │ -
    BALL::VIEW::Scene::startContinuousLoop
    void startContinuousLoop()
    │ │ │ -
    BALL::VIEW::Scene::initializeMembers_
    void initializeMembers_()
    │ │ │ -
    BALL::VIEW::Scene::getCurrentAtom
    Atom * getCurrentAtom()
    Definition scene.h:282
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::handleSceneMessage_
    void handleSceneMessage_(SceneMessage *sm)
    │ │ │ -
    BALL::VIEW::Scene::useVertexBuffers
    bool useVertexBuffers() const
    Definition scene.h:555
    │ │ │ -
    BALL::VIEW::Scene::moveComposites
    void moveComposites(const std::list< Composite * > &composites, Vector3 v)
    │ │ │ -
    BALL::VIEW::Scene::pickObjects
    void pickObjects(const QPoint &pos, list< GeometricObject * > &objects)
    │ │ │ -
    BALL::VIEW::Scene::animation_points_
    std::list< Camera > animation_points_
    Definition scene.h:896
    │ │ │ -
    BALL::VIEW::Scene::getScreenPosition_
    TVector2< float > getScreenPosition_(Vector3 vec)
    │ │ │ -
    BALL::VIEW::Scene::setGLRenderer
    void setGLRenderer(GLRenderer &renderer)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::Scene::mousePressEvent
    virtual void mousePressEvent(QMouseEvent *qmouse_event)
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::LEFT_EYE_WINDOW
    @ LEFT_EYE_WINDOW
    Window into which left eye should be rendered. Indicates same window as CONTROL_WINDOW if no stereo i...
    Definition scene.h:170
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::mouseMoveEvent
    virtual void mouseMoveEvent(QMouseEvent *qmouse_event)
    │ │ │ -
    BALL::VIEW::Scene::old_trackorigin_
    Vector3 old_trackorigin_
    Definition scene.h:861
    │ │ │ -
    BALL::VIEW::Scene::paintGL
    virtual void paintGL()
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::pickParent_
    void pickParent_(QPoint p)
    │ │ │ -
    BALL::VIEW::Scene::resetTracking
    void resetTracking()
    Definition scene.h:481
    │ │ │ -
    BALL::VIEW::Scene::wheelEvent
    virtual void wheelEvent(QWheelEvent *qmouse_event)
    │ │ │ -
    BALL::VIEW::Scene::addToolBarEntries
    virtual void addToolBarEntries(QToolBar *tb)
    │ │ │ -
    BALL::VIEW::Scene::showLightSourcesEnabled
    static bool showLightSourcesEnabled()
    Definition scene.h:378
    │ │ │ -
    BALL::VIEW::Scene::prepareGridTextures
    Position prepareGridTextures(const RegularData3D &grid, const ColorMap &map)
    │ │ │ -
    BALL::VIEW::Scene::setDownsamplingFactor
    void setDownsamplingFactor(float ds_factor)
    │ │ │ -
    BALL::VIEW::Scene::cancel_animation_action_
    QAction * cancel_animation_action_
    Definition scene.h:851
    │ │ │ -
    BALL::VIEW::Scene::overlay_
    QPicture overlay_
    Definition scene.h:928
    │ │ │ -
    BALL::VIEW::Scene::deselect
    void deselect(bool update=true)
    │ │ │ -
    BALL::VIEW::Scene::stereo_right_eye_
    Index stereo_right_eye_
    Definition scene.h:924
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::Scene::createFPSInfo_
    String createFPSInfo_(Renderer *renderer)
    Estimate current fps and convert into a string.
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::updateMaterialForRepresentation
    void updateMaterialForRepresentation(Representation *rep, const Stage::Material &new_material)
    │ │ │ -
    BALL::VIEW::Scene::last_state_
    QByteArray last_state_
    Definition scene.h:907
    │ │ │ -
    BALL::VIEW::Scene::getInteractionModeManager
    InteractionModeManager & getInteractionModeManager()
    Returns a reference to the Scene's interaction mode manager.
    Definition scene.h:641
    │ │ │ -
    BALL::VIEW::Scene::isValid
    virtual bool isValid() const
    │ │ │ -
    BALL::VIEW::Scene::resetCamera_
    virtual void resetCamera_()
    Reset the camera to standard values.
    │ │ │ -
    BALL::VIEW::Scene::buttonPressEvent
    virtual void buttonPressEvent(ButtonEvent *evt)
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::toolbar_edit_controls_
    QToolBar * toolbar_edit_controls_
    Definition scene.h:914
    │ │ │ -
    BALL::VIEW::Scene::system_origin_
    Vector3 system_origin_
    Definition scene.h:860
    │ │ │ -
    BALL::VIEW::Scene::animation_export_PNG_action_
    QAction * animation_export_PNG_action_
    Definition scene.h:852
    │ │ │ -
    BALL::VIEW::Scene::resizeEvent
    virtual void resizeEvent(QResizeEvent *event)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::Scene::getStage
    Stage * getStage()
    Definition scene.h:313
    │ │ │ -
    BALL::VIEW::Scene::setRubberBandVisible
    void setRubberBandVisible(bool show)
    │ │ │ -
    BALL::VIEW::Scene::paintEvent
    virtual void paintEvent(QPaintEvent *e)
    │ │ │ -
    BALL::VIEW::Scene::switch_grid_
    QAction * switch_grid_
    Definition scene.h:857
    │ │ │ -
    BALL::VIEW::Scene::drawLine
    void drawLine(const QPointF &a, const QPointF &b, QPainter *painter=0)
    │ │ │ -
    BALL::VIEW::Scene::material_settings_
    MaterialSettings * material_settings_
    Definition scene.h:887
    │ │ │ -
    BALL::VIEW::Scene::optimizeStructure
    void optimizeStructure()
    │ │ │ -
    BALL::VIEW::Scene::mapViewportTo3D
    Vector3 mapViewportTo3D(int x, int y)
    │ │ │ -
    BALL::VIEW::Scene::isRecording
    bool isRecording() const
    │ │ │ -
    BALL::VIEW::Scene::info_point_
    QPoint info_point_
    Definition scene.h:906
    │ │ │ -
    BALL::VIEW::Scene::stereo_camera_
    Camera stereo_camera_
    Definition scene.h:870
    │ │ │ -
    BALL::VIEW::Scene::active_stereo_action_
    QAction * active_stereo_action_
    Definition scene.h:850
    │ │ │ -
    BALL::VIEW::Scene::activatedOrderItem_
    void activatedOrderItem_(QAction *action)
    │ │ │ -
    BALL::VIEW::Scene::createCoordinateSystemAtOrigin
    void createCoordinateSystemAtOrigin()
    Create an coordinate system at origin.
    │ │ │ -
    BALL::VIEW::Scene::undo_
    vector< EditOperation > undo_
    Definition scene.h:746
    │ │ │ -
    BALL::VIEW::Scene::downsampling_factor_
    static float downsampling_factor_
    Definition scene.h:883
    │ │ │ -
    BALL::VIEW::Scene::renderers_
    std::vector< boost::shared_ptr< RenderSetup > > renderers_
    Definition scene.h:873
    │ │ │ -
    BALL::VIEW::Scene::enterDualStereoDifferentDisplays
    void enterDualStereoDifferentDisplays()
    │ │ │ -
    BALL::VIEW::Scene::getContainers
    std::list< AtomContainer * > getContainers()
    │ │ │ -
    BALL::VIEW::Scene::new_molecule_action_
    QAction * new_molecule_action_
    Definition scene.h:733
    │ │ │ -
    BALL::VIEW::Scene::createNewMolecule
    void createNewMolecule()
    │ │ │ -
    BALL::VIEW::Scene::selectionPressedMoved_
    void selectionPressedMoved_()
    │ │ │ -
    BALL::VIEW::Scene::showExportPNGDialog
    void showExportPNGDialog()
    show an dialog to save an PNG file to
    │ │ │ -
    BALL::VIEW::Scene::stereo_left_eye_
    Index stereo_left_eye_
    Definition scene.h:923
    │ │ │ -
    BALL::VIEW::Scene::exportPNG
    bool exportPNG(const String &filename)
    │ │ │ -
    BALL::VIEW::Scene::setElementCursor
    void setElementCursor(int number)
    │ │ │ -
    BALL::VIEW::Scene::handleRenderToBufferFinishedEvent_
    virtual void handleRenderToBufferFinishedEvent_(RenderToBufferFinishedEvent *evt)
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::newEditOperation
    void newEditOperation(EditOperation &eo)
    │ │ │ -
    BALL::VIEW::Scene::setViewPoint_
    virtual void setViewPoint_()
    Set the viewpoint.
    │ │ │ -
    BALL::VIEW::Scene::clear
    virtual void clear()
    │ │ │ -
    BALL::VIEW::Scene::old_trackrotation_
    Quaternion old_trackrotation_
    Definition scene.h:863
    │ │ │ -
    BALL::VIEW::Scene::writeLights_
    void writeLights_(INIFile &inifile) const
    │ │ │ -
    BALL::VIEW::Scene::renderText_
    void renderText_(QPointF const &point, QString const &text, QPaintDevice *current_dev)
    │ │ │ -
    BALL::VIEW::Scene::fps_
    list< float > fps_
    Definition scene.h:908
    │ │ │ -
    BALL::VIEW::Scene::move
    void move(Vector3 v)
    │ │ │ -
    BALL::VIEW::Scene::customEvent
    virtual void customEvent(QEvent *evt)
    │ │ │ -
    BALL::VIEW::Scene::showExportVRMLDialog
    void showExportVRMLDialog()
    opens the VIEW/DIALOGS/GeometryExportDialog for vrml and stl export
    │ │ │ -
    BALL::VIEW::Scene::dump
    virtual void dump(std::ostream &s=std::cout, Size depth=0) const
    │ │ │ -
    BALL::VIEW::Scene::setWidgetVisible
    virtual void setWidgetVisible(bool state)
    │ │ │ -
    BALL::VIEW::Scene::selectionPressed_
    void selectionPressed_()
    │ │ │ -
    BALL::VIEW::Scene::initializeWidget
    virtual void initializeWidget(MainControl &main_control)
    │ │ │ -
    BALL::VIEW::Scene::update_running_
    bool update_running_
    Definition scene.h:865
    │ │ │ -
    BALL::VIEW::Scene::getMouseWheelSensitivity
    static BALL_DEPRECATED float getMouseWheelSensitivity()
    Definition scene.h:371
    │ │ │ -
    BALL::VIEW::Scene::computeBondOrders
    void computeBondOrders()
    │ │ │ -
    BALL::VIEW::Scene::toggleContinuousLoop
    void toggleContinuousLoop()
    │ │ │ -
    BALL::VIEW::Scene::current_bond_
    Bond * current_bond_
    Definition scene.h:738
    │ │ │ -
    BALL::VIEW::Scene::enterActiveStereo
    void enterActiveStereo()
    │ │ │ -
    BALL::VIEW::Scene::showContextMenu
    void showContextMenu(QPoint pos)
    │ │ │ -
    BALL::VIEW::Scene::setCamera
    void setCamera(const Camera &camera)
    │ │ │ -
    BALL::VIEW::Scene::notify
    void notify(Message *msg)
    Definition scene.h:284
    │ │ │ -
    BALL::VIEW::Scene::offscreen_rendering_
    static bool offscreen_rendering_
    Definition scene.h:910
    │ │ │ -
    BALL::VIEW::Scene::default_font_
    QFont default_font_
    Definition scene.h:926
    │ │ │ -
    BALL::VIEW::Scene::setCursor
    void setCursor(String c)
    │ │ │ -
    BALL::VIEW::Scene::stereoBufferSupportTest
    static bool stereoBufferSupportTest()
    │ │ │ -
    BALL::VIEW::Scene::setFPSEnabled
    void setFPSEnabled(bool state)
    Definition scene.h:471
    │ │ │ -
    BALL::VIEW::Scene::exportScene
    virtual bool exportScene(Renderer &er) const
    │ │ │ -
    BALL::VIEW::Scene::mode_manager_
    InteractionModeManager mode_manager_
    Definition scene.h:930
    │ │ │ -
    BALL::VIEW::Scene::switchRenderer
    void switchRenderer(RenderSetup::RendererType new_type)
    │ │ │ -
    BALL::VIEW::Scene::toolbar_view_controls_
    QToolBar * toolbar_view_controls_
    Definition scene.h:913
    │ │ │ -
    BALL::VIEW::Scene::rotate
    void rotate(float degree_right, float degree_up)
    │ │ │ -
    BALL::VIEW::Scene::getStageSettings
    StageSettings * getStageSettings()
    Definition scene.h:321
    │ │ │ -
    BALL::VIEW::Scene::getAnimationPoints
    std::list< Camera > & getAnimationPoints()
    Definition scene.h:340
    │ │ │ -
    BALL::VIEW::Scene::bondorders_action_
    QAction * bondorders_action_
    Definition scene.h:735
    │ │ │ -
    BALL::VIEW::Scene::transformationEvent6D
    virtual void transformationEvent6D(TransformationEvent6D *evt)
    │ │ │ -
    BALL::VIEW::Scene::getStageSettings
    const StageSettings * getStageSettings() const
    Definition scene.h:325
    │ │ │ -
    BALL::VIEW::Scene::showViewPoint_
    virtual void showViewPoint_()
    Show the viewpoint and the look at point in the statusline of the mainwidget.
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::setupEnvironmentMap
    void setupEnvironmentMap(const QImage &image)
    Try to setup an environment map for all renderers that support it.
    │ │ │ -
    BALL::VIEW::Scene::map3DToViewport
    Vector2 map3DToViewport(const Vector3 &coords)
    │ │ │ -
    BALL::VIEW::Scene::mouseDoubleClickEvent
    virtual void mouseDoubleClickEvent(QMouseEvent *e)
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::initializePreferencesTab
    void initializePreferencesTab(Preferences &preferences)
    │ │ │ -
    BALL::VIEW::Scene::setAnimationSmoothness
    static void setAnimationSmoothness(float value)
    Definition scene.h:344
    │ │ │ -
    BALL::VIEW::Scene::lightsUpdated
    void lightsUpdated(bool redraw=false)
    │ │ │ -
    BALL::VIEW::Scene::init
    virtual void init()
    │ │ │ -
    BALL::VIEW::Scene::motionTrackingEvent
    virtual void motionTrackingEvent(MotionTrackingEvent *evt)
    │ │ │ -
    BALL::VIEW::Scene::Scene
    Scene(QWidget *parent_widget=0, const char *name=NULL, Qt::WindowFlags w_flags=0)
    │ │ │ -
    BALL::VIEW::Scene::eventFilter
    virtual bool eventFilter(QObject *object, QEvent *event)
    │ │ │ -
    BALL::VIEW::Scene::showInfos
    void showInfos()
    Popup informations for object under mouse cursor.
    │ │ │ -
    BALL::VIEW::Scene::create_coordinate_system_
    QMenu * create_coordinate_system_
    Definition scene.h:858
    │ │ │ -
    BALL::VIEW::Scene::tracking_initialized_
    bool tracking_initialized_
    Definition scene.h:862
    │ │ │ -
    BALL::VIEW::Scene::updateAllMaterials
    void updateAllMaterials()
    │ │ │ -
    BALL::VIEW::Scene::gl_renderer_
    GLRenderer * gl_renderer_
    Definition scene.h:874
    │ │ │ -
    BALL::VIEW::Scene::handleDatasetMessage_
    void handleDatasetMessage_(DatasetMessage *dm)
    │ │ │ -
    BALL::VIEW::Scene::want_to_use_vertex_buffer_
    bool want_to_use_vertex_buffer_
    Definition scene.h:902
    │ │ │ -
    BALL::VIEW::Scene::projectionModeChanged
    virtual void projectionModeChanged()
    │ │ │ -
    BALL::VIEW::Scene::writePreferences
    virtual void writePreferences(INIFile &inifile)
    │ │ │ -
    BALL::VIEW::Scene::has_overlay_
    bool has_overlay_
    Definition scene.h:929
    │ │ │ -
    BALL::VIEW::Scene::setFullScreen
    void setFullScreen(bool state)
    │ │ │ -
    BALL::VIEW::Scene::rotateClockwise
    void rotateClockwise(float degree)
    │ │ │ -
    BALL::VIEW::Scene::getDownsamplingFactor
    float getDownsamplingFactor() const
    Definition scene.h:352
    │ │ │ -
    BALL::VIEW::Scene::insert_
    void insert_(int x_, int y_, PDBAtom &atom_)
    │ │ │ -
    BALL::VIEW::Scene::getBondOrderString_
    String getBondOrderString_(Index order)
    │ │ │ -
    BALL::VIEW::Scene::setInfo
    void setInfo(const QString &info_string)
    │ │ │ -
    BALL::VIEW::Scene::getMaterialSettings
    MaterialSettings * getMaterialSettings()
    Definition scene.h:329
    │ │ │ -
    BALL::VIEW::Scene::vrml_nr_
    static Position vrml_nr_
    Definition scene.h:894
    │ │ │ -
    BALL::VIEW::Scene::onNotify
    virtual void onNotify(Message *message)
    │ │ │ -
    BALL::VIEW::Scene::animation_smoothness_
    static float animation_smoothness_
    Definition scene.h:882
    │ │ │ -
    BALL::VIEW::Scene::checkMenu
    virtual void checkMenu(MainControl &main_control)
    │ │ │ -
    BALL::VIEW::Scene::finalizePreferencesTab
    void finalizePreferencesTab(Preferences &preferences)
    │ │ │ -
    BALL::VIEW::Scene::setCurrentBond
    void setCurrentBond(Bond *b)
    Definition scene.h:301
    │ │ │ -
    BALL::VIEW::Scene::setScreenShotNumber
    static void setScreenShotNumber(Position pos)
    Definition scene.h:422
    │ │ │ -
    BALL::VIEW::Scene::getTurnPoint
    const Vector3 & getTurnPoint() const
    Definition scene.h:465
    │ │ │ -
    BALL::VIEW::Scene::applyPreferences
    virtual void applyPreferences()
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::Scene::edit_settings_
    EditSettings * edit_settings_
    Definition scene.h:747
    │ │ │ -
    BALL::VIEW::Scene::usePreview
    bool usePreview() const
    Returns the state of the preview mode.
    Definition scene.h:553
    │ │ │ -
    BALL::VIEW::Scene::screenshot_nr_
    static Position screenshot_nr_
    Definition scene.h:890
    │ │ │ -
    BALL::VIEW::Scene::main_display_
    GLRenderWindow * main_display_
    Definition scene.h:919
    │ │ │ - │ │ │ -
    BALL::VIEW::Scene::dropEvent
    virtual void dropEvent(QDropEvent *e)
    │ │ │ -
    BALL::VIEW::Scene::resetRepresentationsForRenderer_
    virtual void resetRepresentationsForRenderer_(RenderSetup &rs)
    │ │ │ -
    BALL::VIEW::Scene::rotateSystemClockwise_
    void rotateSystemClockwise_()
    │ │ │ -
    BALL::VIEW::Scene::createCoordinateSystem
    void createCoordinateSystem()
    Create an coordinate system at current position.
    │ │ │ -
    BALL::VIEW::Scene::handleRepresentationMessage_
    void handleRepresentationMessage_(RepresentationMessage *rm)
    │ │ │ -
    BALL::VIEW::Scene::fetchPreferences
    virtual void fetchPreferences(INIFile &inifile)
    │ │ │ -
    BALL::VIEW::Scene::light_settings_
    LightSettings * light_settings_
    Definition scene.h:885
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::AnimationThread::setScene
    void setScene(Scene *scene)
    Definition scene.h:950
    │ │ │ -
    BALL::VIEW::AnimationThread::run
    virtual void run()
    Definition scene.h:944
    │ │ │ - │ │ │ - │ │ │ - │ │ │ +
    145 /*_ This maps Atom:Types to Indices of rdf_list_ */
    │ │ │ +
    146 HashMap< Atom::Type, HashMap<Atom::Type, Position> > rdf_indices_;
    │ │ │ +
    147
    │ │ │ +
    148
    │ │ │ +
    149 };
    │ │ │ +
    │ │ │ +
    150
    │ │ │ +
    151} // namespace BALL
    │ │ │ +
    152#endif // BALL__RDFPARAMETER_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ +
    std
    STL namespace.
    │ │ │ + │ │ │ +
    BALL::HashMap
    HashMap class based on the STL map (containing serveral convenience functions)
    Definition hashMap.h:74
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_DEPRECATED
    #define BALL_DEPRECATED
    Definition COMMON/global.h:64
    │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
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    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,1401 +1,132 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _W_I_D_G_E_T_S │ │ │ │ -scene.h │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ +RDFParameter.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_VIEW_WIDGETS_SCENE_H │ │ │ │ -6#define BALL_VIEW_WIDGETS_SCENE_H │ │ │ │ +5#ifndef BALL_STRUCTURE_RDFPARAMETER_H │ │ │ │ +6#define BALL_STRUCTURE_RDFPARAMETER_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H │ │ │ │ -9# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ +8#ifndef BALL_KERNEL_ATOM_H │ │ │ │ +9# include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_VIEW_RENDERING_RENDERERSGLRENDERER_H │ │ │ │ -13# include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_R_E_N_D_E_R_E_R_S_/_g_l_R_e_n_d_e_r_e_r_._h> │ │ │ │ +12#ifndef BALL_STRUCTURE_RADIALDISTRIBUTIONFUNCTION_H │ │ │ │ +13# include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_r_a_d_i_a_l_D_i_s_t_r_i_b_u_t_i_o_n_F_u_n_c_t_i_o_n_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#ifndef BALL_VIEW_KERNEL_COMMON_H │ │ │ │ -17# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_c_o_m_m_o_n_._h> │ │ │ │ +16#ifndef BALL_FORMAT_PARAMETERSECTION_H │ │ │ │ +17# include <_B_A_L_L_/_F_O_R_M_A_T_/_p_a_r_a_m_e_t_e_r_S_e_c_t_i_o_n_._h> │ │ │ │ 18#endif │ │ │ │ 19 │ │ │ │ -20#ifndef BALL_VIEW_RENDERING_RENDERWINDOW_H │ │ │ │ -21# include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_r_e_n_d_e_r_W_i_n_d_o_w_._h> │ │ │ │ +20#ifndef BALL_MOLMEC_PARAMETERS_FORCEFIELDPARAMETERS_H │ │ │ │ +21# include <_B_A_L_L_/_M_O_L_M_E_C_/_P_A_R_A_M_E_T_E_R_/_f_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ 22#endif │ │ │ │ 23 │ │ │ │ -24#ifndef BALL_VIEW_RENDERING_GLRENDERWINDOW_H │ │ │ │ -25# include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h> │ │ │ │ -26#endif │ │ │ │ -27 │ │ │ │ -28#ifndef BALL_VIEW_RENDERING_RENDERSETUP_H │ │ │ │ -29# include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_r_e_n_d_e_r_S_e_t_u_p_._h> │ │ │ │ -30#endif │ │ │ │ -31 │ │ │ │ -32#ifndef BALL_VIEW_DIALOGS_EDITSETTINGS_H │ │ │ │ -33# include <_B_A_L_L_/_V_I_E_W_/_D_I_A_L_O_G_S_/_e_d_i_t_S_e_t_t_i_n_g_s_._h> │ │ │ │ -34#endif │ │ │ │ +24namespace _B_A_L_L │ │ │ │ +25{ │ │ │ │ +_3_1 class _B_A_L_L___E_X_P_O_R_T _R_D_F_P_a_r_a_m_e_t_e_r │ │ │ │ +32 : public _P_a_r_a_m_e_t_e_r_S_e_c_t_i_o_n │ │ │ │ +33 { │ │ │ │ +34 public: │ │ │ │ 35 │ │ │ │ -36#ifndef BALL_VIEW_KERNEL_EDITOPERATION_H │ │ │ │ -37# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_e_d_i_t_O_p_e_r_a_t_i_o_n_._h> │ │ │ │ -38#endif │ │ │ │ -39 │ │ │ │ -40#ifndef BALL_VIEW_KERNEL_MODES_INTERACTIONMODEMANAGER_H │ │ │ │ -41# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_M_O_D_E_S_/_i_n_t_e_r_a_c_t_i_o_n_M_o_d_e_M_a_n_a_g_e_r_._h> │ │ │ │ -42#endif │ │ │ │ -43 │ │ │ │ -44#include │ │ │ │ -45#include │ │ │ │ -46#include │ │ │ │ -47#include │ │ │ │ -48#include │ │ │ │ -49#include │ │ │ │ -50#include │ │ │ │ -51 │ │ │ │ -52#include │ │ │ │ -53 │ │ │ │ -54#ifdef BALL_HAS_RTFACT │ │ │ │ -55 │ │ │ │ -56#ifndef BALL_VIEW_RENDERING_RAYTRACINGRENDERER_H │ │ │ │ -57# include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_R_E_N_D_E_R_E_R_S_/_r_a_y_t_r_a_c_i_n_g_R_e_n_d_e_r_e_r_._h> │ │ │ │ -58#endif │ │ │ │ +36 _B_A_L_L___C_R_E_A_T_E(_R_D_F_P_a_r_a_m_e_t_e_r) │ │ │ │ +37 │ │ │ │ +38 │ │ │ │ +41 │ │ │ │ +42 │ │ │ │ +_4_4 _R_D_F_P_a_r_a_m_e_t_e_r() │ │ │ │ +45 ; │ │ │ │ +46 │ │ │ │ +_5_0 _R_D_F_P_a_r_a_m_e_t_e_r(const _R_D_F_P_a_r_a_m_e_t_e_r& rdf_parameter) │ │ │ │ +51 ; │ │ │ │ +52 │ │ │ │ +_5_5 virtual ~_R_D_F_P_a_r_a_m_e_t_e_r() │ │ │ │ +56 ; │ │ │ │ +57 │ │ │ │ 59 │ │ │ │ -60#endif // BALL_HAS_RTFACT │ │ │ │ -61 │ │ │ │ -62class _Q_M_o_u_s_e_E_v_e_n_t; │ │ │ │ -63class QRubberBand; │ │ │ │ -64class QMenu; │ │ │ │ -65class QImage; │ │ │ │ -66class QAction; │ │ │ │ -67class QWheelEvent; │ │ │ │ -68class QKeyEvent; │ │ │ │ +62 │ │ │ │ +_6_7 const _R_D_F_P_a_r_a_m_e_t_e_r& operator = (const _R_D_F_P_a_r_a_m_e_t_e_r& rdf_parameter) │ │ │ │ +68 ; │ │ │ │ 69 │ │ │ │ -70namespace _B_A_L_L │ │ │ │ -71{ │ │ │ │ -72 class Bond; │ │ │ │ -73 class PDBAtom; │ │ │ │ -74 class AtomContainer; │ │ │ │ -75 │ │ │ │ -76 namespace VIEW │ │ │ │ -77 { │ │ │ │ -78 class ColorMap; │ │ │ │ -79 class InteractionMode; │ │ │ │ -80 class Preferences; │ │ │ │ -81 class LightSettings; │ │ │ │ -82 class StageSettings; │ │ │ │ -83 class MaterialSettings; │ │ │ │ -84 class AnimationThread; │ │ │ │ -85 class ClippingPlane; │ │ │ │ -86 class CompositeMessage; │ │ │ │ -87 class ControlSelectionMessage; │ │ │ │ -88 class RepresentationMessage; │ │ │ │ -89 class DatasetMessage; │ │ │ │ -90 class SceneMessage; │ │ │ │ -91 │ │ │ │ -92 class TransformationEvent6D; │ │ │ │ -93 class MotionTrackingEvent; │ │ │ │ -94 class ButtonEvent; │ │ │ │ -95 class RenderToBufferFinishedEvent; │ │ │ │ -96 │ │ │ │ -_1_3_8 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _S_c_e_n_e │ │ │ │ -139 : public _Q_W_i_d_g_e_t, │ │ │ │ -140 public _M_o_d_u_l_a_r_W_i_d_g_e_t │ │ │ │ -141 { │ │ │ │ -_1_4_2 friend class _A_n_i_m_a_t_i_o_n_T_h_r_e_a_d; │ │ │ │ -_1_4_3 friend class _R_e_n_d_e_r_S_e_t_u_p; │ │ │ │ +_7_2 virtual void clear() │ │ │ │ +73 ; │ │ │ │ +74 │ │ │ │ +76 │ │ │ │ +79 │ │ │ │ +_8_6 _P_o_s_i_t_i_o_n getIndex(_A_t_o_m::Type type_i, _A_t_o_m::Type type_j) const │ │ │ │ +87 ; │ │ │ │ +88 │ │ │ │ +_9_4 const _R_a_d_i_a_l_D_i_s_t_r_i_b_u_t_i_o_n_F_u_n_c_t_i_o_n& getRDF(_A_t_o_m::Type type_i, │ │ │ │ +95 _A_t_o_m::Type type_j) const │ │ │ │ +96 ; │ │ │ │ +97 │ │ │ │ +_1_0_3 const _R_a_d_i_a_l_D_i_s_t_r_i_b_u_t_i_o_n_F_u_n_c_t_i_o_n& getRDF(_P_o_s_i_t_i_o_n index) const │ │ │ │ +104 ; │ │ │ │ +105 │ │ │ │ +107 │ │ │ │ +_1_1_3 virtual bool extractSection(_F_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s& parameters, │ │ │ │ +114 const _S_t_r_i_n_g& section_name) │ │ │ │ +115 ; │ │ │ │ +116 │ │ │ │ +120 │ │ │ │ +_1_2_8 bool hasRDF(_A_t_o_m::Type solvent_atom_type, _A_t_o_m::Type solute_atom_type) │ │ │ │ +129 const ; │ │ │ │ +130 │ │ │ │ +_1_3_4 bool hasParameters(_A_t_o_m::Type solvent_atom_type, │ │ │ │ +135 _A_t_o_m::Type solute_atom_type) const │ │ │ │ +136 ; │ │ │ │ +137 │ │ │ │ +139 │ │ │ │ +140 protected: │ │ │ │ +141 │ │ │ │ +142 /*_ The vector containing all the read RDF representations */ │ │ │ │ +_1_4_3 _s_t_d::vector<_R_a_d_i_a_l_D_i_s_t_r_i_b_u_t_i_o_n_F_u_n_c_t_i_o_n> rdf_list_; │ │ │ │ 144 │ │ │ │ -145#ifdef BALL_HAS_RTFACT │ │ │ │ -146 typedef boost::shared_ptr RaytracingRendererPtr; │ │ │ │ -147 typedef boost::shared_ptr RaytracingWindowPtr; │ │ │ │ -148#endif │ │ │ │ -149 │ │ │ │ -150 Q_OBJECT │ │ │ │ -151 │ │ │ │ -152 public: │ │ │ │ -153 _B_A_L_L___E_M_B_E_D_D_A_B_L_E(_S_c_e_n_e, _M_o_d_u_l_a_r_W_i_d_g_e_t) │ │ │ │ -154 │ │ │ │ -155 │ │ │ │ -158 │ │ │ │ -159 │ │ │ │ -_1_6_4 enum _W_i_n_d_o_w_T_y_p_e │ │ │ │ -165 { │ │ │ │ -_1_6_7 CONTROL_WINDOW = 0, │ │ │ │ -168 │ │ │ │ -_1_7_0 _L_E_F_T___E_Y_E___W_I_N_D_O_W, │ │ │ │ -171 │ │ │ │ -173 RIGHT_EYE_WINDOW │ │ │ │ -_1_7_4 }; │ │ │ │ -175 │ │ │ │ -179 │ │ │ │ -_1_9_0 _S_c_e_n_e(_Q_W_i_d_g_e_t* parent_widget = 0, const char* name = NULL, Qt::WindowFlags │ │ │ │ -w_flags = 0); │ │ │ │ -191 │ │ │ │ -_1_9_4 virtual _~_S_c_e_n_e(); │ │ │ │ -195 │ │ │ │ -_2_0_4 virtual void _c_l_e_a_r(); │ │ │ │ -205 │ │ │ │ -207 │ │ │ │ -209 │ │ │ │ -212 │ │ │ │ -_2_1_9 virtual void _o_n_N_o_t_i_f_y(_M_e_s_s_a_g_e *message); │ │ │ │ -220 │ │ │ │ -_2_2_3 virtual bool _e_x_p_o_r_t_S_c_e_n_e(_R_e_n_d_e_r_e_r &er) const; │ │ │ │ -224 │ │ │ │ -_2_2_5 _S_t_r_i_n_g _g_e_t_B_o_n_d_O_r_d_e_r_S_t_r_i_n_g__(_I_n_d_e_x order); │ │ │ │ -226 │ │ │ │ -228 │ │ │ │ -231 │ │ │ │ -_2_4_1 virtual void _i_n_i_t_i_a_l_i_z_e_W_i_d_g_e_t(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ -242 │ │ │ │ -_2_4_4 virtual void _f_e_t_c_h_P_r_e_f_e_r_e_n_c_e_s(_I_N_I_F_i_l_e& inifile); │ │ │ │ -245 │ │ │ │ -_2_4_7 virtual void _w_r_i_t_e_P_r_e_f_e_r_e_n_c_e_s(_I_N_I_F_i_l_e& inifile); │ │ │ │ -248 │ │ │ │ -_2_5_9 virtual void _c_h_e_c_k_M_e_n_u(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ -260 │ │ │ │ -262 │ │ │ │ -265 │ │ │ │ -_2_6_9 virtual bool _i_s_V_a_l_i_d() const; │ │ │ │ -270 │ │ │ │ -_2_7_7 virtual void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const; │ │ │ │ -278 │ │ │ │ -_2_7_9 void _s_e_t_I_n_f_o(const QString& info_string); │ │ │ │ -_2_8_0 bool _i_s_R_e_c_o_r_d_i_n_g() const; │ │ │ │ -_2_8_1 void _c_a_p_t_u_r_e_C_a_m_e_r_a(); │ │ │ │ -_2_8_2 _A_t_o_m* _g_e_t_C_u_r_r_e_n_t_A_t_o_m() { return current_atom_; } │ │ │ │ -_2_8_3 void _s_e_t_C_u_r_r_e_n_t_A_t_o_m(_A_t_o_m* atom) { current_atom_ = atom; } │ │ │ │ -_2_8_4 void _n_o_t_i_f_y(_M_e_s_s_a_g_e* msg) { notify_(msg); } │ │ │ │ -_2_8_5 _V_e_c_t_o_r_2 _m_a_p_3_D_T_o_V_i_e_w_p_o_r_t(const _V_e_c_t_o_r_3& coords); │ │ │ │ -_2_8_6 _V_e_c_t_o_r_3 _m_a_p_V_i_e_w_p_o_r_t_T_o_3_D(const _V_e_c_t_o_r_2& coords); │ │ │ │ -_2_8_7 _V_e_c_t_o_r_3 _m_a_p_V_i_e_w_p_o_r_t_T_o_3_D(int x, int y); │ │ │ │ -_2_8_8 void _s_e_t_R_u_b_b_e_r_B_a_n_d_G_e_o_m_e_t_r_y(const QRect& rect); │ │ │ │ -_2_8_9 void _s_e_t_R_u_b_b_e_r_B_a_n_d_V_i_s_i_b_l_e(bool show); │ │ │ │ -_2_9_0 void _p_i_c_k_O_b_j_e_c_t_s(const QPoint& pos, list& objects); │ │ │ │ -_2_9_1 void _p_i_c_k_O_b_j_e_c_t_s(const QPoint& pos1, const QPoint& pos2, │ │ │ │ -list& objects); │ │ │ │ -_2_9_2 void _m_e_r_g_e(_C_o_m_p_o_s_i_t_e* a1, _C_o_m_p_o_s_i_t_e* a2); │ │ │ │ -_2_9_3 std::list _g_e_t_C_o_n_t_a_i_n_e_r_s(); │ │ │ │ -_2_9_4 void _e_n_t_e_r_P_i_c_k_i_n_g_M_o_d_e(); │ │ │ │ -_2_9_5 void _e_x_i_t_P_i_c_k_i_n_g_M_o_d_e(); │ │ │ │ -296 │ │ │ │ -_2_9_7 void _d_r_a_w_L_i_n_e(const QPointF& a, const QPointF& b, QPainter* painter = 0); │ │ │ │ -_2_9_8 void _d_r_a_w_L_i_n_e(const _V_e_c_t_o_r_2& a, const _V_e_c_t_o_r_2& b, QPainter* painter = 0); │ │ │ │ -299 │ │ │ │ -_3_0_0 _B_o_n_d* _g_e_t_C_u_r_r_e_n_t_B_o_n_d() { return current_bond_; } │ │ │ │ -_3_0_1 void _s_e_t_C_u_r_r_e_n_t_B_o_n_d(_B_o_n_d* b) { current_bond_ = b; } │ │ │ │ -302 │ │ │ │ -_3_0_3 void _c_h_a_n_g_e_B_o_n_d_O_r_d_e_r(); │ │ │ │ -_3_0_4 void _c_h_a_n_g_e_B_o_n_d_O_r_d_e_r(_I_n_d_e_x delta); │ │ │ │ -_3_0_5 void _a_c_t_i_v_a_t_e_d_O_r_d_e_r_I_t_e_m__(QAction* action); │ │ │ │ -_3_0_6 void _c_r_e_a_t_e_M_o_l_e_c_u_l_e__(); │ │ │ │ -_3_0_7 void _s_e_t_F_o_r_m_a_l_C_h_a_r_g_e__(); │ │ │ │ -308 │ │ │ │ -_3_0_9 void _d_e_s_e_l_e_c_t(bool update=true); │ │ │ │ -_3_1_0 void _g_e_t_C_l_i_c_k_e_d_I_t_e_m_s(const QPoint& p); │ │ │ │ -311 │ │ │ │ -_3_1_3 _S_t_a_g_e* _g_e_t_S_t_a_g_e() │ │ │ │ -314 { return stage_;} │ │ │ │ -315 │ │ │ │ -_3_1_7 const _S_t_a_g_e* _g_e_t_S_t_a_g_e() const │ │ │ │ -318 { return stage_;} │ │ │ │ -319 │ │ │ │ -_3_2_1 _S_t_a_g_e_S_e_t_t_i_n_g_s* _g_e_t_S_t_a_g_e_S_e_t_t_i_n_g_s() │ │ │ │ -322 { return stage_settings_; } │ │ │ │ -323 │ │ │ │ -_3_2_5 const _S_t_a_g_e_S_e_t_t_i_n_g_s* _g_e_t_S_t_a_g_e_S_e_t_t_i_n_g_s() const │ │ │ │ -326 { return stage_settings_; } │ │ │ │ -327 │ │ │ │ -_3_2_9 _M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s* _g_e_t_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s() │ │ │ │ -330 { return material_settings_; } │ │ │ │ -331 │ │ │ │ -_3_3_3 const _M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s* _g_e_t_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s() const │ │ │ │ -334 { return material_settings_; } │ │ │ │ -335 │ │ │ │ -_3_3_7 void _s_e_t_C_a_m_e_r_a(const _C_a_m_e_r_a& camera); │ │ │ │ -338 │ │ │ │ -_3_4_0 std::list& _g_e_t_A_n_i_m_a_t_i_o_n_P_o_i_n_t_s() │ │ │ │ -341 { return animation_points_;} │ │ │ │ -342 │ │ │ │ -_3_4_4 static void _s_e_t_A_n_i_m_a_t_i_o_n_S_m_o_o_t_h_n_e_s_s(float value) │ │ │ │ -345 { animation_smoothness_ = value;} │ │ │ │ -346 │ │ │ │ -_3_4_8 static float _g_e_t_A_n_i_m_a_t_i_o_n_S_m_o_o_t_h_n_e_s_s() │ │ │ │ -349 { return animation_smoothness_;} │ │ │ │ -350 │ │ │ │ -_3_5_2 float _g_e_t_D_o_w_n_s_a_m_p_l_i_n_g_F_a_c_t_o_r() const │ │ │ │ -353 { return downsampling_factor_;} │ │ │ │ -354 │ │ │ │ -_3_5_6 void _s_e_t_D_o_w_n_s_a_m_p_l_i_n_g_F_a_c_t_o_r(float ds_factor); │ │ │ │ -357 │ │ │ │ -_3_5_9 void _s_e_t_D_e_f_a_u_l_t_L_i_g_h_t_i_n_g(bool update_GL = true); │ │ │ │ -360 │ │ │ │ -_3_6_2 _B_A_L_L___D_E_P_R_E_C_A_T_E_D static void _s_e_t_M_o_u_s_e_S_e_n_s_i_t_i_v_i_t_y(float /* sensitivity */) {} │ │ │ │ -363 │ │ │ │ -_3_6_5 _B_A_L_L___D_E_P_R_E_C_A_T_E_D static float _g_e_t_M_o_u_s_e_S_e_n_s_i_t_i_v_i_t_y() { return 0; } │ │ │ │ -366 │ │ │ │ -_3_6_8 _B_A_L_L___D_E_P_R_E_C_A_T_E_D static void _s_e_t_M_o_u_s_e_W_h_e_e_l_S_e_n_s_i_t_i_v_i_t_y(float /* sensitivity │ │ │ │ -*/) {} │ │ │ │ -369 │ │ │ │ -_3_7_1 _B_A_L_L___D_E_P_R_E_C_A_T_E_D static float _g_e_t_M_o_u_s_e_W_h_e_e_l_S_e_n_s_i_t_i_v_i_t_y() { return 0; } │ │ │ │ -372 │ │ │ │ -_3_7_4 static void _s_e_t_S_h_o_w_L_i_g_h_t_S_o_u_r_c_e_s(bool state) │ │ │ │ -375 { show_light_sources_ = state;} │ │ │ │ -376 │ │ │ │ -_3_7_8 static bool _s_h_o_w_L_i_g_h_t_S_o_u_r_c_e_s_E_n_a_b_l_e_d() │ │ │ │ -379 { return show_light_sources_;} │ │ │ │ -380 │ │ │ │ -_3_8_2 _G_L_R_e_n_d_e_r_e_r& _g_e_t_G_L_R_e_n_d_e_r_e_r() │ │ │ │ -383 { return *gl_renderer_;} │ │ │ │ -384 │ │ │ │ -385#ifdef BALL_HAS_RTFACT │ │ │ │ -387 _R_a_y_t_r_a_c_i_n_g_R_e_n_d_e_r_e_r& getRaytracingRenderer() │ │ │ │ -388 { return *rt_renderer_;} │ │ │ │ -389#endif │ │ │ │ -390 │ │ │ │ -_3_9_5 void _s_e_t_G_L_R_e_n_d_e_r_e_r(_G_L_R_e_n_d_e_r_e_r& renderer); │ │ │ │ -396 │ │ │ │ -_3_9_8 static bool _s_t_e_r_e_o_B_u_f_f_e_r_S_u_p_p_o_r_t_T_e_s_t(); │ │ │ │ -399 │ │ │ │ -_4_0_1 bool _i_n_M_o_v_e_M_o_d_e() const; │ │ │ │ -402 │ │ │ │ -_4_0_4 bool _e_x_p_o_r_t_P_N_G(const _S_t_r_i_n_g& filename); │ │ │ │ -405 │ │ │ │ -_4_0_7 virtual void _s_e_t_W_i_d_g_e_t_V_i_s_i_b_l_e(bool state); │ │ │ │ -408 │ │ │ │ -_4_1_0 void _s_e_t_O_f_f_S_c_r_e_e_n_R_e_n_d_e_r_i_n_g(bool enabled, _S_i_z_e factor); │ │ │ │ -411 │ │ │ │ -_4_1_3 virtual void _p_a_i_n_t_E_v_e_n_t(QPaintEvent* e); │ │ │ │ -414 │ │ │ │ -_4_1_6 virtual bool _e_v_e_n_t_F_i_l_t_e_r(_Q_O_b_j_e_c_t* object, _Q_E_v_e_n_t* event); │ │ │ │ -417 │ │ │ │ -_4_1_9 virtual void _p_r_o_j_e_c_t_i_o_n_M_o_d_e_C_h_a_n_g_e_d(); │ │ │ │ -420 │ │ │ │ -_4_2_2 static void _s_e_t_S_c_r_e_e_n_S_h_o_t_N_u_m_b_e_r(_P_o_s_i_t_i_o_n pos) { screenshot_nr_ = pos;} │ │ │ │ -423 │ │ │ │ -_4_2_5 static void _s_e_t_P_O_V_N_u_m_b_e_r(_P_o_s_i_t_i_o_n pos) { pov_nr_ = pos;} │ │ │ │ -426 │ │ │ │ -_4_2_8 static void _s_e_t_V_R_M_L_N_u_m_b_e_r(_P_o_s_i_t_i_o_n pos) {vrml_nr_ = pos;} │ │ │ │ -429 │ │ │ │ -_4_3_1 void _r_o_t_a_t_e(float degree_right, float degree_up); │ │ │ │ -432 │ │ │ │ -_4_3_4 void _r_o_t_a_t_e_C_l_o_c_k_w_i_s_e(float degree); │ │ │ │ -435 │ │ │ │ -_4_4_1 void _m_o_v_e(_V_e_c_t_o_r_3 v); │ │ │ │ -442 │ │ │ │ -443 // TODO: move this and the next function somewhere else... │ │ │ │ -_4_4_9 void _m_o_v_e_C_o_m_p_o_s_i_t_e_s(const std::list& composites, _V_e_c_t_o_r_3 v); │ │ │ │ -450 │ │ │ │ -_4_5_6 void _r_o_t_a_t_e_C_o_m_p_o_s_i_t_e_s(const std::list& composites, float │ │ │ │ -degree_right, float degree_up, float degree_clockwise = 0); │ │ │ │ -457 │ │ │ │ -_4_5_9 bool _i_s_A_n_i_m_a_t_i_o_n_R_u_n_n_i_n_g() const; │ │ │ │ -460 │ │ │ │ -_4_6_2 void _s_e_t_T_u_r_n_P_o_i_n_t(const _V_e_c_t_o_r_3& v) { system_origin_ = v;} │ │ │ │ -463 │ │ │ │ -_4_6_5 const _V_e_c_t_o_r_3& _g_e_t_T_u_r_n_P_o_i_n_t() const { return system_origin_;} │ │ │ │ -466 │ │ │ │ -_4_6_8 void _s_e_t_F_u_l_l_S_c_r_e_e_n(bool state); │ │ │ │ -469 │ │ │ │ -_4_7_1 void _s_e_t_F_P_S_E_n_a_b_l_e_d(bool state) { show_fps_ = state; } │ │ │ │ -472 │ │ │ │ -_4_7_6 void _s_h_o_w_T_e_x_t(const _S_t_r_i_n_g& text, _S_i_z_e font_size = 20); │ │ │ │ -477 │ │ │ │ -_4_7_9 bool _i_s_U_p_d_a_t_e_R_u_n_n_i_n_g() const { return update_running_;} │ │ │ │ -480 │ │ │ │ -_4_8_1 void _r_e_s_e_t_T_r_a_c_k_i_n_g() {tracking_initialized_ = false;} │ │ │ │ -482 │ │ │ │ -483 // TODO: this pretty hacky! │ │ │ │ -_4_8_4 void _u_p_d_a_t_e_A_l_l_M_a_t_e_r_i_a_l_s(); │ │ │ │ -485 │ │ │ │ -_4_8_6 void _u_p_d_a_t_e_M_a_t_e_r_i_a_l_F_o_r_R_e_p_r_e_s_e_n_t_a_t_i_o_n(_R_e_p_r_e_s_e_n_t_a_t_i_o_n* rep, const _S_t_a_g_e_:_: │ │ │ │ -_M_a_t_e_r_i_a_l& new_material); │ │ │ │ -487 │ │ │ │ -_4_8_8 void _l_i_g_h_t_s_U_p_d_a_t_e_d(bool redraw = false); │ │ │ │ -489 │ │ │ │ -_4_9_1 void _s_e_t_u_p_E_n_v_i_r_o_n_m_e_n_t_M_a_p(const QImage& image); │ │ │ │ -492 │ │ │ │ -_4_9_3 _P_o_s_i_t_i_o_n _p_r_e_p_a_r_e_G_r_i_d_T_e_x_t_u_r_e_s(const _R_e_g_u_l_a_r_D_a_t_a_3_D& grid, const _C_o_l_o_r_M_a_p& │ │ │ │ -map); │ │ │ │ -494 │ │ │ │ -_4_9_5 void _u_p_d_a_t_e_G_L(); │ │ │ │ -_4_9_7 void _i_n_i_t_i_a_l_i_z_e_P_r_e_f_e_r_e_n_c_e_s_T_a_b(_P_r_e_f_e_r_e_n_c_e_s &preferences); │ │ │ │ -498 │ │ │ │ -_5_0_0 void _f_i_n_a_l_i_z_e_P_r_e_f_e_r_e_n_c_e_s_T_a_b(_P_r_e_f_e_r_e_n_c_e_s &preferences); │ │ │ │ -501 │ │ │ │ -_5_0_3 virtual void _a_p_p_l_y_P_r_e_f_e_r_e_n_c_e_s(); │ │ │ │ -504 │ │ │ │ -_5_0_6 void _s_h_o_w_C_o_n_t_e_x_t_M_e_n_u(QPoint pos); │ │ │ │ -507 │ │ │ │ -508 // Allow to use the base class setCursor, too │ │ │ │ -509 using QWidget::setCursor; │ │ │ │ -510 │ │ │ │ -_5_1_2 void _s_e_t_C_u_r_s_o_r(_S_t_r_i_n_g c); │ │ │ │ -513 │ │ │ │ -_5_1_5 void _s_e_t_E_l_e_m_e_n_t_C_u_r_s_o_r(int number); │ │ │ │ -516 │ │ │ │ -_5_1_8 virtual void _a_d_d_T_o_o_l_B_a_r_E_n_t_r_i_e_s(QToolBar* tb); │ │ │ │ -519 │ │ │ │ -_5_2_1 virtual void _k_e_y_P_r_e_s_s_E_v_e_n_t(QKeyEvent* e); │ │ │ │ -522 │ │ │ │ -524 public Q_SLOTS: │ │ │ │ -_5_2_6 void _c_r_e_a_t_e_C_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m(); │ │ │ │ -527 │ │ │ │ -_5_2_9 void _c_r_e_a_t_e_C_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m_A_t_O_r_i_g_i_n(); │ │ │ │ -530 │ │ │ │ -_5_3_2 _S_t_r_i_n_g _e_x_p_o_r_t_P_N_G(); │ │ │ │ -533 │ │ │ │ -_5_3_5 void _e_x_p_o_r_t_P_O_V_R_a_y(); │ │ │ │ -536 │ │ │ │ -_5_3_8 void _e_x_p_o_r_t_N_e_x_t_P_O_V_R_a_y(); │ │ │ │ -539 │ │ │ │ -_5_4_1 void _p_r_i_n_t_S_c_e_n_e(); │ │ │ │ -542 │ │ │ │ -_5_4_4 void _s_h_o_w_E_x_p_o_r_t_P_N_G_D_i_a_l_o_g(); │ │ │ │ -545 │ │ │ │ -_5_4_7 void _s_h_o_w_E_x_p_o_r_t_V_R_M_L_D_i_a_l_o_g(); │ │ │ │ -548 │ │ │ │ -_5_5_0 void _s_e_t_P_r_e_v_i_e_w(bool state) { use_preview_ = state; } │ │ │ │ -551 │ │ │ │ -_5_5_3 bool _u_s_e_P_r_e_v_i_e_w() const { return use_preview_; } │ │ │ │ -554 │ │ │ │ -_5_5_5 bool _u_s_e_V_e_r_t_e_x_B_u_f_f_e_r_s() const { return want_to_use_vertex_buffer_; } │ │ │ │ -556 │ │ │ │ -_5_6_0 virtual void _s_w_i_t_c_h_S_h_o_w_W_i_d_g_e_t(); │ │ │ │ -561 │ │ │ │ -_5_6_3 void _s_w_i_t_c_h_R_e_n_d_e_r_e_r(_R_e_n_d_e_r_S_e_t_u_p_:_:_R_e_n_d_e_r_e_r_T_y_p_e new_type); │ │ │ │ -564 │ │ │ │ -_5_6_6 void _a_d_d_G_l_W_i_n_d_o_w(); │ │ │ │ -567 │ │ │ │ -568#ifdef BALL_HAS_RTFACT │ │ │ │ -570 void addRTfactWindow(); │ │ │ │ -571#endif │ │ │ │ -572 │ │ │ │ -_5_7_4 void _e_x_i_t_S_t_e_r_e_o(); │ │ │ │ -575 │ │ │ │ -_5_7_7 void _e_n_t_e_r_S_t_e_r_e_o(); │ │ │ │ -578 │ │ │ │ -_5_8_0 void _e_n_t_e_r_A_c_t_i_v_e_S_t_e_r_e_o(); │ │ │ │ -581 │ │ │ │ -_5_8_3 void _e_n_t_e_r_D_u_a_l_S_t_e_r_e_o(); │ │ │ │ -584 │ │ │ │ -_5_8_6 void _e_n_t_e_r_D_u_a_l_S_t_e_r_e_o_D_i_f_f_e_r_e_n_t_D_i_s_p_l_a_y_s(); │ │ │ │ -587 │ │ │ │ -_5_8_9 void _c_l_e_a_r_R_e_c_o_r_d_e_d_A_n_i_m_a_t_i_o_n(); │ │ │ │ -590 │ │ │ │ -_5_9_2 void _s_t_a_r_t_A_n_i_m_a_t_i_o_n(); │ │ │ │ -593 │ │ │ │ -_5_9_5 void _s_t_o_p_A_n_i_m_a_t_i_o_n(); │ │ │ │ -596 │ │ │ │ -_5_9_8 void _s_w_i_t_c_h_T_o_L_a_s_t_M_o_d_e(); │ │ │ │ -599 │ │ │ │ -_6_0_1 void _s_w_i_t_c_h_S_h_o_w_G_r_i_d(); │ │ │ │ -602 │ │ │ │ -_6_0_4 void _s_h_o_w_I_n_f_o_s(); │ │ │ │ -605 │ │ │ │ -_6_0_7 void _s_e_t_u_p_V_i_e_w_V_o_l_u_m_e(); │ │ │ │ -608 │ │ │ │ -_6_1_0 void _s_t_o_r_e_V_i_e_w_P_o_i_n_t(); │ │ │ │ -611 │ │ │ │ -_6_1_3 void _r_e_s_t_o_r_e_V_i_e_w_P_o_i_n_t(); │ │ │ │ -614 │ │ │ │ -_6_1_6 void _s_t_a_r_t_C_o_n_t_i_n_u_o_u_s_L_o_o_p(); │ │ │ │ -617 │ │ │ │ -_6_1_9 void _s_t_o_p_C_o_n_t_i_n_u_o_u_s_L_o_o_p(); │ │ │ │ -620 │ │ │ │ -_6_2_2 void _t_o_g_g_l_e_C_o_n_t_i_n_u_o_u_s_L_o_o_p(); │ │ │ │ -623 │ │ │ │ -_6_2_5 void _a_p_p_l_y_S_t_e_r_e_o_D_e_f_a_u_l_t_s(); │ │ │ │ -626 │ │ │ │ -627#ifdef BALL_HAS_RTFACT │ │ │ │ -628 RaytracingWindowPtr getWindow(_W_i_n_d_o_w_T_y_p_e aWindowType); │ │ │ │ -629#endif │ │ │ │ -630 │ │ │ │ -_6_3_1 void _c_r_e_a_t_e_N_e_w_M_o_l_e_c_u_l_e(); │ │ │ │ -_6_3_2 void _s_a_t_u_r_a_t_e_W_i_t_h_H_y_d_r_o_g_e_n_s(); │ │ │ │ -_6_3_3 void _o_p_t_i_m_i_z_e_S_t_r_u_c_t_u_r_e(); │ │ │ │ -_6_3_4 void _c_o_m_p_u_t_e_B_o_n_d_O_r_d_e_r_s(); │ │ │ │ -635 │ │ │ │ -636 // slots for communication with PTEDialog │ │ │ │ -_6_3_7 void _s_e_t_E_d_i_t_E_l_e_m_e_n_t_T_y_p_e(int element_number); │ │ │ │ -_6_3_8 int _g_e_t_E_d_i_t_E_l_e_m_e_n_t_T_y_p_e(); │ │ │ │ -639 │ │ │ │ -_6_4_1 _I_n_t_e_r_a_c_t_i_o_n_M_o_d_e_M_a_n_a_g_e_r& _g_e_t_I_n_t_e_r_a_c_t_i_o_n_M_o_d_e_M_a_n_a_g_e_r() { return mode_manager_; │ │ │ │ -} │ │ │ │ -642 │ │ │ │ -644 protected Q_SLOTS: │ │ │ │ -645 │ │ │ │ -649 │ │ │ │ -_6_5_3 virtual void _s_h_o_w_V_i_e_w_P_o_i_n_t__(); │ │ │ │ -654 │ │ │ │ -_6_5_6 virtual void _s_e_t_V_i_e_w_P_o_i_n_t__(); │ │ │ │ -657 │ │ │ │ -_6_5_9 virtual void _r_e_s_e_t_C_a_m_e_r_a__(); │ │ │ │ -660 │ │ │ │ -_6_6_4 virtual void _r_e_s_e_t_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_F_o_r_R_e_n_d_e_r_e_r__(_R_e_n_d_e_r_S_e_t_u_p& rs); │ │ │ │ -665 │ │ │ │ -_6_6_7 virtual void _d_r_o_p_E_v_e_n_t(QDropEvent* e); │ │ │ │ -668 │ │ │ │ -_6_7_0 virtual void _d_r_a_g_E_n_t_e_r_E_v_e_n_t(QDragEnterEvent* e); │ │ │ │ -671 │ │ │ │ -672 // dummy slot for menu entries without immediate action (saves many lines │ │ │ │ -code this way) │ │ │ │ -_6_7_3 void _d_u_m_m_y_S_l_o_t(){} │ │ │ │ -674 │ │ │ │ -676 │ │ │ │ -678 Q_SIGNALS: │ │ │ │ -679 │ │ │ │ -680 // signal for communication with EditOperationDialog │ │ │ │ -_6_8_1 void _n_e_w_E_d_i_t_O_p_e_r_a_t_i_o_n(_E_d_i_t_O_p_e_r_a_t_i_o_n &eo); │ │ │ │ -682 │ │ │ │ -684 protected: │ │ │ │ -685 │ │ │ │ -_6_8_8 void _h_a_n_d_l_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_e_s_s_a_g_e__(_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_e_s_s_a_g_e* rm); │ │ │ │ -689 │ │ │ │ -_6_9_2 void _h_a_n_d_l_e_D_a_t_a_s_e_t_M_e_s_s_a_g_e__(_D_a_t_a_s_e_t_M_e_s_s_a_g_e* dm); │ │ │ │ -693 │ │ │ │ -_6_9_6 void _h_a_n_d_l_e_S_c_e_n_e_M_e_s_s_a_g_e__(_S_c_e_n_e_M_e_s_s_a_g_e* sm); │ │ │ │ -697 │ │ │ │ -_7_0_0 void _h_a_n_d_l_e_C_o_m_p_o_s_i_t_e_M_e_s_s_a_g_e__(_C_o_m_p_o_s_i_t_e_M_e_s_s_a_g_e* cm); │ │ │ │ -701 │ │ │ │ -_7_0_4 void _h_a_n_d_l_e_C_o_n_t_r_o_l_S_e_l_e_c_t_i_o_n_M_e_s_s_a_g_e__(_C_o_n_t_r_o_l_S_e_l_e_c_t_i_o_n_M_e_s_s_a_g_e* csm); │ │ │ │ -705 │ │ │ │ -_7_0_8 virtual void _h_a_n_d_l_e_R_e_n_d_e_r_T_o_B_u_f_f_e_r_F_i_n_i_s_h_e_d_E_v_e_n_t__ │ │ │ │ -(_R_e_n_d_e_r_T_o_B_u_f_f_e_r_F_i_n_i_s_h_e_d_E_v_e_n_t* evt); │ │ │ │ -709 │ │ │ │ -_7_1_4 void _r_e_n_d_e_r_T_e_x_t__(QPointF const& point, QString const& text, _Q_P_a_i_n_t_D_e_v_i_c_e* │ │ │ │ -current_dev); │ │ │ │ -715 │ │ │ │ -_7_2_1 void _i_n_s_e_r_t__(int x_, int y_, _P_D_B_A_t_o_m &atom_); │ │ │ │ -722 │ │ │ │ -_7_2_7 _T_V_e_c_t_o_r_2_<_f_l_o_a_t_> _g_e_t_S_c_r_e_e_n_P_o_s_i_t_i_o_n__(_V_e_c_t_o_r_3 vec); │ │ │ │ -728 │ │ │ │ -_7_2_9 void _i_n_i_t_i_a_l_i_z_e_M_e_m_b_e_r_s__(); │ │ │ │ -730 │ │ │ │ -_7_3_1 void _r_e_n_d_e_r_G_r_i_d__(); │ │ │ │ -732 │ │ │ │ -_7_3_3 QAction *_n_e_w___m_o_l_e_c_u_l_e___a_c_t_i_o_n__, *optimize_action_; │ │ │ │ -_7_3_4 QAction *_a_d_d___h_y_d_r_o_g_e_n_s___a_c_t_i_o_n__; │ │ │ │ -_7_3_5 QAction *_b_o_n_d_o_r_d_e_r_s___a_c_t_i_o_n__; │ │ │ │ -736 │ │ │ │ -_7_3_7 _A_t_o_m* _c_u_r_r_e_n_t___a_t_o_m__; │ │ │ │ -_7_3_8 _B_o_n_d* _c_u_r_r_e_n_t___b_o_n_d__; │ │ │ │ -739 │ │ │ │ -740 // pick atoms/bonds only in highlighted AtomContainer? │ │ │ │ -_7_4_1 static bool _o_n_l_y___h_i_g_h_l_i_g_h_t_e_d__; │ │ │ │ -742 // element for new atoms │ │ │ │ -_7_4_3 int _a_t_o_m_i_c___n_u_m_b_e_r__; │ │ │ │ -744 │ │ │ │ -745 //undo stack │ │ │ │ -_7_4_6 vector _u_n_d_o__; │ │ │ │ -_7_4_7 _E_d_i_t_S_e_t_t_i_n_g_s* _e_d_i_t___s_e_t_t_i_n_g_s__; │ │ │ │ -_7_4_8 QList _t_o_o_l_b_a_r___a_c_t_i_o_n_s___e_d_i_t___c_o_n_t_r_o_l_s__; │ │ │ │ -749 │ │ │ │ -753 │ │ │ │ -_7_5_6 virtual void _i_n_i_t(); │ │ │ │ -757 │ │ │ │ -_7_6_4 virtual void _p_a_i_n_t_G_L(); │ │ │ │ -765 │ │ │ │ -_7_7_2 virtual void _r_e_s_i_z_e_E_v_e_n_t(QResizeEvent* event); │ │ │ │ -773 │ │ │ │ -_7_7_9 virtual void _c_u_s_t_o_m_E_v_e_n_t(_Q_E_v_e_n_t* evt); │ │ │ │ -780 │ │ │ │ -_7_8_4 virtual void _t_r_a_n_s_f_o_r_m_a_t_i_o_n_E_v_e_n_t_6_D(_T_r_a_n_s_f_o_r_m_a_t_i_o_n_E_v_e_n_t_6_D* evt); │ │ │ │ -785 │ │ │ │ -_7_8_9 virtual void _m_o_t_i_o_n_T_r_a_c_k_i_n_g_E_v_e_n_t(_M_o_t_i_o_n_T_r_a_c_k_i_n_g_E_v_e_n_t* evt); │ │ │ │ -790 │ │ │ │ -_7_9_4 virtual void _b_u_t_t_o_n_P_r_e_s_s_E_v_e_n_t(_B_u_t_t_o_n_E_v_e_n_t* evt); │ │ │ │ -795 │ │ │ │ -_7_9_9 virtual void _b_u_t_t_o_n_R_e_l_e_a_s_e_E_v_e_n_t(_B_u_t_t_o_n_E_v_e_n_t* evt); │ │ │ │ -800 │ │ │ │ -_8_0_5 virtual void _m_o_u_s_e_M_o_v_e_E_v_e_n_t(_Q_M_o_u_s_e_E_v_e_n_t* qmouse_event); │ │ │ │ -806 │ │ │ │ -_8_1_1 virtual void _m_o_u_s_e_P_r_e_s_s_E_v_e_n_t(_Q_M_o_u_s_e_E_v_e_n_t* qmouse_event); │ │ │ │ -812 │ │ │ │ -_8_1_7 virtual void _m_o_u_s_e_R_e_l_e_a_s_e_E_v_e_n_t(_Q_M_o_u_s_e_E_v_e_n_t* qmouse_event); │ │ │ │ -818 │ │ │ │ -_8_2_2 virtual void _w_h_e_e_l_E_v_e_n_t(QWheelEvent* qmouse_event); │ │ │ │ -823 │ │ │ │ -_8_2_4 virtual void _m_o_u_s_e_D_o_u_b_l_e_C_l_i_c_k_E_v_e_n_t(_Q_M_o_u_s_e_E_v_e_n_t* e); │ │ │ │ -825 │ │ │ │ -826 //_ │ │ │ │ -_8_2_7 void _a_n_i_m_a_t_e__(); │ │ │ │ -828 │ │ │ │ -_8_2_9 void _r_o_t_a_t_e_S_y_s_t_e_m_C_l_o_c_k_w_i_s_e__(); │ │ │ │ -_8_3_0 void _z_o_o_m_S_y_s_t_e_m__(); │ │ │ │ -831 │ │ │ │ -_8_3_2 void _s_e_l_e_c_t_i_o_n_P_r_e_s_s_e_d__(); │ │ │ │ -_8_3_3 void _s_e_l_e_c_t_i_o_n_P_r_e_s_s_e_d_M_o_v_e_d__(); │ │ │ │ -834 │ │ │ │ -_8_3_5 void _s_e_l_e_c_t_O_b_j_e_c_t_s__(); │ │ │ │ -_8_3_6 void _p_i_c_k_P_a_r_e_n_t__(QPoint p); │ │ │ │ -837 │ │ │ │ -_8_3_8 void _w_r_i_t_e_L_i_g_h_t_s__(_I_N_I_F_i_l_e& inifile) const; │ │ │ │ -839 │ │ │ │ -_8_4_0 void _r_e_a_d_L_i_g_h_t_s__(const _I_N_I_F_i_l_e& inifile); │ │ │ │ -841 │ │ │ │ -_8_4_2 void _c_r_e_a_t_e_C_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m__(bool at_origin); │ │ │ │ -843 │ │ │ │ -_8_4_4 void _r_e_g_i_s_t_e_r_R_e_n_d_e_r_e_r_s__(); │ │ │ │ -845 │ │ │ │ -_8_4_7 _S_t_r_i_n_g _c_r_e_a_t_e_F_P_S_I_n_f_o__(_R_e_n_d_e_r_e_r* renderer); │ │ │ │ -848 │ │ │ │ -849 // Menu entry IDs │ │ │ │ -_8_5_0 QAction *no_stereo_action_, *enter_stereo_action_, *_a_c_t_i_v_e___s_t_e_r_e_o___a_c_t_i_o_n__, │ │ │ │ -*dual_stereo_action_, *dual_stereo_different_display_action_; │ │ │ │ -_8_5_1 QAction *record_animation_action_, *start_animation_action_, │ │ │ │ -*clear_animation_action_, *_c_a_n_c_e_l___a_n_i_m_a_t_i_o_n___a_c_t_i_o_n__; │ │ │ │ -_8_5_2 QAction *animation_export_POV_action_, *animation_export_VRML_action_, │ │ │ │ -*_a_n_i_m_a_t_i_o_n___e_x_p_o_r_t___P_N_G___a_c_t_i_o_n__, *animation_repeat_action_; │ │ │ │ -853 │ │ │ │ -854#ifdef BALL_HAS_RTFACT │ │ │ │ -855 QAction *toggle_continuous_loop_action_; │ │ │ │ -856#endif │ │ │ │ -_8_5_7 QAction *_s_w_i_t_c_h___g_r_i_d__; │ │ │ │ -_8_5_8 QMenu* _c_r_e_a_t_e___c_o_o_r_d_i_n_a_t_e___s_y_s_t_e_m__; │ │ │ │ -859 │ │ │ │ -_8_6_0 _V_e_c_t_o_r_3 _s_y_s_t_e_m___o_r_i_g_i_n__; │ │ │ │ -_8_6_1 _V_e_c_t_o_r_3 _o_l_d___t_r_a_c_k_o_r_i_g_i_n__; │ │ │ │ -_8_6_2 bool _t_r_a_c_k_i_n_g___i_n_i_t_i_a_l_i_z_e_d__; │ │ │ │ -_8_6_3 _Q_u_a_t_e_r_n_i_o_n _o_l_d___t_r_a_c_k_r_o_t_a_t_i_o_n__; │ │ │ │ -864 │ │ │ │ -_8_6_5 bool _u_p_d_a_t_e___r_u_n_n_i_n_g__; │ │ │ │ -866 │ │ │ │ -_8_6_7 QRubberBand* _r_b__; │ │ │ │ -868 │ │ │ │ -_8_6_9 _S_t_a_g_e* _s_t_a_g_e__; │ │ │ │ -_8_7_0 _C_a_m_e_r_a _s_t_e_r_e_o___c_a_m_e_r_a__; │ │ │ │ -_8_7_1 _C_a_m_e_r_a _s_t_o_r_e_d___c_a_m_e_r_a__; │ │ │ │ -872 │ │ │ │ -_8_7_3 std::vector > _r_e_n_d_e_r_e_r_s__; │ │ │ │ -_8_7_4 _G_L_R_e_n_d_e_r_e_r* _g_l___r_e_n_d_e_r_e_r__; │ │ │ │ -875 │ │ │ │ -876#ifdef BALL_HAS_RTFACT │ │ │ │ -877 _R_a_y_t_r_a_c_i_n_g_R_e_n_d_e_r_e_r* rt_renderer_; │ │ │ │ -878 RaytracingWindowPtr rt_window_; │ │ │ │ -879#endif │ │ │ │ -880 │ │ │ │ -_8_8_1 static bool _s_h_o_w___l_i_g_h_t___s_o_u_r_c_e_s__; │ │ │ │ -_8_8_2 static float _a_n_i_m_a_t_i_o_n___s_m_o_o_t_h_n_e_s_s__; │ │ │ │ -_8_8_3 static float _d_o_w_n_s_a_m_p_l_i_n_g___f_a_c_t_o_r__; │ │ │ │ -884 │ │ │ │ -_8_8_5 _L_i_g_h_t_S_e_t_t_i_n_g_s* _l_i_g_h_t___s_e_t_t_i_n_g_s__; │ │ │ │ -_8_8_6 _S_t_a_g_e_S_e_t_t_i_n_g_s* _s_t_a_g_e___s_e_t_t_i_n_g_s__; │ │ │ │ -_8_8_7 _M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s* _m_a_t_e_r_i_a_l___s_e_t_t_i_n_g_s__; │ │ │ │ -888 │ │ │ │ -889 // nr of last png file export │ │ │ │ -_8_9_0 static _P_o_s_i_t_i_o_n _s_c_r_e_e_n_s_h_o_t___n_r__; │ │ │ │ -891 // nr of last pov file export │ │ │ │ -_8_9_2 static _P_o_s_i_t_i_o_n _p_o_v___n_r__; │ │ │ │ -893 //nr of last vrml or stl export │ │ │ │ -_8_9_4 static _P_o_s_i_t_i_o_n _v_r_m_l___n_r__; │ │ │ │ -895 │ │ │ │ -_8_9_6 std::list _a_n_i_m_a_t_i_o_n___p_o_i_n_t_s__; │ │ │ │ -_8_9_7 _A_n_i_m_a_t_i_o_n_T_h_r_e_a_d* _a_n_i_m_a_t_i_o_n___t_h_r_e_a_d__; │ │ │ │ -_8_9_8 bool _s_t_o_p___a_n_i_m_a_t_i_o_n__; │ │ │ │ -899#ifdef BALL_HAS_RTFACT │ │ │ │ -900 bool continuous_loop_; │ │ │ │ -901#endif │ │ │ │ -_9_0_2 bool _w_a_n_t___t_o___u_s_e___v_e_r_t_e_x___b_u_f_f_e_r__; │ │ │ │ -_9_0_3 bool _u_s_e___p_r_e_v_i_e_w__; │ │ │ │ -904 │ │ │ │ -_9_0_5 _P_r_e_c_i_s_e_T_i_m_e _t_i_m_e__; │ │ │ │ -_9_0_6 QPoint _i_n_f_o___p_o_i_n_t__; │ │ │ │ -_9_0_7 QByteArray _l_a_s_t___s_t_a_t_e__; │ │ │ │ -_9_0_8 list _f_p_s__; │ │ │ │ -_9_0_9 bool _s_h_o_w___f_p_s__; │ │ │ │ -_9_1_0 static bool _o_f_f_s_c_r_e_e_n___r_e_n_d_e_r_i_n_g__; │ │ │ │ -_9_1_1 _S_i_z_e _o_f_f_s_c_r_e_e_n___f_a_c_t_o_r__; │ │ │ │ -_9_1_2 _S_i_z_e _f_o_n_t___s_i_z_e__; │ │ │ │ -_9_1_3 QToolBar* _t_o_o_l_b_a_r___v_i_e_w___c_o_n_t_r_o_l_s__; │ │ │ │ -_9_1_4 QToolBar* _t_o_o_l_b_a_r___e_d_i_t___c_o_n_t_r_o_l_s__; │ │ │ │ -_9_1_5 QList _t_o_o_l_b_a_r___a_c_t_i_o_n_s___v_i_e_w___c_o_n_t_r_o_l_s__; │ │ │ │ -916 │ │ │ │ -_9_1_7 QString _i_n_f_o___s_t_r_i_n_g__; │ │ │ │ -918 │ │ │ │ -_9_1_9 _G_L_R_e_n_d_e_r_W_i_n_d_o_w* _m_a_i_n___d_i_s_p_l_a_y__; │ │ │ │ -_9_2_1 _P_o_s_i_t_i_o_n _m_a_i_n___r_e_n_d_e_r_e_r__; │ │ │ │ -922 │ │ │ │ -_9_2_3 _I_n_d_e_x _s_t_e_r_e_o___l_e_f_t___e_y_e__; │ │ │ │ -_9_2_4 _I_n_d_e_x _s_t_e_r_e_o___r_i_g_h_t___e_y_e__; │ │ │ │ -925 │ │ │ │ -_9_2_6 QFont _d_e_f_a_u_l_t___f_o_n_t__; │ │ │ │ -927 │ │ │ │ -_9_2_8 QPicture _o_v_e_r_l_a_y__; │ │ │ │ -_9_2_9 bool _h_a_s___o_v_e_r_l_a_y__; │ │ │ │ -_9_3_0 _I_n_t_e_r_a_c_t_i_o_n_M_o_d_e_M_a_n_a_g_e_r _m_o_d_e___m_a_n_a_g_e_r__; │ │ │ │ -931 }; │ │ │ │ -932 │ │ │ │ -933 │ │ │ │ -_9_3_5 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _A_n_i_m_a_t_i_o_n_T_h_r_e_a_d │ │ │ │ -936 : public _Q_T_h_r_e_a_d │ │ │ │ -937 { │ │ │ │ -938 public: │ │ │ │ -939 │ │ │ │ -_9_4_1 _A_n_i_m_a_t_i_o_n_T_h_r_e_a_d(){}; │ │ │ │ -942 │ │ │ │ -_9_4_4 virtual void _r_u_n() {scene_->animate_();} │ │ │ │ -945 │ │ │ │ -_9_4_7 void _m_y_S_l_e_e_p(_S_i_z_e msec); │ │ │ │ -948 │ │ │ │ -_9_5_0 void _s_e_t_S_c_e_n_e(_S_c_e_n_e* scene) { scene_ = scene;} │ │ │ │ -951 │ │ │ │ -_9_5_3 _S_c_e_n_e* _g_e_t_S_c_e_n_e() { return scene_;} │ │ │ │ -954 │ │ │ │ -955 protected: │ │ │ │ -956 │ │ │ │ -_9_5_7 _S_c_e_n_e* _s_c_e_n_e__; │ │ │ │ -958 }; │ │ │ │ -959 │ │ │ │ -960 } // namespace VIEW │ │ │ │ -961} // namespace BALL │ │ │ │ -962 │ │ │ │ -963#endif // BALL_VIEW_WIDGETS_SCENE_H │ │ │ │ -_r_e_n_d_e_r_W_i_n_d_o_w_._h │ │ │ │ -_r_e_n_d_e_r_S_e_t_u_p_._h │ │ │ │ -_g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h │ │ │ │ -_r_a_y_t_r_a_c_i_n_g_R_e_n_d_e_r_e_r_._h │ │ │ │ -_g_l_R_e_n_d_e_r_e_r_._h │ │ │ │ -_m_o_d_u_l_a_r_W_i_d_g_e_t_._h │ │ │ │ -_e_d_i_t_O_p_e_r_a_t_i_o_n_._h │ │ │ │ -_i_n_t_e_r_a_c_t_i_o_n_M_o_d_e_M_a_n_a_g_e_r_._h │ │ │ │ -_e_d_i_t_S_e_t_t_i_n_g_s_._h │ │ │ │ -_B_A_L_L___E_M_B_E_D_D_A_B_L_E │ │ │ │ -#define BALL_EMBEDDABLE(TYPE, BASE) │ │ │ │ -DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_3_1 │ │ │ │ +145 /*_ This maps Atom:Types to Indices of rdf_list_ */ │ │ │ │ +_1_4_6 _H_a_s_h_M_a_p< _A_t_o_m::Type, _H_a_s_h_M_a_p<_A_t_o_m::Type, _P_o_s_i_t_i_o_n> > rdf_indices_; │ │ │ │ +147 │ │ │ │ +148 │ │ │ │ +149 }; │ │ │ │ +150 │ │ │ │ +151} // namespace BALL │ │ │ │ +152#endif // BALL__RDFPARAMETER_H │ │ │ │ +_r_a_d_i_a_l_D_i_s_t_r_i_b_u_t_i_o_n_F_u_n_c_t_i_o_n_._h │ │ │ │ +_a_t_o_m_._h │ │ │ │ +_p_a_r_a_m_e_t_e_r_S_e_c_t_i_o_n_._h │ │ │ │ +_f_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_s_t_d │ │ │ │ +STL namespace. │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ -DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_P_r_e_c_i_s_e_T_i_m_e │ │ │ │ -DDeeffiinniittiioonn _t_i_m_e_S_t_a_m_p_._h_:_3_8 │ │ │ │ -_B_A_L_L_:_:_T_R_e_g_u_l_a_r_D_a_t_a_3_D_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_M_a_p │ │ │ │ +HashMap class based on the STL map (containing serveral convenience functions) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_M_a_p_._h_:_7_4 │ │ │ │ _B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_I_N_I_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _I_N_I_F_i_l_e_._h_:_2_9 │ │ │ │ +_B_A_L_L_:_:_P_a_r_a_m_e_t_e_r_S_e_c_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _p_a_r_a_m_e_t_e_r_S_e_c_t_i_o_n_._h_:_4_0 │ │ │ │ _B_A_L_L_:_:_A_t_o_m │ │ │ │ DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_B_o_n_d │ │ │ │ -DDeeffiinniittiioonn _b_o_n_d_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_P_D_B_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _P_D_B_A_t_o_m_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_T_Q_u_a_t_e_r_n_i_o_n_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_2_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_C_o_l_o_r_M_a_p │ │ │ │ -DDeeffiinniittiioonn _c_o_l_o_r_M_a_p_._h_:_3_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_e_t_t_i_n_g_s │ │ │ │ -DDeeffiinniittiioonn _e_d_i_t_S_e_t_t_i_n_g_s_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_L_i_g_h_t_S_e_t_t_i_n_g_s │ │ │ │ -DDeeffiinniittiioonn _l_i_g_h_t_S_e_t_t_i_n_g_s_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s │ │ │ │ -DDeeffiinniittiioonn _m_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s_._h_:_3_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ -DDeeffiinniittiioonn _p_r_e_f_e_r_e_n_c_e_s_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_S_e_t_t_i_n_g_s │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_S_e_t_t_i_n_g_s_._h_:_5_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_B_u_t_t_o_n_E_v_e_n_t │ │ │ │ -DDeeffiinniittiioonn _b_u_t_t_o_n_E_v_e_n_t_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_t_i_o_n_T_r_a_c_k_i_n_g_E_v_e_n_t │ │ │ │ -DDeeffiinniittiioonn _m_o_t_i_o_n_T_r_a_c_k_i_n_g_E_v_e_n_t_._h_:_1_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_T_r_a_n_s_f_o_r_m_a_t_i_o_n_E_v_e_n_t_6_D │ │ │ │ -DDeeffiinniittiioonn _t_r_a_n_s_f_o_r_m_a_t_i_o_n_E_v_e_n_t_6_D_._h_:_1_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_O_p_e_r_a_t_i_o_n │ │ │ │ -DDeeffiinniittiioonn _e_d_i_t_O_p_e_r_a_t_i_o_n_._h_:_2_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ -DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_e_s_s_a_g_e │ │ │ │ -DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_D_a_t_a_s_e_t_M_e_s_s_a_g_e │ │ │ │ -DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_1_3_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_C_o_m_p_o_s_i_t_e_M_e_s_s_a_g_e │ │ │ │ -DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_2_0_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_M_e_s_s_a_g_e │ │ │ │ -DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_3_2_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_C_o_n_t_r_o_l_S_e_l_e_c_t_i_o_n_M_e_s_s_a_g_e │ │ │ │ -DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_4_8_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_e_s_s_a_g_e │ │ │ │ -Base class for all messages concerning a Representation. │ │ │ │ -DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_5_7_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_I_n_t_e_r_a_c_t_i_o_n_M_o_d_e_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _i_n_t_e_r_a_c_t_i_o_n_M_o_d_e_M_a_n_a_g_e_r_._h_:_2_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _m_o_d_u_l_a_r_W_i_d_g_e_t_._h_:_6_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h_:_5_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_3_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e_:_:_M_a_t_e_r_i_a_l │ │ │ │ -DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_4_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_C_a_m_e_r_a │ │ │ │ -DDeeffiinniittiioonn _c_a_m_e_r_a_._h_:_2_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_W_i_n_d_o_w │ │ │ │ -DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_W_i_n_d_o_w_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_L_R_e_n_d_e_r_e_r │ │ │ │ -DDeeffiinniittiioonn _g_l_R_e_n_d_e_r_e_r_._h_:_7_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_a_y_t_r_a_c_i_n_g_R_e_n_d_e_r_e_r │ │ │ │ -DDeeffiinniittiioonn _r_a_y_t_r_a_c_i_n_g_R_e_n_d_e_r_e_r_._h_:_3_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_n_d_e_r_e_r │ │ │ │ -DDeeffiinniittiioonn _r_e_n_d_e_r_e_r_._h_:_5_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_n_d_e_r_S_e_t_u_p │ │ │ │ -DDeeffiinniittiioonn _r_e_n_d_e_r_S_e_t_u_p_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_n_d_e_r_S_e_t_u_p_:_:_R_e_n_d_e_r_e_r_T_y_p_e │ │ │ │ -RendererType │ │ │ │ -DDeeffiinniittiioonn _r_e_n_d_e_r_S_e_t_u_p_._h_:_6_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_n_d_e_r_T_o_B_u_f_f_e_r_F_i_n_i_s_h_e_d_E_v_e_n_t │ │ │ │ -DDeeffiinniittiioonn _r_e_n_d_e_r_S_e_t_u_p_._h_:_3_7_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_1_4_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_p_p_l_y_S_t_e_r_e_o_D_e_f_a_u_l_t_s │ │ │ │ -void applyStereoDefaults() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_p_o_v___n_r__ │ │ │ │ -static Position pov_nr_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_9_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_w_i_t_c_h_S_h_o_w_G_r_i_d │ │ │ │ -void switchShowGrid() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_x_i_t_P_i_c_k_i_n_g_M_o_d_e │ │ │ │ -void exitPickingMode() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_h_o_w___f_p_s__ │ │ │ │ -bool show_fps_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_0_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_l_e_c_t_O_b_j_e_c_t_s__ │ │ │ │ -void selectObjects_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_g_i_s_t_e_r_R_e_n_d_e_r_e_r_s__ │ │ │ │ -void registerRenderers_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_d_d___h_y_d_r_o_g_e_n_s___a_c_t_i_o_n__ │ │ │ │ -QAction * add_hydrogens_action_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_3_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_P_O_V_N_u_m_b_e_r │ │ │ │ -static void setPOVNumber(Position pos) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_4_2_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_d_r_a_g_E_n_t_e_r_E_v_e_n_t │ │ │ │ -virtual void dragEnterEvent(QDragEnterEvent *e) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_w_i_t_c_h_S_h_o_w_W_i_d_g_e_t │ │ │ │ -virtual void switchShowWidget() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_S_h_o_w_L_i_g_h_t_S_o_u_r_c_e_s │ │ │ │ -static void setShowLightSources(bool state) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_7_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_b__ │ │ │ │ -QRubberBand * rb_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_6_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_h_a_n_g_e_B_o_n_d_O_r_d_e_r │ │ │ │ -void changeBondOrder(Index delta) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_h_o_w_T_e_x_t │ │ │ │ -void showText(const String &text, Size font_size=20) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_E_d_i_t_E_l_e_m_e_n_t_T_y_p_e │ │ │ │ -int getEditElementType() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_h_a_n_d_l_e_C_o_m_p_o_s_i_t_e_M_e_s_s_a_g_e__ │ │ │ │ -void handleCompositeMessage_(CompositeMessage *cm) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_M_o_u_s_e_S_e_n_s_i_t_i_v_i_t_y │ │ │ │ -static BALL_DEPRECATED void setMouseSensitivity(float) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_6_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_p_r_i_n_t_S_c_e_n_e │ │ │ │ -void printScene() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_O_f_f_S_c_r_e_e_n_R_e_n_d_e_r_i_n_g │ │ │ │ -void setOffScreenRendering(bool enabled, Size factor) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_d_r_a_w_L_i_n_e │ │ │ │ -void drawLine(const Vector2 &a, const Vector2 &b, QPainter *painter=0) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_s_U_p_d_a_t_e_R_u_n_n_i_n_g │ │ │ │ -bool isUpdateRunning() const │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_4_7_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_E_d_i_t_E_l_e_m_e_n_t_T_y_p_e │ │ │ │ -void setEditElementType(int element_number) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_e_r_g_e │ │ │ │ -void merge(Composite *a1, Composite *a2) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_a_t_u_r_a_t_e_W_i_t_h_H_y_d_r_o_g_e_n_s │ │ │ │ -void saturateWithHydrogens() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_G_L_R_e_n_d_e_r_e_r │ │ │ │ -GLRenderer & getGLRenderer() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_8_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_o_r_e_V_i_e_w_P_o_i_n_t │ │ │ │ -void storeViewPoint() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_t_i_m_e__ │ │ │ │ -PreciseTime time_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_0_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_M_o_u_s_e_W_h_e_e_l_S_e_n_s_i_t_i_v_i_t_y │ │ │ │ -static BALL_DEPRECATED void setMouseWheelSensitivity(float) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_6_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_k_e_y_P_r_e_s_s_E_v_e_n_t │ │ │ │ -virtual void keyPressEvent(QKeyEvent *e) │ │ │ │ -Catch key events. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_b_u_t_t_o_n_R_e_l_e_a_s_e_E_v_e_n_t │ │ │ │ -virtual void buttonReleaseEvent(ButtonEvent *evt) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_h_a_n_d_l_e_C_o_n_t_r_o_l_S_e_l_e_c_t_i_o_n_M_e_s_s_a_g_e__ │ │ │ │ -void handleControlSelectionMessage_(ControlSelectionMessage *csm) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_C_l_i_c_k_e_d_I_t_e_m_s │ │ │ │ -void getClickedItems(const QPoint &p) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_o_p___a_n_i_m_a_t_i_o_n__ │ │ │ │ -bool stop_animation_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_9_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_a_g_e___s_e_t_t_i_n_g_s__ │ │ │ │ -StageSettings * stage_settings_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_8_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_C_u_r_r_e_n_t_A_t_o_m │ │ │ │ -void setCurrentAtom(Atom *atom) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_2_8_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_n_f_o___s_t_r_i_n_g__ │ │ │ │ -QString info_string_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_1_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_C_u_r_r_e_n_t_B_o_n_d │ │ │ │ -Bond * getCurrentBond() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_0_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_T_u_r_n_P_o_i_n_t │ │ │ │ -void setTurnPoint(const Vector3 &v) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_4_6_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_o_r_e_d___c_a_m_e_r_a__ │ │ │ │ -Camera stored_camera_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_7_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_R_u_b_b_e_r_B_a_n_d_G_e_o_m_e_t_r_y │ │ │ │ -void setRubberBandGeometry(const QRect &rect) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_x_p_o_r_t_N_e_x_t_P_O_V_R_a_y │ │ │ │ -void exportNextPOVRay() │ │ │ │ -Export to POVRay whithout showing file dialog. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_a_p_V_i_e_w_p_o_r_t_T_o_3_D │ │ │ │ -Vector3 mapViewportTo3D(const Vector2 &coords) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_a_g_e__ │ │ │ │ -Stage * stage_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_6_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_s_t_o_r_e_V_i_e_w_P_o_i_n_t │ │ │ │ -void restoreViewPoint() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_o_p_C_o_n_t_i_n_u_o_u_s_L_o_o_p │ │ │ │ -void stopContinuousLoop() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_D_e_f_a_u_l_t_L_i_g_h_t_i_n_g │ │ │ │ -void setDefaultLighting(bool update_GL=true) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_t_o_o_l_b_a_r___a_c_t_i_o_n_s___e_d_i_t___c_o_n_t_r_o_l_s__ │ │ │ │ -QList< QAction * > toolbar_actions_edit_controls_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_4_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_u_r_r_e_n_t___a_t_o_m__ │ │ │ │ -Atom * current_atom_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_3_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_t_o_o_l_b_a_r___a_c_t_i_o_n_s___v_i_e_w___c_o_n_t_r_o_l_s__ │ │ │ │ -QList< QAction * > toolbar_actions_view_controls_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_1_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_o_f_f_s_c_r_e_e_n___f_a_c_t_o_r__ │ │ │ │ -Size offscreen_factor_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_1_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_M_o_u_s_e_S_e_n_s_i_t_i_v_i_t_y │ │ │ │ -static BALL_DEPRECATED float getMouseSensitivity() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_6_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_o_n_l_y___h_i_g_h_l_i_g_h_t_e_d__ │ │ │ │ -static bool only_highlighted_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_4_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_a_d_L_i_g_h_t_s__ │ │ │ │ -void readLights_(const INIFile &inifile) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_u_s_e___p_r_e_v_i_e_w__ │ │ │ │ -bool use_preview_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_0_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_d_u_m_m_y_S_l_o_t │ │ │ │ -void dummySlot() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_6_7_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_V_R_M_L_N_u_m_b_e_r │ │ │ │ -static void setVRMLNumber(Position pos) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_4_2_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_l_e_a_r_R_e_c_o_r_d_e_d_A_n_i_m_a_t_i_o_n │ │ │ │ -void clearRecordedAnimation() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_S_t_a_g_e │ │ │ │ -const Stage * getStage() const │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_1_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_n_M_o_v_e_M_o_d_e │ │ │ │ -bool inMoveMode() const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_s_A_n_i_m_a_t_i_o_n_R_u_n_n_i_n_g │ │ │ │ -bool isAnimationRunning() const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_o_u_s_e_R_e_l_e_a_s_e_E_v_e_n_t │ │ │ │ -virtual void mouseReleaseEvent(QMouseEvent *qmouse_event) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_p_i_c_k_O_b_j_e_c_t_s │ │ │ │ -void pickObjects(const QPoint &pos1, const QPoint &pos2, list< GeometricObject │ │ │ │ -* > &objects) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_o_t_a_t_e_C_o_m_p_o_s_i_t_e_s │ │ │ │ -void rotateComposites(const std::list< Composite * > &composites, float │ │ │ │ -degree_right, float degree_up, float degree_clockwise=0) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_h_o_w___l_i_g_h_t___s_o_u_r_c_e_s__ │ │ │ │ -static bool show_light_sources_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_8_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_n_i_m_a_t_i_o_n___t_h_r_e_a_d__ │ │ │ │ -AnimationThread * animation_thread_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_9_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_n_i_m_a_t_e__ │ │ │ │ -void animate_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_a_i_n___r_e_n_d_e_r_e_r__ │ │ │ │ -Position main_renderer_ │ │ │ │ -The index of the renderer responsible for the main display. │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_2_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s │ │ │ │ -const MaterialSettings * getMaterialSettings() const │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_3_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_x_p_o_r_t_P_N_G │ │ │ │ -String exportPNG() │ │ │ │ -Export PNG image and return the filename. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_u_p_d_a_t_e_G_L │ │ │ │ -void updateGL() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_A_n_i_m_a_t_i_o_n_S_m_o_o_t_h_n_e_s_s │ │ │ │ -static float getAnimationSmoothness() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_4_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_r_e_a_t_e_C_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m__ │ │ │ │ -void createCoordinateSystem_(bool at_origin) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_P_r_e_v_i_e_w │ │ │ │ -void setPreview(bool state) │ │ │ │ -Enable or disable model previews e.g. while rotating. │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_5_5_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_a_r_t_C_o_n_t_i_n_u_o_u_s_L_o_o_p │ │ │ │ -void startContinuousLoop() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_n_i_t_i_a_l_i_z_e_M_e_m_b_e_r_s__ │ │ │ │ -void initializeMembers_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_C_u_r_r_e_n_t_A_t_o_m │ │ │ │ -Atom * getCurrentAtom() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_2_8_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_a_p_t_u_r_e_C_a_m_e_r_a │ │ │ │ -void captureCamera() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_h_a_n_d_l_e_S_c_e_n_e_M_e_s_s_a_g_e__ │ │ │ │ -void handleSceneMessage_(SceneMessage *sm) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_u_s_e_V_e_r_t_e_x_B_u_f_f_e_r_s │ │ │ │ -bool useVertexBuffers() const │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_5_5_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_o_v_e_C_o_m_p_o_s_i_t_e_s │ │ │ │ -void moveComposites(const std::list< Composite * > &composites, Vector3 v) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_p_i_c_k_O_b_j_e_c_t_s │ │ │ │ -void pickObjects(const QPoint &pos, list< GeometricObject * > &objects) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_n_i_m_a_t_i_o_n___p_o_i_n_t_s__ │ │ │ │ -std::list< Camera > animation_points_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_9_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_S_c_r_e_e_n_P_o_s_i_t_i_o_n__ │ │ │ │ -TVector2< float > getScreenPosition_(Vector3 vec) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_G_L_R_e_n_d_e_r_e_r │ │ │ │ -void setGLRenderer(GLRenderer &renderer) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_u_p_V_i_e_w_V_o_l_u_m_e │ │ │ │ -void setupViewVolume() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_o_p_A_n_i_m_a_t_i_o_n │ │ │ │ -void stopAnimation() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_o_u_s_e_P_r_e_s_s_E_v_e_n_t │ │ │ │ -virtual void mousePressEvent(QMouseEvent *qmouse_event) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_W_i_n_d_o_w_T_y_p_e │ │ │ │ -WindowType │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_1_6_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_L_E_F_T___E_Y_E___W_I_N_D_O_W │ │ │ │ -@ LEFT_EYE_WINDOW │ │ │ │ -Window into which left eye should be rendered. Indicates same window as │ │ │ │ -CONTROL_WINDOW if no stereo i... │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_1_7_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_F_o_r_m_a_l_C_h_a_r_g_e__ │ │ │ │ -void setFormalCharge_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_o_u_s_e_M_o_v_e_E_v_e_n_t │ │ │ │ -virtual void mouseMoveEvent(QMouseEvent *qmouse_event) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_o_l_d___t_r_a_c_k_o_r_i_g_i_n__ │ │ │ │ -Vector3 old_trackorigin_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_6_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_p_a_i_n_t_G_L │ │ │ │ -virtual void paintGL() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_a_r_t_A_n_i_m_a_t_i_o_n │ │ │ │ -void startAnimation() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_p_i_c_k_P_a_r_e_n_t__ │ │ │ │ -void pickParent_(QPoint p) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_s_e_t_T_r_a_c_k_i_n_g │ │ │ │ -void resetTracking() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_4_8_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_w_h_e_e_l_E_v_e_n_t │ │ │ │ -virtual void wheelEvent(QWheelEvent *qmouse_event) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_d_d_T_o_o_l_B_a_r_E_n_t_r_i_e_s │ │ │ │ -virtual void addToolBarEntries(QToolBar *tb) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_h_o_w_L_i_g_h_t_S_o_u_r_c_e_s_E_n_a_b_l_e_d │ │ │ │ -static bool showLightSourcesEnabled() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_7_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_p_r_e_p_a_r_e_G_r_i_d_T_e_x_t_u_r_e_s │ │ │ │ -Position prepareGridTextures(const RegularData3D &grid, const ColorMap &map) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_D_o_w_n_s_a_m_p_l_i_n_g_F_a_c_t_o_r │ │ │ │ -void setDownsamplingFactor(float ds_factor) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_a_n_c_e_l___a_n_i_m_a_t_i_o_n___a_c_t_i_o_n__ │ │ │ │ -QAction * cancel_animation_action_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_5_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_o_v_e_r_l_a_y__ │ │ │ │ -QPicture overlay_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_2_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_d_e_s_e_l_e_c_t │ │ │ │ -void deselect(bool update=true) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_e_r_e_o___r_i_g_h_t___e_y_e__ │ │ │ │ -Index stereo_right_eye_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_2_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_~_S_c_e_n_e │ │ │ │ -virtual ~Scene() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_x_p_o_r_t_P_O_V_R_a_y │ │ │ │ -void exportPOVRay() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_x_i_t_S_t_e_r_e_o │ │ │ │ -void exitStereo() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_r_e_a_t_e_F_P_S_I_n_f_o__ │ │ │ │ -String createFPSInfo_(Renderer *renderer) │ │ │ │ -Estimate current fps and convert into a string. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_n_t_e_r_P_i_c_k_i_n_g_M_o_d_e │ │ │ │ -void enterPickingMode() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_u_p_d_a_t_e_M_a_t_e_r_i_a_l_F_o_r_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -void updateMaterialForRepresentation(Representation *rep, const Stage::Material │ │ │ │ -&new_material) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_l_a_s_t___s_t_a_t_e__ │ │ │ │ -QByteArray last_state_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_0_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_I_n_t_e_r_a_c_t_i_o_n_M_o_d_e_M_a_n_a_g_e_r │ │ │ │ -InteractionModeManager & getInteractionModeManager() │ │ │ │ -Returns a reference to the Scene's interaction mode manager. │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_6_4_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_s_V_a_l_i_d │ │ │ │ -virtual bool isValid() const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_s_e_t_C_a_m_e_r_a__ │ │ │ │ -virtual void resetCamera_() │ │ │ │ -Reset the camera to standard values. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_b_u_t_t_o_n_P_r_e_s_s_E_v_e_n_t │ │ │ │ -virtual void buttonPressEvent(ButtonEvent *evt) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_n_t_e_r_D_u_a_l_S_t_e_r_e_o │ │ │ │ -void enterDualStereo() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_t_o_o_l_b_a_r___e_d_i_t___c_o_n_t_r_o_l_s__ │ │ │ │ -QToolBar * toolbar_edit_controls_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_1_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_y_s_t_e_m___o_r_i_g_i_n__ │ │ │ │ -Vector3 system_origin_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_6_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_n_i_m_a_t_i_o_n___e_x_p_o_r_t___P_N_G___a_c_t_i_o_n__ │ │ │ │ -QAction * animation_export_PNG_action_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_5_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_s_i_z_e_E_v_e_n_t │ │ │ │ -virtual void resizeEvent(QResizeEvent *event) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_w_i_t_c_h_T_o_L_a_s_t_M_o_d_e │ │ │ │ -void switchToLastMode() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_n_t_e_r_S_t_e_r_e_o │ │ │ │ -void enterStereo() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_t_o_m_i_c___n_u_m_b_e_r__ │ │ │ │ -int atomic_number_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_4_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_S_t_a_g_e │ │ │ │ -Stage * getStage() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_1_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_R_u_b_b_e_r_B_a_n_d_V_i_s_i_b_l_e │ │ │ │ -void setRubberBandVisible(bool show) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_p_a_i_n_t_E_v_e_n_t │ │ │ │ -virtual void paintEvent(QPaintEvent *e) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_w_i_t_c_h___g_r_i_d__ │ │ │ │ -QAction * switch_grid_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_5_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_d_r_a_w_L_i_n_e │ │ │ │ -void drawLine(const QPointF &a, const QPointF &b, QPainter *painter=0) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_a_t_e_r_i_a_l___s_e_t_t_i_n_g_s__ │ │ │ │ -MaterialSettings * material_settings_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_8_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_o_p_t_i_m_i_z_e_S_t_r_u_c_t_u_r_e │ │ │ │ -void optimizeStructure() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_a_p_V_i_e_w_p_o_r_t_T_o_3_D │ │ │ │ -Vector3 mapViewportTo3D(int x, int y) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_s_R_e_c_o_r_d_i_n_g │ │ │ │ -bool isRecording() const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_n_f_o___p_o_i_n_t__ │ │ │ │ -QPoint info_point_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_0_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_e_r_e_o___c_a_m_e_r_a__ │ │ │ │ -Camera stereo_camera_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_7_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_c_t_i_v_e___s_t_e_r_e_o___a_c_t_i_o_n__ │ │ │ │ -QAction * active_stereo_action_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_5_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_c_t_i_v_a_t_e_d_O_r_d_e_r_I_t_e_m__ │ │ │ │ -void activatedOrderItem_(QAction *action) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_r_e_a_t_e_C_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m_A_t_O_r_i_g_i_n │ │ │ │ -void createCoordinateSystemAtOrigin() │ │ │ │ -Create an coordinate system at origin. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_u_n_d_o__ │ │ │ │ -vector< EditOperation > undo_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_4_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_d_o_w_n_s_a_m_p_l_i_n_g___f_a_c_t_o_r__ │ │ │ │ -static float downsampling_factor_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_8_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_n_d_e_r_e_r_s__ │ │ │ │ -std::vector< boost::shared_ptr< RenderSetup > > renderers_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_7_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_n_t_e_r_D_u_a_l_S_t_e_r_e_o_D_i_f_f_e_r_e_n_t_D_i_s_p_l_a_y_s │ │ │ │ -void enterDualStereoDifferentDisplays() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_C_o_n_t_a_i_n_e_r_s │ │ │ │ -std::list< AtomContainer * > getContainers() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_n_e_w___m_o_l_e_c_u_l_e___a_c_t_i_o_n__ │ │ │ │ -QAction * new_molecule_action_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_3_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_r_e_a_t_e_N_e_w_M_o_l_e_c_u_l_e │ │ │ │ -void createNewMolecule() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_l_e_c_t_i_o_n_P_r_e_s_s_e_d_M_o_v_e_d__ │ │ │ │ -void selectionPressedMoved_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_h_o_w_E_x_p_o_r_t_P_N_G_D_i_a_l_o_g │ │ │ │ -void showExportPNGDialog() │ │ │ │ -show an dialog to save an PNG file to │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_e_r_e_o___l_e_f_t___e_y_e__ │ │ │ │ -Index stereo_left_eye_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_2_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_x_p_o_r_t_P_N_G │ │ │ │ -bool exportPNG(const String &filename) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_E_l_e_m_e_n_t_C_u_r_s_o_r │ │ │ │ -void setElementCursor(int number) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_h_a_n_d_l_e_R_e_n_d_e_r_T_o_B_u_f_f_e_r_F_i_n_i_s_h_e_d_E_v_e_n_t__ │ │ │ │ -virtual void handleRenderToBufferFinishedEvent_(RenderToBufferFinishedEvent │ │ │ │ -*evt) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_h_a_n_g_e_B_o_n_d_O_r_d_e_r │ │ │ │ -void changeBondOrder() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_n_e_w_E_d_i_t_O_p_e_r_a_t_i_o_n │ │ │ │ -void newEditOperation(EditOperation &eo) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_V_i_e_w_P_o_i_n_t__ │ │ │ │ -virtual void setViewPoint_() │ │ │ │ -Set the viewpoint. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_l_e_a_r │ │ │ │ -virtual void clear() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_o_l_d___t_r_a_c_k_r_o_t_a_t_i_o_n__ │ │ │ │ -Quaternion old_trackrotation_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_6_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_w_r_i_t_e_L_i_g_h_t_s__ │ │ │ │ -void writeLights_(INIFile &inifile) const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_n_d_e_r_T_e_x_t__ │ │ │ │ -void renderText_(QPointF const &point, QString const &text, QPaintDevice │ │ │ │ -*current_dev) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_f_p_s__ │ │ │ │ -list< float > fps_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_0_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_o_v_e │ │ │ │ -void move(Vector3 v) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_u_s_t_o_m_E_v_e_n_t │ │ │ │ -virtual void customEvent(QEvent *evt) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_h_o_w_E_x_p_o_r_t_V_R_M_L_D_i_a_l_o_g │ │ │ │ -void showExportVRMLDialog() │ │ │ │ -opens the VIEW/DIALOGS/GeometryExportDialog for vrml and stl export │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_d_u_m_p │ │ │ │ -virtual void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_W_i_d_g_e_t_V_i_s_i_b_l_e │ │ │ │ -virtual void setWidgetVisible(bool state) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_l_e_c_t_i_o_n_P_r_e_s_s_e_d__ │ │ │ │ -void selectionPressed_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_n_i_t_i_a_l_i_z_e_W_i_d_g_e_t │ │ │ │ -virtual void initializeWidget(MainControl &main_control) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_u_p_d_a_t_e___r_u_n_n_i_n_g__ │ │ │ │ -bool update_running_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_6_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_M_o_u_s_e_W_h_e_e_l_S_e_n_s_i_t_i_v_i_t_y │ │ │ │ -static BALL_DEPRECATED float getMouseWheelSensitivity() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_7_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_o_m_p_u_t_e_B_o_n_d_O_r_d_e_r_s │ │ │ │ -void computeBondOrders() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_t_o_g_g_l_e_C_o_n_t_i_n_u_o_u_s_L_o_o_p │ │ │ │ -void toggleContinuousLoop() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_u_r_r_e_n_t___b_o_n_d__ │ │ │ │ -Bond * current_bond_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_3_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_n_t_e_r_A_c_t_i_v_e_S_t_e_r_e_o │ │ │ │ -void enterActiveStereo() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_h_o_w_C_o_n_t_e_x_t_M_e_n_u │ │ │ │ -void showContextMenu(QPoint pos) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_C_a_m_e_r_a │ │ │ │ -void setCamera(const Camera &camera) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_n_o_t_i_f_y │ │ │ │ -void notify(Message *msg) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_2_8_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_o_f_f_s_c_r_e_e_n___r_e_n_d_e_r_i_n_g__ │ │ │ │ -static bool offscreen_rendering_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_1_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_d_e_f_a_u_l_t___f_o_n_t__ │ │ │ │ -QFont default_font_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_2_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_C_u_r_s_o_r │ │ │ │ -void setCursor(String c) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_t_e_r_e_o_B_u_f_f_e_r_S_u_p_p_o_r_t_T_e_s_t │ │ │ │ -static bool stereoBufferSupportTest() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_F_P_S_E_n_a_b_l_e_d │ │ │ │ -void setFPSEnabled(bool state) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_4_7_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_x_p_o_r_t_S_c_e_n_e │ │ │ │ -virtual bool exportScene(Renderer &er) const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_o_d_e___m_a_n_a_g_e_r__ │ │ │ │ -InteractionModeManager mode_manager_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_3_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_w_i_t_c_h_R_e_n_d_e_r_e_r │ │ │ │ -void switchRenderer(RenderSetup::RendererType new_type) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_t_o_o_l_b_a_r___v_i_e_w___c_o_n_t_r_o_l_s__ │ │ │ │ -QToolBar * toolbar_view_controls_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_1_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_o_t_a_t_e │ │ │ │ -void rotate(float degree_right, float degree_up) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_S_t_a_g_e_S_e_t_t_i_n_g_s │ │ │ │ -StageSettings * getStageSettings() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_2_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_A_n_i_m_a_t_i_o_n_P_o_i_n_t_s │ │ │ │ -std::list< Camera > & getAnimationPoints() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_4_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_b_o_n_d_o_r_d_e_r_s___a_c_t_i_o_n__ │ │ │ │ -QAction * bondorders_action_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_3_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_t_r_a_n_s_f_o_r_m_a_t_i_o_n_E_v_e_n_t_6_D │ │ │ │ -virtual void transformationEvent6D(TransformationEvent6D *evt) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_S_t_a_g_e_S_e_t_t_i_n_g_s │ │ │ │ -const StageSettings * getStageSettings() const │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_2_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_h_o_w_V_i_e_w_P_o_i_n_t__ │ │ │ │ -virtual void showViewPoint_() │ │ │ │ -Show the viewpoint and the look at point in the statusline of the mainwidget. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_z_o_o_m_S_y_s_t_e_m__ │ │ │ │ -void zoomSystem_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_u_p_E_n_v_i_r_o_n_m_e_n_t_M_a_p │ │ │ │ -void setupEnvironmentMap(const QImage &image) │ │ │ │ -Try to setup an environment map for all renderers that support it. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_a_p_3_D_T_o_V_i_e_w_p_o_r_t │ │ │ │ -Vector2 map3DToViewport(const Vector3 &coords) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_o_u_s_e_D_o_u_b_l_e_C_l_i_c_k_E_v_e_n_t │ │ │ │ -virtual void mouseDoubleClickEvent(QMouseEvent *e) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_n_d_e_r_G_r_i_d__ │ │ │ │ -void renderGrid_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_n_i_t_i_a_l_i_z_e_P_r_e_f_e_r_e_n_c_e_s_T_a_b │ │ │ │ -void initializePreferencesTab(Preferences &preferences) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_A_n_i_m_a_t_i_o_n_S_m_o_o_t_h_n_e_s_s │ │ │ │ -static void setAnimationSmoothness(float value) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_4_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_l_i_g_h_t_s_U_p_d_a_t_e_d │ │ │ │ -void lightsUpdated(bool redraw=false) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_n_i_t │ │ │ │ -virtual void init() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_o_t_i_o_n_T_r_a_c_k_i_n_g_E_v_e_n_t │ │ │ │ -virtual void motionTrackingEvent(MotionTrackingEvent *evt) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_S_c_e_n_e │ │ │ │ -Scene(QWidget *parent_widget=0, const char *name=NULL, Qt::WindowFlags │ │ │ │ -w_flags=0) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_v_e_n_t_F_i_l_t_e_r │ │ │ │ -virtual bool eventFilter(QObject *object, QEvent *event) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_h_o_w_I_n_f_o_s │ │ │ │ -void showInfos() │ │ │ │ -Popup informations for object under mouse cursor. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_r_e_a_t_e___c_o_o_r_d_i_n_a_t_e___s_y_s_t_e_m__ │ │ │ │ -QMenu * create_coordinate_system_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_5_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_t_r_a_c_k_i_n_g___i_n_i_t_i_a_l_i_z_e_d__ │ │ │ │ -bool tracking_initialized_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_6_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_u_p_d_a_t_e_A_l_l_M_a_t_e_r_i_a_l_s │ │ │ │ -void updateAllMaterials() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_l___r_e_n_d_e_r_e_r__ │ │ │ │ -GLRenderer * gl_renderer_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_7_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_h_a_n_d_l_e_D_a_t_a_s_e_t_M_e_s_s_a_g_e__ │ │ │ │ -void handleDatasetMessage_(DatasetMessage *dm) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_w_a_n_t___t_o___u_s_e___v_e_r_t_e_x___b_u_f_f_e_r__ │ │ │ │ -bool want_to_use_vertex_buffer_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_0_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_p_r_o_j_e_c_t_i_o_n_M_o_d_e_C_h_a_n_g_e_d │ │ │ │ -virtual void projectionModeChanged() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_w_r_i_t_e_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ -virtual void writePreferences(INIFile &inifile) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_h_a_s___o_v_e_r_l_a_y__ │ │ │ │ -bool has_overlay_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_2_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_F_u_l_l_S_c_r_e_e_n │ │ │ │ -void setFullScreen(bool state) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_o_t_a_t_e_C_l_o_c_k_w_i_s_e │ │ │ │ -void rotateClockwise(float degree) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_D_o_w_n_s_a_m_p_l_i_n_g_F_a_c_t_o_r │ │ │ │ -float getDownsamplingFactor() const │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_5_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_i_n_s_e_r_t__ │ │ │ │ -void insert_(int x_, int y_, PDBAtom &atom_) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_B_o_n_d_O_r_d_e_r_S_t_r_i_n_g__ │ │ │ │ -String getBondOrderString_(Index order) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_I_n_f_o │ │ │ │ -void setInfo(const QString &info_string) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_M_a_t_e_r_i_a_l_S_e_t_t_i_n_g_s │ │ │ │ -MaterialSettings * getMaterialSettings() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_2_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_v_r_m_l___n_r__ │ │ │ │ -static Position vrml_nr_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_9_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_o_n_N_o_t_i_f_y │ │ │ │ -virtual void onNotify(Message *message) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_n_i_m_a_t_i_o_n___s_m_o_o_t_h_n_e_s_s__ │ │ │ │ -static float animation_smoothness_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_8_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_h_e_c_k_M_e_n_u │ │ │ │ -virtual void checkMenu(MainControl &main_control) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_f_i_n_a_l_i_z_e_P_r_e_f_e_r_e_n_c_e_s_T_a_b │ │ │ │ -void finalizePreferencesTab(Preferences &preferences) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_C_u_r_r_e_n_t_B_o_n_d │ │ │ │ -void setCurrentBond(Bond *b) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_3_0_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_e_t_S_c_r_e_e_n_S_h_o_t_N_u_m_b_e_r │ │ │ │ -static void setScreenShotNumber(Position pos) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_4_2_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_g_e_t_T_u_r_n_P_o_i_n_t │ │ │ │ -const Vector3 & getTurnPoint() const │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_4_6_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_p_p_l_y_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ -virtual void applyPreferences() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_f_o_n_t___s_i_z_e__ │ │ │ │ -Size font_size_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_1_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_a_d_d_G_l_W_i_n_d_o_w │ │ │ │ -void addGlWindow() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_e_d_i_t___s_e_t_t_i_n_g_s__ │ │ │ │ -EditSettings * edit_settings_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_7_4_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_u_s_e_P_r_e_v_i_e_w │ │ │ │ -bool usePreview() const │ │ │ │ -Returns the state of the preview mode. │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_5_5_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_s_c_r_e_e_n_s_h_o_t___n_r__ │ │ │ │ -static Position screenshot_nr_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_9_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_m_a_i_n___d_i_s_p_l_a_y__ │ │ │ │ -GLRenderWindow * main_display_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_1_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_r_e_a_t_e_M_o_l_e_c_u_l_e__ │ │ │ │ -void createMolecule_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_d_r_o_p_E_v_e_n_t │ │ │ │ -virtual void dropEvent(QDropEvent *e) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_e_s_e_t_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s_F_o_r_R_e_n_d_e_r_e_r__ │ │ │ │ -virtual void resetRepresentationsForRenderer_(RenderSetup &rs) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_r_o_t_a_t_e_S_y_s_t_e_m_C_l_o_c_k_w_i_s_e__ │ │ │ │ -void rotateSystemClockwise_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_c_r_e_a_t_e_C_o_o_r_d_i_n_a_t_e_S_y_s_t_e_m │ │ │ │ -void createCoordinateSystem() │ │ │ │ -Create an coordinate system at current position. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_h_a_n_d_l_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n_M_e_s_s_a_g_e__ │ │ │ │ -void handleRepresentationMessage_(RepresentationMessage *rm) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_f_e_t_c_h_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ -virtual void fetchPreferences(INIFile &inifile) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e_:_:_l_i_g_h_t___s_e_t_t_i_n_g_s__ │ │ │ │ -LightSettings * light_settings_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_8_8_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_n_i_m_a_t_i_o_n_T_h_r_e_a_d │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_3_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_n_i_m_a_t_i_o_n_T_h_r_e_a_d_:_:_m_y_S_l_e_e_p │ │ │ │ -void mySleep(Size msec) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_n_i_m_a_t_i_o_n_T_h_r_e_a_d_:_:_g_e_t_S_c_e_n_e │ │ │ │ -Scene * getScene() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_5_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_n_i_m_a_t_i_o_n_T_h_r_e_a_d_:_:_s_e_t_S_c_e_n_e │ │ │ │ -void setScene(Scene *scene) │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_5_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_n_i_m_a_t_i_o_n_T_h_r_e_a_d_:_:_r_u_n │ │ │ │ -virtual void run() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_4_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_n_i_m_a_t_i_o_n_T_h_r_e_a_d_:_:_s_c_e_n_e__ │ │ │ │ -Scene * scene_ │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_5_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_n_i_m_a_t_i_o_n_T_h_r_e_a_d_:_:_A_n_i_m_a_t_i_o_n_T_h_r_e_a_d │ │ │ │ -AnimationThread() │ │ │ │ -DDeeffiinniittiioonn _s_c_e_n_e_._h_:_9_4_1 │ │ │ │ -_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_R_a_d_i_a_l_D_i_s_t_r_i_b_u_t_i_o_n_F_u_n_c_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _r_a_d_i_a_l_D_i_s_t_r_i_b_u_t_i_o_n_F_u_n_c_t_i_o_n_._h_:_2_3 │ │ │ │ +_B_A_L_L_:_:_R_D_F_P_a_r_a_m_e_t_e_r │ │ │ │ +DDeeffiinniittiioonn _R_D_F_P_a_r_a_m_e_t_e_r_._h_:_3_3 │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_Q_O_b_j_e_c_t │ │ │ │ -_Q_T_h_r_e_a_d │ │ │ │ -_Q_W_i_d_g_e_t │ │ │ │ -_Q_E_v_e_n_t │ │ │ │ -_Q_P_a_i_n_t_D_e_v_i_c_e │ │ │ │ -_Q_M_o_u_s_e_E_v_e_n_t │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_B_A_L_L___D_E_P_R_E_C_A_T_E_D │ │ │ │ -#define BALL_DEPRECATED │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_6_4 │ │ │ │ -_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ -#define BALL_VIEW_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d89/a08006.html │ │ │ @@ -80,15 +80,15 @@ │ │ │
    BALL::VIEW::MDSimulationThread Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │

    Thread for MDSimulation. │ │ │ More...

    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/threads.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/threads.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::MDSimulationThread:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::SimulationThread │ │ │ @@ -168,15 +168,15 @@ │ │ │   │ │ │ void waitForUpdateOfRepresentations_ () │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Thread for MDSimulation.

    │ │ │ │ │ │ -

    Definition at line 244 of file threads.h.

    │ │ │ +

    Definition at line 244 of file threads.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ MDSimulationThread()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -288,15 +288,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 262 of file threads.h.

    │ │ │ +

    Definition at line 262 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ setSaveImages()

    │ │ │ │ │ │
    │ │ │ @@ -316,15 +316,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 265 of file threads.h.

    │ │ │ +

    Definition at line 265 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ md_

    │ │ │ │ │ │ @@ -341,15 +341,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 268 of file threads.h.

    │ │ │ +

    Definition at line 268 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ save_images_

    │ │ │ │ │ │
    │ │ │ @@ -365,15 +365,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 270 of file threads.h.

    │ │ │ +

    Definition at line 270 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ steps_

    │ │ │ │ │ │
    │ │ │ @@ -389,15 +389,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 269 of file threads.h.

    │ │ │ +

    Definition at line 269 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d8a/a07922.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::VIEW::ModularWidget Class Reference
    Visualisation » Kernel » Widget connectivity and message queuing
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/modularWidget.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/modularWidget.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::ModularWidget:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::Embeddable │ │ │ @@ -130,17 +130,17 @@ │ │ │ virtual void clear () │ │ │   │ │ │
    Management of menu and toolbar entries
    │ │ │ virtual void checkMenu (MainControl &main_control) │ │ │   │ │ │ QAction * insertMenuEntry (Position parent_id, const QString &name, const QObject *receiver=0, const char *slot=0, const String &description="", QKeySequence accel=QKeySequence(), const QString &menu_hint=QString(""), UIOperationMode::OperationMode minimal_mode=UIOperationMode::MODE_ALL) │ │ │   │ │ │ -BALL_DEPRECATED void setMenuHelp (QAction *, const String &) │ │ │ +BALL_DEPRECATED void setMenuHelp (QAction *, const String &) │ │ │   │ │ │ -virtual BALL_DEPRECATED void registerForHelpSystem (const QObject *, const String &) │ │ │ +virtual BALL_DEPRECATED void registerForHelpSystem (const QObject *, const String &) │ │ │   │ │ │ virtual void addToolBarEntries (QToolBar *main_tb) │ │ │   │ │ │ void setIcon (QAction *action, const String &filename, bool add_to_main_toolbar=true) │ │ │   │ │ │
    Preferences handling
    │ │ │ virtual void initializePreferencesTab (Preferences &preferences) │ │ │ @@ -217,15 +217,15 @@ │ │ │   │ │ │ QList< QAction * > main_toolbar_actions_ │ │ │   │ │ │ virtual void dump (std::ostream &s=std::cout, Size depth=0) const │ │ │   │ │ │ void setWorkingDirFromFilename_ (String filename) │ │ │   │ │ │ -virtual BALL_DEPRECATED void showHelp (const String &) │ │ │ +virtual BALL_DEPRECATED void showHelp (const String &) │ │ │   │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -264,15 +264,15 @@ │ │ │

    ModularWidget is a base class for widely independent widget that realize one feature domain. The VIEW framework provides a simple mechanism for Rapid Application Prototyping based on modular widgets. Using these modular widgets and the MainControl class (or more precisely, classes derived from MainControl) applications can be developed in a plug&play style. Inserting an instance of one of these widgets automatically creates the required menus and menu entries in the menubar of the main window, sets up the required connections, and registers the class instance for usage from the embedded Python interpreter (if desired).
    │ │ │ When implementing classes derived from ModularWidget and access to the class from Python is desired, please remember to include the BALL_EMBEDDABLE macro in the public section of your class declaration. Also make sure that the QT class you derive from (e.g. QWidget) is the first base class and ModularWidget second.
    │ │ │
    │ │ │ Remember: A ModularWidget is not notified by the Messages it sends itself!

    See also
    MainControl
    │ │ │
    │ │ │ Embeddable
    │ │ │ │ │ │ -

    Definition at line 60 of file modularWidget.h.

    │ │ │ +

    Definition at line 60 of file modularWidget.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ModularWidget() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Registering

    virtual void initializeWidget (MainControl &main_control)
     
    virtual void finalizeWidget (MainControl &main_control)
     
    │ │ │ @@ -401,15 +401,15 @@ │ │ │
    │ │ │ finalizePreferencesTab
    │ │ │
    │ │ │ applyPreferencesTab
    │ │ │ │ │ │

    Reimplemented in BALL::VIEW::DisplayProperties, BALL::VIEW::ServerWidget, BALL::VIEW::PyWidget, and BALL::VIEW::Scene.

    │ │ │ │ │ │ -

    Definition at line 223 of file modularWidget.h.

    │ │ │ +

    Definition at line 223 of file modularWidget.h.

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    ◆ canHandle()

    │ │ │ │ │ │
    │ │ │ @@ -440,15 +440,15 @@ │ │ │ │ │ │
    See also
    openFile
    │ │ │
    │ │ │ MainControl::openFile
    │ │ │ │ │ │

    Reimplemented in BALL::VIEW::MolecularFileDialog, BALL::VIEW::DatasetControl, BALL::VIEW::PyWidget, and BALL::VIEW::TestFramework.

    │ │ │ │ │ │ -

    Definition at line 140 of file modularWidget.h.

    │ │ │ +

    Definition at line 140 of file modularWidget.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ checkMenu()

    │ │ │ │ │ │
    │ │ │ @@ -534,15 +534,15 @@ │ │ │ │ │ │
    │ │ │
    │ │ │

    Explicit destructor. Calls clear

    See also
    clear
    │ │ │ │ │ │

    Reimplemented from BALL::VIEW::ConnectionObject.

    │ │ │ │ │ │ -

    Definition at line 94 of file modularWidget.h.

    │ │ │ +

    Definition at line 94 of file modularWidget.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ dump()

    │ │ │ │ │ │
    │ │ │ @@ -924,29 +924,29 @@ │ │ │
    │ │ │

    Tell this ModularWidget to open a given file.

    See also
    canHandle
    │ │ │
    │ │ │ MainControl::openFile
    │ │ │ │ │ │

    Reimplemented in BALL::VIEW::MolecularFileDialog, BALL::VIEW::DatasetControl, BALL::VIEW::PyWidget, and BALL::VIEW::TestFramework.

    │ │ │ │ │ │ -

    Definition at line 146 of file modularWidget.h.

    │ │ │ +

    Definition at line 146 of file modularWidget.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ registerForHelpSystem()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -1054,15 +1054,15 @@ │ │ │ │ │ │

    ◆ setMenuHelp()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    virtual BALL_DEPRECATED void BALL::VIEW::ModularWidget::registerForHelpSystem virtual BALL_DEPRECATED void BALL::VIEW::ModularWidget::registerForHelpSystem (const QObject * ,
    │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -1200,15 +1200,15 @@ │ │ │
    │ │ │
    │ │ │
    BALL_DEPRECATED void BALL::VIEW::ModularWidget::setMenuHelp BALL_DEPRECATED void BALL::VIEW::ModularWidget::setMenuHelp (QAction * ,
    │ │ │ │ │ │ │ │ │ @@ -1294,15 +1294,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    virtual BALL_DEPRECATED void BALL::VIEW::ModularWidget::showHelp virtual BALL_DEPRECATED void BALL::VIEW::ModularWidget::showHelp (const String & )
    │ │ │     		│ │ │ protected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 315 of file modularWidget.h.

    │ │ │ +

    Definition at line 315 of file modularWidget.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ main_toolbar_actions_

    │ │ │ │ │ │
    │ │ │ @@ -1318,15 +1318,15 @@ │ │ │
    		│ │ │ protected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 317 of file modularWidget.h.

    │ │ │ +

    Definition at line 317 of file modularWidget.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ show_window_enty_

    │ │ │ │ │ │
    │ │ │ @@ -1342,15 +1342,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 312 of file modularWidget.h.

    │ │ │ +

    Definition at line 312 of file modularWidget.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ window_menu_entry_

    │ │ │ │ │ │
    │ │ │ @@ -1366,15 +1366,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 309 of file modularWidget.h.

    │ │ │ +

    Definition at line 309 of file modularWidget.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d8c/a07958.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members
    │ │ │
    BALL::VIEW::SnapshotManagerInterface Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/snapshotManagerInterface.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/snapshotManagerInterface.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -103,15 +103,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

     SnapshotManagerInterface ()
     
    void setup ()
     
    std::vector< boost::shared_ptr< SnapShotManager > > managers_
     
    std::deque< String > names_
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 15 of file snapshotManagerInterface.h.

    │ │ │ +

    Definition at line 15 of file snapshotManagerInterface.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ SnapshotManagerInterface()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -225,15 +225,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 27 of file snapshotManagerInterface.h.

    │ │ │ +

    Definition at line 27 of file snapshotManagerInterface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ names_

    │ │ │ │ │ │
    │ │ │ @@ -249,15 +249,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 28 of file snapshotManagerInterface.h.

    │ │ │ +

    Definition at line 28 of file snapshotManagerInterface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ num_snapshots_

    │ │ │ │ │ │
    │ │ │ @@ -273,15 +273,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 26 of file snapshotManagerInterface.h.

    │ │ │ +

    Definition at line 26 of file snapshotManagerInterface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d92/a07918.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Member Functions | │ │ │ List of all members
    │ │ │
    BALL::VIEW::RotateMode Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/MODES/rotateMode.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/MODES/rotateMode.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::RotateMode:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::InteractionMode │ │ │ @@ -187,15 +187,15 @@ │ │ │ QAction * main_action_ │ │ │   │ │ │ bool is_current_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 11 of file rotateMode.h.

    │ │ │ +

    Definition at line 11 of file rotateMode.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ RotateMode()

    │ │ │ │ │ │
    │ │ │
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    │ │ │
    │ │ │ │ │ │

    Implements BALL::VIEW::InteractionMode.

    │ │ │ │ │ │ -

    Definition at line 19 of file rotateMode.h.

    │ │ │ +

    Definition at line 19 of file rotateMode.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ mouseDoubleClickEvent()

    │ │ │ │ │ │
    │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d9b/a01379.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: shiftedLVMM.h File Reference │ │ │ +BALL: geneticIndividual.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,36 +65,32 @@ │ │ │
    │ │ │
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    │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    shiftedLVMM.h File Reference
    │ │ │ +
    geneticIndividual.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/MOLMEC/MINIMIZATION/energyMinimizer.h>
    │ │ │ -#include <BALL/MOLMEC/MINIMIZATION/lineSearch.h>
    │ │ │ +
    #include <vector>
    │ │ │ +#include <BALL/DOCKING/GENETICDOCK/genes.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::ShiftedLVMMMinimizer
     
    struct  BALL::ShiftedLVMMMinimizer::Option
     
    struct  BALL::ShiftedLVMMMinimizer::Default
    class  BALL::GeneticIndividual
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ ├── html2text {} │ │ │ │ @@ -1,25 +1,21 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _M_O_L_M_E_C │ │ │ │ - * _M_I_N_I_M_I_Z_A_T_I_O_N │ │ │ │ + * _D_O_C_K_I_N_G │ │ │ │ + * _G_E_N_E_T_I_C_D_O_C_K │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -shiftedLVMM.h File Reference │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_l_i_n_e_S_e_a_r_c_h_._h> │ │ │ │ +geneticIndividual.h File Reference │ │ │ │ +#include │ │ │ │ +#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_g_e_n_e_s_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ - class   _B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t │ │ │ │ +class   _B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d9b/a01379_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: shiftedLVMM.h Source File │ │ │ +BALL: geneticIndividual.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,237 +70,107 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    shiftedLVMM.h
    │ │ │ +
    geneticIndividual.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ -
    2// vi: set ts=2:
    │ │ │ -
    3//
    │ │ │ -
    4// $Id: shiftedLVMM.h,v 1.1.4.6 2007/08/07 09:12:35 aleru Exp $
    │ │ │ -
    5//
    │ │ │ -
    6
    │ │ │ -
    7#ifndef BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H
    │ │ │ -
    8#define BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H
    │ │ │ -
    9
    │ │ │ -
    10#ifndef BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H
    │ │ │ -
    11# include <BALL/MOLMEC/MINIMIZATION/energyMinimizer.h>
    │ │ │ -
    12#endif
    │ │ │ -
    13
    │ │ │ -
    14#ifndef BALL_MOLMEC_MINIMIZATION_LINESEARCH_H
    │ │ │ -
    15# include <BALL/MOLMEC/MINIMIZATION/lineSearch.h>
    │ │ │ -
    16#endif
    │ │ │ -
    17
    │ │ │ -
    18namespace BALL
    │ │ │ -
    19{
    │ │ │ -
    │ │ │ -
    36 class BALL_EXPORT ShiftedLVMMMinimizer
    │ │ │ -
    37 : public EnergyMinimizer
    │ │ │ -
    38 {
    │ │ │ -
    39 public:
    │ │ │ -
    40
    │ │ │ -
    41 BALL_CREATE(ShiftedLVMMMinimizer)
    │ │ │ -
    42
    │ │ │ -
    43
    │ │ │ -
    46
    │ │ │ -
    47
    │ │ │ -
    │ │ │ -
    52 struct Option
    │ │ │ -
    53 {
    │ │ │ -
    56 static const char* UPDATE_METHOD;
    │ │ │ -
    57
    │ │ │ -
    60 static const char* CORRECTION_PARAMETER;
    │ │ │ -
    61
    │ │ │ -
    65 static const char* NUM_OF_COLUMNS;
    │ │ │ -
    66 };
    │ │ │ -
    │ │ │ -
    67
    │ │ │ -
    │ │ │ -
    68 struct BALL_EXPORT Default
    │ │ │ -
    69 {
    │ │ │ -
    73 static const Size UPDATE_METHOD;
    │ │ │ -
    74
    │ │ │ -
    78 static const Size CORRECTION_PARAMETER;
    │ │ │ -
    79
    │ │ │ -
    83 static const Size NUM_OF_COLUMNS;
    │ │ │ -
    84 };
    │ │ │ -
    │ │ │ -
    85
    │ │ │ +Go to the documentation of this file.
    1// ----------------------------------------------------
    │ │ │ +
    2// $Maintainer: Marcel Schumann $
    │ │ │ +
    3// $Authors: Jan Fuhrmann, Marcel Schumann $
    │ │ │ +
    4// ----------------------------------------------------
    │ │ │ +
    5
    │ │ │ +
    6#ifndef BALL_DOCKING_GENETICDOCK_GENETICINDIVIDUAL_H
    │ │ │ +
    7#define BALL_DOCKING_GENETICDOCK_GENETICINDIVIDUAL_H
    │ │ │ +
    8
    │ │ │ +
    9#include <vector>
    │ │ │ +
    10
    │ │ │ +
    11#include <BALL/DOCKING/GENETICDOCK/genes.h>
    │ │ │ +
    12
    │ │ │ +
    13namespace BALL
    │ │ │ +
    14{
    │ │ │ +
    │ │ │ +
    15 class BALL_EXPORT BALL_DEPRECATED GeneticIndividual
    │ │ │ +
    16 {
    │ │ │ +
    17 public:
    │ │ │ +
    20 GeneticIndividual();
    │ │ │ +
    21
    │ │ │ +
    24 GeneticIndividual(const GeneticIndividual& gi);
    │ │ │ +
    25
    │ │ │ +
    28 GeneticIndividual& operator= (const GeneticIndividual& gi);
    │ │ │ +
    29
    │ │ │ +
    32 ~GeneticIndividual();
    │ │ │ +
    33
    │ │ │ +
    36 bool operator<(const GeneticIndividual& gi) const;
    │ │ │ +
    37
    │ │ │ +
    40 void setFitnessValue(const double& d);
    │ │ │ +
    41
    │ │ │ +
    44 double getFitnessValue();
    │ │ │ +
    45
    │ │ │ +
    48 void setAltered(bool b);
    │ │ │ +
    49
    │ │ │ +
    52 bool isAltered();
    │ │ │ +
    53
    │ │ │ +
    56 Size numberOfGenes();
    │ │ │ +
    57
    │ │ │ +
    60 GenericGene* getGene(const Size& i);
    │ │ │ +
    61
    │ │ │ +
    64 void insert(GenericGene* gg);
    │ │ │ +
    65
    │ │ │ +
    68 void mate(GeneticIndividual& parent, GeneticIndividual& offspring);
    │ │ │ +
    69
    │ │ │ +
    72 bool isMutated();
    │ │ │ +
    73
    │ │ │ +
    76 void setMutated(bool);
    │ │ │ +
    77
    │ │ │ +
    80 void randomize();
    │ │ │ +
    81
    │ │ │ +
    82 private:
    │ │ │ +
    83
    │ │ │ +
    86 double fitness_value_;
    │ │ │
    87
    │ │ │ -
    90
    │ │ │ -
    │ │ │ -
    93 enum UpdateMethod
    │ │ │ -
    94 {
    │ │ │ -
    97 RANK_1 = 1,
    │ │ │ -
    98
    │ │ │ -
    101 RANK_2 = 2
    │ │ │ -
    102 };
    │ │ │ -
    │ │ │ -
    103
    │ │ │ -
    │ │ │ -
    106 enum CorrectionParameter
    │ │ │ -
    107 {
    │ │ │ -
    110 UNIT_VALUE = 1,
    │ │ │ -
    111
    │ │ │ -
    114 BALANCING_VALUE = 2,
    │ │ │ -
    115
    │ │ │ -
    118 SQUARE_ROOT = 3,
    │ │ │ -
    119
    │ │ │ -
    122 GEOMETRIC_MEAN = 4,
    │ │ │ -
    123
    │ │ │ -
    126 RATIO_OF_SHIFT_PARAMS = 5
    │ │ │ -
    127 };
    │ │ │ -
    │ │ │ -
    128
    │ │ │ -
    130
    │ │ │ -
    133
    │ │ │ -
    136 ShiftedLVMMMinimizer();
    │ │ │ -
    137
    │ │ │ -
    140 ShiftedLVMMMinimizer(ForceField& force_field);
    │ │ │ -
    141
    │ │ │ -
    144 ShiftedLVMMMinimizer(ForceField& force_field, SnapShotManager *ssm);
    │ │ │ -
    145
    │ │ │ -
    148 ShiftedLVMMMinimizer(ForceField& force_field, SnapShotManager* ssm, const Options& options);
    │ │ │ -
    149
    │ │ │ -
    152 ShiftedLVMMMinimizer(ForceField& force_field, const Options& options);
    │ │ │ -
    153
    │ │ │ -
    156 ShiftedLVMMMinimizer(const ShiftedLVMMMinimizer& rhs);
    │ │ │ -
    157
    │ │ │ -
    160 virtual ~ShiftedLVMMMinimizer();
    │ │ │ -
    161
    │ │ │ -
    163
    │ │ │ -
    166
    │ │ │ -
    169 const ShiftedLVMMMinimizer& operator = (const ShiftedLVMMMinimizer& rhs);
    │ │ │ -
    170
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    172
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    175
    │ │ │ -
    178 virtual bool specificSetup();
    │ │ │ -
    179
    │ │ │ -
    181
    │ │ │ -
    184
    │ │ │ -
    187 void setUpdateMethod(UpdateMethod updt);
    │ │ │ -
    188
    │ │ │ -
    191 UpdateMethod getUpdateMethod() const;
    │ │ │ -
    192
    │ │ │ -
    195 void setCorrectionParameter(CorrectionParameter corr);
    │ │ │ -
    196
    │ │ │ -
    199 CorrectionParameter getCorrectionParameter() const;
    │ │ │ -
    200
    │ │ │ -
    204 void setMaxNumOfColumns(Size num);
    │ │ │ -
    205
    │ │ │ -
    209 Size getMaxNumOfColumns() const;
    │ │ │ -
    210
    │ │ │ -
    217 virtual double findStep();
    │ │ │ -
    218
    │ │ │ -
    222 virtual void updateDirection();
    │ │ │ -
    223
    │ │ │ -
    232 virtual bool minimize(Size iterations = 0, bool resume = false);
    │ │ │ -
    233
    │ │ │ -
    234 protected:
    │ │ │ -
    235
    │ │ │ -
    237
    │ │ │ -
    240
    │ │ │ -
    243 LineSearch line_search_;
    │ │ │ -
    244
    │ │ │ -
    247 bool first_iter_;
    │ │ │ -
    248
    │ │ │ -
    251 Size number_of_atoms_;
    │ │ │ -
    252
    │ │ │ -
    256 Size max_number_of_cols_;
    │ │ │ -
    257
    │ │ │ -
    261 Size curr_number_of_cols_;
    │ │ │ -
    262
    │ │ │ -
    265 Size updt_method_;
    │ │ │ -
    266
    │ │ │ -
    269 Size corr_par_;
    │ │ │ -
    270
    │ │ │ -
    273 double prev_shift_val_;
    │ │ │ -
    274
    │ │ │ -
    277 vector<Vector3> shift_s_;
    │ │ │ -
    278
    │ │ │ -
    281 vector<Vector3> grad_diff_;
    │ │ │ -
    282
    │ │ │ -
    285 vector<float> updt_u_;
    │ │ │ -
    286
    │ │ │ -
    289 vector<float> updt_v_;
    │ │ │ -
    290
    │ │ │ -
    293 vector<Vector3> shifted_direction_;
    │ │ │ -
    294
    │ │ │ -
    298 vector<Vector3> hess_factor_;
    │ │ │ -
    299
    │ │ │ -
    303 vector<Vector3> initial_atoms_;
    │ │ │ -
    304
    │ │ │ -
    306
    │ │ │ -
    307 };
    │ │ │ -
    │ │ │ -
    308} // end of namespace BALL
    │ │ │ -
    309
    │ │ │ -
    310#endif // BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(ForceField &force_field)
    │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::findStep
    virtual double findStep()
    │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(ForceField &force_field, SnapShotManager *ssm)
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::setCorrectionParameter
    void setCorrectionParameter(CorrectionParameter corr)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::initial_atoms_
    vector< Vector3 > initial_atoms_
    Definition shiftedLVMM.h:303
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::getCorrectionParameter
    CorrectionParameter getCorrectionParameter() const
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::setUpdateMethod
    void setUpdateMethod(UpdateMethod updt)
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::specificSetup
    virtual bool specificSetup()
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(const ShiftedLVMMMinimizer &rhs)
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::setMaxNumOfColumns
    void setMaxNumOfColumns(Size num)
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::hess_factor_
    vector< Vector3 > hess_factor_
    Definition shiftedLVMM.h:298
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(ForceField &force_field, const Options &options)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::updateDirection
    virtual void updateDirection()
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::grad_diff_
    vector< Vector3 > grad_diff_
    Definition shiftedLVMM.h:281
    │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::minimize
    virtual bool minimize(Size iterations=0, bool resume=false)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer
    ShiftedLVMMMinimizer(ForceField &force_field, SnapShotManager *ssm, const Options &options)
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::shifted_direction_
    vector< Vector3 > shifted_direction_
    Definition shiftedLVMM.h:293
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::shift_s_
    vector< Vector3 > shift_s_
    Definition shiftedLVMM.h:277
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::getUpdateMethod
    UpdateMethod getUpdateMethod() const
    │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::getMaxNumOfColumns
    Size getMaxNumOfColumns() const
    │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::Option::CORRECTION_PARAMETER
    static const char * CORRECTION_PARAMETER
    Definition shiftedLVMM.h:60
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::Option::UPDATE_METHOD
    static const char * UPDATE_METHOD
    Definition shiftedLVMM.h:56
    │ │ │ -
    BALL::ShiftedLVMMMinimizer::Option::NUM_OF_COLUMNS
    static const char * NUM_OF_COLUMNS
    Definition shiftedLVMM.h:65
    │ │ │ - │ │ │ -
    BALL::ShiftedLVMMMinimizer::Default::CORRECTION_PARAMETER
    static const Size CORRECTION_PARAMETER
    Definition shiftedLVMM.h:78
    │ │ │ - │ │ │ - │ │ │ +
    90 bool altered_;
    │ │ │ +
    91
    │ │ │ +
    94 bool mutated_;
    │ │ │ +
    95
    │ │ │ +
    98 std::vector<GenericGene*> genes_;
    │ │ │ +
    99 };
    │ │ │ +
    │ │ │ +
    100}
    │ │ │ +
    101
    │ │ │ +
    102#endif /* BALL_DOCKING_GENETICDOCK_GENETICINDIVIDUAL_H */
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::GeneticIndividual::operator<
    bool operator<(const GeneticIndividual &gi) const
    │ │ │ + │ │ │ +
    BALL::GeneticIndividual::setFitnessValue
    void setFitnessValue(const double &d)
    │ │ │ +
    BALL::GeneticIndividual::mate
    void mate(GeneticIndividual &parent, GeneticIndividual &offspring)
    │ │ │ +
    BALL::GeneticIndividual::getGene
    GenericGene * getGene(const Size &i)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::GeneticIndividual::insert
    void insert(GenericGene *gg)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::GeneticIndividual::GeneticIndividual
    GeneticIndividual(const GeneticIndividual &gi)
    │ │ │ + │ │ │ │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    BALL_DEPRECATED
    #define BALL_DEPRECATED
    Definition COMMON/global.h:64
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,296 +1,118 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _M_O_L_M_E_C │ │ │ │ - * _M_I_N_I_M_I_Z_A_T_I_O_N │ │ │ │ -shiftedLVMM.h │ │ │ │ + * _D_O_C_K_I_N_G │ │ │ │ + * _G_E_N_E_T_I_C_D_O_C_K │ │ │ │ +geneticIndividual.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ -2// vi: set ts=2: │ │ │ │ -3// │ │ │ │ -4// $Id: shiftedLVMM.h,v 1.1.4.6 2007/08/07 09:12:35 aleru Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H │ │ │ │ -8#define BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H │ │ │ │ -11# include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h> │ │ │ │ -12#endif │ │ │ │ -13 │ │ │ │ -14#ifndef BALL_MOLMEC_MINIMIZATION_LINESEARCH_H │ │ │ │ -15# include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_l_i_n_e_S_e_a_r_c_h_._h> │ │ │ │ -16#endif │ │ │ │ -17 │ │ │ │ -18namespace _B_A_L_L │ │ │ │ -19{ │ │ │ │ -_3_6 class _B_A_L_L___E_X_P_O_R_T _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -37 : public _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r │ │ │ │ -38 { │ │ │ │ -39 public: │ │ │ │ -40 │ │ │ │ -41 _B_A_L_L___C_R_E_A_T_E(_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r) │ │ │ │ -42 │ │ │ │ -43 │ │ │ │ -46 │ │ │ │ -47 │ │ │ │ -_5_2 struct _O_p_t_i_o_n │ │ │ │ -53 { │ │ │ │ -_5_6 static const char* _U_P_D_A_T_E___M_E_T_H_O_D; │ │ │ │ +1// ---------------------------------------------------- │ │ │ │ +2// $Maintainer: Marcel Schumann $ │ │ │ │ +3// $Authors: Jan Fuhrmann, Marcel Schumann $ │ │ │ │ +4// ---------------------------------------------------- │ │ │ │ +5 │ │ │ │ +6#ifndef BALL_DOCKING_GENETICDOCK_GENETICINDIVIDUAL_H │ │ │ │ +7#define BALL_DOCKING_GENETICDOCK_GENETICINDIVIDUAL_H │ │ │ │ +8 │ │ │ │ +9#include │ │ │ │ +10 │ │ │ │ +11#include <_B_A_L_L_/_D_O_C_K_I_N_G_/_G_E_N_E_T_I_C_D_O_C_K_/_g_e_n_e_s_._h> │ │ │ │ +12 │ │ │ │ +13namespace _B_A_L_L │ │ │ │ +14{ │ │ │ │ +_1_5 class _B_A_L_L___E_X_P_O_R_T _B_A_L_L___D_E_P_R_E_C_A_T_E_D _G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l │ │ │ │ +16 { │ │ │ │ +17 public: │ │ │ │ +_2_0 _G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l(); │ │ │ │ +21 │ │ │ │ +_2_4 _G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l(const _G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l& gi); │ │ │ │ +25 │ │ │ │ +_2_8 _G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l& operator= (const _G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l& gi); │ │ │ │ +29 │ │ │ │ +_3_2 _~_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l(); │ │ │ │ +33 │ │ │ │ +_3_6 bool _o_p_e_r_a_t_o_r_<(const _G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l& gi) const; │ │ │ │ +37 │ │ │ │ +_4_0 void _s_e_t_F_i_t_n_e_s_s_V_a_l_u_e(const double& d); │ │ │ │ +41 │ │ │ │ +_4_4 double _g_e_t_F_i_t_n_e_s_s_V_a_l_u_e(); │ │ │ │ +45 │ │ │ │ +_4_8 void _s_e_t_A_l_t_e_r_e_d(bool b); │ │ │ │ +49 │ │ │ │ +_5_2 bool _i_s_A_l_t_e_r_e_d(); │ │ │ │ +53 │ │ │ │ +_5_6 _S_i_z_e _n_u_m_b_e_r_O_f_G_e_n_e_s(); │ │ │ │ 57 │ │ │ │ -_6_0 static const char* _C_O_R_R_E_C_T_I_O_N___P_A_R_A_M_E_T_E_R; │ │ │ │ +_6_0 _G_e_n_e_r_i_c_G_e_n_e* _g_e_t_G_e_n_e(const _S_i_z_e& i); │ │ │ │ 61 │ │ │ │ -_6_5 static const char* _N_U_M___O_F___C_O_L_U_M_N_S; │ │ │ │ -66 }; │ │ │ │ -67 │ │ │ │ -_6_8 struct _B_A_L_L___E_X_P_O_R_T _D_e_f_a_u_l_t │ │ │ │ -69 { │ │ │ │ -_7_3 static const _S_i_z_e _U_P_D_A_T_E___M_E_T_H_O_D; │ │ │ │ -74 │ │ │ │ -_7_8 static const _S_i_z_e _C_O_R_R_E_C_T_I_O_N___P_A_R_A_M_E_T_E_R; │ │ │ │ -79 │ │ │ │ -_8_3 static const _S_i_z_e _N_U_M___O_F___C_O_L_U_M_N_S; │ │ │ │ -84 }; │ │ │ │ -85 │ │ │ │ +_6_4 void _i_n_s_e_r_t(_G_e_n_e_r_i_c_G_e_n_e* gg); │ │ │ │ +65 │ │ │ │ +_6_8 void _m_a_t_e(_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l& parent, _G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l& offspring); │ │ │ │ +69 │ │ │ │ +_7_2 bool _i_s_M_u_t_a_t_e_d(); │ │ │ │ +73 │ │ │ │ +_7_6 void _s_e_t_M_u_t_a_t_e_d(bool); │ │ │ │ +77 │ │ │ │ +_8_0 void _r_a_n_d_o_m_i_z_e(); │ │ │ │ +81 │ │ │ │ +82 private: │ │ │ │ +83 │ │ │ │ +86 double fitness_value_; │ │ │ │ 87 │ │ │ │ -90 │ │ │ │ -_9_3 enum _U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ -94 { │ │ │ │ -_9_7 RANK_1 = 1, │ │ │ │ -98 │ │ │ │ -101 RANK_2 = 2 │ │ │ │ -_1_0_2 }; │ │ │ │ -103 │ │ │ │ -_1_0_6 enum _C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r │ │ │ │ -107 { │ │ │ │ -_1_1_0 UNIT_VALUE = 1, │ │ │ │ -111 │ │ │ │ -_1_1_4 BALANCING_VALUE = 2, │ │ │ │ -115 │ │ │ │ -_1_1_8 SQUARE_ROOT = 3, │ │ │ │ -119 │ │ │ │ -_1_2_2 GEOMETRIC_MEAN = 4, │ │ │ │ -123 │ │ │ │ -126 RATIO_OF_SHIFT_PARAMS = 5 │ │ │ │ -_1_2_7 }; │ │ │ │ -128 │ │ │ │ -130 │ │ │ │ -133 │ │ │ │ -_1_3_6 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(); │ │ │ │ -137 │ │ │ │ -_1_4_0 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ -141 │ │ │ │ -_1_4_4 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field, _S_n_a_p_S_h_o_t_M_a_n_a_g_e_r *ssm); │ │ │ │ -145 │ │ │ │ -_1_4_8 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field, _S_n_a_p_S_h_o_t_M_a_n_a_g_e_r* ssm, const │ │ │ │ -_O_p_t_i_o_n_s& options); │ │ │ │ -149 │ │ │ │ -_1_5_2 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field, const _O_p_t_i_o_n_s& options); │ │ │ │ -153 │ │ │ │ -_1_5_6 _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(const _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r& rhs); │ │ │ │ -157 │ │ │ │ -_1_6_0 virtual _~_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r(); │ │ │ │ -161 │ │ │ │ -163 │ │ │ │ -166 │ │ │ │ -_1_6_9 const _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r& operator = (const _S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r& rhs); │ │ │ │ -170 │ │ │ │ -172 │ │ │ │ -175 │ │ │ │ -_1_7_8 virtual bool _s_p_e_c_i_f_i_c_S_e_t_u_p(); │ │ │ │ -179 │ │ │ │ -181 │ │ │ │ -184 │ │ │ │ -_1_8_7 void _s_e_t_U_p_d_a_t_e_M_e_t_h_o_d(_U_p_d_a_t_e_M_e_t_h_o_d updt); │ │ │ │ -188 │ │ │ │ -_1_9_1 _U_p_d_a_t_e_M_e_t_h_o_d _g_e_t_U_p_d_a_t_e_M_e_t_h_o_d() const; │ │ │ │ -192 │ │ │ │ -_1_9_5 void _s_e_t_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r(_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r corr); │ │ │ │ -196 │ │ │ │ -_1_9_9 _C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r _g_e_t_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r() const; │ │ │ │ -200 │ │ │ │ -_2_0_4 void _s_e_t_M_a_x_N_u_m_O_f_C_o_l_u_m_n_s(_S_i_z_e num); │ │ │ │ -205 │ │ │ │ -_2_0_9 _S_i_z_e _g_e_t_M_a_x_N_u_m_O_f_C_o_l_u_m_n_s() const; │ │ │ │ -210 │ │ │ │ -_2_1_7 virtual double _f_i_n_d_S_t_e_p(); │ │ │ │ -218 │ │ │ │ -_2_2_2 virtual void _u_p_d_a_t_e_D_i_r_e_c_t_i_o_n(); │ │ │ │ -223 │ │ │ │ -_2_3_2 virtual bool _m_i_n_i_m_i_z_e(_S_i_z_e iterations = 0, bool resume = false); │ │ │ │ -233 │ │ │ │ -234 protected: │ │ │ │ -235 │ │ │ │ -237 │ │ │ │ -240 │ │ │ │ -_2_4_3 _L_i_n_e_S_e_a_r_c_h _l_i_n_e___s_e_a_r_c_h__; │ │ │ │ -244 │ │ │ │ -_2_4_7 bool _f_i_r_s_t___i_t_e_r__; │ │ │ │ -248 │ │ │ │ -_2_5_1 _S_i_z_e _n_u_m_b_e_r___o_f___a_t_o_m_s__; │ │ │ │ -252 │ │ │ │ -_2_5_6 _S_i_z_e _m_a_x___n_u_m_b_e_r___o_f___c_o_l_s__; │ │ │ │ -257 │ │ │ │ -_2_6_1 _S_i_z_e _c_u_r_r___n_u_m_b_e_r___o_f___c_o_l_s__; │ │ │ │ -262 │ │ │ │ -_2_6_5 _S_i_z_e _u_p_d_t___m_e_t_h_o_d__; │ │ │ │ -266 │ │ │ │ -_2_6_9 _S_i_z_e _c_o_r_r___p_a_r__; │ │ │ │ -270 │ │ │ │ -_2_7_3 double _p_r_e_v___s_h_i_f_t___v_a_l__; │ │ │ │ -274 │ │ │ │ -_2_7_7 vector _s_h_i_f_t___s__; │ │ │ │ -278 │ │ │ │ -_2_8_1 vector _g_r_a_d___d_i_f_f__; │ │ │ │ -282 │ │ │ │ -_2_8_5 vector _u_p_d_t___u__; │ │ │ │ -286 │ │ │ │ -_2_8_9 vector _u_p_d_t___v__; │ │ │ │ -290 │ │ │ │ -_2_9_3 vector _s_h_i_f_t_e_d___d_i_r_e_c_t_i_o_n__; │ │ │ │ -294 │ │ │ │ -_2_9_8 vector _h_e_s_s___f_a_c_t_o_r__; │ │ │ │ -299 │ │ │ │ -_3_0_3 vector _i_n_i_t_i_a_l___a_t_o_m_s__; │ │ │ │ -304 │ │ │ │ -306 │ │ │ │ -307 }; │ │ │ │ -308} // end of namespace BALL │ │ │ │ -309 │ │ │ │ -310#endif // BALL_MOLMEC_MINIMIZATION_SHIFTEDLVMM_H │ │ │ │ -_l_i_n_e_S_e_a_r_c_h_._h │ │ │ │ -_e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +90 bool altered_; │ │ │ │ +91 │ │ │ │ +94 bool mutated_; │ │ │ │ +95 │ │ │ │ +98 std::vector genes_; │ │ │ │ +99 }; │ │ │ │ +100} │ │ │ │ +101 │ │ │ │ +102#endif /* BALL_DOCKING_GENETICDOCK_GENETICINDIVIDUAL_H */ │ │ │ │ +_g_e_n_e_s_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ -DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ -_B_A_L_L_:_:_S_n_a_p_S_h_o_t_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _s_n_a_p_S_h_o_t_M_a_n_a_g_e_r_._h_:_3_4 │ │ │ │ -_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r │ │ │ │ -DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_3_0 │ │ │ │ -_B_A_L_L_:_:_L_i_n_e_S_e_a_r_c_h │ │ │ │ -DDeeffiinniittiioonn _l_i_n_e_S_e_a_r_c_h_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_3_8 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -ShiftedLVMMMinimizer(ForceField &force_field) │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_~_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -virtual ~ShiftedLVMMMinimizer() │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_f_i_n_d_S_t_e_p │ │ │ │ -virtual double findStep() │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_u_p_d_t___m_e_t_h_o_d__ │ │ │ │ -Size updt_method_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_6_5 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -ShiftedLVMMMinimizer(ForceField &force_field, SnapShotManager *ssm) │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_e_t_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r │ │ │ │ -void setCorrectionParameter(CorrectionParameter corr) │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_c_o_r_r___p_a_r__ │ │ │ │ -Size corr_par_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_6_9 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_c_u_r_r___n_u_m_b_e_r___o_f___c_o_l_s__ │ │ │ │ -Size curr_number_of_cols_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_6_1 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_i_n_i_t_i_a_l___a_t_o_m_s__ │ │ │ │ -vector< Vector3 > initial_atoms_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_3_0_3 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_g_e_t_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r │ │ │ │ -CorrectionParameter getCorrectionParameter() const │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -ShiftedLVMMMinimizer() │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_u_p_d_t___v__ │ │ │ │ -vector< float > updt_v_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_8_9 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_e_t_U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ -void setUpdateMethod(UpdateMethod updt) │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_p_e_c_i_f_i_c_S_e_t_u_p │ │ │ │ -virtual bool specificSetup() │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -ShiftedLVMMMinimizer(const ShiftedLVMMMinimizer &rhs) │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_e_t_M_a_x_N_u_m_O_f_C_o_l_u_m_n_s │ │ │ │ -void setMaxNumOfColumns(Size num) │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_h_e_s_s___f_a_c_t_o_r__ │ │ │ │ -vector< Vector3 > hess_factor_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_9_8 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -ShiftedLVMMMinimizer(ForceField &force_field, const Options &options) │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_n_u_m_b_e_r___o_f___a_t_o_m_s__ │ │ │ │ -Size number_of_atoms_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_5_1 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_C_o_r_r_e_c_t_i_o_n_P_a_r_a_m_e_t_e_r │ │ │ │ -CorrectionParameter │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_1_0_7 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_u_p_d_a_t_e_D_i_r_e_c_t_i_o_n │ │ │ │ -virtual void updateDirection() │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_p_r_e_v___s_h_i_f_t___v_a_l__ │ │ │ │ -double prev_shift_val_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_7_3 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_u_p_d_t___u__ │ │ │ │ -vector< float > updt_u_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_8_5 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_g_r_a_d___d_i_f_f__ │ │ │ │ -vector< Vector3 > grad_diff_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_8_1 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ -UpdateMethod │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_9_4 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_m_i_n_i_m_i_z_e │ │ │ │ -virtual bool minimize(Size iterations=0, bool resume=false) │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_l_i_n_e___s_e_a_r_c_h__ │ │ │ │ -LineSearch line_search_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_4_3 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_f_i_r_s_t___i_t_e_r__ │ │ │ │ -bool first_iter_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_4_7 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r │ │ │ │ -ShiftedLVMMMinimizer(ForceField &force_field, SnapShotManager *ssm, const │ │ │ │ -Options &options) │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_h_i_f_t_e_d___d_i_r_e_c_t_i_o_n__ │ │ │ │ -vector< Vector3 > shifted_direction_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_9_3 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_s_h_i_f_t___s__ │ │ │ │ -vector< Vector3 > shift_s_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_7_7 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_g_e_t_U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ -UpdateMethod getUpdateMethod() const │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_m_a_x___n_u_m_b_e_r___o_f___c_o_l_s__ │ │ │ │ -Size max_number_of_cols_ │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_2_5_6 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_g_e_t_M_a_x_N_u_m_O_f_C_o_l_u_m_n_s │ │ │ │ -Size getMaxNumOfColumns() const │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_C_O_R_R_E_C_T_I_O_N___P_A_R_A_M_E_T_E_R │ │ │ │ -static const char * CORRECTION_PARAMETER │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_6_0 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_U_P_D_A_T_E___M_E_T_H_O_D │ │ │ │ -static const char * UPDATE_METHOD │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_5_6 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_N_U_M___O_F___C_O_L_U_M_N_S │ │ │ │ -static const char * NUM_OF_COLUMNS │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_6_5 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_6_9 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_C_O_R_R_E_C_T_I_O_N___P_A_R_A_M_E_T_E_R │ │ │ │ -static const Size CORRECTION_PARAMETER │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_7_8 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_N_U_M___O_F___C_O_L_U_M_N_S │ │ │ │ -static const Size NUM_OF_COLUMNS │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_8_3 │ │ │ │ -_B_A_L_L_:_:_S_h_i_f_t_e_d_L_V_M_M_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_U_P_D_A_T_E___M_E_T_H_O_D │ │ │ │ -static const Size UPDATE_METHOD │ │ │ │ -DDeeffiinniittiioonn _s_h_i_f_t_e_d_L_V_M_M_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_r_i_c_G_e_n_e │ │ │ │ +DDeeffiinniittiioonn _g_e_n_e_s_._h_:_1_9 │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l │ │ │ │ +DDeeffiinniittiioonn _g_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_._h_:_1_6 │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_r_a_n_d_o_m_i_z_e │ │ │ │ +void randomize() │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_s_e_t_A_l_t_e_r_e_d │ │ │ │ +void setAltered(bool b) │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_g_e_t_F_i_t_n_e_s_s_V_a_l_u_e │ │ │ │ +double getFitnessValue() │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_o_p_e_r_a_t_o_r_< │ │ │ │ +bool operator<(const GeneticIndividual &gi) const │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_i_s_A_l_t_e_r_e_d │ │ │ │ +bool isAltered() │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_s_e_t_F_i_t_n_e_s_s_V_a_l_u_e │ │ │ │ +void setFitnessValue(const double &d) │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_m_a_t_e │ │ │ │ +void mate(GeneticIndividual &parent, GeneticIndividual &offspring) │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_g_e_t_G_e_n_e │ │ │ │ +GenericGene * getGene(const Size &i) │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l │ │ │ │ +GeneticIndividual() │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_n_u_m_b_e_r_O_f_G_e_n_e_s │ │ │ │ +Size numberOfGenes() │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_i_n_s_e_r_t │ │ │ │ +void insert(GenericGene *gg) │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_i_s_M_u_t_a_t_e_d │ │ │ │ +bool isMutated() │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_s_e_t_M_u_t_a_t_e_d │ │ │ │ +void setMutated(bool) │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l │ │ │ │ +GeneticIndividual(const GeneticIndividual &gi) │ │ │ │ +_B_A_L_L_:_:_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l_:_:_~_G_e_n_e_t_i_c_I_n_d_i_v_i_d_u_a_l │ │ │ │ +~GeneticIndividual() │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L___D_E_P_R_E_C_A_T_E_D │ │ │ │ +#define BALL_DEPRECATED │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_6_4 │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d9d/a01760.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: SCWRLRotamerFile.h File Reference │ │ │ +BALL: MMFF94StretchBend.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,39 +65,114 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces
    │ │ │ -
    SCWRLRotamerFile.h File Reference
    │ │ │ +Namespaces | │ │ │ +Macros
    │ │ │ +
    MMFF94StretchBend.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/FORMAT/lineBasedFile.h>
    │ │ │ +
    #include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
    │ │ │ +#include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::SCWRLRotamerFile
     Reads Dunbrack/SCWRL rotamer library files. More...
    class  BALL::MMFF94StretchBend
     
    struct  BALL::MMFF94StretchBend::StretchBend
     
    struct  BALL::MMFF94StretchBend::Bend
     see MMFFANG.PAR More...
     
    struct  BALL::MMFF94StretchBend::Stretch
     
    │ │ │ │ │ │ │ │ │ │ │ │ +

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ +Macros

    #define MMFF94_BENDS_ENABLED   "enable Bends"
     flag to enable BENDS
     
    #define MMFF94_STRETCHES_ENABLED   "enable Stretches"
     flag to enable Stretches
     
    #define MMFF94_STRETCHBENDS_ENABLED   "enable StrechBends"
     flag to enable StretchBends
     
    │ │ │ +

    Macro Definition Documentation

    │ │ │ + │ │ │ +

    ◆ MMFF94_BENDS_ENABLED

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define MMFF94_BENDS_ENABLED   "enable Bends"
    │ │ │ +
    │ │ │ + │ │ │ +

    flag to enable BENDS

    │ │ │ + │ │ │ +

    Definition at line 84 of file MMFF94StretchBend.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ MMFF94_STRETCHBENDS_ENABLED

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define MMFF94_STRETCHBENDS_ENABLED   "enable StrechBends"
    │ │ │ +
    │ │ │ + │ │ │ +

    flag to enable StretchBends

    │ │ │ + │ │ │ +

    Definition at line 90 of file MMFF94StretchBend.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ MMFF94_STRETCHES_ENABLED

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define MMFF94_STRETCHES_ENABLED   "enable Stretches"
    │ │ │ +
    │ │ │ + │ │ │ +

    flag to enable Stretches

    │ │ │ + │ │ │ +

    Definition at line 87 of file MMFF94StretchBend.h.

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    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,20 +1,51 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _F_O_R_M_A_T │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -SCWRLRotamerFile.h File Reference │ │ │ │ -#include <_B_A_L_L_/_F_O_R_M_A_T_/_l_i_n_e_B_a_s_e_d_F_i_l_e_._h> │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _M_M_F_F_9_4 │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _M_a_c_r_o_s │ │ │ │ +MMFF94StretchBend.h File Reference │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_M_F_F_9_4_/_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e │ │ │ │ -  Reads Dunbrack/SCWRL rotamer library files. _M_o_r_e_._._. │ │ │ │ + class   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d │ │ │ │ +  see MMFFANG.PAR _M_o_r_e_._._. │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +MMaaccrrooss │ │ │ │ +#define  _M_M_F_F_9_4___B_E_N_D_S___E_N_A_B_L_E_D   "enable Bends" │ │ │ │ +  flag to enable BENDS │ │ │ │ +  │ │ │ │ +#define  _M_M_F_F_9_4___S_T_R_E_T_C_H_E_S___E_N_A_B_L_E_D   "enable Stretches" │ │ │ │ +  flag to enable Stretches │ │ │ │ +  │ │ │ │ +#define  _M_M_F_F_9_4___S_T_R_E_T_C_H_B_E_N_D_S___E_N_A_B_L_E_D   "enable StrechBends" │ │ │ │ +  flag to enable StretchBends │ │ │ │ +  │ │ │ │ +********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ +********** _?◆_? MMMMFFFF9944__BBEENNDDSS__EENNAABBLLEEDD ********** │ │ │ │ +#define MMFF94_BENDS_ENABLED   "enable Bends" │ │ │ │ +flag to enable BENDS │ │ │ │ +Definition at line _8_4 of file _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h. │ │ │ │ +********** _?◆_? MMMMFFFF9944__SSTTRREETTCCHHBBEENNDDSS__EENNAABBLLEEDD ********** │ │ │ │ +#define MMFF94_STRETCHBENDS_ENABLED   "enable StrechBends" │ │ │ │ +flag to enable StretchBends │ │ │ │ +Definition at line _9_0 of file _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h. │ │ │ │ +********** _?◆_? MMMMFFFF9944__SSTTRREETTCCHHEESS__EENNAABBLLEEDD ********** │ │ │ │ +#define MMFF94_STRETCHES_ENABLED   "enable Stretches" │ │ │ │ +flag to enable Stretches │ │ │ │ +Definition at line _8_7 of file _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d9d/a01760_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: SCWRLRotamerFile.h Source File │ │ │ +BALL: MMFF94StretchBend.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,73 +70,260 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    SCWRLRotamerFile.h
    │ │ │ +
    MMFF94StretchBend.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_FORMAT_SCWRLROTAMERFILE_H
    │ │ │ -
    6#define BALL_FORMAT_SCWRLROTAMERFILE_H
    │ │ │ -
    7
    │ │ │ -
    8#include <BALL/FORMAT/lineBasedFile.h>
    │ │ │ +
    4// $Id: MMFF94StretchBend.h,v 1.1.8.1 2007/03/25 21:25:18 oliver Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H
    │ │ │ +
    8#define BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H
    │ │ │
    9
    │ │ │ -
    10namespace BALL
    │ │ │ -
    11{
    │ │ │ -
    13 class RotamerLibrary;
    │ │ │ -
    │ │ │ -
    22 class BALL_EXPORT SCWRLRotamerFile
    │ │ │ -
    23 : public LineBasedFile
    │ │ │ -
    24 {
    │ │ │ -
    25 public:
    │ │ │ -
    26
    │ │ │ -
    31 SCWRLRotamerFile();
    │ │ │ -
    32
    │ │ │ -
    34 SCWRLRotamerFile(const String& name, File::OpenMode open_mode = std::ios::in);
    │ │ │ -
    35
    │ │ │ -
    37 virtual ~SCWRLRotamerFile();
    │ │ │ +
    10#ifndef BALL_MOLMEC_COMMON_FORCEFIELDCOMPONENT_H
    │ │ │ +
    11# include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
    │ │ │ +
    12#endif
    │ │ │ +
    13
    │ │ │ +
    14#ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
    │ │ │ +
    15# include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
    │ │ │ +
    16#endif
    │ │ │ +
    17
    │ │ │ +
    18namespace BALL
    │ │ │ +
    19{
    │ │ │ +
    20 class MMFF94;
    │ │ │ +
    21
    │ │ │ +
    │ │ │ +
    25 class BALL_EXPORT MMFF94StretchBend
    │ │ │ +
    26 : public ForceFieldComponent
    │ │ │ +
    27 {
    │ │ │ +
    28 public:
    │ │ │ +
    29
    │ │ │ +
    │ │ │ +
    30 struct BALL_EXPORT StretchBend
    │ │ │ +
    31 {
    │ │ │ +
    32 double kba_ijk;
    │ │ │ +
    33 double kba_kji;
    │ │ │ +
    34 double energy; // debug
    │ │ │ +
    35 Index sbtijk;
    │ │ │ +
    36 Index stretch_i_j, stretch_j_k;
    │ │ │ +
    37 Index bend_index;
    │ │ │ +
    38 };
    │ │ │ +
    │ │ │
    39
    │ │ │ -
    40
    │ │ │ -
    45 const SCWRLRotamerFile& operator = (const SCWRLRotamerFile& file);
    │ │ │ -
    46
    │ │ │ -
    48 void operator >> (RotamerLibrary& rotamer_library);
    │ │ │ -
    49
    │ │ │ -
    50 // TODO output operator????
    │ │ │ -
    52
    │ │ │ -
    56 void readSCWRLBackboneDependentLibraryFile(RotamerLibrary& library);
    │ │ │ -
    57
    │ │ │ -
    61 void readSCWRLBackboneIndependentLibraryFile(RotamerLibrary& library);
    │ │ │ -
    62 };
    │ │ │ -
    │ │ │ -
    63} // namespace BALL
    │ │ │ -
    64
    │ │ │ -
    65#endif // BALL_FORMAT_SCWRLROTAMERFILE_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::SCWRLRotamerFile
    Reads Dunbrack/SCWRL rotamer library files.
    Definition SCWRLRotamerFile.h:24
    │ │ │ -
    BALL::SCWRLRotamerFile::readSCWRLBackboneIndependentLibraryFile
    void readSCWRLBackboneIndependentLibraryFile(RotamerLibrary &library)
    │ │ │ -
    BALL::SCWRLRotamerFile::SCWRLRotamerFile
    SCWRLRotamerFile()
    Default constructor.
    │ │ │ -
    BALL::SCWRLRotamerFile::SCWRLRotamerFile
    SCWRLRotamerFile(const String &name, File::OpenMode open_mode=std::ios::in)
    Detailed constructor.
    │ │ │ -
    BALL::SCWRLRotamerFile::~SCWRLRotamerFile
    virtual ~SCWRLRotamerFile()
    Destructor.
    │ │ │ -
    BALL::SCWRLRotamerFile::readSCWRLBackboneDependentLibraryFile
    void readSCWRLBackboneDependentLibraryFile(RotamerLibrary &library)
    │ │ │ -
    BALL::RotamerLibrary
    Rotamer Library Class.
    Definition rotamerLibrary.h:34
    │ │ │ -
    BALL::File::OpenMode
    std::ios::openmode OpenMode
    Definition file.h:165
    │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    │ │ │ +
    41 struct BALL_EXPORT Bend
    │ │ │ +
    42 {
    │ │ │ +
    43 Bend();
    │ │ │ +
    44
    │ │ │ +
    45 double theta0;
    │ │ │ +
    46 double delta_theta;
    │ │ │ +
    47 double theta;
    │ │ │ +
    48 double ka;
    │ │ │ +
    49 Atom* atom1;
    │ │ │ +
    50 Atom* atom2;
    │ │ │ +
    51 Atom* atom3;
    │ │ │ +
    52 bool is_linear;
    │ │ │ +
    53 Position ATIJK;
    │ │ │ +
    54 double energy; // debug
    │ │ │ +
    55 bool emperical; // debug
    │ │ │ +
    56 TVector3<double> n1, n2;
    │ │ │ +
    57 };
    │ │ │ +
    │ │ │ +
    58
    │ │ │ +
    │ │ │ +
    60 struct BALL_EXPORT Stretch
    │ │ │ +
    61 {
    │ │ │ +
    │ │ │ +
    62 Stretch()
    │ │ │ +
    63 : atom1(NULL),
    │ │ │ +
    64 atom2(NULL),
    │ │ │ +
    65 kb(0.0),
    │ │ │ +
    66 r0(0.0),
    │ │ │ +
    67 delta_r(0.0),
    │ │ │ +
    68 sbmb(false),
    │ │ │ +
    69 emperical(false)
    │ │ │ +
    70 {
    │ │ │ +
    71 }
    │ │ │ +
    │ │ │ +
    72
    │ │ │ +
    73 Atom* atom1;
    │ │ │ +
    74 Atom* atom2;
    │ │ │ +
    75 double kb;
    │ │ │ +
    76 double r0;
    │ │ │ +
    77 double delta_r;
    │ │ │ +
    78 bool sbmb;
    │ │ │ +
    79 bool emperical;
    │ │ │ +
    80 Vector3 n;
    │ │ │ +
    81 };
    │ │ │ +
    │ │ │ +
    82
    │ │ │ +
    84 #define MMFF94_BENDS_ENABLED "enable Bends"
    │ │ │ +
    85
    │ │ │ +
    87 #define MMFF94_STRETCHES_ENABLED "enable Stretches"
    │ │ │ +
    88
    │ │ │ +
    90 #define MMFF94_STRETCHBENDS_ENABLED "enable StrechBends"
    │ │ │ +
    91
    │ │ │ +
    92 BALL_CREATE(MMFF94StretchBend)
    │ │ │ +
    93
    │ │ │ +
    94
    │ │ │ +
    96 MMFF94StretchBend();
    │ │ │ +
    97
    │ │ │ +
    100 MMFF94StretchBend(ForceField& force_field);
    │ │ │ +
    101
    │ │ │ +
    104 MMFF94StretchBend(const MMFF94StretchBend& to_copy);
    │ │ │ +
    105
    │ │ │ +
    108 virtual ~MMFF94StretchBend();
    │ │ │ +
    109
    │ │ │ +
    113 virtual bool setup();
    │ │ │ +
    114
    │ │ │ +
    116 virtual double updateEnergy();
    │ │ │ +
    117
    │ │ │ +
    119 virtual double updateBendEnergy();
    │ │ │ +
    120
    │ │ │ +
    122 virtual double updateStretchEnergy();
    │ │ │ +
    123
    │ │ │ +
    125 virtual double updateStretchBendEnergy();
    │ │ │ +
    126
    │ │ │ +
    128 double getStretchEnergy() const;
    │ │ │ +
    129
    │ │ │ +
    131 double getBendEnergy() const;
    │ │ │ +
    132
    │ │ │ +
    134 double getStretchBendEnergy() const;
    │ │ │ +
    135
    │ │ │ +
    137 virtual void updateForces();
    │ │ │ +
    138
    │ │ │ +
    140 virtual void updateBendForces();
    │ │ │ +
    141
    │ │ │ +
    143 virtual void updateStretchForces();
    │ │ │ +
    144
    │ │ │ +
    146 virtual void updateStretchBendForces();
    │ │ │ +
    147
    │ │ │ +
    149 const vector<Bend>& getBends() const { return bends_;}
    │ │ │ +
    150
    │ │ │ +
    152 const vector<Stretch>& getStretches() const { return stretches_;}
    │ │ │ +
    153
    │ │ │ +
    155 const vector<StretchBend>& getStretchBends() const { return stretch_bends_;}
    │ │ │ +
    156
    │ │ │ +
    158 Index calculateSBTIJK(Position angle_type,
    │ │ │ +
    159 bool bond_type1,
    │ │ │ +
    160 bool bond_type2);
    │ │ │ +
    161
    │ │ │ +
    163 Position getBendType(const Bond& bond1, const Bond& bond2,
    │ │ │ +
    164 Atom& atom1, Atom& atom2, Atom& atom3) const;
    │ │ │ +
    165
    │ │ │ +
    167 double calculateBendEmpiricalReferenceAngle(Atom& atom1, Atom& atom2, Atom& atom3) const;
    │ │ │ +
    168
    │ │ │ +
    170 double calculateBendEmpiricalForceConstant(Atom& atom1, Atom& atom2, Atom& atom3, double angle_0) const;
    │ │ │ +
    171
    │ │ │ +
    173 double calculateStretchR0(const Bond& bond);
    │ │ │ +
    174
    │ │ │ +
    176 double calculateStretchConstant(const Bond& bond, double r0);
    │ │ │ +
    177
    │ │ │ +
    178 private:
    │ │ │ +
    179
    │ │ │ +
    180 inline void AddDV3_(Vector3& f3, const TVector3<double> d3);
    │ │ │ +
    181 void calculateDeltas_();
    │ │ │ +
    182 bool setupBends_();
    │ │ │ +
    183 bool setupStretches_();
    │ │ │ +
    184 bool setupStretchBends_();
    │ │ │ +
    185
    │ │ │ +
    186 void errorOccurred_(const String& string,
    │ │ │ +
    187 const Atom& a1, const Atom& a2, const Atom& a3);
    │ │ │ +
    188
    │ │ │ +
    189 vector<Bend> bends_;
    │ │ │ +
    190 vector<Stretch> stretches_;
    │ │ │ +
    191 vector<StretchBend> stretch_bends_;
    │ │ │ +
    192
    │ │ │ +
    193 const MMFF94StretchParameters* stretch_parameters_;
    │ │ │ +
    194 MMFF94BendParameters bend_parameters_;
    │ │ │ +
    195 MMFF94StretchBendParameters sb_parameters_;
    │ │ │ +
    196
    │ │ │ +
    197 static double bend_z_[];
    │ │ │ +
    198 static double bend_c_[];
    │ │ │ +
    199 static String bend_elements_[];
    │ │ │ +
    200
    │ │ │ +
    201 double stretch_energy_;
    │ │ │ +
    202 double bend_energy_;
    │ │ │ +
    203 double stretch_bend_energy_;
    │ │ │ +
    204
    │ │ │ +
    205 MMFF94* mmff94_;
    │ │ │ +
    206 bool stretch_enabled_, bend_enabled_, stretchbend_enabled_;
    │ │ │ +
    207 };
    │ │ │ +
    │ │ │ +
    208} // namespace BALL
    │ │ │ +
    209
    │ │ │ +
    210#endif // BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H
    │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::MMFF94StretchBend::getStretches
    const vector< Stretch > & getStretches() const
    Definition MMFF94StretchBend.h:152
    │ │ │ +
    BALL::MMFF94StretchBend::getBendType
    Position getBendType(const Bond &bond1, const Bond &bond2, Atom &atom1, Atom &atom2, Atom &atom3) const
    │ │ │ +
    BALL::MMFF94StretchBend::getStretchBends
    const vector< StretchBend > & getStretchBends() const
    Definition MMFF94StretchBend.h:155
    │ │ │ +
    BALL::MMFF94StretchBend::calculateBendEmpiricalReferenceAngle
    double calculateBendEmpiricalReferenceAngle(Atom &atom1, Atom &atom2, Atom &atom3) const
    Bend emperical reference angle.
    │ │ │ +
    BALL::MMFF94StretchBend::calculateStretchConstant
    double calculateStretchConstant(const Bond &bond, double r0)
    │ │ │ +
    BALL::MMFF94StretchBend::calculateSBTIJK
    Index calculateSBTIJK(Position angle_type, bool bond_type1, bool bond_type2)
    │ │ │ +
    BALL::MMFF94StretchBend::calculateBendEmpiricalForceConstant
    double calculateBendEmpiricalForceConstant(Atom &atom1, Atom &atom2, Atom &atom3, double angle_0) const
    Bend emperical force constant.
    │ │ │ +
    BALL::MMFF94StretchBend::calculateStretchR0
    double calculateStretchR0(const Bond &bond)
    Calculate the radius value per Schomaker-Stevenson Rule.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,81 +1,335 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _F_O_R_M_A_T │ │ │ │ -SCWRLRotamerFile.h │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _M_M_F_F_9_4 │ │ │ │ +MMFF94StretchBend.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_FORMAT_SCWRLROTAMERFILE_H │ │ │ │ -6#define BALL_FORMAT_SCWRLROTAMERFILE_H │ │ │ │ -7 │ │ │ │ -8#include <_B_A_L_L_/_F_O_R_M_A_T_/_l_i_n_e_B_a_s_e_d_F_i_l_e_._h> │ │ │ │ +4// $Id: MMFF94StretchBend.h,v 1.1.8.1 2007/03/25 21:25:18 oliver Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H │ │ │ │ +8#define BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H │ │ │ │ 9 │ │ │ │ -10namespace _B_A_L_L │ │ │ │ -11{ │ │ │ │ -13 class RotamerLibrary; │ │ │ │ -_2_2 class _B_A_L_L___E_X_P_O_R_T _S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e │ │ │ │ -23 : public _L_i_n_e_B_a_s_e_d_F_i_l_e │ │ │ │ -24 { │ │ │ │ -25 public: │ │ │ │ -26 │ │ │ │ -_3_1 _S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e(); │ │ │ │ -32 │ │ │ │ -_3_4 _S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e(const _S_t_r_i_n_g& name, _F_i_l_e_:_:_O_p_e_n_M_o_d_e open_mode = std::ios:: │ │ │ │ -in); │ │ │ │ -35 │ │ │ │ -_3_7 virtual _~_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e(); │ │ │ │ +10#ifndef BALL_MOLMEC_COMMON_FORCEFIELDCOMPONENT_H │ │ │ │ +11# include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h> │ │ │ │ +12#endif │ │ │ │ +13 │ │ │ │ +14#ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H │ │ │ │ +15# include <_B_A_L_L_/_M_O_L_M_E_C_/_M_M_F_F_9_4_/_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ +16#endif │ │ │ │ +17 │ │ │ │ +18namespace _B_A_L_L │ │ │ │ +19{ │ │ │ │ +20 class MMFF94; │ │ │ │ +21 │ │ │ │ +_2_5 class _B_A_L_L___E_X_P_O_R_T _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ +26 : public _F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t │ │ │ │ +27 { │ │ │ │ +28 public: │ │ │ │ +29 │ │ │ │ +_3_0 struct _B_A_L_L___E_X_P_O_R_T _S_t_r_e_t_c_h_B_e_n_d │ │ │ │ +31 { │ │ │ │ +_3_2 double _k_b_a___i_j_k; │ │ │ │ +_3_3 double _k_b_a___k_j_i; │ │ │ │ +_3_4 double _e_n_e_r_g_y; // debug │ │ │ │ +_3_5 _I_n_d_e_x _s_b_t_i_j_k; │ │ │ │ +_3_6 _I_n_d_e_x _s_t_r_e_t_c_h___i___j, stretch_j_k; │ │ │ │ +_3_7 _I_n_d_e_x _b_e_n_d___i_n_d_e_x; │ │ │ │ +38 }; │ │ │ │ 39 │ │ │ │ -40 │ │ │ │ -_4_5 const _S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e& operator = (const _S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e& file); │ │ │ │ -46 │ │ │ │ -_4_8 void operator >> (_R_o_t_a_m_e_r_L_i_b_r_a_r_y& rotamer_library); │ │ │ │ -49 │ │ │ │ -50 // TODO output operator???? │ │ │ │ -52 │ │ │ │ -_5_6 void _r_e_a_d_S_C_W_R_L_B_a_c_k_b_o_n_e_D_e_p_e_n_d_e_n_t_L_i_b_r_a_r_y_F_i_l_e(_R_o_t_a_m_e_r_L_i_b_r_a_r_y& library); │ │ │ │ -57 │ │ │ │ -_6_1 void _r_e_a_d_S_C_W_R_L_B_a_c_k_b_o_n_e_I_n_d_e_p_e_n_d_e_n_t_L_i_b_r_a_r_y_F_i_l_e(_R_o_t_a_m_e_r_L_i_b_r_a_r_y& library); │ │ │ │ -62 }; │ │ │ │ -63} // namespace BALL │ │ │ │ -64 │ │ │ │ -65#endif // BALL_FORMAT_SCWRLROTAMERFILE_H │ │ │ │ -_l_i_n_e_B_a_s_e_d_F_i_l_e_._h │ │ │ │ +_4_1 struct _B_A_L_L___E_X_P_O_R_T _B_e_n_d │ │ │ │ +42 { │ │ │ │ +_4_3 _B_e_n_d(); │ │ │ │ +44 │ │ │ │ +_4_5 double _t_h_e_t_a_0; │ │ │ │ +_4_6 double _d_e_l_t_a___t_h_e_t_a; │ │ │ │ +_4_7 double _t_h_e_t_a; │ │ │ │ +_4_8 double _k_a; │ │ │ │ +_4_9 _A_t_o_m* _a_t_o_m_1; │ │ │ │ +_5_0 _A_t_o_m* _a_t_o_m_2; │ │ │ │ +_5_1 _A_t_o_m* _a_t_o_m_3; │ │ │ │ +_5_2 bool _i_s___l_i_n_e_a_r; │ │ │ │ +_5_3 _P_o_s_i_t_i_o_n _A_T_I_J_K; │ │ │ │ +_5_4 double _e_n_e_r_g_y; // debug │ │ │ │ +_5_5 bool _e_m_p_e_r_i_c_a_l; // debug │ │ │ │ +_5_6 _T_V_e_c_t_o_r_3_<_d_o_u_b_l_e_> _n_1, n2; │ │ │ │ +57 }; │ │ │ │ +58 │ │ │ │ +_6_0 struct _B_A_L_L___E_X_P_O_R_T _S_t_r_e_t_c_h │ │ │ │ +61 { │ │ │ │ +_6_2 _S_t_r_e_t_c_h() │ │ │ │ +63 : atom1(NULL), │ │ │ │ +64 atom2(NULL), │ │ │ │ +65 kb(0.0), │ │ │ │ +66 r0(0.0), │ │ │ │ +67 delta_r(0.0), │ │ │ │ +68 sbmb(false), │ │ │ │ +69 emperical(false) │ │ │ │ +70 { │ │ │ │ +71 } │ │ │ │ +72 │ │ │ │ +_7_3 _A_t_o_m* _a_t_o_m_1; │ │ │ │ +_7_4 _A_t_o_m* _a_t_o_m_2; │ │ │ │ +_7_5 double _k_b; │ │ │ │ +_7_6 double _r_0; │ │ │ │ +_7_7 double _d_e_l_t_a___r; │ │ │ │ +_7_8 bool _s_b_m_b; │ │ │ │ +_7_9 bool _e_m_p_e_r_i_c_a_l; │ │ │ │ +_8_0 _V_e_c_t_o_r_3 _n; │ │ │ │ +81 }; │ │ │ │ +82 │ │ │ │ +_8_4 #define MMFF94_BENDS_ENABLED "enable Bends" │ │ │ │ +85 │ │ │ │ +_8_7 #define MMFF94_STRETCHES_ENABLED "enable Stretches" │ │ │ │ +88 │ │ │ │ +_9_0 #define MMFF94_STRETCHBENDS_ENABLED "enable StrechBends" │ │ │ │ +91 │ │ │ │ +92 _B_A_L_L___C_R_E_A_T_E(MMFF94StretchBend) │ │ │ │ +93 │ │ │ │ +94 │ │ │ │ +_9_6 _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d(); │ │ │ │ +97 │ │ │ │ +_1_0_0 _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d(_F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ +101 │ │ │ │ +_1_0_4 _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d(const _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d& to_copy); │ │ │ │ +105 │ │ │ │ +_1_0_8 virtual ~_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d(); │ │ │ │ +109 │ │ │ │ +_1_1_3 virtual bool setup(); │ │ │ │ +114 │ │ │ │ +_1_1_6 virtual double updateEnergy(); │ │ │ │ +117 │ │ │ │ +_1_1_9 virtual double updateBendEnergy(); │ │ │ │ +120 │ │ │ │ +_1_2_2 virtual double updateStretchEnergy(); │ │ │ │ +123 │ │ │ │ +_1_2_5 virtual double updateStretchBendEnergy(); │ │ │ │ +126 │ │ │ │ +_1_2_8 double getStretchEnergy() const; │ │ │ │ +129 │ │ │ │ +_1_3_1 double getBendEnergy() const; │ │ │ │ +132 │ │ │ │ +_1_3_4 double getStretchBendEnergy() const; │ │ │ │ +135 │ │ │ │ +_1_3_7 virtual void updateForces(); │ │ │ │ +138 │ │ │ │ +_1_4_0 virtual void updateBendForces(); │ │ │ │ +141 │ │ │ │ +_1_4_3 virtual void updateStretchForces(); │ │ │ │ +144 │ │ │ │ +_1_4_6 virtual void updateStretchBendForces(); │ │ │ │ +147 │ │ │ │ +_1_4_9 const vector<_B_e_n_d>& getBends() const { return bends_;} │ │ │ │ +150 │ │ │ │ +_1_5_2 const vector& _g_e_t_S_t_r_e_t_c_h_e_s() const { return stretches_;} │ │ │ │ +153 │ │ │ │ +_1_5_5 const vector& _g_e_t_S_t_r_e_t_c_h_B_e_n_d_s() const { return │ │ │ │ +stretch_bends_;} │ │ │ │ +156 │ │ │ │ +_1_5_8 _I_n_d_e_x _c_a_l_c_u_l_a_t_e_S_B_T_I_J_K(_P_o_s_i_t_i_o_n angle_type, │ │ │ │ +159 bool bond_type1, │ │ │ │ +160 bool bond_type2); │ │ │ │ +161 │ │ │ │ +_1_6_3 _P_o_s_i_t_i_o_n _g_e_t_B_e_n_d_T_y_p_e(const _B_o_n_d& bond1, const _B_o_n_d& bond2, │ │ │ │ +164 _A_t_o_m& atom1, _A_t_o_m& atom2, _A_t_o_m& atom3) const; │ │ │ │ +165 │ │ │ │ +_1_6_7 double _c_a_l_c_u_l_a_t_e_B_e_n_d_E_m_p_i_r_i_c_a_l_R_e_f_e_r_e_n_c_e_A_n_g_l_e(_A_t_o_m& atom1, _A_t_o_m& atom2, _A_t_o_m& │ │ │ │ +atom3) const; │ │ │ │ +168 │ │ │ │ +_1_7_0 double _c_a_l_c_u_l_a_t_e_B_e_n_d_E_m_p_i_r_i_c_a_l_F_o_r_c_e_C_o_n_s_t_a_n_t(_A_t_o_m& atom1, _A_t_o_m& atom2, _A_t_o_m& │ │ │ │ +atom3, double angle_0) const; │ │ │ │ +171 │ │ │ │ +_1_7_3 double _c_a_l_c_u_l_a_t_e_S_t_r_e_t_c_h_R_0(const _B_o_n_d& bond); │ │ │ │ +174 │ │ │ │ +_1_7_6 double _c_a_l_c_u_l_a_t_e_S_t_r_e_t_c_h_C_o_n_s_t_a_n_t(const _B_o_n_d& bond, double r0); │ │ │ │ +177 │ │ │ │ +178 private: │ │ │ │ +179 │ │ │ │ +180 inline void AddDV3_(_V_e_c_t_o_r_3& f3, const _T_V_e_c_t_o_r_3_<_d_o_u_b_l_e_> d3); │ │ │ │ +181 void calculateDeltas_(); │ │ │ │ +182 bool setupBends_(); │ │ │ │ +183 bool setupStretches_(); │ │ │ │ +184 bool setupStretchBends_(); │ │ │ │ +185 │ │ │ │ +186 void errorOccurred_(const _S_t_r_i_n_g& string, │ │ │ │ +187 const _A_t_o_m& a1, const _A_t_o_m& a2, const _A_t_o_m& a3); │ │ │ │ +188 │ │ │ │ +189 vector bends_; │ │ │ │ +190 vector stretches_; │ │ │ │ +191 vector stretch_bends_; │ │ │ │ +192 │ │ │ │ +193 const _M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s* stretch_parameters_; │ │ │ │ +194 _M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s bend_parameters_; │ │ │ │ +195 _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s sb_parameters_; │ │ │ │ +196 │ │ │ │ +197 static double bend_z_[]; │ │ │ │ +198 static double bend_c_[]; │ │ │ │ +199 static _S_t_r_i_n_g bend_elements_[]; │ │ │ │ +200 │ │ │ │ +201 double stretch_energy_; │ │ │ │ +202 double bend_energy_; │ │ │ │ +203 double stretch_bend_energy_; │ │ │ │ +204 │ │ │ │ +205 _M_M_F_F_9_4* mmff94_; │ │ │ │ +206 bool stretch_enabled_, bend_enabled_, stretchbend_enabled_; │ │ │ │ +207 }; │ │ │ │ +208} // namespace BALL │ │ │ │ +209 │ │ │ │ +210#endif // BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H │ │ │ │ +_M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h │ │ │ │ +_f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ _B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_L_i_n_e_B_a_s_e_d_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _l_i_n_e_B_a_s_e_d_F_i_l_e_._h_:_2_2 │ │ │ │ -_B_A_L_L_:_:_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e │ │ │ │ -Reads Dunbrack/SCWRL rotamer library files. │ │ │ │ -DDeeffiinniittiioonn _S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e_._h_:_2_4 │ │ │ │ -_B_A_L_L_:_:_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e_:_:_r_e_a_d_S_C_W_R_L_B_a_c_k_b_o_n_e_I_n_d_e_p_e_n_d_e_n_t_L_i_b_r_a_r_y_F_i_l_e │ │ │ │ -void readSCWRLBackboneIndependentLibraryFile(RotamerLibrary &library) │ │ │ │ -_B_A_L_L_:_:_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e_:_:_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e │ │ │ │ -SCWRLRotamerFile() │ │ │ │ -Default constructor. │ │ │ │ -_B_A_L_L_:_:_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e_:_:_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e │ │ │ │ -SCWRLRotamerFile(const String &name, File::OpenMode open_mode=std::ios::in) │ │ │ │ -Detailed constructor. │ │ │ │ -_B_A_L_L_:_:_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e_:_:_~_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e │ │ │ │ -virtual ~SCWRLRotamerFile() │ │ │ │ -Destructor. │ │ │ │ -_B_A_L_L_:_:_S_C_W_R_L_R_o_t_a_m_e_r_F_i_l_e_:_:_r_e_a_d_S_C_W_R_L_B_a_c_k_b_o_n_e_D_e_p_e_n_d_e_n_t_L_i_b_r_a_r_y_F_i_l_e │ │ │ │ -void readSCWRLBackboneDependentLibraryFile(RotamerLibrary &library) │ │ │ │ -_B_A_L_L_:_:_R_o_t_a_m_e_r_L_i_b_r_a_r_y │ │ │ │ -Rotamer Library Class. │ │ │ │ -DDeeffiinniittiioonn _r_o_t_a_m_e_r_L_i_b_r_a_r_y_._h_:_3_4 │ │ │ │ -_B_A_L_L_:_:_F_i_l_e_:_:_O_p_e_n_M_o_d_e │ │ │ │ -std::ios::openmode OpenMode │ │ │ │ -DDeeffiinniittiioonn _f_i_l_e_._h_:_1_6_5 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ +_B_A_L_L_:_:_B_o_n_d │ │ │ │ +DDeeffiinniittiioonn _b_o_n_d_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3 │ │ │ │ +DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_1 │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h_:_3_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_._h_:_5_1 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_1_8_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_2_6_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_P_a_r_a_m_e_t_e_r_s_._h_:_3_1_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_2_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_g_e_t_S_t_r_e_t_c_h_e_s │ │ │ │ +const vector< Stretch > & getStretches() const │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_1_5_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_g_e_t_B_e_n_d_T_y_p_e │ │ │ │ +Position getBendType(const Bond &bond1, const Bond &bond2, Atom &atom1, Atom │ │ │ │ +&atom2, Atom &atom3) const │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_g_e_t_S_t_r_e_t_c_h_B_e_n_d_s │ │ │ │ +const vector< StretchBend > & getStretchBends() const │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_1_5_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_B_e_n_d_E_m_p_i_r_i_c_a_l_R_e_f_e_r_e_n_c_e_A_n_g_l_e │ │ │ │ +double calculateBendEmpiricalReferenceAngle(Atom &atom1, Atom &atom2, Atom │ │ │ │ +&atom3) const │ │ │ │ +Bend emperical reference angle. │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_S_t_r_e_t_c_h_C_o_n_s_t_a_n_t │ │ │ │ +double calculateStretchConstant(const Bond &bond, double r0) │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_S_B_T_I_J_K │ │ │ │ +Index calculateSBTIJK(Position angle_type, bool bond_type1, bool bond_type2) │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_B_e_n_d_E_m_p_i_r_i_c_a_l_F_o_r_c_e_C_o_n_s_t_a_n_t │ │ │ │ +double calculateBendEmpiricalForceConstant(Atom &atom1, Atom &atom2, Atom │ │ │ │ +&atom3, double angle_0) const │ │ │ │ +Bend emperical force constant. │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_c_a_l_c_u_l_a_t_e_S_t_r_e_t_c_h_R_0 │ │ │ │ +double calculateStretchR0(const Bond &bond) │ │ │ │ +Calculate the radius value per Schomaker-Stevenson Rule. │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_b_e_n_d___i_n_d_e_x │ │ │ │ +Index bend_index │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_s_t_r_e_t_c_h___i___j │ │ │ │ +Index stretch_i_j │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_k_b_a___i_j_k │ │ │ │ +double kba_ijk │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_s_b_t_i_j_k │ │ │ │ +Index sbtijk │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_e_n_e_r_g_y │ │ │ │ +double energy │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_4 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_B_e_n_d_:_:_k_b_a___k_j_i │ │ │ │ +double kba_kji │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_3_3 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d │ │ │ │ +see MMFFANG.PAR │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_t_h_e_t_a │ │ │ │ +double theta │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_n_1 │ │ │ │ +TVector3< double > n1 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_A_T_I_J_K │ │ │ │ +Position ATIJK │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_3 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_i_s___l_i_n_e_a_r │ │ │ │ +bool is_linear │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_B_e_n_d │ │ │ │ +Bend() │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_t_h_e_t_a_0 │ │ │ │ +double theta0 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_a_t_o_m_2 │ │ │ │ +Atom * atom2 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_e_m_p_e_r_i_c_a_l │ │ │ │ +bool emperical │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_a_t_o_m_1 │ │ │ │ +Atom * atom1 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_k_a │ │ │ │ +double ka │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_d_e_l_t_a___t_h_e_t_a │ │ │ │ +double delta_theta │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_4_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_e_n_e_r_g_y │ │ │ │ +double energy │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_4 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_B_e_n_d_:_:_a_t_o_m_3 │ │ │ │ +Atom * atom3 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_5_1 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_6_1 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_d_e_l_t_a___r │ │ │ │ +double delta_r │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_7 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_k_b │ │ │ │ +double kb │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_5 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_n │ │ │ │ +Vector3 n │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_8_0 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_e_m_p_e_r_i_c_a_l │ │ │ │ +bool emperical │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_9 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_a_t_o_m_2 │ │ │ │ +Atom * atom2 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_s_b_m_b │ │ │ │ +bool sbmb │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_8 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_S_t_r_e_t_c_h │ │ │ │ +Stretch() │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_6_2 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_r_0 │ │ │ │ +double r0 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_6 │ │ │ │ +_B_A_L_L_:_:_M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_:_:_S_t_r_e_t_c_h_:_:_a_t_o_m_1 │ │ │ │ +Atom * atom1 │ │ │ │ +DDeeffiinniittiioonn _M_M_F_F_9_4_S_t_r_e_t_c_h_B_e_n_d_._h_:_7_3 │ │ │ │ +_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/d9f/a07902.html │ │ │ @@ -80,15 +80,15 @@ │ │ │ Protected Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members │ │ │
    BALL::VIEW::InteractionMode Class Referenceabstract
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/MODES/interactionMode.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/MODES/interactionMode.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::InteractionMode:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ QObject │ │ │ @@ -184,15 +184,15 @@ │ │ │ QAction * main_action_ │ │ │   │ │ │ bool is_current_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 24 of file interactionMode.h.

    │ │ │ +

    Definition at line 24 of file interactionMode.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ InteractionMode()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -456,15 +456,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
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    Definition at line 56 of file interactionMode.h.

    │ │ │ +

    Definition at line 56 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ keyPressEvent()

    │ │ │ │ │ │
    │ │ │ @@ -733,15 +733,15 @@ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Reimplemented in BALL::VIEW::EditMode, and BALL::VIEW::MoveMode.

    │ │ │ │ │ │ -

    Definition at line 43 of file interactionMode.h.

    │ │ │ +

    Definition at line 43 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ requestModeChange

    │ │ │ │ │ │
    │ │ │ @@ -787,15 +787,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 57 of file interactionMode.h.

    │ │ │ +

    Definition at line 57 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ setMouseSensitivity()

    │ │ │ │ │ │
    │ │ │ @@ -901,15 +901,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 68 of file interactionMode.h.

    │ │ │ +

    Definition at line 68 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ is_current_

    │ │ │ │ │ │
    │ │ │ @@ -925,15 +925,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 72 of file interactionMode.h.

    │ │ │ +

    Definition at line 72 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ main_action_

    │ │ │ │ │ │
    │ │ │ @@ -949,15 +949,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 71 of file interactionMode.h.

    │ │ │ +

    Definition at line 71 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ mouse_pos_new_

    │ │ │ │ │ │
    │ │ │ @@ -973,15 +973,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 67 of file interactionMode.h.

    │ │ │ +

    Definition at line 67 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ mouse_pos_old_

    │ │ │ │ │ │
    │ │ │ @@ -997,15 +997,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 66 of file interactionMode.h.

    │ │ │ +

    Definition at line 66 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ mouse_sensitivity_

    │ │ │ │ │ │
    │ │ │ @@ -1021,15 +1021,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 69 of file interactionMode.h.

    │ │ │ +

    Definition at line 69 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ mouse_wheel_sensitivity_

    │ │ │ │ │ │
    │ │ │ @@ -1045,15 +1045,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 70 of file interactionMode.h.

    │ │ │ +

    Definition at line 70 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ scene_

    │ │ │ │ │ │
    │ │ │ @@ -1069,15 +1069,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 65 of file interactionMode.h.

    │ │ │ +

    Definition at line 65 of file interactionMode.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/da4/a01631.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: molecule.h File Reference │ │ │ +BALL: knnModel.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,39 +65,39 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    molecule.h File Reference
    │ │ │ +
    knnModel.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/KERNEL/atomContainer.h>
    │ │ │ -#include <BALL/KERNEL/fragment.h>
    │ │ │ -#include <BALL/KERNEL/fragmentIterator.h>
    │ │ │ +
    #include <BALL/QSAR/allModel.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::Molecule
    class  BALL::QSAR::KNNModel
     
    │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ + │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::QSAR
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,21 +1,21 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ + * _Q_S_A_R │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -molecule.h File Reference │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_f_r_a_g_m_e_n_t_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_f_r_a_g_m_e_n_t_I_t_e_r_a_t_o_r_._h> │ │ │ │ +knnModel.h File Reference │ │ │ │ +#include <_B_A_L_L_/_Q_S_A_R_/_a_l_l_M_o_d_e_l_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_M_o_l_e_c_u_l_e │ │ │ │ +class   _B_A_L_L_:_:_Q_S_A_R_:_:_K_N_N_M_o_d_e_l │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +namespace   _B_A_L_L_:_:_Q_S_A_R │ │ │ │ +  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/da4/a01631_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: molecule.h Source File │ │ │ +BALL: knnModel.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,229 +70,71 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    molecule.h
    │ │ │ +
    knnModel.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_KERNEL_MOLECULE_H
    │ │ │ -
    6#define BALL_KERNEL_MOLECULE_H
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    7
    │ │ │ -
    8#ifndef BALL_KERNEL_ATOMCONTAINER_H
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    9# include <BALL/KERNEL/atomContainer.h>
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    10#endif
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    11
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    12#ifndef BALL_KERNEL_FRAGMENT_H
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    13# include <BALL/KERNEL/fragment.h>
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    14#endif
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    15
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    16#ifndef BALL_KERNEL_FRAGMENTITERATOR_H
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    17# include <BALL/KERNEL/fragmentIterator.h>
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    18#endif
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    19
    │ │ │ -
    20namespace BALL
    │ │ │ -
    21{
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    22 class System;
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    23
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    29 class BALL_EXPORT Molecule
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    30 : public AtomContainer
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    31 {
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    32 public:
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    33
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    34 BALL_CREATE_DEEP(Molecule)
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    35
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    36
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    39
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    40
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    42 enum Property
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    43 {
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    44 IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES,
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    45 NUMBER_OF_PROPERTIES
    │ │ │ -
    46 };
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    47
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    49
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    52
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    55 Molecule();
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    56
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    59 Molecule(const Molecule& molecule, bool deep = true);
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    60
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    63 Molecule(const AtomContainer& atomContainer, bool deep = true);
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    64
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    67 Molecule(const String& name);
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    68
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    71 virtual ~Molecule();
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    72
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    74
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    77
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    81 void persistentWrite(PersistenceManager& pm, const char* name = 0) const;
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    82
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    86 void persistentRead(PersistenceManager& pm);
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    87
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    89
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    92
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    97 void set(const Molecule& molecule, bool deep = true);
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    98
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    102 Molecule& operator = (const Molecule& molecule);
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    103
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    108 void get(Molecule& molecule, bool deep = true) const;
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    109
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    113 void swap(Molecule& molecule);
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    114
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    116
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    119
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    123 System* getSystem();
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    124
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    128 const System* getSystem() const;
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    129
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    133 void prepend(Atom& atom);
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    134
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    138 void append(Atom& atom);
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    139
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    143 void insert(Atom& atom);
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    144
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    149 void insertBefore(Atom& atom, Composite& before);
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    150
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    155 void insertAfter(Atom& atom, Composite& after);
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    156
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    160 bool remove(Atom& atom);
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    161
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    165 void prepend(AtomContainer& atom_container);
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    166
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    170 void append(AtomContainer& atom_container);
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    171
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    175 void insert(AtomContainer& atom_container);
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    176
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    181 void insertBefore(AtomContainer& atom_container, Composite& before);
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    182
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    187 void insertAfter(AtomContainer& atom_container, Composite& after);
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    188
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    192 void spliceBefore(AtomContainer& atom_container);
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    193
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    197 void spliceAfter(AtomContainer& atom_container);
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    198
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    204 void splice(AtomContainer& atom_container);
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    205
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    209 bool remove(AtomContainer& atom_container);
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    210
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    212
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    216 virtual bool isMolecule() const { return true; }
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    218
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    222
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    229 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
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    230
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    232
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    237 bool operator == (const Molecule& molecule) const;
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    238
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    242 bool operator != (const Molecule& molecule) const;
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    243
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    244
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    245 BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Fragment)
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    246 BALL_DECLARE_STD_ITERATOR_WRAPPER(Molecule, Fragment, fragments)
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    247
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    248
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    249 protected:
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    250
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    251 Molecule* getMolecule();
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    252
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    253 const Molecule* getMolecule() const;
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    254
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    255 AtomContainer* getSuperAtomContainer();
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    256
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    257 const AtomContainer* getSuperAtomContainer() const;
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    258
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    259 void prepend(Molecule& molecule);
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    260
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    261 void append(Molecule& molecule);
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    262
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    263 void insert(Molecule& molecule);
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    264
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    265 void insertBefore(Molecule& molecule, Composite& composite);
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    266
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    267 void insertAfter(Molecule& molecule, Composite& composite);
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    268
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    269 bool remove(Molecule& molecule);
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    270
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    271 bool isSubAtomContainerOf(const AtomContainer& atom_container) const;
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    272 };
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    273} // namespace BALL
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    274
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    275#endif // BALL_KERNEL_MOLECULE_H
    │ │ │ -
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS
    #define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
    Definition iterator.h:25
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_DECLARE_STD_ITERATOR_WRAPPER
    #define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
    Definition stdIteratorWrapper.h:30
    │ │ │ -
    BALL_CREATE_DEEP
    #define BALL_CREATE_DEEP(name)
    Definition create.h:26
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Molecule::persistentRead
    void persistentRead(PersistenceManager &pm)
    │ │ │ -
    BALL::Molecule::dump
    virtual void dump(std::ostream &s=std::cout, Size depth=0) const
    │ │ │ -
    BALL::Molecule::persistentWrite
    void persistentWrite(PersistenceManager &pm, const char *name=0) const
    │ │ │ -
    BALL::Molecule::getMolecule
    Molecule * getMolecule()
    │ │ │ -
    BALL::Molecule::~Molecule
    virtual ~Molecule()
    │ │ │ -
    BALL::Molecule::insertBefore
    void insertBefore(Molecule &molecule, Composite &composite)
    │ │ │ -
    BALL::Molecule::getSystem
    const System * getSystem() const
    │ │ │ -
    BALL::Molecule::insert
    void insert(AtomContainer &atom_container)
    │ │ │ -
    BALL::Molecule::remove
    bool remove(Atom &atom)
    │ │ │ -
    BALL::Molecule::insertBefore
    void insertBefore(AtomContainer &atom_container, Composite &before)
    │ │ │ -
    BALL::Molecule::splice
    void splice(AtomContainer &atom_container)
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    BALL::Molecule::prepend
    void prepend(Atom &atom)
    │ │ │ -
    BALL::Molecule::swap
    void swap(Molecule &molecule)
    │ │ │ -
    BALL::Molecule::prepend
    void prepend(AtomContainer &atom_container)
    │ │ │ -
    BALL::Molecule::remove
    bool remove(Molecule &molecule)
    │ │ │ -
    BALL::Molecule::set
    void set(const Molecule &molecule, bool deep=true)
    │ │ │ -
    BALL::Molecule::insert
    void insert(Atom &atom)
    │ │ │ -
    BALL::Molecule::get
    void get(Molecule &molecule, bool deep=true) const
    │ │ │ -
    BALL::Molecule::append
    void append(Atom &atom)
    │ │ │ -
    BALL::Molecule::Molecule
    Molecule(const String &name)
    │ │ │ -
    BALL::Molecule::append
    void append(Molecule &molecule)
    │ │ │ -
    BALL::Molecule::Molecule
    Molecule(const AtomContainer &atomContainer, bool deep=true)
    │ │ │ -
    BALL::Molecule::insertAfter
    void insertAfter(AtomContainer &atom_container, Composite &after)
    │ │ │ -
    BALL::Molecule::getSystem
    System * getSystem()
    │ │ │ -
    BALL::Molecule::insertAfter
    void insertAfter(Molecule &molecule, Composite &composite)
    │ │ │ -
    BALL::Molecule::insertBefore
    void insertBefore(Atom &atom, Composite &before)
    │ │ │ -
    BALL::Molecule::spliceBefore
    void spliceBefore(AtomContainer &atom_container)
    │ │ │ -
    BALL::Molecule::insert
    void insert(Molecule &molecule)
    │ │ │ -
    BALL::Molecule::isMolecule
    virtual bool isMolecule() const
    Definition molecule.h:216
    │ │ │ -
    BALL::Molecule::Molecule
    Molecule(const Molecule &molecule, bool deep=true)
    │ │ │ -
    BALL::Molecule::getMolecule
    const Molecule * getMolecule() const
    │ │ │ -
    BALL::Molecule::remove
    bool remove(AtomContainer &atom_container)
    │ │ │ -
    BALL::Molecule::append
    void append(AtomContainer &atom_container)
    │ │ │ -
    BALL::Molecule::getSuperAtomContainer
    const AtomContainer * getSuperAtomContainer() const
    │ │ │ -
    BALL::Molecule::prepend
    void prepend(Molecule &molecule)
    │ │ │ -
    BALL::Molecule::insertAfter
    void insertAfter(Atom &atom, Composite &after)
    │ │ │ -
    BALL::Molecule::spliceAfter
    void spliceAfter(AtomContainer &atom_container)
    │ │ │ -
    BALL::Molecule::getSuperAtomContainer
    AtomContainer * getSuperAtomContainer()
    │ │ │ - │ │ │ -
    BALL::Molecule::isSubAtomContainerOf
    bool isSubAtomContainerOf(const AtomContainer &atom_container) const
    │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    4//
    │ │ │ +
    5
    │ │ │ +
    6#ifndef BALL_QSAR_KNNMODEL_H
    │ │ │ +
    7#define BALL_QSAR_KNNMODEL_H
    │ │ │ +
    8
    │ │ │ +
    9#ifndef BALL_QSAR_ALLMODEL_H
    │ │ │ +
    10#include <BALL/QSAR/allModel.h>
    │ │ │ +
    11#endif
    │ │ │ +
    12
    │ │ │ +
    13namespace BALL
    │ │ │ +
    14{
    │ │ │ +
    15 namespace QSAR
    │ │ │ +
    16 {
    │ │ │ +
    17
    │ │ │ +
    │ │ │ +
    19 class BALL_EXPORT KNNModel : public ALLModel
    │ │ │ +
    20 {
    │ │ │ +
    21 public:
    │ │ │ +
    25 KNNModel(const QSARData& q, int k=3);
    │ │ │ +
    27
    │ │ │ +
    28 void calculateWeights(Eigen::MatrixXd& dist, Eigen::VectorXd& w);
    │ │ │ +
    29
    │ │ │ +
    30 void setParameters(vector<double>& v);
    │ │ │ +
    31
    │ │ │ +
    32 vector<double> getParameters() const;
    │ │ │ +
    33
    │ │ │ +
    34 bool optimizeParameters(int k, int no_steps);
    │ │ │ +
    35
    │ │ │ +
    36 private:
    │ │ │ +
    37 int k_ ;
    │ │ │ +
    38 };
    │ │ │ +
    │ │ │ +
    39 }
    │ │ │ +
    40}
    │ │ │ +
    41
    │ │ │ +
    42#endif // KNNMODEL
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::QSAR::KNNModel::setParameters
    void setParameters(vector< double > &v)
    │ │ │ +
    BALL::QSAR::KNNModel::getParameters
    vector< double > getParameters() const
    │ │ │ +
    BALL::QSAR::KNNModel::KNNModel
    KNNModel(const QSARData &q, int k=3)
    │ │ │ +
    BALL::QSAR::KNNModel::optimizeParameters
    bool optimizeParameters(int k, int no_steps)
    │ │ │ +
    BALL::QSAR::KNNModel::calculateWeights
    void calculateWeights(Eigen::MatrixXd &dist, Eigen::VectorXd &w)
    │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,275 +1,70 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ -molecule.h │ │ │ │ + * _Q_S_A_R │ │ │ │ +knnModel.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_KERNEL_MOLECULE_H │ │ │ │ -6#define BALL_KERNEL_MOLECULE_H │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_KERNEL_ATOMCONTAINER_H │ │ │ │ -9# include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12#ifndef BALL_KERNEL_FRAGMENT_H │ │ │ │ -13# include <_B_A_L_L_/_K_E_R_N_E_L_/_f_r_a_g_m_e_n_t_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16#ifndef BALL_KERNEL_FRAGMENTITERATOR_H │ │ │ │ -17# include <_B_A_L_L_/_K_E_R_N_E_L_/_f_r_a_g_m_e_n_t_I_t_e_r_a_t_o_r_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20namespace _B_A_L_L │ │ │ │ -21{ │ │ │ │ -22 class System; │ │ │ │ -23 │ │ │ │ -_2_9 class _B_A_L_L___E_X_P_O_R_T _M_o_l_e_c_u_l_e │ │ │ │ -30 : public _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -31 { │ │ │ │ -32 public: │ │ │ │ +4// │ │ │ │ +5 │ │ │ │ +6#ifndef BALL_QSAR_KNNMODEL_H │ │ │ │ +7#define BALL_QSAR_KNNMODEL_H │ │ │ │ +8 │ │ │ │ +9#ifndef BALL_QSAR_ALLMODEL_H │ │ │ │ +10#include <_B_A_L_L_/_Q_S_A_R_/_a_l_l_M_o_d_e_l_._h> │ │ │ │ +11#endif │ │ │ │ +12 │ │ │ │ +13namespace _B_A_L_L │ │ │ │ +14{ │ │ │ │ +15 namespace QSAR │ │ │ │ +16 { │ │ │ │ +17 │ │ │ │ +_1_9 class _B_A_L_L___E_X_P_O_R_T _K_N_N_M_o_d_e_l : public _A_L_L_M_o_d_e_l │ │ │ │ +20 { │ │ │ │ +21 public: │ │ │ │ +_2_5 _K_N_N_M_o_d_e_l(const _Q_S_A_R_D_a_t_a& q, int k=3); │ │ │ │ +27 │ │ │ │ +_2_8 void _c_a_l_c_u_l_a_t_e_W_e_i_g_h_t_s(Eigen::MatrixXd& dist, Eigen::VectorXd& w); │ │ │ │ +29 │ │ │ │ +_3_0 void _s_e_t_P_a_r_a_m_e_t_e_r_s(vector& v); │ │ │ │ +31 │ │ │ │ +_3_2 vector _g_e_t_P_a_r_a_m_e_t_e_r_s() const; │ │ │ │ 33 │ │ │ │ -34 _B_A_L_L___C_R_E_A_T_E___D_E_E_P(_M_o_l_e_c_u_l_e) │ │ │ │ +_3_4 bool _o_p_t_i_m_i_z_e_P_a_r_a_m_e_t_e_r_s(int k, int no_steps); │ │ │ │ 35 │ │ │ │ -36 │ │ │ │ -39 │ │ │ │ -40 │ │ │ │ -_4_2 enum _P_r_o_p_e_r_t_y │ │ │ │ -43 { │ │ │ │ -_4_4 IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES, │ │ │ │ -45 NUMBER_OF_PROPERTIES │ │ │ │ -_4_6 }; │ │ │ │ -47 │ │ │ │ -49 │ │ │ │ -52 │ │ │ │ -_5_5 _M_o_l_e_c_u_l_e(); │ │ │ │ -56 │ │ │ │ -_5_9 _M_o_l_e_c_u_l_e(const _M_o_l_e_c_u_l_e& molecule, bool deep = true); │ │ │ │ -60 │ │ │ │ -_6_3 _M_o_l_e_c_u_l_e(const _A_t_o_m_C_o_n_t_a_i_n_e_r& atomContainer, bool deep = true); │ │ │ │ -64 │ │ │ │ -_6_7 _M_o_l_e_c_u_l_e(const _S_t_r_i_n_g& name); │ │ │ │ -68 │ │ │ │ -_7_1 virtual _~_M_o_l_e_c_u_l_e(); │ │ │ │ -72 │ │ │ │ -74 │ │ │ │ -77 │ │ │ │ -_8_1 void _p_e_r_s_i_s_t_e_n_t_W_r_i_t_e(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm, const char* name = 0) const; │ │ │ │ -82 │ │ │ │ -_8_6 void _p_e_r_s_i_s_t_e_n_t_R_e_a_d(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm); │ │ │ │ -87 │ │ │ │ -89 │ │ │ │ -92 │ │ │ │ -_9_7 void _s_e_t(const _M_o_l_e_c_u_l_e& molecule, bool deep = true); │ │ │ │ -98 │ │ │ │ -_1_0_2 _M_o_l_e_c_u_l_e& operator = (const _M_o_l_e_c_u_l_e& molecule); │ │ │ │ -103 │ │ │ │ -_1_0_8 void _g_e_t(_M_o_l_e_c_u_l_e& molecule, bool deep = true) const; │ │ │ │ -109 │ │ │ │ -_1_1_3 void _s_w_a_p(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ -114 │ │ │ │ -116 │ │ │ │ -119 │ │ │ │ -_1_2_3 _S_y_s_t_e_m* _g_e_t_S_y_s_t_e_m(); │ │ │ │ -124 │ │ │ │ -_1_2_8 const _S_y_s_t_e_m* _g_e_t_S_y_s_t_e_m() const; │ │ │ │ -129 │ │ │ │ -_1_3_3 void _p_r_e_p_e_n_d(_A_t_o_m& atom); │ │ │ │ -134 │ │ │ │ -_1_3_8 void _a_p_p_e_n_d(_A_t_o_m& atom); │ │ │ │ -139 │ │ │ │ -_1_4_3 void _i_n_s_e_r_t(_A_t_o_m& atom); │ │ │ │ -144 │ │ │ │ -_1_4_9 void _i_n_s_e_r_t_B_e_f_o_r_e(_A_t_o_m& atom, _C_o_m_p_o_s_i_t_e& before); │ │ │ │ -150 │ │ │ │ -_1_5_5 void _i_n_s_e_r_t_A_f_t_e_r(_A_t_o_m& atom, _C_o_m_p_o_s_i_t_e& after); │ │ │ │ -156 │ │ │ │ -_1_6_0 bool _r_e_m_o_v_e(_A_t_o_m& atom); │ │ │ │ -161 │ │ │ │ -_1_6_5 void _p_r_e_p_e_n_d(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ -166 │ │ │ │ -_1_7_0 void _a_p_p_e_n_d(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ -171 │ │ │ │ -_1_7_5 void _i_n_s_e_r_t(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ -176 │ │ │ │ -_1_8_1 void _i_n_s_e_r_t_B_e_f_o_r_e(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container, _C_o_m_p_o_s_i_t_e& before); │ │ │ │ -182 │ │ │ │ -_1_8_7 void _i_n_s_e_r_t_A_f_t_e_r(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container, _C_o_m_p_o_s_i_t_e& after); │ │ │ │ -188 │ │ │ │ -_1_9_2 void _s_p_l_i_c_e_B_e_f_o_r_e(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ -193 │ │ │ │ -_1_9_7 void _s_p_l_i_c_e_A_f_t_e_r(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ -198 │ │ │ │ -_2_0_4 void _s_p_l_i_c_e(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ -205 │ │ │ │ -_2_0_9 bool _r_e_m_o_v_e(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ -210 │ │ │ │ -212 │ │ │ │ -_2_1_6 virtual bool _i_s_M_o_l_e_c_u_l_e() const { return true; } │ │ │ │ -218 │ │ │ │ -222 │ │ │ │ -_2_2_9 virtual void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const; │ │ │ │ -230 │ │ │ │ -232 │ │ │ │ -_2_3_7 bool operator == (const _M_o_l_e_c_u_l_e& molecule) const; │ │ │ │ -238 │ │ │ │ -_2_4_2 bool operator != (const _M_o_l_e_c_u_l_e& molecule) const; │ │ │ │ -243 │ │ │ │ -244 │ │ │ │ -245 _B_A_L_L___K_E_R_N_E_L___D_E_F_I_N_E___I_T_E_R_A_T_O_R___C_R_E_A_T_O_R_S(_F_r_a_g_m_e_n_t) │ │ │ │ -246 _B_A_L_L___D_E_C_L_A_R_E___S_T_D___I_T_E_R_A_T_O_R___W_R_A_P_P_E_R(_M_o_l_e_c_u_l_e, _F_r_a_g_m_e_n_t, fragments) │ │ │ │ -247 │ │ │ │ -248 │ │ │ │ -249 protected: │ │ │ │ -250 │ │ │ │ -_2_5_1 _M_o_l_e_c_u_l_e* _g_e_t_M_o_l_e_c_u_l_e(); │ │ │ │ -252 │ │ │ │ -_2_5_3 const _M_o_l_e_c_u_l_e* _g_e_t_M_o_l_e_c_u_l_e() const; │ │ │ │ -254 │ │ │ │ -_2_5_5 _A_t_o_m_C_o_n_t_a_i_n_e_r* _g_e_t_S_u_p_e_r_A_t_o_m_C_o_n_t_a_i_n_e_r(); │ │ │ │ -256 │ │ │ │ -_2_5_7 const _A_t_o_m_C_o_n_t_a_i_n_e_r* _g_e_t_S_u_p_e_r_A_t_o_m_C_o_n_t_a_i_n_e_r() const; │ │ │ │ -258 │ │ │ │ -_2_5_9 void _p_r_e_p_e_n_d(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ -260 │ │ │ │ -_2_6_1 void _a_p_p_e_n_d(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ -262 │ │ │ │ -_2_6_3 void _i_n_s_e_r_t(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ -264 │ │ │ │ -_2_6_5 void _i_n_s_e_r_t_B_e_f_o_r_e(_M_o_l_e_c_u_l_e& molecule, _C_o_m_p_o_s_i_t_e& composite); │ │ │ │ -266 │ │ │ │ -_2_6_7 void _i_n_s_e_r_t_A_f_t_e_r(_M_o_l_e_c_u_l_e& molecule, _C_o_m_p_o_s_i_t_e& composite); │ │ │ │ -268 │ │ │ │ -_2_6_9 bool _r_e_m_o_v_e(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ -270 │ │ │ │ -_2_7_1 bool _i_s_S_u_b_A_t_o_m_C_o_n_t_a_i_n_e_r_O_f(const _A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container) const; │ │ │ │ -272 }; │ │ │ │ -273} // namespace BALL │ │ │ │ -274 │ │ │ │ -275#endif // BALL_KERNEL_MOLECULE_H │ │ │ │ -_B_A_L_L___K_E_R_N_E_L___D_E_F_I_N_E___I_T_E_R_A_T_O_R___C_R_E_A_T_O_R_S │ │ │ │ -#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type) │ │ │ │ -DDeeffiinniittiioonn _i_t_e_r_a_t_o_r_._h_:_2_5 │ │ │ │ -_f_r_a_g_m_e_n_t_I_t_e_r_a_t_o_r_._h │ │ │ │ -_f_r_a_g_m_e_n_t_._h │ │ │ │ -_a_t_o_m_C_o_n_t_a_i_n_e_r_._h │ │ │ │ -_B_A_L_L___D_E_C_L_A_R_E___S_T_D___I_T_E_R_A_T_O_R___W_R_A_P_P_E_R │ │ │ │ -#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name) │ │ │ │ -DDeeffiinniittiioonn _s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h_:_3_0 │ │ │ │ -_B_A_L_L___C_R_E_A_T_E___D_E_E_P │ │ │ │ -#define BALL_CREATE_DEEP(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_2_6 │ │ │ │ +36 private: │ │ │ │ +37 int k_ ; │ │ │ │ +38 }; │ │ │ │ +39 } │ │ │ │ +40} │ │ │ │ +41 │ │ │ │ +42#endif // KNNMODEL │ │ │ │ +_a_l_l_M_o_d_e_l_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ -DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h_:_7_3 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_F_r_a_g_m_e_n_t │ │ │ │ -DDeeffiinniittiioonn _f_r_a_g_m_e_n_t_._h_:_2_2 │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e │ │ │ │ -DDeeffiinniittiioonn _m_o_l_e_c_u_l_e_._h_:_3_1 │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_M_o_l_e_c_u_l_e │ │ │ │ -Molecule() │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_e_r_s_i_s_t_e_n_t_R_e_a_d │ │ │ │ -void persistentRead(PersistenceManager &pm) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_d_u_m_p │ │ │ │ -virtual void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_e_r_s_i_s_t_e_n_t_W_r_i_t_e │ │ │ │ -void persistentWrite(PersistenceManager &pm, const char *name=0) const │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_M_o_l_e_c_u_l_e │ │ │ │ -Molecule * getMolecule() │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_~_M_o_l_e_c_u_l_e │ │ │ │ -virtual ~Molecule() │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_B_e_f_o_r_e │ │ │ │ -void insertBefore(Molecule &molecule, Composite &composite) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_S_y_s_t_e_m │ │ │ │ -const System * getSystem() const │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t │ │ │ │ -void insert(AtomContainer &atom_container) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_r_e_m_o_v_e │ │ │ │ -bool remove(Atom &atom) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_B_e_f_o_r_e │ │ │ │ -void insertBefore(AtomContainer &atom_container, Composite &before) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_p_l_i_c_e │ │ │ │ -void splice(AtomContainer &atom_container) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_r_e_p_e_n_d │ │ │ │ -void prepend(Atom &atom) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_w_a_p │ │ │ │ -void swap(Molecule &molecule) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_r_e_p_e_n_d │ │ │ │ -void prepend(AtomContainer &atom_container) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_r_e_m_o_v_e │ │ │ │ -bool remove(Molecule &molecule) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_e_t │ │ │ │ -void set(const Molecule &molecule, bool deep=true) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t │ │ │ │ -void insert(Atom &atom) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t │ │ │ │ -void get(Molecule &molecule, bool deep=true) const │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_a_p_p_e_n_d │ │ │ │ -void append(Atom &atom) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_M_o_l_e_c_u_l_e │ │ │ │ -Molecule(const String &name) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_a_p_p_e_n_d │ │ │ │ -void append(Molecule &molecule) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_M_o_l_e_c_u_l_e │ │ │ │ -Molecule(const AtomContainer &atomContainer, bool deep=true) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_A_f_t_e_r │ │ │ │ -void insertAfter(AtomContainer &atom_container, Composite &after) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_S_y_s_t_e_m │ │ │ │ -System * getSystem() │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_A_f_t_e_r │ │ │ │ -void insertAfter(Molecule &molecule, Composite &composite) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_B_e_f_o_r_e │ │ │ │ -void insertBefore(Atom &atom, Composite &before) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_p_l_i_c_e_B_e_f_o_r_e │ │ │ │ -void spliceBefore(AtomContainer &atom_container) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t │ │ │ │ -void insert(Molecule &molecule) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_s_M_o_l_e_c_u_l_e │ │ │ │ -virtual bool isMolecule() const │ │ │ │ -DDeeffiinniittiioonn _m_o_l_e_c_u_l_e_._h_:_2_1_6 │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_M_o_l_e_c_u_l_e │ │ │ │ -Molecule(const Molecule &molecule, bool deep=true) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_M_o_l_e_c_u_l_e │ │ │ │ -const Molecule * getMolecule() const │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_r_e_m_o_v_e │ │ │ │ -bool remove(AtomContainer &atom_container) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_a_p_p_e_n_d │ │ │ │ -void append(AtomContainer &atom_container) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_S_u_p_e_r_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -const AtomContainer * getSuperAtomContainer() const │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_r_e_p_e_n_d │ │ │ │ -void prepend(Molecule &molecule) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_A_f_t_e_r │ │ │ │ -void insertAfter(Atom &atom, Composite &after) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_p_l_i_c_e_A_f_t_e_r │ │ │ │ -void spliceAfter(AtomContainer &atom_container) │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_S_u_p_e_r_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -AtomContainer * getSuperAtomContainer() │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_P_r_o_p_e_r_t_y │ │ │ │ -Property │ │ │ │ -DDeeffiinniittiioonn _m_o_l_e_c_u_l_e_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_s_S_u_b_A_t_o_m_C_o_n_t_a_i_n_e_r_O_f │ │ │ │ -bool isSubAtomContainerOf(const AtomContainer &atom_container) const │ │ │ │ -_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ -DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_A_L_L_M_o_d_e_l │ │ │ │ +DDeeffiinniittiioonn _a_l_l_M_o_d_e_l_._h_:_2_1 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_K_N_N_M_o_d_e_l │ │ │ │ +DDeeffiinniittiioonn _k_n_n_M_o_d_e_l_._h_:_2_0 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_K_N_N_M_o_d_e_l_:_:_s_e_t_P_a_r_a_m_e_t_e_r_s │ │ │ │ +void setParameters(vector< double > &v) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_K_N_N_M_o_d_e_l_:_:_g_e_t_P_a_r_a_m_e_t_e_r_s │ │ │ │ +vector< double > getParameters() const │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_K_N_N_M_o_d_e_l_:_:_K_N_N_M_o_d_e_l │ │ │ │ +KNNModel(const QSARData &q, int k=3) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_K_N_N_M_o_d_e_l_:_:_o_p_t_i_m_i_z_e_P_a_r_a_m_e_t_e_r_s │ │ │ │ +bool optimizeParameters(int k, int no_steps) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_K_N_N_M_o_d_e_l_:_:_c_a_l_c_u_l_a_t_e_W_e_i_g_h_t_s │ │ │ │ +void calculateWeights(Eigen::MatrixXd &dist, Eigen::VectorXd &w) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_Q_S_A_R_D_a_t_a │ │ │ │ +DDeeffiinniittiioonn _Q_S_A_R_D_a_t_a_._h_:_5_6 │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/da6/a06022.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::PrincipalMomentOfInertiaX Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/QSAR/simpleDescriptors.h>

    │ │ │ +

    #include <BALL/QSAR/simpleDescriptors.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::PrincipalMomentOfInertiaX:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::SimpleBase │ │ │ @@ -104,23 +104,23 @@ │ │ │   │ │ │
    Assignment
    │ │ │ PrincipalMomentOfInertiaX & operator= (const PrincipalMomentOfInertiaX &pmix) │ │ │   │ │ │ - Public Member Functions inherited from BALL::SimpleBase │ │ │  SimpleBase () │ │ │   │ │ │ - SimpleBase (const SimpleBase &sb) │ │ │ + SimpleBase (const SimpleBase &sb) │ │ │   │ │ │  SimpleBase (const String &name) │ │ │   │ │ │  SimpleBase (const String &name, const String &unit) │ │ │   │ │ │ virtual ~SimpleBase () │ │ │   │ │ │ -virtual SimpleBase & operator= (const SimpleBase &sb) │ │ │ +virtual SimpleBase & operator= (const SimpleBase &sb) │ │ │   │ │ │ void computeAllDescriptors (AtomContainer &ac) │ │ │   │ │ │ void setDataFolder (const char *folder) │ │ │   │ │ │ - Public Member Functions inherited from BALL::Descriptor │ │ │  Descriptor () │ │ │ @@ -180,15 +180,15 @@ │ │ │ void calculate_ (AtomContainer &ac) │ │ │   │ │ │ - Protected Member Functions inherited from BALL::Descriptor │ │ │ │ │ │

    Detailed Description

    │ │ │

    This descripor adds up the x-axis component of the principal moment of inertia over all atoms, calculated from the filed coordinates!

    │ │ │ │ │ │ -

    Definition at line 1430 of file simpleDescriptors.h.

    │ │ │ +

    Definition at line 1430 of file simpleDescriptors.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ PrincipalMomentOfInertiaX() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dac/a05506.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Classes | │ │ │ List of all members
    │ │ │
    BALL::JohnsonBoveyShiftProcessor Class Reference
    Molecular Modeling » Nuclear Magnetic Resonance Spectroscopy » Shift modules
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/NMR/johnsonBoveyShiftProcessor.h>

    │ │ │ +

    #include <BALL/NMR/johnsonBoveyShiftProcessor.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::JohnsonBoveyShiftProcessor:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::ShiftModule │ │ │ @@ -200,15 +200,15 @@ │ │ │
    │ │ │ │ │ │ │ │ │
     
    bool valid_
     
    │ │ │

    Detailed Description

    │ │ │

    Shift assignment processor implementing Johnson Bovey theory. <>

    │ │ │ │ │ │ -

    Definition at line 38 of file johnsonBoveyShiftProcessor.h.

    │ │ │ +

    Definition at line 38 of file johnsonBoveyShiftProcessor.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ JohnsonBoveyShiftProcessor()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -537,15 +537,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 118 of file johnsonBoveyShiftProcessor.h.

    │ │ │ +

    Definition at line 118 of file johnsonBoveyShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ atom_list_

    │ │ │ │ │ │
    │ │ │ @@ -561,15 +561,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 117 of file johnsonBoveyShiftProcessor.h.

    │ │ │ +

    Definition at line 117 of file johnsonBoveyShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ expressions_

    │ │ │ │ │ │
    │ │ │ @@ -585,15 +585,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 121 of file johnsonBoveyShiftProcessor.h.

    │ │ │ +

    Definition at line 121 of file johnsonBoveyShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ PROPERTY__RING_CURRENT_SHIFT

    │ │ │ │ │ │
    │ │ │ @@ -610,15 +610,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │

    A symbolic name for the ring current contribution to the chemical shift

    See also
    ShiftModule::PROPERTY__SHIFT
    │ │ │ │ │ │ -

    Definition at line 70 of file johnsonBoveyShiftProcessor.h.

    │ │ │ +

    Definition at line 70 of file johnsonBoveyShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ proton_list_

    │ │ │ │ │ │
    │ │ │ @@ -634,15 +634,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 116 of file johnsonBoveyShiftProcessor.h.

    │ │ │ +

    Definition at line 116 of file johnsonBoveyShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ residues_with_rings_

    │ │ │ │ │ │
    │ │ │ @@ -658,15 +658,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 120 of file johnsonBoveyShiftProcessor.h.

    │ │ │ +

    Definition at line 120 of file johnsonBoveyShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ rings_

    │ │ │ │ │ │
    │ │ │ @@ -682,15 +682,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 119 of file johnsonBoveyShiftProcessor.h.

    │ │ │ +

    Definition at line 119 of file johnsonBoveyShiftProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dad/a00806.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: SASVertex.h File Reference │ │ │ +BALL: bufferedRenderer.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,44 +65,40 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    SASVertex.h File Reference
    │ │ │ +
    bufferedRenderer.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/STRUCTURE/graphVertex.h>
    │ │ │ -#include <BALL/MATHS/vector3.h>
    │ │ │ +
    #include <BALL/VIEW/RENDERING/RENDERERS/renderer.h>
    │ │ │ +#include <BALL/VIEW/RENDERING/renderTarget.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::SASVertex
    class  BALL::VIEW::BufferedRenderer
     
    │ │ │ │ │ │ │ │ │ │ │ │ -

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ + │ │ │

    │ │ │ -Functions

    Storers
    BALL_EXPORT std::ostream & BALL::operator<< (std::ostream &s, const SASVertex &sasvertex)
     
    namespace  BALL::VIEW
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,25 +1,24 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ + * _V_I_E_W │ │ │ │ + * _R_E_N_D_E_R_I_N_G │ │ │ │ + * _R_E_N_D_E_R_E_R_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -SASVertex.h File Reference │ │ │ │ -#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_g_r_a_p_h_V_e_r_t_e_x_._h> │ │ │ │ -#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +bufferedRenderer.h File Reference │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_R_E_N_D_E_R_E_R_S_/_r_e_n_d_e_r_e_r_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_r_e_n_d_e_r_T_a_r_g_e_t_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_S_A_S_V_e_r_t_e_x │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -FFuunnccttiioonnss │ │ │ │ -Storers │ │ │ │ -_B_A_L_L___E_X_P_O_R_T std::ostream &  _B_A_L_L_:_:_o_p_e_r_a_t_o_r_<_< (std::ostream &s, const _S_A_S_V_e_r_t_e_x │ │ │ │ - &sasvertex) │ │ │ │ +namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dad/a00806_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: SASVertex.h Source File │ │ │ +BALL: bufferedRenderer.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,140 +70,152 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    SASVertex.h
    │ │ │ +
    bufferedRenderer.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5#ifndef BALL_STRUCTURE_SASVERTEX_H
    │ │ │ -
    6#define BALL_STRUCTURE_SASVERTEX_H
    │ │ │ +
    5#ifndef BALL_VIEW_RENDERING_RENDERERS_BUFFEREDRENDERER_H
    │ │ │ +
    6#define BALL_VIEW_RENDERING_RENDERERS_BUFFEREDRENDERER_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_STRUCTURE_GRAPHVERTEX_H
    │ │ │ -
    9# include <BALL/STRUCTURE/graphVertex.h>
    │ │ │ +
    8#ifndef BALL_VIEW_RENDERING_RENDERERS_RENDERER_H
    │ │ │ +
    9# include <BALL/VIEW/RENDERING/RENDERERS/renderer.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_MATHS_VECTOR3_H
    │ │ │ -
    13# include <BALL/MATHS/vector3.h>
    │ │ │ +
    12#ifndef BALL_VIEW_RENDERING_RENDERTARGET_H
    │ │ │ +
    13# include <BALL/VIEW/RENDERING/renderTarget.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │
    16namespace BALL
    │ │ │
    17{
    │ │ │ -
    18
    │ │ │ -
    19 class SASEdge;
    │ │ │ -
    20 class SASFace;
    │ │ │ -
    21 class SolventAccessibleSurface;
    │ │ │ -
    22 class TriangulatedSAS;
    │ │ │ -
    23 class SASTriangulator;
    │ │ │ -
    24
    │ │ │ -
    │ │ │ -
    28 class BALL_EXPORT SASVertex : public GraphVertex< SASVertex,SASEdge,SASFace >
    │ │ │ -
    29 {
    │ │ │ -
    30 public:
    │ │ │ -
    31
    │ │ │ -
    41 friend class SASEdge;
    │ │ │ -
    42 friend class SASFace;
    │ │ │ -
    43 friend class SolventAccessibleSurface;
    │ │ │ -
    44 friend class TriangulatedSAS;
    │ │ │ -
    45 friend class SASTriangulator;
    │ │ │ -
    46
    │ │ │ -
    47 BALL_CREATE(SASVertex)
    │ │ │ -
    48
    │ │ │ -
    49
    │ │ │ +
    18 namespace VIEW
    │ │ │ +
    19 {
    │ │ │ +
    │ │ │ +
    29 class BALL_VIEW_EXPORT BufferedRenderer
    │ │ │ +
    30 : public Renderer
    │ │ │ +
    31 {
    │ │ │ +
    32 public:
    │ │ │ +
    33
    │ │ │ +
    │ │ │ +
    34 BufferedRenderer()
    │ │ │ +
    35 : offset_(0),
    │ │ │ +
    36 stride_(0)
    │ │ │ +
    37 { }
    │ │ │ +
    │ │ │ +
    38
    │ │ │ +
    │ │ │ +
    43 bool setFrameBufferFormat(const FrameBufferFormat &format)
    │ │ │ +
    44 {
    │ │ │ +
    45 if (supports(format))
    │ │ │ +
    46 {
    │ │ │ +
    47 bufferFormat = format;
    │ │ │ +
    48 formatUpdated();
    │ │ │ +
    49
    │ │ │ +
    50 return true;
    │ │ │ +
    51 }
    │ │ │
    52
    │ │ │ -
    53
    │ │ │ -
    56 SASVertex()
    │ │ │ -
    57 ;
    │ │ │ -
    58
    │ │ │ -
    66 SASVertex(const SASVertex& sasvertex, bool deep = false)
    │ │ │ -
    67 ;
    │ │ │ +
    53 return false;
    │ │ │ +
    54 }
    │ │ │ +
    │ │ │ +
    55
    │ │ │ +
    │ │ │ +
    62 void renderToBuffer(RenderTarget* renderTarget, const Stage& stage)
    │ │ │ +
    63 {
    │ │ │ +
    64 prepareBufferedRendering(stage);
    │ │ │ +
    65
    │ │ │ +
    66 FrameBufferPtr buffer = renderTarget->getBuffer();
    │ │ │ +
    67 assert(buffer);
    │ │ │
    68
    │ │ │ -
    74 SASVertex(const TVector3<double>& point,
    │ │ │ -
    75 Index index)
    │ │ │ -
    76 ;
    │ │ │ -
    77
    │ │ │ -
    81 virtual ~SASVertex()
    │ │ │ -
    82 ;
    │ │ │ -
    83
    │ │ │ -
    85
    │ │ │ -
    88
    │ │ │ -
    96 void set(const SASVertex& sasvertex, bool deep = false)
    │ │ │ -
    97 ;
    │ │ │ -
    98
    │ │ │ -
    104 SASVertex& operator = (const SASVertex& sasvertex)
    │ │ │ -
    105 ;
    │ │ │ -
    106
    │ │ │ -
    111 void set(const TVector3<double> point,
    │ │ │ -
    112 Index index)
    │ │ │ -
    113 ;
    │ │ │ -
    114
    │ │ │ -
    118 void setPoint(const TVector3<double>& point)
    │ │ │ -
    119 ;
    │ │ │ -
    120
    │ │ │ -
    124 TVector3<double> getPoint() const
    │ │ │ -
    125 ;
    │ │ │ +
    69 if (buffer->getFormat() != bufferFormat)
    │ │ │ +
    70 {
    │ │ │ +
    71 throw Exception::InvalidFormat(__FILE__, __LINE__, "Buffer with wrong framebuffer format supplied");
    │ │ │ +
    72 }
    │ │ │ +
    73
    │ │ │ +
    74 renderToBufferImpl( buffer );
    │ │ │ +
    75
    │ │ │ +
    76 renderTarget->releaseBuffer(buffer);
    │ │ │ +
    77 }
    │ │ │ +
    │ │ │ +
    78
    │ │ │ +
    80 virtual bool supports(const PixelFormat &format) const = 0;
    │ │ │ +
    81
    │ │ │ +
    89 virtual Resolution getSupportedResolution(const Resolution &min, const Resolution &max,
    │ │ │ +
    90 const PixelFormat &format) const = 0;
    │ │ │ +
    91
    │ │ │ +
    94 virtual void setOffset(Size offset) {offset_ = offset;}
    │ │ │ +
    95
    │ │ │ +
    98 virtual void setStride(Size stride) {stride_ = stride;}
    │ │ │ +
    99
    │ │ │ +
    100 protected:
    │ │ │ +
    101
    │ │ │ +
    107 virtual bool supports(const FrameBufferFormat &format) const = 0;
    │ │ │ +
    108
    │ │ │ +
    112 virtual void formatUpdated() = 0;
    │ │ │ +
    113
    │ │ │ +
    116 virtual void prepareBufferedRendering(const Stage& stage) = 0;
    │ │ │ +
    117
    │ │ │ +
    122 virtual void renderToBufferImpl(FrameBufferPtr buffer) = 0;
    │ │ │ +
    123
    │ │ │ +
    125 const FrameBufferFormat &getFrameBufferFormat() const { return bufferFormat; }
    │ │ │
    126
    │ │ │ -
    128
    │ │ │ +
    127 Size offset_;
    │ │ │ +
    128 Size stride_;
    │ │ │ +
    129
    │ │ │ +
    130 private:
    │ │ │
    131
    │ │ │ -
    135 virtual bool operator == (const SASVertex&) const
    │ │ │ -
    136 ;
    │ │ │ +
    132 FrameBufferFormat bufferFormat;
    │ │ │ +
    133 };
    │ │ │ +
    │ │ │ +
    134 } //namespace VIEW
    │ │ │ +
    135
    │ │ │ +
    136} //namespace BALL
    │ │ │
    137
    │ │ │ -
    141 virtual bool operator != (const SASVertex&) const
    │ │ │ -
    142 ;
    │ │ │ -
    143
    │ │ │ -
    148 virtual bool operator *= (const SASVertex&) const
    │ │ │ -
    149 ;
    │ │ │ -
    150
    │ │ │ -
    152
    │ │ │ -
    153 protected:
    │ │ │ -
    154
    │ │ │ -
    155 /*_ @name Attributes
    │ │ │ -
    156 */
    │ │ │ -
    158
    │ │ │ -
    159 /*_ The coordinates of the vertex.
    │ │ │ -
    160 */
    │ │ │ -
    161 TVector3<double> point_;
    │ │ │ -
    162
    │ │ │ -
    164 };
    │ │ │ -
    │ │ │ -
    165
    │ │ │ -
    169
    │ │ │ -
    172 BALL_EXPORT std::ostream& operator << (std::ostream& s, const SASVertex& sasvertex);
    │ │ │ -
    173
    │ │ │ -
    175
    │ │ │ -
    176
    │ │ │ -
    177
    │ │ │ -
    178} // namespace BALL
    │ │ │ -
    179
    │ │ │ -
    180#endif // BALL_STRUCTURE_SASVERTEX_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ -
    std
    STL namespace.
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    138
    │ │ │ +
    139#endif // BALL_VIEW_RENDERING_BUFFEREDRENDERER_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::FrameBufferPtr
    boost::shared_ptr< FrameBuffer > FrameBufferPtr
    Definition renderTarget.h:222
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::BufferedRenderer::supports
    virtual bool supports(const PixelFormat &format) const =0
    │ │ │ +
    BALL::VIEW::BufferedRenderer::formatUpdated
    virtual void formatUpdated()=0
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::BufferedRenderer::getFrameBufferFormat
    const FrameBufferFormat & getFrameBufferFormat() const
    Definition bufferedRenderer.h:125
    │ │ │ +
    BALL::VIEW::BufferedRenderer::supports
    virtual bool supports(const FrameBufferFormat &format) const =0
    │ │ │ +
    BALL::VIEW::BufferedRenderer::renderToBufferImpl
    virtual void renderToBufferImpl(FrameBufferPtr buffer)=0
    │ │ │ +
    BALL::VIEW::BufferedRenderer::setFrameBufferFormat
    bool setFrameBufferFormat(const FrameBufferFormat &format)
    Definition bufferedRenderer.h:43
    │ │ │ +
    BALL::VIEW::BufferedRenderer::prepareBufferedRendering
    virtual void prepareBufferedRendering(const Stage &stage)=0
    │ │ │ +
    BALL::VIEW::BufferedRenderer::setOffset
    virtual void setOffset(Size offset)
    Definition bufferedRenderer.h:94
    │ │ │ +
    BALL::VIEW::BufferedRenderer::getSupportedResolution
    virtual Resolution getSupportedResolution(const Resolution &min, const Resolution &max, const PixelFormat &format) const =0
    │ │ │ +
    BALL::VIEW::BufferedRenderer::setStride
    virtual void setStride(Size stride)
    Definition bufferedRenderer.h:98
    │ │ │ +
    BALL::VIEW::BufferedRenderer::renderToBuffer
    void renderToBuffer(RenderTarget *renderTarget, const Stage &stage)
    Definition bufferedRenderer.h:62
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::RenderTarget::releaseBuffer
    virtual void releaseBuffer(FrameBufferPtr buffer)=0
    │ │ │ +
    BALL::VIEW::RenderTarget::getBuffer
    virtual FrameBufferPtr getBuffer()=0
    │ │ │ + │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,144 +1,177 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ -SASVertex.h │ │ │ │ + * _V_I_E_W │ │ │ │ + * _R_E_N_D_E_R_I_N_G │ │ │ │ + * _R_E_N_D_E_R_E_R_S │ │ │ │ +bufferedRenderer.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_STRUCTURE_SASVERTEX_H │ │ │ │ -6#define BALL_STRUCTURE_SASVERTEX_H │ │ │ │ +5#ifndef BALL_VIEW_RENDERING_RENDERERS_BUFFEREDRENDERER_H │ │ │ │ +6#define BALL_VIEW_RENDERING_RENDERERS_BUFFEREDRENDERER_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_STRUCTURE_GRAPHVERTEX_H │ │ │ │ -9# include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_g_r_a_p_h_V_e_r_t_e_x_._h> │ │ │ │ +8#ifndef BALL_VIEW_RENDERING_RENDERERS_RENDERER_H │ │ │ │ +9# include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_R_E_N_D_E_R_E_R_S_/_r_e_n_d_e_r_e_r_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_MATHS_VECTOR3_H │ │ │ │ -13# include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +12#ifndef BALL_VIEW_RENDERING_RENDERTARGET_H │ │ │ │ +13# include <_B_A_L_L_/_V_I_E_W_/_R_E_N_D_E_R_I_N_G_/_r_e_n_d_e_r_T_a_r_g_e_t_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ 16namespace _B_A_L_L │ │ │ │ 17{ │ │ │ │ -18 │ │ │ │ -19 class SASEdge; │ │ │ │ -20 class SASFace; │ │ │ │ -21 class SolventAccessibleSurface; │ │ │ │ -22 class TriangulatedSAS; │ │ │ │ -23 class SASTriangulator; │ │ │ │ -24 │ │ │ │ -_2_8 class _B_A_L_L___E_X_P_O_R_T _S_A_S_V_e_r_t_e_x : public _G_r_a_p_h_V_e_r_t_e_x< SASVertex,SASEdge,SASFace │ │ │ │ -> │ │ │ │ -29 { │ │ │ │ -30 public: │ │ │ │ -31 │ │ │ │ -_4_1 friend class _S_A_S_E_d_g_e; │ │ │ │ -_4_2 friend class _S_A_S_F_a_c_e; │ │ │ │ -_4_3 friend class _S_o_l_v_e_n_t_A_c_c_e_s_s_i_b_l_e_S_u_r_f_a_c_e; │ │ │ │ -_4_4 friend class _T_r_i_a_n_g_u_l_a_t_e_d_S_A_S; │ │ │ │ -_4_5 friend class _S_A_S_T_r_i_a_n_g_u_l_a_t_o_r; │ │ │ │ -46 │ │ │ │ -47 _B_A_L_L___C_R_E_A_T_E(_S_A_S_V_e_r_t_e_x) │ │ │ │ -48 │ │ │ │ +18 namespace VIEW │ │ │ │ +19 { │ │ │ │ +_2_9 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r │ │ │ │ +30 : public _R_e_n_d_e_r_e_r │ │ │ │ +31 { │ │ │ │ +32 public: │ │ │ │ +33 │ │ │ │ +_3_4 _B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r() │ │ │ │ +35 : offset_(0), │ │ │ │ +36 stride_(0) │ │ │ │ +37 { } │ │ │ │ +38 │ │ │ │ +_4_3 bool _s_e_t_F_r_a_m_e_B_u_f_f_e_r_F_o_r_m_a_t(const _F_r_a_m_e_B_u_f_f_e_r_F_o_r_m_a_t &format) │ │ │ │ +44 { │ │ │ │ +45 if (supports(format)) │ │ │ │ +46 { │ │ │ │ +47 bufferFormat = format; │ │ │ │ +48 formatUpdated(); │ │ │ │ 49 │ │ │ │ +50 return true; │ │ │ │ +51 } │ │ │ │ 52 │ │ │ │ -53 │ │ │ │ -_5_6 _S_A_S_V_e_r_t_e_x() │ │ │ │ -57 ; │ │ │ │ -58 │ │ │ │ -_6_6 _S_A_S_V_e_r_t_e_x(const _S_A_S_V_e_r_t_e_x& sasvertex, bool deep = false) │ │ │ │ -67 ; │ │ │ │ +53 return false; │ │ │ │ +54 } │ │ │ │ +55 │ │ │ │ +_6_2 void _r_e_n_d_e_r_T_o_B_u_f_f_e_r(_R_e_n_d_e_r_T_a_r_g_e_t* renderTarget, const _S_t_a_g_e& stage) │ │ │ │ +63 { │ │ │ │ +64 prepareBufferedRendering(stage); │ │ │ │ +65 │ │ │ │ +66 _F_r_a_m_e_B_u_f_f_e_r_P_t_r buffer = renderTarget->_g_e_t_B_u_f_f_e_r(); │ │ │ │ +67 assert(buffer); │ │ │ │ 68 │ │ │ │ -_7_4 _S_A_S_V_e_r_t_e_x(const _T_V_e_c_t_o_r_3& point, │ │ │ │ -75 _I_n_d_e_x index) │ │ │ │ -76 ; │ │ │ │ -77 │ │ │ │ -_8_1 virtual ~_S_A_S_V_e_r_t_e_x() │ │ │ │ -82 ; │ │ │ │ -83 │ │ │ │ -85 │ │ │ │ -88 │ │ │ │ -_9_6 void set(const _S_A_S_V_e_r_t_e_x& sasvertex, bool deep = false) │ │ │ │ -97 ; │ │ │ │ -98 │ │ │ │ -_1_0_4 _S_A_S_V_e_r_t_e_x& operator = (const _S_A_S_V_e_r_t_e_x& sasvertex) │ │ │ │ -105 ; │ │ │ │ -106 │ │ │ │ -_1_1_1 void set(const _T_V_e_c_t_o_r_3 point, │ │ │ │ -112 _I_n_d_e_x index) │ │ │ │ -113 ; │ │ │ │ -114 │ │ │ │ -_1_1_8 void setPoint(const _T_V_e_c_t_o_r_3& point) │ │ │ │ -119 ; │ │ │ │ -120 │ │ │ │ -_1_2_4 _T_V_e_c_t_o_r_3 getPoint() const │ │ │ │ -125 ; │ │ │ │ +69 if (buffer->getFormat() != bufferFormat) │ │ │ │ +70 { │ │ │ │ +71 throw _E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_F_o_r_m_a_t(__FILE__, __LINE__, "Buffer with wrong │ │ │ │ +framebuffer format supplied"); │ │ │ │ +72 } │ │ │ │ +73 │ │ │ │ +74 renderToBufferImpl( buffer ); │ │ │ │ +75 │ │ │ │ +76 renderTarget->_r_e_l_e_a_s_e_B_u_f_f_e_r(buffer); │ │ │ │ +77 } │ │ │ │ +78 │ │ │ │ +_8_0 virtual bool _s_u_p_p_o_r_t_s(const _P_i_x_e_l_F_o_r_m_a_t &format) const = 0; │ │ │ │ +81 │ │ │ │ +_8_9 virtual _R_e_s_o_l_u_t_i_o_n _g_e_t_S_u_p_p_o_r_t_e_d_R_e_s_o_l_u_t_i_o_n(const _R_e_s_o_l_u_t_i_o_n &min, const │ │ │ │ +_R_e_s_o_l_u_t_i_o_n &max, │ │ │ │ +90 const _P_i_x_e_l_F_o_r_m_a_t &format) const = 0; │ │ │ │ +91 │ │ │ │ +_9_4 virtual void _s_e_t_O_f_f_s_e_t(_S_i_z_e offset) {offset_ = offset;} │ │ │ │ +95 │ │ │ │ +_9_8 virtual void _s_e_t_S_t_r_i_d_e(_S_i_z_e stride) {stride_ = stride;} │ │ │ │ +99 │ │ │ │ +100 protected: │ │ │ │ +101 │ │ │ │ +_1_0_7 virtual bool _s_u_p_p_o_r_t_s(const _F_r_a_m_e_B_u_f_f_e_r_F_o_r_m_a_t &format) const = 0; │ │ │ │ +108 │ │ │ │ +_1_1_2 virtual void _f_o_r_m_a_t_U_p_d_a_t_e_d() = 0; │ │ │ │ +113 │ │ │ │ +_1_1_6 virtual void _p_r_e_p_a_r_e_B_u_f_f_e_r_e_d_R_e_n_d_e_r_i_n_g(const _S_t_a_g_e& stage) = 0; │ │ │ │ +117 │ │ │ │ +_1_2_2 virtual void _r_e_n_d_e_r_T_o_B_u_f_f_e_r_I_m_p_l(_F_r_a_m_e_B_u_f_f_e_r_P_t_r buffer) = 0; │ │ │ │ +123 │ │ │ │ +_1_2_5 const _F_r_a_m_e_B_u_f_f_e_r_F_o_r_m_a_t &_g_e_t_F_r_a_m_e_B_u_f_f_e_r_F_o_r_m_a_t() const { return │ │ │ │ +bufferFormat; } │ │ │ │ 126 │ │ │ │ -128 │ │ │ │ +_1_2_7 _S_i_z_e _o_f_f_s_e_t__; │ │ │ │ +_1_2_8 _S_i_z_e _s_t_r_i_d_e__; │ │ │ │ +129 │ │ │ │ +130 private: │ │ │ │ 131 │ │ │ │ -_1_3_5 virtual bool operator == (const _S_A_S_V_e_r_t_e_x&) const │ │ │ │ -136 ; │ │ │ │ +132 _F_r_a_m_e_B_u_f_f_e_r_F_o_r_m_a_t bufferFormat; │ │ │ │ +133 }; │ │ │ │ +134 } //namespace VIEW │ │ │ │ +135 │ │ │ │ +136} //namespace BALL │ │ │ │ 137 │ │ │ │ -_1_4_1 virtual bool operator != (const _S_A_S_V_e_r_t_e_x&) const │ │ │ │ -142 ; │ │ │ │ -143 │ │ │ │ -_1_4_8 virtual bool operator *= (const _S_A_S_V_e_r_t_e_x&) const │ │ │ │ -149 ; │ │ │ │ -150 │ │ │ │ -152 │ │ │ │ -153 protected: │ │ │ │ -154 │ │ │ │ -155 /*_ @name Attributes │ │ │ │ -156 */ │ │ │ │ -158 │ │ │ │ -159 /*_ The coordinates of the vertex. │ │ │ │ -160 */ │ │ │ │ -_1_6_1 _T_V_e_c_t_o_r_3 point_; │ │ │ │ -162 │ │ │ │ -164 }; │ │ │ │ -165 │ │ │ │ -169 │ │ │ │ -_1_7_2 _B_A_L_L___E_X_P_O_R_T _s_t_d::ostream& operator << (_s_t_d::ostream& s, const _S_A_S_V_e_r_t_e_x& │ │ │ │ -sasvertex); │ │ │ │ -173 │ │ │ │ -175 │ │ │ │ -176 │ │ │ │ -177 │ │ │ │ -178} // namespace BALL │ │ │ │ -179 │ │ │ │ -180#endif // BALL_STRUCTURE_SASVERTEX_H │ │ │ │ -_g_r_a_p_h_V_e_r_t_e_x_._h │ │ │ │ -_v_e_c_t_o_r_3_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ -_s_t_d │ │ │ │ -STL namespace. │ │ │ │ +138 │ │ │ │ +139#endif // BALL_VIEW_RENDERING_BUFFEREDRENDERER_H │ │ │ │ +_r_e_n_d_e_r_T_a_r_g_e_t_._h │ │ │ │ +_r_e_n_d_e_r_e_r_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_1 │ │ │ │ -_B_A_L_L_:_:_G_r_a_p_h_V_e_r_t_e_x │ │ │ │ -DDeeffiinniittiioonn _g_r_a_p_h_V_e_r_t_e_x_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_S_A_S_E_d_g_e │ │ │ │ -DDeeffiinniittiioonn _S_A_S_E_d_g_e_._h_:_3_4 │ │ │ │ -_B_A_L_L_:_:_S_A_S_F_a_c_e │ │ │ │ -DDeeffiinniittiioonn _S_A_S_F_a_c_e_._h_:_3_1 │ │ │ │ -_B_A_L_L_:_:_S_A_S_V_e_r_t_e_x │ │ │ │ -DDeeffiinniittiioonn _S_A_S_V_e_r_t_e_x_._h_:_2_9 │ │ │ │ -_B_A_L_L_:_:_S_o_l_v_e_n_t_A_c_c_e_s_s_i_b_l_e_S_u_r_f_a_c_e │ │ │ │ -DDeeffiinniittiioonn _s_o_l_v_e_n_t_A_c_c_e_s_s_i_b_l_e_S_u_r_f_a_c_e_._h_:_3_9 │ │ │ │ -_B_A_L_L_:_:_T_r_i_a_n_g_u_l_a_t_e_d_S_A_S │ │ │ │ -DDeeffiinniittiioonn _t_r_i_a_n_g_u_l_a_t_e_d_S_A_S_._h_:_6_3 │ │ │ │ -_B_A_L_L_:_:_S_A_S_T_r_i_a_n_g_u_l_a_t_o_r │ │ │ │ -DDeeffiinniittiioonn _t_r_i_a_n_g_u_l_a_t_e_d_S_A_S_._h_:_1_6_1 │ │ │ │ -_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_F_r_a_m_e_B_u_f_f_e_r_P_t_r │ │ │ │ +boost::shared_ptr< FrameBuffer > FrameBufferPtr │ │ │ │ +DDeeffiinniittiioonn _r_e_n_d_e_r_T_a_r_g_e_t_._h_:_2_2_2 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_F_o_r_m_a_t │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_3_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_S_t_a_g_e │ │ │ │ +DDeeffiinniittiioonn _s_t_a_g_e_._h_:_2_3_9 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_i_x_e_l_F_o_r_m_a_t │ │ │ │ +DDeeffiinniittiioonn _p_i_x_e_l_F_o_r_m_a_t_._h_:_6_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r │ │ │ │ +DDeeffiinniittiioonn _b_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_s_u_p_p_o_r_t_s │ │ │ │ +virtual bool supports(const PixelFormat &format) const =0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_f_o_r_m_a_t_U_p_d_a_t_e_d │ │ │ │ +virtual void formatUpdated()=0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_o_f_f_s_e_t__ │ │ │ │ +Size offset_ │ │ │ │ +DDeeffiinniittiioonn _b_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_._h_:_1_2_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r │ │ │ │ +BufferedRenderer() │ │ │ │ +DDeeffiinniittiioonn _b_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_._h_:_3_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_s_t_r_i_d_e__ │ │ │ │ +Size stride_ │ │ │ │ +DDeeffiinniittiioonn _b_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_._h_:_1_2_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_g_e_t_F_r_a_m_e_B_u_f_f_e_r_F_o_r_m_a_t │ │ │ │ +const FrameBufferFormat & getFrameBufferFormat() const │ │ │ │ +DDeeffiinniittiioonn _b_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_._h_:_1_2_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_s_u_p_p_o_r_t_s │ │ │ │ +virtual bool supports(const FrameBufferFormat &format) const =0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_r_e_n_d_e_r_T_o_B_u_f_f_e_r_I_m_p_l │ │ │ │ +virtual void renderToBufferImpl(FrameBufferPtr buffer)=0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_s_e_t_F_r_a_m_e_B_u_f_f_e_r_F_o_r_m_a_t │ │ │ │ +bool setFrameBufferFormat(const FrameBufferFormat &format) │ │ │ │ +DDeeffiinniittiioonn _b_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_._h_:_4_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_p_r_e_p_a_r_e_B_u_f_f_e_r_e_d_R_e_n_d_e_r_i_n_g │ │ │ │ +virtual void prepareBufferedRendering(const Stage &stage)=0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_s_e_t_O_f_f_s_e_t │ │ │ │ +virtual void setOffset(Size offset) │ │ │ │ +DDeeffiinniittiioonn _b_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_._h_:_9_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_g_e_t_S_u_p_p_o_r_t_e_d_R_e_s_o_l_u_t_i_o_n │ │ │ │ +virtual Resolution getSupportedResolution(const Resolution &min, const │ │ │ │ +Resolution &max, const PixelFormat &format) const =0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_s_e_t_S_t_r_i_d_e │ │ │ │ +virtual void setStride(Size stride) │ │ │ │ +DDeeffiinniittiioonn _b_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_._h_:_9_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_B_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_:_:_r_e_n_d_e_r_T_o_B_u_f_f_e_r │ │ │ │ +void renderToBuffer(RenderTarget *renderTarget, const Stage &stage) │ │ │ │ +DDeeffiinniittiioonn _b_u_f_f_e_r_e_d_R_e_n_d_e_r_e_r_._h_:_6_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_R_e_n_d_e_r_e_r │ │ │ │ +DDeeffiinniittiioonn _r_e_n_d_e_r_e_r_._h_:_5_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_R_e_s_o_l_u_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _r_e_n_d_e_r_T_a_r_g_e_t_._h_:_2_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_F_r_a_m_e_B_u_f_f_e_r_F_o_r_m_a_t │ │ │ │ +DDeeffiinniittiioonn _r_e_n_d_e_r_T_a_r_g_e_t_._h_:_4_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_R_e_n_d_e_r_T_a_r_g_e_t │ │ │ │ +DDeeffiinniittiioonn _r_e_n_d_e_r_T_a_r_g_e_t_._h_:_2_2_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_R_e_n_d_e_r_T_a_r_g_e_t_:_:_r_e_l_e_a_s_e_B_u_f_f_e_r │ │ │ │ +virtual void releaseBuffer(FrameBufferPtr buffer)=0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_R_e_n_d_e_r_T_a_r_g_e_t_:_:_g_e_t_B_u_f_f_e_r │ │ │ │ +virtual FrameBufferPtr getBuffer()=0 │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ +#define BALL_VIEW_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dad/a04630.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::SecondaryStructure Class Reference
    Kernel Classes » Miscellaneous
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/KERNEL/secondaryStructure.h>

    │ │ │ +

    #include <BALL/KERNEL/secondaryStructure.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::SecondaryStructure:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::AtomContainer │ │ │ @@ -335,39 +335,39 @@ │ │ │  Apply to all bonds connecting two atoms inside this AtomContainer.
    │ │ │   │ │ │ bool applyInterBond (UnaryProcessor< Bond > &processor) │ │ │  Apply to all bonds connected to atoms outside this AtomContainer.
    │ │ │   │ │ │ - Public Member Functions inherited from BALL::Composite │ │ │ template<typename T > │ │ │ -BALL_INLINE bool apply (UnaryProcessor< T > &processor) │ │ │ +BALL_INLINE bool apply (UnaryProcessor< T > &processor) │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE bool apply (ConstUnaryProcessor< T > &processor) const │ │ │ +BALL_INLINE bool apply (ConstUnaryProcessor< T > &processor) const │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE T * getAncestor (const T &) │ │ │ +BALL_INLINE T * getAncestor (const T &) │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE const T * getAncestor (const T &) const │ │ │ +BALL_INLINE const T * getAncestor (const T &) const │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE T * getPrevious (const T &) │ │ │ +BALL_INLINE T * getPrevious (const T &) │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE const T * getPrevious (const T &dummy) const │ │ │ +BALL_INLINE const T * getPrevious (const T &dummy) const │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE T * getNext (const T &) │ │ │ +BALL_INLINE T * getNext (const T &) │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE const T * getNext (const T &dummy) const │ │ │ +BALL_INLINE const T * getNext (const T &dummy) const │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE bool hasAncestor (const T &dummy) const │ │ │ +BALL_INLINE bool hasAncestor (const T &dummy) const │ │ │   │ │ │  Composite () │ │ │   │ │ │  Composite (const Composite &composite, bool deep=true) │ │ │   │ │ │ virtual ~Composite () │ │ │   │ │ │ @@ -716,18 +716,18 @@ │ │ │ void write (PersistenceManager &pm) const │ │ │   │ │ │ bool read (PersistenceManager &pm) │ │ │   │ │ │ virtual void dump (::std::ostream &s=std::cout, Size depth=0) const │ │ │   │ │ │ - Public Member Functions inherited from BALL::PropertyManager │ │ │ -BALL_INLINE PropertyManager () │ │ │ +BALL_INLINE PropertyManager () │ │ │  Default constructor.
    │ │ │   │ │ │ -BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │ +BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │  Copy constructor.
    │ │ │   │ │ │ virtual ~PropertyManager () │ │ │  Destructor.
    │ │ │   │ │ │ void set (const PropertyManager &property_manager) │ │ │   │ │ │ @@ -840,15 +840,15 @@ │ │ │ - Protected Attributes inherited from BALL::Selectable │ │ │ bool selected_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Secondary structure class. This class is used to represent secondary structure elements of protein chains.

    │ │ │ │ │ │ -

    Definition at line 29 of file secondaryStructure.h.

    │ │ │ +

    Definition at line 29 of file secondaryStructure.h.

    │ │ │

    Member Enumeration Documentation

    │ │ │ │ │ │

    ◆ Type

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -863,15 +863,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    COIL 
    STRAND 
    TURN 
    UNKNOWN 
    NUMBER_OF_TYPES 
    │ │ │ │ │ │ -

    Definition at line 42 of file secondaryStructure.h.

    │ │ │ +

    Definition at line 42 of file secondaryStructure.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ SecondaryStructure() [1/3]

    │ │ │ │ │ │ @@ -1430,15 +1430,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Return the type of secondary structure.

    │ │ │ │ │ │ -

    Definition at line 150 of file secondaryStructure.h.

    │ │ │ +

    Definition at line 150 of file secondaryStructure.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ insert()

    │ │ │ │ │ │
    │ │ │ @@ -1807,15 +1807,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Set the type of secondary structure.

    │ │ │ │ │ │ -

    Definition at line 153 of file secondaryStructure.h.

    │ │ │ +

    Definition at line 153 of file secondaryStructure.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ splice()

    │ │ │ │ │ │
    │ │ │ @@ -1925,15 +1925,15 @@ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    The secondary structure type (helix, strand, coil, turn)

    │ │ │ │ │ │ -

    Definition at line 326 of file secondaryStructure.h.

    │ │ │ +

    Definition at line 326 of file secondaryStructure.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dae/a07994.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members │ │ │
    BALL::VIEW::UpdateRepresentationThread Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/threads.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/threads.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::UpdateRepresentationThread:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::BALLThread │ │ │ @@ -134,15 +134,15 @@ │ │ │  Sends the string as outout to Log.info.
    │ │ │   │ │ │ void waitForUpdateOfRepresentations_ () │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 159 of file threads.h.

    │ │ │ +

    Definition at line 159 of file threads.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ UpdateRepresentationThread()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -177,15 +177,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 175 of file threads.h.

    │ │ │ +

    Definition at line 175 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ run()

    │ │ │ │ │ │
    │ │ │ @@ -233,15 +233,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 171 of file threads.h.

    │ │ │ +

    Definition at line 171 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ rep_

    │ │ │ │ │ │ @@ -258,15 +258,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 180 of file threads.h.

    │ │ │ +

    Definition at line 180 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/db2/a03822.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::ComposedEnergyProcessor Class Reference
    Molecular Modeling » Energy evaluation (non-MM) » Miscellaneous
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/ENERGY/composedEnergyProcessor.h>

    │ │ │ +

    #include <BALL/ENERGY/composedEnergyProcessor.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::ComposedEnergyProcessor:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::EnergyProcessor │ │ │ @@ -173,15 +173,15 @@ │ │ │   │ │ │ bool valid_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    A class for composed energy calculations. Most energies are compositions of several energy contributions. To model this in a convenient way this class is intended to calculate and sum a given list of energy contributions.

    See also
    EnergyProcessor
    │ │ │ │ │ │ -

    Definition at line 34 of file composedEnergyProcessor.h.

    │ │ │ +

    Definition at line 34 of file composedEnergyProcessor.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ComposedEnergyProcessor() [1/3]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -429,15 +429,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 116 of file composedEnergyProcessor.h.

    │ │ │ +

    Definition at line 116 of file composedEnergyProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/db4/a07594.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::VIEW::EditSettings Class Reference
    Visualisation » QT Dialogs
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/DIALOGS/editSettings.h>

    │ │ │ +

    #include <BALL/VIEW/DIALOGS/editSettings.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::EditSettings:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ QWidget │ │ │ @@ -155,15 +155,15 @@ │ │ │ - Protected Member Functions inherited from BALL::VIEW::PreferencesEntry │ │ │ void registerWidgets_ () │ │ │   │ │ │ void registerObject_ (QObject *widget) │ │ │   │ │ │ void unregisterObject_ (QObject *widget) │ │ │   │ │ │ -BALL_DEPRECATED void registerWidgetForHelpSystem_ (const QWidget *, const String &) │ │ │ +BALL_DEPRECATED void registerWidgetForHelpSystem_ (const QWidget *, const String &) │ │ │   │ │ │ void restoreValues_ (bool all, const ValueMap &map) │ │ │   │ │ │ void insertStackEntry_ (QWidget *, const String &name) │ │ │   │ │ │ bool isSupported_ (QObject &widget) │ │ │   │ │ │ @@ -188,15 +188,15 @@ │ │ │

    Detailed Description

    │ │ │

    EditSettings is a widget that will be inserted into the tab dialog Preferences. It contains the following settings:

      │ │ │
    • maximum distance for an atom to be picked
      • │ │ │
    • maximum distance for an bond to be picked
      • │ │ │
    • only atom in highlighted container to be picked?
      • │ │ │
    │ │ │ │ │ │ -

    Definition at line 32 of file editSettings.h.

    │ │ │ +

    Definition at line 32 of file editSettings.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ EditSettings()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/db6/a00692.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: ringAnalyser.h File Reference │ │ │ +BALL: label.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,46 +65,41 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    ringAnalyser.h File Reference
    │ │ │ +
    label.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/KERNEL/atomContainer.h>
    │ │ │ -#include <BALL/CONCEPT/processor.h>
    │ │ │ -#include <BALL/CONCEPT/property.h>
    │ │ │ -#include <vector>
    │ │ │ -#include <set>
    │ │ │ -#include <deque>
    │ │ │ +
    #include <BALL/VIEW/KERNEL/geometricObject.h>
    │ │ │ +#include <BALL/VIEW/DATATYPE/vertex1.h>
    │ │ │ +#include <QtGui/QFont>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │
    │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::RingAnalyser
     Methods for the analysis of the structure of ringsystems. More...
     
    class  BALL::RingAnalyser::Ring
    class  BALL::VIEW::Label
     
    │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ + │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,28 +1,24 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ + * _V_I_E_W │ │ │ │ + * _P_R_I_M_I_T_I_V_E_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -ringAnalyser.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_p_e_r_t_y_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ +label.h File Reference │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_g_e_o_m_e_t_r_i_c_O_b_j_e_c_t_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_v_e_r_t_e_x_1_._h> │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r │ │ │ │ -  Methods for the analysis of the structure of ringsystems. _M_o_r_e_._._. │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │ +  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/db6/a00692_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: ringAnalyser.h Source File │ │ │ +BALL: label.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,197 +70,133 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    ringAnalyser.h
    │ │ │ +
    label.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5#ifndef BALL_STRUCTURE_RINGANALYSER_H
    │ │ │ -
    6#define BALL_STRUCTURE_RINGANALYSER_H
    │ │ │ +
    5#ifndef BALL_VIEW_PRIMITIV_LABEL_H
    │ │ │ +
    6#define BALL_VIEW_PRIMITIV_LABEL_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ -
    9# include <BALL/common.h>
    │ │ │ +
    8#ifndef BALL_VIEW_KERNEL_GEOMETRICOBJECT_H
    │ │ │ +
    9# include <BALL/VIEW/KERNEL/geometricObject.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_KERNEL_ATOMCONTAINER_H
    │ │ │ -
    13# include <BALL/KERNEL/atomContainer.h>
    │ │ │ +
    12#ifndef BALL_VIEW_DATATYPE_VERTEX1_H
    │ │ │ +
    13# include <BALL/VIEW/DATATYPE/vertex1.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │ -
    16#ifndef BALL_CONCEPT_PROCESSOR_H
    │ │ │ -
    17# include <BALL/CONCEPT/processor.h>
    │ │ │ -
    18#endif
    │ │ │ -
    19
    │ │ │ -
    20#ifndef BALL_CONCEPT_PROPERTY_H
    │ │ │ -
    21# include <BALL/CONCEPT/property.h>
    │ │ │ -
    22#endif
    │ │ │ -
    23
    │ │ │ -
    24#include <vector>
    │ │ │ -
    25#include <set>
    │ │ │ -
    26#include <deque>
    │ │ │ -
    27
    │ │ │ -
    28namespace BALL
    │ │ │ -
    29{
    │ │ │ -
    30 class Atom;
    │ │ │ -
    31 class Bond;
    │ │ │ -
    32
    │ │ │ -
    │ │ │ -
    36 class BALL_EXPORT RingAnalyser
    │ │ │ -
    37 : public UnaryProcessor<AtomContainer>
    │ │ │ -
    38 {
    │ │ │ -
    39 public:
    │ │ │ -
    40
    │ │ │ -
    │ │ │ -
    41 enum RingType
    │ │ │ -
    42 {
    │ │ │ -
    43 NONE,
    │ │ │ -
    44 TEMPLATE,
    │ │ │ -
    45 FUSED,
    │ │ │ -
    46 BRIDGED,
    │ │ │ -
    47 SPIRO,
    │ │ │ -
    48 CORE
    │ │ │ -
    49 };
    │ │ │ -
    │ │ │ +
    16#include <QtGui/QFont>
    │ │ │ +
    17
    │ │ │ +
    18namespace BALL
    │ │ │ +
    19{
    │ │ │ +
    20 namespace VIEW
    │ │ │ +
    21 {
    │ │ │ +
    22
    │ │ │ +
    │ │ │ +
    45 class BALL_VIEW_EXPORT Label
    │ │ │ +
    46 : public GeometricObject,
    │ │ │ +
    47 public Vertex
    │ │ │ +
    48 {
    │ │ │ +
    49 public:
    │ │ │
    50
    │ │ │ -
    │ │ │ -
    51 class BALL_EXPORT Ring
    │ │ │ -
    52 : public PropertyManager
    │ │ │ -
    53 {
    │ │ │ -
    54 public:
    │ │ │ -
    56 Ring();
    │ │ │ -
    57
    │ │ │ -
    59 Ring(std::vector<Atom*> const& atoms_);
    │ │ │ -
    60
    │ │ │ -
    62 Position predecessor(Position i) const;
    │ │ │ -
    63
    │ │ │ -
    65 Position successor(Position i) const;
    │ │ │ -
    66
    │ │ │ -
    68 std::vector<Atom*> atoms;
    │ │ │ +
    51 BALL_CREATE(Label)
    │ │ │ +
    52
    │ │ │ +
    53
    │ │ │ +
    56
    │ │ │ +
    57
    │ │ │ +
    68 Label();
    │ │ │
    69
    │ │ │ -
    71 RingType type;
    │ │ │ -
    72
    │ │ │ -
    74 std::set<Bond const*> shared_bonds;
    │ │ │ -
    75 };
    │ │ │ -
    │ │ │ +
    75 Label(const Label& label);
    │ │ │
    76
    │ │ │ -
    79
    │ │ │ -
    83 RingAnalyser();
    │ │ │ +
    78
    │ │ │ +
    80
    │ │ │ +
    83 virtual ~Label();
    │ │ │
    84
    │ │ │ -
    88 virtual ~RingAnalyser();
    │ │ │ -
    90
    │ │ │ -
    93
    │ │ │ -
    95 virtual bool start();
    │ │ │ -
    96
    │ │ │ -
    101 virtual Processor::Result operator ()(AtomContainer& ac);
    │ │ │ +
    91 virtual void clear();
    │ │ │ +
    92
    │ │ │ +
    94
    │ │ │ +
    96
    │ │ │ +
    101 void set(const Label& label);
    │ │ │
    102
    │ │ │ -
    104 virtual bool finish();
    │ │ │ -
    105
    │ │ │ +
    106 const Label& operator = (const Label& label);
    │ │ │
    107
    │ │ │ -
    112 void clear();
    │ │ │ +
    110 void swap(Label& label);
    │ │ │ +
    111
    │ │ │
    113
    │ │ │ -
    120 bool isInRing(const Atom* atom, std::vector<Atom*> const& ring) const;
    │ │ │ -
    121
    │ │ │ -
    128 bool isInRingSystem(const Atom* atom, Index i) const;
    │ │ │ +
    115
    │ │ │ +
    │ │ │ +
    118 void setText(const String& text)
    │ │ │ +
    119 {text_ = text;}
    │ │ │ +
    │ │ │ +
    120
    │ │ │ +
    │ │ │ +
    123 String getText() const
    │ │ │ +
    124 { return text_;}
    │ │ │ +
    │ │ │ +
    125
    │ │ │ +
    128 String getExpandedText() const;
    │ │ │
    129
    │ │ │ -
    137 void sequenceRing(std::vector<Atom*>& ring);
    │ │ │ +
    131 const QFont& getFont() const { return font_;}
    │ │ │ +
    132
    │ │ │ +
    134 void setFont(const QFont& font) { font_ = font;}
    │ │ │ +
    135
    │ │ │ +
    137 void setFontSize(Size size) { font_.setPixelSize(size);}
    │ │ │
    138
    │ │ │ -
    141 Size getNumberOfRingSystems();
    │ │ │ +
    140
    │ │ │
    142
    │ │ │ -
    145 std::vector<Ring> getRingSystem(Position i);
    │ │ │ -
    146
    │ │ │ -
    149 std::vector<Position> getPeelingOrder(Position i);
    │ │ │ -
    150
    │ │ │ -
    151 protected:
    │ │ │ -
    152
    │ │ │ -
    156 void clusterRings_();
    │ │ │ -
    157
    │ │ │ -
    161 void findSharedBonds_();
    │ │ │ -
    162
    │ │ │ -
    166 void peelRings_();
    │ │ │ -
    167
    │ │ │ -
    169 bool isCentralRing_(std::list<Position>::iterator ring, std::list<Position>& unassigned_rings);
    │ │ │ -
    170
    │ │ │ -
    174 bool peelNextRing_(std::list<Position>& unassigned_rings, bool peel_fused = false);
    │ │ │ +
    155 virtual bool isValid() const;
    │ │ │ +
    156
    │ │ │ +
    167 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ +
    168
    │ │ │ +
    169 // Method to get all vertices from a geometric object
    │ │ │ +
    170 virtual void getVertices(vector<Vector3>& vertices) const;
    │ │ │ +
    171
    │ │ │ +
    172 protected:
    │ │ │ +
    173 String text_;
    │ │ │ +
    174 QFont font_;
    │ │ │
    175
    │ │ │ -
    180 bool assignRTD_(std::list<Position>& trial_system);
    │ │ │ -
    181
    │ │ │ -
    183 std::vector<Ring> rings_;
    │ │ │ -
    184
    │ │ │ -
    186 std::vector<std::vector<Position> > ring_systems_;
    │ │ │ -
    187
    │ │ │ -
    189 HashMap<Bond const*, std::deque<Position> > rings_per_bond_;
    │ │ │ -
    190
    │ │ │ -
    192 std::vector<std::vector<Position> > peeling_order_;
    │ │ │ -
    193 };
    │ │ │ +
    177 };
    │ │ │
    │ │ │ -
    194
    │ │ │ -
    195} // namespace BALL
    │ │ │ -
    196
    │ │ │ -
    197#endif // BALL_STRUCTURE_RINGANALYSER_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::PDB::Atom
    char Atom[5]
    Definition PDBdefs.h:257
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::HashMap
    HashMap class based on the STL map (containing serveral convenience functions)
    Definition hashMap.h:74
    │ │ │ - │ │ │ - │ │ │ -
    BALL::RingAnalyser
    Methods for the analysis of the structure of ringsystems.
    Definition ringAnalyser.h:38
    │ │ │ -
    BALL::RingAnalyser::peelNextRing_
    bool peelNextRing_(std::list< Position > &unassigned_rings, bool peel_fused=false)
    │ │ │ -
    BALL::RingAnalyser::start
    virtual bool start()
    Processor method which is called before the operator()-call.
    │ │ │ - │ │ │ -
    BALL::RingAnalyser::finish
    virtual bool finish()
    Processor method which is called after the operator()-call.
    │ │ │ -
    BALL::RingAnalyser::peeling_order_
    std::vector< std::vector< Position > > peeling_order_
    the order in which rings are peeled from their respective ring systems
    Definition ringAnalyser.h:192
    │ │ │ -
    BALL::RingAnalyser::RingAnalyser
    RingAnalyser()
    Default-Constructor.
    │ │ │ -
    BALL::RingAnalyser::getPeelingOrder
    std::vector< Position > getPeelingOrder(Position i)
    │ │ │ -
    BALL::RingAnalyser::isCentralRing_
    bool isCentralRing_(std::list< Position >::iterator ring, std::list< Position > &unassigned_rings)
    │ │ │ -
    BALL::RingAnalyser::isInRingSystem
    bool isInRingSystem(const Atom *atom, Index i) const
    helper-function; determines, whether an atom is part of a certain ring
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::RingAnalyser::~RingAnalyser
    virtual ~RingAnalyser()
    Destructor.
    │ │ │ -
    BALL::RingAnalyser::sequenceRing
    void sequenceRing(std::vector< Atom * > &ring)
    │ │ │ -
    BALL::RingAnalyser::peelRings_
    void peelRings_()
    performs an analysis of the structure of a ringsystem
    │ │ │ -
    BALL::RingAnalyser::getNumberOfRingSystems
    Size getNumberOfRingSystems()
    │ │ │ -
    BALL::RingAnalyser::assignRTD_
    bool assignRTD_(std::list< Position > &trial_system)
    interface for a Ring Template Database (RTD), no functionality yet
    │ │ │ -
    BALL::RingAnalyser::rings_
    std::vector< Ring > rings_
    the smallest set of smallest rings of our molecule
    Definition ringAnalyser.h:183
    │ │ │ -
    BALL::RingAnalyser::ring_systems_
    std::vector< std::vector< Position > > ring_systems_
    the ring systems, stored as indices into the smallest set of smallest rings
    Definition ringAnalyser.h:186
    │ │ │ -
    BALL::RingAnalyser::clusterRings_
    void clusterRings_()
    performs an agglomerative clustering of single rings to ringsystems
    │ │ │ -
    BALL::RingAnalyser::isInRing
    bool isInRing(const Atom *atom, std::vector< Atom * > const &ring) const
    helper-function; determines, whether an atom is part of a certain ring
    │ │ │ -
    BALL::RingAnalyser::getRingSystem
    std::vector< Ring > getRingSystem(Position i)
    │ │ │ -
    BALL::RingAnalyser::rings_per_bond_
    HashMap< Bond const *, std::deque< Position > > rings_per_bond_
    the ring memberships per bond
    Definition ringAnalyser.h:189
    │ │ │ - │ │ │ -
    BALL::RingAnalyser::Ring::predecessor
    Position predecessor(Position i) const
    The predecessor of atom i in the ring.
    │ │ │ -
    BALL::RingAnalyser::Ring::shared_bonds
    std::set< Bond const * > shared_bonds
    the bonds shared with other rings
    Definition ringAnalyser.h:74
    │ │ │ -
    BALL::RingAnalyser::Ring::successor
    Position successor(Position i) const
    The successor of atom i in the ring.
    │ │ │ -
    BALL::RingAnalyser::Ring::Ring
    Ring()
    Default constructor.
    │ │ │ -
    BALL::RingAnalyser::Ring::atoms
    std::vector< Atom * > atoms
    the atoms of this ring
    Definition ringAnalyser.h:68
    │ │ │ -
    BALL::RingAnalyser::Ring::type
    RingType type
    the type of this ring
    Definition ringAnalyser.h:71
    │ │ │ -
    BALL::RingAnalyser::Ring::Ring
    Ring(std::vector< Atom * > const &atoms_)
    Detailed constructor.
    │ │ │ - │ │ │ +
    178
    │ │ │ +
    179 } // namespace VIEW
    │ │ │ +
    180} // namespace BALL
    │ │ │ +
    181
    │ │ │ +
    182#endif // BALL_VIEW_PRIMITIV_LABEL_H
    │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::Label::getFont
    const QFont & getFont() const
    Definition label.h:131
    │ │ │ +
    BALL::VIEW::Label::getText
    String getText() const
    Definition label.h:123
    │ │ │ + │ │ │ +
    BALL::VIEW::Label::dump
    virtual void dump(std::ostream &s=std::cout, Size depth=0) const
    │ │ │ + │ │ │ +
    BALL::VIEW::Label::setFontSize
    void setFontSize(Size size)
    Definition label.h:137
    │ │ │ +
    BALL::VIEW::Label::setFont
    void setFont(const QFont &font)
    Definition label.h:134
    │ │ │ +
    BALL::VIEW::Label::getVertices
    virtual void getVertices(vector< Vector3 > &vertices) const
    │ │ │ +
    BALL::VIEW::Label::isValid
    virtual bool isValid() const
    │ │ │ +
    BALL::VIEW::Label::getExpandedText
    String getExpandedText() const
    │ │ │ │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,268 +1,143 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ -ringAnalyser.h │ │ │ │ + * _V_I_E_W │ │ │ │ + * _P_R_I_M_I_T_I_V_E_S │ │ │ │ +label.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_STRUCTURE_RINGANALYSER_H │ │ │ │ -6#define BALL_STRUCTURE_RINGANALYSER_H │ │ │ │ +5#ifndef BALL_VIEW_PRIMITIV_LABEL_H │ │ │ │ +6#define BALL_VIEW_PRIMITIV_LABEL_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ -9# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +8#ifndef BALL_VIEW_KERNEL_GEOMETRICOBJECT_H │ │ │ │ +9# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_g_e_o_m_e_t_r_i_c_O_b_j_e_c_t_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_KERNEL_ATOMCONTAINER_H │ │ │ │ -13# include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ +12#ifndef BALL_VIEW_DATATYPE_VERTEX1_H │ │ │ │ +13# include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_v_e_r_t_e_x_1_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#ifndef BALL_CONCEPT_PROCESSOR_H │ │ │ │ -17# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20#ifndef BALL_CONCEPT_PROPERTY_H │ │ │ │ -21# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_p_e_r_t_y_._h> │ │ │ │ -22#endif │ │ │ │ -23 │ │ │ │ -24#include │ │ │ │ -25#include │ │ │ │ -26#include │ │ │ │ -27 │ │ │ │ -28namespace _B_A_L_L │ │ │ │ -29{ │ │ │ │ -30 class _A_t_o_m; │ │ │ │ -31 class Bond; │ │ │ │ -32 │ │ │ │ -_3_6 class _B_A_L_L___E_X_P_O_R_T _R_i_n_g_A_n_a_l_y_s_e_r │ │ │ │ -37 : public _U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -38 { │ │ │ │ -39 public: │ │ │ │ -40 │ │ │ │ -_4_1 enum _R_i_n_g_T_y_p_e │ │ │ │ -42 { │ │ │ │ -_4_3 _N_O_N_E, │ │ │ │ -_4_4 _T_E_M_P_L_A_T_E, │ │ │ │ -_4_5 _F_U_S_E_D, │ │ │ │ -_4_6 _B_R_I_D_G_E_D, │ │ │ │ -_4_7 _S_P_I_R_O, │ │ │ │ -48 CORE │ │ │ │ -_4_9 }; │ │ │ │ +16#include │ │ │ │ +17 │ │ │ │ +18namespace _B_A_L_L │ │ │ │ +19{ │ │ │ │ +20 namespace VIEW │ │ │ │ +21 { │ │ │ │ +22 │ │ │ │ +_4_5 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _L_a_b_e_l │ │ │ │ +46 : public _G_e_o_m_e_t_r_i_c_O_b_j_e_c_t, │ │ │ │ +47 public _V_e_r_t_e_x │ │ │ │ +48 { │ │ │ │ +49 public: │ │ │ │ 50 │ │ │ │ -_5_1 class _B_A_L_L___E_X_P_O_R_T _R_i_n_g │ │ │ │ -52 : public _P_r_o_p_e_r_t_y_M_a_n_a_g_e_r │ │ │ │ -53 { │ │ │ │ -54 public: │ │ │ │ -_5_6 _R_i_n_g(); │ │ │ │ +51 _B_A_L_L___C_R_E_A_T_E(_L_a_b_e_l) │ │ │ │ +52 │ │ │ │ +53 │ │ │ │ +56 │ │ │ │ 57 │ │ │ │ -_5_9 _R_i_n_g(std::vector const& atoms_); │ │ │ │ -60 │ │ │ │ -_6_2 _P_o_s_i_t_i_o_n _p_r_e_d_e_c_e_s_s_o_r(_P_o_s_i_t_i_o_n i) const; │ │ │ │ -63 │ │ │ │ -_6_5 _P_o_s_i_t_i_o_n _s_u_c_c_e_s_s_o_r(_P_o_s_i_t_i_o_n i) const; │ │ │ │ -66 │ │ │ │ -_6_8 std::vector _a_t_o_m_s; │ │ │ │ +_6_8 _L_a_b_e_l(); │ │ │ │ 69 │ │ │ │ -_7_1 _R_i_n_g_T_y_p_e _t_y_p_e; │ │ │ │ -72 │ │ │ │ -_7_4 std::set _s_h_a_r_e_d___b_o_n_d_s; │ │ │ │ -75 }; │ │ │ │ +_7_5 _L_a_b_e_l(const _L_a_b_e_l& label); │ │ │ │ 76 │ │ │ │ -79 │ │ │ │ -_8_3 _R_i_n_g_A_n_a_l_y_s_e_r(); │ │ │ │ +78 │ │ │ │ +80 │ │ │ │ +_8_3 virtual ~_L_a_b_e_l(); │ │ │ │ 84 │ │ │ │ -_8_8 virtual _~_R_i_n_g_A_n_a_l_y_s_e_r(); │ │ │ │ -90 │ │ │ │ -93 │ │ │ │ -_9_5 virtual bool _s_t_a_r_t(); │ │ │ │ +_9_1 virtual void clear(); │ │ │ │ +92 │ │ │ │ +94 │ │ │ │ 96 │ │ │ │ -_1_0_1 virtual _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t operator ()(_A_t_o_m_C_o_n_t_a_i_n_e_r& ac); │ │ │ │ +_1_0_1 void set(const _L_a_b_e_l& label); │ │ │ │ 102 │ │ │ │ -_1_0_4 virtual bool _f_i_n_i_s_h(); │ │ │ │ -105 │ │ │ │ +_1_0_6 const _L_a_b_e_l& operator = (const _L_a_b_e_l& label); │ │ │ │ 107 │ │ │ │ -_1_1_2 void _c_l_e_a_r(); │ │ │ │ +_1_1_0 void swap(_L_a_b_e_l& label); │ │ │ │ +111 │ │ │ │ 113 │ │ │ │ -_1_2_0 bool _i_s_I_n_R_i_n_g(const _A_t_o_m* atom, std::vector const& ring) const; │ │ │ │ -121 │ │ │ │ -_1_2_8 bool _i_s_I_n_R_i_n_g_S_y_s_t_e_m(const _A_t_o_m* atom, _I_n_d_e_x i) const; │ │ │ │ +115 │ │ │ │ +_1_1_8 void setText(const _S_t_r_i_n_g& text) │ │ │ │ +119 {text_ = text;} │ │ │ │ +120 │ │ │ │ +_1_2_3 _S_t_r_i_n_g _g_e_t_T_e_x_t() const │ │ │ │ +124 { return text_;} │ │ │ │ +125 │ │ │ │ +_1_2_8 _S_t_r_i_n_g _g_e_t_E_x_p_a_n_d_e_d_T_e_x_t() const; │ │ │ │ 129 │ │ │ │ -_1_3_7 void _s_e_q_u_e_n_c_e_R_i_n_g(std::vector& ring); │ │ │ │ +_1_3_1 const QFont& _g_e_t_F_o_n_t() const { return font_;} │ │ │ │ +132 │ │ │ │ +_1_3_4 void _s_e_t_F_o_n_t(const QFont& font) { font_ = font;} │ │ │ │ +135 │ │ │ │ +_1_3_7 void _s_e_t_F_o_n_t_S_i_z_e(_S_i_z_e size) { font_.setPixelSize(size);} │ │ │ │ 138 │ │ │ │ -_1_4_1 _S_i_z_e _g_e_t_N_u_m_b_e_r_O_f_R_i_n_g_S_y_s_t_e_m_s(); │ │ │ │ +140 │ │ │ │ 142 │ │ │ │ -_1_4_5 std::vector _g_e_t_R_i_n_g_S_y_s_t_e_m(_P_o_s_i_t_i_o_n i); │ │ │ │ -146 │ │ │ │ -_1_4_9 std::vector _g_e_t_P_e_e_l_i_n_g_O_r_d_e_r(_P_o_s_i_t_i_o_n i); │ │ │ │ -150 │ │ │ │ -151 protected: │ │ │ │ -152 │ │ │ │ -_1_5_6 void _c_l_u_s_t_e_r_R_i_n_g_s__(); │ │ │ │ -157 │ │ │ │ -_1_6_1 void _f_i_n_d_S_h_a_r_e_d_B_o_n_d_s__(); │ │ │ │ -162 │ │ │ │ -_1_6_6 void _p_e_e_l_R_i_n_g_s__(); │ │ │ │ -167 │ │ │ │ -_1_6_9 bool _i_s_C_e_n_t_r_a_l_R_i_n_g__(std::list::iterator ring, std:: │ │ │ │ -list& unassigned_rings); │ │ │ │ -170 │ │ │ │ -_1_7_4 bool _p_e_e_l_N_e_x_t_R_i_n_g__(std::list& unassigned_rings, bool peel_fused = │ │ │ │ -false); │ │ │ │ +_1_5_5 virtual bool _i_s_V_a_l_i_d() const; │ │ │ │ +156 │ │ │ │ +_1_6_7 virtual void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const; │ │ │ │ +168 │ │ │ │ +169 // Method to get all vertices from a geometric object │ │ │ │ +_1_7_0 virtual void _g_e_t_V_e_r_t_i_c_e_s(vector& vertices) const; │ │ │ │ +171 │ │ │ │ +172 protected: │ │ │ │ +_1_7_3 _S_t_r_i_n_g _t_e_x_t__; │ │ │ │ +_1_7_4 QFont _f_o_n_t__; │ │ │ │ 175 │ │ │ │ -_1_8_0 bool _a_s_s_i_g_n_R_T_D__(std::list& trial_system); │ │ │ │ +177 }; │ │ │ │ +178 │ │ │ │ +179 } // namespace VIEW │ │ │ │ +180} // namespace BALL │ │ │ │ 181 │ │ │ │ -_1_8_3 std::vector _r_i_n_g_s__; │ │ │ │ -184 │ │ │ │ -_1_8_6 std::vector > _r_i_n_g___s_y_s_t_e_m_s__; │ │ │ │ -187 │ │ │ │ -_1_8_9 _H_a_s_h_M_a_p_<_B_o_n_d_ _c_o_n_s_t_*_,_ _s_t_d_:_:_d_e_q_u_e_<_P_o_s_i_t_i_o_n_> > _r_i_n_g_s___p_e_r___b_o_n_d__; │ │ │ │ -190 │ │ │ │ -_1_9_2 std::vector > _p_e_e_l_i_n_g___o_r_d_e_r__; │ │ │ │ -193 }; │ │ │ │ -194 │ │ │ │ -195} // namespace BALL │ │ │ │ -196 │ │ │ │ -197#endif // BALL_STRUCTURE_RINGANALYSER_H │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_a_t_o_m_C_o_n_t_a_i_n_e_r_._h │ │ │ │ -_p_r_o_p_e_r_t_y_._h │ │ │ │ -_p_r_o_c_e_s_s_o_r_._h │ │ │ │ +182#endif // BALL_VIEW_PRIMITIV_LABEL_H │ │ │ │ +_g_e_o_m_e_t_r_i_c_O_b_j_e_c_t_._h │ │ │ │ +_v_e_r_t_e_x_1_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_:_:_A_t_o_m │ │ │ │ -char Atom[5] │ │ │ │ -DDeeffiinniittiioonn _P_D_B_d_e_f_s_._h_:_2_5_7 │ │ │ │ -_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t │ │ │ │ -int Result │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_6_0 │ │ │ │ -_B_A_L_L_:_:_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_._h_:_3_4_4 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_M_a_p │ │ │ │ -HashMap class based on the STL map (containing serveral convenience functions) │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_M_a_p_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r │ │ │ │ -Methods for the analysis of the structure of ringsystems. │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_3_8 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_p_e_e_l_N_e_x_t_R_i_n_g__ │ │ │ │ -bool peelNextRing_(std::list< Position > &unassigned_rings, bool │ │ │ │ -peel_fused=false) │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_s_t_a_r_t │ │ │ │ -virtual bool start() │ │ │ │ -Processor method which is called before the operator()-call. │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_f_i_n_d_S_h_a_r_e_d_B_o_n_d_s__ │ │ │ │ -void findSharedBonds_() │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_f_i_n_i_s_h │ │ │ │ -virtual bool finish() │ │ │ │ -Processor method which is called after the operator()-call. │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_p_e_e_l_i_n_g___o_r_d_e_r__ │ │ │ │ -std::vector< std::vector< Position > > peeling_order_ │ │ │ │ -the order in which rings are peeled from their respective ring systems │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_1_9_2 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g_A_n_a_l_y_s_e_r │ │ │ │ -RingAnalyser() │ │ │ │ -Default-Constructor. │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_g_e_t_P_e_e_l_i_n_g_O_r_d_e_r │ │ │ │ -std::vector< Position > getPeelingOrder(Position i) │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_i_s_C_e_n_t_r_a_l_R_i_n_g__ │ │ │ │ -bool isCentralRing_(std::list< Position >::iterator ring, std::list< Position > │ │ │ │ -&unassigned_rings) │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_i_s_I_n_R_i_n_g_S_y_s_t_e_m │ │ │ │ -bool isInRingSystem(const Atom *atom, Index i) const │ │ │ │ -helper-function; determines, whether an atom is part of a certain ring │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_c_l_e_a_r │ │ │ │ -void clear() │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g_T_y_p_e │ │ │ │ -RingType │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_4_2 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_S_P_I_R_O │ │ │ │ -@ SPIRO │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_4_7 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_N_O_N_E │ │ │ │ -@ NONE │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_B_R_I_D_G_E_D │ │ │ │ -@ BRIDGED │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_F_U_S_E_D │ │ │ │ -@ FUSED │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_4_5 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_T_E_M_P_L_A_T_E │ │ │ │ -@ TEMPLATE │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_4_4 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_~_R_i_n_g_A_n_a_l_y_s_e_r │ │ │ │ -virtual ~RingAnalyser() │ │ │ │ -Destructor. │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_s_e_q_u_e_n_c_e_R_i_n_g │ │ │ │ -void sequenceRing(std::vector< Atom * > &ring) │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_p_e_e_l_R_i_n_g_s__ │ │ │ │ -void peelRings_() │ │ │ │ -performs an analysis of the structure of a ringsystem │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_g_e_t_N_u_m_b_e_r_O_f_R_i_n_g_S_y_s_t_e_m_s │ │ │ │ -Size getNumberOfRingSystems() │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_a_s_s_i_g_n_R_T_D__ │ │ │ │ -bool assignRTD_(std::list< Position > &trial_system) │ │ │ │ -interface for a Ring Template Database (RTD), no functionality yet │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_r_i_n_g_s__ │ │ │ │ -std::vector< Ring > rings_ │ │ │ │ -the smallest set of smallest rings of our molecule │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_1_8_3 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_r_i_n_g___s_y_s_t_e_m_s__ │ │ │ │ -std::vector< std::vector< Position > > ring_systems_ │ │ │ │ -the ring systems, stored as indices into the smallest set of smallest rings │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_1_8_6 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_c_l_u_s_t_e_r_R_i_n_g_s__ │ │ │ │ -void clusterRings_() │ │ │ │ -performs an agglomerative clustering of single rings to ringsystems │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_i_s_I_n_R_i_n_g │ │ │ │ -bool isInRing(const Atom *atom, std::vector< Atom * > const &ring) const │ │ │ │ -helper-function; determines, whether an atom is part of a certain ring │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_g_e_t_R_i_n_g_S_y_s_t_e_m │ │ │ │ -std::vector< Ring > getRingSystem(Position i) │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_r_i_n_g_s___p_e_r___b_o_n_d__ │ │ │ │ -HashMap< Bond const *, std::deque< Position > > rings_per_bond_ │ │ │ │ -the ring memberships per bond │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_1_8_9 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g_:_:_p_r_e_d_e_c_e_s_s_o_r │ │ │ │ -Position predecessor(Position i) const │ │ │ │ -The predecessor of atom i in the ring. │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g_:_:_s_h_a_r_e_d___b_o_n_d_s │ │ │ │ -std::set< Bond const * > shared_bonds │ │ │ │ -the bonds shared with other rings │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g_:_:_s_u_c_c_e_s_s_o_r │ │ │ │ -Position successor(Position i) const │ │ │ │ -The successor of atom i in the ring. │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g_:_:_R_i_n_g │ │ │ │ -Ring() │ │ │ │ -Default constructor. │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g_:_:_a_t_o_m_s │ │ │ │ -std::vector< Atom * > atoms │ │ │ │ -the atoms of this ring │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_6_8 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g_:_:_t_y_p_e │ │ │ │ -RingType type │ │ │ │ -the type of this ring │ │ │ │ -DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_7_1 │ │ │ │ -_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g_:_:_R_i_n_g │ │ │ │ -Ring(std::vector< Atom * > const &atoms_) │ │ │ │ -Detailed constructor. │ │ │ │ -_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_V_e_r_t_e_x │ │ │ │ +DDeeffiinniittiioonn _v_e_r_t_e_x_1_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_O_b_j_e_c_t │ │ │ │ +DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_O_b_j_e_c_t_._h_:_3_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_g_e_t_F_o_n_t │ │ │ │ +const QFont & getFont() const │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_._h_:_1_3_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_g_e_t_T_e_x_t │ │ │ │ +String getText() const │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_._h_:_1_2_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_f_o_n_t__ │ │ │ │ +QFont font_ │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_._h_:_1_7_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_d_u_m_p │ │ │ │ +virtual void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_t_e_x_t__ │ │ │ │ +String text_ │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_._h_:_1_7_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_s_e_t_F_o_n_t_S_i_z_e │ │ │ │ +void setFontSize(Size size) │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_._h_:_1_3_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_s_e_t_F_o_n_t │ │ │ │ +void setFont(const QFont &font) │ │ │ │ +DDeeffiinniittiioonn _l_a_b_e_l_._h_:_1_3_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_g_e_t_V_e_r_t_i_c_e_s │ │ │ │ +virtual void getVertices(vector< Vector3 > &vertices) const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_i_s_V_a_l_i_d │ │ │ │ +virtual bool isValid() const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_L_a_b_e_l_:_:_g_e_t_E_x_p_a_n_d_e_d_T_e_x_t │ │ │ │ +String getExpandedText() const │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ +#define BALL_VIEW_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/db7/a05562.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::PyCompositeList Class Reference
    Python » Python extensions
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/PYTHON/EXTENSIONS/pyCompositeList.h>

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    #include <BALL/PYTHON/EXTENSIONS/pyCompositeList.h>

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    │ │ │ Inheritance diagram for BALL::PyCompositeList:
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    virtual ~PyCompositeList () throw ()
     Destructor.
     
    │ │ │

    Detailed Description

    │ │ │

    Equivalent for a STL::List of Composite Pointers in Python

    │ │ │ │ │ │ -

    Definition at line 29 of file pyCompositeList.h.

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    Definition at line 29 of file pyCompositeList.h.

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    Member Typedef Documentation

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    ◆ ConstIterator

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    │ │ │
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    typedef std::list<Composite*>::const_iterator BALL::PyCompositeList::ConstIterator
    │ │ │
    │ │ │

    Constant iterator type.

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    Definition at line 54 of file pyCompositeList.h.

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    Definition at line 54 of file pyCompositeList.h.

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    ◆ Iterator

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    │ │ │ @@ -157,15 +157,15 @@ │ │ │ │ │ │ typedef std::list<Composite*>::iterator BALL::PyCompositeList::Iterator │ │ │ │ │ │ │ │ │
    │ │ │

    Iterator type.

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    Definition at line 50 of file pyCompositeList.h.

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    Definition at line 50 of file pyCompositeList.h.

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    ◆ PointerType

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    │ │ │ @@ -174,15 +174,15 @@ │ │ │ │ │ │ typedef Composite** BALL::PyCompositeList::PointerType │ │ │ │ │ │ │ │ │
    │ │ │

    Pointer type

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    Definition at line 46 of file pyCompositeList.h.

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    Definition at line 46 of file pyCompositeList.h.

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    ◆ ValueType

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    │ │ │ @@ -191,15 +191,15 @@ │ │ │ │ │ │ typedef Composite* BALL::PyCompositeList::ValueType │ │ │ │ │ │ │ │ │
    │ │ │

    Composite* type

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    Definition at line 42 of file pyCompositeList.h.

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    Definition at line 42 of file pyCompositeList.h.

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    Constructor & Destructor Documentation

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    ◆ PyCompositeList() [1/6]

    │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/db7/a07866.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::VIEW::DeselectControlsMessage Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/message.h>

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    #include <BALL/VIEW/KERNEL/message.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::DeselectControlsMessage:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::Message │ │ │ @@ -112,15 +112,15 @@ │ │ │   │ │ │ boost::any & data () │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Message send by one GenericControl to notify all other GenericControl instances to deselect their QListView.

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    Definition at line 724 of file message.h.

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    Definition at line 724 of file message.h.

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    Constructor & Destructor Documentation

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    ◆ DeselectControlsMessage()

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    Definition at line 728 of file message.h.

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    Definition at line 728 of file message.h.

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    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/db8/a07990.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members
    │ │ │
    BALL::VIEW::GenerateCrystalThread Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/threads.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/threads.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::GenerateCrystalThread:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::BALLThread │ │ │ @@ -132,15 +132,15 @@ │ │ │  Sends the string as outout to Log.info.
    │ │ │   │ │ │ void waitForUpdateOfRepresentations_ () │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 140 of file threads.h.

    │ │ │ +

    Definition at line 140 of file threads.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ GenerateCrystalThread()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -204,15 +204,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
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    Definition at line 152 of file threads.h.

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    Definition at line 152 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ dialog_

    │ │ │ │ │ │ @@ -229,15 +229,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 155 of file threads.h.

    │ │ │ +

    Definition at line 155 of file threads.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dba/a05906.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::NumberOfCarbon Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/QSAR/simpleDescriptors.h>

    │ │ │ +

    #include <BALL/QSAR/simpleDescriptors.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::NumberOfCarbon:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::SimpleBase │ │ │ @@ -104,23 +104,23 @@ │ │ │   │ │ │
    Assignment
    │ │ │ NumberOfCarbon & operator= (const NumberOfCarbon &nc) │ │ │   │ │ │ - Public Member Functions inherited from BALL::SimpleBase │ │ │  SimpleBase () │ │ │   │ │ │ - SimpleBase (const SimpleBase &sb) │ │ │ + SimpleBase (const SimpleBase &sb) │ │ │   │ │ │  SimpleBase (const String &name) │ │ │   │ │ │  SimpleBase (const String &name, const String &unit) │ │ │   │ │ │ virtual ~SimpleBase () │ │ │   │ │ │ -virtual SimpleBase & operator= (const SimpleBase &sb) │ │ │ +virtual SimpleBase & operator= (const SimpleBase &sb) │ │ │   │ │ │ void computeAllDescriptors (AtomContainer &ac) │ │ │   │ │ │ void setDataFolder (const char *folder) │ │ │   │ │ │ - Public Member Functions inherited from BALL::Descriptor │ │ │  Descriptor () │ │ │ @@ -180,15 +180,15 @@ │ │ │ void calculate_ (AtomContainer &ac) │ │ │   │ │ │ - Protected Member Functions inherited from BALL::Descriptor │ │ │ │ │ │

    Detailed Description

    │ │ │

    This descriptor counts the number of carbon

    │ │ │ │ │ │ -

    Definition at line 294 of file simpleDescriptors.h.

    │ │ │ +

    Definition at line 294 of file simpleDescriptors.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ NumberOfCarbon() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dbd/a04634.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::SecondaryStructureIteratorTraits Class Reference
    Kernel Classes » Iterator Classes
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/KERNEL/secondaryStructureIterator.h>

    │ │ │ +

    #include <BALL/KERNEL/secondaryStructureIterator.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::SecondaryStructureIteratorTraits:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::CompositeIteratorTraits │ │ │ @@ -191,15 +191,15 @@ │ │ │
    │ │ │ │ │ │ │ │ │
    const UnaryPredicate< Composite > * predicate_
     The predicate.
     
    │ │ │

    Detailed Description

    │ │ │

    SecondaryStructureIteratorTraits

    │ │ │ │ │ │ -

    Definition at line 32 of file secondaryStructureIterator.h.

    │ │ │ +

    Definition at line 32 of file secondaryStructureIterator.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ SecondaryStructureIteratorTraits() [1/3]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -216,15 +216,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
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    Definition at line 37 of file secondaryStructureIterator.h.

    │ │ │ +

    Definition at line 37 of file secondaryStructureIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ SecondaryStructureIteratorTraits() [2/3]

    │ │ │ │ │ │
    │ │ │ @@ -244,15 +244,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
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    Definition at line 43 of file secondaryStructureIterator.h.

    │ │ │ +

    Definition at line 43 of file secondaryStructureIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ SecondaryStructureIteratorTraits() [3/3]

    │ │ │ │ │ │
    │ │ │ @@ -282,15 +282,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 49 of file secondaryStructureIterator.h.

    │ │ │ +

    Definition at line 49 of file secondaryStructureIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ operator=()

    │ │ │ │ │ │ @@ -311,15 +311,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 54 of file secondaryStructureIterator.h.

    │ │ │ +

    Definition at line 54 of file secondaryStructureIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ resetPredicate()

    │ │ │ │ │ │
    │ │ │ @@ -338,15 +338,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 60 of file secondaryStructureIterator.h.

    │ │ │ +

    Definition at line 60 of file secondaryStructureIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dbe/a06026.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::PrincipalMomentOfInertiaY Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/QSAR/simpleDescriptors.h>

    │ │ │ +

    #include <BALL/QSAR/simpleDescriptors.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::PrincipalMomentOfInertiaY:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::SimpleBase │ │ │ @@ -104,23 +104,23 @@ │ │ │   │ │ │
    Assignment
    │ │ │ PrincipalMomentOfInertiaY & operator= (const PrincipalMomentOfInertiaY &pmiy) │ │ │   │ │ │ - Public Member Functions inherited from BALL::SimpleBase │ │ │  SimpleBase () │ │ │   │ │ │ - SimpleBase (const SimpleBase &sb) │ │ │ + SimpleBase (const SimpleBase &sb) │ │ │   │ │ │  SimpleBase (const String &name) │ │ │   │ │ │  SimpleBase (const String &name, const String &unit) │ │ │   │ │ │ virtual ~SimpleBase () │ │ │   │ │ │ -virtual SimpleBase & operator= (const SimpleBase &sb) │ │ │ +virtual SimpleBase & operator= (const SimpleBase &sb) │ │ │   │ │ │ void computeAllDescriptors (AtomContainer &ac) │ │ │   │ │ │ void setDataFolder (const char *folder) │ │ │   │ │ │ - Public Member Functions inherited from BALL::Descriptor │ │ │  Descriptor () │ │ │ @@ -180,15 +180,15 @@ │ │ │ void calculate_ (AtomContainer &ac) │ │ │   │ │ │ - Protected Member Functions inherited from BALL::Descriptor │ │ │ │ │ │

    Detailed Description

    │ │ │

    This descriptor adds up the y-axis component of the principal moment of inertia over all atoms, calculated from the filed coordinates!

    │ │ │ │ │ │ -

    Definition at line 1465 of file simpleDescriptors.h.

    │ │ │ +

    Definition at line 1465 of file simpleDescriptors.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ PrincipalMomentOfInertiaY() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc0/a01652.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: extractors.h File Reference │ │ │ +BALL: NMRDescriptors.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,92 +65,51 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Namespaces | │ │ │ -Typedefs | │ │ │ Functions
    │ │ │ -
    extractors.h File Reference
    │ │ │ +
    NMRDescriptors.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/DATATYPE/string.h>
    │ │ │ +
    #include <BALL/common.h>
    │ │ │ +#include <BALL/DATATYPE/hashMap.h>
    │ │ │ +#include <BALL/KERNEL/residue.h>
    │ │ │ +#include <BALL/KERNEL/protein.h>
    │ │ │ +#include <BALL/KERNEL/atomContainer.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -

    │ │ │ -Typedefs

    typedef std::list< Atom * > BALL::AtomList
     
    typedef std::list< Bond * > BALL::BondList
     
    typedef std::list< AtomContainer * > BALL::AtomContainerList
     
    typedef std::list< PDBAtom * > BALL::PDBAtomList
     
    typedef std::list< Residue * > BALL::ResidueList
     
    typedef std::list< Fragment * > BALL::FragmentList
     
    typedef std::list< Molecule * > BALL::MoleculeList
     
    typedef std::list< Protein * > BALL::ProteinList
     
    typedef std::list< SecondaryStructure * > BALL::SecondaryStructureList
     
    typedef std::list< Chain * > BALL::ChainList
     
    typedef std::list< Nucleotide * > BALL::NucleotideList
     
    typedef std::list< NucleicAcid * > BALL::NucleicAcidList
     
    │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ Functions

    BALL_EXPORT AtomList BALL::atoms (const AtomContainer &fragment, const String &expression=String())
     
    BALL_EXPORT AtomList BALL::atoms (const AtomList &atoms, const String &expression)
     
    BALL_EXPORT PDBAtomList BALL::PDBAtoms (const AtomContainer &fragment, const String &expression=String())
     
    BALL_EXPORT BondList BALL::bonds (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT BondList BALL::bonds (const Atom &atom)
     
    BALL_EXPORT AtomContainerList BALL::atomContainers (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT ResidueList BALL::residues (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT FragmentList BALL::fragments (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT MoleculeList BALL::molecules (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT ProteinList BALL::proteins (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT SecondaryStructureList BALL::secondaryStructures (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT ChainList BALL::chains (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT NucleicAcidList BALL::nucleicAcids (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT NucleotideList BALL::nucleotides (const AtomContainer &fragment, bool selected_only=false)
     
    BALL_EXPORT void BALL::calculateResidueChiAngles (const Protein &protein, HashMap< const Residue *, float > &residue_angles)
     
    BALL_EXPORT void BALL::calculateResidueChiAngles (const Chain &fragment, HashMap< const Residue *, float > &residue_angles)
     
    BALL_EXPORT float BALL::calculateResidueChiAngles (const Residue &residue)
     
    BALL_EXPORT void BALL::calculateResidueChi2Angles (const Protein &protein, HashMap< const Residue *, float > &residue_angles)
     
    BALL_EXPORT void BALL::calculateResidueChi2Angles (const Chain &fragment, HashMap< const Residue *, float > &residue_angles)
     
    BALL_EXPORT float BALL::calculateResidueChi2Angles (const Residue &residue)
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,86 +1,37 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ -_N_a_m_e_s_p_a_c_e_s | _T_y_p_e_d_e_f_s | _F_u_n_c_t_i_o_n_s │ │ │ │ -extractors.h File Reference │ │ │ │ + * _Q_S_A_R │ │ │ │ +_N_a_m_e_s_p_a_c_e_s | _F_u_n_c_t_i_o_n_s │ │ │ │ +NMRDescriptors.h File Reference │ │ │ │ #include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_r_e_s_i_d_u_e_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_o_t_e_i_n_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -TTyyppeeddeeffss │ │ │ │ - typedef std::list< _A_t_o_m * >  _B_A_L_L_:_:_A_t_o_m_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _B_o_n_d * >  _B_A_L_L_:_:_B_o_n_d_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _A_t_o_m_C_o_n_t_a_i_n_e_r * >  _B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _P_D_B_A_t_o_m * >  _B_A_L_L_:_:_P_D_B_A_t_o_m_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _R_e_s_i_d_u_e * >  _B_A_L_L_:_:_R_e_s_i_d_u_e_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _F_r_a_g_m_e_n_t * >  _B_A_L_L_:_:_F_r_a_g_m_e_n_t_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _M_o_l_e_c_u_l_e * >  _B_A_L_L_:_:_M_o_l_e_c_u_l_e_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _P_r_o_t_e_i_n * >  _B_A_L_L_:_:_P_r_o_t_e_i_n_L_i_s_t │ │ │ │ -  │ │ │ │ -typedef std::list< _S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e * >  _B_A_L_L_:_:_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _C_h_a_i_n * >  _B_A_L_L_:_:_C_h_a_i_n_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _N_u_c_l_e_o_t_i_d_e * >  _B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_L_i_s_t │ │ │ │ -  │ │ │ │ - typedef std::list< _N_u_c_l_e_i_c_A_c_i_d * >  _B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_L_i_s_t │ │ │ │ -  │ │ │ │ FFuunnccttiioonnss │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _A_t_o_m_L_i_s_t  _B_A_L_L_:_:_a_t_o_m_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r &fragment, │ │ │ │ - const _S_t_r_i_n_g &expression=_S_t_r_i_n_g()) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _A_t_o_m_L_i_s_t  _B_A_L_L_:_:_a_t_o_m_s (const _A_t_o_m_L_i_s_t &atoms, const │ │ │ │ - _S_t_r_i_n_g &expression) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _P_D_B_A_t_o_m_L_i_s_t  _B_A_L_L_:_:_P_D_B_A_t_o_m_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ - &fragment, const _S_t_r_i_n_g &expression=_S_t_r_i_n_g │ │ │ │ - ()) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _B_o_n_d_L_i_s_t  _B_A_L_L_:_:_b_o_n_d_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r &fragment, │ │ │ │ - _b_o_o_l selected_only=false) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _B_o_n_d_L_i_s_t  _B_A_L_L_:_:_b_o_n_d_s (const _A_t_o_m &atom) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _A_t_o_m_C_o_n_t_a_i_n_e_r_L_i_s_t  _B_A_L_L_:_:_a_t_o_m_C_o_n_t_a_i_n_e_r_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ - &fragment, _b_o_o_l selected_only=false) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _R_e_s_i_d_u_e_L_i_s_t  _B_A_L_L_:_:_r_e_s_i_d_u_e_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ - &fragment, _b_o_o_l selected_only=false) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _F_r_a_g_m_e_n_t_L_i_s_t  _B_A_L_L_:_:_f_r_a_g_m_e_n_t_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ - &fragment, _b_o_o_l selected_only=false) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _M_o_l_e_c_u_l_e_L_i_s_t  _B_A_L_L_:_:_m_o_l_e_c_u_l_e_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ - &fragment, _b_o_o_l selected_only=false) │ │ │ │ + _B_A_L_L___E_X_P_O_R_T void  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s (const _P_r_o_t_e_i_n &protein, │ │ │ │ + _H_a_s_h_M_a_p< const _R_e_s_i_d_u_e *, _f_l_o_a_t > &residue_angles) │ │ │ │   │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _P_r_o_t_e_i_n_L_i_s_t  _B_A_L_L_:_:_p_r_o_t_e_i_n_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ - &fragment, _b_o_o_l selected_only=false) │ │ │ │ + _B_A_L_L___E_X_P_O_R_T void  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s (const _C_h_a_i_n &fragment, │ │ │ │ + _H_a_s_h_M_a_p< const _R_e_s_i_d_u_e *, _f_l_o_a_t > &residue_angles) │ │ │ │   │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_L_i_s_t  _B_A_L_L_:_:_s_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_s (const │ │ │ │ - _A_t_o_m_C_o_n_t_a_i_n_e_r &fragment, _b_o_o_l │ │ │ │ - selected_only=false) │ │ │ │ +_B_A_L_L___E_X_P_O_R_T _f_l_o_a_t  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s (const _R_e_s_i_d_u_e &residue) │ │ │ │   │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _C_h_a_i_n_L_i_s_t  _B_A_L_L_:_:_c_h_a_i_n_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ - &fragment, _b_o_o_l selected_only=false) │ │ │ │ + _B_A_L_L___E_X_P_O_R_T void  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s (const _P_r_o_t_e_i_n &protein, │ │ │ │ + _H_a_s_h_M_a_p< const _R_e_s_i_d_u_e *, _f_l_o_a_t > &residue_angles) │ │ │ │   │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _N_u_c_l_e_i_c_A_c_i_d_L_i_s_t  _B_A_L_L_:_:_n_u_c_l_e_i_c_A_c_i_d_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ - &fragment, _b_o_o_l selected_only=false) │ │ │ │ + _B_A_L_L___E_X_P_O_R_T void  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s (const _C_h_a_i_n &fragment, │ │ │ │ + _H_a_s_h_M_a_p< const _R_e_s_i_d_u_e *, _f_l_o_a_t > &residue_angles) │ │ │ │   │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _N_u_c_l_e_o_t_i_d_e_L_i_s_t  _B_A_L_L_:_:_n_u_c_l_e_o_t_i_d_e_s (const _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ - &fragment, _b_o_o_l selected_only=false) │ │ │ │ +_B_A_L_L___E_X_P_O_R_T _f_l_o_a_t  _B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s (const _R_e_s_i_d_u_e &residue) │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc0/a01652_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: extractors.h Source File │ │ │ +BALL: NMRDescriptors.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,136 +70,79 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    extractors.h
    │ │ │ +
    NMRDescriptors.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ -
    2// vi: set ts=2:
    │ │ │ -
    3//
    │ │ │ -
    4// $Id: extractors.h,v 1.2.8.3 2007/03/27 22:41:31 amoll Exp $
    │ │ │ -
    5//
    │ │ │ -
    6// Author:
    │ │ │ -
    7// Oliver Kohlbacher
    │ │ │ -
    8//
    │ │ │ -
    9
    │ │ │ -
    10#ifndef BALL_KERNEL_EXTRACTORS_H
    │ │ │ -
    11#define BALL_KERNEL_EXTRACTORS_H
    │ │ │ -
    12
    │ │ │ -
    13#ifndef BALL_COMMON_H
    │ │ │ -
    14# include <BALL/common.h>
    │ │ │ -
    15#endif
    │ │ │ -
    16
    │ │ │ -
    17#ifndef BALL_DATATYPE_STRING_H
    │ │ │ -
    18# include <BALL/DATATYPE/string.h>
    │ │ │ -
    19#endif
    │ │ │ -
    20
    │ │ │ -
    21namespace BALL
    │ │ │ -
    22{
    │ │ │ +Go to the documentation of this file.
    1#ifndef BALL_QSAR_NMRDESCRIPTORS_H
    │ │ │ +
    2#define BALL_QSAR_NMRDESCRIPTORS_H
    │ │ │ +
    3
    │ │ │ +
    4#ifndef BALL_COMMON_H
    │ │ │ +
    5# include <BALL/common.h>
    │ │ │ +
    6#endif
    │ │ │ +
    7
    │ │ │ +
    8#ifndef BALL_DATATYPE_H
    │ │ │ +
    9# include <BALL/DATATYPE/hashMap.h>
    │ │ │ +
    10#endif
    │ │ │ +
    11
    │ │ │ +
    12#ifndef BALL_KERNEL_RESIDUE_H
    │ │ │ +
    13# include <BALL/KERNEL/residue.h>
    │ │ │ +
    14#endif
    │ │ │ +
    15
    │ │ │ +
    16#ifndef BALL_KERNEL_PROTEIN_H
    │ │ │ +
    17# include <BALL/KERNEL/protein.h>
    │ │ │ +
    18#endif
    │ │ │ +
    19
    │ │ │ +
    20#ifndef BALL_KERNEL_ATOMCONTAINER_H
    │ │ │ +
    21# include <BALL/KERNEL/atomContainer.h>
    │ │ │ +
    22#endif
    │ │ │
    23
    │ │ │ -
    24 class Atom;
    │ │ │ -
    25 class PDBAtom;
    │ │ │ -
    26 class Bond;
    │ │ │ -
    27 class AtomContainer;
    │ │ │ -
    28 class Fragment;
    │ │ │ -
    29 class Molecule;
    │ │ │ -
    30 class Residue;
    │ │ │ -
    31 class SecondaryStructure;
    │ │ │ -
    32 class Chain;
    │ │ │ -
    33 class Protein;
    │ │ │ -
    34 class Nucleotide;
    │ │ │ -
    35 class NucleicAcid;
    │ │ │ -
    36
    │ │ │ -
    51 typedef std::list<Atom*> AtomList;
    │ │ │ -
    53 typedef std::list<Bond*> BondList;
    │ │ │ -
    55 typedef std::list<AtomContainer*> AtomContainerList;
    │ │ │ -
    57 typedef std::list<PDBAtom*> PDBAtomList;
    │ │ │ -
    59 typedef std::list<Residue*> ResidueList;
    │ │ │ -
    61 typedef std::list<Fragment*> FragmentList;
    │ │ │ -
    63 typedef std::list<Molecule*> MoleculeList;
    │ │ │ -
    65 typedef std::list<Protein*> ProteinList;
    │ │ │ -
    67 typedef std::list<SecondaryStructure*> SecondaryStructureList;
    │ │ │ -
    69 typedef std::list<Chain*> ChainList;
    │ │ │ -
    71 typedef std::list<Nucleotide*> NucleotideList;
    │ │ │ -
    73 typedef std::list<NucleicAcid*> NucleicAcidList;
    │ │ │ -
    74
    │ │ │ -
    76
    │ │ │ -
    84
    │ │ │ -
    92 BALL_EXPORT AtomList atoms(const AtomContainer& fragment, const String& expression = String());
    │ │ │ -
    93
    │ │ │ -
    100 BALL_EXPORT AtomList atoms(const AtomList& atoms, const String& expression);
    │ │ │ -
    101
    │ │ │ -
    109 BALL_EXPORT PDBAtomList PDBAtoms(const AtomContainer& fragment, const String& expression = String());
    │ │ │ -
    110
    │ │ │ -
    116 BALL_EXPORT BondList bonds(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    117
    │ │ │ -
    121 BALL_EXPORT BondList bonds(const Atom& atom);
    │ │ │ -
    122
    │ │ │ -
    125 BALL_EXPORT AtomContainerList atomContainers(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    126
    │ │ │ -
    129 BALL_EXPORT ResidueList residues(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    130
    │ │ │ -
    133 BALL_EXPORT FragmentList fragments(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    134
    │ │ │ -
    137 BALL_EXPORT MoleculeList molecules(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    138
    │ │ │ -
    141 BALL_EXPORT ProteinList proteins(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    142
    │ │ │ -
    145 BALL_EXPORT SecondaryStructureList secondaryStructures(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    146
    │ │ │ -
    149 BALL_EXPORT ChainList chains(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    150
    │ │ │ -
    153 BALL_EXPORT NucleicAcidList nucleicAcids(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    154
    │ │ │ -
    157 BALL_EXPORT NucleotideList nucleotides(const AtomContainer& fragment, bool selected_only = false);
    │ │ │ -
    158
    │ │ │ -
    160
    │ │ │ -
    161} // namespace BALL
    │ │ │ -
    162
    │ │ │ -
    163#endif // BALL_KERNEL_EXTRACTORS_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL::atoms
    BALL_EXPORT AtomList atoms(const AtomContainer &fragment, const String &expression=String())
    │ │ │ -
    BALL::AtomList
    std::list< Atom * > AtomList
    Definition extractors.h:51
    │ │ │ - │ │ │ -
    BALL::atomContainers
    BALL_EXPORT AtomContainerList atomContainers(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::NucleotideList
    std::list< Nucleotide * > NucleotideList
    Definition extractors.h:71
    │ │ │ -
    BALL::ResidueList
    std::list< Residue * > ResidueList
    Definition extractors.h:59
    │ │ │ -
    BALL::MoleculeList
    std::list< Molecule * > MoleculeList
    Definition extractors.h:63
    │ │ │ -
    BALL::PDBAtomList
    std::list< PDBAtom * > PDBAtomList
    Definition extractors.h:57
    │ │ │ -
    BALL::PDBAtoms
    BALL_EXPORT PDBAtomList PDBAtoms(const AtomContainer &fragment, const String &expression=String())
    │ │ │ -
    BALL::proteins
    BALL_EXPORT ProteinList proteins(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::BondList
    std::list< Bond * > BondList
    Definition extractors.h:53
    │ │ │ -
    BALL::SecondaryStructureList
    std::list< SecondaryStructure * > SecondaryStructureList
    Definition extractors.h:67
    │ │ │ -
    BALL::molecules
    BALL_EXPORT MoleculeList molecules(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::ChainList
    std::list< Chain * > ChainList
    Definition extractors.h:69
    │ │ │ -
    BALL::nucleotides
    BALL_EXPORT NucleotideList nucleotides(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::fragments
    BALL_EXPORT FragmentList fragments(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::secondaryStructures
    BALL_EXPORT SecondaryStructureList secondaryStructures(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::chains
    BALL_EXPORT ChainList chains(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::AtomContainerList
    std::list< AtomContainer * > AtomContainerList
    Definition extractors.h:55
    │ │ │ -
    BALL::residues
    BALL_EXPORT ResidueList residues(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::nucleicAcids
    BALL_EXPORT NucleicAcidList nucleicAcids(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::ProteinList
    std::list< Protein * > ProteinList
    Definition extractors.h:65
    │ │ │ -
    BALL::FragmentList
    std::list< Fragment * > FragmentList
    Definition extractors.h:61
    │ │ │ -
    BALL::NucleicAcidList
    std::list< NucleicAcid * > NucleicAcidList
    Definition extractors.h:73
    │ │ │ -
    BALL::bonds
    BALL_EXPORT BondList bonds(const AtomContainer &fragment, bool selected_only=false)
    │ │ │ -
    BALL::PDB::Atom
    char Atom[5]
    Definition PDBdefs.h:257
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    24namespace BALL
    │ │ │ +
    25{
    │ │ │ +
    26
    │ │ │ +
    34 BALL_EXPORT void calculateResidueChiAngles(const Protein& protein, HashMap<const Residue*, float>& residue_angles);
    │ │ │ +
    35
    │ │ │ +
    43 BALL_EXPORT void calculateResidueChiAngles( const Chain& fragment,
    │ │ │ +
    44 HashMap<const Residue*,float>& residue_angles);
    │ │ │ +
    45
    │ │ │ +
    49 BALL_EXPORT float calculateResidueChiAngles(const Residue& residue);
    │ │ │ +
    50
    │ │ │ +
    51
    │ │ │ +
    59 BALL_EXPORT void calculateResidueChi2Angles(const Protein& protein, HashMap<const Residue*, float>& residue_angles);
    │ │ │ +
    60
    │ │ │ +
    68 BALL_EXPORT void calculateResidueChi2Angles( const Chain& fragment,
    │ │ │ +
    69 HashMap<const Residue*,float>& residue_angles);
    │ │ │ +
    70
    │ │ │ +
    71
    │ │ │ +
    75 BALL_EXPORT float calculateResidueChi2Angles(const Residue& residue);
    │ │ │ +
    76
    │ │ │ +
    77}
    │ │ │ +
    78
    │ │ │ +
    79#endif
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::calculateResidueChiAngles
    BALL_EXPORT void calculateResidueChiAngles(const Protein &protein, HashMap< const Residue *, float > &residue_angles)
    │ │ │ +
    BALL::calculateResidueChi2Angles
    BALL_EXPORT void calculateResidueChi2Angles(const Protein &protein, HashMap< const Residue *, float > &residue_angles)
    │ │ │ +
    BALL::HashMap
    HashMap class based on the STL map (containing serveral convenience functions)
    Definition hashMap.h:74
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,195 +1,83 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ -extractors.h │ │ │ │ + * _Q_S_A_R │ │ │ │ +NMRDescriptors.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ -2// vi: set ts=2: │ │ │ │ -3// │ │ │ │ -4// $Id: extractors.h,v 1.2.8.3 2007/03/27 22:41:31 amoll Exp $ │ │ │ │ -5// │ │ │ │ -6// Author: │ │ │ │ -7// Oliver Kohlbacher │ │ │ │ -8// │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_KERNEL_EXTRACTORS_H │ │ │ │ -11#define BALL_KERNEL_EXTRACTORS_H │ │ │ │ -12 │ │ │ │ -13#ifndef BALL_COMMON_H │ │ │ │ -14# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -15#endif │ │ │ │ -16 │ │ │ │ -17#ifndef BALL_DATATYPE_STRING_H │ │ │ │ -18# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_s_t_r_i_n_g_._h> │ │ │ │ -19#endif │ │ │ │ -20 │ │ │ │ -21namespace _B_A_L_L │ │ │ │ -22{ │ │ │ │ +1#ifndef BALL_QSAR_NMRDESCRIPTORS_H │ │ │ │ +2#define BALL_QSAR_NMRDESCRIPTORS_H │ │ │ │ +3 │ │ │ │ +4#ifndef BALL_COMMON_H │ │ │ │ +5# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +6#endif │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_DATATYPE_H │ │ │ │ +9# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12#ifndef BALL_KERNEL_RESIDUE_H │ │ │ │ +13# include <_B_A_L_L_/_K_E_R_N_E_L_/_r_e_s_i_d_u_e_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifndef BALL_KERNEL_PROTEIN_H │ │ │ │ +17# include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_o_t_e_i_n_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20#ifndef BALL_KERNEL_ATOMCONTAINER_H │ │ │ │ +21# include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ +22#endif │ │ │ │ 23 │ │ │ │ -24 class _A_t_o_m; │ │ │ │ -25 class PDBAtom; │ │ │ │ -26 class Bond; │ │ │ │ -27 class AtomContainer; │ │ │ │ -28 class Fragment; │ │ │ │ -29 class Molecule; │ │ │ │ -30 class Residue; │ │ │ │ -31 class SecondaryStructure; │ │ │ │ -32 class Chain; │ │ │ │ -33 class Protein; │ │ │ │ -34 class Nucleotide; │ │ │ │ -35 class NucleicAcid; │ │ │ │ -36 │ │ │ │ -_5_1 typedef std::list _A_t_o_m_L_i_s_t; │ │ │ │ -_5_3 typedef std::list _B_o_n_d_L_i_s_t; │ │ │ │ -_5_5 typedef std::list _A_t_o_m_C_o_n_t_a_i_n_e_r_L_i_s_t; │ │ │ │ -_5_7 typedef std::list _P_D_B_A_t_o_m_L_i_s_t; │ │ │ │ -_5_9 typedef std::list _R_e_s_i_d_u_e_L_i_s_t; │ │ │ │ -_6_1 typedef std::list _F_r_a_g_m_e_n_t_L_i_s_t; │ │ │ │ -_6_3 typedef std::list _M_o_l_e_c_u_l_e_L_i_s_t; │ │ │ │ -_6_5 typedef std::list _P_r_o_t_e_i_n_L_i_s_t; │ │ │ │ -_6_7 typedef std::list _S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_L_i_s_t; │ │ │ │ -_6_9 typedef std::list _C_h_a_i_n_L_i_s_t; │ │ │ │ -_7_1 typedef std::list _N_u_c_l_e_o_t_i_d_e_L_i_s_t; │ │ │ │ -_7_3 typedef std::list _N_u_c_l_e_i_c_A_c_i_d_L_i_s_t; │ │ │ │ -74 │ │ │ │ +24namespace _B_A_L_L │ │ │ │ +25{ │ │ │ │ +26 │ │ │ │ +_3_4 _B_A_L_L___E_X_P_O_R_T void _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s(const _P_r_o_t_e_i_n& protein, │ │ │ │ +_H_a_s_h_M_a_p_<_c_o_n_s_t_ _R_e_s_i_d_u_e_*_,_ _f_l_o_a_t_>& residue_angles); │ │ │ │ +35 │ │ │ │ +_4_3 _B_A_L_L___E_X_P_O_R_T void _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s( const _C_h_a_i_n& fragment, │ │ │ │ +44 _H_a_s_h_M_a_p_<_c_o_n_s_t_ _R_e_s_i_d_u_e_*_,_f_l_o_a_t_>& residue_angles); │ │ │ │ +45 │ │ │ │ +_4_9 _B_A_L_L___E_X_P_O_R_T float _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s(const _R_e_s_i_d_u_e& residue); │ │ │ │ +50 │ │ │ │ +51 │ │ │ │ +_5_9 _B_A_L_L___E_X_P_O_R_T void _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s(const _P_r_o_t_e_i_n& protein, │ │ │ │ +_H_a_s_h_M_a_p_<_c_o_n_s_t_ _R_e_s_i_d_u_e_*_,_ _f_l_o_a_t_>& residue_angles); │ │ │ │ +60 │ │ │ │ +_6_8 _B_A_L_L___E_X_P_O_R_T void _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s( const _C_h_a_i_n& fragment, │ │ │ │ +69 _H_a_s_h_M_a_p_<_c_o_n_s_t_ _R_e_s_i_d_u_e_*_,_f_l_o_a_t_>& residue_angles); │ │ │ │ +70 │ │ │ │ +71 │ │ │ │ +_7_5 _B_A_L_L___E_X_P_O_R_T float _c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s(const _R_e_s_i_d_u_e& residue); │ │ │ │ 76 │ │ │ │ -84 │ │ │ │ -_9_2 _B_A_L_L___E_X_P_O_R_T _A_t_o_m_L_i_s_t _a_t_o_m_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, const _S_t_r_i_n_g& │ │ │ │ -expression = _S_t_r_i_n_g()); │ │ │ │ -93 │ │ │ │ -_1_0_0 _B_A_L_L___E_X_P_O_R_T _A_t_o_m_L_i_s_t _a_t_o_m_s(const _A_t_o_m_L_i_s_t& _a_t_o_m_s, const _S_t_r_i_n_g& │ │ │ │ -expression); │ │ │ │ -101 │ │ │ │ -_1_0_9 _B_A_L_L___E_X_P_O_R_T _P_D_B_A_t_o_m_L_i_s_t _P_D_B_A_t_o_m_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, const │ │ │ │ -_S_t_r_i_n_g& expression = _S_t_r_i_n_g()); │ │ │ │ -110 │ │ │ │ -_1_1_6 _B_A_L_L___E_X_P_O_R_T _B_o_n_d_L_i_s_t _b_o_n_d_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, bool │ │ │ │ -selected_only = false); │ │ │ │ -117 │ │ │ │ -_1_2_1 _B_A_L_L___E_X_P_O_R_T _B_o_n_d_L_i_s_t _b_o_n_d_s(const _A_t_o_m& atom); │ │ │ │ -122 │ │ │ │ -_1_2_5 _B_A_L_L___E_X_P_O_R_T _A_t_o_m_C_o_n_t_a_i_n_e_r_L_i_s_t _a_t_o_m_C_o_n_t_a_i_n_e_r_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, │ │ │ │ -bool selected_only = false); │ │ │ │ -126 │ │ │ │ -_1_2_9 _B_A_L_L___E_X_P_O_R_T _R_e_s_i_d_u_e_L_i_s_t _r_e_s_i_d_u_e_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, bool │ │ │ │ -selected_only = false); │ │ │ │ -130 │ │ │ │ -_1_3_3 _B_A_L_L___E_X_P_O_R_T _F_r_a_g_m_e_n_t_L_i_s_t _f_r_a_g_m_e_n_t_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, bool │ │ │ │ -selected_only = false); │ │ │ │ -134 │ │ │ │ -_1_3_7 _B_A_L_L___E_X_P_O_R_T _M_o_l_e_c_u_l_e_L_i_s_t _m_o_l_e_c_u_l_e_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, bool │ │ │ │ -selected_only = false); │ │ │ │ -138 │ │ │ │ -_1_4_1 _B_A_L_L___E_X_P_O_R_T _P_r_o_t_e_i_n_L_i_s_t _p_r_o_t_e_i_n_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, bool │ │ │ │ -selected_only = false); │ │ │ │ -142 │ │ │ │ -_1_4_5 _B_A_L_L___E_X_P_O_R_T _S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_L_i_s_t _s_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& │ │ │ │ -fragment, bool selected_only = false); │ │ │ │ -146 │ │ │ │ -_1_4_9 _B_A_L_L___E_X_P_O_R_T _C_h_a_i_n_L_i_s_t _c_h_a_i_n_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, bool │ │ │ │ -selected_only = false); │ │ │ │ -150 │ │ │ │ -_1_5_3 _B_A_L_L___E_X_P_O_R_T _N_u_c_l_e_i_c_A_c_i_d_L_i_s_t _n_u_c_l_e_i_c_A_c_i_d_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, │ │ │ │ -bool selected_only = false); │ │ │ │ -154 │ │ │ │ -_1_5_7 _B_A_L_L___E_X_P_O_R_T _N_u_c_l_e_o_t_i_d_e_L_i_s_t _n_u_c_l_e_o_t_i_d_e_s(const _A_t_o_m_C_o_n_t_a_i_n_e_r& fragment, bool │ │ │ │ -selected_only = false); │ │ │ │ -158 │ │ │ │ -160 │ │ │ │ -161} // namespace BALL │ │ │ │ -162 │ │ │ │ -163#endif // BALL_KERNEL_EXTRACTORS_H │ │ │ │ +77} │ │ │ │ +78 │ │ │ │ +79#endif │ │ │ │ _c_o_m_m_o_n_._h │ │ │ │ -_s_t_r_i_n_g_._h │ │ │ │ -_B_A_L_L_:_:_a_t_o_m_s │ │ │ │ -BALL_EXPORT AtomList atoms(const AtomContainer &fragment, const String │ │ │ │ -&expression=String()) │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_L_i_s_t │ │ │ │ -std::list< Atom * > AtomList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_5_1 │ │ │ │ +_r_e_s_i_d_u_e_._h │ │ │ │ +_p_r_o_t_e_i_n_._h │ │ │ │ +_a_t_o_m_C_o_n_t_a_i_n_e_r_._h │ │ │ │ +_h_a_s_h_M_a_p_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_a_t_o_m_C_o_n_t_a_i_n_e_r_s │ │ │ │ -BALL_EXPORT AtomContainerList atomContainers(const AtomContainer &fragment, │ │ │ │ -bool selected_only=false) │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_L_i_s_t │ │ │ │ -std::list< Nucleotide * > NucleotideList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_7_1 │ │ │ │ -_B_A_L_L_:_:_R_e_s_i_d_u_e_L_i_s_t │ │ │ │ -std::list< Residue * > ResidueList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_5_9 │ │ │ │ -_B_A_L_L_:_:_M_o_l_e_c_u_l_e_L_i_s_t │ │ │ │ -std::list< Molecule * > MoleculeList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_6_3 │ │ │ │ -_B_A_L_L_:_:_P_D_B_A_t_o_m_L_i_s_t │ │ │ │ -std::list< PDBAtom * > PDBAtomList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_P_D_B_A_t_o_m_s │ │ │ │ -BALL_EXPORT PDBAtomList PDBAtoms(const AtomContainer &fragment, const String │ │ │ │ -&expression=String()) │ │ │ │ -_B_A_L_L_:_:_p_r_o_t_e_i_n_s │ │ │ │ -BALL_EXPORT ProteinList proteins(const AtomContainer &fragment, bool │ │ │ │ -selected_only=false) │ │ │ │ -_B_A_L_L_:_:_B_o_n_d_L_i_s_t │ │ │ │ -std::list< Bond * > BondList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_L_i_s_t │ │ │ │ -std::list< SecondaryStructure * > SecondaryStructureList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_6_7 │ │ │ │ -_B_A_L_L_:_:_m_o_l_e_c_u_l_e_s │ │ │ │ -BALL_EXPORT MoleculeList molecules(const AtomContainer &fragment, bool │ │ │ │ -selected_only=false) │ │ │ │ -_B_A_L_L_:_:_C_h_a_i_n_L_i_s_t │ │ │ │ -std::list< Chain * > ChainList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_6_9 │ │ │ │ -_B_A_L_L_:_:_n_u_c_l_e_o_t_i_d_e_s │ │ │ │ -BALL_EXPORT NucleotideList nucleotides(const AtomContainer &fragment, bool │ │ │ │ -selected_only=false) │ │ │ │ -_B_A_L_L_:_:_f_r_a_g_m_e_n_t_s │ │ │ │ -BALL_EXPORT FragmentList fragments(const AtomContainer &fragment, bool │ │ │ │ -selected_only=false) │ │ │ │ -_B_A_L_L_:_:_s_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e_s │ │ │ │ -BALL_EXPORT SecondaryStructureList secondaryStructures(const AtomContainer │ │ │ │ -&fragment, bool selected_only=false) │ │ │ │ -_B_A_L_L_:_:_c_h_a_i_n_s │ │ │ │ -BALL_EXPORT ChainList chains(const AtomContainer &fragment, bool │ │ │ │ -selected_only=false) │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r_L_i_s_t │ │ │ │ -std::list< AtomContainer * > AtomContainerList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_5_5 │ │ │ │ -_B_A_L_L_:_:_r_e_s_i_d_u_e_s │ │ │ │ -BALL_EXPORT ResidueList residues(const AtomContainer &fragment, bool │ │ │ │ -selected_only=false) │ │ │ │ -_B_A_L_L_:_:_n_u_c_l_e_i_c_A_c_i_d_s │ │ │ │ -BALL_EXPORT NucleicAcidList nucleicAcids(const AtomContainer &fragment, bool │ │ │ │ -selected_only=false) │ │ │ │ -_B_A_L_L_:_:_P_r_o_t_e_i_n_L_i_s_t │ │ │ │ -std::list< Protein * > ProteinList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_6_5 │ │ │ │ -_B_A_L_L_:_:_F_r_a_g_m_e_n_t_L_i_s_t │ │ │ │ -std::list< Fragment * > FragmentList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_6_1 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_L_i_s_t │ │ │ │ -std::list< NucleicAcid * > NucleicAcidList │ │ │ │ -DDeeffiinniittiioonn _e_x_t_r_a_c_t_o_r_s_._h_:_7_3 │ │ │ │ -_B_A_L_L_:_:_b_o_n_d_s │ │ │ │ -BALL_EXPORT BondList bonds(const AtomContainer &fragment, bool │ │ │ │ -selected_only=false) │ │ │ │ -_B_A_L_L_:_:_P_D_B_:_:_A_t_o_m │ │ │ │ -char Atom[5] │ │ │ │ -DDeeffiinniittiioonn _P_D_B_d_e_f_s_._h_:_2_5_7 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_A_n_g_l_e_s │ │ │ │ +BALL_EXPORT void calculateResidueChiAngles(const Protein &protein, HashMap< │ │ │ │ +const Residue *, float > &residue_angles) │ │ │ │ +_B_A_L_L_:_:_c_a_l_c_u_l_a_t_e_R_e_s_i_d_u_e_C_h_i_2_A_n_g_l_e_s │ │ │ │ +BALL_EXPORT void calculateResidueChi2Angles(const Protein &protein, HashMap< │ │ │ │ +const Residue *, float > &residue_angles) │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_M_a_p │ │ │ │ +HashMap class based on the STL map (containing serveral convenience functions) │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_M_a_p_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_C_h_a_i_n │ │ │ │ +DDeeffiinniittiioonn _c_h_a_i_n_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_P_r_o_t_e_i_n │ │ │ │ +DDeeffiinniittiioonn _p_r_o_t_e_i_n_._h_:_3_0 │ │ │ │ +_B_A_L_L_:_:_R_e_s_i_d_u_e │ │ │ │ +DDeeffiinniittiioonn _r_e_s_i_d_u_e_._h_:_3_8 │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc2/a00104.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: fileObserver.h File Reference │ │ │ +BALL: sdGenerator.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,41 +65,49 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    fileObserver.h File Reference
    │ │ │ +
    sdGenerator.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/VIEW/WIDGETS/dockWidget.h>
    │ │ │ -#include <QtCore/QTimer>
    │ │ │ -#include <QtCore/QDateTime>
    │ │ │ +
    #include <BALL/DATATYPE/options.h>
    │ │ │ +#include <BALL/STRUCTURE/ringAnalyser.h>
    │ │ │ +#include <BALL/KERNEL/PDBAtom.h>
    │ │ │ +#include <vector>
    │ │ │ +#include <queue>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::FileObserver
    class  BALL::SDGenerator
     
    struct  BALL::SDGenerator::Option
     Option names. More...
     
    struct  BALL::SDGenerator::Default
     Default values for options. More...
     
    class  BALL::SDGenerator::AtomComparator
     
    │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,24 +1,31 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _W_I_D_G_E_T_S │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -fileObserver.h File Reference │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_W_I_D_G_E_T_S_/_d_o_c_k_W_i_d_g_e_t_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ +sdGenerator.h File Reference │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_r_i_n_g_A_n_a_l_y_s_e_r_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_P_D_B_A_t_o_m_._h> │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_F_i_l_e_O_b_s_e_r_v_e_r │ │ │ │ + class   _B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_O_p_t_i_o_n │ │ │ │ +  _O_p_t_i_o_n names. _M_o_r_e_._._. │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ +  _D_e_f_a_u_l_t values for options. _M_o_r_e_._._. │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_A_t_o_m_C_o_m_p_a_r_a_t_o_r │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │ -  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc2/a00104_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: fileObserver.h Source File │ │ │ +BALL: sdGenerator.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,101 +70,283 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    fileObserver.h
    │ │ │ +
    sdGenerator.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5#ifndef BALL_VIEW_WIDGETS_FILEOBSERVER_H
    │ │ │ -
    6#define BALL_VIEW_WIDGETS_FILEOBSERVER_H
    │ │ │ +
    5#ifndef BALL_STRUCTURE_SDGENERATOR_H
    │ │ │ +
    6#define BALL_STRUCTURE_SDGENERATOR_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_VIEW_WIDGETS_DOCKWIDGET_H
    │ │ │ -
    9# include <BALL/VIEW/WIDGETS/dockWidget.h>
    │ │ │ +
    8#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ +
    9# include <BALL/DATATYPE/options.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#include <QtCore/QTimer>
    │ │ │ -
    13#include <QtCore/QDateTime>
    │ │ │ -
    14
    │ │ │ -
    15class QAction;
    │ │ │ -
    16
    │ │ │ -
    17namespace BALL
    │ │ │ -
    18{
    │ │ │ -
    19 namespace VIEW
    │ │ │ -
    20 {
    │ │ │ -
    │ │ │ -
    34 class BALL_VIEW_EXPORT FileObserver
    │ │ │ -
    35 : public DockWidget
    │ │ │ -
    36 {
    │ │ │ -
    37 Q_OBJECT
    │ │ │ -
    38
    │ │ │ -
    39 public:
    │ │ │ -
    40
    │ │ │ -
    41 BALL_EMBEDDABLE(FileObserver,DockWidget)
    │ │ │ -
    42
    │ │ │ -
    43
    │ │ │ -
    44 FileObserver(QWidget *parent = 0, const char *name = 0);
    │ │ │ -
    45
    │ │ │ -
    47 virtual ~FileObserver();
    │ │ │ -
    48
    │ │ │ -
    49 //
    │ │ │ -
    50 virtual void initializeWidget(MainControl& main_control);
    │ │ │ -
    51
    │ │ │ -
    52 //
    │ │ │ -
    53 virtual void checkMenu(MainControl& main_control);
    │ │ │ -
    54
    │ │ │ -
    56 void setFileName(String filename);
    │ │ │ -
    57
    │ │ │ -
    59 String getFileName() const;
    │ │ │ -
    60
    │ │ │ -
    62 void setUpdateInterval(Size msec);
    │ │ │ -
    63
    │ │ │ -
    64 public Q_SLOTS:
    │ │ │ -
    65
    │ │ │ -
    67 void updateFile();
    │ │ │ -
    68
    │ │ │ -
    70 void start();
    │ │ │ -
    71
    │ │ │ -
    73 void stop();
    │ │ │ -
    74
    │ │ │ -
    76 void chooseFile();
    │ │ │ +
    12#ifndef BALL_STRUCTURE_RINGANALYSER_H
    │ │ │ +
    13# include <BALL/STRUCTURE/ringAnalyser.h>
    │ │ │ +
    14#endif
    │ │ │ +
    15
    │ │ │ +
    16#ifndef BALL_KERNEL_PDBATOM_H
    │ │ │ +
    17# include <BALL/KERNEL/PDBAtom.h>
    │ │ │ +
    18#endif
    │ │ │ +
    19
    │ │ │ +
    20#include <vector>
    │ │ │ +
    21#include <queue>
    │ │ │ +
    22
    │ │ │ +
    23namespace BALL
    │ │ │ +
    24{
    │ │ │ +
    25 class System;
    │ │ │ +
    26 class Atom;
    │ │ │ +
    27
    │ │ │ +
    │ │ │ +
    33 class BALL_EXPORT SDGenerator
    │ │ │ +
    34 {
    │ │ │ +
    35 public:
    │ │ │ +
    36
    │ │ │ +
    │ │ │ +
    40 enum Property
    │ │ │ +
    41 {
    │ │ │ +
    42 FIRST_SDGENERATOR_PROPERTY = PDBAtom::NUMBER_OF_PROPERTIES+1,
    │ │ │ +
    43 IN_RING,
    │ │ │ +
    44 CORE_CHAIN,
    │ │ │ +
    45 DEPOSITED,
    │ │ │ +
    46 FXAS,
    │ │ │ +
    47 EQAS,
    │ │ │ +
    48 HEAD,
    │ │ │ +
    49 EDGE,
    │ │ │ +
    50 ASSEMBLED,
    │ │ │ +
    51 ZIG,
    │ │ │ +
    52 ZAG,
    │ │ │ +
    53 INITIALIZED_HEAD_CFS,
    │ │ │ +
    54 LAST_SDGENERATOR_PROPERTY
    │ │ │ +
    55 };
    │ │ │ +
    │ │ │ +
    56
    │ │ │ +
    │ │ │ +
    61 struct BALL_EXPORT Option
    │ │ │ +
    62 {
    │ │ │ +
    65 static const char* SHOW_HYDROGENS;
    │ │ │ +
    66
    │ │ │ +
    70 static const char* STANDARD_BOND_LENGTH;
    │ │ │ +
    71 };
    │ │ │ +
    │ │ │ +
    72
    │ │ │ +
    │ │ │ +
    74 struct BALL_EXPORT Default
    │ │ │ +
    75 {
    │ │ │ +
    76 static const bool SHOW_HYDROGENS;
    │ │ │
    77
    │ │ │ -
    78 protected:
    │ │ │ -
    79
    │ │ │ -
    80 QAction* start_action_, *stop_action_;
    │ │ │ -
    81
    │ │ │ -
    82 QTimer timer_;
    │ │ │ -
    83 String file_name_;
    │ │ │ -
    84 QDateTime last_vis_time_;
    │ │ │ -
    85 };
    │ │ │ -
    │ │ │ -
    86
    │ │ │ -
    87} } // namespaces
    │ │ │ -
    88
    │ │ │ -
    89#endif // BALL_VIEW_WIDGETS_FILEOBSERVER_H
    │ │ │ - │ │ │ -
    BALL_EMBEDDABLE
    #define BALL_EMBEDDABLE(TYPE, BASE)
    Definition embeddable.h:31
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ +
    78 static const float STANDARD_BOND_LENGTH;
    │ │ │ +
    79 };
    │ │ │ +
    │ │ │ +
    81
    │ │ │ +
    85
    │ │ │ +
    89 SDGenerator(bool show_hydrogens = false);
    │ │ │ +
    90
    │ │ │ +
    94 virtual ~SDGenerator();
    │ │ │ +
    96
    │ │ │ +
    101 Options options;
    │ │ │ +
    103
    │ │ │ +
    109 void setDefaultOptions();
    │ │ │ +
    111
    │ │ │ +
    116 void generateSD(System& molecule_sys);
    │ │ │ +
    117
    │ │ │ +
    121 void clear();
    │ │ │ +
    122
    │ │ │ +
    123 protected:
    │ │ │ +
    124
    │ │ │ +
    │ │ │ +
    127 class AtomComparator
    │ │ │ +
    128 {
    │ │ │ +
    129 public:
    │ │ │ +
    │ │ │ +
    130 bool operator() (Atom const* first, Atom const* second) const
    │ │ │ +
    131 {
    │ │ │ +
    132 Size first_value = first->getProperty("SDGenerator::PRIORITY").getUnsignedInt();
    │ │ │ +
    133 Size second_value = second->getProperty("SDGenerator::PRIORITY").getUnsignedInt();
    │ │ │ +
    134
    │ │ │ +
    135 return first_value < second_value;
    │ │ │ +
    136 }
    │ │ │ +
    │ │ │ +
    137 };
    │ │ │ +
    │ │ │ +
    138
    │ │ │ +
    143 void prepare_();
    │ │ │ +
    144
    │ │ │ +
    149 void constructRingSystem_(Position current_ring_system);
    │ │ │ +
    150
    │ │ │ +
    151 // Obtain the CFS from the properties of the atom...
    │ │ │ +
    152 Angle getCFS_(Atom const* atom, bool hi);
    │ │ │ +
    153
    │ │ │ +
    154 // Convert a vector into the corresponding CFS angle
    │ │ │ +
    155 Angle computeCFS_(Vector3 const& input);
    │ │ │ +
    156
    │ │ │ +
    157 // store the CFS for an atom
    │ │ │ +
    158 void setCFS_(Atom* atom, Angle cfs, bool high);
    │ │ │ +
    159
    │ │ │ +
    160 // push the CFS before it is overwritten
    │ │ │ +
    161 void pushCFS_(Atom* atom);
    │ │ │ +
    162
    │ │ │ +
    163 // retrieve backup CVS values
    │ │ │ +
    164 Angle getBackupCFS_(Atom const*, bool hi);
    │ │ │ +
    165
    │ │ │ +
    166 // Compute the CFS values for a full regular polygon
    │ │ │ +
    167 void computeCoreCFS_(RingAnalyser::Ring& ring, bool clockwise);
    │ │ │ +
    168
    │ │ │ +
    169 //
    │ │ │ +
    170 Angle computeAngularSeparation_(Atom* seed);
    │ │ │ +
    171
    │ │ │ +
    172 //
    │ │ │ +
    173 Angle computeAngularDemand_(Atom* seed);
    │ │ │ +
    174
    │ │ │ +
    175 //
    │ │ │ +
    176 std::vector<Atom*> sequenceSubstituents_(Atom* seed);
    │ │ │ +
    177
    │ │ │ +
    180 void computeShelleyPriorities_();
    │ │ │ +
    181
    │ │ │ +
    184 void buildRegularPolygon_(RingAnalyser::Ring& ring, Position first_anchor_index, bool clockwise);
    │ │ │ +
    185
    │ │ │ +
    188 void buildOpenPolygon_(RingAnalyser::Ring& ring, Position first_anchor_index, Position second_anchor_index);
    │ │ │ +
    189
    │ │ │ +
    196 void attachCore_(Position current_ring, std::vector<RingAnalyser::Ring>& current_system, float x_start);
    │ │ │ +
    197
    │ │ │ +
    203 void attachTemplate_(Position current_ring, std::vector<RingAnalyser::Ring>& current_system);
    │ │ │ +
    204
    │ │ │ +
    210 void attachFused_(Position current_ring, std::vector<RingAnalyser::Ring>& current_system);
    │ │ │ +
    211
    │ │ │ +
    217 void attachBridged_(Position current_ring, std::vector<RingAnalyser::Ring>& current_system);
    │ │ │ +
    218
    │ │ │ +
    224 void attachSpiro_(Position current_ring, std::vector<RingAnalyser::Ring>& current_system);
    │ │ │ +
    225
    │ │ │ +
    227 void computeAdjacencyMatrix_(std::vector<Atom*>& chain, std::vector<bool>& result);
    │ │ │ +
    228
    │ │ │ +
    230 static bool compareChains_(const vector<Atom*>& x, const vector<Atom*>& y);
    │ │ │ +
    231
    │ │ │ +
    235 void treatChains_();
    │ │ │ +
    236
    │ │ │ +
    237 //
    │ │ │ +
    238 void smoothCFSAngle_(Atom* seed);
    │ │ │ +
    239
    │ │ │ +
    240 //
    │ │ │ +
    241 void placeSubstituent_(Atom* seed, Atom* head, Atom* next);
    │ │ │ +
    242
    │ │ │ +
    243 //
    │ │ │ +
    244 void depositPFU_(Atom* seed_atom, Atom* next_neighbour);
    │ │ │ +
    245
    │ │ │ +
    246 //
    │ │ │ +
    247 void checkOverlap_(Atom* atom);
    │ │ │ +
    248
    │ │ │ +
    249 //Check whether the ring is clockwise or not
    │ │ │ +
    250 bool ringIsClockwise_(const RingAnalyser::Ring& ring, Index start_index = 0) const;
    │ │ │ +
    251
    │ │ │ +
    255 void assembleSD_();
    │ │ │ +
    256
    │ │ │ +
    257 // The backtracking for our Floyd-Warshall implementation
    │ │ │ +
    258 void findFloydWarshallPath_(std::vector<int>& path, std::vector<Index>& next, Size remaining_atoms, Position i, Position j, std::list<Index>& output);
    │ │ │ +
    259
    │ │ │ +
    261 RingAnalyser ring_analyser_;
    │ │ │ +
    262
    │ │ │ +
    264 std::list<std::list<Atom*> > chains_;
    │ │ │ +
    265
    │ │ │ +
    267 std::priority_queue<Atom*, std::vector<Atom*>, AtomComparator> redraw_queue_;
    │ │ │ +
    268
    │ │ │ +
    270 System* system_;
    │ │ │ +
    271 };
    │ │ │ +
    │ │ │ +
    272
    │ │ │ +
    273} // namepspace BALL
    │ │ │ +
    274
    │ │ │ +
    275#endif
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::PDB::Atom
    char Atom[5]
    Definition PDBdefs.h:257
    │ │ │ +
    BALL::NamedProperty::getUnsignedInt
    unsigned int getUnsignedInt() const
    │ │ │ +
    BALL::PropertyManager::getProperty
    const NamedProperty & getProperty(const std::string &name) const
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::RingAnalyser
    Methods for the analysis of the structure of ringsystems.
    Definition ringAnalyser.h:38
    │ │ │ + │ │ │ + │ │ │ +
    BALL::SDGenerator::placeSubstituent_
    void placeSubstituent_(Atom *seed, Atom *head, Atom *next)
    │ │ │ +
    BALL::SDGenerator::computeAdjacencyMatrix_
    void computeAdjacencyMatrix_(std::vector< Atom * > &chain, std::vector< bool > &result)
    Compute adjacency matrix of the given atoms.
    │ │ │ +
    BALL::SDGenerator::SDGenerator
    SDGenerator(bool show_hydrogens=false)
    │ │ │ + │ │ │ +
    BALL::SDGenerator::computeShelleyPriorities_
    void computeShelleyPriorities_()
    │ │ │ +
    BALL::SDGenerator::redraw_queue_
    std::priority_queue< Atom *, std::vector< Atom * >, AtomComparator > redraw_queue_
    our redraw queue
    Definition sdGenerator.h:267
    │ │ │ +
    BALL::SDGenerator::system_
    System * system_
    the system we are working on
    Definition sdGenerator.h:270
    │ │ │ +
    BALL::SDGenerator::pushCFS_
    void pushCFS_(Atom *atom)
    │ │ │ +
    BALL::SDGenerator::Property
    Property
    Properties, used to describe atoms and their status.
    Definition sdGenerator.h:41
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::SDGenerator::setDefaultOptions
    void setDefaultOptions()
    │ │ │ +
    BALL::SDGenerator::computeAngularSeparation_
    Angle computeAngularSeparation_(Atom *seed)
    │ │ │ +
    BALL::SDGenerator::ringIsClockwise_
    bool ringIsClockwise_(const RingAnalyser::Ring &ring, Index start_index=0) const
    │ │ │ +
    BALL::SDGenerator::buildOpenPolygon_
    void buildOpenPolygon_(RingAnalyser::Ring &ring, Position first_anchor_index, Position second_anchor_index)
    │ │ │ +
    BALL::SDGenerator::attachBridged_
    void attachBridged_(Position current_ring, std::vector< RingAnalyser::Ring > &current_system)
    attach a bridged ring to a (partially) constructed ringsystem
    │ │ │ +
    BALL::SDGenerator::getCFS_
    Angle getCFS_(Atom const *atom, bool hi)
    │ │ │ +
    BALL::SDGenerator::sequenceSubstituents_
    std::vector< Atom * > sequenceSubstituents_(Atom *seed)
    │ │ │ +
    BALL::SDGenerator::buildRegularPolygon_
    void buildRegularPolygon_(RingAnalyser::Ring &ring, Position first_anchor_index, bool clockwise)
    │ │ │ +
    BALL::SDGenerator::depositPFU_
    void depositPFU_(Atom *seed_atom, Atom *next_neighbour)
    │ │ │ +
    BALL::SDGenerator::attachTemplate_
    void attachTemplate_(Position current_ring, std::vector< RingAnalyser::Ring > &current_system)
    attach a ring template to a (partially) constructed ringsystem (no functionality yet)
    │ │ │ +
    BALL::SDGenerator::setCFS_
    void setCFS_(Atom *atom, Angle cfs, bool high)
    │ │ │ +
    BALL::SDGenerator::options
    Options options
    options
    Definition sdGenerator.h:101
    │ │ │ +
    BALL::SDGenerator::generateSD
    void generateSD(System &molecule_sys)
    Generates a structure Diagram from the input System.
    │ │ │ +
    BALL::SDGenerator::attachCore_
    void attachCore_(Position current_ring, std::vector< RingAnalyser::Ring > &current_system, float x_start)
    construct the core-ring as a regular polygon
    │ │ │ +
    BALL::SDGenerator::smoothCFSAngle_
    void smoothCFSAngle_(Atom *seed)
    │ │ │ +
    BALL::SDGenerator::chains_
    std::list< std::list< Atom * > > chains_
    all chains
    Definition sdGenerator.h:264
    │ │ │ +
    BALL::SDGenerator::attachSpiro_
    void attachSpiro_(Position current_ring, std::vector< RingAnalyser::Ring > &current_system)
    attach a spiro ring to a (partially) constructed ringsystem
    │ │ │ +
    BALL::SDGenerator::compareChains_
    static bool compareChains_(const vector< Atom * > &x, const vector< Atom * > &y)
    Comparator for chains of atoms.
    │ │ │ +
    BALL::SDGenerator::prepare_
    void prepare_()
    Distinguishes between ring-atoms and core-chain-atoms, removes all H-Atoms from the System.
    │ │ │ +
    BALL::SDGenerator::~SDGenerator
    virtual ~SDGenerator()
    │ │ │ +
    BALL::SDGenerator::treatChains_
    void treatChains_()
    cluster and arrange all chains in the system
    │ │ │ +
    BALL::SDGenerator::getBackupCFS_
    Angle getBackupCFS_(Atom const *, bool hi)
    │ │ │ +
    BALL::SDGenerator::computeCFS_
    Angle computeCFS_(Vector3 const &input)
    │ │ │ +
    BALL::SDGenerator::checkOverlap_
    void checkOverlap_(Atom *atom)
    │ │ │ +
    BALL::SDGenerator::computeAngularDemand_
    Angle computeAngularDemand_(Atom *seed)
    │ │ │ +
    BALL::SDGenerator::computeCoreCFS_
    void computeCoreCFS_(RingAnalyser::Ring &ring, bool clockwise)
    │ │ │ +
    BALL::SDGenerator::constructRingSystem_
    void constructRingSystem_(Position current_ring_system)
    Constructs a ringsystem, providing the atoms with relative 2D-coordinates, starting in the point of o...
    │ │ │ +
    BALL::SDGenerator::attachFused_
    void attachFused_(Position current_ring, std::vector< RingAnalyser::Ring > &current_system)
    attach a fused ring to a (partially) constructed ringsystem
    │ │ │ + │ │ │ +
    BALL::SDGenerator::findFloydWarshallPath_
    void findFloydWarshallPath_(std::vector< int > &path, std::vector< Index > &next, Size remaining_atoms, Position i, Position j, std::list< Index > &output)
    │ │ │ +
    BALL::SDGenerator::ring_analyser_
    RingAnalyser ring_analyser_
    The ring analyser containing all information about ring systems.
    Definition sdGenerator.h:261
    │ │ │ + │ │ │ +
    BALL::SDGenerator::Option::STANDARD_BOND_LENGTH
    static const char * STANDARD_BOND_LENGTH
    Definition sdGenerator.h:70
    │ │ │ +
    BALL::SDGenerator::Option::SHOW_HYDROGENS
    static const char * SHOW_HYDROGENS
    Definition sdGenerator.h:65
    │ │ │ +
    BALL::SDGenerator::Default
    Default values for options.
    Definition sdGenerator.h:75
    │ │ │ +
    BALL::SDGenerator::Default::SHOW_HYDROGENS
    static const bool SHOW_HYDROGENS
    Definition sdGenerator.h:76
    │ │ │ +
    BALL::SDGenerator::Default::STANDARD_BOND_LENGTH
    static const float STANDARD_BOND_LENGTH
    Definition sdGenerator.h:78
    │ │ │ + │ │ │ + │ │ │ │ │ │ - │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,99 +1,402 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _W_I_D_G_E_T_S │ │ │ │ -fileObserver.h │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ +sdGenerator.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_VIEW_WIDGETS_FILEOBSERVER_H │ │ │ │ -6#define BALL_VIEW_WIDGETS_FILEOBSERVER_H │ │ │ │ +5#ifndef BALL_STRUCTURE_SDGENERATOR_H │ │ │ │ +6#define BALL_STRUCTURE_SDGENERATOR_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_VIEW_WIDGETS_DOCKWIDGET_H │ │ │ │ -9# include <_B_A_L_L_/_V_I_E_W_/_W_I_D_G_E_T_S_/_d_o_c_k_W_i_d_g_e_t_._h> │ │ │ │ +8#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ +9# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#include │ │ │ │ -13#include │ │ │ │ -14 │ │ │ │ -15class QAction; │ │ │ │ -16 │ │ │ │ -17namespace _B_A_L_L │ │ │ │ -18{ │ │ │ │ -19 namespace VIEW │ │ │ │ -20 { │ │ │ │ -_3_4 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _F_i_l_e_O_b_s_e_r_v_e_r │ │ │ │ -35 : public _D_o_c_k_W_i_d_g_e_t │ │ │ │ -36 { │ │ │ │ -37 Q_OBJECT │ │ │ │ -38 │ │ │ │ -39 public: │ │ │ │ -40 │ │ │ │ -41 _B_A_L_L___E_M_B_E_D_D_A_B_L_E(_F_i_l_e_O_b_s_e_r_v_e_r,_D_o_c_k_W_i_d_g_e_t) │ │ │ │ -42 │ │ │ │ -43 │ │ │ │ -_4_4 _F_i_l_e_O_b_s_e_r_v_e_r(_Q_W_i_d_g_e_t *parent = 0, const char *name = 0); │ │ │ │ -45 │ │ │ │ -_4_7 virtual ~_F_i_l_e_O_b_s_e_r_v_e_r(); │ │ │ │ -48 │ │ │ │ -49 // │ │ │ │ -_5_0 virtual void initializeWidget(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ -51 │ │ │ │ -52 // │ │ │ │ -_5_3 virtual void checkMenu(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ -54 │ │ │ │ -_5_6 void setFileName(_S_t_r_i_n_g filename); │ │ │ │ -57 │ │ │ │ -_5_9 _S_t_r_i_n_g getFileName() const; │ │ │ │ -60 │ │ │ │ -_6_2 void setUpdateInterval(_S_i_z_e msec); │ │ │ │ -63 │ │ │ │ -64 public Q_SLOTS: │ │ │ │ -65 │ │ │ │ -_6_7 void updateFile(); │ │ │ │ -68 │ │ │ │ -_7_0 void start(); │ │ │ │ -71 │ │ │ │ -_7_3 void stop(); │ │ │ │ -74 │ │ │ │ -_7_6 void chooseFile(); │ │ │ │ +12#ifndef BALL_STRUCTURE_RINGANALYSER_H │ │ │ │ +13# include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_r_i_n_g_A_n_a_l_y_s_e_r_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifndef BALL_KERNEL_PDBATOM_H │ │ │ │ +17# include <_B_A_L_L_/_K_E_R_N_E_L_/_P_D_B_A_t_o_m_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20#include │ │ │ │ +21#include │ │ │ │ +22 │ │ │ │ +23namespace _B_A_L_L │ │ │ │ +24{ │ │ │ │ +25 class System; │ │ │ │ +26 class _A_t_o_m; │ │ │ │ +27 │ │ │ │ +_3_3 class _B_A_L_L___E_X_P_O_R_T _S_D_G_e_n_e_r_a_t_o_r │ │ │ │ +34 { │ │ │ │ +35 public: │ │ │ │ +36 │ │ │ │ +_4_0 enum _P_r_o_p_e_r_t_y │ │ │ │ +41 { │ │ │ │ +_4_2 FIRST_SDGENERATOR_PROPERTY = PDBAtom::NUMBER_OF_PROPERTIES+1, │ │ │ │ +_4_3 _I_N___R_I_N_G, │ │ │ │ +_4_4 _C_O_R_E___C_H_A_I_N, │ │ │ │ +_4_5 _D_E_P_O_S_I_T_E_D, │ │ │ │ +_4_6 _F_X_A_S, │ │ │ │ +_4_7 _E_Q_A_S, │ │ │ │ +_4_8 _H_E_A_D, │ │ │ │ +_4_9 _E_D_G_E, │ │ │ │ +_5_0 _A_S_S_E_M_B_L_E_D, │ │ │ │ +_5_1 _Z_I_G, │ │ │ │ +_5_2 _Z_A_G, │ │ │ │ +_5_3 _I_N_I_T_I_A_L_I_Z_E_D___H_E_A_D___C_F_S, │ │ │ │ +54 LAST_SDGENERATOR_PROPERTY │ │ │ │ +_5_5 }; │ │ │ │ +56 │ │ │ │ +_6_1 struct _B_A_L_L___E_X_P_O_R_T _O_p_t_i_o_n │ │ │ │ +62 { │ │ │ │ +_6_5 static const char* _S_H_O_W___H_Y_D_R_O_G_E_N_S; │ │ │ │ +66 │ │ │ │ +_7_0 static const char* _S_T_A_N_D_A_R_D___B_O_N_D___L_E_N_G_T_H; │ │ │ │ +71 }; │ │ │ │ +72 │ │ │ │ +_7_4 struct _B_A_L_L___E_X_P_O_R_T _D_e_f_a_u_l_t │ │ │ │ +75 { │ │ │ │ +_7_6 static const bool _S_H_O_W___H_Y_D_R_O_G_E_N_S; │ │ │ │ 77 │ │ │ │ -78 protected: │ │ │ │ -79 │ │ │ │ -_8_0 QAction* start_action_, *stop_action_; │ │ │ │ +_7_8 static const float _S_T_A_N_D_A_R_D___B_O_N_D___L_E_N_G_T_H; │ │ │ │ +79 }; │ │ │ │ 81 │ │ │ │ -_8_2 QTimer timer_; │ │ │ │ -_8_3 _S_t_r_i_n_g file_name_; │ │ │ │ -_8_4 QDateTime last_vis_time_; │ │ │ │ -85 }; │ │ │ │ -86 │ │ │ │ -87} } // namespaces │ │ │ │ -88 │ │ │ │ -89#endif // BALL_VIEW_WIDGETS_FILEOBSERVER_H │ │ │ │ -_d_o_c_k_W_i_d_g_e_t_._h │ │ │ │ -_B_A_L_L___E_M_B_E_D_D_A_B_L_E │ │ │ │ -#define BALL_EMBEDDABLE(TYPE, BASE) │ │ │ │ -DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_3_1 │ │ │ │ +85 │ │ │ │ +_8_9 _S_D_G_e_n_e_r_a_t_o_r(bool show_hydrogens = false); │ │ │ │ +90 │ │ │ │ +_9_4 virtual _~_S_D_G_e_n_e_r_a_t_o_r(); │ │ │ │ +96 │ │ │ │ +_1_0_1 _O_p_t_i_o_n_s _o_p_t_i_o_n_s; │ │ │ │ +103 │ │ │ │ +_1_0_9 void _s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s(); │ │ │ │ +111 │ │ │ │ +_1_1_6 void _g_e_n_e_r_a_t_e_S_D(_S_y_s_t_e_m& molecule_sys); │ │ │ │ +117 │ │ │ │ +_1_2_1 void _c_l_e_a_r(); │ │ │ │ +122 │ │ │ │ +123 protected: │ │ │ │ +124 │ │ │ │ +_1_2_7 class _A_t_o_m_C_o_m_p_a_r_a_t_o_r │ │ │ │ +128 { │ │ │ │ +129 public: │ │ │ │ +_1_3_0 bool operator() (_A_t_o_m const* first, _A_t_o_m const* second) const │ │ │ │ +131 { │ │ │ │ +132 _S_i_z_e first_value = first->_g_e_t_P_r_o_p_e_r_t_y("SDGenerator:: │ │ │ │ +PRIORITY")._g_e_t_U_n_s_i_g_n_e_d_I_n_t(); │ │ │ │ +133 _S_i_z_e second_value = second->_g_e_t_P_r_o_p_e_r_t_y("SDGenerator:: │ │ │ │ +PRIORITY")._g_e_t_U_n_s_i_g_n_e_d_I_n_t(); │ │ │ │ +134 │ │ │ │ +135 return first_value < second_value; │ │ │ │ +136 } │ │ │ │ +137 }; │ │ │ │ +138 │ │ │ │ +_1_4_3 void _p_r_e_p_a_r_e__(); │ │ │ │ +144 │ │ │ │ +_1_4_9 void _c_o_n_s_t_r_u_c_t_R_i_n_g_S_y_s_t_e_m__(_P_o_s_i_t_i_o_n current_ring_system); │ │ │ │ +150 │ │ │ │ +151 // Obtain the CFS from the properties of the atom... │ │ │ │ +_1_5_2 _A_n_g_l_e _g_e_t_C_F_S__(_A_t_o_m const* atom, bool hi); │ │ │ │ +153 │ │ │ │ +154 // Convert a vector into the corresponding CFS angle │ │ │ │ +_1_5_5 _A_n_g_l_e _c_o_m_p_u_t_e_C_F_S__(_V_e_c_t_o_r_3 const& input); │ │ │ │ +156 │ │ │ │ +157 // store the CFS for an atom │ │ │ │ +_1_5_8 void _s_e_t_C_F_S__(_A_t_o_m* atom, _A_n_g_l_e cfs, bool high); │ │ │ │ +159 │ │ │ │ +160 // push the CFS before it is overwritten │ │ │ │ +_1_6_1 void _p_u_s_h_C_F_S__(_A_t_o_m* atom); │ │ │ │ +162 │ │ │ │ +163 // retrieve backup CVS values │ │ │ │ +_1_6_4 _A_n_g_l_e _g_e_t_B_a_c_k_u_p_C_F_S__(_A_t_o_m const*, bool hi); │ │ │ │ +165 │ │ │ │ +166 // Compute the CFS values for a full regular polygon │ │ │ │ +_1_6_7 void _c_o_m_p_u_t_e_C_o_r_e_C_F_S__(_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g& ring, bool clockwise); │ │ │ │ +168 │ │ │ │ +169 // │ │ │ │ +_1_7_0 _A_n_g_l_e _c_o_m_p_u_t_e_A_n_g_u_l_a_r_S_e_p_a_r_a_t_i_o_n__(_A_t_o_m* seed); │ │ │ │ +171 │ │ │ │ +172 // │ │ │ │ +_1_7_3 _A_n_g_l_e _c_o_m_p_u_t_e_A_n_g_u_l_a_r_D_e_m_a_n_d__(_A_t_o_m* seed); │ │ │ │ +174 │ │ │ │ +175 // │ │ │ │ +_1_7_6 std::vector _s_e_q_u_e_n_c_e_S_u_b_s_t_i_t_u_e_n_t_s__(_A_t_o_m* seed); │ │ │ │ +177 │ │ │ │ +_1_8_0 void _c_o_m_p_u_t_e_S_h_e_l_l_e_y_P_r_i_o_r_i_t_i_e_s__(); │ │ │ │ +181 │ │ │ │ +_1_8_4 void _b_u_i_l_d_R_e_g_u_l_a_r_P_o_l_y_g_o_n__(_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g& ring, _P_o_s_i_t_i_o_n │ │ │ │ +first_anchor_index, bool clockwise); │ │ │ │ +185 │ │ │ │ +_1_8_8 void _b_u_i_l_d_O_p_e_n_P_o_l_y_g_o_n__(_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g& ring, _P_o_s_i_t_i_o_n │ │ │ │ +first_anchor_index, _P_o_s_i_t_i_o_n second_anchor_index); │ │ │ │ +189 │ │ │ │ +_1_9_6 void _a_t_t_a_c_h_C_o_r_e__(_P_o_s_i_t_i_o_n current_ring, std::vector& │ │ │ │ +current_system, float x_start); │ │ │ │ +197 │ │ │ │ +_2_0_3 void _a_t_t_a_c_h_T_e_m_p_l_a_t_e__(_P_o_s_i_t_i_o_n current_ring, std::vector& current_system); │ │ │ │ +204 │ │ │ │ +_2_1_0 void _a_t_t_a_c_h_F_u_s_e_d__(_P_o_s_i_t_i_o_n current_ring, std::vector& │ │ │ │ +current_system); │ │ │ │ +211 │ │ │ │ +_2_1_7 void _a_t_t_a_c_h_B_r_i_d_g_e_d__(_P_o_s_i_t_i_o_n current_ring, std::vector& │ │ │ │ +current_system); │ │ │ │ +218 │ │ │ │ +_2_2_4 void _a_t_t_a_c_h_S_p_i_r_o__(_P_o_s_i_t_i_o_n current_ring, std::vector& │ │ │ │ +current_system); │ │ │ │ +225 │ │ │ │ +_2_2_7 void _c_o_m_p_u_t_e_A_d_j_a_c_e_n_c_y_M_a_t_r_i_x__(std::vector& chain, std::vector& │ │ │ │ +result); │ │ │ │ +228 │ │ │ │ +_2_3_0 static bool _c_o_m_p_a_r_e_C_h_a_i_n_s__(const vector& x, const vector& y); │ │ │ │ +231 │ │ │ │ +_2_3_5 void _t_r_e_a_t_C_h_a_i_n_s__(); │ │ │ │ +236 │ │ │ │ +237 // │ │ │ │ +_2_3_8 void _s_m_o_o_t_h_C_F_S_A_n_g_l_e__(_A_t_o_m* seed); │ │ │ │ +239 │ │ │ │ +240 // │ │ │ │ +_2_4_1 void _p_l_a_c_e_S_u_b_s_t_i_t_u_e_n_t__(_A_t_o_m* seed, _A_t_o_m* head, _A_t_o_m* next); │ │ │ │ +242 │ │ │ │ +243 // │ │ │ │ +_2_4_4 void _d_e_p_o_s_i_t_P_F_U__(_A_t_o_m* seed_atom, _A_t_o_m* next_neighbour); │ │ │ │ +245 │ │ │ │ +246 // │ │ │ │ +_2_4_7 void _c_h_e_c_k_O_v_e_r_l_a_p__(_A_t_o_m* atom); │ │ │ │ +248 │ │ │ │ +249 //Check whether the ring is clockwise or not │ │ │ │ +_2_5_0 bool _r_i_n_g_I_s_C_l_o_c_k_w_i_s_e__(const _R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g& ring, _I_n_d_e_x start_index = │ │ │ │ +0) const; │ │ │ │ +251 │ │ │ │ +_2_5_5 void _a_s_s_e_m_b_l_e_S_D__(); │ │ │ │ +256 │ │ │ │ +257 // The backtracking for our Floyd-Warshall implementation │ │ │ │ +_2_5_8 void _f_i_n_d_F_l_o_y_d_W_a_r_s_h_a_l_l_P_a_t_h__(std::vector& path, std::vector& │ │ │ │ +next, _S_i_z_e remaining_atoms, _P_o_s_i_t_i_o_n i, _P_o_s_i_t_i_o_n j, std::list& output); │ │ │ │ +259 │ │ │ │ +_2_6_1 _R_i_n_g_A_n_a_l_y_s_e_r _r_i_n_g___a_n_a_l_y_s_e_r__; │ │ │ │ +262 │ │ │ │ +_2_6_4 std::list > _c_h_a_i_n_s__; │ │ │ │ +265 │ │ │ │ +_2_6_7 std::priority_queue, _A_t_o_m_C_o_m_p_a_r_a_t_o_r> │ │ │ │ +_r_e_d_r_a_w___q_u_e_u_e__; │ │ │ │ +268 │ │ │ │ +_2_7_0 _S_y_s_t_e_m* _s_y_s_t_e_m__; │ │ │ │ +271 }; │ │ │ │ +272 │ │ │ │ +273} // namepspace BALL │ │ │ │ +274 │ │ │ │ +275#endif │ │ │ │ +_r_i_n_g_A_n_a_l_y_s_e_r_._h │ │ │ │ +_P_D_B_A_t_o_m_._h │ │ │ │ +_o_p_t_i_o_n_s_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ -DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_D_o_c_k_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _d_o_c_k_W_i_d_g_e_t_._h_:_2_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_F_i_l_e_O_b_s_e_r_v_e_r │ │ │ │ -DDeeffiinniittiioonn _f_i_l_e_O_b_s_e_r_v_e_r_._h_:_3_6 │ │ │ │ +_B_A_L_L_:_:_P_D_B_:_:_A_t_o_m │ │ │ │ +char Atom[5] │ │ │ │ +DDeeffiinniittiioonn _P_D_B_d_e_f_s_._h_:_2_5_7 │ │ │ │ +_B_A_L_L_:_:_N_a_m_e_d_P_r_o_p_e_r_t_y_:_:_g_e_t_U_n_s_i_g_n_e_d_I_n_t │ │ │ │ +unsigned int getUnsignedInt() const │ │ │ │ +_B_A_L_L_:_:_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r_:_:_g_e_t_P_r_o_p_e_r_t_y │ │ │ │ +const NamedProperty & getProperty(const std::string &name) const │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ +_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ +DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ +_B_A_L_L_:_:_T_A_n_g_l_e_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r │ │ │ │ +Methods for the analysis of the structure of ringsystems. │ │ │ │ +DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_R_i_n_g_A_n_a_l_y_s_e_r_:_:_R_i_n_g │ │ │ │ +DDeeffiinniittiioonn _r_i_n_g_A_n_a_l_y_s_e_r_._h_:_5_3 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_3_4 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_p_l_a_c_e_S_u_b_s_t_i_t_u_e_n_t__ │ │ │ │ +void placeSubstituent_(Atom *seed, Atom *head, Atom *next) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_o_m_p_u_t_e_A_d_j_a_c_e_n_c_y_M_a_t_r_i_x__ │ │ │ │ +void computeAdjacencyMatrix_(std::vector< Atom * > &chain, std::vector< bool > │ │ │ │ +&result) │ │ │ │ +Compute adjacency matrix of the given atoms. │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_S_D_G_e_n_e_r_a_t_o_r │ │ │ │ +SDGenerator(bool show_hydrogens=false) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_a_s_s_e_m_b_l_e_S_D__ │ │ │ │ +void assembleSD_() │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_o_m_p_u_t_e_S_h_e_l_l_e_y_P_r_i_o_r_i_t_i_e_s__ │ │ │ │ +void computeShelleyPriorities_() │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_r_e_d_r_a_w___q_u_e_u_e__ │ │ │ │ +std::priority_queue< Atom *, std::vector< Atom * >, AtomComparator > │ │ │ │ +redraw_queue_ │ │ │ │ +our redraw queue │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_2_6_7 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_s_y_s_t_e_m__ │ │ │ │ +System * system_ │ │ │ │ +the system we are working on │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_2_7_0 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_p_u_s_h_C_F_S__ │ │ │ │ +void pushCFS_(Atom *atom) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_P_r_o_p_e_r_t_y │ │ │ │ +Property │ │ │ │ +Properties, used to describe atoms and their status. │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_4_1 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_D_E_P_O_S_I_T_E_D │ │ │ │ +@ DEPOSITED │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_4_5 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_E_Q_A_S │ │ │ │ +@ EQAS │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_4_7 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_I_N___R_I_N_G │ │ │ │ +@ IN_RING │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_4_3 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_H_E_A_D │ │ │ │ +@ HEAD │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_F_X_A_S │ │ │ │ +@ FXAS │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_4_6 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_Z_A_G │ │ │ │ +@ ZAG │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_5_2 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_I_N_I_T_I_A_L_I_Z_E_D___H_E_A_D___C_F_S │ │ │ │ +@ INITIALIZED_HEAD_CFS │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_5_3 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_Z_I_G │ │ │ │ +@ ZIG │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_5_1 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_A_S_S_E_M_B_L_E_D │ │ │ │ +@ ASSEMBLED │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_E_D_G_E │ │ │ │ +@ EDGE │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_4_9 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_C_O_R_E___C_H_A_I_N │ │ │ │ +@ CORE_CHAIN │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_4_4 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s │ │ │ │ +void setDefaultOptions() │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_o_m_p_u_t_e_A_n_g_u_l_a_r_S_e_p_a_r_a_t_i_o_n__ │ │ │ │ +Angle computeAngularSeparation_(Atom *seed) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_r_i_n_g_I_s_C_l_o_c_k_w_i_s_e__ │ │ │ │ +bool ringIsClockwise_(const RingAnalyser::Ring &ring, Index start_index=0) │ │ │ │ +const │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_b_u_i_l_d_O_p_e_n_P_o_l_y_g_o_n__ │ │ │ │ +void buildOpenPolygon_(RingAnalyser::Ring &ring, Position first_anchor_index, │ │ │ │ +Position second_anchor_index) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_a_t_t_a_c_h_B_r_i_d_g_e_d__ │ │ │ │ +void attachBridged_(Position current_ring, std::vector< RingAnalyser::Ring > │ │ │ │ +¤t_system) │ │ │ │ +attach a bridged ring to a (partially) constructed ringsystem │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_g_e_t_C_F_S__ │ │ │ │ +Angle getCFS_(Atom const *atom, bool hi) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_s_e_q_u_e_n_c_e_S_u_b_s_t_i_t_u_e_n_t_s__ │ │ │ │ +std::vector< Atom * > sequenceSubstituents_(Atom *seed) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_b_u_i_l_d_R_e_g_u_l_a_r_P_o_l_y_g_o_n__ │ │ │ │ +void buildRegularPolygon_(RingAnalyser::Ring &ring, Position │ │ │ │ +first_anchor_index, bool clockwise) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_d_e_p_o_s_i_t_P_F_U__ │ │ │ │ +void depositPFU_(Atom *seed_atom, Atom *next_neighbour) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_a_t_t_a_c_h_T_e_m_p_l_a_t_e__ │ │ │ │ +void attachTemplate_(Position current_ring, std::vector< RingAnalyser::Ring > │ │ │ │ +¤t_system) │ │ │ │ +attach a ring template to a (partially) constructed ringsystem (no │ │ │ │ +functionality yet) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_s_e_t_C_F_S__ │ │ │ │ +void setCFS_(Atom *atom, Angle cfs, bool high) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_o_p_t_i_o_n_s │ │ │ │ +Options options │ │ │ │ +options │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_1_0_1 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_g_e_n_e_r_a_t_e_S_D │ │ │ │ +void generateSD(System &molecule_sys) │ │ │ │ +Generates a structure Diagram from the input System. │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_a_t_t_a_c_h_C_o_r_e__ │ │ │ │ +void attachCore_(Position current_ring, std::vector< RingAnalyser::Ring > │ │ │ │ +¤t_system, float x_start) │ │ │ │ +construct the core-ring as a regular polygon │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_s_m_o_o_t_h_C_F_S_A_n_g_l_e__ │ │ │ │ +void smoothCFSAngle_(Atom *seed) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_h_a_i_n_s__ │ │ │ │ +std::list< std::list< Atom * > > chains_ │ │ │ │ +all chains │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_2_6_4 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_a_t_t_a_c_h_S_p_i_r_o__ │ │ │ │ +void attachSpiro_(Position current_ring, std::vector< RingAnalyser::Ring > │ │ │ │ +¤t_system) │ │ │ │ +attach a spiro ring to a (partially) constructed ringsystem │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_o_m_p_a_r_e_C_h_a_i_n_s__ │ │ │ │ +static bool compareChains_(const vector< Atom * > &x, const vector< Atom * > │ │ │ │ +&y) │ │ │ │ +Comparator for chains of atoms. │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_p_r_e_p_a_r_e__ │ │ │ │ +void prepare_() │ │ │ │ +Distinguishes between ring-atoms and core-chain-atoms, removes all H-Atoms from │ │ │ │ +the System. │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_~_S_D_G_e_n_e_r_a_t_o_r │ │ │ │ +virtual ~SDGenerator() │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_t_r_e_a_t_C_h_a_i_n_s__ │ │ │ │ +void treatChains_() │ │ │ │ +cluster and arrange all chains in the system │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_g_e_t_B_a_c_k_u_p_C_F_S__ │ │ │ │ +Angle getBackupCFS_(Atom const *, bool hi) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_o_m_p_u_t_e_C_F_S__ │ │ │ │ +Angle computeCFS_(Vector3 const &input) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_h_e_c_k_O_v_e_r_l_a_p__ │ │ │ │ +void checkOverlap_(Atom *atom) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_o_m_p_u_t_e_A_n_g_u_l_a_r_D_e_m_a_n_d__ │ │ │ │ +Angle computeAngularDemand_(Atom *seed) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_o_m_p_u_t_e_C_o_r_e_C_F_S__ │ │ │ │ +void computeCoreCFS_(RingAnalyser::Ring &ring, bool clockwise) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_o_n_s_t_r_u_c_t_R_i_n_g_S_y_s_t_e_m__ │ │ │ │ +void constructRingSystem_(Position current_ring_system) │ │ │ │ +Constructs a ringsystem, providing the atoms with relative 2D-coordinates, │ │ │ │ +starting in the point of o... │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_a_t_t_a_c_h_F_u_s_e_d__ │ │ │ │ +void attachFused_(Position current_ring, std::vector< RingAnalyser::Ring > │ │ │ │ +¤t_system) │ │ │ │ +attach a fused ring to a (partially) constructed ringsystem │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_c_l_e_a_r │ │ │ │ +void clear() │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_f_i_n_d_F_l_o_y_d_W_a_r_s_h_a_l_l_P_a_t_h__ │ │ │ │ +void findFloydWarshallPath_(std::vector< int > &path, std::vector< Index > │ │ │ │ +&next, Size remaining_atoms, Position i, Position j, std::list< Index > │ │ │ │ +&output) │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_r_i_n_g___a_n_a_l_y_s_e_r__ │ │ │ │ +RingAnalyser ring_analyser_ │ │ │ │ +The ring analyser containing all information about ring systems. │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_2_6_1 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_O_p_t_i_o_n │ │ │ │ +Option names. │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_6_2 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_O_p_t_i_o_n_:_:_S_T_A_N_D_A_R_D___B_O_N_D___L_E_N_G_T_H │ │ │ │ +static const char * STANDARD_BOND_LENGTH │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_7_0 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_O_p_t_i_o_n_:_:_S_H_O_W___H_Y_D_R_O_G_E_N_S │ │ │ │ +static const char * SHOW_HYDROGENS │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_6_5 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ +Default values for options. │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_7_5 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_D_e_f_a_u_l_t_:_:_S_H_O_W___H_Y_D_R_O_G_E_N_S │ │ │ │ +static const bool SHOW_HYDROGENS │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_7_6 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_D_e_f_a_u_l_t_:_:_S_T_A_N_D_A_R_D___B_O_N_D___L_E_N_G_T_H │ │ │ │ +static const float STANDARD_BOND_LENGTH │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_7_8 │ │ │ │ +_B_A_L_L_:_:_S_D_G_e_n_e_r_a_t_o_r_:_:_A_t_o_m_C_o_m_p_a_r_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _s_d_G_e_n_e_r_a_t_o_r_._h_:_1_2_8 │ │ │ │ +_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_Q_W_i_d_g_e_t │ │ │ │ -_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ -#define BALL_VIEW_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc2/a08070.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members │ │ │
    BALL::VIEW::ModelProcessor Class Reference
    Visualisation » Model Processors
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/MODELS/modelProcessor.h>

    │ │ │ +

    #include <BALL/VIEW/MODELS/modelProcessor.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::ModelProcessor:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::UnaryProcessor< Composite > │ │ │ @@ -147,18 +147,18 @@ │ │ │ virtual bool start () │ │ │   │ │ │ virtual bool finish () │ │ │   │ │ │ virtual Processor::Result operator() (Composite &) │ │ │   │ │ │ - Public Member Functions inherited from BALL::PropertyManager │ │ │ -BALL_INLINE PropertyManager () │ │ │ +BALL_INLINE PropertyManager () │ │ │  Default constructor.
    │ │ │   │ │ │ -BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │ +BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │  Copy constructor.
    │ │ │   │ │ │ virtual ~PropertyManager () │ │ │  Destructor.
    │ │ │   │ │ │ virtual void destroy () │ │ │  Clears all properties.
    │ │ │ @@ -266,15 +266,15 @@ │ │ │ │ │ │

    Detailed Description

    │ │ │

    Base class for all model processors. Every model processor has a list with all GeometricObject 's it has created. It also stores the drawing precision, it will use for creating new models. You can apply model processors like every other UnaryProcessor for Composite 's:
    │ │ │ 

      Molecule m;
│ │ │    ModelProcessor model_processor;
│ │ │    m.apply(model_processor);
│ │ │
    │ │ │ -

    Definition at line 37 of file modelProcessor.h.

    │ │ │ +

    Definition at line 37 of file modelProcessor.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ModelProcessor() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -387,15 +387,15 @@ │ │ │ │ │ │
    │ │ │
    │ │ │

    Needed in derived classes, which store references to the Composite instances they worked on. Here only needed for a common interface and therefore empty.

    │ │ │ │ │ │

    Reimplemented in BALL::VIEW::AtomBondModelBaseProcessor, and BALL::VIEW::AddSurfaceModel.

    │ │ │ │ │ │ -

    Definition at line 65 of file modelProcessor.h.

    │ │ │ +

    Definition at line 65 of file modelProcessor.h.

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    │ │ │
    │ │ │ │ │ │

    ◆ createGeometricObjects()

    │ │ │ │ │ │
    │ │ │ @@ -417,15 +417,15 @@ │ │ │ │ │ │ │ │ │
    │ │ │

    Method to create geometric objects. This method is called in Representation::update() after all operator() was called for all Composites. To be overloaded in derived classes

    │ │ │ │ │ │

    Reimplemented in BALL::VIEW::AtomBondModelBaseProcessor, BALL::VIEW::AddBackboneModel, BALL::VIEW::AddBallAndStickModel, BALL::VIEW::LabelModel, and BALL::VIEW::AddSurfaceModel.

    │ │ │ │ │ │ -

    Definition at line 97 of file modelProcessor.h.

    │ │ │ +

    Definition at line 97 of file modelProcessor.h.

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    │ │ │
    │ │ │ │ │ │

    ◆ dump()

    │ │ │ │ │ │
    │ │ │ @@ -457,15 +457,15 @@ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Reimplemented in BALL::VIEW::AtomBondModelBaseProcessor, BALL::VIEW::AddBackboneModel, BALL::VIEW::AddBallAndStickModel, BALL::VIEW::AddLineModel, BALL::VIEW::AddSurfaceModel, and BALL::VIEW::AddVanDerWaalsModel.

    │ │ │ │ │ │ -

    Definition at line 69 of file modelProcessor.h.

    │ │ │ +

    Definition at line 69 of file modelProcessor.h.

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    │ │ │
    │ │ │ │ │ │

    ◆ getDrawingPrecision()

    │ │ │ │ │ │
    │ │ │ @@ -503,15 +503,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Return the list with the created geometric objects.

    │ │ │ │ │ │ -

    Definition at line 73 of file modelProcessor.h.

    │ │ │ +

    Definition at line 73 of file modelProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getGeometricObjects() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -532,15 +532,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Return the list with the created geometric objects.

    │ │ │ │ │ │ -

    Definition at line 77 of file modelProcessor.h.

    │ │ │ +

    Definition at line 77 of file modelProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getSurfaceDrawingPrecision()

    │ │ │ │ │ │
    │ │ │ @@ -576,15 +576,15 @@ │ │ │ │ │ │ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 59 of file modelProcessor.h.

    │ │ │ +

    Definition at line 59 of file modelProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setDrawingPrecision()

    │ │ │ │ │ │
    │ │ │ @@ -637,15 +637,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 106 of file modelProcessor.h.

    │ │ │ +

    Definition at line 106 of file modelProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ geometric_objects_

    │ │ │ │ │ │
    │ │ │ @@ -661,15 +661,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 103 of file modelProcessor.h.

    │ │ │ +

    Definition at line 103 of file modelProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ surface_drawing_precision_

    │ │ │ │ │ │
    │ │ │ @@ -685,15 +685,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 109 of file modelProcessor.h.

    │ │ │ +

    Definition at line 109 of file modelProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc4/a00443.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: peptideDialog.h File Reference │ │ │ +BALL: editSingleShortcut.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -72,26 +72,28 @@ │ │ │
  • include
  • BALL
  • VIEW
  • DIALOGS
    • │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    peptideDialog.h File Reference
    │ │ │ +
    editSingleShortcut.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/COMMON/global.h>
    │ │ │ -#include <BALL/STRUCTURE/peptideBuilder.h>
    │ │ │ -#include <BALL/VIEW/UIC/ui_peptideDialog.h>
    │ │ │ +
    #include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ +#include <BALL/VIEW/KERNEL/shortcutRegistry.h>
    │ │ │ +#include <BALL/VIEW/KERNEL/modularWidget.h>
    │ │ │ +#include <BALL/VIEW/UIC/ui_editSingleShortcut.h>
    │ │ │ +#include <QtWidgets/QDialog>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::PeptideDialog
    class  BALL::VIEW::EditSingleShortcut
     
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -3,21 +3,23 @@ │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ * _D_I_A_L_O_G_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -peptideDialog.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_p_e_p_t_i_d_e_B_u_i_l_d_e_r_._h> │ │ │ │ -#include │ │ │ │ +editSingleShortcut.h File Reference │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_s_h_o_r_t_c_u_t_R_e_g_i_s_t_r_y_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc4/a00443_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: peptideDialog.h Source File │ │ │ +BALL: editSingleShortcut.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -74,175 +74,128 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    peptideDialog.h
    │ │ │ +
    editSingleShortcut.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_VIEW_DIALOGS_PEPTIDEDIALOG_H
    │ │ │ -
    6#define BALL_VIEW_DIALOGS_PEPTIDEDIALOG_H
    │ │ │ -
    7
    │ │ │ -
    8#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ -
    9# include <BALL/COMMON/global.h>
    │ │ │ -
    10#endif
    │ │ │ -
    11
    │ │ │ -
    12#ifndef BALL_STRUCTURE_PEPTIDEBUILDER_H
    │ │ │ -
    13#include <BALL/STRUCTURE/peptideBuilder.h>
    │ │ │ -
    14#endif
    │ │ │ -
    15
    │ │ │ -
    16#include <BALL/VIEW/UIC/ui_peptideDialog.h>
    │ │ │ -
    17
    │ │ │ -
    18namespace BALL
    │ │ │ -
    19{
    │ │ │ -
    20 namespace VIEW
    │ │ │ -
    21 {
    │ │ │ -
    │ │ │ -
    25 class BALL_VIEW_EXPORT PeptideDialog
    │ │ │ -
    26 : public QDialog,
    │ │ │ -
    27 public Ui_PeptideDialogData,
    │ │ │ -
    28 public Peptides::PeptideBuilder
    │ │ │ -
    29 {
    │ │ │ -
    30 Q_OBJECT
    │ │ │ +
    4//
    │ │ │ +
    5
    │ │ │ +
    6#ifndef BALL_VIEW_DIALOGS_EDITSINGLESHORTCUT_H
    │ │ │ +
    7#define BALL_VIEW_DIALOGS_EDITSINGLESHORTCUT_H
    │ │ │ +
    8
    │ │ │ +
    9#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY
    │ │ │ +
    10# include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ +
    11#endif
    │ │ │ +
    12
    │ │ │ +
    13#ifndef BALL_VIEW_KERNEL_SHORTCUTREGISTRY_H
    │ │ │ +
    14# include <BALL/VIEW/KERNEL/shortcutRegistry.h>
    │ │ │ +
    15#endif
    │ │ │ +
    16
    │ │ │ +
    17#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H
    │ │ │ +
    18# include <BALL/VIEW/KERNEL/modularWidget.h>
    │ │ │ +
    19#endif
    │ │ │ +
    20
    │ │ │ +
    21#include <BALL/VIEW/UIC/ui_editSingleShortcut.h>
    │ │ │ +
    22
    │ │ │ +
    23#include <QtWidgets/QDialog>
    │ │ │ +
    24
    │ │ │ +
    25class QModelIndex;
    │ │ │ +
    26
    │ │ │ +
    27namespace BALL
    │ │ │ +
    28{
    │ │ │ +
    29 namespace VIEW
    │ │ │ +
    30 {
    │ │ │
    31
    │ │ │ -
    32 public:
    │ │ │ -
    33
    │ │ │ -
    35 PeptideDialog( QWidget* parent = 0, const char* name = "PeptideDialog", Qt::WindowFlags fl = 0 );
    │ │ │ -
    36
    │ │ │ -
    38 ~PeptideDialog() {}
    │ │ │ -
    39
    │ │ │ -
    41 String getSequence();
    │ │ │ -
    42
    │ │ │ -
    44 Protein* getProtein() { return protein_;}
    │ │ │ -
    45
    │ │ │ -
    46 public Q_SLOTS:
    │ │ │ -
    47
    │ │ │ -
    49 void ala_pressed() {insert_('a');}
    │ │ │ -
    50
    │ │ │ -
    52 void arg_pressed() {insert_('r');}
    │ │ │ -
    53
    │ │ │ -
    55 void asn_pressed() {insert_('n');}
    │ │ │ -
    56
    │ │ │ -
    58 void asp_pressed() {insert_('d');}
    │ │ │ -
    59
    │ │ │ -
    61 void cys_pressed() {insert_('c');}
    │ │ │ -
    62
    │ │ │ -
    64 void gln_pressed() {insert_('q');}
    │ │ │ -
    65
    │ │ │ -
    67 void glu_pressed() {insert_('e');}
    │ │ │ -
    68
    │ │ │ -
    70 void gly_pressed() {insert_('g');}
    │ │ │ -
    71
    │ │ │ -
    73 void his_pressed() {insert_('h');}
    │ │ │ -
    74
    │ │ │ -
    76 void ile_pressed() {insert_('i');}
    │ │ │ -
    77
    │ │ │ -
    79 void leu_pressed() {insert_('l');}
    │ │ │ -
    80
    │ │ │ -
    82 void lys_pressed() {insert_('k');}
    │ │ │ -
    83
    │ │ │ -
    85 void met_pressed() {insert_('m');}
    │ │ │ -
    86
    │ │ │ -
    88 void phe_pressed() {insert_('f');}
    │ │ │ -
    89
    │ │ │ -
    91 void pro_pressed() {insert_('p');}
    │ │ │ -
    92
    │ │ │ -
    94 void ser_pressed() {insert_('s');}
    │ │ │ -
    95
    │ │ │ -
    97 void thr_pressed() {insert_('t');}
    │ │ │ -
    98
    │ │ │ -
    100 void trp_pressed() {insert_('w');}
    │ │ │ -
    101
    │ │ │ -
    103 void tyr_pressed() {insert_('y');}
    │ │ │ -
    104
    │ │ │ -
    106 void val_pressed() {insert_('v');}
    │ │ │ -
    107
    │ │ │ -
    109 void back_pressed();
    │ │ │ -
    110
    │ │ │ -
    112 void close_pressed();
    │ │ │ -
    113
    │ │ │ -
    115 void angle_changed();
    │ │ │ -
    116
    │ │ │ -
    118 void insert_seq();
    │ │ │ -
    119
    │ │ │ -
    121 void prolineActivated();
    │ │ │ -
    122
    │ │ │ -
    124 void prolineDeactivated();
    │ │ │ -
    125
    │ │ │ -
    127 virtual bool eventFilter(QObject* object, QEvent* event);
    │ │ │ -
    128
    │ │ │ -
    129 protected:
    │ │ │ -
    130
    │ │ │ -
    131 void insert_(char a);
    │ │ │ -
    132
    │ │ │ -
    133 void truncString_(String& data);
    │ │ │ -
    134
    │ │ │ -
    135 bool isAminoAcid_(char a) const;
    │ │ │ -
    136
    │ │ │ -
    137 Protein* protein_;
    │ │ │ -
    138 static String all_amino_acids_;
    │ │ │ -
    139 };
    │ │ │ -
    │ │ │ -
    140
    │ │ │ -
    141} } // namespaces
    │ │ │ -
    142#endif
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::PeptideDialog::isAminoAcid_
    bool isAminoAcid_(char a) const
    │ │ │ -
    BALL::VIEW::PeptideDialog::truncString_
    void truncString_(String &data)
    │ │ │ -
    BALL::VIEW::PeptideDialog::eventFilter
    virtual bool eventFilter(QObject *object, QEvent *event)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::PeptideDialog::PeptideDialog
    PeptideDialog(QWidget *parent=0, const char *name="PeptideDialog", Qt::WindowFlags fl=0)
    Constructor.
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ +
    │ │ │ +
    35 class BALL_VIEW_EXPORT EditSingleShortcut
    │ │ │ +
    36 : public QDialog,
    │ │ │ +
    37 public Ui_EditSingleShortcutData
    │ │ │ +
    38 {
    │ │ │ +
    39 // macro needed for Qt's slot mechanism:
    │ │ │ +
    40 Q_OBJECT
    │ │ │ +
    41
    │ │ │ +
    42 public:
    │ │ │ +
    43
    │ │ │ +
    45 EditSingleShortcut(QWidget* parent = NULL, const char* name = "EditSingleShortcut", Qt::WindowFlags fl = 0 );
    │ │ │ +
    46
    │ │ │ +
    47 QKeySequence const& getKeySequence() const { return new_sequence_; }
    │ │ │ +
    48
    │ │ │ +
    49 void setIndex(const QModelIndex& index);
    │ │ │ +
    50 void reset();
    │ │ │ +
    51 void setup(const QString& shortcut);
    │ │ │ +
    52
    │ │ │ +
    53 public Q_SLOTS:
    │ │ │ +
    54 virtual void accept();
    │ │ │ +
    55 virtual void reject();
    │ │ │ +
    56
    │ │ │ +
    57 protected Q_SLOTS:
    │ │ │ +
    58 void modeChanged_(bool toggled);
    │ │ │ +
    59
    │ │ │ +
    60 protected:
    │ │ │ +
    61 bool is_recording_;
    │ │ │ +
    62
    │ │ │ +
    63 unsigned int modifiers_;
    │ │ │ +
    64 int key_;
    │ │ │ +
    65 QKeySequence new_sequence_;
    │ │ │ +
    66
    │ │ │ +
    68 void setErrorText(QString error);
    │ │ │ +
    69
    │ │ │ +
    71 void setShortcutText(QString new_keysequence);
    │ │ │ +
    72
    │ │ │ +
    73 void updateText_();
    │ │ │ +
    74 void changeMode_(bool mode);
    │ │ │ +
    75
    │ │ │ +
    76 void keyPressEvent(QKeyEvent* evt);
    │ │ │ +
    77 void keyReleaseEvent(QKeyEvent* evt);
    │ │ │ +
    78
    │ │ │ +
    79 void startRecording_();
    │ │ │ +
    80 void stopRecording_();
    │ │ │ +
    81 };
    │ │ │ +
    │ │ │ +
    82
    │ │ │ +
    83 }
    │ │ │ +
    84}
    │ │ │ +
    85
    │ │ │ +
    86#endif
    │ │ │ +
    87
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::EditSingleShortcut::EditSingleShortcut
    EditSingleShortcut(QWidget *parent=NULL, const char *name="EditSingleShortcut", Qt::WindowFlags fl=0)
    Constructor.
    │ │ │ +
    BALL::VIEW::EditSingleShortcut::keyPressEvent
    void keyPressEvent(QKeyEvent *evt)
    │ │ │ + │ │ │ +
    BALL::VIEW::EditSingleShortcut::keyReleaseEvent
    void keyReleaseEvent(QKeyEvent *evt)
    │ │ │ + │ │ │ +
    BALL::VIEW::EditSingleShortcut::modeChanged_
    void modeChanged_(bool toggled)
    │ │ │ + │ │ │ +
    BALL::VIEW::EditSingleShortcut::setIndex
    void setIndex(const QModelIndex &index)
    │ │ │ + │ │ │ +
    BALL::VIEW::EditSingleShortcut::setShortcutText
    void setShortcutText(QString new_keysequence)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::EditSingleShortcut::getKeySequence
    QKeySequence const & getKeySequence() const
    Definition editSingleShortcut.h:47
    │ │ │ +
    BALL::VIEW::EditSingleShortcut::setup
    void setup(const QString &shortcut)
    │ │ │ +
    BALL::VIEW::EditSingleShortcut::setErrorText
    void setErrorText(QString error)
    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -2,238 +2,152 @@ │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ * _D_I_A_L_O_G_S │ │ │ │ -peptideDialog.h │ │ │ │ +editSingleShortcut.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_VIEW_DIALOGS_PEPTIDEDIALOG_H │ │ │ │ -6#define BALL_VIEW_DIALOGS_PEPTIDEDIALOG_H │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ -9# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12#ifndef BALL_STRUCTURE_PEPTIDEBUILDER_H │ │ │ │ -13#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_p_e_p_t_i_d_e_B_u_i_l_d_e_r_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16#include │ │ │ │ -17 │ │ │ │ -18namespace _B_A_L_L │ │ │ │ -19{ │ │ │ │ -20 namespace VIEW │ │ │ │ -21 { │ │ │ │ -_2_5 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _P_e_p_t_i_d_e_D_i_a_l_o_g │ │ │ │ -26 : public _Q_D_i_a_l_o_g, │ │ │ │ -27 public Ui_PeptideDialogData, │ │ │ │ -28 public _P_e_p_t_i_d_e_s_:_:_P_e_p_t_i_d_e_B_u_i_l_d_e_r │ │ │ │ -29 { │ │ │ │ -30 Q_OBJECT │ │ │ │ +4// │ │ │ │ +5 │ │ │ │ +6#ifndef BALL_VIEW_DIALOGS_EDITSINGLESHORTCUT_H │ │ │ │ +7#define BALL_VIEW_DIALOGS_EDITSINGLESHORTCUT_H │ │ │ │ +8 │ │ │ │ +9#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY │ │ │ │ +10# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h> │ │ │ │ +11#endif │ │ │ │ +12 │ │ │ │ +13#ifndef BALL_VIEW_KERNEL_SHORTCUTREGISTRY_H │ │ │ │ +14# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_s_h_o_r_t_c_u_t_R_e_g_i_s_t_r_y_._h> │ │ │ │ +15#endif │ │ │ │ +16 │ │ │ │ +17#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H │ │ │ │ +18# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ +19#endif │ │ │ │ +20 │ │ │ │ +21#include │ │ │ │ +22 │ │ │ │ +23#include │ │ │ │ +24 │ │ │ │ +25class QModelIndex; │ │ │ │ +26 │ │ │ │ +27namespace _B_A_L_L │ │ │ │ +28{ │ │ │ │ +29 namespace VIEW │ │ │ │ +30 { │ │ │ │ 31 │ │ │ │ -32 public: │ │ │ │ -33 │ │ │ │ -_3_5 _P_e_p_t_i_d_e_D_i_a_l_o_g( _Q_W_i_d_g_e_t* parent = 0, const char* name = "PeptideDialog", Qt:: │ │ │ │ -WindowFlags fl = 0 ); │ │ │ │ -36 │ │ │ │ -_3_8 _~_P_e_p_t_i_d_e_D_i_a_l_o_g() {} │ │ │ │ -39 │ │ │ │ -_4_1 _S_t_r_i_n_g _g_e_t_S_e_q_u_e_n_c_e(); │ │ │ │ -42 │ │ │ │ -_4_4 _P_r_o_t_e_i_n* _g_e_t_P_r_o_t_e_i_n() { return protein_;} │ │ │ │ -45 │ │ │ │ -46 public Q_SLOTS: │ │ │ │ -47 │ │ │ │ -_4_9 void _a_l_a___p_r_e_s_s_e_d() {insert_('a');} │ │ │ │ -50 │ │ │ │ -_5_2 void _a_r_g___p_r_e_s_s_e_d() {insert_('r');} │ │ │ │ -53 │ │ │ │ -_5_5 void _a_s_n___p_r_e_s_s_e_d() {insert_('n');} │ │ │ │ +_3_5 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t │ │ │ │ +36 : public _Q_D_i_a_l_o_g, │ │ │ │ +37 public Ui_EditSingleShortcutData │ │ │ │ +38 { │ │ │ │ +39 // macro needed for Qt's slot mechanism: │ │ │ │ +40 Q_OBJECT │ │ │ │ +41 │ │ │ │ +42 public: │ │ │ │ +43 │ │ │ │ +_4_5 _E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t(_Q_W_i_d_g_e_t* parent = NULL, const char* name = │ │ │ │ +"EditSingleShortcut", Qt::WindowFlags fl = 0 ); │ │ │ │ +46 │ │ │ │ +_4_7 QKeySequence const& _g_e_t_K_e_y_S_e_q_u_e_n_c_e() const { return new_sequence_; } │ │ │ │ +48 │ │ │ │ +_4_9 void _s_e_t_I_n_d_e_x(const QModelIndex& index); │ │ │ │ +_5_0 void _r_e_s_e_t(); │ │ │ │ +_5_1 void _s_e_t_u_p(const QString& shortcut); │ │ │ │ +52 │ │ │ │ +53 public Q_SLOTS: │ │ │ │ +_5_4 virtual void _a_c_c_e_p_t(); │ │ │ │ +_5_5 virtual void _r_e_j_e_c_t(); │ │ │ │ 56 │ │ │ │ -_5_8 void _a_s_p___p_r_e_s_s_e_d() {insert_('d');} │ │ │ │ +57 protected Q_SLOTS: │ │ │ │ +_5_8 void _m_o_d_e_C_h_a_n_g_e_d__(bool toggled); │ │ │ │ 59 │ │ │ │ -_6_1 void _c_y_s___p_r_e_s_s_e_d() {insert_('c');} │ │ │ │ +60 protected: │ │ │ │ +_6_1 bool _i_s___r_e_c_o_r_d_i_n_g__; │ │ │ │ 62 │ │ │ │ -_6_4 void _g_l_n___p_r_e_s_s_e_d() {insert_('q');} │ │ │ │ -65 │ │ │ │ -_6_7 void _g_l_u___p_r_e_s_s_e_d() {insert_('e');} │ │ │ │ -68 │ │ │ │ -_7_0 void _g_l_y___p_r_e_s_s_e_d() {insert_('g');} │ │ │ │ -71 │ │ │ │ -_7_3 void _h_i_s___p_r_e_s_s_e_d() {insert_('h');} │ │ │ │ -74 │ │ │ │ -_7_6 void _i_l_e___p_r_e_s_s_e_d() {insert_('i');} │ │ │ │ -77 │ │ │ │ -_7_9 void _l_e_u___p_r_e_s_s_e_d() {insert_('l');} │ │ │ │ -80 │ │ │ │ -_8_2 void _l_y_s___p_r_e_s_s_e_d() {insert_('k');} │ │ │ │ -83 │ │ │ │ -_8_5 void _m_e_t___p_r_e_s_s_e_d() {insert_('m');} │ │ │ │ -86 │ │ │ │ -_8_8 void _p_h_e___p_r_e_s_s_e_d() {insert_('f');} │ │ │ │ -89 │ │ │ │ -_9_1 void _p_r_o___p_r_e_s_s_e_d() {insert_('p');} │ │ │ │ -92 │ │ │ │ -_9_4 void _s_e_r___p_r_e_s_s_e_d() {insert_('s');} │ │ │ │ -95 │ │ │ │ -_9_7 void _t_h_r___p_r_e_s_s_e_d() {insert_('t');} │ │ │ │ -98 │ │ │ │ -_1_0_0 void _t_r_p___p_r_e_s_s_e_d() {insert_('w');} │ │ │ │ -101 │ │ │ │ -_1_0_3 void _t_y_r___p_r_e_s_s_e_d() {insert_('y');} │ │ │ │ -104 │ │ │ │ -_1_0_6 void _v_a_l___p_r_e_s_s_e_d() {insert_('v');} │ │ │ │ -107 │ │ │ │ -_1_0_9 void _b_a_c_k___p_r_e_s_s_e_d(); │ │ │ │ -110 │ │ │ │ -_1_1_2 void _c_l_o_s_e___p_r_e_s_s_e_d(); │ │ │ │ -113 │ │ │ │ -_1_1_5 void _a_n_g_l_e___c_h_a_n_g_e_d(); │ │ │ │ -116 │ │ │ │ -_1_1_8 void _i_n_s_e_r_t___s_e_q(); │ │ │ │ -119 │ │ │ │ -_1_2_1 void _p_r_o_l_i_n_e_A_c_t_i_v_a_t_e_d(); │ │ │ │ -122 │ │ │ │ -_1_2_4 void _p_r_o_l_i_n_e_D_e_a_c_t_i_v_a_t_e_d(); │ │ │ │ -125 │ │ │ │ -_1_2_7 virtual bool _e_v_e_n_t_F_i_l_t_e_r(_Q_O_b_j_e_c_t* object, _Q_E_v_e_n_t* event); │ │ │ │ -128 │ │ │ │ -129 protected: │ │ │ │ -130 │ │ │ │ -_1_3_1 void _i_n_s_e_r_t__(char a); │ │ │ │ -132 │ │ │ │ -_1_3_3 void _t_r_u_n_c_S_t_r_i_n_g__(_S_t_r_i_n_g& data); │ │ │ │ -134 │ │ │ │ -_1_3_5 bool _i_s_A_m_i_n_o_A_c_i_d__(char a) const; │ │ │ │ -136 │ │ │ │ -_1_3_7 _P_r_o_t_e_i_n* _p_r_o_t_e_i_n__; │ │ │ │ -_1_3_8 static _S_t_r_i_n_g _a_l_l___a_m_i_n_o___a_c_i_d_s__; │ │ │ │ -139 }; │ │ │ │ -140 │ │ │ │ -141} } // namespaces │ │ │ │ -142#endif │ │ │ │ -_p_e_p_t_i_d_e_B_u_i_l_d_e_r_._h │ │ │ │ +_6_3 unsigned int _m_o_d_i_f_i_e_r_s__; │ │ │ │ +_6_4 int _k_e_y__; │ │ │ │ +_6_5 QKeySequence _n_e_w___s_e_q_u_e_n_c_e__; │ │ │ │ +66 │ │ │ │ +_6_8 void _s_e_t_E_r_r_o_r_T_e_x_t(QString error); │ │ │ │ +69 │ │ │ │ +_7_1 void _s_e_t_S_h_o_r_t_c_u_t_T_e_x_t(QString new_keysequence); │ │ │ │ +72 │ │ │ │ +_7_3 void _u_p_d_a_t_e_T_e_x_t__(); │ │ │ │ +_7_4 void _c_h_a_n_g_e_M_o_d_e__(bool mode); │ │ │ │ +75 │ │ │ │ +_7_6 void _k_e_y_P_r_e_s_s_E_v_e_n_t(QKeyEvent* evt); │ │ │ │ +_7_7 void _k_e_y_R_e_l_e_a_s_e_E_v_e_n_t(QKeyEvent* evt); │ │ │ │ +78 │ │ │ │ +_7_9 void _s_t_a_r_t_R_e_c_o_r_d_i_n_g__(); │ │ │ │ +_8_0 void _s_t_o_p_R_e_c_o_r_d_i_n_g__(); │ │ │ │ +81 }; │ │ │ │ +82 │ │ │ │ +83 } │ │ │ │ +84} │ │ │ │ +85 │ │ │ │ +86#endif │ │ │ │ +87 │ │ │ │ +_m_o_d_u_l_a_r_W_i_d_g_e_t_._h │ │ │ │ +_p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h │ │ │ │ +_s_h_o_r_t_c_u_t_R_e_g_i_s_t_r_y_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_P_r_o_t_e_i_n │ │ │ │ -DDeeffiinniittiioonn _p_r_o_t_e_i_n_._h_:_3_0 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_P_e_p_t_i_d_e_B_u_i_l_d_e_r │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_B_u_i_l_d_e_r_._h_:_9_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_2_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_g_l_y___p_r_e_s_s_e_d │ │ │ │ -void gly_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_7_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_m_e_t___p_r_e_s_s_e_d │ │ │ │ -void met_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_8_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_a_s_n___p_r_e_s_s_e_d │ │ │ │ -void asn_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_5_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_i_n_s_e_r_t___s_e_q │ │ │ │ -void insert_seq() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_t_y_r___p_r_e_s_s_e_d │ │ │ │ -void tyr_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_1_0_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_a_s_p___p_r_e_s_s_e_d │ │ │ │ -void asp_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_5_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_p_r_o_l_i_n_e_A_c_t_i_v_a_t_e_d │ │ │ │ -void prolineActivated() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_c_y_s___p_r_e_s_s_e_d │ │ │ │ -void cys_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_6_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_g_l_n___p_r_e_s_s_e_d │ │ │ │ -void gln_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_6_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_~_P_e_p_t_i_d_e_D_i_a_l_o_g │ │ │ │ -~PeptideDialog() │ │ │ │ -Destructor. │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_3_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_h_i_s___p_r_e_s_s_e_d │ │ │ │ -void his_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_7_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_i_s_A_m_i_n_o_A_c_i_d__ │ │ │ │ -bool isAminoAcid_(char a) const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_t_r_u_n_c_S_t_r_i_n_g__ │ │ │ │ -void truncString_(String &data) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_e_v_e_n_t_F_i_l_t_e_r │ │ │ │ -virtual bool eventFilter(QObject *object, QEvent *event) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_g_e_t_S_e_q_u_e_n_c_e │ │ │ │ -String getSequence() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_t_r_p___p_r_e_s_s_e_d │ │ │ │ -void trp_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_1_0_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_a_n_g_l_e___c_h_a_n_g_e_d │ │ │ │ -void angle_changed() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_l_y_s___p_r_e_s_s_e_d │ │ │ │ -void lys_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_8_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_a_r_g___p_r_e_s_s_e_d │ │ │ │ -void arg_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_5_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_t_h_r___p_r_e_s_s_e_d │ │ │ │ -void thr_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_9_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_g_l_u___p_r_e_s_s_e_d │ │ │ │ -void glu_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_6_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g │ │ │ │ -PeptideDialog(QWidget *parent=0, const char *name="PeptideDialog", Qt:: │ │ │ │ -WindowFlags fl=0) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t │ │ │ │ +DDeeffiinniittiioonn _e_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_s_t_a_r_t_R_e_c_o_r_d_i_n_g__ │ │ │ │ +void startRecording_() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_a_c_c_e_p_t │ │ │ │ +virtual void accept() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_m_o_d_i_f_i_e_r_s__ │ │ │ │ +unsigned int modifiers_ │ │ │ │ +DDeeffiinniittiioonn _e_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_._h_:_6_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t │ │ │ │ +EditSingleShortcut(QWidget *parent=NULL, const char *name="EditSingleShortcut", │ │ │ │ +Qt::WindowFlags fl=0) │ │ │ │ Constructor. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_i_n_s_e_r_t__ │ │ │ │ -void insert_(char a) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_s_e_r___p_r_e_s_s_e_d │ │ │ │ -void ser_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_9_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_b_a_c_k___p_r_e_s_s_e_d │ │ │ │ -void back_pressed() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_a_l_l___a_m_i_n_o___a_c_i_d_s__ │ │ │ │ -static String all_amino_acids_ │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_1_3_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_l_e_u___p_r_e_s_s_e_d │ │ │ │ -void leu_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_7_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_p_r_o_t_e_i_n__ │ │ │ │ -Protein * protein_ │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_1_3_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_i_l_e___p_r_e_s_s_e_d │ │ │ │ -void ile_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_7_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_p_h_e___p_r_e_s_s_e_d │ │ │ │ -void phe_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_8_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_g_e_t_P_r_o_t_e_i_n │ │ │ │ -Protein * getProtein() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_4_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_c_l_o_s_e___p_r_e_s_s_e_d │ │ │ │ -void close_pressed() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_a_l_a___p_r_e_s_s_e_d │ │ │ │ -void ala_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_4_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_p_r_o_l_i_n_e_D_e_a_c_t_i_v_a_t_e_d │ │ │ │ -void prolineDeactivated() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_v_a_l___p_r_e_s_s_e_d │ │ │ │ -void val_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_1_0_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_e_p_t_i_d_e_D_i_a_l_o_g_:_:_p_r_o___p_r_e_s_s_e_d │ │ │ │ -void pro_pressed() │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_D_i_a_l_o_g_._h_:_9_1 │ │ │ │ -_Q_O_b_j_e_c_t │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_k_e_y_P_r_e_s_s_E_v_e_n_t │ │ │ │ +void keyPressEvent(QKeyEvent *evt) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_i_s___r_e_c_o_r_d_i_n_g__ │ │ │ │ +bool is_recording_ │ │ │ │ +DDeeffiinniittiioonn _e_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_._h_:_6_1 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_k_e_y_R_e_l_e_a_s_e_E_v_e_n_t │ │ │ │ +void keyReleaseEvent(QKeyEvent *evt) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_c_h_a_n_g_e_M_o_d_e__ │ │ │ │ +void changeMode_(bool mode) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_m_o_d_e_C_h_a_n_g_e_d__ │ │ │ │ +void modeChanged_(bool toggled) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_r_e_j_e_c_t │ │ │ │ +virtual void reject() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_s_e_t_I_n_d_e_x │ │ │ │ +void setIndex(const QModelIndex &index) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_k_e_y__ │ │ │ │ +int key_ │ │ │ │ +DDeeffiinniittiioonn _e_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_._h_:_6_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_s_e_t_S_h_o_r_t_c_u_t_T_e_x_t │ │ │ │ +void setShortcutText(QString new_keysequence) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_r_e_s_e_t │ │ │ │ +void reset() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_n_e_w___s_e_q_u_e_n_c_e__ │ │ │ │ +QKeySequence new_sequence_ │ │ │ │ +DDeeffiinniittiioonn _e_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_._h_:_6_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_u_p_d_a_t_e_T_e_x_t__ │ │ │ │ +void updateText_() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_s_t_o_p_R_e_c_o_r_d_i_n_g__ │ │ │ │ +void stopRecording_() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_g_e_t_K_e_y_S_e_q_u_e_n_c_e │ │ │ │ +QKeySequence const & getKeySequence() const │ │ │ │ +DDeeffiinniittiioonn _e_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_._h_:_4_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_s_e_t_u_p │ │ │ │ +void setup(const QString &shortcut) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_E_d_i_t_S_i_n_g_l_e_S_h_o_r_t_c_u_t_:_:_s_e_t_E_r_r_o_r_T_e_x_t │ │ │ │ +void setErrorText(QString error) │ │ │ │ _Q_D_i_a_l_o_g │ │ │ │ _Q_W_i_d_g_e_t │ │ │ │ -_Q_E_v_e_n_t │ │ │ │ -_g_l_o_b_a_l_._h │ │ │ │ _B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ #define BALL_VIEW_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc4/a06778.html │ │ │ @@ -76,27 +76,27 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::FPTBondOrderStrategy::DPJoinMapComparator_ Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h>

    │ │ │ +

    #include <BALL/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h>

    │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    bool operator() (DPConfig_ const *leftp, DPConfig_ const *rightp) const
     
    int compare (DPConfig_ const *leftp, DPConfig_ const *rightp) const
     
    │ │ │

    Detailed Description

    │ │ │

    A comparator, which searches DPConfigs in a DPJoinMap. Two DPConfigs are equal, if they have the same bond values, even if they have different consumed valences.

    │ │ │ │ │ │ -

    Definition at line 817 of file FPTBondOrderStrategy.h.

    │ │ │ +

    Definition at line 817 of file FPTBondOrderStrategy.h.

    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ compare()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc4/a08318.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::VIEW::VRMLRenderer Class Reference
    Visualisation » Renderer
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/RENDERING/RENDERERS/VRMLRenderer.h>

    │ │ │ +

    #include <BALL/VIEW/RENDERING/RENDERERS/VRMLRenderer.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::VRMLRenderer:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::Renderer │ │ │ @@ -323,15 +323,15 @@ │ │ │
    │ │ │

    Detailed Description

    │ │ │

    VRMLRenderer class. This class walks over all the geometric primitives in a Scene and exports them into a data file in the VRML format, which can be used to render the same scene externally.
    │ │ │
    │ │ │ This is unmaintained code!

    │ │ │
    Deprecated:
    Use STL renderer instead
    │ │ │ │ │ │ -

    Definition at line 40 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 40 of file VRMLRenderer.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ VRMLRenderer() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -595,15 +595,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 119 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 119 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ outheader_()

    │ │ │ │ │ │
    │ │ │ @@ -623,15 +623,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 116 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 116 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ renderLine_()

    │ │ │ │ │ │
    │ │ │ @@ -914,15 +914,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ bigY

    │ │ │ │ │ │
    │ │ │ @@ -938,15 +938,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ bigZ

    │ │ │ │ │ │
    │ │ │ @@ -962,15 +962,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ current_indent_

    │ │ │ │ │ │
    │ │ │ @@ -986,15 +986,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 135 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 135 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ height

    │ │ │ │ │ │
    │ │ │ @@ -1002,15 +1002,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Size BALL::VIEW::VRMLRenderer::height
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 122 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 122 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ origin_

    │ │ │ │ │ │
    │ │ │ @@ -1026,15 +1026,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 133 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 133 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ outfile_

    │ │ │ │ │ │
    │ │ │ @@ -1050,15 +1050,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 131 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 131 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ rotation_

    │ │ │ │ │ │
    │ │ │ @@ -1074,15 +1074,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 134 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 134 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ scalingUsed

    │ │ │ │ │ │
    │ │ │ @@ -1098,15 +1098,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 141 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 141 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ smallX

    │ │ │ │ │ │
    │ │ │ @@ -1122,15 +1122,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ smallY

    │ │ │ │ │ │
    │ │ │ @@ -1146,15 +1146,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ smallZ

    │ │ │ │ │ │
    │ │ │ @@ -1170,15 +1170,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 138 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ width

    │ │ │ │ │ │
    │ │ │ @@ -1186,15 +1186,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Size BALL::VIEW::VRMLRenderer::width
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 122 of file VRMLRenderer.h.

    │ │ │ +

    Definition at line 122 of file VRMLRenderer.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc6/a08386.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::VIEW::TreeWidget Class Reference
    Visualisation » Modular Widgets
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/WIDGETS/genericControl.h>

    │ │ │ +

    #include <BALL/VIEW/WIDGETS/genericControl.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::TreeWidget:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ QTreeWidget │ │ │ @@ -97,15 +97,15 @@ │ │ │   │ │ │ void selectItems (const list< QTreeWidgetItem * > &items) │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Base class for all control widgets.

    │ │ │ │ │ │ -

    Definition at line 25 of file genericControl.h.

    │ │ │ +

    Definition at line 25 of file genericControl.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ TreeWidget()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc8/a01124.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: modelFactory.h File Reference │ │ │ +BALL: uhligCavFreeEnergyProcessor.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,41 +65,43 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    modelFactory.h File Reference
    │ │ │ +
    uhligCavFreeEnergyProcessor.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/CONCEPT/factory.h>
    │ │ │ -#include <BALL/QSAR/Model.h>
    │ │ │ -#include <BALL/QSAR/QSARData.h>
    │ │ │ +
    #include <BALL/common.h>
    │ │ │ +#include <BALL/ENERGY/energyProcessor.h>
    │ │ │ +#include <BALL/DATATYPE/options.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │
    │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::QSAR::ModelFactory< T >
    class  BALL::UhligCavFreeEnergyProcessor
     
    struct  BALL::UhligCavFreeEnergyProcessor::Option
     
    struct  BALL::UhligCavFreeEnergyProcessor::Default
     
    │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::QSAR
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,23 +1,25 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ + * _S_O_L_V_A_T_I_O_N │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -modelFactory.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_f_a_c_t_o_r_y_._h> │ │ │ │ -#include <_B_A_L_L_/_Q_S_A_R_/_M_o_d_e_l_._h> │ │ │ │ -#include <_B_A_L_L_/_Q_S_A_R_/_Q_S_A_R_D_a_t_a_._h> │ │ │ │ +uhligCavFreeEnergyProcessor.h File Reference │ │ │ │ +#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_E_N_E_R_G_Y_/_e_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y_<_ _T_ _> │ │ │ │ + class   _B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_Q_S_A_R │ │ │ │ -  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dc8/a01124_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: modelFactory.h Source File │ │ │ +BALL: uhligCavFreeEnergyProcessor.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,88 +70,138 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    modelFactory.h
    │ │ │ +
    uhligCavFreeEnergyProcessor.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_QSAR_MODELFACTORY_H
    │ │ │ -
    6#define BALL_QSAR_MODELFACTORY_H
    │ │ │ -
    7
    │ │ │ -
    8#ifndef BALL_CONCEPT_FACTORY_H
    │ │ │ -
    9#include <BALL/CONCEPT/factory.h>
    │ │ │ -
    10#endif
    │ │ │ -
    11
    │ │ │ -
    12#ifndef MODEL
    │ │ │ -
    13#include <BALL/QSAR/Model.h>
    │ │ │ -
    14#endif
    │ │ │ -
    15
    │ │ │ -
    16#ifndef QSARH
    │ │ │ -
    17#include <BALL/QSAR/QSARData.h>
    │ │ │ -
    18#endif
    │ │ │ -
    19
    │ │ │ -
    20namespace BALL
    │ │ │ -
    21{
    │ │ │ -
    22 namespace QSAR
    │ │ │ -
    23 {
    │ │ │ -
    24 //typedef Model* (*CreateMethod) (const QSARData& q);
    │ │ │ -
    25
    │ │ │ -
    28 template <typename T>
    │ │ │ -
    │ │ │ -
    29 class ModelFactory
    │ │ │ -
    30 {
    │ │ │ -
    31 public:
    │ │ │ -
    32
    │ │ │ -
    │ │ │ -
    33 static T* create(const QSARData& q)
    │ │ │ -
    34 {
    │ │ │ -
    35 return new T(q);
    │ │ │ -
    36 }
    │ │ │ -
    │ │ │ -
    37
    │ │ │ -
    │ │ │ -
    38 static T* createKernel1(const QSARData& q, int k, double p1, double p2)
    │ │ │ -
    39 {
    │ │ │ -
    40 return new T(q,k,p1,p2);
    │ │ │ -
    41 }
    │ │ │ -
    │ │ │ -
    42
    │ │ │ -
    │ │ │ -
    43 static T* createKernel2(const QSARData& q, String s1, String s2)
    │ │ │ -
    44 {
    │ │ │ -
    45 return new T(q,s1,s2);
    │ │ │ -
    46 }
    │ │ │ -
    │ │ │ -
    47 };
    │ │ │ -
    │ │ │ -
    48 }
    │ │ │ -
    49}
    │ │ │ -
    50
    │ │ │ -
    51#endif // BALL_QSAR_MODELFACTORY_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::QSAR::ModelFactory::createKernel1
    static T * createKernel1(const QSARData &q, int k, double p1, double p2)
    Definition modelFactory.h:38
    │ │ │ -
    BALL::QSAR::ModelFactory::createKernel2
    static T * createKernel2(const QSARData &q, String s1, String s2)
    Definition modelFactory.h:43
    │ │ │ -
    BALL::QSAR::ModelFactory::create
    static T * create(const QSARData &q)
    Definition modelFactory.h:33
    │ │ │ - │ │ │ +
    4// $Id: uhligCavFreeEnergyProcessor.h,v 1.19 2005/12/23 17:02:00 amoll Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_SOLVATION_UHLIGCAVFREEENERGYPROCESSOR_H
    │ │ │ +
    8#define BALL_SOLVATION_UHLIGCAVFREEENERGYPROCESSOR_H
    │ │ │ +
    9
    │ │ │ +
    10#ifndef BALL_COMMON_H
    │ │ │ +
    11# include <BALL/common.h>
    │ │ │ +
    12#endif
    │ │ │ +
    13
    │ │ │ +
    14#ifndef BALL_ENERGY_ENERGYPROCESSOR_H
    │ │ │ +
    15# include <BALL/ENERGY/energyProcessor.h>
    │ │ │ +
    16#endif
    │ │ │ +
    17
    │ │ │ +
    18#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ +
    19# include <BALL/DATATYPE/options.h>
    │ │ │ +
    20#endif
    │ │ │ +
    21
    │ │ │ +
    22namespace BALL
    │ │ │ +
    23{
    │ │ │ +
    │ │ │ +
    30 class BALL_EXPORT UhligCavFreeEnergyProcessor
    │ │ │ +
    31 : public EnergyProcessor
    │ │ │ +
    32 {
    │ │ │ +
    33
    │ │ │ +
    34 public:
    │ │ │ +
    35
    │ │ │ +
    │ │ │ +
    40 struct Option
    │ │ │ +
    41 {
    │ │ │ +
    47 static const char* VERBOSITY;
    │ │ │ +
    48
    │ │ │ +
    56 static const char* PROBE_RADIUS;
    │ │ │ +
    57
    │ │ │ +
    65 static const char* SURFACE_TENSION;
    │ │ │ +
    66
    │ │ │ +
    74 static const char* CONSTANT;
    │ │ │ +
    75
    │ │ │ +
    76 };
    │ │ │ +
    │ │ │ +
    77
    │ │ │ +
    │ │ │ +
    82 struct Default
    │ │ │ +
    83 {
    │ │ │ +
    87 static const int VERBOSITY;
    │ │ │ +
    88
    │ │ │ +
    94 static const float PROBE_RADIUS;
    │ │ │ +
    95
    │ │ │ +
    106 static const float SURFACE_TENSION;
    │ │ │ +
    107
    │ │ │ +
    116 static const float CONSTANT;
    │ │ │ +
    117
    │ │ │ +
    118 };
    │ │ │ +
    │ │ │ +
    119
    │ │ │ +
    123
    │ │ │ +
    126 UhligCavFreeEnergyProcessor();
    │ │ │ +
    127
    │ │ │ +
    130 UhligCavFreeEnergyProcessor(const UhligCavFreeEnergyProcessor& proc);
    │ │ │ +
    131
    │ │ │ +
    134 virtual ~UhligCavFreeEnergyProcessor();
    │ │ │ +
    135
    │ │ │ +
    137
    │ │ │ +
    140
    │ │ │ +
    143 const UhligCavFreeEnergyProcessor& operator = (const UhligCavFreeEnergyProcessor& proc);
    │ │ │ +
    144
    │ │ │ +
    147 virtual void clear();
    │ │ │ +
    148
    │ │ │ +
    150
    │ │ │ +
    153
    │ │ │ +
    156 bool operator == (const UhligCavFreeEnergyProcessor& proc) const;
    │ │ │ +
    157
    │ │ │ +
    159
    │ │ │ +
    162
    │ │ │ +
    165 virtual bool finish();
    │ │ │ +
    166
    │ │ │ +
    168
    │ │ │ +
    171
    │ │ │ +
    174 Options options;
    │ │ │ +
    175
    │ │ │ +
    177
    │ │ │ +
    178 private:
    │ │ │ +
    179
    │ │ │ +
    180 void setDefaultOptions();
    │ │ │ +
    181
    │ │ │ +
    182 };
    │ │ │ +
    │ │ │ +
    183}
    │ │ │ +
    184
    │ │ │ +
    185#endif // BALL_SOLVATION_UHLIGCAVFREEENERGYPROCESSOR_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::UhligCavFreeEnergyProcessor::UhligCavFreeEnergyProcessor
    UhligCavFreeEnergyProcessor(const UhligCavFreeEnergyProcessor &proc)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,80 +1,154 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ -modelFactory.h │ │ │ │ + * _S_O_L_V_A_T_I_O_N │ │ │ │ +uhligCavFreeEnergyProcessor.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_QSAR_MODELFACTORY_H │ │ │ │ -6#define BALL_QSAR_MODELFACTORY_H │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_CONCEPT_FACTORY_H │ │ │ │ -9#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_f_a_c_t_o_r_y_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12#ifndef MODEL │ │ │ │ -13#include <_B_A_L_L_/_Q_S_A_R_/_M_o_d_e_l_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16#ifndef QSARH │ │ │ │ -17#include <_B_A_L_L_/_Q_S_A_R_/_Q_S_A_R_D_a_t_a_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20namespace _B_A_L_L │ │ │ │ -21{ │ │ │ │ -22 namespace QSAR │ │ │ │ -23 { │ │ │ │ -24 //typedef Model* (*CreateMethod) (const QSARData& q); │ │ │ │ -25 │ │ │ │ -28 template │ │ │ │ -_2_9 class _M_o_d_e_l_F_a_c_t_o_r_y │ │ │ │ -30 { │ │ │ │ -31 public: │ │ │ │ -32 │ │ │ │ -_3_3 static T* _c_r_e_a_t_e(const _Q_S_A_R_D_a_t_a& q) │ │ │ │ -34 { │ │ │ │ -35 return new T(q); │ │ │ │ -36 } │ │ │ │ -37 │ │ │ │ -_3_8 static T* _c_r_e_a_t_e_K_e_r_n_e_l_1(const _Q_S_A_R_D_a_t_a& q, int k, double p1, double p2) │ │ │ │ -39 { │ │ │ │ -40 return new T(q,k,p1,p2); │ │ │ │ -41 } │ │ │ │ -42 │ │ │ │ -_4_3 static T* _c_r_e_a_t_e_K_e_r_n_e_l_2(const _Q_S_A_R_D_a_t_a& q, _S_t_r_i_n_g s1, _S_t_r_i_n_g s2) │ │ │ │ -44 { │ │ │ │ -45 return new T(q,s1,s2); │ │ │ │ -46 } │ │ │ │ -47 }; │ │ │ │ -48 } │ │ │ │ -49} │ │ │ │ -50 │ │ │ │ -51#endif // BALL_QSAR_MODELFACTORY_H │ │ │ │ -_Q_S_A_R_D_a_t_a_._h │ │ │ │ -_M_o_d_e_l_._h │ │ │ │ -_f_a_c_t_o_r_y_._h │ │ │ │ +4// $Id: uhligCavFreeEnergyProcessor.h,v 1.19 2005/12/23 17:02:00 amoll Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_SOLVATION_UHLIGCAVFREEENERGYPROCESSOR_H │ │ │ │ +8#define BALL_SOLVATION_UHLIGCAVFREEENERGYPROCESSOR_H │ │ │ │ +9 │ │ │ │ +10#ifndef BALL_COMMON_H │ │ │ │ +11# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +12#endif │ │ │ │ +13 │ │ │ │ +14#ifndef BALL_ENERGY_ENERGYPROCESSOR_H │ │ │ │ +15# include <_B_A_L_L_/_E_N_E_R_G_Y_/_e_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h> │ │ │ │ +16#endif │ │ │ │ +17 │ │ │ │ +18#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ +19# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +20#endif │ │ │ │ +21 │ │ │ │ +22namespace _B_A_L_L │ │ │ │ +23{ │ │ │ │ +_3_0 class _B_A_L_L___E_X_P_O_R_T _U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +31 : public _E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +32 { │ │ │ │ +33 │ │ │ │ +34 public: │ │ │ │ +35 │ │ │ │ +_4_0 struct _O_p_t_i_o_n │ │ │ │ +41 { │ │ │ │ +_4_7 static const char* _V_E_R_B_O_S_I_T_Y; │ │ │ │ +48 │ │ │ │ +_5_6 static const char* _P_R_O_B_E___R_A_D_I_U_S; │ │ │ │ +57 │ │ │ │ +_6_5 static const char* _S_U_R_F_A_C_E___T_E_N_S_I_O_N; │ │ │ │ +66 │ │ │ │ +_7_4 static const char* _C_O_N_S_T_A_N_T; │ │ │ │ +75 │ │ │ │ +76 }; │ │ │ │ +77 │ │ │ │ +_8_2 struct _D_e_f_a_u_l_t │ │ │ │ +83 { │ │ │ │ +_8_7 static const int _V_E_R_B_O_S_I_T_Y; │ │ │ │ +88 │ │ │ │ +_9_4 static const float _P_R_O_B_E___R_A_D_I_U_S; │ │ │ │ +95 │ │ │ │ +_1_0_6 static const float _S_U_R_F_A_C_E___T_E_N_S_I_O_N; │ │ │ │ +107 │ │ │ │ +_1_1_6 static const float _C_O_N_S_T_A_N_T; │ │ │ │ +117 │ │ │ │ +118 }; │ │ │ │ +119 │ │ │ │ +123 │ │ │ │ +_1_2_6 _U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r(); │ │ │ │ +127 │ │ │ │ +_1_3_0 _U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r(const _U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r& proc); │ │ │ │ +131 │ │ │ │ +_1_3_4 virtual _~_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r(); │ │ │ │ +135 │ │ │ │ +137 │ │ │ │ +140 │ │ │ │ +_1_4_3 const _U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r& operator = (const │ │ │ │ +_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r& proc); │ │ │ │ +144 │ │ │ │ +_1_4_7 virtual void _c_l_e_a_r(); │ │ │ │ +148 │ │ │ │ +150 │ │ │ │ +153 │ │ │ │ +_1_5_6 bool operator == (const _U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r& proc) const; │ │ │ │ +157 │ │ │ │ +159 │ │ │ │ +162 │ │ │ │ +_1_6_5 virtual bool _f_i_n_i_s_h(); │ │ │ │ +166 │ │ │ │ +168 │ │ │ │ +171 │ │ │ │ +_1_7_4 _O_p_t_i_o_n_s _o_p_t_i_o_n_s; │ │ │ │ +175 │ │ │ │ +177 │ │ │ │ +178 private: │ │ │ │ +179 │ │ │ │ +180 void setDefaultOptions(); │ │ │ │ +181 │ │ │ │ +182 }; │ │ │ │ +183} │ │ │ │ +184 │ │ │ │ +185#endif // BALL_SOLVATION_UHLIGCAVFREEENERGYPROCESSOR_H │ │ │ │ +_c_o_m_m_o_n_._h │ │ │ │ +_o_p_t_i_o_n_s_._h │ │ │ │ +_e_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y │ │ │ │ -DDeeffiinniittiioonn _m_o_d_e_l_F_a_c_t_o_r_y_._h_:_3_0 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y_:_:_c_r_e_a_t_e_K_e_r_n_e_l_1 │ │ │ │ -static T * createKernel1(const QSARData &q, int k, double p1, double p2) │ │ │ │ -DDeeffiinniittiioonn _m_o_d_e_l_F_a_c_t_o_r_y_._h_:_3_8 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y_:_:_c_r_e_a_t_e_K_e_r_n_e_l_2 │ │ │ │ -static T * createKernel2(const QSARData &q, String s1, String s2) │ │ │ │ -DDeeffiinniittiioonn _m_o_d_e_l_F_a_c_t_o_r_y_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_M_o_d_e_l_F_a_c_t_o_r_y_:_:_c_r_e_a_t_e │ │ │ │ -static T * create(const QSARData &q) │ │ │ │ -DDeeffiinniittiioonn _m_o_d_e_l_F_a_c_t_o_r_y_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_Q_S_A_R_D_a_t_a │ │ │ │ -DDeeffiinniittiioonn _Q_S_A_R_D_a_t_a_._h_:_5_6 │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _e_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_f_i_n_i_s_h │ │ │ │ +virtual bool finish() │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_c_l_e_a_r │ │ │ │ +virtual void clear() │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +UhligCavFreeEnergyProcessor() │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_~_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +virtual ~UhligCavFreeEnergyProcessor() │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r │ │ │ │ +UhligCavFreeEnergyProcessor(const UhligCavFreeEnergyProcessor &proc) │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_o_p_t_i_o_n_s │ │ │ │ +Options options │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_1_7_4 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_4_1 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_C_O_N_S_T_A_N_T │ │ │ │ +static const char * CONSTANT │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_R_O_B_E___R_A_D_I_U_S │ │ │ │ +static const char * PROBE_RADIUS │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_5_6 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_V_E_R_B_O_S_I_T_Y │ │ │ │ +static const char * VERBOSITY │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_4_7 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_S_U_R_F_A_C_E___T_E_N_S_I_O_N │ │ │ │ +static const char * SURFACE_TENSION │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_6_5 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_8_3 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_S_U_R_F_A_C_E___T_E_N_S_I_O_N │ │ │ │ +static const float SURFACE_TENSION │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_1_0_6 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_V_E_R_B_O_S_I_T_Y │ │ │ │ +static const int VERBOSITY │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_8_7 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_R_O_B_E___R_A_D_I_U_S │ │ │ │ +static const float PROBE_RADIUS │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_9_4 │ │ │ │ +_B_A_L_L_:_:_U_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_C_O_N_S_T_A_N_T │ │ │ │ +static const float CONSTANT │ │ │ │ +DDeeffiinniittiioonn _u_h_l_i_g_C_a_v_F_r_e_e_E_n_e_r_g_y_P_r_o_c_e_s_s_o_r_._h_:_1_1_6 │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dca/a04906.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Classes | │ │ │ List of all members
    │ │ │
    BALL::TSurface< T > Class Template Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/MATHS/surface.h>

    │ │ │ +

    #include <BALL/MATHS/surface.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Classes

    class  Triangle
     
    │ │ │ │ │ │ │ │ │

    │ │ │ @@ -193,15 +193,15 @@ │ │ │

     the triangles
     
    │ │ │

    Detailed Description

    │ │ │
    template<typename T>
    │ │ │ class BALL::TSurface< T >

    Generic Three-dimensional Surface class. This class describes a three-dimensional triangulated surface. Each triangle is represented by three indices to vertices (as described by the TSurface::Triangle ). Each of the vertices has a position and possibly a normal vector associated.

    │ │ │ │ │ │ -

    Definition at line 27 of file surface.h.

    │ │ │ +

    Definition at line 27 of file surface.h.

    │ │ │

    Member Typedef Documentation

    │ │ │ │ │ │

    ◆ Normal

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ @@ -211,15 +211,15 @@ │ │ │ typedef TVector3<T> BALL::TSurface< T >::Normal │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    A normal.

    │ │ │ │ │ │ -

    Definition at line 62 of file surface.h.

    │ │ │ +

    Definition at line 62 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ Vertex

    │ │ │ │ │ │
    │ │ │ @@ -231,15 +231,15 @@ │ │ │ typedef TVector3<T> BALL::TSurface< T >::Vertex │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    A vertex.

    │ │ │ │ │ │ -

    Definition at line 59 of file surface.h.

    │ │ │ +

    Definition at line 59 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ TSurface() [1/2]

    │ │ │ │ │ │ @@ -254,15 +254,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    This is required for windows dlls

    │ │ │ │ │ │ -

    Definition at line 202 of file surface.h.

    │ │ │ +

    Definition at line 202 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ TSurface() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -276,15 +276,15 @@ │ │ │ const TSurface< T > &  │ │ │ surface) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 207 of file surface.h.

    │ │ │ +

    Definition at line 207 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ~TSurface()

    │ │ │ │ │ │
    │ │ │ @@ -305,15 +305,15 @@ │ │ │ │ │ │ │ │ │ virtual │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 215 of file surface.h.

    │ │ │ +

    Definition at line 215 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ clear()

    │ │ │ │ │ │ @@ -327,84 +327,84 @@ │ │ │ ( │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 220 of file surface.h.

    │ │ │ +

    Definition at line 220 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ clearNormals()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TSurface< T >::clearNormals BALL_INLINE void BALL::TSurface< T >::clearNormals ()
    │ │ │
    │ │ │ │ │ │

    Clear all normals.

    │ │ │ │ │ │ -

    Definition at line 460 of file surface.h.

    │ │ │ +

    Definition at line 460 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ clearTriangles()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TSurface< T >::clearTriangles BALL_INLINE void BALL::TSurface< T >::clearTriangles ()
    │ │ │
    │ │ │ │ │ │

    Clear all triangles.

    │ │ │ │ │ │ -

    Definition at line 388 of file surface.h.

    │ │ │ +

    Definition at line 388 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ clearVertices()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TSurface< T >::clearVertices BALL_INLINE void BALL::TSurface< T >::clearVertices ()
    │ │ │
    │ │ │ │ │ │

    Clear all vertices.

    │ │ │ │ │ │ -

    Definition at line 424 of file surface.h.

    │ │ │ +

    Definition at line 424 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ get()

    │ │ │ │ │ │
    │ │ │ @@ -418,15 +418,15 @@ │ │ │ TSurface< T > &  │ │ │ surface) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 245 of file surface.h.

    │ │ │ +

    Definition at line 245 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getArea()

    │ │ │ │ │ │
    │ │ │ @@ -440,228 +440,228 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Compute the surface area. The area is computed as the sum of the areas of all triangles.

    │ │ │ │ │ │ -

    Definition at line 328 of file surface.h.

    │ │ │ +

    Definition at line 328 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNormal() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE TSurface< T >::Normal & BALL::TSurface< T >::getNormal BALL_INLINE TSurface< T >::Normal & BALL::TSurface< T >::getNormal (Position index)
    │ │ │
    │ │ │ │ │ │

    Return the position of a normal.

    │ │ │ │ │ │ -

    Definition at line 446 of file surface.h.

    │ │ │ +

    Definition at line 446 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getNormal() [2/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE const TSurface< T >::Normal & BALL::TSurface< T >::getNormal BALL_INLINE const TSurface< T >::Normal & BALL::TSurface< T >::getNormal (Position index) const
    │ │ │
    │ │ │ │ │ │

    Return the position of a normal.

    │ │ │ │ │ │ -

    Definition at line 453 of file surface.h.

    │ │ │ +

    Definition at line 453 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getNumberOfNormals()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE Size BALL::TSurface< T >::getNumberOfNormals BALL_INLINE Size BALL::TSurface< T >::getNumberOfNormals () const
    │ │ │
    │ │ │ │ │ │

    Return the number of normals.

    │ │ │ │ │ │ -

    Definition at line 367 of file surface.h.

    │ │ │ +

    Definition at line 367 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getNumberOfTriangles()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE Size BALL::TSurface< T >::getNumberOfTriangles BALL_INLINE Size BALL::TSurface< T >::getNumberOfTriangles () const
    │ │ │
    │ │ │ │ │ │

    Return the number of triangles.

    │ │ │ │ │ │ -

    Definition at line 353 of file surface.h.

    │ │ │ +

    Definition at line 353 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getNumberOfVertices()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE Size BALL::TSurface< T >::getNumberOfVertices BALL_INLINE Size BALL::TSurface< T >::getNumberOfVertices () const
    │ │ │
    │ │ │ │ │ │

    Return the number of vertices.

    │ │ │ │ │ │ -

    Definition at line 360 of file surface.h.

    │ │ │ +

    Definition at line 360 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getTriangle() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE TSurface< T >::Triangle & BALL::TSurface< T >::getTriangle BALL_INLINE TSurface< T >::Triangle & BALL::TSurface< T >::getTriangle (Position index)
    │ │ │
    │ │ │ │ │ │

    Return a triangle with a given index.

    │ │ │ │ │ │ -

    Definition at line 374 of file surface.h.

    │ │ │ +

    Definition at line 374 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getTriangle() [2/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE const TSurface< T >::Triangle & BALL::TSurface< T >::getTriangle BALL_INLINE const TSurface< T >::Triangle & BALL::TSurface< T >::getTriangle (Position index) const
    │ │ │
    │ │ │ │ │ │

    Return a triangle with a given index.

    │ │ │ │ │ │ -

    Definition at line 381 of file surface.h.

    │ │ │ +

    Definition at line 381 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getVertex() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE TSurface< T >::Vertex & BALL::TSurface< T >::getVertex BALL_INLINE TSurface< T >::Vertex & BALL::TSurface< T >::getVertex (Position index)
    │ │ │
    │ │ │ │ │ │

    Return the position of a vertex.

    │ │ │ │ │ │ -

    Definition at line 410 of file surface.h.

    │ │ │ +

    Definition at line 410 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getVertex() [2/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE const TSurface< T >::Vertex & BALL::TSurface< T >::getVertex BALL_INLINE const TSurface< T >::Vertex & BALL::TSurface< T >::getVertex (Position index) const
    │ │ │
    │ │ │ │ │ │

    Return the position of a vertex.

    │ │ │ │ │ │ -

    Definition at line 417 of file surface.h.

    │ │ │ +

    Definition at line 417 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ operator!=()

    │ │ │ │ │ │
    │ │ │ @@ -675,15 +675,15 @@ │ │ │ const TSurface< T > &  │ │ │ surface) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 480 of file surface.h.

    │ │ │ +

    Definition at line 480 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator=()

    │ │ │ │ │ │
    │ │ │ @@ -697,15 +697,15 @@ │ │ │ const TSurface< T > &  │ │ │ surface) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 236 of file surface.h.

    │ │ │ +

    Definition at line 236 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator==()

    │ │ │ │ │ │
    │ │ │ @@ -719,87 +719,87 @@ │ │ │ const TSurface< T > &  │ │ │ surface) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 344 of file surface.h.

    │ │ │ +

    Definition at line 344 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ pushBackNormal()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TSurface< T >::pushBackNormal BALL_INLINE void BALL::TSurface< T >::pushBackNormal (const Normal & n)
    │ │ │
    │ │ │ │ │ │

    Add a normal.

    │ │ │ │ │ │ -

    Definition at line 474 of file surface.h.

    │ │ │ +

    Definition at line 474 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ pushBackTriangle()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TSurface< T >::pushBackTriangle BALL_INLINE void BALL::TSurface< T >::pushBackTriangle (const Triangle & triangle)
    │ │ │
    │ │ │ │ │ │

    Add a triangle.

    │ │ │ │ │ │ -

    Definition at line 402 of file surface.h.

    │ │ │ +

    Definition at line 402 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ pushBackVertex()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TSurface< T >::pushBackVertex BALL_INLINE void BALL::TSurface< T >::pushBackVertex (const Vertex & vertex)
    │ │ │
    │ │ │ │ │ │

    Add a vertex.

    │ │ │ │ │ │ -

    Definition at line 439 of file surface.h.

    │ │ │ +

    Definition at line 439 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ readMSMSFile()

    │ │ │ │ │ │
    │ │ │ @@ -829,87 +829,87 @@ │ │ │

    Read from MSMS file. Read the contents of the vertex and faces file created by Michael Sanners software MSMS.

    Exceptions
    │ │ │ │ │ │ │ │ │
    Exception::FileNotFoundif the file could not be opened
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 253 of file surface.h.

    │ │ │ +

    Definition at line 253 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ resizeNormals()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TSurface< T >::resizeNormals BALL_INLINE void BALL::TSurface< T >::resizeNormals (Size size)
    │ │ │
    │ │ │ │ │ │

    Resize the normal array.

    │ │ │ │ │ │ -

    Definition at line 467 of file surface.h.

    │ │ │ +

    Definition at line 467 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ resizeTriangles()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TSurface< T >::resizeTriangles BALL_INLINE void BALL::TSurface< T >::resizeTriangles (Size size)
    │ │ │
    │ │ │ │ │ │

    Resize the triangle array.

    │ │ │ │ │ │ -

    Definition at line 395 of file surface.h.

    │ │ │ +

    Definition at line 395 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ resizeVertices()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TSurface< T >::resizeVertices BALL_INLINE void BALL::TSurface< T >::resizeVertices (Size size)
    │ │ │
    │ │ │ │ │ │

    Resize the vertex array.

    │ │ │ │ │ │ -

    Definition at line 431 of file surface.h.

    │ │ │ +

    Definition at line 431 of file surface.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ set()

    │ │ │ │ │ │
    │ │ │ @@ -923,15 +923,15 @@ │ │ │ const TSurface< T > &  │ │ │ surface) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 228 of file surface.h.

    │ │ │ +

    Definition at line 228 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ normal

    │ │ │ │ │ │ @@ -944,15 +944,15 @@ │ │ │ vector<Normal> BALL::TSurface< T >::normal │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    the normals for each vertex

    │ │ │ │ │ │ -

    Definition at line 188 of file surface.h.

    │ │ │ +

    Definition at line 188 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ triangle

    │ │ │ │ │ │
    │ │ │ @@ -964,15 +964,15 @@ │ │ │ vector<Triangle> BALL::TSurface< T >::triangle │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    the triangles

    │ │ │ │ │ │ -

    Definition at line 191 of file surface.h.

    │ │ │ +

    Definition at line 191 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ vertex

    │ │ │ │ │ │
    │ │ │ @@ -984,15 +984,15 @@ │ │ │ vector<Vertex> BALL::TSurface< T >::vertex │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    the vertices

    │ │ │ │ │ │ -

    Definition at line 185 of file surface.h.

    │ │ │ +

    Definition at line 185 of file surface.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dce/a01946.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: list.h File Reference │ │ │ +BALL: empiricalHSShiftProcessor.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,34 +65,48 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    list.h File Reference
    │ │ │ +
    empiricalHSShiftProcessor.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/CONCEPT/visitor.h>
    │ │ │ -#include <BALL/CONCEPT/processor.h>
    │ │ │ -#include <list>
    │ │ │ +
    #include <BALL/MATHS/cubicSpline2D.h>
    │ │ │ +#include <BALL/MATHS/cubicSpline1D.h>
    │ │ │ +#include <BALL/FORMAT/genericMolFile.h>
    │ │ │ +#include <BALL/NMR/shiftModule.h>
    │ │ │ +#include <BALL/KERNEL/expression.h>
    │ │ │ +#include <BALL/DATATYPE/options.h>
    │ │ │ +#include <set>
    │ │ │ +#include <map>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::List< Value >
    class  BALL::EmpiricalHSShiftProcessor
     
    struct  BALL::EmpiricalHSShiftProcessor::Option
     Option names. More...
     
    struct  BALL::EmpiricalHSShiftProcessor::Default
     Default values for options. More...
     
    class  BALL::EmpiricalHSShiftProcessor::PropertiesForShift_
     
    class  BALL::EmpiricalHSShiftProcessor::ShiftHyperSurface_
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ ├── html2text {} │ │ │ │ @@ -1,22 +1,36 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _D_A_T_A_T_Y_P_E │ │ │ │ + * _N_M_R │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -list.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_v_i_s_i_t_o_r_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ -#include │ │ │ │ +empiricalHSShiftProcessor.h File Reference │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_c_u_b_i_c_S_p_l_i_n_e_2_D_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_c_u_b_i_c_S_p_l_i_n_e_1_D_._h> │ │ │ │ +#include <_B_A_L_L_/_F_O_R_M_A_T_/_g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h> │ │ │ │ +#include <_B_A_L_L_/_N_M_R_/_s_h_i_f_t_M_o_d_u_l_e_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_e_x_p_r_e_s_s_i_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_L_i_s_t_<_ _V_a_l_u_e_ _> │ │ │ │ + class   _B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ +  _O_p_t_i_o_n names. _M_o_r_e_._._. │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ +  _D_e_f_a_u_l_t values for options. _M_o_r_e_._._. │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t__ │ │ │ │ +  │ │ │ │ + class   _B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__ │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dce/a01946_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: list.h Source File │ │ │ +BALL: empiricalHSShiftProcessor.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,271 +70,442 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    list.h
    │ │ │ +
    empiricalHSShiftProcessor.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ -
    2// vi: set ts=2:
    │ │ │ -
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_DATATYPE_LIST_H
    │ │ │ -
    6#define BALL_DATATYPE_LIST_H
    │ │ │ +Go to the documentation of this file.
    1#ifndef BALL_NMR_EMPIRICALHSSHIFTPROCESSOR_H
    │ │ │ +
    2#define BALL_NMR_EMPIRICALHSSHIFTPROCESSOR_H
    │ │ │ +
    3
    │ │ │ +
    4#ifndef BALL_MATHS_CUBICSPLINE2D_H
    │ │ │ +
    5# include <BALL/MATHS/cubicSpline2D.h>
    │ │ │ +
    6#endif
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_COMMON_H
    │ │ │ -
    9# include <BALL/common.h>
    │ │ │ +
    8#ifndef BALL_MATHS_CUBICSPLINE1D_H
    │ │ │ +
    9# include <BALL/MATHS/cubicSpline1D.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_CONCEPT_VISITOR_H
    │ │ │ -
    13# include <BALL/CONCEPT/visitor.h>
    │ │ │ -
    14#endif
    │ │ │ -
    15
    │ │ │ -
    16#ifndef BALL_CONCEPT_PROCESSOR_H
    │ │ │ -
    17# include <BALL/CONCEPT/processor.h>
    │ │ │ -
    18#endif
    │ │ │ -
    19
    │ │ │ -
    20#include <list>
    │ │ │ -
    21
    │ │ │ -
    22#ifdef BALL_COMPILER_GXX || BALL_COMPILER_LLVM
    │ │ │ -
    23#warning "This header file is deprecated and should not be used in new code! As a replacement for BALL::List the use of std::list is strongly suggested."
    │ │ │ -
    24#endif
    │ │ │ -
    25
    │ │ │ -
    26namespace BALL
    │ │ │ -
    27{
    │ │ │ -
    33 template <typename Value>
    │ │ │ -
    │ │ │ -
    34 class List
    │ │ │ -
    35 : public std::list<Value>
    │ │ │ -
    36 {
    │ │ │ -
    37 public:
    │ │ │ -
    38
    │ │ │ -
    42
    │ │ │ -
    45 typedef typename std::list<Value>::iterator Iterator;
    │ │ │ -
    46 // for STL compatibility
    │ │ │ -
    47 typedef typename std::list<Value>::iterator iterator;
    │ │ │ -
    48
    │ │ │ -
    51 typedef typename std::list<Value>::const_iterator ConstIterator;
    │ │ │ -
    52 // for STL compatibility
    │ │ │ -
    53 typedef typename std::list<Value>::const_iterator const_iterator;
    │ │ │ -
    54
    │ │ │ -
    56
    │ │ │ -
    58
    │ │ │ -
    59 BALL_CREATE_DEEP(List)
    │ │ │ -
    60
    │ │ │ -
    61
    │ │ │ -
    │ │ │ -
    64 List()
    │ │ │ -
    65 : std::list<Value>()
    │ │ │ -
    66 {
    │ │ │ -
    67 }
    │ │ │ -
    │ │ │ -
    68
    │ │ │ -
    │ │ │ -
    74 List(const List& new_list, bool /* deep = true */)
    │ │ │ -
    75 : std::list<Value>(new_list)
    │ │ │ -
    76 {
    │ │ │ -
    77 }
    │ │ │ -
    │ │ │ -
    78
    │ │ │ -
    │ │ │ -
    81 void destroy()
    │ │ │ -
    82 {
    │ │ │ -
    83 std::list<Value>::clear();
    │ │ │ -
    84 }
    │ │ │ -
    │ │ │ -
    85
    │ │ │ -
    │ │ │ -
    88 virtual ~List()
    │ │ │ -
    89 {
    │ │ │ -
    90 std::list<Value>::clear();
    │ │ │ -
    91 }
    │ │ │ +
    12
    │ │ │ +
    13#ifndef BALL_FORMAT_GENERICMOLFILE_H
    │ │ │ +
    14# include <BALL/FORMAT/genericMolFile.h>
    │ │ │ +
    15#endif
    │ │ │ +
    16
    │ │ │ +
    17#ifndef BALL_NMR_SHIFT_MODULE_H
    │ │ │ +
    18# include<BALL/NMR/shiftModule.h>
    │ │ │ +
    19#endif
    │ │ │ +
    20
    │ │ │ +
    21#ifndef BALL_KERNEL_EXPRESSION_H
    │ │ │ +
    22# include<BALL/KERNEL/expression.h>
    │ │ │ +
    23#endif
    │ │ │ +
    24
    │ │ │ +
    25#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ +
    26# include <BALL/DATATYPE/options.h>
    │ │ │ +
    27#endif
    │ │ │ +
    28
    │ │ │ +
    29
    │ │ │ +
    30#include <set>
    │ │ │ +
    31#include <map>
    │ │ │ +
    32
    │ │ │ +
    33namespace BALL
    │ │ │ +
    34{
    │ │ │ +
    35 class Atom;
    │ │ │ +
    36
    │ │ │ +
    │ │ │ +
    40 class BALL_EXPORT EmpiricalHSShiftProcessor
    │ │ │ +
    41 : public ShiftModule
    │ │ │ +
    42 {
    │ │ │ +
    43 public:
    │ │ │ +
    44
    │ │ │ +
    45 BALL_CREATE(EmpiricalHSShiftProcessor)
    │ │ │ +
    46
    │ │ │ +
    47 static const int VERBOSITY_LEVEL_CRITICAL;
    │ │ │ +
    48 static const int VERBOSITY_LEVEL_DEBUG;
    │ │ │ +
    49
    │ │ │ +
    │ │ │ +
    54 struct BALL_EXPORT Option
    │ │ │ +
    55 {
    │ │ │ +
    58 static const char* VERBOSITY;
    │ │ │ +
    59
    │ │ │ +
    60 };
    │ │ │
    │ │ │ +
    61
    │ │ │ +
    │ │ │ +
    63 struct BALL_EXPORT Default
    │ │ │ +
    64 {
    │ │ │ +
    65 static const int VERBOSITY;
    │ │ │ +
    66 };
    │ │ │ +
    │ │ │ +
    67
    │ │ │ +
    69
    │ │ │ +
    70
    │ │ │ +
    74
    │ │ │ +
    78 static const char* PROPERTY__EHS_SHIFT;
    │ │ │ +
    79
    │ │ │ +
    81
    │ │ │ +
    84
    │ │ │ +
    87 EmpiricalHSShiftProcessor();
    │ │ │ +
    88
    │ │ │ +
    91 virtual ~EmpiricalHSShiftProcessor();
    │ │ │
    92
    │ │ │
    94
    │ │ │ -
    96
    │ │ │ -
    │ │ │ -
    101 void set(const List& list, bool /* deep */ = true)
    │ │ │ -
    102 {
    │ │ │ -
    103 std::list<Value>::clear();
    │ │ │ -
    104
    │ │ │ -
    105 ConstIterator it = list.begin();
    │ │ │ -
    106 for ( ; it != list.end(); ++it)
    │ │ │ -
    107 {
    │ │ │ -
    108 std::list<Value>::push_back(const_cast<Value&>(*it));
    │ │ │ -
    109 }
    │ │ │ -
    110 }
    │ │ │ -
    │ │ │ -
    111
    │ │ │ -
    │ │ │ -
    114 const List& operator = (const List& list)
    │ │ │ -
    115 {
    │ │ │ -
    116 set(list);
    │ │ │ -
    117 return *this;
    │ │ │ -
    118 }
    │ │ │ -
    │ │ │ -
    119
    │ │ │ -
    │ │ │ -
    121 void get(List& list, bool deep = true) const
    │ │ │ -
    122 {
    │ │ │ -
    123 list.set(*this, deep);
    │ │ │ -
    124 }
    │ │ │ -
    │ │ │ -
    125
    │ │ │ -
    │ │ │ -
    127 void swap(List& list)
    │ │ │ -
    128 {
    │ │ │ -
    129 List<Value> temp;
    │ │ │ -
    130 temp.set(*this);
    │ │ │ -
    131 (*this).set(list);
    │ │ │ -
    132 list.set(temp);
    │ │ │ -
    133 }
    │ │ │ -
    │ │ │ -
    134
    │ │ │ -
    136
    │ │ │ -
    138
    │ │ │ -
    │ │ │ -
    141 Size getSize() const
    │ │ │ -
    142 {
    │ │ │ -
    143 return (Size)std::list<Value>::size();
    │ │ │ -
    144 }
    │ │ │ -
    │ │ │ -
    145
    │ │ │ -
    │ │ │ -
    150 bool remove(const Value& item)
    │ │ │ -
    151 {
    │ │ │ -
    152 Iterator it = std::list<Value>::begin();
    │ │ │ -
    153 for (; it != std::list<Value>::end(); ++it)
    │ │ │ -
    154 {
    │ │ │ -
    155 if (*it == item)
    │ │ │ -
    156 {
    │ │ │ -
    157 std::list<Value>::erase(it);
    │ │ │ -
    158 return true;
    │ │ │ -
    159 }
    │ │ │ -
    160 }
    │ │ │ -
    161 return false;
    │ │ │ -
    162 }
    │ │ │ -
    │ │ │ -
    163
    │ │ │ -
    165
    │ │ │ -
    167
    │ │ │ -
    │ │ │ -
    171 bool isEmpty() const
    │ │ │ -
    172 {
    │ │ │ -
    173 return (std::list<Value>::size() == 0);
    │ │ │ -
    174 }
    │ │ │ -
    │ │ │ -
    175
    │ │ │ +
    97
    │ │ │ +
    130 virtual void init();
    │ │ │ +
    131
    │ │ │ +
    133
    │ │ │ +
    136
    │ │ │ +
    142 virtual bool start();
    │ │ │ +
    143
    │ │ │ +
    144
    │ │ │ +
    157 virtual Processor::Result operator () (Composite& composite);
    │ │ │ +
    158
    │ │ │ +
    176 virtual bool finish();
    │ │ │
    177
    │ │ │
    179
    │ │ │ -
    184 virtual void host(Visitor<List<Value> >& visitor);
    │ │ │ -
    185
    │ │ │ -
    187
    │ │ │ +
    183 Options options;
    │ │ │ +
    184
    │ │ │ +
    187 void setDefaultOptions();
    │ │ │
    189
    │ │ │ -
    │ │ │ -
    194 bool apply(UnaryProcessor<Value>& processor)
    │ │ │ -
    195 {
    │ │ │ -
    196 if (!processor.start()) return false;
    │ │ │ -
    197
    │ │ │ -
    198 for (Iterator it = std::list<Value>::begin(); it != std::list<Value>::end(); ++it)
    │ │ │ -
    199 {
    │ │ │ -
    200 Processor::Result result = processor(*it);
    │ │ │ -
    201 if (result <= Processor::BREAK)
    │ │ │ -
    202 {
    │ │ │ -
    203 return (result == Processor::BREAK);
    │ │ │ -
    204 }
    │ │ │ -
    205 }
    │ │ │ +
    190 protected:
    │ │ │ +
    191
    │ │ │ +
    192
    │ │ │ +
    193 /*_ Neested class providing atom properties for the shift computations
    │ │ │ +
    194 * */
    │ │ │ +
    │ │ │ +
    195 class BALL_EXPORT PropertiesForShift_
    │ │ │ +
    196 {
    │ │ │ +
    197 public:
    │ │ │ +
    198
    │ │ │ +
    201 PropertiesForShift_(int verbosity_ = EmpiricalHSShiftProcessor::VERBOSITY_LEVEL_CRITICAL);
    │ │ │ +
    202
    │ │ │ +
    205 Atom* current_atom;
    │ │ │
    206
    │ │ │ -
    207 return processor.finish();
    │ │ │ -
    208 }
    │ │ │ -
    │ │ │ -
    209
    │ │ │ -
    211
    │ │ │ -
    │ │ │ -
    215 bool operator == (const List<Value>& list) const
    │ │ │ -
    216 {
    │ │ │ -
    217 if (std::list<Value>::size() != list.size())
    │ │ │ -
    218 {
    │ │ │ -
    219 return false;
    │ │ │ -
    220 }
    │ │ │ -
    221
    │ │ │ -
    222 typename List<Value>::ConstIterator this_it = std::list<Value>::begin();
    │ │ │ -
    223 typename List<Value>::ConstIterator list_it = list.begin();
    │ │ │ +
    223 bool computeProperties_(Atom* atom, std::set<String> properties);
    │ │ │
    224
    │ │ │ -
    225 for (; this_it != std::list<Value>::end(); ++this_it)
    │ │ │ -
    226 {
    │ │ │ -
    227 if (!(*this_it == *list_it))
    │ │ │ -
    228 {
    │ │ │ -
    229 return false;
    │ │ │ -
    230 }
    │ │ │ -
    231 ++list_it;
    │ │ │ -
    232 }
    │ │ │ -
    233 return true;
    │ │ │ -
    234 }
    │ │ │ -
    │ │ │ -
    235
    │ │ │ -
    │ │ │ -
    239 bool operator != (const List<Value>& list) const
    │ │ │ -
    240 {
    │ │ │ -
    241 return !(*this == list);
    │ │ │ -
    242 }
    │ │ │ -
    │ │ │ -
    243
    │ │ │ -
    244 };
    │ │ │ -
    │ │ │ -
    245
    │ │ │ -
    246 template <typename Value>
    │ │ │ -
    │ │ │ -
    247 void List<Value>::host(Visitor<List<Value> >& visitor)
    │ │ │ -
    248 {
    │ │ │ -
    249 visitor.visit(*this);
    │ │ │ -
    250 }
    │ │ │ -
    │ │ │ -
    251} // namespace BALL
    │ │ │ -
    252
    │ │ │ -
    253#endif // BALL_DATATYPE_LIST_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_CREATE_DEEP
    #define BALL_CREATE_DEEP(name)
    Definition create.h:26
    │ │ │ -
    std
    STL namespace.
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::UnaryProcessor::start
    virtual bool start()
    Definition processor.h:92
    │ │ │ -
    BALL::UnaryProcessor::finish
    virtual bool finish()
    Definition processor.h:99
    │ │ │ - │ │ │ - │ │ │ -
    BALL::List::operator=
    const List & operator=(const List &list)
    Definition list.h:114
    │ │ │ -
    BALL::List::operator!=
    bool operator!=(const List< Value > &list) const
    Definition list.h:239
    │ │ │ -
    BALL::List::apply
    bool apply(UnaryProcessor< Value > &processor)
    Definition list.h:194
    │ │ │ -
    BALL::List::destroy
    void destroy()
    Definition list.h:81
    │ │ │ -
    BALL::List::operator==
    bool operator==(const List< Value > &list) const
    Definition list.h:215
    │ │ │ -
    BALL::List::Iterator
    std::list< Value >::iterator Iterator
    Definition list.h:45
    │ │ │ -
    BALL::List::swap
    void swap(List &list)
    Swaps the contents of two lists.
    Definition list.h:127
    │ │ │ -
    BALL::List::set
    void set(const List &list, bool=true)
    Definition list.h:101
    │ │ │ -
    BALL::List::ConstIterator
    std::list< Value >::const_iterator ConstIterator
    Definition list.h:51
    │ │ │ -
    BALL::List::const_iterator
    std::list< Value >::const_iterator const_iterator
    Definition list.h:53
    │ │ │ -
    BALL::List::get
    void get(List &list, bool deep=true) const
    Assign the content of a list to another.
    Definition list.h:121
    │ │ │ -
    BALL::List::host
    virtual void host(Visitor< List< Value > > &visitor)
    Definition list.h:247
    │ │ │ -
    BALL::List::remove
    bool remove(const Value &item)
    Definition list.h:150
    │ │ │ -
    BALL::List::getSize
    Size getSize() const
    Definition list.h:141
    │ │ │ -
    BALL::List::isEmpty
    bool isEmpty() const
    Definition list.h:171
    │ │ │ -
    BALL::List::~List
    virtual ~List()
    Definition list.h:88
    │ │ │ -
    BALL::List::List
    List(const List &new_list, bool)
    Definition list.h:74
    │ │ │ -
    BALL::List::iterator
    std::list< Value >::iterator iterator
    Definition list.h:47
    │ │ │ - │ │ │ +
    236 std::pair<float, String> operator [] (const String& property_name);
    │ │ │ +
    237
    │ │ │ +
    242 static bool isDiscrete(String property);
    │ │ │ +
    243
    │ │ │ +
    247 static bool isMixed(String property);
    │ │ │ +
    248
    │ │ │ +
    249 protected:
    │ │ │ +
    250
    │ │ │ +
    251 // Storing the atoms properties
    │ │ │ +
    252 // ...as numerical value
    │ │ │ +
    253 std::map<String, float> properties_real_;
    │ │ │ +
    254 // ... as alphanumerical/discrete value
    │ │ │ +
    255 std::map<String, String> properties_string_;
    │ │ │ +
    256
    │ │ │ +
    257 protected:
    │ │ │ +
    258
    │ │ │ +
    259 float getChiAngle_(Residue* residue);
    │ │ │ +
    260 float getChi2Angle_(Residue* residue);
    │ │ │ +
    261 char getAminoAcid_(Residue* residue);
    │ │ │ +
    262 char getSecondaryStructure_(Residue* residue);
    │ │ │ +
    263 float getHA_HBondLen_(Residue* residue);
    │ │ │ +
    264 float getHA2_HBondLen_(Residue* residue);
    │ │ │ +
    265 float getHN_HBondLen_(Residue* residue);
    │ │ │ +
    266 float getO_HBondLen_(Residue* residue);
    │ │ │ +
    267 bool hasDisulfidBond_(Residue* residue);
    │ │ │ +
    268 bool hasHA_HBond_(Residue* residue);
    │ │ │ +
    269 bool hasHA2_HBond_(Residue* residue);
    │ │ │ +
    270 bool hasHN_HBond_(Residue* residue);
    │ │ │ +
    271 bool hasO_HBond_(Residue* residue);
    │ │ │ +
    272
    │ │ │ +
    273 private:
    │ │ │ +
    274 // verbosity of the classes methods
    │ │ │ +
    275 int verbosity_;
    │ │ │ +
    276 }; // end of nested class
    │ │ │ +
    │ │ │ +
    277
    │ │ │ +
    278
    │ │ │ +
    279 /*_ Neested class handling the empirical hypersurfaces.
    │ │ │ +
    280 **/
    │ │ │ +
    281
    │ │ │ +
    │ │ │ +
    282 class ShiftHyperSurface_
    │ │ │ +
    283 {
    │ │ │ +
    284 public:
    │ │ │ +
    285 typedef std::map<String, std::map<String, float> > tabletype;
    │ │ │ +
    286
    │ │ │ +
    290
    │ │ │ +
    │ │ │ +
    291 enum HYPERSURFACE__TYPE{
    │ │ │ +
    292 REAL__REAL,
    │ │ │ +
    293 REAL__DISCRETE,
    │ │ │ +
    294 DISCRETE__REAL, // not used
    │ │ │ +
    295 DISCRETE__DISCRETE,
    │ │ │ +
    296 CHI__REAL, // not used
    │ │ │ +
    297 REAL__CHI,
    │ │ │ +
    298 CHI__DISCRETE,
    │ │ │ +
    299 DISCRETE__CHI,
    │ │ │ +
    300 CHI__CHI,
    │ │ │ +
    301 SINGLE__REAL,
    │ │ │ +
    302 SINGLE__DISCRETE,
    │ │ │ +
    303 SINGLE__CHI
    │ │ │ +
    304 };
    │ │ │ +
    │ │ │ +
    305
    │ │ │ +
    306 /*_ Constructors and Destructors.
    │ │ │ +
    307 */
    │ │ │ +
    308 ShiftHyperSurface_(int verbosity = EmpiricalHSShiftProcessor::VERBOSITY_LEVEL_CRITICAL);
    │ │ │ +
    309
    │ │ │ +
    310 /*_ Detailed constructor.
    │ │ │ +
    311 * Creates a ShiftHyperSurface given the <b>filename<\b> of the data file,
    │ │ │ +
    312 * the atom type, and the two property types according to its deduced
    │ │ │ +
    313 * hypersurface types (see {\tt HYPERSURFACE__TYPE()}).
    │ │ │ +
    314 *
    │ │ │ +
    315 * If the data file cannot be found, no hypersurface is created.
    │ │ │ +
    316 *
    │ │ │ +
    317 * In the special case that the two properties have the same type, we create just one table entry in
    │ │ │ +
    318 * {\tt table_} or just one spline { \tt in s1d_ }.
    │ │ │ +
    319 *
    │ │ │ +
    320 * In case of hypersurfaces of type {\tt REAL__DISCRETE} the splines default values are set to the
    │ │ │ +
    321 * row-averages if given specified in the datafile.
    │ │ │ +
    322 *
    │ │ │ +
    323 * In case of hypersurfaces of type {\tt REAL__CHI, REAL__REAL } the splines default values are
    │ │ │ +
    324 * set to the splines averages.
    │ │ │ +
    325 *
    │ │ │ +
    326 * In all cases but look-up tables the bounds for the splines are set as specified in
    │ │ │ +
    327 * the datafile if specified.
    │ │ │ +
    328 *
    │ │ │ +
    329 * Note:
    │ │ │ +
    330 * The spline or value can be accessed
    │ │ │ +
    331 * by the {\tt operator () } given __not__ the property-value, but the property name.
    │ │ │ +
    332 *
    │ │ │ +
    333 * @throws BALL::Exception::FileNotFound
    │ │ │ +
    334 */
    │ │ │ +
    335 ShiftHyperSurface_(String filename, String /* atomtype */,
    │ │ │ +
    336 String firstproperty, String secondproperty,
    │ │ │ +
    337 int verbosity = EmpiricalHSShiftProcessor::VERBOSITY_LEVEL_CRITICAL);
    │ │ │ +
    338
    │ │ │ +
    341 virtual ~ShiftHyperSurface_();
    │ │ │ +
    342
    │ │ │ +
    352 float operator () (PropertiesForShift_& properties);
    │ │ │ +
    353
    │ │ │ +
    357 bool isvalid(){return !invalid_;}
    │ │ │ +
    358
    │ │ │ +
    359 // Returns the total average given in the input file.
    │ │ │ +
    360 float getTotalAverage() {return average_;}
    │ │ │ +
    361
    │ │ │ +
    362 private:
    │ │ │ +
    363
    │ │ │ +
    364 // Computes the average of the look-up table values.
    │ │ │ +
    365 float getTableAverage_();
    │ │ │ +
    366
    │ │ │ +
    367 // Computes the row average of the look-up table given a row name.
    │ │ │ +
    368 float getTableRowAverage_(const std::map<String, float>& row);
    │ │ │ +
    369
    │ │ │ +
    370 // Computes the column average of the look-up table given a column name.
    │ │ │ +
    371 float getTableColumnAverage_(const String& name);
    │ │ │ +
    372
    │ │ │ +
    377 bool tableHasColumn_(const String& name) ;
    │ │ │ +
    378
    │ │ │ +
    398 void parseDataFile_(BALL::File& file, String filename) ;
    │ │ │ +
    399
    │ │ │ +
    400 // Method to convert a vector of strings into a vector of floats {/tt output}.
    │ │ │ +
    401 void convertToReal_(const vector<String>& input, vector<float>& output);
    │ │ │ +
    402
    │ │ │ +
    406 void setType_(String firstproperty, String secondproperty);
    │ │ │ +
    407
    │ │ │ +
    408 // The type of the hypersurface.
    │ │ │ +
    409 int type_;
    │ │ │ +
    410
    │ │ │ +
    411 // The properties of the hypersurface.
    │ │ │ +
    412 String first_property_;
    │ │ │ +
    413 String second_property_;
    │ │ │ +
    414
    │ │ │ +
    415 // The hypersurface can be a 2D spline, 1D spline or a look-up table.
    │ │ │ +
    416 CubicSpline2D s2d_;
    │ │ │ +
    417 std::map <String, CubicSpline1D > s1d_;
    │ │ │ +
    418 // Note: access of the look--up table: first the discrete key x, second the numerical key y.
    │ │ │ +
    419 std::map <String, std::map<String, float> > table_;
    │ │ │ +
    420
    │ │ │ +
    421 // The averages of the hypersurface as read from the file.
    │ │ │ +
    422 // //TODO rename to row_defaults
    │ │ │ +
    423 std::map <String, float> row_averages_;
    │ │ │ +
    424 std::map <String, float> col_averages_;
    │ │ │ +
    425
    │ │ │ +
    426 // The spacing in x and y direction as read from the file.
    │ │ │ +
    427 float row_spacing_;
    │ │ │ +
    428 float col_spacing_;
    │ │ │ +
    429
    │ │ │ +
    430 // Flag to store whether the spline we created is valid.
    │ │ │ +
    431 bool invalid_;
    │ │ │ +
    432
    │ │ │ +
    433 // The average over the complete hypersurface as read from the file.
    │ │ │ +
    434 // Note: this average maybe weighted in non-obvious ways!
    │ │ │ +
    435 float average_;
    │ │ │ +
    436
    │ │ │ +
    437 // verbosity of the method
    │ │ │ +
    438 int verbosity_;
    │ │ │ +
    439
    │ │ │ +
    440 // The underlying data of the hypersurface as read from the file.
    │ │ │ +
    441 vector<String> y_axis_values_;
    │ │ │ +
    442 vector<vector<String> > x_axis_values_;
    │ │ │ +
    443 vector<vector<float> > sample_values_;
    │ │ │ +
    444 };
    │ │ │ +
    │ │ │ +
    445
    │ │ │ +
    446
    │ │ │ +
    447
    │ │ │ +
    448
    │ │ │ +
    449 /*_ The target atoms collected by {\tt operator ()}.
    │ │ │ +
    450 */
    │ │ │ +
    451 std::vector<PropertiesForShift_> targets_;
    │ │ │ +
    452
    │ │ │ +
    453 /*_ The target atom types stored as a vector of strings collected from the ini-file
    │ │ │ +
    454 * by {\tt init ()}.
    │ │ │ +
    455 */
    │ │ │ +
    456 vector<String> target_names_;
    │ │ │ +
    457
    │ │ │ +
    458 /*_ The target properties used for determine the
    │ │ │ +
    459 * empirical hypersurface shifts. The properties are collected
    │ │ │ +
    460 * from the ini-file by {\tt init ()} and are stored per target atom
    │ │ │ +
    461 * in the same order as the target_names.
    │ │ │ +
    462 */
    │ │ │ +
    463 vector< std::set<String> > target_property_names_;
    │ │ │ +
    464
    │ │ │ +
    465 /*_ The file names of the files storing the property-data-splines for computing the
    │ │ │ +
    466 * shift contributions are stored in a map, whose key is the pair of
    │ │ │ +
    467 * properties, to which the splines belong.
    │ │ │ +
    468 * The maps are stored per target atom type in the same order as the target_names.
    │ │ │ +
    469 * The files are specified in the section {\tt EmpiricalShiftHyperSurfaces}
    │ │ │ +
    470 * of the file {\tt ShiftX.ini} and are collected by {\tt init ()}.
    │ │ │ +
    471 */
    │ │ │ +
    472 vector< std::map< std::pair<String, String>, String > > property_files_;
    │ │ │ +
    473
    │ │ │ +
    474 /*_ The property pairs for each atom type are stored in this map.
    │ │ │ +
    475 * The map is created in {\tt init ()}.
    │ │ │ +
    476 **/
    │ │ │ +
    477 std::map< String, vector< std::pair<String, String> > > property_pairs_;
    │ │ │ +
    478
    │ │ │ +
    479 /*_ The hypersurfaces are precomputed by {\tt init()}
    │ │ │ +
    480 * and then are stored per atom type in a map with key atom_type of
    │ │ │ +
    481 * maps with the property pair as key.
    │ │ │ +
    482 */
    │ │ │ +
    483
    │ │ │ +
    484 std::map<String, std::map <std::pair<String, String>,EmpiricalHSShiftProcessor::ShiftHyperSurface_> > hypersurfaces_;
    │ │ │ +
    485
    │ │ │ +
    486 /*_ Option to exclude prolins from the shift computations.
    │ │ │ +
    487 Default is false.
    │ │ │ +
    488 */
    │ │ │ +
    489 bool exclude_prolins_;
    │ │ │ +
    490
    │ │ │ +
    491 // Map containing possible correction terms for ssbonds.
    │ │ │ +
    492 std::map<String, float> ssbond_correction_;
    │ │ │ +
    493
    │ │ │ +
    494 private:
    │ │ │ +
    495
    │ │ │ +
    496 /*_ Some debugging functions printing parameter/effector/target information
    │ │ │ +
    497 * to the Log stream.
    │ │ │ +
    498 */
    │ │ │ +
    499 void printParameters_();
    │ │ │ +
    500 void printTargets_();
    │ │ │ +
    501
    │ │ │ +
    502 /*_ A function to perform some ShiftX-y postprocessing:
    │ │ │ +
    503 add for all CA-atoms 0.2 times the EF-shift-value of the bound HA-atoms.
    │ │ │ +
    504 Due to some reason ShiftX does not perform this postprocessing
    │ │ │ +
    505 for the empirical Hypersurface contributions.
    │ │ │ +
    506 */
    │ │ │ +
    507 void postprocessing_();
    │ │ │ +
    508
    │ │ │ +
    510 int verbosity_;
    │ │ │ +
    511
    │ │ │ +
    512 };// end of class
    │ │ │ +
    │ │ │ +
    513} // end of namespace
    │ │ │ +
    514#endif // BALL_NMR_EMPIRICALHSSHIFTPROCESSOR_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ + │ │ │ +
    BALL::PDB::Atom
    char Atom[5]
    Definition PDBdefs.h:257
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::EmpiricalHSShiftProcessor::ssbond_correction_
    std::map< String, float > ssbond_correction_
    Definition empiricalHSShiftProcessor.h:492
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::EmpiricalHSShiftProcessor::property_files_
    vector< std::map< std::pair< String, String >, String > > property_files_
    Definition empiricalHSShiftProcessor.h:472
    │ │ │ +
    BALL::EmpiricalHSShiftProcessor::targets_
    std::vector< PropertiesForShift_ > targets_
    Definition empiricalHSShiftProcessor.h:451
    │ │ │ +
    BALL::EmpiricalHSShiftProcessor::property_pairs_
    std::map< String, vector< std::pair< String, String > > > property_pairs_
    Definition empiricalHSShiftProcessor.h:477
    │ │ │ +
    BALL::EmpiricalHSShiftProcessor::hypersurfaces_
    std::map< String, std::map< std::pair< String, String >, EmpiricalHSShiftProcessor::ShiftHyperSurface_ > > hypersurfaces_
    Definition empiricalHSShiftProcessor.h:484
    │ │ │ +
    BALL::EmpiricalHSShiftProcessor::target_property_names_
    vector< std::set< String > > target_property_names_
    Definition empiricalHSShiftProcessor.h:463
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::EmpiricalHSShiftProcessor::PropertiesForShift_::computeProperties_
    bool computeProperties_(Atom *atom, std::set< String > properties)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::EmpiricalHSShiftProcessor::PropertiesForShift_::PropertiesForShift_
    PropertiesForShift_(int verbosity_=EmpiricalHSShiftProcessor::VERBOSITY_LEVEL_CRITICAL)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::EmpiricalHSShiftProcessor::ShiftHyperSurface_::tabletype
    std::map< String, std::map< String, float > > tabletype
    Definition empiricalHSShiftProcessor.h:285
    │ │ │ + │ │ │ +
    BALL::EmpiricalHSShiftProcessor::ShiftHyperSurface_::ShiftHyperSurface_
    ShiftHyperSurface_(String filename, String, String firstproperty, String secondproperty, int verbosity=EmpiricalHSShiftProcessor::VERBOSITY_LEVEL_CRITICAL)
    │ │ │ + │ │ │ +
    BALL::EmpiricalHSShiftProcessor::ShiftHyperSurface_::ShiftHyperSurface_
    ShiftHyperSurface_(int verbosity=EmpiricalHSShiftProcessor::VERBOSITY_LEVEL_CRITICAL)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,284 +1,549 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _D_A_T_A_T_Y_P_E │ │ │ │ -list.h │ │ │ │ + * _N_M_R │ │ │ │ +empiricalHSShiftProcessor.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ -2// vi: set ts=2: │ │ │ │ -3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_DATATYPE_LIST_H │ │ │ │ -6#define BALL_DATATYPE_LIST_H │ │ │ │ +1#ifndef BALL_NMR_EMPIRICALHSSHIFTPROCESSOR_H │ │ │ │ +2#define BALL_NMR_EMPIRICALHSSHIFTPROCESSOR_H │ │ │ │ +3 │ │ │ │ +4#ifndef BALL_MATHS_CUBICSPLINE2D_H │ │ │ │ +5# include <_B_A_L_L_/_M_A_T_H_S_/_c_u_b_i_c_S_p_l_i_n_e_2_D_._h> │ │ │ │ +6#endif │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_COMMON_H │ │ │ │ -9# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +8#ifndef BALL_MATHS_CUBICSPLINE1D_H │ │ │ │ +9# include <_B_A_L_L_/_M_A_T_H_S_/_c_u_b_i_c_S_p_l_i_n_e_1_D_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_CONCEPT_VISITOR_H │ │ │ │ -13# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_v_i_s_i_t_o_r_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16#ifndef BALL_CONCEPT_PROCESSOR_H │ │ │ │ -17# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20#include │ │ │ │ -21 │ │ │ │ -22#ifdef BALL_COMPILER_GXX || BALL_COMPILER_LLVM │ │ │ │ -23#warning "This header file is deprecated and should not be used in new code! │ │ │ │ -As a replacement for BALL::List the use of std::list is strongly suggested." │ │ │ │ -24#endif │ │ │ │ -25 │ │ │ │ -26namespace _B_A_L_L │ │ │ │ -27{ │ │ │ │ -33 template │ │ │ │ -_3_4 class _L_i_s_t │ │ │ │ -35 : public std::list │ │ │ │ -36 { │ │ │ │ -37 public: │ │ │ │ -38 │ │ │ │ -42 │ │ │ │ -_4_5 typedef typename std::list::iterator _I_t_e_r_a_t_o_r; │ │ │ │ -46 // for STL compatibility │ │ │ │ -_4_7 typedef typename std::list::iterator _i_t_e_r_a_t_o_r; │ │ │ │ -48 │ │ │ │ -_5_1 typedef typename std::list::const_iterator _C_o_n_s_t_I_t_e_r_a_t_o_r; │ │ │ │ -52 // for STL compatibility │ │ │ │ -_5_3 typedef typename std::list::const_iterator _c_o_n_s_t___i_t_e_r_a_t_o_r; │ │ │ │ -54 │ │ │ │ -56 │ │ │ │ -58 │ │ │ │ -59 _B_A_L_L___C_R_E_A_T_E___D_E_E_P(_L_i_s_t) │ │ │ │ -60 │ │ │ │ +12 │ │ │ │ +13#ifndef BALL_FORMAT_GENERICMOLFILE_H │ │ │ │ +14# include <_B_A_L_L_/_F_O_R_M_A_T_/_g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h> │ │ │ │ +15#endif │ │ │ │ +16 │ │ │ │ +17#ifndef BALL_NMR_SHIFT_MODULE_H │ │ │ │ +18# include<_B_A_L_L_/_N_M_R_/_s_h_i_f_t_M_o_d_u_l_e_._h> │ │ │ │ +19#endif │ │ │ │ +20 │ │ │ │ +21#ifndef BALL_KERNEL_EXPRESSION_H │ │ │ │ +22# include<_B_A_L_L_/_K_E_R_N_E_L_/_e_x_p_r_e_s_s_i_o_n_._h> │ │ │ │ +23#endif │ │ │ │ +24 │ │ │ │ +25#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ +26# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +27#endif │ │ │ │ +28 │ │ │ │ +29 │ │ │ │ +30#include │ │ │ │ +31#include │ │ │ │ +32 │ │ │ │ +33namespace _B_A_L_L │ │ │ │ +34{ │ │ │ │ +35 class _A_t_o_m; │ │ │ │ +36 │ │ │ │ +_4_0 class _B_A_L_L___E_X_P_O_R_T _E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r │ │ │ │ +41 : public _S_h_i_f_t_M_o_d_u_l_e │ │ │ │ +42 { │ │ │ │ +43 public: │ │ │ │ +44 │ │ │ │ +45 _B_A_L_L___C_R_E_A_T_E(_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r) │ │ │ │ +46 │ │ │ │ +_4_7 static const int VERBOSITY_LEVEL_CRITICAL; │ │ │ │ +_4_8 static const int VERBOSITY_LEVEL_DEBUG; │ │ │ │ +49 │ │ │ │ +_5_4 struct _B_A_L_L___E_X_P_O_R_T _O_p_t_i_o_n │ │ │ │ +55 { │ │ │ │ +_5_8 static const char* _V_E_R_B_O_S_I_T_Y; │ │ │ │ +59 │ │ │ │ +60 }; │ │ │ │ 61 │ │ │ │ -_6_4 _L_i_s_t() │ │ │ │ -65 : _s_t_d::list() │ │ │ │ -66 { │ │ │ │ -67 } │ │ │ │ -68 │ │ │ │ -_7_4 _L_i_s_t(const _L_i_s_t& new_list, bool /* deep = true */) │ │ │ │ -75 : _s_t_d::list(new_list) │ │ │ │ -76 { │ │ │ │ -77 } │ │ │ │ -78 │ │ │ │ -_8_1 void _d_e_s_t_r_o_y() │ │ │ │ -82 { │ │ │ │ -83 std::list::clear(); │ │ │ │ -84 } │ │ │ │ -85 │ │ │ │ -_8_8 virtual _~_L_i_s_t() │ │ │ │ -89 { │ │ │ │ -90 std::list::clear(); │ │ │ │ -91 } │ │ │ │ +_6_3 struct _B_A_L_L___E_X_P_O_R_T _D_e_f_a_u_l_t │ │ │ │ +64 { │ │ │ │ +_6_5 static const int _V_E_R_B_O_S_I_T_Y; │ │ │ │ +66 }; │ │ │ │ +67 │ │ │ │ +69 │ │ │ │ +70 │ │ │ │ +74 │ │ │ │ +_7_8 static const char* _P_R_O_P_E_R_T_Y_____E_H_S___S_H_I_F_T; │ │ │ │ +79 │ │ │ │ +81 │ │ │ │ +84 │ │ │ │ +_8_7 _E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r(); │ │ │ │ +88 │ │ │ │ +_9_1 virtual _~_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r(); │ │ │ │ 92 │ │ │ │ 94 │ │ │ │ -96 │ │ │ │ -_1_0_1 void _s_e_t(const _L_i_s_t& list, bool /* deep */ = true) │ │ │ │ -102 { │ │ │ │ -103 std::list::clear(); │ │ │ │ -104 │ │ │ │ -105 _C_o_n_s_t_I_t_e_r_a_t_o_r it = list.begin(); │ │ │ │ -106 for ( ; it != list.end(); ++it) │ │ │ │ -107 { │ │ │ │ -108 std::list::push_back(const_cast(*it)); │ │ │ │ -109 } │ │ │ │ -110 } │ │ │ │ -111 │ │ │ │ -_1_1_4 const _L_i_s_t& _o_p_e_r_a_t_o_r_ _=_ (const _L_i_s_t& list) │ │ │ │ -115 { │ │ │ │ -116 _s_e_t(list); │ │ │ │ -117 return *this; │ │ │ │ -118 } │ │ │ │ -119 │ │ │ │ -_1_2_1 void _g_e_t(_L_i_s_t& list, bool deep = true) const │ │ │ │ -122 { │ │ │ │ -123 list._s_e_t(*this, deep); │ │ │ │ -124 } │ │ │ │ -125 │ │ │ │ -_1_2_7 void _s_w_a_p(_L_i_s_t& list) │ │ │ │ -128 { │ │ │ │ -129 _L_i_s_t_<_V_a_l_u_e_> temp; │ │ │ │ -130 temp._s_e_t(*this); │ │ │ │ -131 (*this).set(list); │ │ │ │ -132 list._s_e_t(temp); │ │ │ │ -133 } │ │ │ │ -134 │ │ │ │ +97 │ │ │ │ +_1_3_0 virtual void _i_n_i_t(); │ │ │ │ +131 │ │ │ │ +133 │ │ │ │ 136 │ │ │ │ -138 │ │ │ │ -_1_4_1 _S_i_z_e _g_e_t_S_i_z_e() const │ │ │ │ -142 { │ │ │ │ -143 return (_S_i_z_e)std::list::size(); │ │ │ │ -144 } │ │ │ │ -145 │ │ │ │ -_1_5_0 bool _r_e_m_o_v_e(const Value& item) │ │ │ │ -151 { │ │ │ │ -152 _I_t_e_r_a_t_o_r it = std::list::begin(); │ │ │ │ -153 for (; it != std::list::end(); ++it) │ │ │ │ -154 { │ │ │ │ -155 if (*it == item) │ │ │ │ -156 { │ │ │ │ -157 std::list::erase(it); │ │ │ │ -158 return true; │ │ │ │ -159 } │ │ │ │ -160 } │ │ │ │ -161 return false; │ │ │ │ -162 } │ │ │ │ -163 │ │ │ │ -165 │ │ │ │ -167 │ │ │ │ -_1_7_1 bool _i_s_E_m_p_t_y() const │ │ │ │ -172 { │ │ │ │ -173 return (std::list::size() == 0); │ │ │ │ -174 } │ │ │ │ -175 │ │ │ │ +_1_4_2 virtual bool _s_t_a_r_t(); │ │ │ │ +143 │ │ │ │ +144 │ │ │ │ +_1_5_7 virtual _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t operator () (_C_o_m_p_o_s_i_t_e& composite); │ │ │ │ +158 │ │ │ │ +_1_7_6 virtual bool _f_i_n_i_s_h(); │ │ │ │ 177 │ │ │ │ 179 │ │ │ │ -184 virtual void _h_o_s_t(_V_i_s_i_t_o_r<_L_i_s_t_<_V_a_l_u_e_> >& visitor); │ │ │ │ -185 │ │ │ │ -187 │ │ │ │ +_1_8_3 _O_p_t_i_o_n_s _o_p_t_i_o_n_s; │ │ │ │ +184 │ │ │ │ +_1_8_7 void _s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s(); │ │ │ │ 189 │ │ │ │ -_1_9_4 bool _a_p_p_l_y(_U_n_a_r_y_P_r_o_c_e_s_s_o_r_<_V_a_l_u_e_>& processor) │ │ │ │ -195 { │ │ │ │ -196 if (!processor._s_t_a_r_t()) return false; │ │ │ │ -197 │ │ │ │ -198 for (_I_t_e_r_a_t_o_r it = std::list::begin(); it != std::list::end │ │ │ │ -(); ++it) │ │ │ │ -199 { │ │ │ │ -200 _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t result = processor(*it); │ │ │ │ -201 if (result <= _P_r_o_c_e_s_s_o_r_:_:_B_R_E_A_K) │ │ │ │ -202 { │ │ │ │ -203 return (result == _P_r_o_c_e_s_s_o_r_:_:_B_R_E_A_K); │ │ │ │ -204 } │ │ │ │ -205 } │ │ │ │ +190 protected: │ │ │ │ +191 │ │ │ │ +192 │ │ │ │ +193 /*_ Neested class providing atom properties for the shift computations │ │ │ │ +194 * */ │ │ │ │ +_1_9_5 class _B_A_L_L___E_X_P_O_R_T _P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t__ │ │ │ │ +196 { │ │ │ │ +197 public: │ │ │ │ +198 │ │ │ │ +_2_0_1 _P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t__(int verbosity_ = EmpiricalHSShiftProcessor:: │ │ │ │ +VERBOSITY_LEVEL_CRITICAL); │ │ │ │ +202 │ │ │ │ +_2_0_5 _A_t_o_m* _c_u_r_r_e_n_t___a_t_o_m; │ │ │ │ 206 │ │ │ │ -207 return processor._f_i_n_i_s_h(); │ │ │ │ -208 } │ │ │ │ -209 │ │ │ │ -211 │ │ │ │ -_2_1_5 bool _o_p_e_r_a_t_o_r_ _=_=_ (const _L_i_s_t_<_V_a_l_u_e_>& list) const │ │ │ │ -216 { │ │ │ │ -217 if (std::list::size() != list.size()) │ │ │ │ -218 { │ │ │ │ -219 return false; │ │ │ │ -220 } │ │ │ │ -221 │ │ │ │ -222 typename _L_i_s_t_<_V_a_l_u_e_>_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r this_it = std::list::begin(); │ │ │ │ -223 typename _L_i_s_t_<_V_a_l_u_e_>_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r list_it = list.begin(); │ │ │ │ +_2_2_3 bool _c_o_m_p_u_t_e_P_r_o_p_e_r_t_i_e_s__(_A_t_o_m* atom, std::set properties); │ │ │ │ 224 │ │ │ │ -225 for (; this_it != std::list::end(); ++this_it) │ │ │ │ -226 { │ │ │ │ -227 if (!(*this_it == *list_it)) │ │ │ │ -228 { │ │ │ │ -229 return false; │ │ │ │ -230 } │ │ │ │ -231 ++list_it; │ │ │ │ -232 } │ │ │ │ -233 return true; │ │ │ │ -234 } │ │ │ │ -235 │ │ │ │ -_2_3_9 bool _o_p_e_r_a_t_o_r_ _!_=_ (const _L_i_s_t_<_V_a_l_u_e_>& list) const │ │ │ │ -240 { │ │ │ │ -241 return !(*this == list); │ │ │ │ -242 } │ │ │ │ +_2_3_6 std::pair operator [] (const _S_t_r_i_n_g& property_name); │ │ │ │ +237 │ │ │ │ +_2_4_2 static bool _i_s_D_i_s_c_r_e_t_e(_S_t_r_i_n_g property); │ │ │ │ 243 │ │ │ │ -244 }; │ │ │ │ -245 │ │ │ │ -246 template │ │ │ │ -_2_4_7 void _L_i_s_t_<_V_a_l_u_e_>_:_:_h_o_s_t(_V_i_s_i_t_o_r<_L_i_s_t_<_V_a_l_u_e_> >& visitor) │ │ │ │ -248 { │ │ │ │ -249 visitor.visit(*this); │ │ │ │ -250 } │ │ │ │ -251} // namespace BALL │ │ │ │ -252 │ │ │ │ -253#endif // BALL_DATATYPE_LIST_H │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_v_i_s_i_t_o_r_._h │ │ │ │ -_p_r_o_c_e_s_s_o_r_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E___D_E_E_P │ │ │ │ -#define BALL_CREATE_DEEP(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_2_6 │ │ │ │ -_s_t_d │ │ │ │ -STL namespace. │ │ │ │ +_2_4_7 static bool _i_s_M_i_x_e_d(_S_t_r_i_n_g property); │ │ │ │ +248 │ │ │ │ +249 protected: │ │ │ │ +250 │ │ │ │ +251 // Storing the atoms properties │ │ │ │ +252 // ...as numerical value │ │ │ │ +_2_5_3 std::map _p_r_o_p_e_r_t_i_e_s___r_e_a_l__; │ │ │ │ +254 // ... as alphanumerical/discrete value │ │ │ │ +_2_5_5 std::map _p_r_o_p_e_r_t_i_e_s___s_t_r_i_n_g__; │ │ │ │ +256 │ │ │ │ +257 protected: │ │ │ │ +258 │ │ │ │ +_2_5_9 float _g_e_t_C_h_i_A_n_g_l_e__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_0 float _g_e_t_C_h_i_2_A_n_g_l_e__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_1 char _g_e_t_A_m_i_n_o_A_c_i_d__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_2 char _g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_3 float _g_e_t_H_A___H_B_o_n_d_L_e_n__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_4 float _g_e_t_H_A_2___H_B_o_n_d_L_e_n__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_5 float _g_e_t_H_N___H_B_o_n_d_L_e_n__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_6 float _g_e_t_O___H_B_o_n_d_L_e_n__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_7 bool _h_a_s_D_i_s_u_l_f_i_d_B_o_n_d__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_8 bool _h_a_s_H_A___H_B_o_n_d__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_6_9 bool _h_a_s_H_A_2___H_B_o_n_d__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_7_0 bool _h_a_s_H_N___H_B_o_n_d__(_R_e_s_i_d_u_e* residue); │ │ │ │ +_2_7_1 bool _h_a_s_O___H_B_o_n_d__(_R_e_s_i_d_u_e* residue); │ │ │ │ +272 │ │ │ │ +273 private: │ │ │ │ +274 // verbosity of the classes methods │ │ │ │ +275 int verbosity_; │ │ │ │ +276 }; // end of nested class │ │ │ │ +277 │ │ │ │ +278 │ │ │ │ +279 /*_ Neested class handling the empirical hypersurfaces. │ │ │ │ +280 **/ │ │ │ │ +281 │ │ │ │ +_2_8_2 class _S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__ │ │ │ │ +283 { │ │ │ │ +284 public: │ │ │ │ +_2_8_5 typedef std::map > _t_a_b_l_e_t_y_p_e; │ │ │ │ +286 │ │ │ │ +290 │ │ │ │ +_2_9_1 enum _H_Y_P_E_R_S_U_R_F_A_C_E_____T_Y_P_E{ │ │ │ │ +_2_9_2 _R_E_A_L_____R_E_A_L, │ │ │ │ +_2_9_3 _R_E_A_L_____D_I_S_C_R_E_T_E, │ │ │ │ +_2_9_4 _D_I_S_C_R_E_T_E_____R_E_A_L, // not used │ │ │ │ +_2_9_5 _D_I_S_C_R_E_T_E_____D_I_S_C_R_E_T_E, │ │ │ │ +_2_9_6 _C_H_I_____R_E_A_L, // not used │ │ │ │ +_2_9_7 _R_E_A_L_____C_H_I, │ │ │ │ +_2_9_8 _C_H_I_____D_I_S_C_R_E_T_E, │ │ │ │ +_2_9_9 _D_I_S_C_R_E_T_E_____C_H_I, │ │ │ │ +_3_0_0 _C_H_I_____C_H_I, │ │ │ │ +_3_0_1 _S_I_N_G_L_E_____R_E_A_L, │ │ │ │ +_3_0_2 _S_I_N_G_L_E_____D_I_S_C_R_E_T_E, │ │ │ │ +303 SINGLE__CHI │ │ │ │ +_3_0_4 }; │ │ │ │ +305 │ │ │ │ +306 /*_ Constructors and Destructors. │ │ │ │ +307 */ │ │ │ │ +_3_0_8 _S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__(int verbosity = EmpiricalHSShiftProcessor:: │ │ │ │ +VERBOSITY_LEVEL_CRITICAL); │ │ │ │ +309 │ │ │ │ +310 /*_ Detailed constructor. │ │ │ │ +311 * Creates a ShiftHyperSurface given the filename<\b> of the data file, │ │ │ │ +312 * the atom type, and the two property types according to its deduced │ │ │ │ +313 * hypersurface types (see {\tt HYPERSURFACE__TYPE()}). │ │ │ │ +314 * │ │ │ │ +315 * If the data file cannot be found, no hypersurface is created. │ │ │ │ +316 * │ │ │ │ +317 * In the special case that the two properties have the same type, we create │ │ │ │ +just one table entry in │ │ │ │ +318 * {\tt table_} or just one spline { \tt in s1d_ }. │ │ │ │ +319 * │ │ │ │ +320 * In case of hypersurfaces of type {\tt REAL__DISCRETE} the splines default │ │ │ │ +values are set to the │ │ │ │ +321 * row-averages if given specified in the datafile. │ │ │ │ +322 * │ │ │ │ +323 * In case of hypersurfaces of type {\tt REAL__CHI, REAL__REAL } the splines │ │ │ │ +default values are │ │ │ │ +324 * set to the splines averages. │ │ │ │ +325 * │ │ │ │ +326 * In all cases but look-up tables the bounds for the splines are set as │ │ │ │ +specified in │ │ │ │ +327 * the datafile if specified. │ │ │ │ +328 * │ │ │ │ +329 * Note: │ │ │ │ +330 * The spline or value can be accessed │ │ │ │ +331 * by the {\tt operator () } given __not__ the property-value, but the │ │ │ │ +property name. │ │ │ │ +332 * │ │ │ │ +333 * @throws BALL::Exception::FileNotFound │ │ │ │ +334 */ │ │ │ │ +_3_3_5 _S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__(_S_t_r_i_n_g filename, _S_t_r_i_n_g /* atomtype */, │ │ │ │ +336 _S_t_r_i_n_g firstproperty, _S_t_r_i_n_g secondproperty, │ │ │ │ +337 int verbosity = EmpiricalHSShiftProcessor::VERBOSITY_LEVEL_CRITICAL); │ │ │ │ +338 │ │ │ │ +_3_4_1 virtual _~_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__(); │ │ │ │ +342 │ │ │ │ +_3_5_2 float operator () (_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t__& properties); │ │ │ │ +353 │ │ │ │ +_3_5_7 bool _i_s_v_a_l_i_d(){return !invalid_;} │ │ │ │ +358 │ │ │ │ +359 // Returns the total average given in the input file. │ │ │ │ +_3_6_0 float _g_e_t_T_o_t_a_l_A_v_e_r_a_g_e() {return average_;} │ │ │ │ +361 │ │ │ │ +362 private: │ │ │ │ +363 │ │ │ │ +364 // Computes the average of the look-up table values. │ │ │ │ +365 float getTableAverage_(); │ │ │ │ +366 │ │ │ │ +367 // Computes the row average of the look-up table given a row name. │ │ │ │ +368 float getTableRowAverage_(const std::map& row); │ │ │ │ +369 │ │ │ │ +370 // Computes the column average of the look-up table given a column name. │ │ │ │ +371 float getTableColumnAverage_(const _S_t_r_i_n_g& name); │ │ │ │ +372 │ │ │ │ +377 bool tableHasColumn_(const _S_t_r_i_n_g& name) ; │ │ │ │ +378 │ │ │ │ +398 void parseDataFile_(_B_A_L_L_:_:_F_i_l_e& file, _S_t_r_i_n_g filename) ; │ │ │ │ +399 │ │ │ │ +400 // Method to convert a vector of strings into a vector of floats {/tt │ │ │ │ +output}. │ │ │ │ +401 void convertToReal_(const vector& input, vector& output); │ │ │ │ +402 │ │ │ │ +406 void setType_(_S_t_r_i_n_g firstproperty, _S_t_r_i_n_g secondproperty); │ │ │ │ +407 │ │ │ │ +408 // The type of the hypersurface. │ │ │ │ +409 int type_; │ │ │ │ +410 │ │ │ │ +411 // The properties of the hypersurface. │ │ │ │ +412 _S_t_r_i_n_g first_property_; │ │ │ │ +413 _S_t_r_i_n_g second_property_; │ │ │ │ +414 │ │ │ │ +415 // The hypersurface can be a 2D spline, 1D spline or a look-up table. │ │ │ │ +416 _C_u_b_i_c_S_p_l_i_n_e_2_D s2d_; │ │ │ │ +417 std::map s1d_; │ │ │ │ +418 // Note: access of the look--up table: first the discrete key x, second the │ │ │ │ +numerical key y. │ │ │ │ +419 std::map > table_; │ │ │ │ +420 │ │ │ │ +421 // The averages of the hypersurface as read from the file. │ │ │ │ +422 // //TODO rename to row_defaults │ │ │ │ +423 std::map row_averages_; │ │ │ │ +424 std::map col_averages_; │ │ │ │ +425 │ │ │ │ +426 // The spacing in x and y direction as read from the file. │ │ │ │ +427 float row_spacing_; │ │ │ │ +428 float col_spacing_; │ │ │ │ +429 │ │ │ │ +430 // Flag to store whether the spline we created is valid. │ │ │ │ +431 bool invalid_; │ │ │ │ +432 │ │ │ │ +433 // The average over the complete hypersurface as read from the file. │ │ │ │ +434 // Note: this average maybe weighted in non-obvious ways! │ │ │ │ +435 float average_; │ │ │ │ +436 │ │ │ │ +437 // verbosity of the method │ │ │ │ +438 int verbosity_; │ │ │ │ +439 │ │ │ │ +440 // The underlying data of the hypersurface as read from the file. │ │ │ │ +441 vector y_axis_values_; │ │ │ │ +442 vector > x_axis_values_; │ │ │ │ +443 vector > sample_values_; │ │ │ │ +444 }; │ │ │ │ +445 │ │ │ │ +446 │ │ │ │ +447 │ │ │ │ +448 │ │ │ │ +449 /*_ The target atoms collected by {\tt operator ()}. │ │ │ │ +450 */ │ │ │ │ +_4_5_1 std::vector _t_a_r_g_e_t_s__; │ │ │ │ +452 │ │ │ │ +453 /*_ The target atom types stored as a vector of strings collected from the │ │ │ │ +ini-file │ │ │ │ +454 * by {\tt init ()}. │ │ │ │ +455 */ │ │ │ │ +_4_5_6 vector _t_a_r_g_e_t___n_a_m_e_s__; │ │ │ │ +457 │ │ │ │ +458 /*_ The target properties used for determine the │ │ │ │ +459 * empirical hypersurface shifts. The properties are collected │ │ │ │ +460 * from the ini-file by {\tt init ()} and are stored per target atom │ │ │ │ +461 * in the same order as the target_names. │ │ │ │ +462 */ │ │ │ │ +_4_6_3 vector< std::set > _t_a_r_g_e_t___p_r_o_p_e_r_t_y___n_a_m_e_s__; │ │ │ │ +464 │ │ │ │ +465 /*_ The file names of the files storing the property-data-splines for │ │ │ │ +computing the │ │ │ │ +466 * shift contributions are stored in a map, whose key is the pair of │ │ │ │ +467 * properties, to which the splines belong. │ │ │ │ +468 * The maps are stored per target atom type in the same order as the │ │ │ │ +target_names. │ │ │ │ +469 * The files are specified in the section {\tt EmpiricalShiftHyperSurfaces} │ │ │ │ +470 * of the file {\tt ShiftX.ini} and are collected by {\tt init ()}. │ │ │ │ +471 */ │ │ │ │ +_4_7_2 vector< std::map< std::pair, _S_t_r_i_n_g > > _p_r_o_p_e_r_t_y___f_i_l_e_s__; │ │ │ │ +473 │ │ │ │ +474 /*_ The property pairs for each atom type are stored in this map. │ │ │ │ +475 * The map is created in {\tt init ()}. │ │ │ │ +476 **/ │ │ │ │ +_4_7_7 std::map< String, vector< std::pair > > _p_r_o_p_e_r_t_y___p_a_i_r_s__; │ │ │ │ +478 │ │ │ │ +479 /*_ The hypersurfaces are precomputed by {\tt init()} │ │ │ │ +480 * and then are stored per atom type in a map with key atom_type of │ │ │ │ +481 * maps with the property pair as key. │ │ │ │ +482 */ │ │ │ │ +483 │ │ │ │ +_4_8_4 std::map,_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__> > _h_y_p_e_r_s_u_r_f_a_c_e_s__; │ │ │ │ +485 │ │ │ │ +486 /*_ Option to exclude prolins from the shift computations. │ │ │ │ +487 Default is false. │ │ │ │ +488 */ │ │ │ │ +_4_8_9 bool _e_x_c_l_u_d_e___p_r_o_l_i_n_s__; │ │ │ │ +490 │ │ │ │ +491 // Map containing possible correction terms for ssbonds. │ │ │ │ +_4_9_2 std::map _s_s_b_o_n_d___c_o_r_r_e_c_t_i_o_n__; │ │ │ │ +493 │ │ │ │ +494 private: │ │ │ │ +495 │ │ │ │ +496 /*_ Some debugging functions printing parameter/effector/target information │ │ │ │ +497 * to the Log stream. │ │ │ │ +498 */ │ │ │ │ +499 void printParameters_(); │ │ │ │ +500 void printTargets_(); │ │ │ │ +501 │ │ │ │ +502 /*_ A function to perform some ShiftX-y postprocessing: │ │ │ │ +503 add for all CA-atoms 0.2 times the EF-shift-value of the bound HA-atoms. │ │ │ │ +504 Due to some reason ShiftX does not perform this postprocessing │ │ │ │ +505 for the empirical Hypersurface contributions. │ │ │ │ +506 */ │ │ │ │ +507 void postprocessing_(); │ │ │ │ +508 │ │ │ │ +510 int verbosity_; │ │ │ │ +511 │ │ │ │ +512 };// end of class │ │ │ │ +513} // end of namespace │ │ │ │ +514#endif // BALL_NMR_EMPIRICALHSSHIFTPROCESSOR_H │ │ │ │ +_e_x_p_r_e_s_s_i_o_n_._h │ │ │ │ +_g_e_n_e_r_i_c_M_o_l_F_i_l_e_._h │ │ │ │ +_c_u_b_i_c_S_p_l_i_n_e_1_D_._h │ │ │ │ +_c_u_b_i_c_S_p_l_i_n_e_2_D_._h │ │ │ │ +_s_h_i_f_t_M_o_d_u_l_e_._h │ │ │ │ +_o_p_t_i_o_n_s_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r_:_:_B_R_E_A_K │ │ │ │ -@ BREAK │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_4_7 │ │ │ │ +_B_A_L_L_:_:_P_D_B_:_:_A_t_o_m │ │ │ │ +char Atom[5] │ │ │ │ +DDeeffiinniittiioonn _P_D_B_d_e_f_s_._h_:_2_5_7 │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ _B_A_L_L_:_:_P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t │ │ │ │ int Result │ │ │ │ DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_6_0 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_s_t_a_r_t │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ +_B_A_L_L_:_:_R_e_s_i_d_u_e │ │ │ │ +DDeeffiinniittiioonn _r_e_s_i_d_u_e_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_C_u_b_i_c_S_p_l_i_n_e_2_D │ │ │ │ +DDeeffiinniittiioonn _c_u_b_i_c_S_p_l_i_n_e_2_D_._h_:_1_8 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_4_2 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_s_s_b_o_n_d___c_o_r_r_e_c_t_i_o_n__ │ │ │ │ +std::map< String, float > ssbond_correction_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_4_9_2 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_o_p_t_i_o_n_s │ │ │ │ +Options options │ │ │ │ +options │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_1_8_3 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_s_t_a_r_t │ │ │ │ virtual bool start() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_9_2 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r_:_:_f_i_n_i_s_h │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_t_a_r_g_e_t___n_a_m_e_s__ │ │ │ │ +vector< String > target_names_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_4_5_6 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_R_O_P_E_R_T_Y_____E_H_S___S_H_I_F_T │ │ │ │ +static const char * PROPERTY__EHS_SHIFT │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_7_8 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_e_x_c_l_u_d_e___p_r_o_l_i_n_s__ │ │ │ │ +bool exclude_prolins_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_4_8_9 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s │ │ │ │ +void setDefaultOptions() │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_i_n_i_t │ │ │ │ +virtual void init() │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_f_i_n_i_s_h │ │ │ │ virtual bool finish() │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_V_i_s_i_t_o_r │ │ │ │ -DDeeffiinniittiioonn _v_i_s_i_t_o_r_._h_:_2_3 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ -const List & operator=(const List &list) │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_1_1_4 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_o_p_e_r_a_t_o_r_!_= │ │ │ │ -bool operator!=(const List< Value > &list) const │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_2_3_9 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_a_p_p_l_y │ │ │ │ -bool apply(UnaryProcessor< Value > &processor) │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_1_9_4 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_d_e_s_t_r_o_y │ │ │ │ -void destroy() │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_8_1 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_o_p_e_r_a_t_o_r_=_= │ │ │ │ -bool operator==(const List< Value > &list) const │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_2_1_5 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_I_t_e_r_a_t_o_r │ │ │ │ -std::list< Value >::iterator Iterator │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_4_5 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_s_w_a_p │ │ │ │ -void swap(List &list) │ │ │ │ -Swaps the contents of two lists. │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_1_2_7 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_s_e_t │ │ │ │ -void set(const List &list, bool=true) │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_1_0_1 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ -std::list< Value >::const_iterator ConstIterator │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_5_1 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_c_o_n_s_t___i_t_e_r_a_t_o_r │ │ │ │ -std::list< Value >::const_iterator const_iterator │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_g_e_t │ │ │ │ -void get(List &list, bool deep=true) const │ │ │ │ -Assign the content of a list to another. │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_1_2_1 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_h_o_s_t │ │ │ │ -virtual void host(Visitor< List< Value > > &visitor) │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_2_4_7 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_r_e_m_o_v_e │ │ │ │ -bool remove(const Value &item) │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_1_5_0 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_g_e_t_S_i_z_e │ │ │ │ -Size getSize() const │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_1_4_1 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_i_s_E_m_p_t_y │ │ │ │ -bool isEmpty() const │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_1_7_1 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_~_L_i_s_t │ │ │ │ -virtual ~List() │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_8_8 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_L_i_s_t │ │ │ │ -List(const List &new_list, bool) │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_L_i_s_t_:_:_i_t_e_r_a_t_o_r │ │ │ │ -std::list< Value >::iterator iterator │ │ │ │ -DDeeffiinniittiioonn _l_i_s_t_._h_:_4_7 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_~_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r │ │ │ │ +virtual ~EmpiricalHSShiftProcessor() │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_p_r_o_p_e_r_t_y___f_i_l_e_s__ │ │ │ │ +vector< std::map< std::pair< String, String >, String > > property_files_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_4_7_2 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_t_a_r_g_e_t_s__ │ │ │ │ +std::vector< PropertiesForShift_ > targets_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_4_5_1 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_p_r_o_p_e_r_t_y___p_a_i_r_s__ │ │ │ │ +std::map< String, vector< std::pair< String, String > > > property_pairs_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_4_7_7 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_h_y_p_e_r_s_u_r_f_a_c_e_s__ │ │ │ │ +std::map< String, std::map< std::pair< String, String >, │ │ │ │ +EmpiricalHSShiftProcessor::ShiftHyperSurface_ > > hypersurfaces_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_4_8_4 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_t_a_r_g_e_t___p_r_o_p_e_r_t_y___n_a_m_e_s__ │ │ │ │ +vector< std::set< String > > target_property_names_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_4_6_3 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r │ │ │ │ +EmpiricalHSShiftProcessor() │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ +Option names. │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_5_5 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_V_E_R_B_O_S_I_T_Y │ │ │ │ +static const char * VERBOSITY │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_5_8 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ +Default values for options. │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_6_4 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_V_E_R_B_O_S_I_T_Y │ │ │ │ +static const int VERBOSITY │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_6_5 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t__ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_1_9_6 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_h_a_s_H_A___H_B_o_n_d__ │ │ │ │ +bool hasHA_HBond_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_h_a_s_D_i_s_u_l_f_i_d_B_o_n_d__ │ │ │ │ +bool hasDisulfidBond_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_g_e_t_S_e_c_o_n_d_a_r_y_S_t_r_u_c_t_u_r_e__ │ │ │ │ +char getSecondaryStructure_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_g_e_t_C_h_i_2_A_n_g_l_e__ │ │ │ │ +float getChi2Angle_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_c_u_r_r_e_n_t___a_t_o_m │ │ │ │ +Atom * current_atom │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_0_5 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_g_e_t_O___H_B_o_n_d_L_e_n__ │ │ │ │ +float getO_HBondLen_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_g_e_t_A_m_i_n_o_A_c_i_d__ │ │ │ │ +char getAminoAcid_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_h_a_s_H_A_2___H_B_o_n_d__ │ │ │ │ +bool hasHA2_HBond_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_i_s_M_i_x_e_d │ │ │ │ +static bool isMixed(String property) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_g_e_t_H_A_2___H_B_o_n_d_L_e_n__ │ │ │ │ +float getHA2_HBondLen_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_c_o_m_p_u_t_e_P_r_o_p_e_r_t_i_e_s__ │ │ │ │ +bool computeProperties_(Atom *atom, std::set< String > properties) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_h_a_s_H_N___H_B_o_n_d__ │ │ │ │ +bool hasHN_HBond_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_i_s_D_i_s_c_r_e_t_e │ │ │ │ +static bool isDiscrete(String property) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_h_a_s_O___H_B_o_n_d__ │ │ │ │ +bool hasO_HBond_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t__ │ │ │ │ +PropertiesForShift_(int verbosity_=EmpiricalHSShiftProcessor:: │ │ │ │ +VERBOSITY_LEVEL_CRITICAL) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_g_e_t_H_N___H_B_o_n_d_L_e_n__ │ │ │ │ +float getHN_HBondLen_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_p_r_o_p_e_r_t_i_e_s___r_e_a_l__ │ │ │ │ +std::map< String, float > properties_real_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_5_3 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_p_r_o_p_e_r_t_i_e_s___s_t_r_i_n_g__ │ │ │ │ +std::map< String, String > properties_string_ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_5_5 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_g_e_t_H_A___H_B_o_n_d_L_e_n__ │ │ │ │ +float getHA_HBondLen_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_P_r_o_p_e_r_t_i_e_s_F_o_r_S_h_i_f_t___:_:_g_e_t_C_h_i_A_n_g_l_e__ │ │ │ │ +float getChiAngle_(Residue *residue) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__ │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_8_3 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_i_s_v_a_l_i_d │ │ │ │ +bool isvalid() │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_3_5_7 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_t_a_b_l_e_t_y_p_e │ │ │ │ +std::map< String, std::map< String, float > > tabletype │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_8_5 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_~_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__ │ │ │ │ +virtual ~ShiftHyperSurface_() │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__ │ │ │ │ +ShiftHyperSurface_(String filename, String, String firstproperty, String │ │ │ │ +secondproperty, int verbosity=EmpiricalHSShiftProcessor:: │ │ │ │ +VERBOSITY_LEVEL_CRITICAL) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_g_e_t_T_o_t_a_l_A_v_e_r_a_g_e │ │ │ │ +float getTotalAverage() │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_3_6_0 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e__ │ │ │ │ +ShiftHyperSurface_(int verbosity=EmpiricalHSShiftProcessor:: │ │ │ │ +VERBOSITY_LEVEL_CRITICAL) │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_H_Y_P_E_R_S_U_R_F_A_C_E_____T_Y_P_E │ │ │ │ +HYPERSURFACE__TYPE │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_9_1 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_R_E_A_L_____C_H_I │ │ │ │ +@ REAL__CHI │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_9_7 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_C_H_I_____D_I_S_C_R_E_T_E │ │ │ │ +@ CHI__DISCRETE │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_9_8 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_D_I_S_C_R_E_T_E_____D_I_S_C_R_E_T_E │ │ │ │ +@ DISCRETE__DISCRETE │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_9_5 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_R_E_A_L_____D_I_S_C_R_E_T_E │ │ │ │ +@ REAL__DISCRETE │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_9_3 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_D_I_S_C_R_E_T_E_____R_E_A_L │ │ │ │ +@ DISCRETE__REAL │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_9_4 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_S_I_N_G_L_E_____D_I_S_C_R_E_T_E │ │ │ │ +@ SINGLE__DISCRETE │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_3_0_2 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_D_I_S_C_R_E_T_E_____C_H_I │ │ │ │ +@ DISCRETE__CHI │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_9_9 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_S_I_N_G_L_E_____R_E_A_L │ │ │ │ +@ SINGLE__REAL │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_3_0_1 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_C_H_I_____R_E_A_L │ │ │ │ +@ CHI__REAL │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_9_6 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_C_H_I_____C_H_I │ │ │ │ +@ CHI__CHI │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_3_0_0 │ │ │ │ +_B_A_L_L_:_:_E_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_:_:_S_h_i_f_t_H_y_p_e_r_S_u_r_f_a_c_e___:_:_R_E_A_L_____R_E_A_L │ │ │ │ +@ REAL__REAL │ │ │ │ +DDeeffiinniittiioonn _e_m_p_i_r_i_c_a_l_H_S_S_h_i_f_t_P_r_o_c_e_s_s_o_r_._h_:_2_9_2 │ │ │ │ +_B_A_L_L_:_:_S_h_i_f_t_M_o_d_u_l_e │ │ │ │ +DDeeffiinniittiioonn _s_h_i_f_t_M_o_d_u_l_e_._h_:_4_3 │ │ │ │ +_B_A_L_L_:_:_F_i_l_e │ │ │ │ +DDeeffiinniittiioonn _f_i_l_e_._h_:_1_3_6 │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dd1/a08022.html │ │ │ @@ -80,15 +80,15 @@ │ │ │ Protected Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members
    │ │ │
    BALL::VIEW::AddBackboneModel Class Reference
    Visualisation » Model Processors
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/MODELS/backboneModel.h>

    │ │ │ +

    #include <BALL/VIEW/MODELS/backboneModel.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::AddBackboneModel:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::ModelProcessor │ │ │ @@ -164,18 +164,18 @@ │ │ │  UnaryProcessor (const UnaryProcessor &) │ │ │   │ │ │ virtual ~UnaryProcessor () │ │ │   │ │ │ virtual bool finish () │ │ │   │ │ │ - Public Member Functions inherited from BALL::PropertyManager │ │ │ -BALL_INLINE PropertyManager () │ │ │ +BALL_INLINE PropertyManager () │ │ │  Default constructor.
    │ │ │   │ │ │ -BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │ +BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │  Copy constructor.
    │ │ │   │ │ │ virtual ~PropertyManager () │ │ │  Destructor.
    │ │ │   │ │ │ virtual void destroy () │ │ │  Clears all properties.
    │ │ │ @@ -374,15 +374,15 @@ │ │ │   │ │ │ typedef const ArgumentType * const_argument_pointer │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    AddBackboneModel class. The class AddBackboneModel is a model processor that creates a backbone model through the CA-atoms of the processed Composite object. For information about the processor concept see Processor in the BALL documentation.

    │ │ │ │ │ │ -

    Definition at line 41 of file backboneModel.h.

    │ │ │ +

    Definition at line 41 of file backboneModel.h.

    │ │ │

    Member Enumeration Documentation

    │ │ │ │ │ │

    ◆ ModelTypes

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -401,15 +401,15 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    Enumerator
    TUBE 
    RIBBON 
    NUCLEIC_ACID 
    │ │ │ │ │ │ -

    Definition at line 64 of file backboneModel.h.

    │ │ │ +

    Definition at line 64 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ AddBackboneModel() [1/2]

    │ │ │ │ │ │ @@ -1013,15 +1013,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 115 of file backboneModel.h.

    │ │ │ +

    Definition at line 115 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ interpolate_()

    │ │ │ │ │ │
    │ │ │ @@ -1101,15 +1101,15 @@ │ │ │ inlineprotectedvirtual │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Reimplemented in BALL::VIEW::AddCartoonModel.

    │ │ │ │ │ │ -

    Definition at line 144 of file backboneModel.h.

    │ │ │ +

    Definition at line 144 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ refineModelParts_()

    │ │ │ │ │ │
    │ │ │ @@ -1189,15 +1189,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 126 of file backboneModel.h.

    │ │ │ +

    Definition at line 126 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setRibbonMode()

    │ │ │ │ │ │
    │ │ │ @@ -1217,15 +1217,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 122 of file backboneModel.h.

    │ │ │ +

    Definition at line 122 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setTubeRadius()

    │ │ │ │ │ │
    │ │ │ @@ -1245,15 +1245,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 111 of file backboneModel.h.

    │ │ │ +

    Definition at line 111 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ start()

    │ │ │ │ │ │
    │ │ │ @@ -1298,15 +1298,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 173 of file backboneModel.h.

    │ │ │ +

    Definition at line 173 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ care_for_SS_

    │ │ │ │ │ │
    │ │ │ @@ -1322,15 +1322,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 168 of file backboneModel.h.

    │ │ │ +

    Definition at line 168 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ dummy_chain_

    │ │ │ │ │ │
    │ │ │ @@ -1346,15 +1346,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 178 of file backboneModel.h.

    │ │ │ +

    Definition at line 178 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ dummy_protein_

    │ │ │ │ │ │
    │ │ │ @@ -1370,15 +1370,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 177 of file backboneModel.h.

    │ │ │ +

    Definition at line 177 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ dummy_ss_

    │ │ │ │ │ │
    │ │ │ @@ -1394,15 +1394,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 179 of file backboneModel.h.

    │ │ │ +

    Definition at line 179 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ guide_points_

    │ │ │ │ │ │
    │ │ │ @@ -1418,15 +1418,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 171 of file backboneModel.h.

    │ │ │ +

    Definition at line 171 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ interpolated_points_

    │ │ │ │ │ │
    │ │ │ @@ -1442,15 +1442,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 172 of file backboneModel.h.

    │ │ │ +

    Definition at line 172 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ interpolation_steps_

    │ │ │ │ │ │
    │ │ │ @@ -1466,15 +1466,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 163 of file backboneModel.h.

    │ │ │ +

    Definition at line 163 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ last_protein_

    │ │ │ │ │ │
    │ │ │ @@ -1490,15 +1490,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 181 of file backboneModel.h.

    │ │ │ +

    Definition at line 181 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ middle_ribbon_

    │ │ │ │ │ │
    │ │ │ @@ -1514,15 +1514,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 186 of file backboneModel.h.

    │ │ │ +

    Definition at line 186 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ middle_slide_

    │ │ │ │ │ │
    │ │ │ @@ -1538,15 +1538,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 185 of file backboneModel.h.

    │ │ │ +

    Definition at line 185 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ model_parts_

    │ │ │ │ │ │
    │ │ │ @@ -1562,15 +1562,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 175 of file backboneModel.h.

    │ │ │ +

    Definition at line 175 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ number_of_ribbons_

    │ │ │ │ │ │
    │ │ │ @@ -1586,15 +1586,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 165 of file backboneModel.h.

    │ │ │ +

    Definition at line 165 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ offsets_

    │ │ │ │ │ │
    │ │ │ @@ -1610,15 +1610,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 174 of file backboneModel.h.

    │ │ │ +

    Definition at line 174 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ residues_to_be_rendered_

    │ │ │ │ │ │
    │ │ │ @@ -1634,15 +1634,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 180 of file backboneModel.h.

    │ │ │ +

    Definition at line 180 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ribbon_height_

    │ │ │ │ │ │
    │ │ │ @@ -1658,15 +1658,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 167 of file backboneModel.h.

    │ │ │ +

    Definition at line 167 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ribbon_mode_

    │ │ │ │ │ │
    │ │ │ @@ -1682,15 +1682,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 169 of file backboneModel.h.

    │ │ │ +

    Definition at line 169 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ribbon_width_

    │ │ │ │ │ │
    │ │ │ @@ -1706,15 +1706,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 166 of file backboneModel.h.

    │ │ │ +

    Definition at line 166 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ slides_

    │ │ │ │ │ │
    │ │ │ @@ -1730,15 +1730,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 184 of file backboneModel.h.

    │ │ │ +

    Definition at line 184 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ slides_angle_

    │ │ │ │ │ │
    │ │ │ @@ -1754,15 +1754,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 187 of file backboneModel.h.

    │ │ │ +

    Definition at line 187 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ss_

    │ │ │ │ │ │
    │ │ │ @@ -1778,15 +1778,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 182 of file backboneModel.h.

    │ │ │ +

    Definition at line 182 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ temp_matrix_

    │ │ │ │ │ │
    │ │ │ @@ -1802,15 +1802,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 188 of file backboneModel.h.

    │ │ │ +

    Definition at line 188 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ tube_radius_

    │ │ │ │ │ │
    │ │ │ @@ -1826,15 +1826,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 160 of file backboneModel.h.

    │ │ │ +

    Definition at line 160 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ xs_

    │ │ │ │ │ │
    │ │ │ @@ -1850,15 +1850,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 189 of file backboneModel.h.

    │ │ │ +

    Definition at line 189 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ys_

    │ │ │ │ │ │
    │ │ │ @@ -1874,15 +1874,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 189 of file backboneModel.h.

    │ │ │ +

    Definition at line 189 of file backboneModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dd2/a04190.html │ │ │ @@ -76,44 +76,44 @@ │ │ │
    │ │ │ Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::PDB::RecordEXPDTA Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/FORMAT/PDBdefs.h>

    │ │ │ +

    #include <BALL/FORMAT/PDBdefs.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Attributes

    RecordType record_type
     
    RecordName record_name
     
    Continuation continuation
     
    SList technique
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 634 of file PDBdefs.h.

    │ │ │ +

    Definition at line 634 of file PDBdefs.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ continuation

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Continuation BALL::PDB::RecordEXPDTA::continuation
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 638 of file PDBdefs.h.

    │ │ │ +

    Definition at line 638 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ record_name

    │ │ │ │ │ │
    │ │ │ @@ -121,15 +121,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    RecordName BALL::PDB::RecordEXPDTA::record_name
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 637 of file PDBdefs.h.

    │ │ │ +

    Definition at line 637 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ record_type

    │ │ │ │ │ │
    │ │ │ @@ -137,15 +137,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    RecordType BALL::PDB::RecordEXPDTA::record_type
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 636 of file PDBdefs.h.

    │ │ │ +

    Definition at line 636 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ technique

    │ │ │ │ │ │
    │ │ │ @@ -153,15 +153,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    SList BALL::PDB::RecordEXPDTA::technique
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 639 of file PDBdefs.h.

    │ │ │ +

    Definition at line 639 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dd3/a07574.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::VIEW::DockProgressDialog Class Reference
    Visualisation » QT Dialogs
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/DIALOGS/dockProgressDialog.h>

    │ │ │ +

    #include <BALL/VIEW/DIALOGS/dockProgressDialog.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::DockProgressDialog:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ QDialog │ │ │ @@ -113,15 +113,15 @@ │ │ │   │ │ │ void updateProgress_ () │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Dialog for showing the progress during a docking calculation.

    │ │ │ │ │ │ -

    Definition at line 33 of file dockProgressDialog.h.

    │ │ │ +

    Definition at line 33 of file dockProgressDialog.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ DockProgressDialog()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dd3/a07870.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::VIEW::TransformationMessage Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/KERNEL/message.h>

    │ │ │ +

    #include <BALL/VIEW/KERNEL/message.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::TransformationMessage:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::Message │ │ │ @@ -117,15 +117,15 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    bool isDeletable () const
     
    boost::any & data ()
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 734 of file message.h.

    │ │ │ +

    Definition at line 734 of file message.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ TransformationMessage() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -178,15 +178,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 750 of file message.h.

    │ │ │ +

    Definition at line 750 of file message.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ setMatrix()

    │ │ │ │ │ │
    │ │ │ @@ -206,15 +206,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 746 of file message.h.

    │ │ │ +

    Definition at line 746 of file message.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dd6/a04238.html │ │ │ @@ -76,42 +76,42 @@ │ │ │
    │ │ │ Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::PDB::RecordJRNL Struct Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/FORMAT/PDBdefs.h>

    │ │ │ +

    #include <BALL/FORMAT/PDBdefs.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Attributes

    RecordType record_type
     
    RecordName record_name
     
    LString text
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 775 of file PDBdefs.h.

    │ │ │ +

    Definition at line 775 of file PDBdefs.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ record_name

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    RecordName BALL::PDB::RecordJRNL::record_name
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 778 of file PDBdefs.h.

    │ │ │ +

    Definition at line 778 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ record_type

    │ │ │ │ │ │
    │ │ │ @@ -119,15 +119,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    RecordType BALL::PDB::RecordJRNL::record_type
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 777 of file PDBdefs.h.

    │ │ │ +

    Definition at line 777 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ text

    │ │ │ │ │ │
    │ │ │ @@ -135,15 +135,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    LString BALL::PDB::RecordJRNL::text
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 779 of file PDBdefs.h.

    │ │ │ +

    Definition at line 779 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/ddb/a00542.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: atomOverview.h File Reference │ │ │ +BALL: UIOperationMode.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,37 +65,33 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    atomOverview.h File Reference
    │ │ │ +
    UIOperationMode.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/COMMON/global.h>
    │ │ │ -#include <BALL/CONCEPT/composite.h>
    │ │ │ -#include <BALL/VIEW/UIC/ui_atomOverview.h>
    │ │ │ +
    #include <BALL/COMMON/global.h>
    │ │ │ +#include <BALL/SYSTEM/mutex.h>
    │ │ │ +#include <boost/shared_ptr.hpp>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::AtomOverview
     
    class  BALL::VIEW::AtomOverview::OverviewProcessor
     
    class  BALL::VIEW::AtomOverview::ApplyProcessor
    class  BALL::VIEW::UIOperationMode
     
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,27 +1,23 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ - * _D_I_A_L_O_G_S │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -atomOverview.h File Reference │ │ │ │ +UIOperationMode.h File Reference │ │ │ │ #include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_c_o_m_p_o_s_i_t_e_._h> │ │ │ │ -#include │ │ │ │ +#include <_B_A_L_L_/_S_Y_S_T_E_M_/_m_u_t_e_x_._h> │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_A_p_p_l_y_P_r_o_c_e_s_s_o_r │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/ddb/a00542_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: atomOverview.h Source File │ │ │ +BALL: UIOperationMode.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,196 +70,108 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    atomOverview.h
    │ │ │ +
    UIOperationMode.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5#ifndef BALL_VIEW_DIALOGS_ATOMOVERVIEW_H
    │ │ │ -
    6#define BALL_VIEW_DIALOGS_ATOMOVERVIEW_H
    │ │ │ +
    5#ifndef BALL_VIEW_KERNEL_UIOPERATIONMODE_H
    │ │ │ +
    6#define BALL_VIEW_KERNEL_UIOPERATIONMODE_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ -
    9# include <BALL/COMMON/global.h>
    │ │ │ +
    8#ifndef BALL_CONCEPT_EMBEDDABLE_H
    │ │ │ +
    9# include <BALL/COMMON/global.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_CONCEPT_COMPOSITE_H
    │ │ │ -
    13# include <BALL/CONCEPT/composite.h>
    │ │ │ +
    12#ifndef BALL_SYSTEM_MUTEX_H
    │ │ │ +
    13# include <BALL/SYSTEM/mutex.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │ -
    16#include <BALL/VIEW/UIC/ui_atomOverview.h>
    │ │ │ +
    16#include <boost/shared_ptr.hpp>
    │ │ │
    17
    │ │ │
    18namespace BALL
    │ │ │
    19{
    │ │ │ -
    20 class AtomContainer;
    │ │ │ -
    21
    │ │ │ -
    22 namespace VIEW
    │ │ │ -
    23 {
    │ │ │ -
    24 class MainControl;
    │ │ │ -
    25
    │ │ │ -
    │ │ │ -
    32 class BALL_VIEW_EXPORT AtomOverview
    │ │ │ -
    33 : public QDialog,
    │ │ │ -
    34 public Ui_AtomOverviewData
    │ │ │ -
    35 {
    │ │ │ -
    36 Q_OBJECT
    │ │ │ -
    37
    │ │ │ -
    38 public:
    │ │ │ -
    39
    │ │ │ -
    │ │ │ -
    41 class BALL_VIEW_EXPORT OverviewProcessor
    │ │ │ -
    42 : public UnaryProcessor<Composite>
    │ │ │ -
    43 {
    │ │ │ -
    44 public:
    │ │ │ -
    45
    │ │ │ -
    46 BALL_CREATE(OverviewProcessor)
    │ │ │ -
    47
    │ │ │ -
    48
    │ │ │ -
    49 OverviewProcessor();
    │ │ │ -
    50
    │ │ │ -
    52 OverviewProcessor(const OverviewProcessor& model_processor);
    │ │ │ +
    20 namespace VIEW
    │ │ │ +
    21 {
    │ │ │ +
    │ │ │ +
    25 class BALL_VIEW_EXPORT UIOperationMode
    │ │ │ +
    26 {
    │ │ │ +
    27 public:
    │ │ │ +
    28
    │ │ │ +
    │ │ │ +
    29 enum OperationMode
    │ │ │ +
    30 {
    │ │ │ +
    31 MODE_FULL = 0,
    │ │ │ +
    32 MODE_ADVANCED,
    │ │ │ +
    33 MODE_KIOSK,
    │ │ │ +
    34 MODE_ALL
    │ │ │ +
    35 };
    │ │ │ +
    │ │ │ +
    36
    │ │ │ +
    37 virtual ~UIOperationMode();
    │ │ │ +
    38
    │ │ │ +
    39 static UIOperationMode& instance();
    │ │ │ +
    40
    │ │ │ +
    41 OperationMode getMode();
    │ │ │ +
    42 void setMode(OperationMode new_mode);
    │ │ │ +
    43
    │ │ │ +
    44 bool isFull();
    │ │ │ +
    45 bool isAdvanced();
    │ │ │ +
    46 bool isKiosk();
    │ │ │ +
    47
    │ │ │ +
    48 protected:
    │ │ │ +
    49 // prevent outside use of constructors
    │ │ │ +
    50 UIOperationMode();
    │ │ │ +
    51 UIOperationMode(const UIOperationMode&);
    │ │ │ +
    52 const UIOperationMode& operator=(const UIOperationMode&);
    │ │ │
    53
    │ │ │ -
    55 virtual ~OverviewProcessor();
    │ │ │ +
    54 // our instance pointer
    │ │ │ +
    55 static boost::shared_ptr<UIOperationMode> instance_;
    │ │ │
    56
    │ │ │ -
    58 Processor::Result operator() (Composite& composite);
    │ │ │ -
    59
    │ │ │ -
    61 void setTable(QTableWidget* widget) { table_ = widget;}
    │ │ │ -
    62
    │ │ │ -
    64 void showOnlySelection(bool state) {only_selection_ = state;}
    │ │ │ -
    65
    │ │ │ -
    66 protected:
    │ │ │ -
    67
    │ │ │ -
    68 QTableWidget* table_;
    │ │ │ -
    69 bool only_selection_;
    │ │ │ -
    70 };
    │ │ │ -
    │ │ │ -
    71
    │ │ │ -
    │ │ │ -
    73 class BALL_VIEW_EXPORT ApplyProcessor
    │ │ │ -
    74 : public UnaryProcessor<Composite>
    │ │ │ -
    75 {
    │ │ │ -
    76 public:
    │ │ │ -
    77
    │ │ │ -
    78 BALL_CREATE(ApplyProcessor)
    │ │ │ -
    79
    │ │ │ -
    80
    │ │ │ -
    81 ApplyProcessor();
    │ │ │ -
    82
    │ │ │ -
    84 ApplyProcessor(const ApplyProcessor& model_processor);
    │ │ │ -
    85
    │ │ │ -
    87 virtual ~ApplyProcessor();
    │ │ │ -
    88
    │ │ │ -
    90 Processor::Result operator() (Composite& composite);
    │ │ │ -
    91
    │ │ │ -
    93 void setTable(QTableWidget* widget) { table_ = widget; row_ = 0;}
    │ │ │ -
    94
    │ │ │ -
    96 void setMainControl(MainControl* main_control) {main_control_ = main_control;}
    │ │ │ -
    97
    │ │ │ -
    99 void showOnlySelection(bool state) {only_selection_ = state;}
    │ │ │ -
    100
    │ │ │ -
    101 protected:
    │ │ │ -
    102
    │ │ │ -
    103 QTableWidget* table_;
    │ │ │ -
    104 Position row_;
    │ │ │ -
    105 bool only_selection_;
    │ │ │ -
    106 MainControl* main_control_;
    │ │ │ -
    107 };
    │ │ │ -
    │ │ │ -
    108
    │ │ │ -
    109
    │ │ │ -
    113
    │ │ │ -
    118 AtomOverview(QWidget *parent = NULL, const char *name = "AtomOverview");
    │ │ │ -
    119
    │ │ │ -
    121
    │ │ │ -
    124
    │ │ │ -
    127 virtual ~AtomOverview();
    │ │ │ -
    128
    │ │ │ -
    130
    │ │ │ -
    133
    │ │ │ -
    135 void setParent(AtomContainer* ac);
    │ │ │ -
    136
    │ │ │ -
    138 void showOnlySelection(bool state) {only_selection_ = state;}
    │ │ │ -
    139
    │ │ │ -
    141
    │ │ │ -
    144
    │ │ │ -
    145 protected Q_SLOTS:
    │ │ │ -
    146
    │ │ │ -
    152 virtual void accept();
    │ │ │ -
    153
    │ │ │ -
    154 void itemChanged(QTableWidgetItem* item);
    │ │ │ -
    155 void itemActivated(QTableWidgetItem* item);
    │ │ │ -
    156
    │ │ │ -
    157 protected:
    │ │ │ -
    158
    │ │ │ -
    159 void restoreItem_(QTableWidgetItem* item);
    │ │ │ -
    160
    │ │ │ -
    161 AtomContainer* parent_;
    │ │ │ -
    162 OverviewProcessor processor_;
    │ │ │ -
    163 ApplyProcessor apply_processor_;
    │ │ │ -
    164 String item_backup_;
    │ │ │ -
    165 bool ignore_;
    │ │ │ -
    166 bool only_selection_;
    │ │ │ -
    167 };
    │ │ │ -
    │ │ │ -
    168
    │ │ │ -
    169} } // namespaces
    │ │ │ -
    170
    │ │ │ -
    171#endif // BALL_VIEW_DIALOGS_AtomOverview_H
    │ │ │ - │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::AtomOverview::itemActivated
    void itemActivated(QTableWidgetItem *item)
    │ │ │ - │ │ │ -
    BALL::VIEW::AtomOverview::apply_processor_
    ApplyProcessor apply_processor_
    Definition atomOverview.h:163
    │ │ │ -
    BALL::VIEW::AtomOverview::processor_
    OverviewProcessor processor_
    Definition atomOverview.h:162
    │ │ │ -
    BALL::VIEW::AtomOverview::showOnlySelection
    void showOnlySelection(bool state)
    Definition atomOverview.h:138
    │ │ │ -
    BALL::VIEW::AtomOverview::restoreItem_
    void restoreItem_(QTableWidgetItem *item)
    │ │ │ -
    BALL::VIEW::AtomOverview::setParent
    void setParent(AtomContainer *ac)
    │ │ │ - │ │ │ -
    BALL::VIEW::AtomOverview::itemChanged
    void itemChanged(QTableWidgetItem *item)
    │ │ │ -
    BALL::VIEW::AtomOverview::parent_
    AtomContainer * parent_
    Definition atomOverview.h:161
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::AtomOverview::AtomOverview
    AtomOverview(QWidget *parent=NULL, const char *name="AtomOverview")
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::AtomOverview::ApplyProcessor::setMainControl
    void setMainControl(MainControl *main_control)
    Definition atomOverview.h:96
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ +
    57 static Mutex create_mutex_;
    │ │ │ +
    58
    │ │ │ +
    59 OperationMode mode_;
    │ │ │ +
    60 };
    │ │ │ +
    │ │ │ +
    61 }
    │ │ │ +
    62}
    │ │ │ +
    63
    │ │ │ +
    64#endif // BALL_VIEW_KERNEL_UIOPERATIONMODE_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::UIOperationMode::instance
    static UIOperationMode & instance()
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::UIOperationMode::instance_
    static boost::shared_ptr< UIOperationMode > instance_
    Definition UIOperationMode.h:55
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::UIOperationMode::setMode
    void setMode(OperationMode new_mode)
    │ │ │ + │ │ │ +
    BALL::VIEW::UIOperationMode::operator=
    const UIOperationMode & operator=(const UIOperationMode &)
    │ │ │ +
    BALL::VIEW::UIOperationMode::UIOperationMode
    UIOperationMode(const UIOperationMode &)
    │ │ │ + │ │ │ + │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,236 +1,121 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ - * _D_I_A_L_O_G_S │ │ │ │ -atomOverview.h │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ +UIOperationMode.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_VIEW_DIALOGS_ATOMOVERVIEW_H │ │ │ │ -6#define BALL_VIEW_DIALOGS_ATOMOVERVIEW_H │ │ │ │ +5#ifndef BALL_VIEW_KERNEL_UIOPERATIONMODE_H │ │ │ │ +6#define BALL_VIEW_KERNEL_UIOPERATIONMODE_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ +8#ifndef BALL_CONCEPT_EMBEDDABLE_H │ │ │ │ 9# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_CONCEPT_COMPOSITE_H │ │ │ │ -13# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_c_o_m_p_o_s_i_t_e_._h> │ │ │ │ +12#ifndef BALL_SYSTEM_MUTEX_H │ │ │ │ +13# include <_B_A_L_L_/_S_Y_S_T_E_M_/_m_u_t_e_x_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#include │ │ │ │ +16#include │ │ │ │ 17 │ │ │ │ 18namespace _B_A_L_L │ │ │ │ 19{ │ │ │ │ -20 class AtomContainer; │ │ │ │ -21 │ │ │ │ -22 namespace VIEW │ │ │ │ -23 { │ │ │ │ -24 class MainControl; │ │ │ │ -25 │ │ │ │ -_3_2 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _A_t_o_m_O_v_e_r_v_i_e_w │ │ │ │ -33 : public _Q_D_i_a_l_o_g, │ │ │ │ -34 public Ui_AtomOverviewData │ │ │ │ -35 { │ │ │ │ -36 Q_OBJECT │ │ │ │ -37 │ │ │ │ -38 public: │ │ │ │ -39 │ │ │ │ -_4_1 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r │ │ │ │ -42 : public _U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -43 { │ │ │ │ -44 public: │ │ │ │ -45 │ │ │ │ -46 _B_A_L_L___C_R_E_A_T_E(_O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r) │ │ │ │ +20 namespace VIEW │ │ │ │ +21 { │ │ │ │ +_2_5 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e │ │ │ │ +26 { │ │ │ │ +27 public: │ │ │ │ +28 │ │ │ │ +_2_9 enum _O_p_e_r_a_t_i_o_n_M_o_d_e │ │ │ │ +30 { │ │ │ │ +_3_1 MODE_FULL = 0, │ │ │ │ +_3_2 _M_O_D_E___A_D_V_A_N_C_E_D, │ │ │ │ +_3_3 _M_O_D_E___K_I_O_S_K, │ │ │ │ +34 MODE_ALL │ │ │ │ +_3_5 }; │ │ │ │ +36 │ │ │ │ +_3_7 virtual _~_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e(); │ │ │ │ +38 │ │ │ │ +_3_9 static _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e& _i_n_s_t_a_n_c_e(); │ │ │ │ +40 │ │ │ │ +_4_1 _O_p_e_r_a_t_i_o_n_M_o_d_e _g_e_t_M_o_d_e(); │ │ │ │ +_4_2 void _s_e_t_M_o_d_e(_O_p_e_r_a_t_i_o_n_M_o_d_e new_mode); │ │ │ │ +43 │ │ │ │ +_4_4 bool _i_s_F_u_l_l(); │ │ │ │ +_4_5 bool _i_s_A_d_v_a_n_c_e_d(); │ │ │ │ +_4_6 bool _i_s_K_i_o_s_k(); │ │ │ │ 47 │ │ │ │ -48 │ │ │ │ -_4_9 _O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r(); │ │ │ │ -50 │ │ │ │ -_5_2 _O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r(const _O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r& model_processor); │ │ │ │ +48 protected: │ │ │ │ +49 // prevent outside use of constructors │ │ │ │ +_5_0 _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e(); │ │ │ │ +_5_1 _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e(const _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e&); │ │ │ │ +_5_2 const _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e& _o_p_e_r_a_t_o_r_=(const _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e&); │ │ │ │ 53 │ │ │ │ -_5_5 virtual ~_O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r(); │ │ │ │ +54 // our instance pointer │ │ │ │ +_5_5 static boost::shared_ptr _i_n_s_t_a_n_c_e__; │ │ │ │ 56 │ │ │ │ -_5_8 _P_r_o_c_e_s_s_o_r::_R_e_s_u_l_t operator() (_C_o_m_p_o_s_i_t_e& composite); │ │ │ │ -59 │ │ │ │ -_6_1 void setTable(_Q_T_a_b_l_e_W_i_d_g_e_t* widget) { table_ = widget;} │ │ │ │ -62 │ │ │ │ -_6_4 void _s_h_o_w_O_n_l_y_S_e_l_e_c_t_i_o_n(bool state) {only_selection_ = state;} │ │ │ │ -65 │ │ │ │ -66 protected: │ │ │ │ -67 │ │ │ │ -_6_8 _Q_T_a_b_l_e_W_i_d_g_e_t* _t_a_b_l_e__; │ │ │ │ -_6_9 bool _o_n_l_y___s_e_l_e_c_t_i_o_n__; │ │ │ │ -70 }; │ │ │ │ -71 │ │ │ │ -_7_3 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _A_p_p_l_y_P_r_o_c_e_s_s_o_r │ │ │ │ -74 : public _U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -75 { │ │ │ │ -76 public: │ │ │ │ -77 │ │ │ │ -78 _B_A_L_L___C_R_E_A_T_E(_A_p_p_l_y_P_r_o_c_e_s_s_o_r) │ │ │ │ -79 │ │ │ │ -80 │ │ │ │ -_8_1 _A_p_p_l_y_P_r_o_c_e_s_s_o_r(); │ │ │ │ -82 │ │ │ │ -_8_4 _A_p_p_l_y_P_r_o_c_e_s_s_o_r(const _A_p_p_l_y_P_r_o_c_e_s_s_o_r& model_processor); │ │ │ │ -85 │ │ │ │ -_8_7 virtual ~_A_p_p_l_y_P_r_o_c_e_s_s_o_r(); │ │ │ │ -88 │ │ │ │ -_9_0 _P_r_o_c_e_s_s_o_r::_R_e_s_u_l_t operator() (_C_o_m_p_o_s_i_t_e& composite); │ │ │ │ -91 │ │ │ │ -_9_3 void setTable(_Q_T_a_b_l_e_W_i_d_g_e_t* widget) { table_ = widget; row_ = 0;} │ │ │ │ -94 │ │ │ │ -_9_6 void _s_e_t_M_a_i_n_C_o_n_t_r_o_l(_M_a_i_n_C_o_n_t_r_o_l* main_control) {main_control_ = │ │ │ │ -main_control;} │ │ │ │ -97 │ │ │ │ -_9_9 void _s_h_o_w_O_n_l_y_S_e_l_e_c_t_i_o_n(bool state) {only_selection_ = state;} │ │ │ │ -100 │ │ │ │ -101 protected: │ │ │ │ -102 │ │ │ │ -_1_0_3 _Q_T_a_b_l_e_W_i_d_g_e_t* _t_a_b_l_e__; │ │ │ │ -_1_0_4 _P_o_s_i_t_i_o_n _r_o_w__; │ │ │ │ -_1_0_5 bool _o_n_l_y___s_e_l_e_c_t_i_o_n__; │ │ │ │ -_1_0_6 _M_a_i_n_C_o_n_t_r_o_l* _m_a_i_n___c_o_n_t_r_o_l__; │ │ │ │ -107 }; │ │ │ │ -108 │ │ │ │ -109 │ │ │ │ -113 │ │ │ │ -_1_1_8 _A_t_o_m_O_v_e_r_v_i_e_w(_Q_W_i_d_g_e_t *parent = NULL, const char *name = "AtomOverview"); │ │ │ │ -119 │ │ │ │ -121 │ │ │ │ -124 │ │ │ │ -_1_2_7 virtual _~_A_t_o_m_O_v_e_r_v_i_e_w(); │ │ │ │ -128 │ │ │ │ -130 │ │ │ │ -133 │ │ │ │ -_1_3_5 void _s_e_t_P_a_r_e_n_t(_A_t_o_m_C_o_n_t_a_i_n_e_r* ac); │ │ │ │ -136 │ │ │ │ -_1_3_8 void _s_h_o_w_O_n_l_y_S_e_l_e_c_t_i_o_n(bool state) {only_selection_ = state;} │ │ │ │ -139 │ │ │ │ -141 │ │ │ │ -144 │ │ │ │ -145 protected Q_SLOTS: │ │ │ │ -146 │ │ │ │ -_1_5_2 virtual void _a_c_c_e_p_t(); │ │ │ │ -153 │ │ │ │ -_1_5_4 void _i_t_e_m_C_h_a_n_g_e_d(QTableWidgetItem* item); │ │ │ │ -_1_5_5 void _i_t_e_m_A_c_t_i_v_a_t_e_d(QTableWidgetItem* item); │ │ │ │ -156 │ │ │ │ -157 protected: │ │ │ │ -158 │ │ │ │ -_1_5_9 void _r_e_s_t_o_r_e_I_t_e_m__(QTableWidgetItem* item); │ │ │ │ -160 │ │ │ │ -_1_6_1 _A_t_o_m_C_o_n_t_a_i_n_e_r* _p_a_r_e_n_t__; │ │ │ │ -_1_6_2 _O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r _p_r_o_c_e_s_s_o_r__; │ │ │ │ -_1_6_3 _A_p_p_l_y_P_r_o_c_e_s_s_o_r _a_p_p_l_y___p_r_o_c_e_s_s_o_r__; │ │ │ │ -_1_6_4 _S_t_r_i_n_g _i_t_e_m___b_a_c_k_u_p__; │ │ │ │ -_1_6_5 bool _i_g_n_o_r_e__; │ │ │ │ -_1_6_6 bool _o_n_l_y___s_e_l_e_c_t_i_o_n__; │ │ │ │ -167 }; │ │ │ │ -168 │ │ │ │ -169} } // namespaces │ │ │ │ -170 │ │ │ │ -171#endif // BALL_VIEW_DIALOGS_AtomOverview_H │ │ │ │ -_c_o_m_p_o_s_i_t_e_._h │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_5_7 static _M_u_t_e_x _c_r_e_a_t_e___m_u_t_e_x__; │ │ │ │ +58 │ │ │ │ +_5_9 _O_p_e_r_a_t_i_o_n_M_o_d_e _m_o_d_e__; │ │ │ │ +60 }; │ │ │ │ +61 } │ │ │ │ +62} │ │ │ │ +63 │ │ │ │ +64#endif // BALL_VIEW_KERNEL_UIOPERATIONMODE_H │ │ │ │ +_m_u_t_e_x_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ -DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_6_0 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_R_e_s_u_l_t │ │ │ │ -DDeeffiinniittiioonn _r_e_s_u_l_t_._h_:_2_2 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_i_g_n_o_r_e__ │ │ │ │ -bool ignore_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_6_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_i_t_e_m_A_c_t_i_v_a_t_e_d │ │ │ │ -void itemActivated(QTableWidgetItem *item) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_i_t_e_m___b_a_c_k_u_p__ │ │ │ │ -String item_backup_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_6_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_a_p_p_l_y___p_r_o_c_e_s_s_o_r__ │ │ │ │ -ApplyProcessor apply_processor_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_6_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_p_r_o_c_e_s_s_o_r__ │ │ │ │ -OverviewProcessor processor_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_6_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_s_h_o_w_O_n_l_y_S_e_l_e_c_t_i_o_n │ │ │ │ -void showOnlySelection(bool state) │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_3_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_r_e_s_t_o_r_e_I_t_e_m__ │ │ │ │ -void restoreItem_(QTableWidgetItem *item) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_s_e_t_P_a_r_e_n_t │ │ │ │ -void setParent(AtomContainer *ac) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_o_n_l_y___s_e_l_e_c_t_i_o_n__ │ │ │ │ -bool only_selection_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_6_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_i_t_e_m_C_h_a_n_g_e_d │ │ │ │ -void itemChanged(QTableWidgetItem *item) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_p_a_r_e_n_t__ │ │ │ │ -AtomContainer * parent_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_6_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_~_A_t_o_m_O_v_e_r_v_i_e_w │ │ │ │ -virtual ~AtomOverview() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_a_c_c_e_p_t │ │ │ │ -virtual void accept() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_A_t_o_m_O_v_e_r_v_i_e_w │ │ │ │ -AtomOverview(QWidget *parent=NULL, const char *name="AtomOverview") │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r_:_:_s_h_o_w_O_n_l_y_S_e_l_e_c_t_i_o_n │ │ │ │ -void showOnlySelection(bool state) │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_6_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r_:_:_o_n_l_y___s_e_l_e_c_t_i_o_n__ │ │ │ │ -bool only_selection_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_6_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_O_v_e_r_v_i_e_w_P_r_o_c_e_s_s_o_r_:_:_t_a_b_l_e__ │ │ │ │ -QTableWidget * table_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_6_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_A_p_p_l_y_P_r_o_c_e_s_s_o_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_7_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_A_p_p_l_y_P_r_o_c_e_s_s_o_r_:_:_o_n_l_y___s_e_l_e_c_t_i_o_n__ │ │ │ │ -bool only_selection_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_0_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_A_p_p_l_y_P_r_o_c_e_s_s_o_r_:_:_m_a_i_n___c_o_n_t_r_o_l__ │ │ │ │ -MainControl * main_control_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_0_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_A_p_p_l_y_P_r_o_c_e_s_s_o_r_:_:_s_e_t_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ -void setMainControl(MainControl *main_control) │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_9_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_A_p_p_l_y_P_r_o_c_e_s_s_o_r_:_:_t_a_b_l_e__ │ │ │ │ -QTableWidget * table_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_0_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_A_p_p_l_y_P_r_o_c_e_s_s_o_r_:_:_s_h_o_w_O_n_l_y_S_e_l_e_c_t_i_o_n │ │ │ │ -void showOnlySelection(bool state) │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_A_t_o_m_O_v_e_r_v_i_e_w_:_:_A_p_p_l_y_P_r_o_c_e_s_s_o_r_:_:_r_o_w__ │ │ │ │ -Position row_ │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_O_v_e_r_v_i_e_w_._h_:_1_0_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ -DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_Q_D_i_a_l_o_g │ │ │ │ -_Q_T_a_b_l_e_W_i_d_g_e_t │ │ │ │ -_Q_W_i_d_g_e_t │ │ │ │ +_B_A_L_L_:_:_T_M_u_t_e_x_<_ _B_A_L_L___D_E_F_A_U_L_T___M_U_T_E_X___T_Y_P_E_ _> │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e │ │ │ │ +DDeeffiinniittiioonn _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h_:_2_6 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_i_s_A_d_v_a_n_c_e_d │ │ │ │ +bool isAdvanced() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e │ │ │ │ +UIOperationMode() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_g_e_t_M_o_d_e │ │ │ │ +OperationMode getMode() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_i_n_s_t_a_n_c_e │ │ │ │ +static UIOperationMode & instance() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_c_r_e_a_t_e___m_u_t_e_x__ │ │ │ │ +static Mutex create_mutex_ │ │ │ │ +DDeeffiinniittiioonn _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_~_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e │ │ │ │ +virtual ~UIOperationMode() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_i_n_s_t_a_n_c_e__ │ │ │ │ +static boost::shared_ptr< UIOperationMode > instance_ │ │ │ │ +DDeeffiinniittiioonn _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h_:_5_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_O_p_e_r_a_t_i_o_n_M_o_d_e │ │ │ │ +OperationMode │ │ │ │ +DDeeffiinniittiioonn _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h_:_3_0 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_M_O_D_E___K_I_O_S_K │ │ │ │ +@ MODE_KIOSK │ │ │ │ +DDeeffiinniittiioonn _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h_:_3_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_M_O_D_E___A_D_V_A_N_C_E_D │ │ │ │ +@ MODE_ADVANCED │ │ │ │ +DDeeffiinniittiioonn _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_i_s_F_u_l_l │ │ │ │ +bool isFull() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_s_e_t_M_o_d_e │ │ │ │ +void setMode(OperationMode new_mode) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_i_s_K_i_o_s_k │ │ │ │ +bool isKiosk() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ +const UIOperationMode & operator=(const UIOperationMode &) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e │ │ │ │ +UIOperationMode(const UIOperationMode &) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_m_o_d_e__ │ │ │ │ +OperationMode mode_ │ │ │ │ +DDeeffiinniittiioonn _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h_:_5_9 │ │ │ │ _g_l_o_b_a_l_._h │ │ │ │ _B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ #define BALL_VIEW_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/ddb/a06430.html │ │ │ @@ -78,15 +78,15 @@ │ │ │ Protected Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members │ │ │
    BALL::Rescoring3D Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SCORING/FUNCTIONS/rescoring3D.h>

    │ │ │ +

    #include <BALL/SCORING/FUNCTIONS/rescoring3D.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::Rescoring3D:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::Rescoring │ │ │ @@ -170,15 +170,15 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
    String name_
     
    std::ofstream stddev_out_
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 15 of file rescoring3D.h.

    │ │ │ +

    Definition at line 15 of file rescoring3D.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ Rescoring3D()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -366,15 +366,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 37 of file rescoring3D.h.

    │ │ │ +

    Definition at line 37 of file rescoring3D.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ reg3D_grid_names_

    │ │ │ │ │ │
    │ │ │ @@ -391,15 +391,15 @@ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │

    the names for the RegularData3D-grids to be created by generateRegularData3DGrids()

    │ │ │ │ │ │ -

    Definition at line 40 of file rescoring3D.h.

    │ │ │ +

    Definition at line 40 of file rescoring3D.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ resolution_

    │ │ │ │ │ │
    │ │ │ @@ -415,15 +415,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 36 of file rescoring3D.h.

    │ │ │ +

    Definition at line 36 of file rescoring3D.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ sizeX_

    │ │ │ │ │ │
    │ │ │ @@ -439,15 +439,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 33 of file rescoring3D.h.

    │ │ │ +

    Definition at line 33 of file rescoring3D.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ sizeY_

    │ │ │ │ │ │
    │ │ │ @@ -463,15 +463,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 34 of file rescoring3D.h.

    │ │ │ +

    Definition at line 34 of file rescoring3D.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ sizeZ_

    │ │ │ │ │ │
    │ │ │ @@ -487,15 +487,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 35 of file rescoring3D.h.

    │ │ │ +

    Definition at line 35 of file rescoring3D.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/ddc/a06626.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Static Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::UhligCavFreeEnergyProcessor::Default Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SOLVATION/uhligCavFreeEnergyProcessor.h>

    │ │ │ +

    #include <BALL/SOLVATION/uhligCavFreeEnergyProcessor.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -92,15 +92,15 @@ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Static Public Attributes

    static const int VERBOSITY
     
    static const float PROBE_RADIUS
     
     
    static const float CONSTANT
     
    │ │ │

    Detailed Description

    │ │ │

    Default values for cavitation free energy calculations. These values represent the default settings for the calculations of the cavitation free energy.

    │ │ │ │ │ │ -

    Definition at line 82 of file uhligCavFreeEnergyProcessor.h.

    │ │ │ +

    Definition at line 82 of file uhligCavFreeEnergyProcessor.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ CONSTANT

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -117,15 +117,15 @@ │ │ │ │ │ │
    │ │ │
    │ │ │

    Default additive constant. This additive constant was also found by fitting aginst experimental data Default::SURFACE_TENSION . In contrast to Simonson/Br{"u}nger it is not zero but $0.921 │ │ │ \mathrm{kcal}\cdot\mathrm{mol}^{-1} = 3.855 │ │ │ \mathrm{kJ}\cdot\mathrm{mol}^{-1}$.

    See also
    Option::CONSTANT
    │ │ │ │ │ │ -

    Definition at line 116 of file uhligCavFreeEnergyProcessor.h.

    │ │ │ +

    Definition at line 116 of file uhligCavFreeEnergyProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ PROBE_RADIUS

    │ │ │ │ │ │
    │ │ │ @@ -142,15 +142,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │

    Default probe radius. This probe radius is the one suggested by Reiss et al. in their paper (1.385 $ A $).

    See also
    Option::PROBE_RADIUS
    │ │ │ │ │ │ -

    Definition at line 94 of file uhligCavFreeEnergyProcessor.h.

    │ │ │ +

    Definition at line 94 of file uhligCavFreeEnergyProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ SURFACE_TENSION

    │ │ │ │ │ │
    │ │ │ @@ -169,15 +169,15 @@ │ │ │ │ │ │ │ │ │
    │ │ │

    Default surface tension. This is a surface tension obtained by fitting calculated solvation free energies of several small solutes against experimantel data. The value ( $5.41 \mathrm{cal}\cdot\mathrm{mol}^{-1}\cdot A^{-2} = │ │ │ 22.635 \mathrm{J}\cdot\mathrm{mol}^{-1}\cdot A^{-2}$) slightly differs from the value suggested by Simonson/Br{"u}nger in their paper ( $6 \mathrm{cal}\cdot\mathrm{mol}^{-1}\cdot A^{-2} = 25.1 │ │ │ \mathrm{J}\cdot\mathrm{mol}^{-1}\cdot A^{-2}$).

    See also
    Option::SURFACE_TENSION
    │ │ │ │ │ │ -

    Definition at line 106 of file uhligCavFreeEnergyProcessor.h.

    │ │ │ +

    Definition at line 106 of file uhligCavFreeEnergyProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ VERBOSITY

    │ │ │ │ │ │
    │ │ │ @@ -194,15 +194,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │

    Default verbosity level.

    See also
    Option::VERBOSITY
    │ │ │ │ │ │ -

    Definition at line 87 of file uhligCavFreeEnergyProcessor.h.

    │ │ │ +

    Definition at line 87 of file uhligCavFreeEnergyProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/de2/a01442.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: forceField.h File Reference │ │ │ +BALL: maths.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,47 +65,28 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    │ │ │ -Classes | │ │ │ -Namespaces
    │ │ │ -
    forceField.h File Reference
    │ │ │ +
    maths.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/KERNEL/system.h>
    │ │ │ -#include <BALL/DATATYPE/options.h>
    │ │ │ -#include <BALL/CONCEPT/timeStamp.h>
    │ │ │ -#include <BALL/MOLMEC/PARAMETER/forceFieldParameters.h>
    │ │ │ -#include <BALL/MOLMEC/PARAMETER/atomTypes.h>
    │ │ │ -#include <BALL/MOLMEC/COMMON/periodicBoundary.h>
    │ │ │ -#include <BALL/MOLMEC/COMMON/atomVector.h>
    │ │ │ -#include <vector>
    │ │ │ -#include <BALL/MOLMEC/COMMON/forceField.iC>
    │ │ │ +
    #include <BALL/MATHS/analyticalGeometry.h>
    │ │ │ +#include <BALL/MATHS/angle.h>
    │ │ │ +#include <BALL/MATHS/box3.h>
    │ │ │ +#include <BALL/MATHS/matrix44.h>
    │ │ │ +#include <BALL/MATHS/quaternion.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -

    │ │ │ -Classes

    class  BALL::ForceField
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -

    │ │ │ -Namespaces

    namespace  BALL
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,29 +1,15 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _M_O_L_M_E_C │ │ │ │ - * _C_O_M_M_O_N │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -forceField.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_t_i_m_e_S_t_a_m_p_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_P_A_R_A_M_E_T_E_R_/_f_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_P_A_R_A_M_E_T_E_R_/_a_t_o_m_T_y_p_e_s_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h> │ │ │ │ -#include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_a_t_o_m_V_e_c_t_o_r_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ +maths.h File Reference │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_a_n_a_l_y_t_i_c_a_l_G_e_o_m_e_t_r_y_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_a_n_g_l_e_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_b_o_x_3_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_m_a_t_r_i_x_4_4_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_q_u_a_t_e_r_n_i_o_n_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ -  │ │ │ │ -NNaammeessppaacceess │ │ │ │ -namespace   _B_A_L_L │ │ │ │ -  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/de2/a01442_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: forceField.h Source File │ │ │ +BALL: maths.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,325 +70,57 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    forceField.h
    │ │ │ +
    maths.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4// $Id: forceField.h,v 1.33 2005/12/23 17:01:51 amoll Exp $
    │ │ │ -
    5//
    │ │ │ -
    6
    │ │ │ -
    7#ifndef BALL_MOLMEC_COMMON_FORCEFIELD_H
    │ │ │ -
    8#define BALL_MOLMEC_COMMON_FORCEFIELD_H
    │ │ │ -
    9
    │ │ │ -
    10#ifndef BALL_COMMON_H
    │ │ │ -
    11# include <BALL/common.h>
    │ │ │ -
    12#endif
    │ │ │ -
    13
    │ │ │ -
    14#ifndef BALL_KERNEL_SYSTEM_H
    │ │ │ -
    15# include <BALL/KERNEL/system.h>
    │ │ │ -
    16#endif
    │ │ │ -
    17
    │ │ │ -
    18#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ -
    19# include <BALL/DATATYPE/options.h>
    │ │ │ -
    20#endif
    │ │ │ -
    21
    │ │ │ -
    22#ifndef BALL_CONCEPT_TIMESTAMP_H
    │ │ │ -
    23# include <BALL/CONCEPT/timeStamp.h>
    │ │ │ -
    24#endif
    │ │ │ -
    25
    │ │ │ -
    26#ifndef BALL_MOLMEC_PARAMETER_FORCEFIELDPARAMETERS_H
    │ │ │ -
    27# include <BALL/MOLMEC/PARAMETER/forceFieldParameters.h>
    │ │ │ -
    28#endif
    │ │ │ -
    29
    │ │ │ -
    30#ifndef BALL_MOLMEC_PARAMETER_ATOMTYPES_H
    │ │ │ -
    31# include <BALL/MOLMEC/PARAMETER/atomTypes.h>
    │ │ │ -
    32#endif
    │ │ │ -
    33
    │ │ │ -
    34#ifndef BALL_MOLMEC_COMMON_PERIODIC_BOUNDARY_H
    │ │ │ -
    35# include <BALL/MOLMEC/COMMON/periodicBoundary.h>
    │ │ │ -
    36#endif
    │ │ │ -
    37
    │ │ │ -
    38#ifndef BALL_MOLMEC_COMMON_ATOMVECTOR_H
    │ │ │ -
    39# include <BALL/MOLMEC/COMMON/atomVector.h>
    │ │ │ -
    40#endif
    │ │ │ -
    41
    │ │ │ -
    42#include <vector>
    │ │ │ -
    43
    │ │ │ -
    44namespace BALL
    │ │ │ -
    45{
    │ │ │ -
    46 class ForceFieldComponent;
    │ │ │ -
    47
    │ │ │ -
    │ │ │ -
    85 class BALL_EXPORT ForceField
    │ │ │ -
    86 {
    │ │ │ -
    87 public:
    │ │ │ -
    88
    │ │ │ -
    89 friend class ForceFieldComponent;
    │ │ │ -
    90
    │ │ │ -
    94
    │ │ │ -
    99 typedef std::vector<std::pair<Atom*, Atom*> > PairVector;
    │ │ │ -
    100
    │ │ │ -
    102
    │ │ │ -
    105
    │ │ │ -
    106 BALL_CREATE(ForceField)
    │ │ │ -
    107
    │ │ │ -
    108
    │ │ │ -
    112 ForceField();
    │ │ │ -
    113
    │ │ │ -
    118 ForceField(System& system);
    │ │ │ -
    119
    │ │ │ -
    124 ForceField(System& system, const Options& options);
    │ │ │ -
    125
    │ │ │ -
    128 ForceField(const ForceField& force_field);
    │ │ │ -
    129
    │ │ │ -
    132 virtual ~ForceField();
    │ │ │ -
    133
    │ │ │ -
    136 virtual void clear()
    │ │ │ -
    137 ;
    │ │ │ -
    138
    │ │ │ -
    140
    │ │ │ -
    143
    │ │ │ -
    146 ForceField& operator = (const ForceField& force_field);
    │ │ │ -
    147
    │ │ │ -
    149
    │ │ │ -
    152
    │ │ │ -
    157 bool isValid() const
    │ │ │ -
    158 ;
    │ │ │ -
    159
    │ │ │ -
    161
    │ │ │ -
    164
    │ │ │ -
    167 bool setup(System& system);
    │ │ │ -
    168
    │ │ │ -
    171 bool setup(System& system, const Options& options);
    │ │ │ -
    172
    │ │ │ -
    177 virtual bool specificSetup();
    │ │ │ -
    178
    │ │ │ -
    183 void setMaximumNumberOfErrors(Size nr);
    │ │ │ -
    184
    │ │ │ -
    188 Size getMaximumNumberOfErrors() const;
    │ │ │ -
    189
    │ │ │ -
    191 HashSet<const Atom*>& getUnassignedAtoms();
    │ │ │ -
    192
    │ │ │ -
    194
    │ │ │ -
    197
    │ │ │ -
    200 void setName(const String& name);
    │ │ │ -
    201
    │ │ │ -
    204 String getName() const;
    │ │ │ -
    205
    │ │ │ -
    208 Size getNumberOfAtoms() const;
    │ │ │ -
    209
    │ │ │ -
    217 Size getNumberOfMovableAtoms() const;
    │ │ │ -
    218
    │ │ │ -
    221 BALL_INLINE
    │ │ │ -
    222 const AtomVector& getAtoms() const ;
    │ │ │ -
    223
    │ │ │ -
    226 BALL_INLINE
    │ │ │ -
    227 System* getSystem() ;
    │ │ │ -
    228
    │ │ │ -
    231 BALL_INLINE
    │ │ │ -
    232 const System* getSystem() const ;
    │ │ │ -
    233
    │ │ │ -
    236 BALL_INLINE
    │ │ │ -
    237 bool getUseSelection() const ;
    │ │ │ -
    238
    │ │ │ -
    241 BALL_INLINE
    │ │ │ -
    242 void disableSelection() ;
    │ │ │ -
    243
    │ │ │ -
    246 BALL_INLINE
    │ │ │ -
    247 void enableSelection() ;
    │ │ │ -
    248
    │ │ │ -
    250 BALL_INLINE
    │ │ │ -
    251 bool isSelectionEnabled() const ;
    │ │ │ -
    252
    │ │ │ -
    255 ForceFieldParameters& getParameters();
    │ │ │ -
    256
    │ │ │ -
    259 Size countComponents() const;
    │ │ │ -
    260
    │ │ │ -
    268 const TimeStamp& getUpdateTime() const
    │ │ │ -
    269 ;
    │ │ │ -
    270
    │ │ │ -
    278 const TimeStamp& getSetupTime() const
    │ │ │ -
    279 ;
    │ │ │ -
    280
    │ │ │ -
    285 void insertComponent(ForceFieldComponent* force_field_component);
    │ │ │ -
    286
    │ │ │ -
    290 void removeComponent(const ForceFieldComponent* force_field_component);
    │ │ │ -
    291
    │ │ │ -
    294 void removeComponent(const String& name);
    │ │ │ -
    295
    │ │ │ -
    301 ForceFieldComponent* getComponent(const Size index) const;
    │ │ │ -
    302
    │ │ │ -
    306 ForceFieldComponent* getComponent(const String& name) const;
    │ │ │ -
    307
    │ │ │ -
    313 double getEnergy() const;
    │ │ │ -
    314
    │ │ │ -
    317 double updateEnergy();
    │ │ │ -
    318
    │ │ │ -
    321 void updateForces();
    │ │ │ -
    322
    │ │ │ -
    325 double getRMSGradient() const;
    │ │ │ -
    326
    │ │ │ -
    331 virtual Size getUpdateFrequency() const;
    │ │ │ -
    332
    │ │ │ -
    342 virtual void update();
    │ │ │ -
    343
    │ │ │ -
    │ │ │ -
    347 virtual String getResults() const
    │ │ │ -
    348 { return "undefined";}
    │ │ │ -
    │ │ │ -
    349
    │ │ │ -
    350 //_ Report an error and increase the error counter
    │ │ │ -
    351 std::ostream& error();
    │ │ │ -
    352
    │ │ │ -
    354
    │ │ │ -
    357
    │ │ │ -
    360 Options options;
    │ │ │ -
    361
    │ │ │ -
    364 PeriodicBoundary periodic_boundary;
    │ │ │ -
    365
    │ │ │ -
    367
    │ │ │ -
    368 protected:
    │ │ │ -
    369 /*_ Collect all atoms into the atoms_ vector.
    │ │ │ -
    370 */
    │ │ │ -
    371 void collectAtoms_(const System& system);
    │ │ │ -
    372
    │ │ │ -
    373 /*_ Sort the atom vector wrt selection.
    │ │ │ -
    374 */
    │ │ │ -
    375 void sortSelectedAtomVector_();
    │ │ │ -
    376
    │ │ │ -
    380 virtual void performRequiredUpdates_();
    │ │ │ -
    381
    │ │ │ -
    382 /*_ @name Protected Attributes
    │ │ │ -
    383 */
    │ │ │ -
    384 //_@{
    │ │ │ -
    385
    │ │ │ -
    386 /*_ The system the force field is bound to
    │ │ │ -
    387 */
    │ │ │ -
    388 System* system_;
    │ │ │ -
    389
    │ │ │ -
    390 /*_ The atoms in the simulated system
    │ │ │ -
    391 */
    │ │ │ -
    392 AtomVector atoms_;
    │ │ │ -
    393
    │ │ │ -
    394 /*_ An object containing the force field parameters read from a file
    │ │ │ -
    395 */
    │ │ │ -
    396 ForceFieldParameters parameters_;
    │ │ │ -
    397
    │ │ │ -
    398 /*_ The boolean variable indicates if the setup of the force field was successful
    │ │ │ -
    399 */
    │ │ │ -
    400 bool valid_;
    │ │ │ -
    401
    │ │ │ -
    402 /*_ The force field name
    │ │ │ -
    403 */
    │ │ │ -
    404 String name_;
    │ │ │ -
    405
    │ │ │ -
    406 /*_ The total energy
    │ │ │ -
    407 */
    │ │ │ -
    408 double energy_;
    │ │ │ -
    409
    │ │ │ -
    410 /*_ The components of the force field
    │ │ │ -
    411 */
    │ │ │ -
    412 vector<ForceFieldComponent*> components_;
    │ │ │ -
    413
    │ │ │ -
    414 /*_ The number of movable atoms in the force field
    │ │ │ -
    415 */
    │ │ │ -
    416 Size number_of_movable_atoms_;
    │ │ │ -
    417
    │ │ │ -
    418 /*_ Do we have to check whether atoms are selected?
    │ │ │ -
    419 */
    │ │ │ -
    420 bool use_selection_;
    │ │ │ -
    421
    │ │ │ -
    422 /*_ This flag can temporarily disable the selection.
    │ │ │ -
    423 */
    │ │ │ -
    424 bool selection_enabled_;
    │ │ │ -
    425
    │ │ │ -
    426 /*_ The time of the last call to update.
    │ │ │ -
    427 */
    │ │ │ -
    428 TimeStamp update_time_stamp_;
    │ │ │ -
    429
    │ │ │ -
    430 /*_ The time of the last call to setup.
    │ │ │ -
    431 */
    │ │ │ -
    432 TimeStamp setup_time_stamp_;
    │ │ │ -
    433
    │ │ │ -
    434 //_ Atoms, for which the setup of the force field fails
    │ │ │ -
    435 HashSet<const Atom*> unassigned_atoms_;
    │ │ │ -
    436
    │ │ │ -
    437 //_ max number of unassigned atoms
    │ │ │ -
    438 Size max_number_of_errors_;
    │ │ │ -
    439
    │ │ │ -
    440 Size number_of_errors_;
    │ │ │ -
    441
    │ │ │ -
    442 //_@}
    │ │ │ -
    443 };
    │ │ │ -
    │ │ │ -
    444
    │ │ │ -
    445# ifndef BALL_NO_INLINE_FUNCTIONS
    │ │ │ -
    446# include <BALL/MOLMEC/COMMON/forceField.iC>
    │ │ │ -
    447# endif
    │ │ │ -
    448
    │ │ │ -
    449} // namespace BALL
    │ │ │ -
    450
    │ │ │ -
    451#endif // BALL_MOLMEC_COMMON_FORCEFIELD_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_INLINE
    #define BALL_INLINE
    Definition debug.h:15
    │ │ │ -
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::ForceField::error
    std::ostream & error()
    │ │ │ -
    BALL::ForceField::periodic_boundary
    PeriodicBoundary periodic_boundary
    Definition forceField.h:364
    │ │ │ -
    BALL::ForceField::PairVector
    std::vector< std::pair< Atom *, Atom * > > PairVector
    Definition forceField.h:99
    │ │ │ -
    BALL::ForceField::max_number_of_errors_
    Size max_number_of_errors_
    Definition forceField.h:438
    │ │ │ - │ │ │ -
    BALL::ForceField::number_of_movable_atoms_
    Size number_of_movable_atoms_
    Definition forceField.h:416
    │ │ │ - │ │ │ -
    BALL::ForceField::parameters_
    ForceFieldParameters parameters_
    Definition forceField.h:396
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ForceField::components_
    vector< ForceFieldComponent * > components_
    Definition forceField.h:412
    │ │ │ -
    BALL::ForceField::collectAtoms_
    void collectAtoms_(const System &system)
    │ │ │ - │ │ │ -
    BALL::ForceField::sortSelectedAtomVector_
    void sortSelectedAtomVector_()
    │ │ │ -
    BALL::ForceField::atoms_
    AtomVector atoms_
    Definition forceField.h:392
    │ │ │ -
    BALL::ForceField::setup_time_stamp_
    TimeStamp setup_time_stamp_
    Definition forceField.h:432
    │ │ │ -
    BALL::ForceField::performRequiredUpdates_
    virtual void performRequiredUpdates_()
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::ForceField::update_time_stamp_
    TimeStamp update_time_stamp_
    Definition forceField.h:428
    │ │ │ -
    BALL::ForceField::unassigned_atoms_
    HashSet< const Atom * > unassigned_atoms_
    Definition forceField.h:435
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ - │ │ │ +
    4// $Id: maths.h,v 1.2 2002/02/27 12:18:18 sturm Exp $
    │ │ │ +
    5// MATHS header file
    │ │ │ +
    6// collective header file for all headers in BALL/MATHS
    │ │ │ +
    7
    │ │ │ +
    8#ifndef BALL_MATHS_H
    │ │ │ +
    9#define BALL_MATHS_H
    │ │ │ +
    10
    │ │ │ +
    11#ifndef BALL_MATHS_ANALYTICALGEOMETRY_H
    │ │ │ +
    12# include <BALL/MATHS/analyticalGeometry.h>
    │ │ │ +
    13#endif
    │ │ │ +
    14
    │ │ │ +
    15#ifndef BALL_MATHS_ANGLE_H
    │ │ │ +
    16# include <BALL/MATHS/angle.h>
    │ │ │ +
    17#endif
    │ │ │ +
    18
    │ │ │ +
    19#ifndef BALL_MATHS_BOX3_H
    │ │ │ +
    20# include <BALL/MATHS/box3.h>
    │ │ │ +
    21#endif
    │ │ │ +
    22
    │ │ │ +
    23#ifndef BALL_MATHS_MATRIX44_H
    │ │ │ +
    24# include <BALL/MATHS/matrix44.h>
    │ │ │ +
    25#endif
    │ │ │ +
    26
    │ │ │ +
    27#ifndef BALL_MATHS_QUATERNION_H
    │ │ │ +
    28# include <BALL/MATHS/quaternion.h>
    │ │ │ +
    29#endif
    │ │ │ +
    30
    │ │ │ +
    31#endif // BALL_MATHS_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,371 +1,46 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _M_O_L_M_E_C │ │ │ │ - * _C_O_M_M_O_N │ │ │ │ -forceField.h │ │ │ │ +maths.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: forceField.h,v 1.33 2005/12/23 17:01:51 amoll Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_MOLMEC_COMMON_FORCEFIELD_H │ │ │ │ -8#define BALL_MOLMEC_COMMON_FORCEFIELD_H │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_COMMON_H │ │ │ │ -11# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -12#endif │ │ │ │ -13 │ │ │ │ -14#ifndef BALL_KERNEL_SYSTEM_H │ │ │ │ -15# include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ -16#endif │ │ │ │ -17 │ │ │ │ -18#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ -19# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ -20#endif │ │ │ │ -21 │ │ │ │ -22#ifndef BALL_CONCEPT_TIMESTAMP_H │ │ │ │ -23# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_t_i_m_e_S_t_a_m_p_._h> │ │ │ │ -24#endif │ │ │ │ -25 │ │ │ │ -26#ifndef BALL_MOLMEC_PARAMETER_FORCEFIELDPARAMETERS_H │ │ │ │ -27# include <_B_A_L_L_/_M_O_L_M_E_C_/_P_A_R_A_M_E_T_E_R_/_f_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s_._h> │ │ │ │ -28#endif │ │ │ │ -29 │ │ │ │ -30#ifndef BALL_MOLMEC_PARAMETER_ATOMTYPES_H │ │ │ │ -31# include <_B_A_L_L_/_M_O_L_M_E_C_/_P_A_R_A_M_E_T_E_R_/_a_t_o_m_T_y_p_e_s_._h> │ │ │ │ -32#endif │ │ │ │ -33 │ │ │ │ -34#ifndef BALL_MOLMEC_COMMON_PERIODIC_BOUNDARY_H │ │ │ │ -35# include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h> │ │ │ │ -36#endif │ │ │ │ -37 │ │ │ │ -38#ifndef BALL_MOLMEC_COMMON_ATOMVECTOR_H │ │ │ │ -39# include <_B_A_L_L_/_M_O_L_M_E_C_/_C_O_M_M_O_N_/_a_t_o_m_V_e_c_t_o_r_._h> │ │ │ │ -40#endif │ │ │ │ -41 │ │ │ │ -42#include │ │ │ │ -43 │ │ │ │ -44namespace _B_A_L_L │ │ │ │ -45{ │ │ │ │ -46 class ForceFieldComponent; │ │ │ │ -47 │ │ │ │ -_8_5 class _B_A_L_L___E_X_P_O_R_T _F_o_r_c_e_F_i_e_l_d │ │ │ │ -86 { │ │ │ │ -87 public: │ │ │ │ -88 │ │ │ │ -_8_9 friend class _F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t; │ │ │ │ -90 │ │ │ │ -94 │ │ │ │ -_9_9 typedef std::vector > _P_a_i_r_V_e_c_t_o_r; │ │ │ │ -100 │ │ │ │ -102 │ │ │ │ -105 │ │ │ │ -106 _B_A_L_L___C_R_E_A_T_E(_F_o_r_c_e_F_i_e_l_d) │ │ │ │ -107 │ │ │ │ -108 │ │ │ │ -_1_1_2 _F_o_r_c_e_F_i_e_l_d(); │ │ │ │ -113 │ │ │ │ -_1_1_8 _F_o_r_c_e_F_i_e_l_d(_S_y_s_t_e_m& system); │ │ │ │ -119 │ │ │ │ -_1_2_4 _F_o_r_c_e_F_i_e_l_d(_S_y_s_t_e_m& system, const _O_p_t_i_o_n_s& options); │ │ │ │ -125 │ │ │ │ -_1_2_8 _F_o_r_c_e_F_i_e_l_d(const _F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ -129 │ │ │ │ -_1_3_2 virtual ~_F_o_r_c_e_F_i_e_l_d(); │ │ │ │ -133 │ │ │ │ -_1_3_6 virtual void clear() │ │ │ │ -137 ; │ │ │ │ -138 │ │ │ │ -140 │ │ │ │ -143 │ │ │ │ -_1_4_6 _F_o_r_c_e_F_i_e_l_d& operator = (const _F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ -147 │ │ │ │ -149 │ │ │ │ -152 │ │ │ │ -_1_5_7 bool isValid() const │ │ │ │ -158 ; │ │ │ │ -159 │ │ │ │ -161 │ │ │ │ -164 │ │ │ │ -_1_6_7 bool setup(_S_y_s_t_e_m& system); │ │ │ │ -168 │ │ │ │ -_1_7_1 bool setup(_S_y_s_t_e_m& system, const _O_p_t_i_o_n_s& options); │ │ │ │ -172 │ │ │ │ -_1_7_7 virtual bool specificSetup(); │ │ │ │ -178 │ │ │ │ -_1_8_3 void setMaximumNumberOfErrors(_S_i_z_e nr); │ │ │ │ -184 │ │ │ │ -_1_8_8 _S_i_z_e getMaximumNumberOfErrors() const; │ │ │ │ -189 │ │ │ │ -_1_9_1 _H_a_s_h_S_e_t& getUnassignedAtoms(); │ │ │ │ -192 │ │ │ │ -194 │ │ │ │ -197 │ │ │ │ -_2_0_0 void setName(const _S_t_r_i_n_g& name); │ │ │ │ -201 │ │ │ │ -_2_0_4 _S_t_r_i_n_g getName() const; │ │ │ │ -205 │ │ │ │ -_2_0_8 _S_i_z_e getNumberOfAtoms() const; │ │ │ │ -209 │ │ │ │ -_2_1_7 _S_i_z_e getNumberOfMovableAtoms() const; │ │ │ │ -218 │ │ │ │ -221 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_2_2 const _A_t_o_m_V_e_c_t_o_r& getAtoms() const ; │ │ │ │ -223 │ │ │ │ -226 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_2_7 _S_y_s_t_e_m* getSystem() ; │ │ │ │ -228 │ │ │ │ -231 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_3_2 const _S_y_s_t_e_m* getSystem() const ; │ │ │ │ -233 │ │ │ │ -236 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_3_7 bool getUseSelection() const ; │ │ │ │ -238 │ │ │ │ -241 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_4_2 void disableSelection() ; │ │ │ │ -243 │ │ │ │ -246 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_4_7 void enableSelection() ; │ │ │ │ -248 │ │ │ │ -250 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_2_5_1 bool isSelectionEnabled() const ; │ │ │ │ -252 │ │ │ │ -_2_5_5 _F_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s& getParameters(); │ │ │ │ -256 │ │ │ │ -_2_5_9 _S_i_z_e countComponents() const; │ │ │ │ -260 │ │ │ │ -_2_6_8 const _T_i_m_e_S_t_a_m_p& getUpdateTime() const │ │ │ │ -269 ; │ │ │ │ -270 │ │ │ │ -_2_7_8 const _T_i_m_e_S_t_a_m_p& getSetupTime() const │ │ │ │ -279 ; │ │ │ │ -280 │ │ │ │ -_2_8_5 void insertComponent(_F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t* force_field_component); │ │ │ │ -286 │ │ │ │ -_2_9_0 void removeComponent(const _F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t* force_field_component); │ │ │ │ -291 │ │ │ │ -_2_9_4 void removeComponent(const _S_t_r_i_n_g& name); │ │ │ │ -295 │ │ │ │ -_3_0_1 _F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t* getComponent(const _S_i_z_e index) const; │ │ │ │ -302 │ │ │ │ -_3_0_6 _F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t* getComponent(const _S_t_r_i_n_g& name) const; │ │ │ │ -307 │ │ │ │ -_3_1_3 double getEnergy() const; │ │ │ │ -314 │ │ │ │ -_3_1_7 double updateEnergy(); │ │ │ │ -318 │ │ │ │ -_3_2_1 void updateForces(); │ │ │ │ -322 │ │ │ │ -_3_2_5 double getRMSGradient() const; │ │ │ │ -326 │ │ │ │ -_3_3_1 virtual _S_i_z_e getUpdateFrequency() const; │ │ │ │ -332 │ │ │ │ -_3_4_2 virtual void update(); │ │ │ │ -343 │ │ │ │ -_3_4_7 virtual _S_t_r_i_n_g getResults() const │ │ │ │ -348 { return "undefined";} │ │ │ │ -349 │ │ │ │ -350 //_ Report an error and increase the error counter │ │ │ │ -_3_5_1 std::ostream& _e_r_r_o_r(); │ │ │ │ -352 │ │ │ │ -354 │ │ │ │ -357 │ │ │ │ -_3_6_0 _O_p_t_i_o_n_s _o_p_t_i_o_n_s; │ │ │ │ -361 │ │ │ │ -_3_6_4 _P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y _p_e_r_i_o_d_i_c___b_o_u_n_d_a_r_y; │ │ │ │ -365 │ │ │ │ -367 │ │ │ │ -368 protected: │ │ │ │ -369 /*_ Collect all atoms into the atoms_ vector. │ │ │ │ -370 */ │ │ │ │ -_3_7_1 void _c_o_l_l_e_c_t_A_t_o_m_s__(const _S_y_s_t_e_m& system); │ │ │ │ -372 │ │ │ │ -373 /*_ Sort the atom vector wrt selection. │ │ │ │ -374 */ │ │ │ │ -_3_7_5 void _s_o_r_t_S_e_l_e_c_t_e_d_A_t_o_m_V_e_c_t_o_r__(); │ │ │ │ -376 │ │ │ │ -_3_8_0 virtual void _p_e_r_f_o_r_m_R_e_q_u_i_r_e_d_U_p_d_a_t_e_s__(); │ │ │ │ -381 │ │ │ │ -382 /*_ @name Protected Attributes │ │ │ │ -383 */ │ │ │ │ -384 //_@{ │ │ │ │ -385 │ │ │ │ -386 /*_ The system the force field is bound to │ │ │ │ -387 */ │ │ │ │ -_3_8_8 _S_y_s_t_e_m* _s_y_s_t_e_m__; │ │ │ │ -389 │ │ │ │ -390 /*_ The atoms in the simulated system │ │ │ │ -391 */ │ │ │ │ -_3_9_2 _A_t_o_m_V_e_c_t_o_r _a_t_o_m_s__; │ │ │ │ -393 │ │ │ │ -394 /*_ An object containing the force field parameters read from a file │ │ │ │ -395 */ │ │ │ │ -_3_9_6 _F_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s _p_a_r_a_m_e_t_e_r_s__; │ │ │ │ -397 │ │ │ │ -398 /*_ The boolean variable indicates if the setup of the force field was │ │ │ │ -successful │ │ │ │ -399 */ │ │ │ │ -_4_0_0 bool _v_a_l_i_d__; │ │ │ │ -401 │ │ │ │ -402 /*_ The force field name │ │ │ │ -403 */ │ │ │ │ -_4_0_4 _S_t_r_i_n_g _n_a_m_e__; │ │ │ │ -405 │ │ │ │ -406 /*_ The total energy │ │ │ │ -407 */ │ │ │ │ -_4_0_8 double _e_n_e_r_g_y__; │ │ │ │ -409 │ │ │ │ -410 /*_ The components of the force field │ │ │ │ -411 */ │ │ │ │ -_4_1_2 vector _c_o_m_p_o_n_e_n_t_s__; │ │ │ │ -413 │ │ │ │ -414 /*_ The number of movable atoms in the force field │ │ │ │ -415 */ │ │ │ │ -_4_1_6 _S_i_z_e _n_u_m_b_e_r___o_f___m_o_v_a_b_l_e___a_t_o_m_s__; │ │ │ │ -417 │ │ │ │ -418 /*_ Do we have to check whether atoms are selected? │ │ │ │ -419 */ │ │ │ │ -_4_2_0 bool _u_s_e___s_e_l_e_c_t_i_o_n__; │ │ │ │ -421 │ │ │ │ -422 /*_ This flag can temporarily disable the selection. │ │ │ │ -423 */ │ │ │ │ -_4_2_4 bool _s_e_l_e_c_t_i_o_n___e_n_a_b_l_e_d__; │ │ │ │ -425 │ │ │ │ -426 /*_ The time of the last call to update. │ │ │ │ -427 */ │ │ │ │ -_4_2_8 _T_i_m_e_S_t_a_m_p _u_p_d_a_t_e___t_i_m_e___s_t_a_m_p__; │ │ │ │ -429 │ │ │ │ -430 /*_ The time of the last call to setup. │ │ │ │ -431 */ │ │ │ │ -_4_3_2 _T_i_m_e_S_t_a_m_p _s_e_t_u_p___t_i_m_e___s_t_a_m_p__; │ │ │ │ -433 │ │ │ │ -434 //_ Atoms, for which the setup of the force field fails │ │ │ │ -_4_3_5 _H_a_s_h_S_e_t_<_c_o_n_s_t_ _A_t_o_m_*_> _u_n_a_s_s_i_g_n_e_d___a_t_o_m_s__; │ │ │ │ -436 │ │ │ │ -437 //_ max number of unassigned atoms │ │ │ │ -_4_3_8 _S_i_z_e _m_a_x___n_u_m_b_e_r___o_f___e_r_r_o_r_s__; │ │ │ │ -439 │ │ │ │ -_4_4_0 _S_i_z_e _n_u_m_b_e_r___o_f___e_r_r_o_r_s__; │ │ │ │ -441 │ │ │ │ -442 //_@} │ │ │ │ -443 }; │ │ │ │ -444 │ │ │ │ -445# ifndef BALL_NO_INLINE_FUNCTIONS │ │ │ │ -446# include │ │ │ │ -447# endif │ │ │ │ -448 │ │ │ │ -449} // namespace BALL │ │ │ │ -450 │ │ │ │ -451#endif // BALL_MOLMEC_COMMON_FORCEFIELD_H │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_f_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s_._h │ │ │ │ -_a_t_o_m_T_y_p_e_s_._h │ │ │ │ -_p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h │ │ │ │ -_a_t_o_m_V_e_c_t_o_r_._h │ │ │ │ -_o_p_t_i_o_n_s_._h │ │ │ │ -_t_i_m_e_S_t_a_m_p_._h │ │ │ │ -_B_A_L_L___I_N_L_I_N_E │ │ │ │ -#define BALL_INLINE │ │ │ │ -DDeeffiinniittiioonn _d_e_b_u_g_._h_:_1_5 │ │ │ │ -_B_A_L_L___C_R_E_A_T_E │ │ │ │ -#define BALL_CREATE(name) │ │ │ │ -DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ -_B_A_L_L │ │ │ │ -DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_T_i_m_e_S_t_a_m_p │ │ │ │ -DDeeffiinniittiioonn _t_i_m_e_S_t_a_m_p_._h_:_1_7_2 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_S_e_t │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_S_e_t_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ -DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ -DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_A_t_o_m_V_e_c_t_o_r │ │ │ │ -DDeeffiinniittiioonn _a_t_o_m_V_e_c_t_o_r_._h_:_3_1 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_e_r_r_o_r │ │ │ │ -std::ostream & error() │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_p_e_r_i_o_d_i_c___b_o_u_n_d_a_r_y │ │ │ │ -PeriodicBoundary periodic_boundary │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_3_6_4 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_P_a_i_r_V_e_c_t_o_r │ │ │ │ -std::vector< std::pair< Atom *, Atom * > > PairVector │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_9_9 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_m_a_x___n_u_m_b_e_r___o_f___e_r_r_o_r_s__ │ │ │ │ -Size max_number_of_errors_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_3_8 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_o_p_t_i_o_n_s │ │ │ │ -Options options │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_3_6_0 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_n_u_m_b_e_r___o_f___m_o_v_a_b_l_e___a_t_o_m_s__ │ │ │ │ -Size number_of_movable_atoms_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_1_6 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_u_s_e___s_e_l_e_c_t_i_o_n__ │ │ │ │ -bool use_selection_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_2_0 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_p_a_r_a_m_e_t_e_r_s__ │ │ │ │ -ForceFieldParameters parameters_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_3_9_6 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_n_a_m_e__ │ │ │ │ -String name_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_0_4 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_s_y_s_t_e_m__ │ │ │ │ -System * system_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_3_8_8 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_c_o_m_p_o_n_e_n_t_s__ │ │ │ │ -vector< ForceFieldComponent * > components_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_1_2 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_c_o_l_l_e_c_t_A_t_o_m_s__ │ │ │ │ -void collectAtoms_(const System &system) │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_n_u_m_b_e_r___o_f___e_r_r_o_r_s__ │ │ │ │ -Size number_of_errors_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_4_0 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_s_o_r_t_S_e_l_e_c_t_e_d_A_t_o_m_V_e_c_t_o_r__ │ │ │ │ -void sortSelectedAtomVector_() │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_a_t_o_m_s__ │ │ │ │ -AtomVector atoms_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_3_9_2 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_s_e_t_u_p___t_i_m_e___s_t_a_m_p__ │ │ │ │ -TimeStamp setup_time_stamp_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_3_2 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_p_e_r_f_o_r_m_R_e_q_u_i_r_e_d_U_p_d_a_t_e_s__ │ │ │ │ -virtual void performRequiredUpdates_() │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_e_n_e_r_g_y__ │ │ │ │ -double energy_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_0_8 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_v_a_l_i_d__ │ │ │ │ -bool valid_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_0_0 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_s_e_l_e_c_t_i_o_n___e_n_a_b_l_e_d__ │ │ │ │ -bool selection_enabled_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_2_4 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_u_p_d_a_t_e___t_i_m_e___s_t_a_m_p__ │ │ │ │ -TimeStamp update_time_stamp_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_2_8 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_:_:_u_n_a_s_s_i_g_n_e_d___a_t_o_m_s__ │ │ │ │ -HashSet< const Atom * > unassigned_atoms_ │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_4_3_5 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_C_o_m_p_o_n_e_n_t_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_P_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y │ │ │ │ -DDeeffiinniittiioonn _p_e_r_i_o_d_i_c_B_o_u_n_d_a_r_y_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s │ │ │ │ -DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_P_a_r_a_m_e_t_e_r_s_._h_:_3_1 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ -_s_y_s_t_e_m_._h │ │ │ │ +4// $Id: maths.h,v 1.2 2002/02/27 12:18:18 sturm Exp $ │ │ │ │ +5// MATHS header file │ │ │ │ +6// collective header file for all headers in BALL/MATHS │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_MATHS_H │ │ │ │ +9#define BALL_MATHS_H │ │ │ │ +10 │ │ │ │ +11#ifndef BALL_MATHS_ANALYTICALGEOMETRY_H │ │ │ │ +12# include <_B_A_L_L_/_M_A_T_H_S_/_a_n_a_l_y_t_i_c_a_l_G_e_o_m_e_t_r_y_._h> │ │ │ │ +13#endif │ │ │ │ +14 │ │ │ │ +15#ifndef BALL_MATHS_ANGLE_H │ │ │ │ +16# include <_B_A_L_L_/_M_A_T_H_S_/_a_n_g_l_e_._h> │ │ │ │ +17#endif │ │ │ │ +18 │ │ │ │ +19#ifndef BALL_MATHS_BOX3_H │ │ │ │ +20# include <_B_A_L_L_/_M_A_T_H_S_/_b_o_x_3_._h> │ │ │ │ +21#endif │ │ │ │ +22 │ │ │ │ +23#ifndef BALL_MATHS_MATRIX44_H │ │ │ │ +24# include <_B_A_L_L_/_M_A_T_H_S_/_m_a_t_r_i_x_4_4_._h> │ │ │ │ +25#endif │ │ │ │ +26 │ │ │ │ +27#ifndef BALL_MATHS_QUATERNION_H │ │ │ │ +28# include <_B_A_L_L_/_M_A_T_H_S_/_q_u_a_t_e_r_n_i_o_n_._h> │ │ │ │ +29#endif │ │ │ │ +30 │ │ │ │ +31#endif // BALL_MATHS_H │ │ │ │ +_q_u_a_t_e_r_n_i_o_n_._h │ │ │ │ +_a_n_g_l_e_._h │ │ │ │ +_m_a_t_r_i_x_4_4_._h │ │ │ │ +_a_n_a_l_y_t_i_c_a_l_G_e_o_m_e_t_r_y_._h │ │ │ │ +_b_o_x_3_._h │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/de3/a04138.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Public Attributes | │ │ │ List of all members │ │ │
    BALL::PDB::RecordCON061 Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/FORMAT/PDBdefs.h>

    │ │ │ +

    #include <BALL/FORMAT/PDBdefs.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    void clear ()
     
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ @@ -97,15 +97,15 @@ │ │ │

    Integer atom_serial_number
     
    Integer bond_atom [4]
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 497 of file PDBdefs.h.

    │ │ │ +

    Definition at line 497 of file PDBdefs.h.

    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ clear()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -122,15 +122,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
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    Definition at line 504 of file PDBdefs.h.

    │ │ │ +

    Definition at line 504 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ atom_serial_number

    │ │ │ │ │ │ @@ -139,15 +139,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Integer BALL::PDB::RecordCON061::atom_serial_number
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 501 of file PDBdefs.h.

    │ │ │ +

    Definition at line 501 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ bond_atom

    │ │ │ │ │ │
    │ │ │ @@ -155,15 +155,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Integer BALL::PDB::RecordCON061::bond_atom[4]
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 502 of file PDBdefs.h.

    │ │ │ +

    Definition at line 502 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ record_name

    │ │ │ │ │ │
    │ │ │ @@ -171,15 +171,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    RecordName BALL::PDB::RecordCON061::record_name
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 500 of file PDBdefs.h.

    │ │ │ +

    Definition at line 500 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ record_type

    │ │ │ │ │ │
    │ │ │ @@ -187,15 +187,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    RecordType BALL::PDB::RecordCON061::record_type
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 499 of file PDBdefs.h.

    │ │ │ +

    Definition at line 499 of file PDBdefs.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/de6/a04814.html │ │ │ @@ -76,40 +76,40 @@ │ │ │
    │ │ │ Public Types | │ │ │ List of all members
    │ │ │
    BALL::FloatTraits Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/MATHS/fftwCommon.h>

    │ │ │ +

    #include <BALL/MATHS/fftwCommon.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Types

    typedef float ComplexPrecision
     
    typedef fftwf_plan FftwPlan
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 22 of file fftwCommon.h.

    │ │ │ +

    Definition at line 22 of file fftwCommon.h.

    │ │ │

    Member Typedef Documentation

    │ │ │ │ │ │

    ◆ ComplexPrecision

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef float BALL::FloatTraits::ComplexPrecision
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 24 of file fftwCommon.h.

    │ │ │ +

    Definition at line 24 of file fftwCommon.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ FftwPlan

    │ │ │ │ │ │
    │ │ │ @@ -117,15 +117,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef fftwf_plan BALL::FloatTraits::FftwPlan
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 25 of file fftwCommon.h.

    │ │ │ +

    Definition at line 25 of file fftwCommon.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/de9/a03530.html │ │ │ @@ -79,15 +79,15 @@ │ │ │
    BALL::HashMap< Key, T > Class Template Reference
    │ │ │ │ │ │
    │ │ │ │ │ │

    HashMap class based on the STL map (containing serveral convenience functions) │ │ │ More...

    │ │ │ │ │ │ -

    #include <BALL/DATATYPE/hashMap.h>

    │ │ │ +

    #include <BALL/DATATYPE/hashMap.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::HashMap< Key, T >:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::StringHashMap< String > │ │ │ @@ -156,15 +156,15 @@ │ │ │ Size size () const │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │
    template<class Key, class T>
    │ │ │ class BALL::HashMap< Key, T >

    HashMap class based on the STL map (containing serveral convenience functions)

    │ │ │ │ │ │ -

    Definition at line 73 of file hashMap.h.

    │ │ │ +

    Definition at line 73 of file hashMap.h.

    │ │ │

    Member Typedef Documentation

    │ │ │ │ │ │

    ◆ Base

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ @@ -172,15 +172,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef boost::unordered_map<Key, T> BALL::HashMap< Key, T >::Base
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 93 of file hashMap.h.

    │ │ │ +

    Definition at line 93 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ ConstIterator

    │ │ │ │ │ │
    │ │ │ @@ -190,15 +190,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Base::const_iterator BALL::HashMap< Key, T >::ConstIterator
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 98 of file hashMap.h.

    │ │ │ +

    Definition at line 98 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ Iterator

    │ │ │ │ │ │
    │ │ │ @@ -208,15 +208,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Base::iterator BALL::HashMap< Key, T >::Iterator
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 97 of file hashMap.h.

    │ │ │ +

    Definition at line 97 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ KeyType

    │ │ │ │ │ │
    │ │ │ @@ -226,15 +226,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Key BALL::HashMap< Key, T >::KeyType
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 95 of file hashMap.h.

    │ │ │ +

    Definition at line 95 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ PointerType

    │ │ │ │ │ │
    │ │ │ @@ -244,15 +244,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Base::value_type* BALL::HashMap< Key, T >::PointerType
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 96 of file hashMap.h.

    │ │ │ +

    Definition at line 96 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ ValueType

    │ │ │ │ │ │
    │ │ │ @@ -262,15 +262,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Base::value_type BALL::HashMap< Key, T >::ValueType
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 94 of file hashMap.h.

    │ │ │ +

    Definition at line 94 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ has()

    │ │ │ │ │ │ @@ -295,15 +295,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Test whether the map contains the given key.

    │ │ │ │ │ │ -

    Definition at line 102 of file hashMap.h.

    │ │ │ +

    Definition at line 102 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator==()

    │ │ │ │ │ │
    │ │ │ @@ -319,15 +319,15 @@ │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Equality operator. Check whether two two hashmaps contain the same elements. O(n) runtime.

    │ │ │ │ │ │ -

    Definition at line 144 of file hashMap.h.

    │ │ │ +

    Definition at line 144 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator[]() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -343,15 +343,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Return a mutable reference to the element whose key is key. If an element with the key key does not exist, it is inserted.

    │ │ │ │ │ │ -

    Definition at line 165 of file hashMap.h.

    │ │ │ +

    Definition at line 165 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator[]() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -373,15 +373,15 @@ │ │ │
    Exceptions
    │ │ │ │ │ │ │ │ │
    IllegalKeyif the given key does not exist
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 130 of file hashMap.h.

    │ │ │ +

    Definition at line 130 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ size()

    │ │ │ │ │ │
    │ │ │ @@ -403,15 +403,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Return the size of the hash map. TODO: Remove this. This narrows the precision of size_t! (But of course breaks persistence...)

    │ │ │ │ │ │ -

    Definition at line 122 of file hashMap.h.

    │ │ │ +

    Definition at line 122 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/deb/a01508.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: vector3.h File Reference │ │ │ +BALL: circle3.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -72,48 +72,41 @@ │ │ │
  • include
  • BALL
  • MATHS
    • │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    vector3.h File Reference
    │ │ │ +
    circle3.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/COMMON/exception.h>
    │ │ │ -#include <BALL/CONCEPT/persistenceManager.h>
    │ │ │ -#include <BALL/MATHS/angle.h>
    │ │ │ -#include <BALL/MATHS/common.h>
    │ │ │ +
    #include <BALL/COMMON/exception.h>
    │ │ │ +#include <BALL/MATHS/vector3.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::TVector3< T >
    class  BALL::TCircle3< T >
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │

    Global binary operators for three-dimensional vectors.

    typedef TVector3< float > BALL::Vector3
     
    template class BALL_EXPORT BALL::TVector3< float >
     
    template<typename T >
    BALL_INLINE TVector3< T > BALL::operator* (const T &a, const TVector3< T > &b)
     
    template<typename T >
    std::istream & BALL::operator>> (std::istream &s, TVector3< T > &vector)
     
    template<typename T >
    std::ostream & BALL::operator<< (std::ostream &s, const TVector3< T > &vector)
     

    Storers

    typedef TCircle3< float > BALL::Circle3
     
    template<typename T >
    std::istream & BALL::operator>> (std::istream &s, TCircle3< T > &circle)
     
    template<typename T >
    std::ostream & BALL::operator<< (std::ostream &s, const TCircle3< T > &circle)
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -2,38 +2,30 @@ │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _M_A_T_H_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -vector3.h File Reference │ │ │ │ +circle3.h File Reference │ │ │ │ #include <_B_A_L_L_/_C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h> │ │ │ │ -#include <_B_A_L_L_/_M_A_T_H_S_/_a_n_g_l_e_._h> │ │ │ │ -#include <_B_A_L_L_/_M_A_T_H_S_/_c_o_m_m_o_n_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _T_ _> │ │ │ │ +class   _B_A_L_L_:_:_T_C_i_r_c_l_e_3_<_ _T_ _> │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -********** GGlloobbaall bbiinnaarryy ooppeerraattoorrss ffoorr tthhrreeee--ddiimmeennssiioonnaall vveeccttoorrss.. ********** │ │ │ │ - typedef _T_V_e_c_t_o_r_3< _f_l_o_a_t >  _B_A_L_L_:_:_V_e_c_t_o_r_3 │ │ │ │ -  │ │ │ │ -template class _B_A_L_L___E_X_P_O_R_T  _B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ -  │ │ │ │ -template │ │ │ │ - _B_A_L_L___I_N_L_I_N_E _T_V_e_c_t_o_r_3< T >  _B_A_L_L_:_:_o_p_e_r_a_t_o_r_* (const T &a, const _T_V_e_c_t_o_r_3< T > │ │ │ │ - &b) │ │ │ │ +********** SSttoorreerrss ********** │ │ │ │ +typedef _T_C_i_r_c_l_e_3< _f_l_o_a_t >  _B_A_L_L_:_:_C_i_r_c_l_e_3 │ │ │ │   │ │ │ │ template │ │ │ │ - std::istream &  _B_A_L_L_:_:_o_p_e_r_a_t_o_r_>_> (std::istream &s, _T_V_e_c_t_o_r_3< T > │ │ │ │ - &vector) │ │ │ │ + std::istream &  _B_A_L_L_:_:_o_p_e_r_a_t_o_r_>_> (std::istream &s, _T_C_i_r_c_l_e_3< T > │ │ │ │ + &circle) │ │ │ │   │ │ │ │ template │ │ │ │ - std::ostream &  _B_A_L_L_:_:_o_p_e_r_a_t_o_r_<_< (std::ostream &s, const _T_V_e_c_t_o_r_3< │ │ │ │ - T > &vector) │ │ │ │ + std::ostream &  _B_A_L_L_:_:_o_p_e_r_a_t_o_r_<_< (std::ostream &s, const _T_C_i_r_c_l_e_3< T │ │ │ │ + > &circle) │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/deb/a01508_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: vector3.h Source File │ │ │ +BALL: circle3.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -74,1161 +74,307 @@ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    vector3.h
    │ │ │ +
    circle3.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_MATHS_VECTOR3_H
    │ │ │ -
    6#define BALL_MATHS_VECTOR3_H
    │ │ │ -
    7
    │ │ │ -
    8#ifndef BALL_COMMON_EXCEPTION_H
    │ │ │ -
    9# include <BALL/COMMON/exception.h>
    │ │ │ -
    10#endif
    │ │ │ -
    11
    │ │ │ -
    12#ifndef BALL_CONCEPT_PERSISTENCEMANAGER_H
    │ │ │ -
    13# include <BALL/CONCEPT/persistenceManager.h>
    │ │ │ -
    14#endif
    │ │ │ -
    15
    │ │ │ -
    16#ifndef BALL_MATHS_ANGLE_H
    │ │ │ -
    17# include <BALL/MATHS/angle.h>
    │ │ │ -
    18#endif
    │ │ │ -
    19
    │ │ │ -
    20#ifndef BALL_MATHS_COMMON_H
    │ │ │ -
    21# include <BALL/MATHS/common.h>
    │ │ │ -
    22#endif
    │ │ │ -
    23
    │ │ │ -
    24#ifdef BALL_HAS_IEEEFP_H
    │ │ │ -
    25# include <ieeefp.h>
    │ │ │ -
    26#endif
    │ │ │ -
    27
    │ │ │ +
    4// $Id: circle3.h,v 1.42 2004/07/05 20:57:28 oliver Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_MATHS_CIRCLE3_H
    │ │ │ +
    8#define BALL_MATHS_CIRCLE3_H
    │ │ │ +
    9
    │ │ │ +
    10#ifndef BALL_COMMON_EXCEPTION_H
    │ │ │ +
    11# include <BALL/COMMON/exception.h>
    │ │ │ +
    12#endif
    │ │ │ +
    13
    │ │ │ +
    14#ifndef BALL_MATHS_VECTOR3_H
    │ │ │ +
    15# include <BALL/MATHS/vector3.h>
    │ │ │ +
    16#endif
    │ │ │ +
    17
    │ │ │ +
    18
    │ │ │ +
    19namespace BALL
    │ │ │ +
    20{
    │ │ │ +
    26 template <typename T>
    │ │ │ +
    27 class TCircle3;
    │ │ │
    28
    │ │ │ -
    29namespace BALL
    │ │ │ -
    30{
    │ │ │ +
    34 template <typename T>
    │ │ │ +
    35 std::istream& operator >> (std::istream& s, TCircle3<T>& circle);
    │ │ │
    36
    │ │ │ -
    37 template <typename T>
    │ │ │ -
    38 class TVector3;
    │ │ │ -
    39
    │ │ │ -
    43
    │ │ │ -
    47 template <typename T>
    │ │ │ -
    48 BALL_INLINE
    │ │ │ -
    49 TVector3<T> operator * (const T& a, const TVector3<T>& b);
    │ │ │ +
    38 template <typename T>
    │ │ │ +
    39 std::ostream& operator << (std::ostream& s, const TCircle3<T>& circle);
    │ │ │ +
    41
    │ │ │ +
    44 template <typename T>
    │ │ │ +
    │ │ │ +
    45 class TCircle3
    │ │ │ +
    46 {
    │ │ │ +
    47 public:
    │ │ │ +
    48
    │ │ │ +
    49 BALL_CREATE(TCircle3<T>)
    │ │ │
    50
    │ │ │ -
    55 template <typename T>
    │ │ │ -
    56 std::istream& operator >> (std::istream& s, TVector3<T>& vector);
    │ │ │ -
    57
    │ │ │ -
    62 template <typename T>
    │ │ │ -
    63 std::ostream& operator << (std::ostream& s, const TVector3<T>& vector);
    │ │ │ -
    64
    │ │ │ -
    66
    │ │ │ -
    69 template <typename T>
    │ │ │ -
    │ │ │ -
    70 class TVector3
    │ │ │ -
    71 {
    │ │ │ -
    72 public:
    │ │ │ -
    73
    │ │ │ -
    77
    │ │ │ -
    │ │ │ -
    82 TVector3();
    │ │ │ -
    83
    │ │ │ -
    │ │ │ -
    90 explicit TVector3(const T* ptr);
    │ │ │ -
    91
    │ │ │ -
    │ │ │ -
    97 explicit TVector3(const T& value);
    │ │ │ -
    98
    │ │ │ -
    102 template<typename T2>
    │ │ │ -
    103 explicit TVector3(const TVector3<T2>& vec);
    │ │ │ -
    104
    │ │ │ -
    │ │ │ -
    111 TVector3(const T& vx, const T& vy, const T& vz);
    │ │ │ +
    51
    │ │ │ +
    54
    │ │ │ +
    55
    │ │ │ +
    │ │ │ +
    59 TCircle3()
    │ │ │ +
    60 : p(),
    │ │ │ +
    61 n(),
    │ │ │ +
    62 radius(0)
    │ │ │ +
    63 {
    │ │ │ +
    64 }
    │ │ │ +
    │ │ │ +
    65
    │ │ │ +
    │ │ │ +
    70 TCircle3(const TCircle3& circle)
    │ │ │ +
    71 : p(circle.p),
    │ │ │ +
    72 n(circle.n),
    │ │ │ +
    73 radius(circle.radius)
    │ │ │ +
    74 {
    │ │ │ +
    75 }
    │ │ │ +
    │ │ │ +
    76
    │ │ │ +
    │ │ │ +
    83 TCircle3(const TVector3<T>& point, const TVector3<T>& normal, const T& radius)
    │ │ │ +
    84 : p(point),
    │ │ │ +
    85 n(normal),
    │ │ │ +
    86 radius(radius)
    │ │ │ +
    87 {
    │ │ │ +
    88 }
    │ │ │ +
    │ │ │ +
    89
    │ │ │ +
    │ │ │ +
    94 virtual ~TCircle3()
    │ │ │ +
    95 {
    │ │ │ +
    96 }
    │ │ │ +
    │ │ │ +
    97
    │ │ │ +
    │ │ │ +
    101 virtual void clear()
    │ │ │ +
    102 {
    │ │ │ +
    103 p.clear();
    │ │ │ +
    104 n.clear();
    │ │ │ +
    105 radius = (T)0;
    │ │ │ +
    106 }
    │ │ │ +
    │ │ │ +
    107
    │ │ │ +
    109
    │ │ │
    112
    │ │ │ -
    │ │ │ -
    117 TVector3(const TVector3& vector);
    │ │ │ -
    118
    │ │ │ -
    │ │ │ -
    128 TVector3(const T& r, const TAngle<T>& phi, const TAngle<T>& theta);
    │ │ │ -
    129
    │ │ │ +
    │ │ │ +
    116 void swap(TCircle3& circle)
    │ │ │ +
    117 {
    │ │ │ +
    118 TVector3<T> temp_vector(p);
    │ │ │ +
    119 p = circle.p;
    │ │ │ +
    120 circle.p = temp_vector;
    │ │ │ +
    121
    │ │ │ +
    122 temp_vector = n;
    │ │ │ +
    123 n = circle.n;
    │ │ │ +
    124 circle.n = temp_vector;
    │ │ │ +
    125
    │ │ │ +
    126 T temp = radius;
    │ │ │ +
    127 radius = circle.radius;
    │ │ │ +
    128 circle.radius = temp;
    │ │ │ +
    129 }
    │ │ │ +
    │ │ │ +
    130
    │ │ │
    │ │ │ -
    134 ~TVector3();
    │ │ │ -
    135
    │ │ │ -
    │ │ │ -
    139 void clear();
    │ │ │ +
    134 void set(const TCircle3& circle)
    │ │ │ +
    135 {
    │ │ │ +
    136 p = circle.p;
    │ │ │ +
    137 n = circle.n;
    │ │ │ +
    138 radius = circle.radius;
    │ │ │ +
    139 }
    │ │ │ +
    │ │ │
    140
    │ │ │ -
    142
    │ │ │ -
    146
    │ │ │ -
    │ │ │ -
    153 void set(const T* ptr);
    │ │ │ -
    154
    │ │ │ -
    │ │ │ -
    159 void set(const T& value);
    │ │ │ -
    160
    │ │ │ -
    │ │ │ -
    166 void set(const T& vx, const T& vy, const T& vz);
    │ │ │ -
    167
    │ │ │ -
    171 void set(const TVector3& vector);
    │ │ │ -
    172
    │ │ │ -
    │ │ │ -
    185 void set(const T& r, const TAngle<T>& phi, const TAngle<T>& theta);
    │ │ │ -
    186
    │ │ │ -
    191 TVector3& operator = (const TVector3& v);
    │ │ │ -
    192
    │ │ │ -
    │ │ │ -
    197 TVector3& operator = (T value);
    │ │ │ -
    198
    │ │ │ -
    │ │ │ -
    204 TVector3& operator = (const T* ptr);
    │ │ │ -
    205
    │ │ │ -
    │ │ │ -
    212 void get(T* ptr) const;
    │ │ │ -
    213
    │ │ │ -
    │ │ │ -
    219 void get(T& x, T& y, T& z) const;
    │ │ │ -
    220
    │ │ │ -
    225 void get(TVector3& vector) const;
    │ │ │ -
    226
    │ │ │ -
    │ │ │ -
    234 void get(T& r, TAngle<T>& phi, TAngle<T>& theta) const;
    │ │ │ +
    │ │ │ +
    146 void set(const TVector3<T>& point, const TVector3<T>& normal, const T& rad)
    │ │ │ +
    147 {
    │ │ │ +
    148 p = point;
    │ │ │ +
    149 n = normal;
    │ │ │ +
    150 radius = rad;
    │ │ │ +
    151 }
    │ │ │ +
    │ │ │ +
    152
    │ │ │ +
    │ │ │ +
    157 TCircle3& operator = (const TCircle3& circle)
    │ │ │ +
    158 {
    │ │ │ +
    159 p = circle.p;
    │ │ │ +
    160 n = circle.n;
    │ │ │ +
    161 radius = circle.radius;
    │ │ │ +
    162
    │ │ │ +
    163 return *this;
    │ │ │ +
    164 }
    │ │ │ +
    │ │ │ +
    165
    │ │ │ +
    │ │ │ +
    170 void get(TCircle3& circle) const
    │ │ │ +
    171 {
    │ │ │ +
    172 circle.p = p;
    │ │ │ +
    173 circle.n = n;
    │ │ │ +
    174 circle.radius = radius;
    │ │ │ +
    175 }
    │ │ │ +
    │ │ │ +
    176
    │ │ │ +
    │ │ │ +
    182 void get(TVector3<T>& point, TVector3<T>& normal, T& rhs) const
    │ │ │ +
    183
    │ │ │ +
    184 {
    │ │ │ +
    185 point = p;
    │ │ │ +
    186 normal = n;
    │ │ │ +
    187 rhs = radius;
    │ │ │ +
    188 }
    │ │ │ +
    │ │ │ +
    189
    │ │ │ +
    191
    │ │ │ +
    194
    │ │ │ +
    │ │ │ +
    198 bool operator == (const TCircle3& circle) const
    │ │ │ +
    199 {
    │ │ │ +
    200 return (p == circle.p && n == circle.n && Maths::isEqual(radius, circle.radius));
    │ │ │ +
    201 }
    │ │ │ +
    │ │ │ +
    202
    │ │ │ +
    │ │ │ +
    206 bool operator != (const TCircle3& circle) const
    │ │ │ +
    207 {
    │ │ │ +
    208 return (p != circle.p || n != circle.n || Maths::isNotEqual(radius, circle.radius));
    │ │ │ +
    209 }
    │ │ │ +
    │ │ │ +
    210
    │ │ │ +
    │ │ │ +
    217 bool has(const TVector3<T>& point, bool on_surface = false) const
    │ │ │ +
    218 {
    │ │ │ +
    219 if (on_surface)
    │ │ │ +
    220 {
    │ │ │ +
    221 return (Maths::isZero(n * (point - p))
    │ │ │ +
    222 && Maths::isEqual(p.getDistance(point), radius));
    │ │ │ +
    223 }
    │ │ │ +
    224 else
    │ │ │ +
    225 {
    │ │ │ +
    226 return (Maths::isZero(n * (point - p))
    │ │ │ +
    227 && Maths::isLessOrEqual(p.getDistance(point), radius));
    │ │ │ +
    228 }
    │ │ │ +
    229 }
    │ │ │ +
    │ │ │ +
    230
    │ │ │ +
    232
    │ │ │
    235
    │ │ │ -
    │ │ │ -
    239 void swap(TVector3& vector);
    │ │ │ -
    240
    │ │ │ -
    │ │ │ -
    246 T getLength() const;
    │ │ │ -
    247
    │ │ │ -
    │ │ │ -
    253 T getSquareLength() const;
    │ │ │ -
    254
    │ │ │ -
    │ │ │ -
    261 TVector3& normalize();
    │ │ │ +
    │ │ │ +
    240 bool isValid() const
    │ │ │ +
    241 {
    │ │ │ +
    242 return true;
    │ │ │ +
    243 }
    │ │ │ +
    │ │ │ +
    244
    │ │ │ +
    │ │ │ +
    251 void dump(std::ostream& s = std::cout, Size depth = 0) const
    │ │ │ +
    252 {
    │ │ │ +
    253 BALL_DUMP_STREAM_PREFIX(s);
    │ │ │ +
    254
    │ │ │ +
    255 BALL_DUMP_HEADER(s, this, this);
    │ │ │ +
    256
    │ │ │ +
    257 BALL_DUMP_DEPTH(s, depth);
    │ │ │ +
    258 s << " position: " << p << std::endl;
    │ │ │ +
    259
    │ │ │ +
    260 BALL_DUMP_DEPTH(s, depth);
    │ │ │ +
    261 s << " normal: " << n << std::endl;
    │ │ │
    262
    │ │ │ -
    │ │ │ -
    267 TVector3& negate();
    │ │ │ -
    268
    │ │ │ -
    │ │ │ -
    271 static const TVector3& getZero();
    │ │ │ -
    272
    │ │ │ -
    │ │ │ -
    276 static const TVector3& getUnit();
    │ │ │ -
    277
    │ │ │ -
    │ │ │ -
    281 T& operator [] (Position position);
    │ │ │ -
    282
    │ │ │ -
    │ │ │ -
    286 const T& operator [] (Position position) const;
    │ │ │ -
    288
    │ │ │ -
    292
    │ │ │ -
    │ │ │ -
    295 const TVector3& operator + () const;
    │ │ │ -
    296
    │ │ │ -
    │ │ │ -
    299 TVector3 operator - () const;
    │ │ │ -
    300
    │ │ │ -
    303 TVector3 operator + (const TVector3& b) const;
    │ │ │ -
    304
    │ │ │ -
    307 TVector3 operator - (const TVector3& b) const;
    │ │ │ -
    308
    │ │ │ -
    │ │ │ -
    314 TVector3& operator += (const TVector3& vector);
    │ │ │ -
    315
    │ │ │ -
    │ │ │ -
    320 TVector3& operator -= (const TVector3& vector);
    │ │ │ -
    321
    │ │ │ -
    │ │ │ -
    327 TVector3 operator * (const T& scalar) const;
    │ │ │ -
    328
    │ │ │ -
    │ │ │ -
    334 TVector3& operator *= (const T& scalar);
    │ │ │ -
    335
    │ │ │ -
    │ │ │ -
    342 TVector3 operator / (const T& lambda) const;
    │ │ │ -
    343
    │ │ │ -
    │ │ │ -
    349 TVector3& operator /= (const T& lambda);
    │ │ │ -
    350
    │ │ │ -
    354 T operator * (const TVector3& vector) const;
    │ │ │ -
    355
    │ │ │ -
    │ │ │ -
    359 TVector3 operator % (const TVector3& vector) const;
    │ │ │ -
    360
    │ │ │ -
    │ │ │ -
    364 TVector3& operator %= (const TVector3& vector);
    │ │ │ -
    365
    │ │ │ -
    367
    │ │ │ -
    371
    │ │ │ -
    │ │ │ -
    374 T getDistance(const TVector3& vector) const;
    │ │ │ -
    375
    │ │ │ -
    │ │ │ -
    378 T getSquareDistance(const TVector3& vector) const;
    │ │ │ -
    379
    │ │ │ -
    │ │ │ -
    384 TAngle<T> getAngle(const TVector3& vector) const;
    │ │ │ -
    385
    │ │ │ -
    │ │ │ -
    389 TVector3 getOrthogonalProjection(const TVector3& direction) const;
    │ │ │ -
    390
    │ │ │ -
    │ │ │ -
    397 static TVector3 getPerpendicularNormalization
    │ │ │ -
    398 (const TVector3& a, const TVector3& b, const TVector3& c);
    │ │ │ -
    399
    │ │ │ -
    │ │ │ -
    407 static T getTripleProduct (const TVector3<T>& a, const TVector3<T>& b, const TVector3<T>& c);
    │ │ │ -
    408
    │ │ │ -
    410
    │ │ │ -
    414
    │ │ │ -
    │ │ │ -
    420 bool operator == (const TVector3& vector) const;
    │ │ │ -
    421
    │ │ │ -
    │ │ │ -
    427 bool operator != (const TVector3& vector) const;
    │ │ │ -
    428
    │ │ │ -
    │ │ │ -
    430 bool operator < (const TVector3& vector) const;
    │ │ │ -
    431
    │ │ │ -
    432
    │ │ │ -
    │ │ │ -
    437 bool isZero() const;
    │ │ │ -
    438
    │ │ │ -
    │ │ │ -
    441 bool isOrthogonalTo(const TVector3& vector) const;
    │ │ │ -
    442
    │ │ │ -
    444
    │ │ │ -
    445
    │ │ │ -
    449
    │ │ │ -
    │ │ │ -
    452 void write(PersistenceManager& pm) const;
    │ │ │ -
    453
    │ │ │ -
    │ │ │ -
    456 bool read(PersistenceManager& pm);
    │ │ │ -
    457
    │ │ │ -
    459
    │ │ │ -
    463
    │ │ │ -
    │ │ │ -
    470 void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ -
    471
    │ │ │ -
    │ │ │ -
    476 bool isValid() const;
    │ │ │ -
    477
    │ │ │ -
    479
    │ │ │ -
    480
    │ │ │ -
    486
    │ │ │ -
    489 T x;
    │ │ │ -
    490
    │ │ │ -
    493 T y;
    │ │ │ -
    494
    │ │ │ -
    497 T z;
    │ │ │ -
    499
    │ │ │ -
    500 private:
    │ │ │ -
    501
    │ │ │ -
    502 TAngle<T> getAngle_(const T& a, const T& b) const
    │ │ │ -
    503 {
    │ │ │ -
    504 TAngle<T> angle;
    │ │ │ -
    505
    │ │ │ -
    506 if (Maths::isNotZero(a))
    │ │ │ -
    507 {
    │ │ │ -
    508 angle = atan(b / a);
    │ │ │ -
    509 }
    │ │ │ -
    510 else
    │ │ │ -
    511 {
    │ │ │ -
    512 angle = Maths::sgn(b) * Constants::PI / 2;
    │ │ │ -
    513 }
    │ │ │ -
    514
    │ │ │ -
    515 if (Maths::isLess(a, 0))
    │ │ │ -
    516 {
    │ │ │ -
    517 angle += Constants::PI;
    │ │ │ -
    518 }
    │ │ │ -
    519
    │ │ │ -
    520 if (Maths::isLess(angle.value, 0))
    │ │ │ -
    521 {
    │ │ │ -
    522 return (Angle)(angle.value += 2.0 * Constants::PI);
    │ │ │ -
    523 }
    │ │ │ -
    524 else
    │ │ │ -
    525 {
    │ │ │ -
    526 return angle;
    │ │ │ -
    527 }
    │ │ │ -
    528 }
    │ │ │ -
    529 };
    │ │ │ -
    531
    │ │ │ -
    532 template <typename T>
    │ │ │ -
    533 BALL_INLINE
    │ │ │ -
    │ │ │ -
    534 TVector3<T>::TVector3()
    │ │ │ -
    535 : x(0),
    │ │ │ -
    536 y(0),
    │ │ │ -
    537 z(0)
    │ │ │ -
    538 {
    │ │ │ -
    539 }
    │ │ │ -
    │ │ │ -
    540
    │ │ │ -
    541 template <typename T>
    │ │ │ -
    542 BALL_INLINE
    │ │ │ -
    │ │ │ -
    543 TVector3<T>::TVector3(const T* ptr)
    │ │ │ -
    544 {
    │ │ │ -
    545 if (ptr == 0)
    │ │ │ -
    546 {
    │ │ │ -
    547 throw Exception::NullPointer(__FILE__, __LINE__);
    │ │ │ -
    548 }
    │ │ │ -
    549
    │ │ │ -
    550 x = *ptr++;
    │ │ │ -
    551 y = *ptr++;
    │ │ │ -
    552 z = *ptr;
    │ │ │ -
    553 }
    │ │ │ -
    │ │ │ -
    554
    │ │ │ -
    555 template <typename T>
    │ │ │ -
    556 BALL_INLINE
    │ │ │ -
    │ │ │ -
    557 TVector3<T>::TVector3(const T& value)
    │ │ │ -
    558 : x(value),
    │ │ │ -
    559 y(value),
    │ │ │ -
    560 z(value)
    │ │ │ -
    561 {
    │ │ │ -
    562 }
    │ │ │ -
    │ │ │ -
    563
    │ │ │ -
    564 template <typename T> template <typename T2>
    │ │ │ -
    565 BALL_INLINE
    │ │ │ -
    │ │ │ -
    566 TVector3<T>::TVector3(const TVector3<T2>& vec)
    │ │ │ -
    567 : x((T)vec.x),
    │ │ │ -
    568 y((T)vec.y),
    │ │ │ -
    569 z((T)vec.z)
    │ │ │ -
    570 {
    │ │ │ -
    571 }
    │ │ │ -
    │ │ │ -
    572
    │ │ │ -
    573 template <typename T>
    │ │ │ -
    574 BALL_INLINE
    │ │ │ -
    │ │ │ -
    575 TVector3<T>::TVector3(const T& vx, const T& vy, const T& vz)
    │ │ │ -
    576 : x(vx),
    │ │ │ -
    577 y(vy),
    │ │ │ -
    578 z(vz)
    │ │ │ -
    579 {
    │ │ │ -
    580 }
    │ │ │ -
    │ │ │ -
    581
    │ │ │ -
    582 template <typename T>
    │ │ │ -
    583 BALL_INLINE
    │ │ │ -
    │ │ │ -
    584 TVector3<T>::TVector3(const TVector3& vector)
    │ │ │ -
    585 : x(vector.x),
    │ │ │ -
    586 y(vector.y),
    │ │ │ -
    587 z(vector.z)
    │ │ │ -
    588 {
    │ │ │ -
    589 }
    │ │ │ -
    │ │ │ -
    590
    │ │ │ -
    591 template <typename T>
    │ │ │ -
    592 BALL_INLINE
    │ │ │ -
    │ │ │ -
    593 TVector3<T>::TVector3(const T& r, const TAngle<T>& phi, const TAngle<T>& theta)
    │ │ │ -
    594 : x(r * cos(phi) * sin(theta)),
    │ │ │ -
    595 y(r * sin(phi) * sin(theta)),
    │ │ │ -
    596 z(r * cos(theta))
    │ │ │ -
    597 {
    │ │ │ -
    598 }
    │ │ │ -
    │ │ │ -
    599
    │ │ │ -
    600 template <typename T>
    │ │ │ -
    601 BALL_INLINE
    │ │ │ -
    │ │ │ -
    602 TVector3<T>::~TVector3()
    │ │ │ -
    603 {
    │ │ │ -
    604 }
    │ │ │ -
    │ │ │ -
    605
    │ │ │ -
    606 template <typename T>
    │ │ │ -
    607 BALL_INLINE
    │ │ │ -
    │ │ │ -
    608 void TVector3<T>::clear()
    │ │ │ -
    609 {
    │ │ │ -
    610 x = y = z = (T)0;
    │ │ │ -
    611 }
    │ │ │ -
    │ │ │ -
    612
    │ │ │ -
    613 template <typename T>
    │ │ │ -
    614 BALL_INLINE
    │ │ │ -
    │ │ │ -
    615 void TVector3<T>::set(const T* ptr)
    │ │ │ -
    616 {
    │ │ │ -
    617 if (ptr == 0)
    │ │ │ -
    618 throw Exception::NullPointer(__FILE__, __LINE__);
    │ │ │ -
    619
    │ │ │ -
    620 x = *ptr++;
    │ │ │ -
    621 y = *ptr++;
    │ │ │ -
    622 z = *ptr;
    │ │ │ -
    623 }
    │ │ │ -
    │ │ │ -
    624
    │ │ │ -
    625 template <typename T>
    │ │ │ -
    626 BALL_INLINE
    │ │ │ -
    │ │ │ -
    627 void TVector3<T>::set(const T& value)
    │ │ │ -
    628 {
    │ │ │ -
    629 x = value;
    │ │ │ -
    630 y = value;
    │ │ │ -
    631 z = value;
    │ │ │ -
    632 }
    │ │ │ -
    │ │ │ -
    633
    │ │ │ -
    634 template <typename T>
    │ │ │ -
    635 BALL_INLINE
    │ │ │ -
    │ │ │ -
    636 void TVector3<T>::set(const T& vx, const T& vy, const T& vz)
    │ │ │ -
    637 {
    │ │ │ -
    638 x = vx;
    │ │ │ -
    639 y = vy;
    │ │ │ -
    640 z = vz;
    │ │ │ -
    641 }
    │ │ │ -
    │ │ │ -
    642
    │ │ │ -
    643 template <typename T>
    │ │ │ -
    644 BALL_INLINE
    │ │ │ -
    645 void TVector3<T>::set(const TVector3<T>& vector)
    │ │ │ -
    646 {
    │ │ │ -
    647 x = vector.x;
    │ │ │ -
    648 y = vector.y;
    │ │ │ -
    649 z = vector.z;
    │ │ │ -
    650 }
    │ │ │ -
    651
    │ │ │ -
    652 template <typename T>
    │ │ │ -
    653 BALL_INLINE
    │ │ │ -
    │ │ │ -
    654 void TVector3<T>::set(const T& r, const TAngle<T> &phi, const TAngle<T> &theta)
    │ │ │ -
    655 {
    │ │ │ -
    656 x = r * cos(phi) * sin(theta);
    │ │ │ -
    657 y = r * sin(phi) * sin(theta);
    │ │ │ -
    658 z = r * cos(theta);
    │ │ │ -
    659 }
    │ │ │ -
    │ │ │ -
    660
    │ │ │ -
    661 template <typename T>
    │ │ │ -
    662 BALL_INLINE
    │ │ │ -
    │ │ │ -
    663 TVector3<T>& TVector3<T>::operator = (const T* ptr)
    │ │ │ -
    664 {
    │ │ │ -
    665 if (ptr == 0)
    │ │ │ -
    666 {
    │ │ │ -
    667 throw Exception::NullPointer(__FILE__, __LINE__);
    │ │ │ -
    668 }
    │ │ │ -
    669
    │ │ │ -
    670 x = *ptr++;
    │ │ │ -
    671 y = *ptr++;
    │ │ │ -
    672 z = *ptr;
    │ │ │ -
    673
    │ │ │ -
    674 return *this;
    │ │ │ -
    675 }
    │ │ │ -
    │ │ │ -
    676
    │ │ │ -
    677 template <typename T>
    │ │ │ -
    678 BALL_INLINE
    │ │ │ -
    679 TVector3<T>& TVector3<T>::operator = (const TVector3<T>& vector)
    │ │ │ -
    680 {
    │ │ │ -
    681 x = vector.x;
    │ │ │ -
    682 y = vector.y;
    │ │ │ -
    683 z = vector.z;
    │ │ │ -
    684
    │ │ │ -
    685 return *this;
    │ │ │ -
    686 }
    │ │ │ -
    687
    │ │ │ -
    688 template <typename T>
    │ │ │ -
    689 BALL_INLINE
    │ │ │ -
    │ │ │ -
    690 TVector3<T>& TVector3<T>::operator = (T value)
    │ │ │ -
    691 {
    │ │ │ -
    692 x = y = z = value;
    │ │ │ -
    693
    │ │ │ -
    694 return *this;
    │ │ │ -
    695 }
    │ │ │ -
    │ │ │ -
    696
    │ │ │ -
    697 template <typename T>
    │ │ │ -
    698 BALL_INLINE
    │ │ │ -
    │ │ │ -
    699 void TVector3<T>::get(T* ptr) const
    │ │ │ -
    700 {
    │ │ │ -
    701 if (ptr == 0)
    │ │ │ -
    702 {
    │ │ │ -
    703 throw Exception::NullPointer(__FILE__, __LINE__);
    │ │ │ -
    704 }
    │ │ │ -
    705
    │ │ │ -
    706 *ptr++ = x;
    │ │ │ -
    707 *ptr++ = y;
    │ │ │ -
    708 *ptr = z;
    │ │ │ -
    709 }
    │ │ │ -
    │ │ │ -
    710
    │ │ │ -
    711 template <typename T>
    │ │ │ -
    712 BALL_INLINE
    │ │ │ -
    │ │ │ -
    713 void TVector3<T>::get(T& new_x, T& new_y, T& new_z) const
    │ │ │ -
    714 {
    │ │ │ -
    715 new_x = x;
    │ │ │ -
    716 new_y = y;
    │ │ │ -
    717 new_z = z;
    │ │ │ -
    718 }
    │ │ │ -
    │ │ │ -
    719
    │ │ │ -
    720 template <typename T>
    │ │ │ -
    721 BALL_INLINE
    │ │ │ -
    722 void TVector3<T>::get(TVector3<T>& vector) const
    │ │ │ -
    723 {
    │ │ │ -
    724 vector.x = x;
    │ │ │ -
    725 vector.y = y;
    │ │ │ -
    726 vector.z = z;
    │ │ │ -
    727 }
    │ │ │ -
    728
    │ │ │ -
    729 template <typename T>
    │ │ │ -
    730 BALL_INLINE
    │ │ │ -
    │ │ │ -
    731 void TVector3<T>::get(T& r, TAngle<T>& phi, TAngle<T>& theta) const
    │ │ │ -
    732 {
    │ │ │ -
    733 r = sqrt(x * x + y * y + z * z);
    │ │ │ -
    734 phi = (Angle)getAngle_(x, y);
    │ │ │ -
    735 theta = getAngle_(z, sqrt(x * x + y * y));
    │ │ │ -
    736 }
    │ │ │ -
    │ │ │ -
    737
    │ │ │ -
    738 template <typename T>
    │ │ │ -
    739 BALL_INLINE
    │ │ │ -
    │ │ │ -
    740 void TVector3<T>::swap(TVector3<T>& vector)
    │ │ │ -
    741 {
    │ │ │ -
    742 T temp = x;
    │ │ │ -
    743 x = vector.x;
    │ │ │ -
    744 vector.x = temp;
    │ │ │ -
    745
    │ │ │ -
    746 temp = y;
    │ │ │ -
    747 y = vector.y;
    │ │ │ -
    748 vector.y = temp;
    │ │ │ -
    749
    │ │ │ -
    750 temp = z;
    │ │ │ -
    751 z = vector.z;
    │ │ │ -
    752 vector.z = temp;
    │ │ │ -
    753 }
    │ │ │ -
    │ │ │ -
    754
    │ │ │ -
    755 template <typename T>
    │ │ │ -
    756 BALL_INLINE
    │ │ │ -
    │ │ │ -
    757 T TVector3<T>::getLength() const
    │ │ │ -
    758 {
    │ │ │ -
    759 return (T)sqrt(x * x + y * y + z * z);
    │ │ │ -
    760 }
    │ │ │ -
    │ │ │ -
    761
    │ │ │ -
    762 template <typename T>
    │ │ │ -
    763 BALL_INLINE
    │ │ │ -
    │ │ │ -
    764 T TVector3<T>::getSquareLength() const
    │ │ │ -
    765 {
    │ │ │ -
    766 return (x * x + y * y + z * z);
    │ │ │ -
    767 }
    │ │ │ -
    │ │ │ -
    768
    │ │ │ -
    769 template <typename T>
    │ │ │ -
    │ │ │ -
    770 TVector3<T>& TVector3<T>::normalize()
    │ │ │ -
    771 {
    │ │ │ -
    772 T len = sqrt(x * x + y * y + z * z);
    │ │ │ -
    773
    │ │ │ -
    774 if (Maths::isZero(len))
    │ │ │ -
    775 {
    │ │ │ -
    776 throw Exception::DivisionByZero(__FILE__, __LINE__);
    │ │ │ -
    777 }
    │ │ │ -
    778
    │ │ │ -
    779 x /= len;
    │ │ │ -
    780 y /= len;
    │ │ │ -
    781 z /= len;
    │ │ │ -
    782
    │ │ │ -
    783 return *this;
    │ │ │ -
    784 }
    │ │ │ -
    │ │ │ -
    785
    │ │ │ -
    786 template <typename T>
    │ │ │ -
    787 BALL_INLINE
    │ │ │ -
    │ │ │ -
    788 TVector3<T>& TVector3<T>::negate()
    │ │ │ -
    789 {
    │ │ │ -
    790 x *= -1;
    │ │ │ -
    791 y *= -1;
    │ │ │ -
    792 z *= -1;
    │ │ │ -
    793 return *this;
    │ │ │ -
    794 }
    │ │ │ -
    │ │ │ -
    795
    │ │ │ -
    796 template <typename T>
    │ │ │ -
    797 BALL_INLINE
    │ │ │ -
    │ │ │ -
    798 const TVector3<T>& TVector3<T>::getZero()
    │ │ │ -
    799 {
    │ │ │ -
    800 static TVector3<T> null_vector(0, 0, 0);
    │ │ │ -
    801 return null_vector;
    │ │ │ -
    802 }
    │ │ │ -
    │ │ │ -
    803
    │ │ │ -
    804 template <typename T>
    │ │ │ -
    805 BALL_INLINE
    │ │ │ -
    │ │ │ -
    806 const TVector3<T>& TVector3<T>::getUnit()
    │ │ │ -
    807 {
    │ │ │ -
    808 static TVector3<T> unit_vector(1, 1, 1);
    │ │ │ -
    809 return unit_vector;
    │ │ │ -
    810 }
    │ │ │ -
    │ │ │ -
    811
    │ │ │ -
    812 template <typename T>
    │ │ │ -
    813 BALL_INLINE
    │ │ │ -
    │ │ │ -
    814 T& TVector3<T>::operator [] (Position position)
    │ │ │ -
    815 {
    │ │ │ -
    816 if (position > 2)
    │ │ │ -
    817 {
    │ │ │ -
    818 throw Exception::IndexOverflow(__FILE__, __LINE__, position);
    │ │ │ -
    819 }
    │ │ │ -
    820 switch (position)
    │ │ │ -
    821 {
    │ │ │ -
    822 case 0: return x;
    │ │ │ -
    823 case 1: return y;
    │ │ │ -
    824 case 2:
    │ │ │ -
    825 default:
    │ │ │ -
    826 return z;
    │ │ │ -
    827 }
    │ │ │ -
    828 }
    │ │ │ -
    │ │ │ -
    829
    │ │ │ -
    830 template <typename T>
    │ │ │ -
    831 BALL_INLINE
    │ │ │ -
    │ │ │ -
    832 const T& TVector3<T>::operator [] (Position position) const
    │ │ │ -
    833 {
    │ │ │ -
    834 if (position > 2)
    │ │ │ -
    835 {
    │ │ │ -
    836 throw Exception::IndexOverflow(__FILE__, __LINE__);
    │ │ │ -
    837 }
    │ │ │ -
    838 switch (position)
    │ │ │ -
    839 {
    │ │ │ -
    840 case 0: return x;
    │ │ │ -
    841 case 1: return y;
    │ │ │ -
    842 case 2:
    │ │ │ -
    843 default:
    │ │ │ -
    844 return z;
    │ │ │ -
    845 }
    │ │ │ -
    846 }
    │ │ │ -
    │ │ │ -
    847
    │ │ │ -
    848 template <typename T>
    │ │ │ -
    849 BALL_INLINE
    │ │ │ -
    │ │ │ -
    850 const TVector3<T>& TVector3<T>::operator + () const
    │ │ │ -
    851 {
    │ │ │ -
    852 return *this;
    │ │ │ -
    853 }
    │ │ │ -
    │ │ │ -
    854
    │ │ │ -
    855 template <typename T>
    │ │ │ -
    856 BALL_INLINE
    │ │ │ -
    │ │ │ -
    857 TVector3<T> TVector3<T>::operator - () const
    │ │ │ -
    858 {
    │ │ │ -
    859 return TVector3<T>(-x, -y, -z);
    │ │ │ -
    860 }
    │ │ │ -
    │ │ │ -
    861
    │ │ │ -
    862 template <typename T>
    │ │ │ -
    863 BALL_INLINE
    │ │ │ -
    │ │ │ -
    864 TVector3<T>& TVector3<T>::operator += (const TVector3<T>& vector)
    │ │ │ -
    865 {
    │ │ │ -
    866 x += vector.x;
    │ │ │ -
    867 y += vector.y;
    │ │ │ -
    868 z += vector.z;
    │ │ │ -
    869
    │ │ │ -
    870 return *this;
    │ │ │ -
    871 }
    │ │ │ -
    │ │ │ -
    872
    │ │ │ -
    873 template <typename T>
    │ │ │ -
    874 BALL_INLINE
    │ │ │ -
    │ │ │ -
    875 TVector3<T>& TVector3<T>::operator -= (const TVector3<T>& vector)
    │ │ │ -
    876 {
    │ │ │ -
    877 x -= vector.x;
    │ │ │ -
    878 y -= vector.y;
    │ │ │ -
    879 z -= vector.z;
    │ │ │ -
    880
    │ │ │ -
    881 return *this;
    │ │ │ -
    882 }
    │ │ │ -
    │ │ │ -
    883
    │ │ │ -
    884 template <typename T>
    │ │ │ -
    885 BALL_INLINE
    │ │ │ -
    │ │ │ -
    886 TVector3<T> TVector3<T>::operator * (const T& scalar) const
    │ │ │ -
    887 {
    │ │ │ -
    888 return TVector3<T>(x * scalar, y * scalar, z * scalar);
    │ │ │ -
    889 }
    │ │ │ -
    │ │ │ -
    890
    │ │ │ -
    891 template <typename T>
    │ │ │ -
    892 BALL_INLINE
    │ │ │ -
    │ │ │ -
    893 TVector3<T>& TVector3<T>::operator *= (const T &scalar)
    │ │ │ -
    894 {
    │ │ │ -
    895 x *= scalar;
    │ │ │ -
    896 y *= scalar;
    │ │ │ -
    897 z *= scalar;
    │ │ │ -
    898
    │ │ │ -
    899 return *this;
    │ │ │ -
    900 }
    │ │ │ -
    │ │ │ -
    901
    │ │ │ -
    902 template <typename T>
    │ │ │ -
    │ │ │ -
    903 TVector3<T> TVector3<T>::operator / (const T& lambda) const
    │ │ │ -
    904 {
    │ │ │ -
    905 if (lambda == (T)0)
    │ │ │ -
    906 {
    │ │ │ -
    907 throw Exception::DivisionByZero(__FILE__, __LINE__);
    │ │ │ -
    908 }
    │ │ │ -
    909 return TVector3<T>(x / lambda, y / lambda, z / lambda);
    │ │ │ -
    910 }
    │ │ │ -
    │ │ │ -
    911
    │ │ │ -
    912 template <typename T>
    │ │ │ -
    │ │ │ -
    913 TVector3<T>& TVector3<T>::operator /= (const T& lambda)
    │ │ │ -
    914 {
    │ │ │ -
    915 if (lambda == (T)0)
    │ │ │ -
    916 {
    │ │ │ -
    917 throw Exception::DivisionByZero(__FILE__, __LINE__);
    │ │ │ -
    918 }
    │ │ │ -
    919 x /= lambda;
    │ │ │ -
    920 y /= lambda;
    │ │ │ -
    921 z /= lambda;
    │ │ │ -
    922
    │ │ │ -
    923 return *this;
    │ │ │ -
    924 }
    │ │ │ -
    │ │ │ -
    925
    │ │ │ -
    926 template <typename T>
    │ │ │ -
    927 BALL_INLINE
    │ │ │ -
    928 T TVector3<T>::operator * (const TVector3<T>& vector) const
    │ │ │ -
    929 {
    │ │ │ -
    930 return (x * vector.x + y * vector.y + z * vector.z);
    │ │ │ -
    931 }
    │ │ │ -
    932
    │ │ │ -
    933 template <typename T>
    │ │ │ -
    │ │ │ -
    934 TVector3<T> TVector3<T>::operator % (const TVector3<T>& v) const
    │ │ │ -
    935 {
    │ │ │ -
    936 return TVector3(y * v.z - z * v.y, z * v.x - x * v.z, x * v.y - y * v.x);
    │ │ │ -
    937 }
    │ │ │ -
    │ │ │ -
    938
    │ │ │ -
    939 template <typename T>
    │ │ │ -
    940 BALL_INLINE
    │ │ │ -
    │ │ │ -
    941 TVector3<T>& TVector3<T>::operator %= (const TVector3<T>& v)
    │ │ │ -
    942 {
    │ │ │ -
    943 set(y * v.z - z * v.y, z * v.x - x * v.z, x * v.y - y * v.x);
    │ │ │ -
    944 return *this;
    │ │ │ -
    945 }
    │ │ │ -
    │ │ │ -
    946
    │ │ │ -
    947 template <typename T>
    │ │ │ -
    948 BALL_INLINE
    │ │ │ -
    │ │ │ -
    949 T TVector3<T>::getDistance(const TVector3<T>& v) const
    │ │ │ -
    950 {
    │ │ │ -
    951 T dx = x - v.x;
    │ │ │ -
    952 T dy = y - v.y;
    │ │ │ -
    953 T dz = z - v.z;
    │ │ │ -
    954
    │ │ │ -
    955 return (T)sqrt(dx * dx + dy * dy + dz * dz);
    │ │ │ -
    956 }
    │ │ │ -
    │ │ │ -
    957
    │ │ │ -
    958 template <typename T>
    │ │ │ -
    959 BALL_INLINE T
    │ │ │ -
    │ │ │ -
    960 TVector3<T>::getSquareDistance(const TVector3<T>& v) const
    │ │ │ -
    961 {
    │ │ │ -
    962 T dx = x - v.x;
    │ │ │ -
    963 T dy = y - v.y;
    │ │ │ -
    964 T dz = z - v.z;
    │ │ │ -
    965
    │ │ │ -
    966 return (dx * dx + dy * dy + dz * dz);
    │ │ │ -
    967 }
    │ │ │ -
    │ │ │ -
    968
    │ │ │ -
    969 template <typename T>
    │ │ │ -
    970 BALL_INLINE
    │ │ │ -
    │ │ │ -
    971 TAngle<T> TVector3<T>::getAngle(const TVector3<T>& vector) const
    │ │ │ -
    972 {
    │ │ │ -
    973 T length_product = getSquareLength() * vector.getSquareLength();
    │ │ │ -
    974
    │ │ │ -
    975 if (length_product == (T)0)
    │ │ │ -
    976 {
    │ │ │ -
    977 throw Exception::DivisionByZero(__FILE__, __LINE__);
    │ │ │ -
    978 }
    │ │ │ -
    979
    │ │ │ -
    980 T acos_arg = ((*this) * vector) / sqrt(length_product);
    │ │ │ -
    981
    │ │ │ -
    982 // ensure that the argument of acos is in the correct range
    │ │ │ -
    983 // (might happen if the angle between the two vectors is
    │ │ │ -
    984 // very close to zero)
    │ │ │ -
    985 if (fabs(acos_arg) > 1.0)
    │ │ │ -
    986 {
    │ │ │ -
    987 return (TAngle<T>)0.0;
    │ │ │ -
    988 }
    │ │ │ -
    989
    │ │ │ -
    990 return (TAngle<T>)acos(acos_arg);
    │ │ │ -
    991 }
    │ │ │ -
    │ │ │ -
    992
    │ │ │ -
    993 template <typename T>
    │ │ │ -
    994 BALL_INLINE
    │ │ │ -
    │ │ │ -
    995 TVector3<T> TVector3<T>::getOrthogonalProjection(const TVector3<T>& direction) const
    │ │ │ -
    996 {
    │ │ │ -
    997 return ((direction * (*this)) / (direction * direction) * direction);
    │ │ │ -
    998 }
    │ │ │ -
    │ │ │ -
    999
    │ │ │ -
    1000 template <typename T>
    │ │ │ -
    │ │ │ -
    1001 TVector3<T> TVector3<T>::getPerpendicularNormalization
    │ │ │ -
    1002 (const TVector3<T> &a, const TVector3<T> &b, const TVector3<T> &c)
    │ │ │ -
    1003 {
    │ │ │ -
    1004 TVector3 diff1(b.x - a.x, b.y - a.y, b.z - a.z);
    │ │ │ -
    1005 TVector3 diff2(b.x - c.x, b.y - c.y, b.z - c.z);
    │ │ │ -
    1006
    │ │ │ -
    1007 return TVector3
    │ │ │ -
    1008 (diff1.y * diff2.z - diff1.z * diff2.y,
    │ │ │ -
    1009 diff1.z * diff2.x - diff1.x * diff2.z,
    │ │ │ -
    1010 diff1.x * diff2.y - diff1.y * diff2.x);
    │ │ │ -
    1011 }
    │ │ │ -
    │ │ │ -
    1012
    │ │ │ -
    1013 template <typename T>
    │ │ │ -
    1014 BALL_INLINE
    │ │ │ -
    │ │ │ -
    1015 T TVector3<T>::getTripleProduct
    │ │ │ -
    1016 (const TVector3<T>& a,
    │ │ │ -
    1017 const TVector3<T>& b,
    │ │ │ -
    1018 const TVector3<T>& c)
    │ │ │ -
    1019 {
    │ │ │ -
    1020 return ( a.x * (b.y * c.z - b.z * c.y)
    │ │ │ -
    1021 + a.y * (b.z * c.x - b.x * c.z)
    │ │ │ -
    1022 + a.z * (b.x * c.y - b.y * c.x));
    │ │ │ -
    1023 }
    │ │ │ -
    │ │ │ -
    1024
    │ │ │ -
    1025 template <typename T>
    │ │ │ -
    1026 BALL_INLINE
    │ │ │ -
    │ │ │ -
    1027 bool TVector3<T>::operator == (const TVector3<T>& v) const
    │ │ │ -
    1028 {
    │ │ │ -
    1029 return (Maths::isEqual(x, v.x) && Maths::isEqual(y, v.y) && Maths::isEqual(z, v.z));
    │ │ │ -
    1030 }
    │ │ │ -
    │ │ │ -
    1031
    │ │ │ -
    1032 template <typename T>
    │ │ │ -
    1033 BALL_INLINE
    │ │ │ -
    │ │ │ -
    1034 bool TVector3<T>::operator < (const TVector3<T>& v) const
    │ │ │ -
    1035 {
    │ │ │ -
    1036 return (x < v.x || y < v.y || z < v.z);
    │ │ │ -
    1037 }
    │ │ │ -
    │ │ │ -
    1038
    │ │ │ -
    1039
    │ │ │ -
    1040 template <typename T>
    │ │ │ -
    1041 BALL_INLINE
    │ │ │ -
    │ │ │ -
    1042 bool TVector3<T>::operator != (const TVector3<T>& v) const
    │ │ │ -
    1043 {
    │ │ │ -
    1044 return (Maths::isNotEqual(x, v.x) || Maths::isNotEqual(y, v.y) || Maths::isNotEqual(z, v.z));
    │ │ │ -
    1045 }
    │ │ │ -
    │ │ │ -
    1046
    │ │ │ -
    1047 template <typename T>
    │ │ │ -
    1048 BALL_INLINE
    │ │ │ -
    │ │ │ -
    1049 bool TVector3<T>::isOrthogonalTo(const TVector3<T>& v) const
    │ │ │ -
    1050 {
    │ │ │ -
    1051 return Maths::isZero((*this) * v);
    │ │ │ -
    1052 }
    │ │ │ -
    │ │ │ -
    1053
    │ │ │ -
    1054 template <typename T>
    │ │ │ -
    1055 BALL_INLINE
    │ │ │ -
    │ │ │ -
    1056 bool TVector3<T>::isValid() const
    │ │ │ -
    1057 {
    │ │ │ -
    1058 return true;
    │ │ │ -
    1059 }
    │ │ │ -
    │ │ │ -
    │ │ │ -
    1060
    │ │ │ -
    1061 template <typename T>
    │ │ │ -
    1062 BALL_INLINE
    │ │ │ -
    │ │ │ -
    1063 bool TVector3<T>::isZero() const
    │ │ │ -
    1064 {
    │ │ │ -
    1065 return (Maths::isZero(x) && Maths::isZero(y) && Maths::isZero(z));
    │ │ │ -
    1066 }
    │ │ │ -
    │ │ │ -
    1067
    │ │ │ -
    1068 template <typename T>
    │ │ │ -
    │ │ │ -
    1069 void TVector3<T>::dump(std::ostream& s, Size depth) const
    │ │ │ -
    1070 {
    │ │ │ -
    1071 BALL_DUMP_STREAM_PREFIX(s);
    │ │ │ -
    1072
    │ │ │ -
    1073 BALL_DUMP_HEADER(s, this, this);
    │ │ │ -
    1074
    │ │ │ -
    1075 BALL_DUMP_DEPTH(s, depth);
    │ │ │ -
    1076 s << " (x = " << x << ", y = " << y << ", z = " << z << ")" << std::endl;
    │ │ │ -
    1077
    │ │ │ -
    1078 BALL_DUMP_STREAM_SUFFIX(s);
    │ │ │ -
    1079 }
    │ │ │ -
    │ │ │ -
    │ │ │ -
    1080
    │ │ │ -
    1084 typedef TVector3<float> Vector3;
    │ │ │ -
    1085
    │ │ │ -
    1086 template <typename T>
    │ │ │ -
    1087 BALL_INLINE
    │ │ │ -
    1088 TVector3<T> TVector3<T>::operator + (const TVector3<T>& b) const
    │ │ │ -
    1089 {
    │ │ │ -
    1090 return TVector3<T>(x + b.x, y + b.y, z + b.z);
    │ │ │ -
    1091 }
    │ │ │ -
    1092
    │ │ │ -
    1093 template <typename T>
    │ │ │ -
    1094 BALL_INLINE
    │ │ │ -
    1095 TVector3<T> TVector3<T>::operator - (const TVector3<T>& b) const
    │ │ │ -
    1096 {
    │ │ │ -
    1097 return TVector3<T>(x - b.x, y - b.y, z - b.z);
    │ │ │ -
    1098 }
    │ │ │ -
    1099
    │ │ │ -
    1100 template <typename T>
    │ │ │ -
    │ │ │ -
    1101 void TVector3<T>::write(PersistenceManager& pm) const
    │ │ │ -
    1102 {
    │ │ │ -
    1103 pm.writePrimitive(x, "x");
    │ │ │ -
    1104 pm.writePrimitive(y, "y");
    │ │ │ -
    1105 pm.writePrimitive(z, "z");
    │ │ │ -
    1106 }
    │ │ │ -
    │ │ │ -
    1107
    │ │ │ -
    1108 template <typename T>
    │ │ │ -
    │ │ │ -
    1109 bool TVector3<T>::read(PersistenceManager& pm)
    │ │ │ -
    1110 {
    │ │ │ -
    1111 pm.readPrimitive(x, "x");
    │ │ │ -
    1112 pm.readPrimitive(y, "y");
    │ │ │ -
    1113 pm.readPrimitive(z, "z");
    │ │ │ -
    1114
    │ │ │ -
    1115 return true;
    │ │ │ -
    1116 }
    │ │ │ -
    │ │ │ -
    │ │ │ -
    1117
    │ │ │ -
    1118
    │ │ │ -
    1119 template <typename T>
    │ │ │ -
    1120 BALL_INLINE
    │ │ │ -
    │ │ │ -
    1121 TVector3<T> operator * (const T& scalar, const TVector3<T>& vector)
    │ │ │ -
    1122 {
    │ │ │ -
    1123 return TVector3<T>(scalar * vector.x, scalar * vector.y, scalar * vector.z);
    │ │ │ -
    1124 }
    │ │ │ -
    │ │ │ -
    1125
    │ │ │ -
    1126 template <typename T>
    │ │ │ -
    │ │ │ -
    1127 std::istream& operator >> (std::istream& s, TVector3<T>& v)
    │ │ │ -
    1128 {
    │ │ │ -
    1129 char c;
    │ │ │ -
    1130 s >> c >> v.x >> v.y >> v.z >> c;
    │ │ │ -
    1131
    │ │ │ -
    1132 return s;
    │ │ │ -
    1133 }
    │ │ │ -
    │ │ │ -
    1134
    │ │ │ -
    1135 template <typename T>
    │ │ │ -
    │ │ │ -
    1136 std::ostream& operator << (std::ostream& s, const TVector3<T>& v)
    │ │ │ -
    1137 {
    │ │ │ -
    1138 s << "(" << v.x << ' ' << v.y << ' ' << v.z << ')';
    │ │ │ -
    1139
    │ │ │ -
    1140 return s;
    │ │ │ -
    1141 }
    │ │ │ -
    │ │ │ -
    1142// required for visual studio
    │ │ │ -
    1143#ifdef BALL_COMPILER_MSVC
    │ │ │ -
    1144#include <vector>
    │ │ │ -
    1145extern template class BALL_EXPORT std::vector<Vector3>;
    │ │ │ -
    1146#endif
    │ │ │ -
    1147
    │ │ │ -
    1148extern template class BALL_EXPORT TVector3<float>;
    │ │ │ -
    1149
    │ │ │ -
    1150}// namespace BALL
    │ │ │ -
    1151
    │ │ │ -
    1152#endif // BALL_MATHS_VECTOR3_H
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ +
    263 BALL_DUMP_DEPTH(s, depth);
    │ │ │ +
    264 s << " radius: " << radius << std::endl;
    │ │ │ +
    265
    │ │ │ +
    266 BALL_DUMP_STREAM_SUFFIX(s);
    │ │ │ +
    267 }
    │ │ │
    │ │ │ +
    268
    │ │ │ +
    270
    │ │ │ +
    273
    │ │ │ +
    277 TVector3<T> p;
    │ │ │ +
    278
    │ │ │ +
    282 TVector3<T> n;
    │ │ │ +
    283
    │ │ │ +
    287 T radius;
    │ │ │ +
    288
    │ │ │ +
    290 };
    │ │ │
    │ │ │ +
    292
    │ │ │ +
    294#ifdef BALL_COMPILER_MSVC
    │ │ │ +
    295 template class BALL_EXPORT TCircle3<float>;
    │ │ │ +
    296#endif
    │ │ │ +
    297
    │ │ │ +
    301 typedef TCircle3<float> Circle3;
    │ │ │ +
    302
    │ │ │ +
    306 template <typename T>
    │ │ │ +
    │ │ │ +
    307 std::istream& operator >> (std::istream& s, TCircle3<T>& circle)
    │ │ │ +
    308 {
    │ │ │ +
    309 char c;
    │ │ │ +
    310 s >> c;
    │ │ │ +
    311 s >> circle.p >> circle.n >> circle.radius;
    │ │ │ +
    312 s >> c;
    │ │ │ +
    313 return s;
    │ │ │ +
    314 }
    │ │ │
    │ │ │ - │ │ │ - │ │ │ -
    BALL_DUMP_STREAM_PREFIX
    #define BALL_DUMP_STREAM_PREFIX(os)
    Definition macros.h:391
    │ │ │ -
    BALL_DUMP_STREAM_SUFFIX
    #define BALL_DUMP_STREAM_SUFFIX(os)
    Definition macros.h:395
    │ │ │ -
    BALL_DUMP_DEPTH
    #define BALL_DUMP_DEPTH(os, depth)
    Definition macros.h:390
    │ │ │ -
    BALL_DUMP_HEADER
    #define BALL_DUMP_HEADER(os, cl, ob)
    Definition macros.h:393
    │ │ │ -
    BALL_INLINE
    #define BALL_INLINE
    Definition debug.h:15
    │ │ │ +
    315
    │ │ │ +
    323 template <typename T>
    │ │ │ +
    │ │ │ +
    324 std::ostream& operator << (std::ostream& s, const TCircle3<T>& circle)
    │ │ │ +
    325 {
    │ │ │ +
    326 return s << '(' << circle.p
    │ │ │ +
    327 << ' ' << circle.n
    │ │ │ +
    328 << ' ' << circle.radius
    │ │ │ +
    329 << ')';
    │ │ │ +
    330 }
    │ │ │ +
    │ │ │ +
    331
    │ │ │ +
    332} // namespace BALL
    │ │ │ +
    333
    │ │ │ +
    334#endif // BALL_MATHS_CIRCLE3_H
    │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ +
    BALL_DUMP_STREAM_PREFIX
    #define BALL_DUMP_STREAM_PREFIX(os)
    Definition macros.h:391
    │ │ │ +
    BALL_DUMP_STREAM_SUFFIX
    #define BALL_DUMP_STREAM_SUFFIX(os)
    Definition macros.h:395
    │ │ │ +
    BALL_DUMP_DEPTH
    #define BALL_DUMP_DEPTH(os, depth)
    Definition macros.h:390
    │ │ │ +
    BALL_DUMP_HEADER
    #define BALL_DUMP_HEADER(os, cl, ob)
    Definition macros.h:393
    │ │ │
    BALL::operator<<
    BALL_EXPORT std::ostream & operator<<(std::ostream &os, const Exception::GeneralException &e)
    │ │ │ - │ │ │ -
    BALL::operator*
    BALL_INLINE TAngle< T > operator*(const T &val, const TAngle< T > &angle)
    Definition angle.h:704
    │ │ │ -
    BALL::TVector3< float >
    template class BALL_EXPORT TVector3< float >
    │ │ │ -
    BALL::Vector3
    TVector3< float > Vector3
    Definition vector3.h:1084
    │ │ │ -
    BALL::Angle
    TAngle< float > Angle
    Definition angle.h:697
    │ │ │ -
    BALL::operator>>
    std::istream & operator>>(std::istream &is, TRegularData1D< ValueType > &grid)
    Input operator.
    Definition regularData1D.h:802
    │ │ │ -
    BALL::Constants::PI
    BALL_EXTERN_VARIABLE const double PI
    PI.
    Definition constants.h:35
    │ │ │ -
    BALL::Maths::isNotZero
    bool isNotZero(const T &t)
    Definition MATHS/common.h:200
    │ │ │ -
    BALL::Maths::isNotEqual
    bool isNotEqual(const T1 &a, const T2 &b)
    Definition MATHS/common.h:224
    │ │ │ -
    BALL::Maths::isLess
    bool isLess(const T1 &a, const T2 &b)
    Definition MATHS/common.h:236
    │ │ │ -
    BALL::Maths::isZero
    bool isZero(const T &t)
    Definition MATHS/common.h:189
    │ │ │ -
    BALL::Maths::sgn
    T sgn(const T &t)
    Definition MATHS/common.h:138
    │ │ │ -
    BALL::Maths::isEqual
    bool isEqual(const T1 &a, const T2 &b)
    Definition MATHS/common.h:212
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::PersistenceManager::readPrimitive
    bool readPrimitive(T &t, const char *name)
    Definition persistenceManager.h:827
    │ │ │ -
    BALL::PersistenceManager::writePrimitive
    void writePrimitive(const T &t, const char *name)
    Definition persistenceManager.h:818
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::TVector3::getLength
    T getLength() const
    Definition vector3.h:757
    │ │ │ -
    BALL::TVector3::getDistance
    T getDistance(const TVector3 &vector) const
    Definition vector3.h:949
    │ │ │ -
    BALL::TVector3::operator/=
    TVector3 & operator/=(const T &lambda)
    Definition vector3.h:913
    │ │ │ -
    BALL::TVector3::getAngle
    TAngle< T > getAngle(const TVector3 &vector) const
    Definition vector3.h:971
    │ │ │ -
    BALL::TVector3::operator==
    bool operator==(const TVector3 &vector) const
    Definition vector3.h:1027
    │ │ │ -
    BALL::TVector3::operator!=
    bool operator!=(const TVector3 &vector) const
    Definition vector3.h:1042
    │ │ │ -
    BALL::TVector3::TVector3
    TVector3(const T &value)
    Definition vector3.h:557
    │ │ │ -
    BALL::TVector3::operator[]
    T & operator[](Position position)
    Definition vector3.h:814
    │ │ │ -
    BALL::TVector3::get
    void get(T &x, T &y, T &z) const
    Definition vector3.h:713
    │ │ │ -
    BALL::TVector3::operator-
    TVector3 operator-() const
    Definition vector3.h:857
    │ │ │ -
    BALL::TVector3::isZero
    bool isZero() const
    Definition vector3.h:1063
    │ │ │ -
    BALL::TVector3::get
    void get(TVector3 &vector) const
    │ │ │ -
    BALL::TVector3::set
    void set(const T &value)
    Definition vector3.h:627
    │ │ │ -
    BALL::TVector3::TVector3
    TVector3(const T *ptr)
    Definition vector3.h:543
    │ │ │ -
    BALL::TVector3::operator%=
    TVector3 & operator%=(const TVector3 &vector)
    Definition vector3.h:941
    │ │ │ - │ │ │ -
    BALL::TVector3::swap
    void swap(TVector3 &vector)
    Definition vector3.h:740
    │ │ │ -
    BALL::TVector3::getZero
    static const TVector3 & getZero()
    Definition vector3.h:798
    │ │ │ - │ │ │ -
    BALL::TVector3::negate
    TVector3 & negate()
    Definition vector3.h:788
    │ │ │ -
    BALL::TVector3::set
    void set(const TVector3 &vector)
    │ │ │ -
    BALL::TVector3::TVector3
    TVector3(const TVector3< T2 > &vec)
    │ │ │ -
    BALL::TVector3::operator-=
    TVector3 & operator-=(const TVector3 &vector)
    Definition vector3.h:875
    │ │ │ -
    BALL::TVector3::read
    bool read(PersistenceManager &pm)
    Definition vector3.h:1109
    │ │ │ -
    BALL::TVector3::operator%
    TVector3 operator%(const TVector3 &vector) const
    Definition vector3.h:934
    │ │ │ -
    BALL::TVector3::getSquareLength
    T getSquareLength() const
    Definition vector3.h:764
    │ │ │ -
    BALL::TVector3::getPerpendicularNormalization
    static TVector3 getPerpendicularNormalization(const TVector3 &a, const TVector3 &b, const TVector3 &c)
    Definition vector3.h:1002
    │ │ │ -
    BALL::TVector3::TVector3
    TVector3(const TVector3 &vector)
    Definition vector3.h:584
    │ │ │ -
    BALL::TVector3::operator=
    TVector3 & operator=(const TVector3 &v)
    │ │ │ -
    BALL::TVector3::operator*
    TVector3 operator*(const T &scalar) const
    Definition vector3.h:886
    │ │ │ -
    BALL::TVector3::set
    void set(const T &vx, const T &vy, const T &vz)
    Definition vector3.h:636
    │ │ │ -
    BALL::TVector3::get
    void get(T &r, TAngle< T > &phi, TAngle< T > &theta) const
    Definition vector3.h:731
    │ │ │ -
    BALL::TVector3::getTripleProduct
    static T getTripleProduct(const TVector3< T > &a, const TVector3< T > &b, const TVector3< T > &c)
    Definition vector3.h:1016
    │ │ │ -
    BALL::TVector3::operator+=
    TVector3 & operator+=(const TVector3 &vector)
    Definition vector3.h:864
    │ │ │ -
    BALL::TVector3::operator/
    TVector3 operator/(const T &lambda) const
    Definition vector3.h:903
    │ │ │ - │ │ │ -
    BALL::TVector3::normalize
    TVector3 & normalize()
    Definition vector3.h:770
    │ │ │ -
    BALL::TVector3::set
    void set(const T *ptr)
    Definition vector3.h:615
    │ │ │ -
    BALL::TVector3::operator+
    const TVector3 & operator+() const
    Definition vector3.h:850
    │ │ │ -
    BALL::TVector3::isOrthogonalTo
    bool isOrthogonalTo(const TVector3 &vector) const
    Definition vector3.h:1049
    │ │ │ -
    BALL::TVector3::write
    void write(PersistenceManager &pm) const
    Definition vector3.h:1101
    │ │ │ -
    BALL::TVector3::isValid
    bool isValid() const
    Definition vector3.h:1056
    │ │ │ -
    BALL::TVector3::clear
    void clear()
    Definition vector3.h:608
    │ │ │ -
    BALL::TVector3::dump
    void dump(std::ostream &s=std::cout, Size depth=0) const
    Definition vector3.h:1069
    │ │ │ -
    BALL::TVector3::set
    void set(const T &r, const TAngle< T > &phi, const TAngle< T > &theta)
    Definition vector3.h:654
    │ │ │ -
    BALL::TVector3::operator*=
    TVector3 & operator*=(const T &scalar)
    Definition vector3.h:893
    │ │ │ -
    BALL::TVector3::operator<
    bool operator<(const TVector3 &vector) const
    Needed for MSVC.
    Definition vector3.h:1034
    │ │ │ -
    BALL::TVector3::getUnit
    static const TVector3 & getUnit()
    Definition vector3.h:806
    │ │ │ -
    BALL::TVector3::getOrthogonalProjection
    TVector3 getOrthogonalProjection(const TVector3 &direction) const
    Definition vector3.h:995
    │ │ │ -
    BALL::TVector3::get
    void get(T *ptr) const
    Definition vector3.h:699
    │ │ │ -
    BALL::TVector3::TVector3
    TVector3(const T &vx, const T &vy, const T &vz)
    Definition vector3.h:575
    │ │ │ -
    BALL::TVector3::TVector3
    TVector3(const T &r, const TAngle< T > &phi, const TAngle< T > &theta)
    Definition vector3.h:593
    │ │ │ - │ │ │ -
    BALL::TVector3::getSquareDistance
    T getSquareDistance(const TVector3 &vector) const
    Definition vector3.h:960
    │ │ │ - │ │ │ +
    BALL::Circle3
    TCircle3< float > Circle3
    Definition circle3.h:301
    │ │ │ + │ │ │ +
    BALL::operator>>
    std::istream & operator>>(std::istream &is, TRegularData1D< ValueType > &grid)
    Input operator.
    Definition regularData1D.h:802
    │ │ │ +
    BALL::Maths::isNotEqual
    bool isNotEqual(const T1 &a, const T2 &b)
    Definition MATHS/common.h:224
    │ │ │ +
    BALL::Maths::isZero
    bool isZero(const T &t)
    Definition MATHS/common.h:189
    │ │ │ +
    BALL::Maths::isLessOrEqual
    bool isLessOrEqual(const T1 &a, const T2 &b)
    Definition MATHS/common.h:249
    │ │ │ +
    BALL::Maths::isEqual
    bool isEqual(const T1 &a, const T2 &b)
    Definition MATHS/common.h:212
    │ │ │ + │ │ │ +
    BALL::TCircle3::TCircle3
    TCircle3(const TCircle3 &circle)
    Definition circle3.h:70
    │ │ │ +
    BALL::TCircle3::isValid
    bool isValid() const
    Definition circle3.h:240
    │ │ │ +
    BALL::TCircle3::operator!=
    bool operator!=(const TCircle3 &circle) const
    Definition circle3.h:206
    │ │ │ +
    BALL::TCircle3::TCircle3
    TCircle3(const TVector3< T > &point, const TVector3< T > &normal, const T &radius)
    Definition circle3.h:83
    │ │ │ +
    BALL::TCircle3::has
    bool has(const TVector3< T > &point, bool on_surface=false) const
    Definition circle3.h:217
    │ │ │ +
    BALL::TCircle3::p
    TVector3< T > p
    Definition circle3.h:277
    │ │ │ +
    BALL::TCircle3::~TCircle3
    virtual ~TCircle3()
    Definition circle3.h:94
    │ │ │ +
    BALL::TCircle3::set
    void set(const TVector3< T > &point, const TVector3< T > &normal, const T &rad)
    Definition circle3.h:146
    │ │ │ +
    BALL::TCircle3::get
    void get(TCircle3 &circle) const
    Definition circle3.h:170
    │ │ │ +
    BALL::TCircle3::swap
    void swap(TCircle3 &circle)
    Definition circle3.h:116
    │ │ │ +
    BALL::TCircle3::get
    void get(TVector3< T > &point, TVector3< T > &normal, T &rhs) const
    Definition circle3.h:182
    │ │ │ +
    BALL::TCircle3::dump
    void dump(std::ostream &s=std::cout, Size depth=0) const
    Definition circle3.h:251
    │ │ │ + │ │ │ +
    BALL::TCircle3::n
    TVector3< T > n
    Definition circle3.h:282
    │ │ │ +
    BALL::TCircle3::clear
    virtual void clear()
    Definition circle3.h:101
    │ │ │ +
    BALL::TCircle3::operator=
    TCircle3 & operator=(const TCircle3 &circle)
    Definition circle3.h:157
    │ │ │ +
    BALL::TCircle3::operator==
    bool operator==(const TCircle3 &circle) const
    Definition circle3.h:198
    │ │ │ +
    BALL::TCircle3::set
    void set(const TCircle3 &circle)
    Definition circle3.h:134
    │ │ │ + │ │ │ │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ - │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ + │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,1109 +1,333 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _M_A_T_H_S │ │ │ │ -vector3.h │ │ │ │ +circle3.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_MATHS_VECTOR3_H │ │ │ │ -6#define BALL_MATHS_VECTOR3_H │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_COMMON_EXCEPTION_H │ │ │ │ -9# include <_B_A_L_L_/_C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12#ifndef BALL_CONCEPT_PERSISTENCEMANAGER_H │ │ │ │ -13# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16#ifndef BALL_MATHS_ANGLE_H │ │ │ │ -17# include <_B_A_L_L_/_M_A_T_H_S_/_a_n_g_l_e_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20#ifndef BALL_MATHS_COMMON_H │ │ │ │ -21# include <_B_A_L_L_/_M_A_T_H_S_/_c_o_m_m_o_n_._h> │ │ │ │ -22#endif │ │ │ │ -23 │ │ │ │ -24#ifdef BALL_HAS_IEEEFP_H │ │ │ │ -25# include │ │ │ │ -26#endif │ │ │ │ -27 │ │ │ │ +4// $Id: circle3.h,v 1.42 2004/07/05 20:57:28 oliver Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_MATHS_CIRCLE3_H │ │ │ │ +8#define BALL_MATHS_CIRCLE3_H │ │ │ │ +9 │ │ │ │ +10#ifndef BALL_COMMON_EXCEPTION_H │ │ │ │ +11# include <_B_A_L_L_/_C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h> │ │ │ │ +12#endif │ │ │ │ +13 │ │ │ │ +14#ifndef BALL_MATHS_VECTOR3_H │ │ │ │ +15# include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +16#endif │ │ │ │ +17 │ │ │ │ +18 │ │ │ │ +19namespace _B_A_L_L │ │ │ │ +20{ │ │ │ │ +26 template │ │ │ │ +27 class TCircle3; │ │ │ │ 28 │ │ │ │ -29namespace _B_A_L_L │ │ │ │ -30{ │ │ │ │ +34 template │ │ │ │ +35 std::istream& _o_p_e_r_a_t_o_r_ _>_>_ (std::istream& s, TCircle3& circle); │ │ │ │ 36 │ │ │ │ -37 template │ │ │ │ -38 class TVector3; │ │ │ │ -39 │ │ │ │ -43 │ │ │ │ -47 template │ │ │ │ -48 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -49 TVector3 _o_p_e_r_a_t_o_r_ _*_ (const T& a, const TVector3& b); │ │ │ │ +38 template │ │ │ │ +39 std::ostream& _o_p_e_r_a_t_o_r_ _<_<_ (std::ostream& s, const TCircle3& circle); │ │ │ │ +41 │ │ │ │ +44 template │ │ │ │ +_4_5 class _T_C_i_r_c_l_e_3 │ │ │ │ +46 { │ │ │ │ +47 public: │ │ │ │ +48 │ │ │ │ +49 _B_A_L_L___C_R_E_A_T_E(_T_C_i_r_c_l_e_3_<_T_>) │ │ │ │ 50 │ │ │ │ -55 template │ │ │ │ -56 std::istream& _o_p_e_r_a_t_o_r_ _>_>_ (std::istream& s, TVector3& vector); │ │ │ │ -57 │ │ │ │ -62 template │ │ │ │ -63 std::ostream& _o_p_e_r_a_t_o_r_ _<_<_ (std::ostream& s, const TVector3& vector); │ │ │ │ -64 │ │ │ │ -66 │ │ │ │ -69 template │ │ │ │ -_7_0 class _T_V_e_c_t_o_r_3 │ │ │ │ -71 { │ │ │ │ -72 public: │ │ │ │ -73 │ │ │ │ -77 │ │ │ │ -_8_2 _T_V_e_c_t_o_r_3(); │ │ │ │ -83 │ │ │ │ -_9_0 explicit _T_V_e_c_t_o_r_3(const T* ptr); │ │ │ │ -91 │ │ │ │ -_9_7 explicit _T_V_e_c_t_o_r_3(const T& value); │ │ │ │ -98 │ │ │ │ -102 template │ │ │ │ -_1_0_3 explicit _T_V_e_c_t_o_r_3(const _T_V_e_c_t_o_r_3_<_T_2_>& vec); │ │ │ │ -104 │ │ │ │ -_1_1_1 _T_V_e_c_t_o_r_3(const T& vx, const T& vy, const T& vz); │ │ │ │ +51 │ │ │ │ +54 │ │ │ │ +55 │ │ │ │ +_5_9 _T_C_i_r_c_l_e_3() │ │ │ │ +60 : _p(), │ │ │ │ +61 _n(), │ │ │ │ +62 _r_a_d_i_u_s(0) │ │ │ │ +63 { │ │ │ │ +64 } │ │ │ │ +65 │ │ │ │ +_7_0 _T_C_i_r_c_l_e_3(const _T_C_i_r_c_l_e_3& circle) │ │ │ │ +71 : _p(circle._p), │ │ │ │ +72 _n(circle._n), │ │ │ │ +73 _r_a_d_i_u_s(circle._r_a_d_i_u_s) │ │ │ │ +74 { │ │ │ │ +75 } │ │ │ │ +76 │ │ │ │ +_8_3 _T_C_i_r_c_l_e_3(const _T_V_e_c_t_o_r_3_<_T_>& point, const _T_V_e_c_t_o_r_3_<_T_>& normal, const T& │ │ │ │ +_r_a_d_i_u_s) │ │ │ │ +84 : _p(point), │ │ │ │ +85 _n(normal), │ │ │ │ +86 _r_a_d_i_u_s(_r_a_d_i_u_s) │ │ │ │ +87 { │ │ │ │ +88 } │ │ │ │ +89 │ │ │ │ +_9_4 virtual _~_T_C_i_r_c_l_e_3() │ │ │ │ +95 { │ │ │ │ +96 } │ │ │ │ +97 │ │ │ │ +_1_0_1 virtual void _c_l_e_a_r() │ │ │ │ +102 { │ │ │ │ +103 _p.clear(); │ │ │ │ +104 _n.clear(); │ │ │ │ +105 _r_a_d_i_u_s = (T)0; │ │ │ │ +106 } │ │ │ │ +107 │ │ │ │ +109 │ │ │ │ 112 │ │ │ │ -_1_1_7 _T_V_e_c_t_o_r_3(const _T_V_e_c_t_o_r_3& vector); │ │ │ │ -118 │ │ │ │ -_1_2_8 _T_V_e_c_t_o_r_3(const T& r, const _T_A_n_g_l_e_<_T_>& phi, const _T_A_n_g_l_e_<_T_>& theta); │ │ │ │ -129 │ │ │ │ -_1_3_4 _~_T_V_e_c_t_o_r_3(); │ │ │ │ -135 │ │ │ │ -_1_3_9 void _c_l_e_a_r(); │ │ │ │ +_1_1_6 void _s_w_a_p(_T_C_i_r_c_l_e_3& circle) │ │ │ │ +117 { │ │ │ │ +118 _T_V_e_c_t_o_r_3_<_T_> temp_vector(_p); │ │ │ │ +119 _p = circle._p; │ │ │ │ +120 circle._p = temp_vector; │ │ │ │ +121 │ │ │ │ +122 temp_vector = _n; │ │ │ │ +123 _n = circle._n; │ │ │ │ +124 circle._n = temp_vector; │ │ │ │ +125 │ │ │ │ +126 T temp = _r_a_d_i_u_s; │ │ │ │ +127 _r_a_d_i_u_s = circle._r_a_d_i_u_s; │ │ │ │ +128 circle._r_a_d_i_u_s = temp; │ │ │ │ +129 } │ │ │ │ +130 │ │ │ │ +_1_3_4 void _s_e_t(const _T_C_i_r_c_l_e_3& circle) │ │ │ │ +135 { │ │ │ │ +136 _p = circle._p; │ │ │ │ +137 _n = circle._n; │ │ │ │ +138 _r_a_d_i_u_s = circle._r_a_d_i_u_s; │ │ │ │ +139 } │ │ │ │ 140 │ │ │ │ -142 │ │ │ │ -146 │ │ │ │ -_1_5_3 void _s_e_t(const T* ptr); │ │ │ │ -154 │ │ │ │ -_1_5_9 void _s_e_t(const T& value); │ │ │ │ -160 │ │ │ │ -_1_6_6 void _s_e_t(const T& vx, const T& vy, const T& vz); │ │ │ │ -167 │ │ │ │ -_1_7_1 void _s_e_t(const _T_V_e_c_t_o_r_3& vector); │ │ │ │ -172 │ │ │ │ -_1_8_5 void _s_e_t(const T& r, const _T_A_n_g_l_e_<_T_>& phi, const _T_A_n_g_l_e_<_T_>& theta); │ │ │ │ -186 │ │ │ │ -_1_9_1 _T_V_e_c_t_o_r_3& _o_p_e_r_a_t_o_r_ _=_ (const _T_V_e_c_t_o_r_3& v); │ │ │ │ -192 │ │ │ │ -_1_9_7 _T_V_e_c_t_o_r_3& _o_p_e_r_a_t_o_r_ _=_ (T value); │ │ │ │ -198 │ │ │ │ -_2_0_4 _T_V_e_c_t_o_r_3& _o_p_e_r_a_t_o_r_ _=_ (const T* ptr); │ │ │ │ -205 │ │ │ │ -_2_1_2 void _g_e_t(T* ptr) const; │ │ │ │ -213 │ │ │ │ -_2_1_9 void _g_e_t(T& _x, T& _y, T& _z) const; │ │ │ │ -220 │ │ │ │ -_2_2_5 void _g_e_t(_T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -226 │ │ │ │ -_2_3_4 void _g_e_t(T& r, _T_A_n_g_l_e_<_T_>& phi, _T_A_n_g_l_e_<_T_>& theta) const; │ │ │ │ +_1_4_6 void _s_e_t(const _T_V_e_c_t_o_r_3_<_T_>& point, const _T_V_e_c_t_o_r_3_<_T_>& normal, const T& rad) │ │ │ │ +147 { │ │ │ │ +148 _p = point; │ │ │ │ +149 _n = normal; │ │ │ │ +150 _r_a_d_i_u_s = rad; │ │ │ │ +151 } │ │ │ │ +152 │ │ │ │ +_1_5_7 _T_C_i_r_c_l_e_3& _o_p_e_r_a_t_o_r_ _=_ (const _T_C_i_r_c_l_e_3& circle) │ │ │ │ +158 { │ │ │ │ +159 _p = circle._p; │ │ │ │ +160 _n = circle._n; │ │ │ │ +161 _r_a_d_i_u_s = circle._r_a_d_i_u_s; │ │ │ │ +162 │ │ │ │ +163 return *this; │ │ │ │ +164 } │ │ │ │ +165 │ │ │ │ +_1_7_0 void _g_e_t(_T_C_i_r_c_l_e_3& circle) const │ │ │ │ +171 { │ │ │ │ +172 circle._p = _p; │ │ │ │ +173 circle._n = _n; │ │ │ │ +174 circle._r_a_d_i_u_s = _r_a_d_i_u_s; │ │ │ │ +175 } │ │ │ │ +176 │ │ │ │ +_1_8_2 void _g_e_t(_T_V_e_c_t_o_r_3_<_T_>& point, _T_V_e_c_t_o_r_3_<_T_>& normal, T& rhs) const │ │ │ │ +183 │ │ │ │ +184 { │ │ │ │ +185 point = _p; │ │ │ │ +186 normal = _n; │ │ │ │ +187 rhs = _r_a_d_i_u_s; │ │ │ │ +188 } │ │ │ │ +189 │ │ │ │ +191 │ │ │ │ +194 │ │ │ │ +_1_9_8 bool _o_p_e_r_a_t_o_r_ _=_=_ (const _T_C_i_r_c_l_e_3& circle) const │ │ │ │ +199 { │ │ │ │ +200 return (_p == circle._p && _n == circle._n && _M_a_t_h_s_:_:_i_s_E_q_u_a_l(_r_a_d_i_u_s, │ │ │ │ +circle._r_a_d_i_u_s)); │ │ │ │ +201 } │ │ │ │ +202 │ │ │ │ +_2_0_6 bool _o_p_e_r_a_t_o_r_ _!_=_ (const _T_C_i_r_c_l_e_3& circle) const │ │ │ │ +207 { │ │ │ │ +208 return (_p != circle._p || _n != circle._n || _M_a_t_h_s_:_:_i_s_N_o_t_E_q_u_a_l(_r_a_d_i_u_s, │ │ │ │ +circle._r_a_d_i_u_s)); │ │ │ │ +209 } │ │ │ │ +210 │ │ │ │ +_2_1_7 bool _h_a_s(const _T_V_e_c_t_o_r_3_<_T_>& point, bool on_surface = false) const │ │ │ │ +218 { │ │ │ │ +219 if (on_surface) │ │ │ │ +220 { │ │ │ │ +221 return (_M_a_t_h_s_:_:_i_s_Z_e_r_o(_n * (point - _p)) │ │ │ │ +222 && _M_a_t_h_s_:_:_i_s_E_q_u_a_l(_p.getDistance(point), _r_a_d_i_u_s)); │ │ │ │ +223 } │ │ │ │ +224 else │ │ │ │ +225 { │ │ │ │ +226 return (_M_a_t_h_s_:_:_i_s_Z_e_r_o(_n * (point - _p)) │ │ │ │ +227 && _M_a_t_h_s_:_:_i_s_L_e_s_s_O_r_E_q_u_a_l(_p.getDistance(point), _r_a_d_i_u_s)); │ │ │ │ +228 } │ │ │ │ +229 } │ │ │ │ +230 │ │ │ │ +232 │ │ │ │ 235 │ │ │ │ -_2_3_9 void _s_w_a_p(_T_V_e_c_t_o_r_3& vector); │ │ │ │ -240 │ │ │ │ -_2_4_6 T _g_e_t_L_e_n_g_t_h() const; │ │ │ │ -247 │ │ │ │ -_2_5_3 T _g_e_t_S_q_u_a_r_e_L_e_n_g_t_h() const; │ │ │ │ +_2_4_0 bool _i_s_V_a_l_i_d() const │ │ │ │ +241 { │ │ │ │ +242 return true; │ │ │ │ +243 } │ │ │ │ +244 │ │ │ │ +_2_5_1 void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const │ │ │ │ +252 { │ │ │ │ +253 _B_A_L_L___D_U_M_P___S_T_R_E_A_M___P_R_E_F_I_X(s); │ │ │ │ 254 │ │ │ │ -_2_6_1 _T_V_e_c_t_o_r_3& _n_o_r_m_a_l_i_z_e(); │ │ │ │ +255 _B_A_L_L___D_U_M_P___H_E_A_D_E_R(s, this, this); │ │ │ │ +256 │ │ │ │ +257 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ +258 s << " position: " << _p << std::endl; │ │ │ │ +259 │ │ │ │ +260 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ +261 s << " normal: " << _n << std::endl; │ │ │ │ 262 │ │ │ │ -_2_6_7 _T_V_e_c_t_o_r_3& _n_e_g_a_t_e(); │ │ │ │ +263 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ +264 s << " radius: " << _r_a_d_i_u_s << std::endl; │ │ │ │ +265 │ │ │ │ +266 _B_A_L_L___D_U_M_P___S_T_R_E_A_M___S_U_F_F_I_X(s); │ │ │ │ +267 } │ │ │ │ 268 │ │ │ │ -_2_7_1 static const _T_V_e_c_t_o_r_3& _g_e_t_Z_e_r_o(); │ │ │ │ -272 │ │ │ │ -_2_7_6 static const _T_V_e_c_t_o_r_3& _g_e_t_U_n_i_t(); │ │ │ │ -277 │ │ │ │ -_2_8_1 T& _o_p_e_r_a_t_o_r_ _[_]_ (_P_o_s_i_t_i_o_n position); │ │ │ │ -282 │ │ │ │ -_2_8_6 const T& _o_p_e_r_a_t_o_r_ _[_]_ (_P_o_s_i_t_i_o_n position) const; │ │ │ │ +270 │ │ │ │ +273 │ │ │ │ +_2_7_7 _T_V_e_c_t_o_r_3_<_T_> _p; │ │ │ │ +278 │ │ │ │ +_2_8_2 _T_V_e_c_t_o_r_3_<_T_> _n; │ │ │ │ +283 │ │ │ │ +_2_8_7 T _r_a_d_i_u_s; │ │ │ │ 288 │ │ │ │ +290 }; │ │ │ │ 292 │ │ │ │ -_2_9_5 const _T_V_e_c_t_o_r_3& _o_p_e_r_a_t_o_r_ _+_ () const; │ │ │ │ -296 │ │ │ │ -_2_9_9 _T_V_e_c_t_o_r_3 _o_p_e_r_a_t_o_r_ _-_ () const; │ │ │ │ -300 │ │ │ │ -_3_0_3 _T_V_e_c_t_o_r_3 _o_p_e_r_a_t_o_r_ _+_ (const _T_V_e_c_t_o_r_3& b) const; │ │ │ │ -304 │ │ │ │ -_3_0_7 _T_V_e_c_t_o_r_3 _o_p_e_r_a_t_o_r_ _-_ (const _T_V_e_c_t_o_r_3& b) const; │ │ │ │ -308 │ │ │ │ -_3_1_4 _T_V_e_c_t_o_r_3& _o_p_e_r_a_t_o_r_ _+_=_ (const _T_V_e_c_t_o_r_3& vector); │ │ │ │ +294#ifdef BALL_COMPILER_MSVC │ │ │ │ +295 template class _B_A_L_L___E_X_P_O_R_T _T_C_i_r_c_l_e_3_<_f_l_o_a_t_>; │ │ │ │ +296#endif │ │ │ │ +297 │ │ │ │ +_3_0_1 typedef _T_C_i_r_c_l_e_3_<_f_l_o_a_t_> _C_i_r_c_l_e_3; │ │ │ │ +302 │ │ │ │ +306 template │ │ │ │ +_3_0_7 std::istream& _o_p_e_r_a_t_o_r_ _>_>_ (std::istream& s, _T_C_i_r_c_l_e_3_<_T_>& circle) │ │ │ │ +308 { │ │ │ │ +309 char c; │ │ │ │ +310 s >> c; │ │ │ │ +311 s >> circle._p >> circle._n >> circle._r_a_d_i_u_s; │ │ │ │ +312 s >> c; │ │ │ │ +313 return s; │ │ │ │ +314 } │ │ │ │ 315 │ │ │ │ -_3_2_0 _T_V_e_c_t_o_r_3& _o_p_e_r_a_t_o_r_ _-_=_ (const _T_V_e_c_t_o_r_3& vector); │ │ │ │ -321 │ │ │ │ -_3_2_7 _T_V_e_c_t_o_r_3 _o_p_e_r_a_t_o_r_ _*_ (const T& scalar) const; │ │ │ │ -328 │ │ │ │ -_3_3_4 _T_V_e_c_t_o_r_3& _o_p_e_r_a_t_o_r_ _*_=_ (const T& scalar); │ │ │ │ -335 │ │ │ │ -_3_4_2 _T_V_e_c_t_o_r_3 _o_p_e_r_a_t_o_r_ _/_ (const T& lambda) const; │ │ │ │ -343 │ │ │ │ -_3_4_9 _T_V_e_c_t_o_r_3& _o_p_e_r_a_t_o_r_ _/_=_ (const T& lambda); │ │ │ │ -350 │ │ │ │ -_3_5_4 T _o_p_e_r_a_t_o_r_ _*_ (const _T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -355 │ │ │ │ -_3_5_9 _T_V_e_c_t_o_r_3 _o_p_e_r_a_t_o_r_ _%_ (const _T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -360 │ │ │ │ -_3_6_4 _T_V_e_c_t_o_r_3& _o_p_e_r_a_t_o_r_ _%_=_ (const _T_V_e_c_t_o_r_3& vector); │ │ │ │ -365 │ │ │ │ -367 │ │ │ │ -371 │ │ │ │ -_3_7_4 T _g_e_t_D_i_s_t_a_n_c_e(const _T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -375 │ │ │ │ -_3_7_8 T _g_e_t_S_q_u_a_r_e_D_i_s_t_a_n_c_e(const _T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -379 │ │ │ │ -_3_8_4 _T_A_n_g_l_e_<_T_> _g_e_t_A_n_g_l_e(const _T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -385 │ │ │ │ -_3_8_9 _T_V_e_c_t_o_r_3 _g_e_t_O_r_t_h_o_g_o_n_a_l_P_r_o_j_e_c_t_i_o_n(const _T_V_e_c_t_o_r_3& direction) const; │ │ │ │ -390 │ │ │ │ -_3_9_7 static _T_V_e_c_t_o_r_3 _g_e_t_P_e_r_p_e_n_d_i_c_u_l_a_r_N_o_r_m_a_l_i_z_a_t_i_o_n │ │ │ │ -398 (const _T_V_e_c_t_o_r_3& a, const _T_V_e_c_t_o_r_3& b, const _T_V_e_c_t_o_r_3& c); │ │ │ │ -399 │ │ │ │ -_4_0_7 static T _g_e_t_T_r_i_p_l_e_P_r_o_d_u_c_t (const _T_V_e_c_t_o_r_3_<_T_>& a, const _T_V_e_c_t_o_r_3_<_T_>& b, │ │ │ │ -const _T_V_e_c_t_o_r_3_<_T_>& c); │ │ │ │ -408 │ │ │ │ -410 │ │ │ │ -414 │ │ │ │ -_4_2_0 bool _o_p_e_r_a_t_o_r_ _=_=_ (const _T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -421 │ │ │ │ -_4_2_7 bool _o_p_e_r_a_t_o_r_ _!_=_ (const _T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -428 │ │ │ │ -_4_3_0 bool _o_p_e_r_a_t_o_r_ _<_ (const _T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -431 │ │ │ │ -432 │ │ │ │ -_4_3_7 bool _i_s_Z_e_r_o() const; │ │ │ │ -438 │ │ │ │ -_4_4_1 bool _i_s_O_r_t_h_o_g_o_n_a_l_T_o(const _T_V_e_c_t_o_r_3& vector) const; │ │ │ │ -442 │ │ │ │ -444 │ │ │ │ -445 │ │ │ │ -449 │ │ │ │ -_4_5_2 void _w_r_i_t_e(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm) const; │ │ │ │ -453 │ │ │ │ -_4_5_6 bool _r_e_a_d(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm); │ │ │ │ -457 │ │ │ │ -459 │ │ │ │ -463 │ │ │ │ -_4_7_0 void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const; │ │ │ │ -471 │ │ │ │ -_4_7_6 bool _i_s_V_a_l_i_d() const; │ │ │ │ -477 │ │ │ │ -479 │ │ │ │ -480 │ │ │ │ -486 │ │ │ │ -_4_8_9 T _x; │ │ │ │ -490 │ │ │ │ -_4_9_3 T _y; │ │ │ │ -494 │ │ │ │ -_4_9_7 T _z; │ │ │ │ -499 │ │ │ │ -500 private: │ │ │ │ -501 │ │ │ │ -502 _T_A_n_g_l_e_<_T_> getAngle_(const T& a, const T& b) const │ │ │ │ -503 { │ │ │ │ -504 _T_A_n_g_l_e_<_T_> angle; │ │ │ │ -505 │ │ │ │ -506 if (_M_a_t_h_s_:_:_i_s_N_o_t_Z_e_r_o(a)) │ │ │ │ -507 { │ │ │ │ -508 angle = atan(b / a); │ │ │ │ -509 } │ │ │ │ -510 else │ │ │ │ -511 { │ │ │ │ -512 angle = _M_a_t_h_s_:_:_s_g_n(b) * _C_o_n_s_t_a_n_t_s_:_:_P_I / 2; │ │ │ │ -513 } │ │ │ │ -514 │ │ │ │ -515 if (_M_a_t_h_s_:_:_i_s_L_e_s_s(a, 0)) │ │ │ │ -516 { │ │ │ │ -517 angle += _C_o_n_s_t_a_n_t_s_:_:_P_I; │ │ │ │ -518 } │ │ │ │ -519 │ │ │ │ -520 if (_M_a_t_h_s_:_:_i_s_L_e_s_s(angle._v_a_l_u_e, 0)) │ │ │ │ -521 { │ │ │ │ -522 return (_A_n_g_l_e)(angle._v_a_l_u_e += 2.0 * _C_o_n_s_t_a_n_t_s_:_:_P_I); │ │ │ │ -523 } │ │ │ │ -524 else │ │ │ │ -525 { │ │ │ │ -526 return angle; │ │ │ │ -527 } │ │ │ │ -528 } │ │ │ │ -529 }; │ │ │ │ -531 │ │ │ │ -532 template │ │ │ │ -533 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_5_3_4 _T_V_e_c_t_o_r_3_<_T_>_:_:_T_V_e_c_t_o_r_3() │ │ │ │ -535 : x(0), │ │ │ │ -536 y(0), │ │ │ │ -537 z(0) │ │ │ │ -538 { │ │ │ │ -539 } │ │ │ │ -540 │ │ │ │ -541 template │ │ │ │ -542 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_5_4_3 _T_V_e_c_t_o_r_3_<_T_>_:_:_T_V_e_c_t_o_r_3(const T* ptr) │ │ │ │ -544 { │ │ │ │ -545 if (ptr == 0) │ │ │ │ -546 { │ │ │ │ -547 throw _E_x_c_e_p_t_i_o_n_:_:_N_u_l_l_P_o_i_n_t_e_r(__FILE__, __LINE__); │ │ │ │ -548 } │ │ │ │ -549 │ │ │ │ -550 x = *ptr++; │ │ │ │ -551 y = *ptr++; │ │ │ │ -552 z = *ptr; │ │ │ │ -553 } │ │ │ │ -554 │ │ │ │ -555 template │ │ │ │ -556 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_5_5_7 _T_V_e_c_t_o_r_3_<_T_>_:_:_T_V_e_c_t_o_r_3(const T& value) │ │ │ │ -558 : x(value), │ │ │ │ -559 y(value), │ │ │ │ -560 z(value) │ │ │ │ -561 { │ │ │ │ -562 } │ │ │ │ -563 │ │ │ │ -564 template template │ │ │ │ -565 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_5_6_6 _T_V_e_c_t_o_r_3_<_T_>_:_:_T_V_e_c_t_o_r_3(const _T_V_e_c_t_o_r_3_<_T_2_>& vec) │ │ │ │ -567 : x((T)vec.x), │ │ │ │ -568 y((T)vec.y), │ │ │ │ -569 z((T)vec.z) │ │ │ │ -570 { │ │ │ │ -571 } │ │ │ │ -572 │ │ │ │ -573 template │ │ │ │ -574 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_5_7_5 _T_V_e_c_t_o_r_3_<_T_>_:_:_T_V_e_c_t_o_r_3(const T& vx, const T& vy, const T& vz) │ │ │ │ -576 : x(vx), │ │ │ │ -577 y(vy), │ │ │ │ -578 z(vz) │ │ │ │ -579 { │ │ │ │ -580 } │ │ │ │ -581 │ │ │ │ -582 template │ │ │ │ -583 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_5_8_4 _T_V_e_c_t_o_r_3_<_T_>_:_:_T_V_e_c_t_o_r_3(const _T_V_e_c_t_o_r_3& vector) │ │ │ │ -585 : x(vector.x), │ │ │ │ -586 y(vector.y), │ │ │ │ -587 z(vector.z) │ │ │ │ -588 { │ │ │ │ -589 } │ │ │ │ -590 │ │ │ │ -591 template │ │ │ │ -592 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_5_9_3 _T_V_e_c_t_o_r_3_<_T_>_:_:_T_V_e_c_t_o_r_3(const T& r, const _T_A_n_g_l_e_<_T_>& phi, const _T_A_n_g_l_e_<_T_>& │ │ │ │ -theta) │ │ │ │ -594 : x(r * cos(phi) * sin(theta)), │ │ │ │ -595 y(r * sin(phi) * sin(theta)), │ │ │ │ -596 z(r * cos(theta)) │ │ │ │ -597 { │ │ │ │ -598 } │ │ │ │ -599 │ │ │ │ -600 template │ │ │ │ -601 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_6_0_2 _T_V_e_c_t_o_r_3_<_T_>_:_:_~_T_V_e_c_t_o_r_3() │ │ │ │ -603 { │ │ │ │ -604 } │ │ │ │ -605 │ │ │ │ -606 template │ │ │ │ -607 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_6_0_8 void _T_V_e_c_t_o_r_3_<_T_>_:_:_c_l_e_a_r() │ │ │ │ -609 { │ │ │ │ -610 x = y = z = (T)0; │ │ │ │ -611 } │ │ │ │ -612 │ │ │ │ -613 template │ │ │ │ -614 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_6_1_5 void _T_V_e_c_t_o_r_3_<_T_>_:_:_s_e_t(const T* ptr) │ │ │ │ -616 { │ │ │ │ -617 if (ptr == 0) │ │ │ │ -618 throw _E_x_c_e_p_t_i_o_n_:_:_N_u_l_l_P_o_i_n_t_e_r(__FILE__, __LINE__); │ │ │ │ -619 │ │ │ │ -620 x = *ptr++; │ │ │ │ -621 y = *ptr++; │ │ │ │ -622 z = *ptr; │ │ │ │ -623 } │ │ │ │ -624 │ │ │ │ -625 template │ │ │ │ -626 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_6_2_7 void _T_V_e_c_t_o_r_3_<_T_>_:_:_s_e_t(const T& value) │ │ │ │ -628 { │ │ │ │ -629 x = value; │ │ │ │ -630 y = value; │ │ │ │ -631 z = value; │ │ │ │ -632 } │ │ │ │ -633 │ │ │ │ -634 template │ │ │ │ -635 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_6_3_6 void _T_V_e_c_t_o_r_3_<_T_>_:_:_s_e_t(const T& vx, const T& vy, const T& vz) │ │ │ │ -637 { │ │ │ │ -638 x = vx; │ │ │ │ -639 y = vy; │ │ │ │ -640 z = vz; │ │ │ │ -641 } │ │ │ │ -642 │ │ │ │ -643 template │ │ │ │ -644 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -645 void _T_V_e_c_t_o_r_3_<_T_>_:_:_s_e_t(const _T_V_e_c_t_o_r_3_<_T_>& vector) │ │ │ │ -646 { │ │ │ │ -647 x = vector._x; │ │ │ │ -648 y = vector._y; │ │ │ │ -649 z = vector._z; │ │ │ │ -650 } │ │ │ │ -651 │ │ │ │ -652 template │ │ │ │ -653 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_6_5_4 void _T_V_e_c_t_o_r_3_<_T_>_:_:_s_e_t(const T& r, const _T_A_n_g_l_e_<_T_> &phi, const _T_A_n_g_l_e_<_T_> │ │ │ │ -&theta) │ │ │ │ -655 { │ │ │ │ -656 x = r * cos(phi) * sin(theta); │ │ │ │ -657 y = r * sin(phi) * sin(theta); │ │ │ │ -658 z = r * cos(theta); │ │ │ │ -659 } │ │ │ │ -660 │ │ │ │ -661 template │ │ │ │ -662 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_6_6_3 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _=_ (const T* ptr) │ │ │ │ -664 { │ │ │ │ -665 if (ptr == 0) │ │ │ │ -666 { │ │ │ │ -667 throw _E_x_c_e_p_t_i_o_n_:_:_N_u_l_l_P_o_i_n_t_e_r(__FILE__, __LINE__); │ │ │ │ -668 } │ │ │ │ -669 │ │ │ │ -670 x = *ptr++; │ │ │ │ -671 y = *ptr++; │ │ │ │ -672 z = *ptr; │ │ │ │ -673 │ │ │ │ -674 return *this; │ │ │ │ -675 } │ │ │ │ -676 │ │ │ │ -677 template │ │ │ │ -678 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -679 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _=_ (const _T_V_e_c_t_o_r_3_<_T_>& vector) │ │ │ │ -680 { │ │ │ │ -681 x = vector._x; │ │ │ │ -682 y = vector._y; │ │ │ │ -683 z = vector._z; │ │ │ │ -684 │ │ │ │ -685 return *this; │ │ │ │ -686 } │ │ │ │ -687 │ │ │ │ -688 template │ │ │ │ -689 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_6_9_0 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _=_ (T value) │ │ │ │ -691 { │ │ │ │ -692 x = y = z = value; │ │ │ │ -693 │ │ │ │ -694 return *this; │ │ │ │ -695 } │ │ │ │ -696 │ │ │ │ -697 template │ │ │ │ -698 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_6_9_9 void _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t(T* ptr) const │ │ │ │ -700 { │ │ │ │ -701 if (ptr == 0) │ │ │ │ -702 { │ │ │ │ -703 throw _E_x_c_e_p_t_i_o_n_:_:_N_u_l_l_P_o_i_n_t_e_r(__FILE__, __LINE__); │ │ │ │ -704 } │ │ │ │ -705 │ │ │ │ -706 *ptr++ = x; │ │ │ │ -707 *ptr++ = y; │ │ │ │ -708 *ptr = z; │ │ │ │ -709 } │ │ │ │ -710 │ │ │ │ -711 template │ │ │ │ -712 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_7_1_3 void _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t(T& new_x, T& new_y, T& new_z) const │ │ │ │ -714 { │ │ │ │ -715 new_x = x; │ │ │ │ -716 new_y = y; │ │ │ │ -717 new_z = z; │ │ │ │ -718 } │ │ │ │ -719 │ │ │ │ -720 template │ │ │ │ -721 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -722 void _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t(_T_V_e_c_t_o_r_3_<_T_>& vector) const │ │ │ │ -723 { │ │ │ │ -724 vector._x = x; │ │ │ │ -725 vector._y = y; │ │ │ │ -726 vector._z = z; │ │ │ │ -727 } │ │ │ │ -728 │ │ │ │ -729 template │ │ │ │ -730 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_7_3_1 void _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t(T& r, _T_A_n_g_l_e_<_T_>& phi, _T_A_n_g_l_e_<_T_>& theta) const │ │ │ │ -732 { │ │ │ │ -733 r = sqrt(x * x + y * y + z * z); │ │ │ │ -734 phi = (_A_n_g_l_e)getAngle_(x, y); │ │ │ │ -735 theta = getAngle_(z, sqrt(x * x + y * y)); │ │ │ │ -736 } │ │ │ │ -737 │ │ │ │ -738 template │ │ │ │ -739 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_7_4_0 void _T_V_e_c_t_o_r_3_<_T_>_:_:_s_w_a_p(_T_V_e_c_t_o_r_3_<_T_>& vector) │ │ │ │ -741 { │ │ │ │ -742 T temp = x; │ │ │ │ -743 x = vector._x; │ │ │ │ -744 vector._x = temp; │ │ │ │ -745 │ │ │ │ -746 temp = y; │ │ │ │ -747 y = vector._y; │ │ │ │ -748 vector._y = temp; │ │ │ │ -749 │ │ │ │ -750 temp = z; │ │ │ │ -751 z = vector._z; │ │ │ │ -752 vector._z = temp; │ │ │ │ -753 } │ │ │ │ -754 │ │ │ │ -755 template │ │ │ │ -756 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_7_5_7 T _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_L_e_n_g_t_h() const │ │ │ │ -758 { │ │ │ │ -759 return (T)sqrt(x * x + y * y + z * z); │ │ │ │ -760 } │ │ │ │ -761 │ │ │ │ -762 template │ │ │ │ -763 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_7_6_4 T _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_S_q_u_a_r_e_L_e_n_g_t_h() const │ │ │ │ -765 { │ │ │ │ -766 return (x * x + y * y + z * z); │ │ │ │ -767 } │ │ │ │ -768 │ │ │ │ -769 template │ │ │ │ -_7_7_0 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_n_o_r_m_a_l_i_z_e() │ │ │ │ -771 { │ │ │ │ -772 T len = sqrt(x * x + y * y + z * z); │ │ │ │ -773 │ │ │ │ -774 if (_M_a_t_h_s_:_:_i_s_Z_e_r_o(len)) │ │ │ │ -775 { │ │ │ │ -776 throw _E_x_c_e_p_t_i_o_n_:_:_D_i_v_i_s_i_o_n_B_y_Z_e_r_o(__FILE__, __LINE__); │ │ │ │ -777 } │ │ │ │ -778 │ │ │ │ -779 x /= len; │ │ │ │ -780 y /= len; │ │ │ │ -781 z /= len; │ │ │ │ -782 │ │ │ │ -783 return *this; │ │ │ │ -784 } │ │ │ │ -785 │ │ │ │ -786 template │ │ │ │ -787 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_7_8_8 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_n_e_g_a_t_e() │ │ │ │ -789 { │ │ │ │ -790 x *= -1; │ │ │ │ -791 y *= -1; │ │ │ │ -792 z *= -1; │ │ │ │ -793 return *this; │ │ │ │ -794 } │ │ │ │ -795 │ │ │ │ -796 template │ │ │ │ -797 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_7_9_8 const _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_Z_e_r_o() │ │ │ │ -799 { │ │ │ │ -800 static _T_V_e_c_t_o_r_3_<_T_> null_vector(0, 0, 0); │ │ │ │ -801 return null_vector; │ │ │ │ -802 } │ │ │ │ -803 │ │ │ │ -804 template │ │ │ │ -805 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_8_0_6 const _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_U_n_i_t() │ │ │ │ -807 { │ │ │ │ -808 static _T_V_e_c_t_o_r_3_<_T_> unit_vector(1, 1, 1); │ │ │ │ -809 return unit_vector; │ │ │ │ -810 } │ │ │ │ -811 │ │ │ │ -812 template │ │ │ │ -813 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_8_1_4 T& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _[_]_ (_P_o_s_i_t_i_o_n position) │ │ │ │ -815 { │ │ │ │ -816 if (position > 2) │ │ │ │ -817 { │ │ │ │ -818 throw _E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_O_v_e_r_f_l_o_w(__FILE__, __LINE__, position); │ │ │ │ -819 } │ │ │ │ -820 switch (position) │ │ │ │ -821 { │ │ │ │ -822 case 0: return x; │ │ │ │ -823 case 1: return y; │ │ │ │ -824 case 2: │ │ │ │ -825 default: │ │ │ │ -826 return z; │ │ │ │ -827 } │ │ │ │ -828 } │ │ │ │ -829 │ │ │ │ -830 template │ │ │ │ -831 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_8_3_2 const T& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _[_]_ (_P_o_s_i_t_i_o_n position) const │ │ │ │ -833 { │ │ │ │ -834 if (position > 2) │ │ │ │ -835 { │ │ │ │ -836 throw _E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_O_v_e_r_f_l_o_w(__FILE__, __LINE__); │ │ │ │ -837 } │ │ │ │ -838 switch (position) │ │ │ │ -839 { │ │ │ │ -840 case 0: return x; │ │ │ │ -841 case 1: return y; │ │ │ │ -842 case 2: │ │ │ │ -843 default: │ │ │ │ -844 return z; │ │ │ │ -845 } │ │ │ │ -846 } │ │ │ │ -847 │ │ │ │ -848 template │ │ │ │ -849 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_8_5_0 const _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _+_ () const │ │ │ │ -851 { │ │ │ │ -852 return *this; │ │ │ │ -853 } │ │ │ │ -854 │ │ │ │ -855 template │ │ │ │ -856 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_8_5_7 _T_V_e_c_t_o_r_3_<_T_> _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _-_ () const │ │ │ │ -858 { │ │ │ │ -859 return _T_V_e_c_t_o_r_3_<_T_>(-x, -y, -z); │ │ │ │ -860 } │ │ │ │ -861 │ │ │ │ -862 template │ │ │ │ -863 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_8_6_4 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _+_=_ (const _T_V_e_c_t_o_r_3_<_T_>& vector) │ │ │ │ -865 { │ │ │ │ -866 x += vector._x; │ │ │ │ -867 y += vector._y; │ │ │ │ -868 z += vector._z; │ │ │ │ -869 │ │ │ │ -870 return *this; │ │ │ │ -871 } │ │ │ │ -872 │ │ │ │ -873 template │ │ │ │ -874 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_8_7_5 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _-_=_ (const _T_V_e_c_t_o_r_3_<_T_>& vector) │ │ │ │ -876 { │ │ │ │ -877 x -= vector._x; │ │ │ │ -878 y -= vector._y; │ │ │ │ -879 z -= vector._z; │ │ │ │ -880 │ │ │ │ -881 return *this; │ │ │ │ -882 } │ │ │ │ -883 │ │ │ │ -884 template │ │ │ │ -885 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_8_8_6 _T_V_e_c_t_o_r_3_<_T_> _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _*_ (const T& scalar) const │ │ │ │ -887 { │ │ │ │ -888 return _T_V_e_c_t_o_r_3_<_T_>(x * scalar, y * scalar, z * scalar); │ │ │ │ -889 } │ │ │ │ -890 │ │ │ │ -891 template │ │ │ │ -892 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_8_9_3 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _*_=_ (const T &scalar) │ │ │ │ -894 { │ │ │ │ -895 x *= scalar; │ │ │ │ -896 y *= scalar; │ │ │ │ -897 z *= scalar; │ │ │ │ -898 │ │ │ │ -899 return *this; │ │ │ │ -900 } │ │ │ │ -901 │ │ │ │ -902 template │ │ │ │ -_9_0_3 _T_V_e_c_t_o_r_3_<_T_> _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _/_ (const T& lambda) const │ │ │ │ -904 { │ │ │ │ -905 if (lambda == (T)0) │ │ │ │ -906 { │ │ │ │ -907 throw _E_x_c_e_p_t_i_o_n_:_:_D_i_v_i_s_i_o_n_B_y_Z_e_r_o(__FILE__, __LINE__); │ │ │ │ -908 } │ │ │ │ -909 return _T_V_e_c_t_o_r_3_<_T_>(x / lambda, y / lambda, z / lambda); │ │ │ │ -910 } │ │ │ │ -911 │ │ │ │ -912 template │ │ │ │ -_9_1_3 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _/_=_ (const T& lambda) │ │ │ │ -914 { │ │ │ │ -915 if (lambda == (T)0) │ │ │ │ -916 { │ │ │ │ -917 throw _E_x_c_e_p_t_i_o_n_:_:_D_i_v_i_s_i_o_n_B_y_Z_e_r_o(__FILE__, __LINE__); │ │ │ │ -918 } │ │ │ │ -919 x /= lambda; │ │ │ │ -920 y /= lambda; │ │ │ │ -921 z /= lambda; │ │ │ │ -922 │ │ │ │ -923 return *this; │ │ │ │ -924 } │ │ │ │ -925 │ │ │ │ -926 template │ │ │ │ -927 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -928 T _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _*_ (const _T_V_e_c_t_o_r_3_<_T_>& vector) const │ │ │ │ -929 { │ │ │ │ -930 return (x * vector._x + y * vector._y + z * vector._z); │ │ │ │ -931 } │ │ │ │ -932 │ │ │ │ -933 template │ │ │ │ -_9_3_4 _T_V_e_c_t_o_r_3_<_T_> _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _%_ (const _T_V_e_c_t_o_r_3_<_T_>& v) const │ │ │ │ -935 { │ │ │ │ -936 return _T_V_e_c_t_o_r_3(y * v._z - z * v._y, z * v._x - x * v._z, x * v._y - y * v._x); │ │ │ │ -937 } │ │ │ │ -938 │ │ │ │ -939 template │ │ │ │ -940 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_9_4_1 _T_V_e_c_t_o_r_3_<_T_>& _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _%_=_ (const _T_V_e_c_t_o_r_3_<_T_>& v) │ │ │ │ -942 { │ │ │ │ -943 set(y * v._z - z * v._y, z * v._x - x * v._z, x * v._y - y * v._x); │ │ │ │ -944 return *this; │ │ │ │ -945 } │ │ │ │ -946 │ │ │ │ -947 template │ │ │ │ -948 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_9_4_9 T _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_D_i_s_t_a_n_c_e(const _T_V_e_c_t_o_r_3_<_T_>& v) const │ │ │ │ -950 { │ │ │ │ -951 T dx = x - v._x; │ │ │ │ -952 T dy = y - v._y; │ │ │ │ -953 T dz = z - v._z; │ │ │ │ -954 │ │ │ │ -955 return (T)sqrt(dx * dx + dy * dy + dz * dz); │ │ │ │ -956 } │ │ │ │ -957 │ │ │ │ -958 template │ │ │ │ -959 _B_A_L_L___I_N_L_I_N_E T │ │ │ │ -_9_6_0 _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_S_q_u_a_r_e_D_i_s_t_a_n_c_e(const _T_V_e_c_t_o_r_3_<_T_>& v) const │ │ │ │ -961 { │ │ │ │ -962 T dx = x - v._x; │ │ │ │ -963 T dy = y - v._y; │ │ │ │ -964 T dz = z - v._z; │ │ │ │ -965 │ │ │ │ -966 return (dx * dx + dy * dy + dz * dz); │ │ │ │ -967 } │ │ │ │ -968 │ │ │ │ -969 template │ │ │ │ -970 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_9_7_1 _T_A_n_g_l_e_<_T_> _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_A_n_g_l_e(const _T_V_e_c_t_o_r_3_<_T_>& vector) const │ │ │ │ -972 { │ │ │ │ -973 T length_product = getSquareLength() * vector._g_e_t_S_q_u_a_r_e_L_e_n_g_t_h(); │ │ │ │ -974 │ │ │ │ -975 if (length_product == (T)0) │ │ │ │ -976 { │ │ │ │ -977 throw _E_x_c_e_p_t_i_o_n_:_:_D_i_v_i_s_i_o_n_B_y_Z_e_r_o(__FILE__, __LINE__); │ │ │ │ -978 } │ │ │ │ -979 │ │ │ │ -980 T acos_arg = ((*this) * vector) / sqrt(length_product); │ │ │ │ -981 │ │ │ │ -982 // ensure that the argument of acos is in the correct range │ │ │ │ -983 // (might happen if the angle between the two vectors is │ │ │ │ -984 // very close to zero) │ │ │ │ -985 if (fabs(acos_arg) > 1.0) │ │ │ │ -986 { │ │ │ │ -987 return (_T_A_n_g_l_e_<_T_>)0.0; │ │ │ │ -988 } │ │ │ │ -989 │ │ │ │ -990 return (_T_A_n_g_l_e_<_T_>)acos(acos_arg); │ │ │ │ -991 } │ │ │ │ -992 │ │ │ │ -993 template │ │ │ │ -994 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_9_9_5 _T_V_e_c_t_o_r_3_<_T_> _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_O_r_t_h_o_g_o_n_a_l_P_r_o_j_e_c_t_i_o_n(const _T_V_e_c_t_o_r_3_<_T_>& │ │ │ │ -direction) const │ │ │ │ -996 { │ │ │ │ -997 return ((direction * (*this)) / (direction * direction) * direction); │ │ │ │ -998 } │ │ │ │ -999 │ │ │ │ -1000 template │ │ │ │ -_1_0_0_1 _T_V_e_c_t_o_r_3_<_T_> _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_P_e_r_p_e_n_d_i_c_u_l_a_r_N_o_r_m_a_l_i_z_a_t_i_o_n │ │ │ │ -1002 (const _T_V_e_c_t_o_r_3_<_T_> &a, const _T_V_e_c_t_o_r_3_<_T_> &b, const _T_V_e_c_t_o_r_3_<_T_> &c) │ │ │ │ -1003 { │ │ │ │ -1004 _T_V_e_c_t_o_r_3 diff1(b._x - a._x, b._y - a._y, b._z - a._z); │ │ │ │ -1005 _T_V_e_c_t_o_r_3 diff2(b._x - c.x, b._y - c.y, b._z - c.z); │ │ │ │ -1006 │ │ │ │ -1007 return _T_V_e_c_t_o_r_3 │ │ │ │ -1008 (diff1._y * diff2._z - diff1._z * diff2._y, │ │ │ │ -1009 diff1._z * diff2._x - diff1._x * diff2._z, │ │ │ │ -1010 diff1._x * diff2._y - diff1._y * diff2._x); │ │ │ │ -1011 } │ │ │ │ -1012 │ │ │ │ -1013 template │ │ │ │ -1014 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_0_1_5 T _T_V_e_c_t_o_r_3_<_T_>_:_:_g_e_t_T_r_i_p_l_e_P_r_o_d_u_c_t │ │ │ │ -1016 (const _T_V_e_c_t_o_r_3_<_T_>& a, │ │ │ │ -1017 const _T_V_e_c_t_o_r_3_<_T_>& b, │ │ │ │ -1018 const _T_V_e_c_t_o_r_3_<_T_>& c) │ │ │ │ -1019 { │ │ │ │ -1020 return ( a._x * (b._y * c.z - b._z * c.y) │ │ │ │ -1021 + a._y * (b._z * c.x - b._x * c.z) │ │ │ │ -1022 + a._z * (b._x * c.y - b._y * c.x)); │ │ │ │ -1023 } │ │ │ │ -1024 │ │ │ │ -1025 template │ │ │ │ -1026 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_0_2_7 bool _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _=_=_ (const _T_V_e_c_t_o_r_3_<_T_>& v) const │ │ │ │ -1028 { │ │ │ │ -1029 return (_M_a_t_h_s_:_:_i_s_E_q_u_a_l(x, v._x) && _M_a_t_h_s_:_:_i_s_E_q_u_a_l(y, v._y) && _M_a_t_h_s_:_:_i_s_E_q_u_a_l │ │ │ │ -(z, v._z)); │ │ │ │ -1030 } │ │ │ │ -1031 │ │ │ │ -1032 template │ │ │ │ -1033 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_0_3_4 bool _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _<_ (const _T_V_e_c_t_o_r_3_<_T_>& v) const │ │ │ │ -1035 { │ │ │ │ -1036 return (x < v._x || y < v._y || z < v._z); │ │ │ │ -1037 } │ │ │ │ -1038 │ │ │ │ -1039 │ │ │ │ -1040 template │ │ │ │ -1041 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_0_4_2 bool _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _!_=_ (const _T_V_e_c_t_o_r_3_<_T_>& v) const │ │ │ │ -1043 { │ │ │ │ -1044 return (_M_a_t_h_s_:_:_i_s_N_o_t_E_q_u_a_l(x, v._x) || _M_a_t_h_s_:_:_i_s_N_o_t_E_q_u_a_l(y, v._y) || _M_a_t_h_s_:_: │ │ │ │ -_i_s_N_o_t_E_q_u_a_l(z, v._z)); │ │ │ │ -1045 } │ │ │ │ -1046 │ │ │ │ -1047 template │ │ │ │ -1048 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_0_4_9 bool _T_V_e_c_t_o_r_3_<_T_>_:_:_i_s_O_r_t_h_o_g_o_n_a_l_T_o(const _T_V_e_c_t_o_r_3_<_T_>& v) const │ │ │ │ -1050 { │ │ │ │ -1051 return _M_a_t_h_s_:_:_i_s_Z_e_r_o((*this) * v); │ │ │ │ -1052 } │ │ │ │ -1053 │ │ │ │ -1054 template │ │ │ │ -1055 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_0_5_6 bool _T_V_e_c_t_o_r_3_<_T_>_:_:_i_s_V_a_l_i_d() const │ │ │ │ -1057 { │ │ │ │ -1058 return true; │ │ │ │ -1059 } │ │ │ │ -1060 │ │ │ │ -1061 template │ │ │ │ -1062 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_0_6_3 bool _T_V_e_c_t_o_r_3_<_T_>_:_:_i_s_Z_e_r_o() const │ │ │ │ -1064 { │ │ │ │ -1065 return (_M_a_t_h_s_:_:_i_s_Z_e_r_o(x) && _M_a_t_h_s_:_:_i_s_Z_e_r_o(y) && _M_a_t_h_s_:_:_i_s_Z_e_r_o(z)); │ │ │ │ -1066 } │ │ │ │ -1067 │ │ │ │ -1068 template │ │ │ │ -_1_0_6_9 void _T_V_e_c_t_o_r_3_<_T_>_:_:_d_u_m_p(std::ostream& s, _S_i_z_e depth) const │ │ │ │ -1070 { │ │ │ │ -1071 _B_A_L_L___D_U_M_P___S_T_R_E_A_M___P_R_E_F_I_X(s); │ │ │ │ -1072 │ │ │ │ -1073 _B_A_L_L___D_U_M_P___H_E_A_D_E_R(s, this, this); │ │ │ │ -1074 │ │ │ │ -1075 _B_A_L_L___D_U_M_P___D_E_P_T_H(s, depth); │ │ │ │ -1076 s << " (x = " << x << ", y = " << y << ", z = " << z << ")" << std::endl; │ │ │ │ -1077 │ │ │ │ -1078 _B_A_L_L___D_U_M_P___S_T_R_E_A_M___S_U_F_F_I_X(s); │ │ │ │ -1079 } │ │ │ │ -1080 │ │ │ │ -_1_0_8_4 typedef _T_V_e_c_t_o_r_3_<_f_l_o_a_t_> _V_e_c_t_o_r_3; │ │ │ │ -1085 │ │ │ │ -1086 template │ │ │ │ -1087 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -1088 _T_V_e_c_t_o_r_3_<_T_> _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _+_ (const _T_V_e_c_t_o_r_3_<_T_>& b) const │ │ │ │ -1089 { │ │ │ │ -1090 return _T_V_e_c_t_o_r_3_<_T_>(x + b._x, y + b._y, z + b._z); │ │ │ │ -1091 } │ │ │ │ -1092 │ │ │ │ -1093 template │ │ │ │ -1094 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -1095 TVector3 _T_V_e_c_t_o_r_3_<_T_>_:_:_o_p_e_r_a_t_o_r_ _-_ (const TVector3& b) const │ │ │ │ -1096 { │ │ │ │ -1097 return TVector3(x - b.x, y - b.y, z - b.z); │ │ │ │ -1098 } │ │ │ │ -1099 │ │ │ │ -1100 template │ │ │ │ -_1_1_0_1 void _T_V_e_c_t_o_r_3_<_T_>_:_:_w_r_i_t_e(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm) const │ │ │ │ -1102 { │ │ │ │ -1103 pm._w_r_i_t_e_P_r_i_m_i_t_i_v_e(x, "x"); │ │ │ │ -1104 pm._w_r_i_t_e_P_r_i_m_i_t_i_v_e(y, "y"); │ │ │ │ -1105 pm._w_r_i_t_e_P_r_i_m_i_t_i_v_e(z, "z"); │ │ │ │ -1106 } │ │ │ │ -1107 │ │ │ │ -1108 template │ │ │ │ -_1_1_0_9 bool _T_V_e_c_t_o_r_3_<_T_>_:_:_r_e_a_d(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm) │ │ │ │ -1110 { │ │ │ │ -1111 pm._r_e_a_d_P_r_i_m_i_t_i_v_e(x, "x"); │ │ │ │ -1112 pm._r_e_a_d_P_r_i_m_i_t_i_v_e(y, "y"); │ │ │ │ -1113 pm._r_e_a_d_P_r_i_m_i_t_i_v_e(z, "z"); │ │ │ │ -1114 │ │ │ │ -1115 return true; │ │ │ │ -1116 } │ │ │ │ -1117 │ │ │ │ -1118 │ │ │ │ -1119 template │ │ │ │ -1120 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_1_2_1 _T_V_e_c_t_o_r_3_<_T_> _o_p_e_r_a_t_o_r_ _*_ (const T& scalar, const _T_V_e_c_t_o_r_3_<_T_>& vector) │ │ │ │ -1122 { │ │ │ │ -1123 return _T_V_e_c_t_o_r_3_<_T_>(scalar * vector._x, scalar * vector._y, scalar * │ │ │ │ -vector._z); │ │ │ │ -1124 } │ │ │ │ -1125 │ │ │ │ -1126 template │ │ │ │ -_1_1_2_7 std::istream& _o_p_e_r_a_t_o_r_ _>_>_ (std::istream& s, _T_V_e_c_t_o_r_3_<_T_>& v) │ │ │ │ -1128 { │ │ │ │ -1129 char c; │ │ │ │ -1130 s >> c >> v._x >> v._y >> v._z >> c; │ │ │ │ -1131 │ │ │ │ -1132 return s; │ │ │ │ -1133 } │ │ │ │ -1134 │ │ │ │ -1135 template │ │ │ │ -_1_1_3_6 std::ostream& _o_p_e_r_a_t_o_r_ _<_<_ (std::ostream& s, const _T_V_e_c_t_o_r_3_<_T_>& v) │ │ │ │ -1137 { │ │ │ │ -1138 s << "(" << v._x << ' ' << v._y << ' ' << v._z << ')'; │ │ │ │ -1139 │ │ │ │ -1140 return s; │ │ │ │ -1141 } │ │ │ │ -1142// required for visual studio │ │ │ │ -1143#ifdef BALL_COMPILER_MSVC │ │ │ │ -1144#include │ │ │ │ -1145extern template class _B_A_L_L___E_X_P_O_R_T std::vector; │ │ │ │ -1146#endif │ │ │ │ -1147 │ │ │ │ -1148extern template class _B_A_L_L___E_X_P_O_R_T _T_V_e_c_t_o_r_3_<_f_l_o_a_t_>; │ │ │ │ -1149 │ │ │ │ -1150}// namespace BALL │ │ │ │ -1151 │ │ │ │ -1152#endif // BALL_MATHS_VECTOR3_H │ │ │ │ -_a_n_g_l_e_._h │ │ │ │ -_p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h │ │ │ │ +323 template │ │ │ │ +_3_2_4 std::ostream& _o_p_e_r_a_t_o_r_ _<_<_ (std::ostream& s, const _T_C_i_r_c_l_e_3_<_T_>& circle) │ │ │ │ +325 { │ │ │ │ +326 return s << '(' << circle._p │ │ │ │ +327 << ' ' << circle._n │ │ │ │ +328 << ' ' << circle._r_a_d_i_u_s │ │ │ │ +329 << ')'; │ │ │ │ +330 } │ │ │ │ +331 │ │ │ │ +332} // namespace BALL │ │ │ │ +333 │ │ │ │ +334#endif // BALL_MATHS_CIRCLE3_H │ │ │ │ +_v_e_c_t_o_r_3_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ _B_A_L_L___D_U_M_P___S_T_R_E_A_M___P_R_E_F_I_X │ │ │ │ #define BALL_DUMP_STREAM_PREFIX(os) │ │ │ │ DDeeffiinniittiioonn _m_a_c_r_o_s_._h_:_3_9_1 │ │ │ │ _B_A_L_L___D_U_M_P___S_T_R_E_A_M___S_U_F_F_I_X │ │ │ │ #define BALL_DUMP_STREAM_SUFFIX(os) │ │ │ │ DDeeffiinniittiioonn _m_a_c_r_o_s_._h_:_3_9_5 │ │ │ │ _B_A_L_L___D_U_M_P___D_E_P_T_H │ │ │ │ #define BALL_DUMP_DEPTH(os, depth) │ │ │ │ DDeeffiinniittiioonn _m_a_c_r_o_s_._h_:_3_9_0 │ │ │ │ _B_A_L_L___D_U_M_P___H_E_A_D_E_R │ │ │ │ #define BALL_DUMP_HEADER(os, cl, ob) │ │ │ │ DDeeffiinniittiioonn _m_a_c_r_o_s_._h_:_3_9_3 │ │ │ │ -_B_A_L_L___I_N_L_I_N_E │ │ │ │ -#define BALL_INLINE │ │ │ │ -DDeeffiinniittiioonn _d_e_b_u_g_._h_:_1_5 │ │ │ │ _B_A_L_L_:_:_o_p_e_r_a_t_o_r_<_< │ │ │ │ BALL_EXPORT std::ostream & operator<<(std::ostream &os, const Exception:: │ │ │ │ GeneralException &e) │ │ │ │ +_B_A_L_L_:_:_C_i_r_c_l_e_3 │ │ │ │ +TCircle3< float > Circle3 │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_3_0_1 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_o_p_e_r_a_t_o_r_* │ │ │ │ -BALL_INLINE TAngle< T > operator*(const T &val, const TAngle< T > &angle) │ │ │ │ -DDeeffiinniittiioonn _a_n_g_l_e_._h_:_7_0_4 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ -template class BALL_EXPORT TVector3< float > │ │ │ │ -_B_A_L_L_:_:_V_e_c_t_o_r_3 │ │ │ │ -TVector3< float > Vector3 │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_8_4 │ │ │ │ -_B_A_L_L_:_:_A_n_g_l_e │ │ │ │ -TAngle< float > Angle │ │ │ │ -DDeeffiinniittiioonn _a_n_g_l_e_._h_:_6_9_7 │ │ │ │ _B_A_L_L_:_:_o_p_e_r_a_t_o_r_>_> │ │ │ │ std::istream & operator>>(std::istream &is, TRegularData1D< ValueType > &grid) │ │ │ │ Input operator. │ │ │ │ DDeeffiinniittiioonn _r_e_g_u_l_a_r_D_a_t_a_1_D_._h_:_8_0_2 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_a_n_t_s_:_:_P_I │ │ │ │ -BALL_EXTERN_VARIABLE const double PI │ │ │ │ -PI. │ │ │ │ -DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_M_a_t_h_s_:_:_i_s_N_o_t_Z_e_r_o │ │ │ │ -bool isNotZero(const T &t) │ │ │ │ -DDeeffiinniittiioonn _M_A_T_H_S_/_c_o_m_m_o_n_._h_:_2_0_0 │ │ │ │ _B_A_L_L_:_:_M_a_t_h_s_:_:_i_s_N_o_t_E_q_u_a_l │ │ │ │ bool isNotEqual(const T1 &a, const T2 &b) │ │ │ │ DDeeffiinniittiioonn _M_A_T_H_S_/_c_o_m_m_o_n_._h_:_2_2_4 │ │ │ │ -_B_A_L_L_:_:_M_a_t_h_s_:_:_i_s_L_e_s_s │ │ │ │ -bool isLess(const T1 &a, const T2 &b) │ │ │ │ -DDeeffiinniittiioonn _M_A_T_H_S_/_c_o_m_m_o_n_._h_:_2_3_6 │ │ │ │ _B_A_L_L_:_:_M_a_t_h_s_:_:_i_s_Z_e_r_o │ │ │ │ bool isZero(const T &t) │ │ │ │ DDeeffiinniittiioonn _M_A_T_H_S_/_c_o_m_m_o_n_._h_:_1_8_9 │ │ │ │ -_B_A_L_L_:_:_M_a_t_h_s_:_:_s_g_n │ │ │ │ -T sgn(const T &t) │ │ │ │ -DDeeffiinniittiioonn _M_A_T_H_S_/_c_o_m_m_o_n_._h_:_1_3_8 │ │ │ │ +_B_A_L_L_:_:_M_a_t_h_s_:_:_i_s_L_e_s_s_O_r_E_q_u_a_l │ │ │ │ +bool isLessOrEqual(const T1 &a, const T2 &b) │ │ │ │ +DDeeffiinniittiioonn _M_A_T_H_S_/_c_o_m_m_o_n_._h_:_2_4_9 │ │ │ │ _B_A_L_L_:_:_M_a_t_h_s_:_:_i_s_E_q_u_a_l │ │ │ │ bool isEqual(const T1 &a, const T2 &b) │ │ │ │ DDeeffiinniittiioonn _M_A_T_H_S_/_c_o_m_m_o_n_._h_:_2_1_2 │ │ │ │ -_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_O_v_e_r_f_l_o_w │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_6_4 │ │ │ │ -_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_u_l_l_P_o_i_n_t_e_r │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_6_0 │ │ │ │ -_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_D_i_v_i_s_i_o_n_B_y_Z_e_r_o │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_3_4_2 │ │ │ │ -_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h_:_7_3 │ │ │ │ -_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_:_:_r_e_a_d_P_r_i_m_i_t_i_v_e │ │ │ │ -bool readPrimitive(T &t, const char *name) │ │ │ │ -DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h_:_8_2_7 │ │ │ │ -_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_:_:_w_r_i_t_e_P_r_i_m_i_t_i_v_e │ │ │ │ -void writePrimitive(const T &t, const char *name) │ │ │ │ -DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h_:_8_1_8 │ │ │ │ -_B_A_L_L_:_:_T_A_n_g_l_e │ │ │ │ -DDeeffiinniittiioonn _a_n_g_l_e_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_T_A_n_g_l_e_:_:_v_a_l_u_e │ │ │ │ -T value │ │ │ │ -DDeeffiinniittiioonn _a_n_g_l_e_._h_:_3_7_7 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_1 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_L_e_n_g_t_h │ │ │ │ -T getLength() const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_5_7 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_D_i_s_t_a_n_c_e │ │ │ │ -T getDistance(const TVector3 &vector) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_9_4_9 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_/_= │ │ │ │ -TVector3 & operator/=(const T &lambda) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_9_1_3 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_A_n_g_l_e │ │ │ │ -TAngle< T > getAngle(const TVector3 &vector) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_9_7_1 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_=_= │ │ │ │ -bool operator==(const TVector3 &vector) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_2_7 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_!_= │ │ │ │ -bool operator!=(const TVector3 &vector) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_4_2 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -TVector3(const T &value) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_5_5_7 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_[_] │ │ │ │ -T & operator[](Position position) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_8_1_4 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t │ │ │ │ -void get(T &x, T &y, T &z) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_1_3 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_- │ │ │ │ -TVector3 operator-() const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_8_5_7 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_i_s_Z_e_r_o │ │ │ │ -bool isZero() const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_6_3 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t │ │ │ │ -void get(TVector3 &vector) const │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_s_e_t │ │ │ │ -void set(const T &value) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_6_2_7 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -TVector3(const T *ptr) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_5_4_3 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_%_= │ │ │ │ -TVector3 & operator%=(const TVector3 &vector) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_9_4_1 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_x │ │ │ │ -T x │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_4_8_9 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_s_w_a_p │ │ │ │ -void swap(TVector3 &vector) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_4_0 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_Z_e_r_o │ │ │ │ -static const TVector3 & getZero() │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_9_8 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_~_T_V_e_c_t_o_r_3 │ │ │ │ -~TVector3() │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_6_0_2 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_n_e_g_a_t_e │ │ │ │ -TVector3 & negate() │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_8_8 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_s_e_t │ │ │ │ -void set(const TVector3 &vector) │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -TVector3(const TVector3< T2 > &vec) │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_-_= │ │ │ │ -TVector3 & operator-=(const TVector3 &vector) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_8_7_5 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_r_e_a_d │ │ │ │ -bool read(PersistenceManager &pm) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_1_0_9 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_% │ │ │ │ -TVector3 operator%(const TVector3 &vector) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_9_3_4 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_S_q_u_a_r_e_L_e_n_g_t_h │ │ │ │ -T getSquareLength() const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_6_4 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_P_e_r_p_e_n_d_i_c_u_l_a_r_N_o_r_m_a_l_i_z_a_t_i_o_n │ │ │ │ -static TVector3 getPerpendicularNormalization(const TVector3 &a, const TVector3 │ │ │ │ -&b, const TVector3 &c) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_0_2 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -TVector3(const TVector3 &vector) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_5_8_4 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ -TVector3 & operator=(const TVector3 &v) │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_* │ │ │ │ -TVector3 operator*(const T &scalar) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_8_8_6 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_s_e_t │ │ │ │ -void set(const T &vx, const T &vy, const T &vz) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_6_3_6 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t │ │ │ │ -void get(T &r, TAngle< T > &phi, TAngle< T > &theta) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_3_1 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_T_r_i_p_l_e_P_r_o_d_u_c_t │ │ │ │ -static T getTripleProduct(const TVector3< T > &a, const TVector3< T > &b, const │ │ │ │ -TVector3< T > &c) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_1_6 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_+_= │ │ │ │ -TVector3 & operator+=(const TVector3 &vector) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_8_6_4 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_/ │ │ │ │ -TVector3 operator/(const T &lambda) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_9_0_3 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_y │ │ │ │ -T y │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_4_9_3 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_n_o_r_m_a_l_i_z_e │ │ │ │ -TVector3 & normalize() │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_7_0 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_s_e_t │ │ │ │ -void set(const T *ptr) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_6_1_5 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_+ │ │ │ │ -const TVector3 & operator+() const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_8_5_0 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_i_s_O_r_t_h_o_g_o_n_a_l_T_o │ │ │ │ -bool isOrthogonalTo(const TVector3 &vector) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_4_9 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_w_r_i_t_e │ │ │ │ -void write(PersistenceManager &pm) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_1_0_1 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_i_s_V_a_l_i_d │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3 │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_4_6 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_T_C_i_r_c_l_e_3 │ │ │ │ +TCircle3(const TCircle3 &circle) │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_7_0 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_i_s_V_a_l_i_d │ │ │ │ bool isValid() const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_5_6 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_c_l_e_a_r │ │ │ │ -void clear() │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_6_0_8 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_d_u_m_p │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_2_4_0 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_o_p_e_r_a_t_o_r_!_= │ │ │ │ +bool operator!=(const TCircle3 &circle) const │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_2_0_6 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_T_C_i_r_c_l_e_3 │ │ │ │ +TCircle3(const TVector3< T > &point, const TVector3< T > &normal, const T │ │ │ │ +&radius) │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_8_3 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_h_a_s │ │ │ │ +bool has(const TVector3< T > &point, bool on_surface=false) const │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_2_1_7 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_p │ │ │ │ +TVector3< T > p │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_2_7_7 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_~_T_C_i_r_c_l_e_3 │ │ │ │ +virtual ~TCircle3() │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_9_4 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_s_e_t │ │ │ │ +void set(const TVector3< T > &point, const TVector3< T > &normal, const T &rad) │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_1_4_6 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_g_e_t │ │ │ │ +void get(TCircle3 &circle) const │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_1_7_0 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_s_w_a_p │ │ │ │ +void swap(TCircle3 &circle) │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_1_1_6 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_g_e_t │ │ │ │ +void get(TVector3< T > &point, TVector3< T > &normal, T &rhs) const │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_1_8_2 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_d_u_m_p │ │ │ │ void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_6_9 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_s_e_t │ │ │ │ -void set(const T &r, const TAngle< T > &phi, const TAngle< T > &theta) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_6_5_4 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_*_= │ │ │ │ -TVector3 & operator*=(const T &scalar) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_8_9_3 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_o_p_e_r_a_t_o_r_< │ │ │ │ -bool operator<(const TVector3 &vector) const │ │ │ │ -Needed for MSVC. │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_1_0_3_4 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_U_n_i_t │ │ │ │ -static const TVector3 & getUnit() │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_8_0_6 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_O_r_t_h_o_g_o_n_a_l_P_r_o_j_e_c_t_i_o_n │ │ │ │ -TVector3 getOrthogonalProjection(const TVector3 &direction) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_9_9_5 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t │ │ │ │ -void get(T *ptr) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_6_9_9 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -TVector3(const T &vx, const T &vy, const T &vz) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_5_7_5 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -TVector3(const T &r, const TAngle< T > &phi, const TAngle< T > &theta) │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_5_9_3 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_T_V_e_c_t_o_r_3 │ │ │ │ -TVector3() │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_5_3_4 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_g_e_t_S_q_u_a_r_e_D_i_s_t_a_n_c_e │ │ │ │ -T getSquareDistance(const TVector3 &vector) const │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_9_6_0 │ │ │ │ -_B_A_L_L_:_:_T_V_e_c_t_o_r_3_:_:_z │ │ │ │ -T z │ │ │ │ -DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_4_9_7 │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_2_5_1 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_r_a_d_i_u_s │ │ │ │ +T radius │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_2_8_7 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_n │ │ │ │ +TVector3< T > n │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_2_8_2 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_c_l_e_a_r │ │ │ │ +virtual void clear() │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_1_0_1 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ +TCircle3 & operator=(const TCircle3 &circle) │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_1_5_7 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_o_p_e_r_a_t_o_r_=_= │ │ │ │ +bool operator==(const TCircle3 &circle) const │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_1_9_8 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3_:_:_s_e_t │ │ │ │ +void set(const TCircle3 &circle) │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_1_3_4 │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3 │ │ │ │ +DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_1 │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ _e_x_c_e_p_t_i_o_n_._h │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dec/a06822.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Classes | │ │ │ List of all members
    │ │ │
    BALL::BuildBondsProcessor Class Reference
    Molecular Modeling » Molecular Structure » Miscellaneous
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/STRUCTURE/buildBondsProcessor.h>

    │ │ │ +

    #include <BALL/STRUCTURE/buildBondsProcessor.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::BuildBondsProcessor:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::UnaryProcessor< AtomContainer > │ │ │ @@ -204,15 +204,15 @@ │ │ │   │ │ │ typedef const ArgumentType * const_argument_pointer │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Bond creation processor

    │ │ │ │ │ │ -

    Definition at line 34 of file buildBondsProcessor.h.

    │ │ │ +

    Definition at line 34 of file buildBondsProcessor.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ BuildBondsProcessor() [1/3]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -424,15 +424,15 @@ │ │ │ inline │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    Return the bond length Hashmap.

    │ │ │ │ │ │ -

    Definition at line 136 of file buildBondsProcessor.h.

    │ │ │ +

    Definition at line 136 of file buildBondsProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getMaxBondLength_()

    │ │ │ │ │ │
    │ │ │ @@ -777,15 +777,15 @@ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    structure where bond order distances are stored in

    │ │ │ │ │ │ -

    Definition at line 181 of file buildBondsProcessor.h.

    │ │ │ +

    Definition at line 181 of file buildBondsProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ max_bond_lengths_

    │ │ │ │ │ │
    │ │ │ @@ -803,15 +803,15 @@ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    structure were the bond maxima stored in (used in buildBonds_)

    │ │ │ │ │ │ -

    Definition at line 184 of file buildBondsProcessor.h.

    │ │ │ +

    Definition at line 184 of file buildBondsProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ max_length_

    │ │ │ │ │ │
    │ │ │ @@ -829,15 +829,15 @@ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    parameter which holds the longest possible bond

    │ │ │ │ │ │ -

    Definition at line 207 of file buildBondsProcessor.h.

    │ │ │ +

    Definition at line 207 of file buildBondsProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ min_bond_lengths_

    │ │ │ │ │ │
    │ │ │ @@ -855,15 +855,15 @@ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    structure were the bond minima stored in (used in buildBonds_)

    │ │ │ │ │ │ -

    Definition at line 187 of file buildBondsProcessor.h.

    │ │ │ +

    Definition at line 187 of file buildBondsProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ num_bonds_

    │ │ │ │ │ │
    │ │ │ @@ -881,15 +881,15 @@ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    number of bonds, which are created during the processor call

    │ │ │ │ │ │ -

    Definition at line 178 of file buildBondsProcessor.h.

    │ │ │ +

    Definition at line 178 of file buildBondsProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ options

    │ │ │ │ │ │
    │ │ │ @@ -899,15 +899,15 @@ │ │ │ Options BALL::BuildBondsProcessor::options │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    options

    │ │ │ │ │ │ -

    Definition at line 151 of file buildBondsProcessor.h.

    │ │ │ +

    Definition at line 151 of file buildBondsProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dee/a04014.html │ │ │ @@ -80,15 +80,15 @@ │ │ │
    BALL::NMRStarFile Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │

    This class provides methods for reading and assigning chemical shifts. │ │ │ More...

    │ │ │ │ │ │ -

    #include <BALL/FORMAT/NMRStarFile.h>

    │ │ │ +

    #include <BALL/FORMAT/NMRStarFile.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::NMRStarFile:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::CIFFile │ │ │ @@ -588,29 +588,29 @@ │ │ │
    if (condition.hasType("pressure"))
    │ │ │
    pressure = condition.values["pressure"];
    │ │ │
    │ │ │
    cout << "NMR conditions: " << pH << ", " << temperature << ", " << pressure << endl;
    │ │ │
    }
    │ │ │
    BALL::Peptides::GetSequence
    BALL_EXPORT OneLetterAASequence GetSequence(const Protein &protein)
    │ │ │
    BALL::String::size
    size_t size() const BALL_NOEXCEPT
    │ │ │ -
    BALL::NMRStarFile
    This class provides methods for reading and assigning chemical shifts.
    Definition NMRStarFile.h:115
    │ │ │ +
    BALL::NMRStarFile
    This class provides methods for reading and assigning chemical shifts.
    Definition NMRStarFile.h:115
    │ │ │
    BALL::NMRStarFile::getChemicalUnitByLabel
    const MolecularSystem::ChemicalUnit & getChemicalUnitByLabel(String const &label) const
    │ │ │ - │ │ │ -
    BALL::NMRStarFile::MolecularSystem::getChemicalUnit
    ChemicalUnit const & getChemicalUnit(Position i) const
    Definition NMRStarFile.h:399
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::ShiftModule::PROPERTY__EXPERIMENTAL__SHIFT
    static const char * PROPERTY__EXPERIMENTAL__SHIFT
    Definition shiftModule.h:59
    │ │ │ + │ │ │ +
    BALL::NMRStarFile::MolecularSystem::getChemicalUnit
    ChemicalUnit const & getChemicalUnit(Position i) const
    Definition NMRStarFile.h:399
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::ShiftModule::PROPERTY__EXPERIMENTAL__SHIFT
    static const char * PROPERTY__EXPERIMENTAL__SHIFT
    Definition shiftModule.h:59
    │ │ │ │ │ │
    │ │ │ -

    Definition at line 113 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 113 of file NMRStarFile.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ NMRStarFile() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -859,15 +859,15 @@ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
    │ │ │

    Get the entry information

    │ │ │ │ │ │ -

    Definition at line 678 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 678 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getMolecularInformation() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -887,15 +887,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Get the molecular information

    │ │ │ │ │ │ -

    Definition at line 686 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 686 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getMolecularInformation() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -915,15 +915,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Get the molecular information

    │ │ │ │ │ │ -

    Definition at line 682 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 682 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getMonomericPolymer() [1/4]

    │ │ │ │ │ │
    │ │ │ @@ -1040,15 +1040,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get all Monomeric Polymers.

    │ │ │ │ │ │ -

    Definition at line 822 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 822 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNMRData()

    │ │ │ │ │ │
    │ │ │ @@ -1207,15 +1207,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the spectrometers.

    │ │ │ │ │ │ -

    Definition at line 774 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 774 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNMRSpectrometers() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1236,15 +1236,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the spectrometers.

    │ │ │ │ │ │ -

    Definition at line 776 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 776 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNumberOfAtoms()

    │ │ │ │ │ │
    │ │ │ @@ -1283,15 +1283,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the number of monomeric polymers in the file.

    │ │ │ │ │ │ -

    Definition at line 819 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 819 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNumberOfNMRSpectrometers()

    │ │ │ │ │ │
    │ │ │ @@ -1312,15 +1312,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the number of nmr spectrometers.

    │ │ │ │ │ │ -

    Definition at line 779 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 779 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNumberOfSampleConditions()

    │ │ │ │ │ │
    │ │ │ @@ -1341,15 +1341,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the number of sample conditions.

    │ │ │ │ │ │ -

    Definition at line 721 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 721 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNumberOfSamples()

    │ │ │ │ │ │
    │ │ │ @@ -1370,15 +1370,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the number of samples.

    │ │ │ │ │ │ -

    Definition at line 736 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 736 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNumberOfShiftReferenceSets()

    │ │ │ │ │ │
    │ │ │ @@ -1399,15 +1399,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the number of shift reference sets.

    │ │ │ │ │ │ -

    Definition at line 757 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 757 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getNumberOfShiftsAssigned()

    │ │ │ │ │ │
    │ │ │ @@ -1427,15 +1427,15 @@ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │

    Return the number of atoms assigned a chemical shift

    │ │ │ │ │ │ -

    Definition at line 670 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 670 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getResidueSequence()

    │ │ │ │ │ │
    │ │ │ @@ -1516,15 +1516,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the i-th SampleCondition.

    │ │ │ │ │ │ -

    Definition at line 715 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 715 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getSampleCondition() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1546,15 +1546,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the i-th SampleCondition.

    │ │ │ │ │ │ -

    Definition at line 718 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 718 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getSampleConditionByName() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -1613,15 +1613,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the sample conditions.

    │ │ │ │ │ │ -

    Definition at line 727 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 727 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getSampleConditions() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1642,15 +1642,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the sample conditions.

    │ │ │ │ │ │ -

    Definition at line 724 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 724 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getSamples()

    │ │ │ │ │ │
    │ │ │ @@ -1671,15 +1671,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the samples.

    │ │ │ │ │ │ -

    Definition at line 732 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 732 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getShiftReferenceSet() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -1701,15 +1701,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the i-th shift reference set.

    │ │ │ │ │ │ -

    Definition at line 763 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 763 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getShiftReferenceSet() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1731,15 +1731,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the i-th shift reference set.

    │ │ │ │ │ │ -

    Definition at line 765 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 765 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getShiftReferenceSetByName() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -1800,15 +1800,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the shift reference sets.

    │ │ │ │ │ │ -

    Definition at line 752 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 752 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getShiftReferenceSets() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1829,15 +1829,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Get the shift reference sets.

    │ │ │ │ │ │ -

    Definition at line 754 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 754 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ hasCshifts()

    │ │ │ │ │ │
    │ │ │ @@ -1858,15 +1858,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Check, whether this NMRFile provides carbon shifts.

    │ │ │ │ │ │ -

    Definition at line 855 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 855 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ hasHshifts()

    │ │ │ │ │ │
    │ │ │ @@ -1887,15 +1887,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Check, whether this NMRFile provides hydrogen shifts.

    │ │ │ │ │ │ -

    Definition at line 852 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 852 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ hasMonomericPolymer()

    │ │ │ │ │ │
    │ │ │ @@ -1936,15 +1936,15 @@ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │

    Check, whether this NMRFile provides nitrogen shifts.

    │ │ │ │ │ │ -

    Definition at line 858 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 858 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ hasSample()

    │ │ │ │ │ │
    │ │ │ @@ -2148,15 +2148,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 119 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 119 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ INT_VALUE_NA

    │ │ │ │ │ │
    │ │ │ @@ -2172,15 +2172,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 120 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 120 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ POSITION_VALUE_NA

    │ │ │ │ │ │
    │ │ │ @@ -2196,15 +2196,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 122 of file NMRStarFile.h.

    │ │ │ +

    Definition at line 122 of file NMRStarFile.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dfe/a02102.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: main.C File Reference │ │ │ +BALL: mainframe.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,101 +70,35 @@ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -Functions
    │ │ │ -
    main.C File Reference
    │ │ │ +Classes | │ │ │ +Namespaces
    │ │ │ +
    mainframe.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <QtWidgets/QApplication>
    │ │ │ -#include <QtWidgets/QMessageBox>
    │ │ │ -#include <QtCore/QTranslator>
    │ │ │ -#include "mainframe.h"
    │ │ │ -#include <BALL/SYSTEM/path.h>
    │ │ │ -#include <BALL/SYSTEM/directory.h>
    │ │ │ +
    #include <BALL/VIEW/KERNEL/mainControl.h>
    │ │ │ +#include <BALL/VIEW/WIDGETS/scene.h>
    │ │ │ +#include <QtWidgets/QWidget>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ +

    │ │ │ -Functions

    void logMessages (QtMsgType type, const QMessageLogContext &context, const QString &message)
     
    int main (int argc, char **argv)
     

    │ │ │ +Classes

    class  BALL::Mainframe
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ +Namespaces

    namespace  BALL
     
    │ │ │ -

    Function Documentation

    │ │ │ - │ │ │ -

    ◆ logMessages()

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    void logMessages (QtMsgType type,
    const QMessageLogContext & context,
    const QString & message 
    )
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 14 of file main.C.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -

    ◆ main()

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    int main (int argc,
    char ** argv 
    )
    │ │ │ -
    │ │ │ - │ │ │ -

    Definition at line 46 of file main.C.

    │ │ │ - │ │ │ -
    │ │ │ -
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,36 +1,21 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _s_o_u_r_c_e │ │ │ │ * _A_P_P_L_I_C_A_T_I_O_N_S │ │ │ │ * _B_A_L_L_V_I_E_W │ │ │ │ -_F_u_n_c_t_i_o_n_s │ │ │ │ -main.C File Reference │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include "_m_a_i_n_f_r_a_m_e_._h" │ │ │ │ -#include <_B_A_L_L_/_S_Y_S_T_E_M_/_p_a_t_h_._h> │ │ │ │ -#include <_B_A_L_L_/_S_Y_S_T_E_M_/_d_i_r_e_c_t_o_r_y_._h> │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ +mainframe.h File Reference │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_a_i_n_C_o_n_t_r_o_l_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_W_I_D_G_E_T_S_/_s_c_e_n_e_._h> │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -FFuunnccttiioonnss │ │ │ │ -void  _l_o_g_M_e_s_s_a_g_e_s (QtMsgType type, const QMessageLogContext &context, const │ │ │ │ - QString &message) │ │ │ │ +CCllaasssseess │ │ │ │ +class   _B_A_L_L_:_:_M_a_i_n_f_r_a_m_e │ │ │ │   │ │ │ │ - int  _m_a_i_n (int argc, char **argv) │ │ │ │ +NNaammeessppaacceess │ │ │ │ +namespace   _B_A_L_L │ │ │ │   │ │ │ │ -********** FFuunnccttiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ -********** _?◆_? llooggMMeessssaaggeess(()) ********** │ │ │ │ -void logMessages ( QtMsgType  ttyyppee, │ │ │ │ - const QMessageLogContext &  ccoonntteexxtt, │ │ │ │ - const QString &  mmeessssaaggee  │ │ │ │ - ) │ │ │ │ -Definition at line _1_4 of file _m_a_i_n_._C. │ │ │ │ -********** _?◆_? mmaaiinn(()) ********** │ │ │ │ -int main ( int  aarrggcc, │ │ │ │ - char **  aarrggvv  │ │ │ │ - ) │ │ │ │ -Definition at line _4_6 of file _m_a_i_n_._C. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d0/dfe/a02102_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: main.C Source File │ │ │ +BALL: mainframe.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -74,240 +74,102 @@ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    main.C
    │ │ │ +
    mainframe.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5// order of includes is important: first qapplication, then BALL includes
    │ │ │ -
    6#include <QtWidgets/QApplication>
    │ │ │ -
    7#include <QtWidgets/QMessageBox>
    │ │ │ -
    8#include <QtCore/QTranslator>
    │ │ │ -
    9
    │ │ │ -
    10#include "mainframe.h"
    │ │ │ -
    11#include <BALL/SYSTEM/path.h>
    │ │ │ -
    12#include <BALL/SYSTEM/directory.h>
    │ │ │ -
    13
    │ │ │ -
    │ │ │ -
    14void logMessages(QtMsgType type, const QMessageLogContext& context, const QString& message)
    │ │ │ -
    15{
    │ │ │ -
    16 BALL::String s(message.toStdString());
    │ │ │ -
    17 if (s.hasPrefix("QTextBrowser")) return;
    │ │ │ -
    18
    │ │ │ -
    19 switch ( type ) {
    │ │ │ -
    20 case QtDebugMsg:
    │ │ │ -
    21 BALL::Log.info() << message.toStdString() << " " << (context.file ? context.file : "(unknown context)")
    │ │ │ -
    22 << " " << context.line
    │ │ │ -
    23 << " " << (context.function ? context.function : "(unknown function)") << std::endl;
    │ │ │ -
    24 break;
    │ │ │ -
    25 case QtWarningMsg:
    │ │ │ -
    26 BALL::Log.warn() << message.toStdString() << " " << (context.file ? context.file : "(unknown context)")
    │ │ │ -
    27 << " " << context.line
    │ │ │ -
    28 << " " << (context.function ? context.function : "(unknown function)") << std::endl;
    │ │ │ -
    29 break;
    │ │ │ -
    30 case QtFatalMsg:
    │ │ │ -
    31 fprintf( stderr, "Fatal: %s\n", message.toLatin1().constData() );
    │ │ │ -
    32 abort(); // deliberately core dump
    │ │ │ -
    33 case QtCriticalMsg:
    │ │ │ -
    34 fprintf( stderr, "Critical: %s\n", message.toLatin1().constData() );
    │ │ │ -
    35 abort(); // deliberately core dump
    │ │ │ -
    36 default:
    │ │ │ -
    37 break;
    │ │ │ -
    38 }
    │ │ │ -
    39}
    │ │ │ +
    5#ifndef BALL_APPLICATIONS_BALLVIEW_MAINFRAME_H
    │ │ │ +
    6#define BALL_APPLICATIONS_BALLVIEW_MAINFRAME_H
    │ │ │ +
    7
    │ │ │ +
    8#ifndef BALL_VIEW_KERNEL_MAINCONTROL_H
    │ │ │ +
    9# include <BALL/VIEW/KERNEL/mainControl.h>
    │ │ │ +
    10#endif
    │ │ │ +
    11
    │ │ │ +
    12#ifndef BALL_VIEW_WIDGETS_SCENE_H
    │ │ │ +
    13# include <BALL/VIEW/WIDGETS/scene.h>
    │ │ │ +
    14#endif
    │ │ │ +
    15
    │ │ │ +
    16#include <QtWidgets/QWidget>
    │ │ │ +
    17
    │ │ │ +
    18namespace BALL
    │ │ │ +
    19{
    │ │ │ +
    20 using namespace BALL::VIEW;
    │ │ │ +
    21
    │ │ │ +
    │ │ │ +
    22 class Mainframe
    │ │ │ +
    23 : public BALL::VIEW::MainControl
    │ │ │ +
    24 {
    │ │ │ +
    25 Q_OBJECT
    │ │ │ +
    26
    │ │ │ +
    27 public:
    │ │ │ +
    28
    │ │ │ +
    30 BALL_EMBEDDABLE(Mainframe, MainControl)
    │ │ │ +
    31
    │ │ │ +
    32
    │ │ │ +
    33 Mainframe(QWidget* parent = 0, const char* name = 0);
    │ │ │ +
    34
    │ │ │ +
    36 virtual ~Mainframe();
    │ │ │ +
    37
    │ │ │ +
    38 public Q_SLOTS:
    │ │ │ +
    39
    │ │ │ +
    41 void show();
    │ │ │ +
    42
    │ │ │ +
    44 bool eventFilter(QObject*, QEvent* e);
    │ │ │ +
    45
    │ │ │ +
    47 void reset();
    │ │ │ +
    48
    │ │ │ +
    49 // Help menu
    │ │ │ +
    50 void about();
    │ │ │ +
    51
    │ │ │ +
    52 void checkMenus();
    │ │ │ +
    53
    │ │ │ +
    54 protected:
    │ │ │ +
    55 void changeEvent(QEvent* evt);
    │ │ │ +
    56 void setupPluginHandlers_();
    │ │ │ +
    57
    │ │ │ +
    58 Scene* scene_;
    │ │ │ +
    59 QAction* save_project_action_;
    │ │ │ +
    60 QAction* qload_action_, *qsave_action_;
    │ │ │ +
    61 };
    │ │ │
    │ │ │ -
    40
    │ │ │ -
    41
    │ │ │ -
    42// uncomment this to use debugging to std::cout!
    │ │ │ -
    43//#undef BALL_OS_WINDOWS
    │ │ │ -
    44
    │ │ │ -
    45#ifndef BALL_OS_WINDOWS
    │ │ │ -
    │ │ │ -
    46int main(int argc, char **argv)
    │ │ │ -
    47{
    │ │ │ -
    48#else
    │ │ │ -
    49int WINAPI WinMain(HINSTANCE, HINSTANCE, PSTR cmd_line, int)
    │ │ │ -
    50{
    │ │ │ -
    51 int argc = __argc;
    │ │ │ -
    52 char** argv = __argv;
    │ │ │ -
    53#endif
    │ │ │ -
    54
    │ │ │ -
    55 qInstallMessageHandler(logMessages);
    │ │ │ -
    56
    │ │ │ -
    57 // *sigh* this is required as long as Qt does not correctly paint on OpenGL 2 contexts
    │ │ │ -
    58 //QGL::setPreferredPaintEngine(QPaintEngine::OpenGL);
    │ │ │ -
    59
    │ │ │ -
    60 QApplication application(argc, argv);
    │ │ │ -
    61
    │ │ │ -
    62 QStringList arguments = application.arguments();
    │ │ │ -
    63 QStringList::const_iterator arg_it;
    │ │ │ +
    62
    │ │ │ +
    63} // namespace BALL
    │ │ │
    64
    │ │ │ -
    65 bool kiosk_mode = false;
    │ │ │ -
    66 for (arg_it = arguments.constBegin(); arg_it != arguments.constEnd(); ++arg_it)
    │ │ │ -
    67 {
    │ │ │ -
    68 if (arg_it->toLocal8Bit() == "-kiosk")
    │ │ │ -
    69 {
    │ │ │ -
    70 kiosk_mode = true;
    │ │ │ -
    71 }
    │ │ │ -
    72 }
    │ │ │ -
    73
    │ │ │ -
    74 if (kiosk_mode)
    │ │ │ -
    75 {
    │ │ │ -
    76 BALL::VIEW::UIOperationMode::instance().setMode(BALL::VIEW::UIOperationMode::MODE_KIOSK);
    │ │ │ -
    77 }
    │ │ │ -
    78
    │ │ │ -
    79 // =============== testing for opengl support ======================================
    │ │ │ -
    80 if (!QGLFormat::hasOpenGL())
    │ │ │ -
    81 {
    │ │ │ -
    82 QMessageBox::critical(0, "Error while starting BALLView",
    │ │ │ -
    83 "Your computer has no OpenGL support, please install the correct drivers. Aborting for now...",
    │ │ │ -
    84 QMessageBox::Ok, Qt::NoButton, Qt::NoButton);
    │ │ │ -
    85 return -1;
    │ │ │ -
    86 }
    │ │ │ -
    87
    │ │ │ -
    88 BALL::String home_dir = BALL::Directory::getUserHomeDir();
    │ │ │ -
    89
    │ │ │ -
    90 // =============== load translations =====================
    │ │ │ -
    91 BALL::INIFile f(home_dir + BALL::FileSystem::PATH_SEPARATOR + ".BALLView");
    │ │ │ -
    92 f.read();
    │ │ │ -
    93
    │ │ │ -
    94 if (f.hasEntry("GENERAL", "language"))
    │ │ │ -
    95 {
    │ │ │ -
    96 QString str = f.getValue("GENERAL", "language").c_str();
    │ │ │ -
    97
    │ │ │ -
    98 if (str != "en_US")
    │ │ │ -
    99 {
    │ │ │ -
    100 QString loc = "BALLView-" + str;
    │ │ │ -
    101
    │ │ │ -
    102 BALL::Path p;
    │ │ │ -
    103 QStringList dpaths = QString(p.getDataPath().c_str()).split("\n");
    │ │ │ -
    104
    │ │ │ -
    105 QTranslator* translator = new QTranslator(&application);
    │ │ │ -
    106 Q_FOREACH(QString s, dpaths)
    │ │ │ -
    107 {
    │ │ │ -
    108 translator->load(loc, s + "BALLView/translations");
    │ │ │ -
    109 if (!translator->isEmpty())
    │ │ │ -
    110 {
    │ │ │ -
    111 QCoreApplication::installTranslator(translator);
    │ │ │ -
    112 break;
    │ │ │ -
    113 }
    │ │ │ -
    114 }
    │ │ │ -
    115 }
    │ │ │ -
    116 }
    │ │ │ -
    117
    │ │ │ -
    118 // =============== testing if we can write in current directory =====================
    │ │ │ -
    119 if (home_dir == "")
    │ │ │ -
    120 {
    │ │ │ -
    121 try
    │ │ │ -
    122 {
    │ │ │ -
    123 BALL::String temp_file_name;
    │ │ │ -
    124 BALL::File::createTemporaryFilename(temp_file_name);
    │ │ │ -
    125 BALL::File out(temp_file_name, std::ios::out);
    │ │ │ -
    126 out << "test" << std::endl;
    │ │ │ -
    127 out.remove();
    │ │ │ -
    128 }
    │ │ │ -
    129 catch(...)
    │ │ │ -
    130 {
    │ │ │ -
    131 QMessageBox::warning(0, "Error while starting BALLView",
    │ │ │ -
    132 QString("You dont have write access to the current working directory\n") +
    │ │ │ -
    133 "and BALLView can not find your home directory. This can cause\n" +
    │ │ │ -
    134 "unexpected behaviour. Please start BALLView from your homedir with\n" +
    │ │ │ -
    135 "absolute path (e.g. C:\\Programs\\BALLView\\BALLView).\n");
    │ │ │ -
    136 }
    │ │ │ -
    137 }
    │ │ │ -
    138
    │ │ │ -
    139 // =============== initialize Mainframe ============================================
    │ │ │ -
    140 // Create the mainframe.
    │ │ │ -
    141 BALL::Mainframe mainframe(0, "Mainframe");
    │ │ │ -
    142
    │ │ │ -
    143 // can we use the users homedir as working dir?
    │ │ │ -
    144 if (home_dir != "")
    │ │ │ -
    145 {
    │ │ │ -
    146 mainframe.setWorkingDir(home_dir);
    │ │ │ -
    147 }
    │ │ │ -
    148
    │ │ │ -
    149 // Register the mainfram (required for Python support).
    │ │ │ -
    150 mainframe.setIdentifier("Mainframe");
    │ │ │ -
    151 mainframe.registerThis();
    │ │ │ -
    152
    │ │ │ -
    153 // Show the main window.
    │ │ │ -
    154 mainframe.show();
    │ │ │ -
    155
    │ │ │ -
    156 // =============== parsing command line arguments ==================================
    │ │ │ -
    157 // If there are additional command line arguments, interpret them as files to open or logging flag.
    │ │ │ -
    158 for (BALL::Index i = 1; i < argc; ++i)
    │ │ │ -
    159 {
    │ │ │ -
    160 BALL::String argument(argv[i]);
    │ │ │ -
    161 if (argument == "-l")
    │ │ │ -
    162 {
    │ │ │ -
    163 mainframe.enableLoggingToFile();
    │ │ │ -
    164 continue;
    │ │ │ -
    165 }
    │ │ │ -
    166 else if (argument == "-kiosk")
    │ │ │ -
    167 {
    │ │ │ -
    168 // the kiosk mode has already been handled
    │ │ │ -
    169 continue;
    │ │ │ -
    170 }
    │ │ │ -
    171
    │ │ │ -
    172 mainframe.openFile(argument);
    │ │ │ -
    173 }
    │ │ │ -
    174
    │ │ │ -
    175 // enable ending of program from python script
    │ │ │ -
    176 if (mainframe.isAboutToQuit())
    │ │ │ -
    177 {
    │ │ │ -
    178 mainframe.aboutToExit();
    │ │ │ -
    179 return 0;
    │ │ │ -
    180 }
    │ │ │ -
    181
    │ │ │ -
    182 // Hand over control to the application.
    │ │ │ -
    183 return application.exec();
    │ │ │ -
    184}
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    logMessages
    void logMessages(QtMsgType type, const QMessageLogContext &context, const QString &message)
    Definition main.C:14
    │ │ │ -
    main
    int main(int argc, char **argv)
    Definition main.C:46
    │ │ │ -
    BALL::Log
    BALL_EXPORT LogStream Log
    │ │ │ -
    BALL::LogStream::info
    LogStream & info(int n=0)
    │ │ │ -
    BALL::LogStream::warn
    LogStream & warn(int n=0)
    │ │ │ -
    BALL::Embeddable::registerThis
    virtual void registerThis()
    │ │ │ -
    BALL::Embeddable::setIdentifier
    void setIdentifier(const String &identifier)
    │ │ │ - │ │ │ -
    BALL::String::hasPrefix
    bool hasPrefix(const String &s) const
    True, if the string starts with s
    │ │ │ -
    BALL::String::c_str
    const char * c_str() const BALL_NOEXCEPT
    │ │ │ - │ │ │ - │ │ │ -
    BALL::INIFile::getValue
    String getValue(const String &section, const String &key) const
    │ │ │ -
    BALL::INIFile::hasEntry
    bool hasEntry(const String &section, const String &key) const
    │ │ │ -
    BALL::Directory::getUserHomeDir
    static String getUserHomeDir()
    Get the home directory of the current user.
    │ │ │ - │ │ │ -
    BALL::File::createTemporaryFilename
    static bool createTemporaryFilename(String &temporary, const String &suffix=".TMP")
    │ │ │ -
    BALL::File::remove
    static bool remove(String name)
    │ │ │ -
    BALL::FileSystem::PATH_SEPARATOR
    static const char PATH_SEPARATOR
    Definition fileSystem.h:52
    │ │ │ - │ │ │ -
    BALL::Path::getDataPath
    String getDataPath()
    │ │ │ -
    BALL::VIEW::MainControl::openFile
    virtual void openFile(const String &file)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::MainControl::aboutToExit
    virtual void aboutToExit()
    │ │ │ -
    BALL::VIEW::MainControl::setWorkingDir
    void setWorkingDir(const String &dir)
    Set the working directory for the next file dialog and file operation to the given directory.
    │ │ │ -
    BALL::VIEW::UIOperationMode::instance
    static UIOperationMode & instance()
    │ │ │ - │ │ │ -
    BALL::VIEW::UIOperationMode::setMode
    void setMode(OperationMode new_mode)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ +
    65#endif // BALL_APPLICATIONS_BALLVIEW_MAINFRAME_H
    │ │ │ + │ │ │ + │ │ │ +
    BALL_EMBEDDABLE
    #define BALL_EMBEDDABLE(TYPE, BASE)
    Definition embeddable.h:31
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Mainframe::qload_action_
    QAction * qload_action_
    Definition mainframe.h:60
    │ │ │ + │ │ │ +
    BALL::Mainframe::setupPluginHandlers_
    void setupPluginHandlers_()
    Definition mainframe.C:393
    │ │ │ +
    BALL::Mainframe::eventFilter
    bool eventFilter(QObject *, QEvent *e)
    Catch key events.
    Definition mainframe.C:209
    │ │ │ +
    BALL::Mainframe::~Mainframe
    virtual ~Mainframe()
    Definition mainframe.C:201
    │ │ │ +
    BALL::Mainframe::scene_
    Scene * scene_
    Definition mainframe.h:58
    │ │ │ +
    BALL::Mainframe::changeEvent
    void changeEvent(QEvent *evt)
    Definition mainframe.C:373
    │ │ │ +
    BALL::Mainframe::save_project_action_
    QAction * save_project_action_
    Definition mainframe.h:59
    │ │ │ +
    BALL::Mainframe::checkMenus
    void checkMenus()
    Definition mainframe.C:272
    │ │ │ +
    BALL::Mainframe::reset
    void reset()
    remove all loaded Molecules and Representations, reset Coloring options
    Definition mainframe.C:256
    │ │ │ +
    BALL::Mainframe::qsave_action_
    QAction * qsave_action_
    Definition mainframe.h:60
    │ │ │ + │ │ │ + │ │ │ + │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,287 +1,127 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _s_o_u_r_c_e │ │ │ │ * _A_P_P_L_I_C_A_T_I_O_N_S │ │ │ │ * _B_A_L_L_V_I_E_W │ │ │ │ -main.C │ │ │ │ +mainframe.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5// order of includes is important: first qapplication, then BALL includes │ │ │ │ -6#include │ │ │ │ -7#include │ │ │ │ -8#include │ │ │ │ -9 │ │ │ │ -10#include "_m_a_i_n_f_r_a_m_e_._h" │ │ │ │ -11#include <_B_A_L_L_/_S_Y_S_T_E_M_/_p_a_t_h_._h> │ │ │ │ -12#include <_B_A_L_L_/_S_Y_S_T_E_M_/_d_i_r_e_c_t_o_r_y_._h> │ │ │ │ -13 │ │ │ │ -_1_4void _l_o_g_M_e_s_s_a_g_e_s(QtMsgType type, const QMessageLogContext& context, const │ │ │ │ -QString& message) │ │ │ │ -15{ │ │ │ │ -16 _B_A_L_L_:_:_S_t_r_i_n_g s(message.toStdString()); │ │ │ │ -17 if (s._h_a_s_P_r_e_f_i_x("QTextBrowser")) return; │ │ │ │ -18 │ │ │ │ -19 switch ( type ) { │ │ │ │ -20 case QtDebugMsg: │ │ │ │ -21 _B_A_L_L_:_:_L_o_g._i_n_f_o() << message.toStdString() << " " << (context.file ? │ │ │ │ -context.file : "(unknown context)") │ │ │ │ -22 << " " << context.line │ │ │ │ -23 << " " << (context.function ? context.function : "(unknown function)") << │ │ │ │ -std::endl; │ │ │ │ -24 break; │ │ │ │ -25 case QtWarningMsg: │ │ │ │ -26 _B_A_L_L_:_:_L_o_g._w_a_r_n() << message.toStdString() << " " << (context.file ? │ │ │ │ -context.file : "(unknown context)") │ │ │ │ -27 << " " << context.line │ │ │ │ -28 << " " << (context.function ? context.function : "(unknown function)") << │ │ │ │ -std::endl; │ │ │ │ -29 break; │ │ │ │ -30 case QtFatalMsg: │ │ │ │ -31 fprintf( stderr, "Fatal: %s\n", message.toLatin1().constData() ); │ │ │ │ -32 abort(); // deliberately core dump │ │ │ │ -33 case QtCriticalMsg: │ │ │ │ -34 fprintf( stderr, "Critical: %s\n", message.toLatin1().constData() ); │ │ │ │ -35 abort(); // deliberately core dump │ │ │ │ -36 default: │ │ │ │ -37 break; │ │ │ │ -38 } │ │ │ │ -39} │ │ │ │ -40 │ │ │ │ -41 │ │ │ │ -42// uncomment this to use debugging to std::cout! │ │ │ │ -43//#undef BALL_OS_WINDOWS │ │ │ │ -44 │ │ │ │ -45#ifndef BALL_OS_WINDOWS │ │ │ │ -_4_6int _m_a_i_n(int argc, char **argv) │ │ │ │ -47{ │ │ │ │ -48#else │ │ │ │ -49int WINAPI WinMain(HINSTANCE, HINSTANCE, PSTR cmd_line, int) │ │ │ │ -50{ │ │ │ │ -51 int argc = __argc; │ │ │ │ -52 char** argv = __argv; │ │ │ │ -53#endif │ │ │ │ -54 │ │ │ │ -55 qInstallMessageHandler(_l_o_g_M_e_s_s_a_g_e_s); │ │ │ │ -56 │ │ │ │ -57 // *sigh* this is required as long as Qt does not correctly paint on OpenGL │ │ │ │ -2 contexts │ │ │ │ -58 //QGL::setPreferredPaintEngine(QPaintEngine::OpenGL); │ │ │ │ -59 │ │ │ │ -60 QApplication application(argc, argv); │ │ │ │ -61 │ │ │ │ -62 QStringList arguments = application.arguments(); │ │ │ │ -63 QStringList::const_iterator arg_it; │ │ │ │ +5#ifndef BALL_APPLICATIONS_BALLVIEW_MAINFRAME_H │ │ │ │ +6#define BALL_APPLICATIONS_BALLVIEW_MAINFRAME_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_VIEW_KERNEL_MAINCONTROL_H │ │ │ │ +9# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_a_i_n_C_o_n_t_r_o_l_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12#ifndef BALL_VIEW_WIDGETS_SCENE_H │ │ │ │ +13# include <_B_A_L_L_/_V_I_E_W_/_W_I_D_G_E_T_S_/_s_c_e_n_e_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#include │ │ │ │ +17 │ │ │ │ +18namespace _B_A_L_L │ │ │ │ +19{ │ │ │ │ +20 using namespace _B_A_L_L_:_:_V_I_E_W; │ │ │ │ +21 │ │ │ │ +_2_2 class _M_a_i_n_f_r_a_m_e │ │ │ │ +23 : public _B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ +24 { │ │ │ │ +25 Q_OBJECT │ │ │ │ +26 │ │ │ │ +27 public: │ │ │ │ +28 │ │ │ │ +30 _B_A_L_L___E_M_B_E_D_D_A_B_L_E(_M_a_i_n_f_r_a_m_e, _M_a_i_n_C_o_n_t_r_o_l) │ │ │ │ +31 │ │ │ │ +32 │ │ │ │ +33 _M_a_i_n_f_r_a_m_e(_Q_W_i_d_g_e_t* parent = 0, const char* name = 0); │ │ │ │ +34 │ │ │ │ +36 virtual _~_M_a_i_n_f_r_a_m_e(); │ │ │ │ +37 │ │ │ │ +38 public Q_SLOTS: │ │ │ │ +39 │ │ │ │ +41 void _s_h_o_w(); │ │ │ │ +42 │ │ │ │ +44 bool _e_v_e_n_t_F_i_l_t_e_r(_Q_O_b_j_e_c_t*, _Q_E_v_e_n_t* e); │ │ │ │ +45 │ │ │ │ +47 void _r_e_s_e_t(); │ │ │ │ +48 │ │ │ │ +49 // Help menu │ │ │ │ +50 void _a_b_o_u_t(); │ │ │ │ +51 │ │ │ │ +52 void _c_h_e_c_k_M_e_n_u_s(); │ │ │ │ +53 │ │ │ │ +54 protected: │ │ │ │ +55 void _c_h_a_n_g_e_E_v_e_n_t(_Q_E_v_e_n_t* evt); │ │ │ │ +56 void _s_e_t_u_p_P_l_u_g_i_n_H_a_n_d_l_e_r_s__(); │ │ │ │ +57 │ │ │ │ +_5_8 _S_c_e_n_e* _s_c_e_n_e__; │ │ │ │ +_5_9 QAction* _s_a_v_e___p_r_o_j_e_c_t___a_c_t_i_o_n__; │ │ │ │ +_6_0 QAction* _q_l_o_a_d___a_c_t_i_o_n__, *_q_s_a_v_e___a_c_t_i_o_n__; │ │ │ │ +61 }; │ │ │ │ +62 │ │ │ │ +63} // namespace BALL │ │ │ │ 64 │ │ │ │ -65 bool kiosk_mode = false; │ │ │ │ -66 for (arg_it = arguments.constBegin(); arg_it != arguments.constEnd(); │ │ │ │ -++arg_it) │ │ │ │ -67 { │ │ │ │ -68 if (arg_it->toLocal8Bit() == "-kiosk") │ │ │ │ -69 { │ │ │ │ -70 kiosk_mode = true; │ │ │ │ -71 } │ │ │ │ -72 } │ │ │ │ -73 │ │ │ │ -74 if (kiosk_mode) │ │ │ │ -75 { │ │ │ │ -76 _B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_i_n_s_t_a_n_c_e()._s_e_t_M_o_d_e(_B_A_L_L_:_:_V_I_E_W_:_: │ │ │ │ -_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_M_O_D_E___K_I_O_S_K); │ │ │ │ -77 } │ │ │ │ -78 │ │ │ │ -79 // =============== testing for opengl support │ │ │ │ -====================================== │ │ │ │ -80 if (!QGLFormat::hasOpenGL()) │ │ │ │ -81 { │ │ │ │ -82 QMessageBox::critical(0, "Error while starting BALLView", │ │ │ │ -83 "Your computer has no OpenGL support, please install the correct drivers. │ │ │ │ -Aborting for now...", │ │ │ │ -84 QMessageBox::Ok, Qt::NoButton, Qt::NoButton); │ │ │ │ -85 return -1; │ │ │ │ -86 } │ │ │ │ -87 │ │ │ │ -88 _B_A_L_L_:_:_S_t_r_i_n_g home_dir = _B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_g_e_t_U_s_e_r_H_o_m_e_D_i_r(); │ │ │ │ -89 │ │ │ │ -90 // =============== load translations ===================== │ │ │ │ -91 _B_A_L_L_:_:_I_N_I_F_i_l_e f(home_dir + _B_A_L_L_:_:_F_i_l_e_S_y_s_t_e_m_:_:_P_A_T_H___S_E_P_A_R_A_T_O_R + ".BALLView"); │ │ │ │ -92 f._r_e_a_d(); │ │ │ │ -93 │ │ │ │ -94 if (f._h_a_s_E_n_t_r_y("GENERAL", "language")) │ │ │ │ -95 { │ │ │ │ -96 QString str = f._g_e_t_V_a_l_u_e("GENERAL", "language")._c___s_t_r(); │ │ │ │ -97 │ │ │ │ -98 if (str != "en_US") │ │ │ │ -99 { │ │ │ │ -100 QString loc = "BALLView-" + str; │ │ │ │ -101 │ │ │ │ -102 _B_A_L_L_:_:_P_a_t_h p; │ │ │ │ -103 QStringList dpaths = QString(p._g_e_t_D_a_t_a_P_a_t_h()._c___s_t_r()).split("\n"); │ │ │ │ -104 │ │ │ │ -105 QTranslator* translator = new QTranslator(&application); │ │ │ │ -106 Q_FOREACH(QString s, dpaths) │ │ │ │ -107 { │ │ │ │ -108 translator->load(loc, s + "BALLView/translations"); │ │ │ │ -109 if (!translator->isEmpty()) │ │ │ │ -110 { │ │ │ │ -111 QCoreApplication::installTranslator(translator); │ │ │ │ -112 break; │ │ │ │ -113 } │ │ │ │ -114 } │ │ │ │ -115 } │ │ │ │ -116 } │ │ │ │ -117 │ │ │ │ -118 // =============== testing if we can write in current directory │ │ │ │ -===================== │ │ │ │ -119 if (home_dir == "") │ │ │ │ -120 { │ │ │ │ -121 try │ │ │ │ -122 { │ │ │ │ -123 _B_A_L_L_:_:_S_t_r_i_n_g temp_file_name; │ │ │ │ -124 _B_A_L_L_:_:_F_i_l_e_:_:_c_r_e_a_t_e_T_e_m_p_o_r_a_r_y_F_i_l_e_n_a_m_e(temp_file_name); │ │ │ │ -125 _B_A_L_L_:_:_F_i_l_e out(temp_file_name, std::ios::out); │ │ │ │ -126 out << "test" << std::endl; │ │ │ │ -127 out._r_e_m_o_v_e(); │ │ │ │ -128 } │ │ │ │ -129 catch(...) │ │ │ │ -130 { │ │ │ │ -131 QMessageBox::warning(0, "Error while starting BALLView", │ │ │ │ -132 QString("You dont have write access to the current working directory\n") + │ │ │ │ -133 "and BALLView can not find your home directory. This can cause\n" + │ │ │ │ -134 "unexpected behaviour. Please start BALLView from your homedir with\n" + │ │ │ │ -135 "absolute path (e.g. C:\\Programs\\BALLView\\BALLView).\n"); │ │ │ │ -136 } │ │ │ │ -137 } │ │ │ │ -138 │ │ │ │ -139 // =============== initialize Mainframe │ │ │ │ -============================================ │ │ │ │ -140 // Create the mainframe. │ │ │ │ -141 _B_A_L_L_:_:_M_a_i_n_f_r_a_m_e mainframe(0, "Mainframe"); │ │ │ │ -142 │ │ │ │ -143 // can we use the users homedir as working dir? │ │ │ │ -144 if (home_dir != "") │ │ │ │ -145 { │ │ │ │ -146 mainframe._s_e_t_W_o_r_k_i_n_g_D_i_r(home_dir); │ │ │ │ -147 } │ │ │ │ -148 │ │ │ │ -149 // Register the mainfram (required for Python support). │ │ │ │ -150 mainframe._s_e_t_I_d_e_n_t_i_f_i_e_r("Mainframe"); │ │ │ │ -151 mainframe._r_e_g_i_s_t_e_r_T_h_i_s(); │ │ │ │ -152 │ │ │ │ -153 // Show the main window. │ │ │ │ -154 mainframe._s_h_o_w(); │ │ │ │ -155 │ │ │ │ -156 // =============== parsing command line arguments │ │ │ │ -================================== │ │ │ │ -157 // If there are additional command line arguments, interpret them as files │ │ │ │ -to open or logging flag. │ │ │ │ -158 for (_B_A_L_L_:_:_I_n_d_e_x i = 1; i < argc; ++i) │ │ │ │ -159 { │ │ │ │ -160 _B_A_L_L_:_:_S_t_r_i_n_g argument(argv[i]); │ │ │ │ -161 if (argument == "-l") │ │ │ │ -162 { │ │ │ │ -163 mainframe._e_n_a_b_l_e_L_o_g_g_i_n_g_T_o_F_i_l_e(); │ │ │ │ -164 continue; │ │ │ │ -165 } │ │ │ │ -166 else if (argument == "-kiosk") │ │ │ │ -167 { │ │ │ │ -168 // the kiosk mode has already been handled │ │ │ │ -169 continue; │ │ │ │ -170 } │ │ │ │ -171 │ │ │ │ -172 mainframe._o_p_e_n_F_i_l_e(argument); │ │ │ │ -173 } │ │ │ │ -174 │ │ │ │ -175 // enable ending of program from python script │ │ │ │ -176 if (mainframe._i_s_A_b_o_u_t_T_o_Q_u_i_t()) │ │ │ │ -177 { │ │ │ │ -178 mainframe._a_b_o_u_t_T_o_E_x_i_t(); │ │ │ │ -179 return 0; │ │ │ │ -180 } │ │ │ │ -181 │ │ │ │ -182 // Hand over control to the application. │ │ │ │ -183 return application.exec(); │ │ │ │ -184} │ │ │ │ -_p_a_t_h_._h │ │ │ │ -_d_i_r_e_c_t_o_r_y_._h │ │ │ │ -_m_a_i_n_f_r_a_m_e_._h │ │ │ │ -_l_o_g_M_e_s_s_a_g_e_s │ │ │ │ -void logMessages(QtMsgType type, const QMessageLogContext &context, const │ │ │ │ -QString &message) │ │ │ │ -DDeeffiinniittiioonn _m_a_i_n_._C_:_1_4 │ │ │ │ -_m_a_i_n │ │ │ │ -int main(int argc, char **argv) │ │ │ │ -DDeeffiinniittiioonn _m_a_i_n_._C_:_4_6 │ │ │ │ -_B_A_L_L_:_:_L_o_g │ │ │ │ -BALL_EXPORT LogStream Log │ │ │ │ -_B_A_L_L_:_:_L_o_g_S_t_r_e_a_m_:_:_i_n_f_o │ │ │ │ -LogStream & info(int n=0) │ │ │ │ -_B_A_L_L_:_:_L_o_g_S_t_r_e_a_m_:_:_w_a_r_n │ │ │ │ -LogStream & warn(int n=0) │ │ │ │ -_B_A_L_L_:_:_E_m_b_e_d_d_a_b_l_e_:_:_r_e_g_i_s_t_e_r_T_h_i_s │ │ │ │ -virtual void registerThis() │ │ │ │ -_B_A_L_L_:_:_E_m_b_e_d_d_a_b_l_e_:_:_s_e_t_I_d_e_n_t_i_f_i_e_r │ │ │ │ -void setIdentifier(const String &identifier) │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g_:_:_h_a_s_P_r_e_f_i_x │ │ │ │ -bool hasPrefix(const String &s) const │ │ │ │ -True, if the string starts with s │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g_:_:_c___s_t_r │ │ │ │ -const char * c_str() const BALL_NOEXCEPT │ │ │ │ -_B_A_L_L_:_:_I_N_I_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _I_N_I_F_i_l_e_._h_:_2_9 │ │ │ │ -_B_A_L_L_:_:_I_N_I_F_i_l_e_:_:_r_e_a_d │ │ │ │ -bool read() │ │ │ │ -_B_A_L_L_:_:_I_N_I_F_i_l_e_:_:_g_e_t_V_a_l_u_e │ │ │ │ -String getValue(const String §ion, const String &key) const │ │ │ │ -_B_A_L_L_:_:_I_N_I_F_i_l_e_:_:_h_a_s_E_n_t_r_y │ │ │ │ -bool hasEntry(const String §ion, const String &key) const │ │ │ │ -_B_A_L_L_:_:_D_i_r_e_c_t_o_r_y_:_:_g_e_t_U_s_e_r_H_o_m_e_D_i_r │ │ │ │ -static String getUserHomeDir() │ │ │ │ -Get the home directory of the current user. │ │ │ │ -_B_A_L_L_:_:_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _f_i_l_e_._h_:_1_3_6 │ │ │ │ -_B_A_L_L_:_:_F_i_l_e_:_:_c_r_e_a_t_e_T_e_m_p_o_r_a_r_y_F_i_l_e_n_a_m_e │ │ │ │ -static bool createTemporaryFilename(String &temporary, const String │ │ │ │ -&suffix=".TMP") │ │ │ │ -_B_A_L_L_:_:_F_i_l_e_:_:_r_e_m_o_v_e │ │ │ │ -static bool remove(String name) │ │ │ │ -_B_A_L_L_:_:_F_i_l_e_S_y_s_t_e_m_:_:_P_A_T_H___S_E_P_A_R_A_T_O_R │ │ │ │ -static const char PATH_SEPARATOR │ │ │ │ -DDeeffiinniittiioonn _f_i_l_e_S_y_s_t_e_m_._h_:_5_2 │ │ │ │ -_B_A_L_L_:_:_P_a_t_h │ │ │ │ -DDeeffiinniittiioonn _p_a_t_h_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_P_a_t_h_:_:_g_e_t_D_a_t_a_P_a_t_h │ │ │ │ -String getDataPath() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_:_:_o_p_e_n_F_i_l_e │ │ │ │ -virtual void openFile(const String &file) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_:_:_i_s_A_b_o_u_t_T_o_Q_u_i_t │ │ │ │ -bool isAboutToQuit() │ │ │ │ -DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_6_9_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_:_:_e_n_a_b_l_e_L_o_g_g_i_n_g_T_o_F_i_l_e │ │ │ │ -void enableLoggingToFile() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_:_:_a_b_o_u_t_T_o_E_x_i_t │ │ │ │ -virtual void aboutToExit() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l_:_:_s_e_t_W_o_r_k_i_n_g_D_i_r │ │ │ │ -void setWorkingDir(const String &dir) │ │ │ │ -Set the working directory for the next file dialog and file operation to the │ │ │ │ -given directory. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_i_n_s_t_a_n_c_e │ │ │ │ -static UIOperationMode & instance() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_M_O_D_E___K_I_O_S_K │ │ │ │ -@ MODE_KIOSK │ │ │ │ -DDeeffiinniittiioonn _U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_U_I_O_p_e_r_a_t_i_o_n_M_o_d_e_:_:_s_e_t_M_o_d_e │ │ │ │ -void setMode(OperationMode new_mode) │ │ │ │ +65#endif // BALL_APPLICATIONS_BALLVIEW_MAINFRAME_H │ │ │ │ +_m_a_i_n_C_o_n_t_r_o_l_._h │ │ │ │ +_s_c_e_n_e_._h │ │ │ │ +_B_A_L_L___E_M_B_E_D_D_A_B_L_E │ │ │ │ +#define BALL_EMBEDDABLE(TYPE, BASE) │ │ │ │ +DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_3_1 │ │ │ │ +_B_A_L_L │ │ │ │ +DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W │ │ │ │ +DDeeffiinniittiioonn _c_o_n_s_t_r_a_i_n_t_s_._h_:_3_5 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_S_c_e_n_e │ │ │ │ +DDeeffiinniittiioonn _s_c_e_n_e_._h_:_1_4_1 │ │ │ │ _B_A_L_L_:_:_M_a_i_n_f_r_a_m_e │ │ │ │ DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._h_:_2_4 │ │ │ │ _B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_s_h_o_w │ │ │ │ void show() │ │ │ │ DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._C_:_2_8_1 │ │ │ │ -_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_q_l_o_a_d___a_c_t_i_o_n__ │ │ │ │ +QAction * qload_action_ │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._h_:_6_0 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_a_b_o_u_t │ │ │ │ +void about() │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._C_:_3_4_9 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_s_e_t_u_p_P_l_u_g_i_n_H_a_n_d_l_e_r_s__ │ │ │ │ +void setupPluginHandlers_() │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._C_:_3_9_3 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_e_v_e_n_t_F_i_l_t_e_r │ │ │ │ +bool eventFilter(QObject *, QEvent *e) │ │ │ │ +Catch key events. │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._C_:_2_0_9 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_~_M_a_i_n_f_r_a_m_e │ │ │ │ +virtual ~Mainframe() │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._C_:_2_0_1 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_s_c_e_n_e__ │ │ │ │ +Scene * scene_ │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._h_:_5_8 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_c_h_a_n_g_e_E_v_e_n_t │ │ │ │ +void changeEvent(QEvent *evt) │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._C_:_3_7_3 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_s_a_v_e___p_r_o_j_e_c_t___a_c_t_i_o_n__ │ │ │ │ +QAction * save_project_action_ │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._h_:_5_9 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_c_h_e_c_k_M_e_n_u_s │ │ │ │ +void checkMenus() │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._C_:_2_7_2 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_r_e_s_e_t │ │ │ │ +void reset() │ │ │ │ +remove all loaded Molecules and Representations, reset Coloring options │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._C_:_2_5_6 │ │ │ │ +_B_A_L_L_:_:_M_a_i_n_f_r_a_m_e_:_:_q_s_a_v_e___a_c_t_i_o_n__ │ │ │ │ +QAction * qsave_action_ │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_f_r_a_m_e_._h_:_6_0 │ │ │ │ +_Q_O_b_j_e_c_t │ │ │ │ +_Q_W_i_d_g_e_t │ │ │ │ +_Q_E_v_e_n_t │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d00/a05646.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::QSAR::PredictionConfiguration Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/QSAR/configIO.h>

    │ │ │ +

    #include <BALL/QSAR/configIO.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

     PredictionConfiguration ()
     
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ @@ -103,15 +103,15 @@ │ │ │

    bool print_expected
     
    bool done
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 121 of file configIO.h.

    │ │ │ +

    Definition at line 121 of file configIO.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ PredictionConfiguration()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -135,15 +135,15 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    String BALL::QSAR::PredictionConfiguration::data
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 126 of file configIO.h.

    │ │ │ +

    Definition at line 126 of file configIO.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ done

    │ │ │ │ │ │
    │ │ │ @@ -151,15 +151,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    bool BALL::QSAR::PredictionConfiguration::done
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 131 of file configIO.h.

    │ │ │ +

    Definition at line 131 of file configIO.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ model

    │ │ │ │ │ │
    │ │ │ @@ -167,15 +167,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    String BALL::QSAR::PredictionConfiguration::model
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 125 of file configIO.h.

    │ │ │ +

    Definition at line 125 of file configIO.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ output

    │ │ │ │ │ │
    │ │ │ @@ -183,15 +183,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    String BALL::QSAR::PredictionConfiguration::output
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 127 of file configIO.h.

    │ │ │ +

    Definition at line 127 of file configIO.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ print_expected

    │ │ │ │ │ │
    │ │ │ @@ -199,15 +199,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    bool BALL::QSAR::PredictionConfiguration::print_expected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 130 of file configIO.h.

    │ │ │ +

    Definition at line 130 of file configIO.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ statistic

    │ │ │ │ │ │
    │ │ │ @@ -215,15 +215,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    int BALL::QSAR::PredictionConfiguration::statistic
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 128 of file configIO.h.

    │ │ │ +

    Definition at line 128 of file configIO.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ statistic_name

    │ │ │ │ │ │
    │ │ │ @@ -231,15 +231,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    String BALL::QSAR::PredictionConfiguration::statistic_name
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 129 of file configIO.h.

    │ │ │ +

    Definition at line 129 of file configIO.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d03/a04778.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::TAngle< T > Class Template Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/MATHS/angle.h>

    │ │ │ +

    #include <BALL/MATHS/angle.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Types

    Enums
    enum  Range { RANGE__UNLIMITED = 0 │ │ │ , RANGE__UNSIGNED = 1 │ │ │ , RANGE__SIGNED = 2 │ │ │ @@ -189,15 +189,15 @@ │ │ │
    static T toDegree (const T &radian)
     
    │ │ │

    Detailed Description

    │ │ │
    template<typename T>
    │ │ │ class BALL::TAngle< T >

    Generic Angle Class. Use this class to describe angles. The TAngle class permits the conversion from degree to radians and is the return type of all functions used to calculate angles.

    │ │ │ │ │ │ -

    Definition at line 52 of file angle.h.

    │ │ │ +

    Definition at line 52 of file angle.h.

    │ │ │

    Member Enumeration Documentation

    │ │ │ │ │ │

    ◆ Range

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ @@ -211,15 +211,15 @@ │ │ │

    form of the angle range: RANGE__UNLIMITED = 0 no limitations RANGE__UNSIGNED = 1 0 <= angle <= 360, 0 <= angle <= PI * 2 RANGE__SIGNED = 2 -180 <= angle <= 180, -PI <= angle <= PI

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Enumerator
    RANGE__UNLIMITED 
    RANGE__UNSIGNED 
    RANGE__SIGNED 
    │ │ │ │ │ │ -

    Definition at line 67 of file angle.h.

    │ │ │ +

    Definition at line 67 of file angle.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ TAngle() [1/3]

    │ │ │ │ │ │ @@ -234,15 +234,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Default constructor. Creates a new angle object. Its value is set to 0.

    │ │ │ │ │ │ -

    Definition at line 384 of file angle.h.

    │ │ │ +

    Definition at line 384 of file angle.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ TAngle() [2/3]

    │ │ │ │ │ │
    │ │ │ @@ -262,15 +262,15 @@ │ │ │

    Copy constructor. Create a copy of a TAngle object. Copies are always shallow.

    Parameters
    │ │ │ │ │ │ │ │ │
    anglethe object to be copied
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 390 of file angle.h.

    │ │ │ +

    Definition at line 390 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ TAngle() [3/3]

    │ │ │ │ │ │
    │ │ │ @@ -309,15 +309,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    new_valuethe value of the angle object
    radiantrue if new_value is in radians, false otherwise
    │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 396 of file angle.h.

    │ │ │ +

    Definition at line 396 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ~TAngle()

    │ │ │ │ │ │
    │ │ │ @@ -339,15 +339,15 @@ │ │ │ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
    │ │ │

    Destructor.

    │ │ │ │ │ │ -

    Definition at line 104 of file angle.h.

    │ │ │ +

    Definition at line 104 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ clear()

    │ │ │ │ │ │ @@ -370,15 +370,15 @@ │ │ │ │ │ │ inlinevirtual │ │ │ │ │ │ │ │ │
    │ │ │

    Clear method The value is set to 0.

    │ │ │ │ │ │ -

    Definition at line 111 of file angle.h.

    │ │ │ +

    Definition at line 111 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ dump()

    │ │ │ │ │ │
    │ │ │ @@ -409,15 +409,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    s- output stream where to output the internal state of {*this}
    depth- the dumping depth
    │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 681 of file angle.h.

    │ │ │ +

    Definition at line 681 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ get() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -448,15 +448,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    valthe variable to assign the value to
    radianif set to true assigns the value in radians (default).
    │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 442 of file angle.h.

    │ │ │ +

    Definition at line 442 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ get() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -476,15 +476,15 @@ │ │ │

    Assign the value to another angle.

    Parameters
    │ │ │ │ │ │ │ │ │
    anglethe angle to assign the value to
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 436 of file angle.h.

    │ │ │ +

    Definition at line 436 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ isEquivalent()

    │ │ │ │ │ │
    │ │ │ @@ -505,15 +505,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to compare with
    │ │ │ │ │ │ │ │ │
    Returns
    bool, true if {*this} angle is equal to value
    │ │ │ │ │ │ -

    Definition at line 664 of file angle.h.

    │ │ │ +

    Definition at line 664 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ isValid()

    │ │ │ │ │ │
    │ │ │ @@ -527,15 +527,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Test whether instance is valid. Always returns true

    Returns
    bool true
    │ │ │ │ │ │ -

    Definition at line 675 of file angle.h.

    │ │ │ +

    Definition at line 675 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ negate()

    │ │ │ │ │ │
    │ │ │ @@ -549,15 +549,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Negate the angle

    │ │ │ │ │ │ -

    Definition at line 513 of file angle.h.

    │ │ │ +

    Definition at line 513 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ normalize()

    │ │ │ │ │ │
    │ │ │ @@ -577,15 +577,15 @@ │ │ │

    Normalize the angle over a given range. RANGE__UNLIMITED = 0 no limitations. RANGE__UNSIGNED = 1 $0 \le \mathtt{angle} \le 360, 0 \le angle \le 2 \pi$. RANGE__SIGNED = 2 $-180 \le \mathtt{angle} \le 180, -\pi \le \mathtt{angle} \le \pi$.

    Parameters
    │ │ │ │ │ │ │ │ │
    rangethe range of the angle
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 478 of file angle.h.

    │ │ │ +

    Definition at line 478 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator T()

    │ │ │ │ │ │
    │ │ │ @@ -599,15 +599,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Cast operator

    Returns
    value in radians
    │ │ │ │ │ │ -

    Definition at line 448 of file angle.h.

    │ │ │ +

    Definition at line 448 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator!=()

    │ │ │ │ │ │
    │ │ │ @@ -628,15 +628,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to compare with
    │ │ │ │ │ │ │ │ │
    Returns
    bool, true if the two angles are not equal
    │ │ │ │ │ │ -

    Definition at line 627 of file angle.h.

    │ │ │ +

    Definition at line 627 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator*=() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -657,15 +657,15 @@ │ │ │ │ │ │ │ │ │
    valthe value to multiply by
    │ │ │ │ │ │ │ │ │
    Returns
    TAngle, {*this}
    │ │ │ │ │ │ -

    Definition at line 578 of file angle.h.

    │ │ │ +

    Definition at line 578 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator*=() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -686,15 +686,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to multiply by
    │ │ │ │ │ │ │ │ │
    Returns
    TAngle, {*this}
    │ │ │ │ │ │ -

    Definition at line 571 of file angle.h.

    │ │ │ +

    Definition at line 571 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator+() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -708,15 +708,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Positive sign.

    │ │ │ │ │ │ -

    Definition at line 519 of file angle.h.

    │ │ │ +

    Definition at line 519 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator+() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -737,15 +737,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to add
    │ │ │ │ │ │ │ │ │
    Returns
    TAngle, the new angle
    │ │ │ │ │ │ -

    Definition at line 545 of file angle.h.

    │ │ │ +

    Definition at line 545 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator+=() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -766,15 +766,15 @@ │ │ │ │ │ │ │ │ │
    valthe value to add
    │ │ │ │ │ │ │ │ │
    Returns
    TAngle, {*this}
    │ │ │ │ │ │ -

    Definition at line 538 of file angle.h.

    │ │ │ +

    Definition at line 538 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator+=() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -795,15 +795,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to add
    │ │ │ │ │ │ │ │ │
    Returns
    TAngle, {*this}
    │ │ │ │ │ │ -

    Definition at line 531 of file angle.h.

    │ │ │ +

    Definition at line 531 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator-() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -817,15 +817,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Negative sign.

    │ │ │ │ │ │ -

    Definition at line 525 of file angle.h.

    │ │ │ +

    Definition at line 525 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator-() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -846,15 +846,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to substract
    │ │ │ │ │ │ │ │ │
    Returns
    TAngle, the new angle
    │ │ │ │ │ │ -

    Definition at line 565 of file angle.h.

    │ │ │ +

    Definition at line 565 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator-=() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -875,15 +875,15 @@ │ │ │ │ │ │ │ │ │
    valthe value to substract
    │ │ │ │ │ │ │ │ │
    Returns
    TAngle, {*this}
    │ │ │ │ │ │ -

    Definition at line 558 of file angle.h.

    │ │ │ +

    Definition at line 558 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator-=() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -904,15 +904,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to substract
    │ │ │ │ │ │ │ │ │
    Returns
    TAngle, {*this}
    │ │ │ │ │ │ -

    Definition at line 551 of file angle.h.

    │ │ │ +

    Definition at line 551 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator/()

    │ │ │ │ │ │
    │ │ │ @@ -939,15 +939,15 @@ │ │ │
    Exceptions
    │ │ │ │ │ │ │ │ │
    Exception::DivisionByZeroif val is zero
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 610 of file angle.h.

    │ │ │ +

    Definition at line 610 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator/=() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -974,15 +974,15 @@ │ │ │
    Exceptions
    │ │ │ │ │ │ │ │ │
    Exception::DivisionByZeroif val is zero
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 597 of file angle.h.

    │ │ │ +

    Definition at line 597 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator/=() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1009,15 +1009,15 @@ │ │ │
    Exceptions
    │ │ │ │ │ │ │ │ │
    Exception::DivisionByZeroif angle is zero
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 585 of file angle.h.

    │ │ │ +

    Definition at line 585 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator<() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -1038,15 +1038,15 @@ │ │ │ │ │ │ │ │ │
    valthe value to compare with
    │ │ │ │ │ │ │ │ │
    Returns
    bool, true if {*this} angle is smaller than value
    │ │ │ │ │ │ -

    Definition at line 639 of file angle.h.

    │ │ │ +

    Definition at line 639 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator<() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1067,15 +1067,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to compare with
    │ │ │ │ │ │ │ │ │
    Returns
    bool, true if {*this} angle is smaller than value
    │ │ │ │ │ │ -

    Definition at line 633 of file angle.h.

    │ │ │ +

    Definition at line 633 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator<=()

    │ │ │ │ │ │
    │ │ │ @@ -1096,15 +1096,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to compare with
    │ │ │ │ │ │ │ │ │
    Returns
    bool, true if {*this} angle is smaller or equal than value
    │ │ │ │ │ │ -

    Definition at line 645 of file angle.h.

    │ │ │ +

    Definition at line 645 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator=() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -1124,15 +1124,15 @@ │ │ │

    Assignment operator for floats. Assign a float value to the angle. The assigned value has to be in radians!

    Parameters
    │ │ │ │ │ │ │ │ │
    new_valuethe new value
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 429 of file angle.h.

    │ │ │ +

    Definition at line 429 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator=() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1147,15 +1147,15 @@ │ │ │ angle) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Assignment operator

    │ │ │ │ │ │ -

    Definition at line 422 of file angle.h.

    │ │ │ +

    Definition at line 422 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator==()

    │ │ │ │ │ │
    │ │ │ @@ -1176,15 +1176,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to compare with
    │ │ │ │ │ │ │ │ │
    Returns
    bool, true if the two angles are equal
    │ │ │ │ │ │ -

    Definition at line 621 of file angle.h.

    │ │ │ +

    Definition at line 621 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator>()

    │ │ │ │ │ │
    │ │ │ @@ -1205,15 +1205,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to compare with
    │ │ │ │ │ │ │ │ │
    Returns
    bool, true if {*this} angle is greater than value
    │ │ │ │ │ │ -

    Definition at line 657 of file angle.h.

    │ │ │ +

    Definition at line 657 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ operator>=()

    │ │ │ │ │ │
    │ │ │ @@ -1234,15 +1234,15 @@ │ │ │ │ │ │ │ │ │
    anglethe angle to compare with
    │ │ │ │ │ │ │ │ │
    Returns
    bool, true if {*this} angle is greater or equal than value
    │ │ │ │ │ │ -

    Definition at line 651 of file angle.h.

    │ │ │ +

    Definition at line 651 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ set() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -1273,15 +1273,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    new_valuethe value of the angle object
    radiantrue if new_value is in radians, false otherwise
    │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 416 of file angle.h.

    │ │ │ +

    Definition at line 416 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ set() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1301,15 +1301,15 @@ │ │ │

    Assign an Angle object from another.

    Parameters
    │ │ │ │ │ │ │ │ │
    anglethe angle object to be assigned from
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 410 of file angle.h.

    │ │ │ +

    Definition at line 410 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ swap()

    │ │ │ │ │ │
    │ │ │ @@ -1324,15 +1324,15 @@ │ │ │ angle) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Swap the contents of two angles.

    │ │ │ │ │ │ -

    Definition at line 402 of file angle.h.

    │ │ │ +

    Definition at line 402 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ toDegree() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -1346,15 +1346,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Return the value of the angle

    Returns
    value in degrees
    │ │ │ │ │ │ -

    Definition at line 465 of file angle.h.

    │ │ │ +

    Definition at line 465 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ toDegree() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1383,15 +1383,15 @@ │ │ │ │ │ │ │ │ │
    radianthe value in radians
    │ │ │ │ │ │ │ │ │
    Returns
    T the value in degrees
    │ │ │ │ │ │ -

    Definition at line 471 of file angle.h.

    │ │ │ +

    Definition at line 471 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ toRadian() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -1405,15 +1405,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Return the value of the angle

    Returns
    value in radians
    │ │ │ │ │ │ -

    Definition at line 454 of file angle.h.

    │ │ │ +

    Definition at line 454 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ toRadian() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1442,15 +1442,15 @@ │ │ │ │ │ │ │ │ │
    degreethe value in degrees
    │ │ │ │ │ │ │ │ │
    Returns
    T the value in radians
    │ │ │ │ │ │ -

    Definition at line 460 of file angle.h.

    │ │ │ +

    Definition at line 460 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ value

    │ │ │ │ │ │ @@ -1462,15 +1462,15 @@ │ │ │ │ │ │ T BALL::TAngle< T >::value │ │ │ │ │ │ │ │ │
    │ │ │

    The value

    │ │ │ │ │ │ -

    Definition at line 377 of file angle.h.

    │ │ │ +

    Definition at line 377 of file angle.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d03/a06386.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::EnergeticEvaluation Class Reference
    Molecular Modeling » Molecular Structure » Docking of molecular structures
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SCORING/FUNCTIONS/energeticEvaluation.h>

    │ │ │ +

    #include <BALL/SCORING/FUNCTIONS/energeticEvaluation.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::EnergeticEvaluation:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::ForceFieldEvaluation │ │ │ @@ -101,15 +101,15 @@ │ │ │   │ │ │ virtual std::vector< ConformationSet::Conformation > operator() (ConformationSet &conformations) │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Base class for energetic evaluators of docking results. This trivial class will return the identity scoring, leaving permutation and score unchanged.

    │ │ │ │ │ │ -

    Definition at line 20 of file energeticEvaluation.h.

    │ │ │ +

    Definition at line 20 of file energeticEvaluation.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ EnergeticEvaluation()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d04/a00713.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: peptides.h File Reference │ │ │ +BALL: point.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,81 +65,40 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    peptides.h File Reference
    │ │ │ +
    point.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/KERNEL/protein.h>
    │ │ │ -#include <BALL/DATATYPE/options.h>
    │ │ │ -#include <BALL/CONCEPT/embeddable.h>
    │ │ │ +
    #include <BALL/VIEW/KERNEL/geometricObject.h>
    │ │ │ +#include <BALL/VIEW/DATATYPE/vertex1.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │
    │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::Peptides::NameConverter
     This class provides conversion of atom names between naming schemata. More...
     
    struct  BALL::Peptides::NameConverter::Option
     Option names. More...
     
    struct  BALL::Peptides::NameConverter::Default
     Default values for options. More...
    class  BALL::VIEW::Point
     
    │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ -

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::Peptides
    namespace  BALL::VIEW
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -

    │ │ │ -Typedefs

    Type definitions
    typedef std::list< String > BALL::Peptides::ThreeLetterAASequence
     An amino acid sequence in three-letter code.
     
    typedef String BALL::Peptides::OneLetterAASequence
     An amino acid sequence in one-letter code.
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │

    │ │ │ -Functions

    Amino acid sequence conversion
    BALL_EXPORT char BALL::Peptides::OneLetterCode (const String &aa)
     
    BALL_EXPORT String BALL::Peptides::ThreeLetterCode (char aa)
     
    BALL_EXPORT bool BALL::Peptides::IsOneLetterCode (char aa)
     
    BALL_EXPORT bool BALL::Peptides::IsThreeLetterCode (const String &aa)
     
    BALL_EXPORT OneLetterAASequence BALL::Peptides::ThreeLetterToOneLetter (const ThreeLetterAASequence &sequence)
     
    BALL_EXPORT ThreeLetterAASequence BALL::Peptides::OneLetterToThreeLetter (const OneLetterAASequence &sequence)
     
    BALL_EXPORT OneLetterAASequence BALL::Peptides::GetSequence (const Protein &protein)
     
    BALL_EXPORT OneLetterAASequence BALL::Peptides::GetSequence (const Chain &chain)
     
    BALL_EXPORT OneLetterAASequence BALL::Peptides::GetSequence (ResidueConstIterator it)
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,67 +1,23 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ + * _V_I_E_W │ │ │ │ + * _P_R_I_M_I_T_I_V_E_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -peptides.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_o_t_e_i_n_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_e_m_b_e_d_d_a_b_l_e_._h> │ │ │ │ +point.h File Reference │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_g_e_o_m_e_t_r_i_c_O_b_j_e_c_t_._h> │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_v_e_r_t_e_x_1_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ - class   _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r │ │ │ │ -  This class provides conversion of atom names between naming schemata. │ │ │ │ - _M_o_r_e_._._. │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_O_p_t_i_o_n │ │ │ │ -  _O_p_t_i_o_n names. _M_o_r_e_._._. │ │ │ │ -  │ │ │ │ -struct   _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_D_e_f_a_u_l_t │ │ │ │ -  _D_e_f_a_u_l_t values for options. _M_o_r_e_._._. │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_P_o_i_n_t │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_P_e_p_t_i_d_e_s │ │ │ │ -  │ │ │ │ -TTyyppeeddeeffss │ │ │ │ -Type definitions │ │ │ │ -typedef std::list< _S_t_r_i_n_g >  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_T_h_r_e_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e │ │ │ │ -  An amino acid sequence in three-letter code. │ │ │ │ -  │ │ │ │ - typedef _S_t_r_i_n_g  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e │ │ │ │ -  An amino acid sequence in one-letter code. │ │ │ │ -  │ │ │ │ -FFuunnccttiioonnss │ │ │ │ -Amino acid sequence conversion │ │ │ │ - _B_A_L_L___E_X_P_O_R_T char  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_O_n_e_L_e_t_t_e_r_C_o_d_e (const _S_t_r_i_n_g │ │ │ │ - &aa) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _S_t_r_i_n_g  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_T_h_r_e_e_L_e_t_t_e_r_C_o_d_e (char aa) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _b_o_o_l  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_I_s_O_n_e_L_e_t_t_e_r_C_o_d_e (char aa) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _b_o_o_l  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_I_s_T_h_r_e_e_L_e_t_t_e_r_C_o_d_e (const │ │ │ │ - _S_t_r_i_n_g &aa) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_T_h_r_e_e_L_e_t_t_e_r_T_o_O_n_e_L_e_t_t_e_r │ │ │ │ - (const _T_h_r_e_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e &sequence) │ │ │ │ -  │ │ │ │ -_B_A_L_L___E_X_P_O_R_T _T_h_r_e_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_O_n_e_L_e_t_t_e_r_T_o_T_h_r_e_e_L_e_t_t_e_r │ │ │ │ - (const _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e &sequence) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_G_e_t_S_e_q_u_e_n_c_e (const _P_r_o_t_e_i_n │ │ │ │ - &protein) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_G_e_t_S_e_q_u_e_n_c_e (const _C_h_a_i_n │ │ │ │ - &chain) │ │ │ │ -  │ │ │ │ - _B_A_L_L___E_X_P_O_R_T _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e  _B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_G_e_t_S_e_q_u_e_n_c_e │ │ │ │ - (_R_e_s_i_d_u_e_C_o_n_s_t_I_t_e_r_a_t_o_r it) │ │ │ │ +namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d04/a00713_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: peptides.h Source File │ │ │ +BALL: point.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,193 +70,101 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    peptides.h
    │ │ │ +
    point.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_STRUCTURE_PEPTIDES_H
    │ │ │ -
    6#define BALL_STRUCTURE_PEPTIDES_H
    │ │ │ -
    7
    │ │ │ -
    8#ifndef BALL_COMMON_H
    │ │ │ -
    9# include <BALL/common.h>
    │ │ │ -
    10#endif
    │ │ │ -
    11
    │ │ │ -
    12#ifndef BALL_KERNEL_PROTEIN_H
    │ │ │ -
    13# include <BALL/KERNEL/protein.h>
    │ │ │ -
    14#endif
    │ │ │ -
    15
    │ │ │ -
    16#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ -
    17# include <BALL/DATATYPE/options.h>
    │ │ │ -
    18#endif
    │ │ │ -
    19
    │ │ │ -
    20#ifndef BALL_CONCEPT_EMBEDDABLE_H
    │ │ │ -
    21# include <BALL/CONCEPT/embeddable.h>
    │ │ │ -
    22#endif
    │ │ │ -
    23
    │ │ │ -
    24namespace BALL
    │ │ │ -
    25{
    │ │ │ -
    26
    │ │ │ -
    27 namespace Peptides
    │ │ │ -
    28 {
    │ │ │ -
    33
    │ │ │ -
    35 typedef std::list<String> ThreeLetterAASequence;
    │ │ │ -
    36
    │ │ │ -
    38 typedef String OneLetterAASequence;
    │ │ │ -
    40
    │ │ │ +
    4// $Id: point.h,v 1.10.16.1 2007-03-25 21:26:10 oliver Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_VIEW_PRIMITIVES_POINT_H
    │ │ │ +
    8#define BALL_VIEW_PRIMITIVES_POINT_H
    │ │ │ +
    9
    │ │ │ +
    10#ifndef BALL_VIEW_KERNEL_GEOMETRICOBJECT_H
    │ │ │ +
    11# include <BALL/VIEW/KERNEL/geometricObject.h>
    │ │ │ +
    12#endif
    │ │ │ +
    13
    │ │ │ +
    14#ifndef BALL_VIEW_DATATYPE_VERTEX1_H
    │ │ │ +
    15# include <BALL/VIEW/DATATYPE/vertex1.h>
    │ │ │ +
    16#endif
    │ │ │ +
    17
    │ │ │ +
    18namespace BALL
    │ │ │ +
    19{
    │ │ │ +
    20 namespace VIEW
    │ │ │ +
    21 {
    │ │ │ +
    22
    │ │ │ +
    │ │ │ +
    34 class BALL_VIEW_EXPORT Point
    │ │ │ +
    35 : public GeometricObject,
    │ │ │ +
    36 public Vertex
    │ │ │ +
    37 {
    │ │ │ +
    38 public:
    │ │ │ +
    39
    │ │ │ +
    40 BALL_CREATE(Point)
    │ │ │ +
    41
    │ │ │ +
    42
    │ │ │
    45
    │ │ │ -
    50 BALL_EXPORT char OneLetterCode(const String& aa);
    │ │ │ -
    51
    │ │ │ -
    57 BALL_EXPORT String ThreeLetterCode(char aa);
    │ │ │ -
    58
    │ │ │ -
    64 BALL_EXPORT bool IsOneLetterCode(char aa);
    │ │ │ -
    65
    │ │ │ -
    71 BALL_EXPORT bool IsThreeLetterCode(const String& aa);
    │ │ │ -
    72
    │ │ │ -
    76 BALL_EXPORT OneLetterAASequence ThreeLetterToOneLetter(const ThreeLetterAASequence& sequence);
    │ │ │ -
    77
    │ │ │ -
    81 BALL_EXPORT ThreeLetterAASequence OneLetterToThreeLetter(const OneLetterAASequence& sequence);
    │ │ │ -
    82
    │ │ │ -
    88 BALL_EXPORT OneLetterAASequence GetSequence(const Protein& protein);
    │ │ │ -
    89
    │ │ │ -
    95 BALL_EXPORT OneLetterAASequence GetSequence(const Chain& chain);
    │ │ │ -
    96
    │ │ │ -
    102 BALL_EXPORT OneLetterAASequence GetSequence(ResidueConstIterator it);
    │ │ │ -
    104
    │ │ │ -
    106//
    │ │ │ -
    108
    │ │ │ -
    │ │ │ -
    150 class BALL_EXPORT NameConverter
    │ │ │ -
    151 : public Embeddable
    │ │ │ -
    152 {
    │ │ │ -
    153 public:
    │ │ │ -
    154 BALL_EMBEDDABLE(NameConverter, Embeddable)
    │ │ │ -
    155
    │ │ │ -
    156
    │ │ │ -
    159
    │ │ │ -
    160 static const String VALUE_NA;
    │ │ │ -
    161
    │ │ │ -
    │ │ │ -
    163 struct BALL_EXPORT Option
    │ │ │ -
    164 {
    │ │ │ -
    167 static const char* INIFile;
    │ │ │ -
    168
    │ │ │ -
    171 static const char* PSEUDO_ATOMS_INIFile;
    │ │ │ -
    172
    │ │ │ -
    173 };
    │ │ │ -
    │ │ │ -
    174
    │ │ │ -
    │ │ │ -
    176 struct BALL_EXPORT Default
    │ │ │ -
    177 {
    │ │ │ -
    178 static const String INIFile;
    │ │ │ -
    179 static const String PSEUDO_ATOMS_INIFile;
    │ │ │ -
    180 };
    │ │ │ -
    │ │ │ -
    181
    │ │ │ -
    184 NameConverter();
    │ │ │ -
    185
    │ │ │ -
    187 virtual ~NameConverter() {}
    │ │ │ -
    188
    │ │ │ -
    191 void setDefaultOptions();
    │ │ │ -
    192
    │ │ │ -
    198 bool supportsNamingScheme(const String& scheme_name) const;
    │ │ │ -
    199
    │ │ │ -
    205 bool supportsPseudoAtomNamingScheme(const String& scheme_name) const;
    │ │ │ -
    206
    │ │ │ -
    214 String convertName(const String& amino_acid, const String& old_atom_name,
    │ │ │ -
    215 const String& old_naming_scheme, const String& new_naming_scheme) const;
    │ │ │ -
    216
    │ │ │ -
    226 bool matches(const String& amino_acid, const String& old_atom_name,
    │ │ │ -
    227 const String& old_naming_scheme, const String& new_atom_name,
    │ │ │ -
    228 const String& new_naming_scheme) const;
    │ │ │ -
    229
    │ │ │ -
    241 std::vector<String> resolvePseudoAtoms(const String& amino_acid, const String& atom_name,
    │ │ │ -
    242 const String& old_naming_scheme, const String& new_naming_scheme) const;
    │ │ │ -
    243
    │ │ │ -
    248 Options options;
    │ │ │ -
    250
    │ │ │ -
    251 protected:
    │ │ │ -
    252
    │ │ │ -
    256 void readConversionTable_();
    │ │ │ -
    257
    │ │ │ -
    261 void readPseudoAtomsConversionTable_();
    │ │ │ -
    262
    │ │ │ -
    263 std::vector<String> conventions_;
    │ │ │ -
    264 std::vector< std::vector <String> > conversion_table_;
    │ │ │ -
    265
    │ │ │ -
    266 std::vector<String> pseudo_conventions_;
    │ │ │ -
    267 std::vector< std::vector <std::vector <String> > > pseudo_conversion_table_;
    │ │ │ -
    268
    │ │ │ -
    269 //TODO: unse a StringHashMap of amino acid names to simplify the access
    │ │ │ -
    270 };
    │ │ │ -
    │ │ │ -
    271
    │ │ │ -
    272 } // namespace Peptides
    │ │ │ -
    273
    │ │ │ -
    274} // namespace BALL
    │ │ │ -
    275
    │ │ │ -
    276#endif // BALL_STRUCTURE_PEPTIDES_H_
    │ │ │ -
    277
    │ │ │ -
    278
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_EMBEDDABLE
    #define BALL_EMBEDDABLE(TYPE, BASE)
    Definition embeddable.h:31
    │ │ │ - │ │ │ -
    BALL::ResidueConstIterator
    ConstBidirectionalIterator< Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraits > ResidueConstIterator
    Definition residueIterator.h:67
    │ │ │ -
    BALL::Peptides::ThreeLetterToOneLetter
    BALL_EXPORT OneLetterAASequence ThreeLetterToOneLetter(const ThreeLetterAASequence &sequence)
    │ │ │ -
    BALL::Peptides::GetSequence
    BALL_EXPORT OneLetterAASequence GetSequence(const Protein &protein)
    │ │ │ -
    BALL::Peptides::OneLetterCode
    BALL_EXPORT char OneLetterCode(const String &aa)
    │ │ │ -
    BALL::Peptides::IsOneLetterCode
    BALL_EXPORT bool IsOneLetterCode(char aa)
    │ │ │ -
    BALL::Peptides::ThreeLetterAASequence
    std::list< String > ThreeLetterAASequence
    An amino acid sequence in three-letter code.
    Definition peptides.h:35
    │ │ │ -
    BALL::Peptides::OneLetterToThreeLetter
    BALL_EXPORT ThreeLetterAASequence OneLetterToThreeLetter(const OneLetterAASequence &sequence)
    │ │ │ -
    BALL::Peptides::IsThreeLetterCode
    BALL_EXPORT bool IsThreeLetterCode(const String &aa)
    │ │ │ -
    BALL::Peptides::ThreeLetterCode
    BALL_EXPORT String ThreeLetterCode(char aa)
    │ │ │ -
    BALL::Peptides::OneLetterAASequence
    String OneLetterAASequence
    An amino acid sequence in one-letter code.
    Definition peptides.h:38
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Peptides::NameConverter
    This class provides conversion of atom names between naming schemata.
    Definition peptides.h:152
    │ │ │ -
    BALL::Peptides::NameConverter::~NameConverter
    virtual ~NameConverter()
    Destructor.
    Definition peptides.h:187
    │ │ │ -
    BALL::Peptides::NameConverter::pseudo_conversion_table_
    std::vector< std::vector< std::vector< String > > > pseudo_conversion_table_
    Definition peptides.h:267
    │ │ │ -
    BALL::Peptides::NameConverter::supportsPseudoAtomNamingScheme
    bool supportsPseudoAtomNamingScheme(const String &scheme_name) const
    │ │ │ - │ │ │ -
    BALL::Peptides::NameConverter::pseudo_conventions_
    std::vector< String > pseudo_conventions_
    Definition peptides.h:266
    │ │ │ -
    BALL::Peptides::NameConverter::conversion_table_
    std::vector< std::vector< String > > conversion_table_
    Definition peptides.h:264
    │ │ │ -
    BALL::Peptides::NameConverter::resolvePseudoAtoms
    std::vector< String > resolvePseudoAtoms(const String &amino_acid, const String &atom_name, const String &old_naming_scheme, const String &new_naming_scheme) const
    │ │ │ - │ │ │ -
    BALL::Peptides::NameConverter::matches
    bool matches(const String &amino_acid, const String &old_atom_name, const String &old_naming_scheme, const String &new_atom_name, const String &new_naming_scheme) const
    │ │ │ - │ │ │ -
    BALL::Peptides::NameConverter::supportsNamingScheme
    bool supportsNamingScheme(const String &scheme_name) const
    │ │ │ -
    BALL::Peptides::NameConverter::conventions_
    std::vector< String > conventions_
    Definition peptides.h:263
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Peptides::NameConverter::convertName
    String convertName(const String &amino_acid, const String &old_atom_name, const String &old_naming_scheme, const String &new_naming_scheme) const
    │ │ │ - │ │ │ -
    BALL::Peptides::NameConverter::Option::PSEUDO_ATOMS_INIFile
    static const char * PSEUDO_ATOMS_INIFile
    Definition peptides.h:171
    │ │ │ - │ │ │ -
    BALL::Peptides::NameConverter::Default
    Default values for options.
    Definition peptides.h:177
    │ │ │ -
    BALL::Peptides::NameConverter::Default::PSEUDO_ATOMS_INIFile
    static const String PSEUDO_ATOMS_INIFile
    Definition peptides.h:179
    │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    46
    │ │ │ +
    52 Point();
    │ │ │ +
    53
    │ │ │ +
    56 Point(const Point& point);
    │ │ │ +
    57
    │ │ │ +
    59
    │ │ │ +
    61
    │ │ │ +
    64 virtual ~Point();
    │ │ │ +
    65
    │ │ │ +
    70 virtual void clear();
    │ │ │ +
    71
    │ │ │ +
    73
    │ │ │ +
    76
    │ │ │ +
    79 void set(const Point& point);
    │ │ │ +
    80
    │ │ │ +
    84 const Point& operator = (const Point& point);
    │ │ │ +
    85
    │ │ │ +
    90 void swap(Point& point);
    │ │ │ +
    91
    │ │ │ +
    93
    │ │ │ +
    95
    │ │ │ +
    98 virtual bool isValid() const;
    │ │ │ +
    99
    │ │ │ +
    110 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ +
    111
    │ │ │ +
    112 // Method to get all vertices from a geometric object
    │ │ │ +
    113 virtual void getVertices(vector<Vector3>& vertices) const;
    │ │ │ +
    114
    │ │ │ +
    116
    │ │ │ +
    117 };
    │ │ │ +
    │ │ │ +
    118
    │ │ │ +
    119 } // namespace VIEW
    │ │ │ +
    120} // namespace BALL
    │ │ │ +
    121
    │ │ │ +
    122#endif // BALL_VIEW_PRIMITIVES_POINT_H
    │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ +
    std
    STL namespace.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,251 +1,99 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _S_T_R_U_C_T_U_R_E │ │ │ │ -peptides.h │ │ │ │ + * _V_I_E_W │ │ │ │ + * _P_R_I_M_I_T_I_V_E_S │ │ │ │ +point.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_STRUCTURE_PEPTIDES_H │ │ │ │ -6#define BALL_STRUCTURE_PEPTIDES_H │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_COMMON_H │ │ │ │ -9# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12#ifndef BALL_KERNEL_PROTEIN_H │ │ │ │ -13# include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_o_t_e_i_n_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ -17# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ -18#endif │ │ │ │ -19 │ │ │ │ -20#ifndef BALL_CONCEPT_EMBEDDABLE_H │ │ │ │ -21# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_e_m_b_e_d_d_a_b_l_e_._h> │ │ │ │ -22#endif │ │ │ │ -23 │ │ │ │ -24namespace _B_A_L_L │ │ │ │ -25{ │ │ │ │ -26 │ │ │ │ -27 namespace Peptides │ │ │ │ -28 { │ │ │ │ -33 │ │ │ │ -_3_5 typedef std::list _T_h_r_e_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e; │ │ │ │ -36 │ │ │ │ -_3_8 typedef _S_t_r_i_n_g _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e; │ │ │ │ -40 │ │ │ │ +4// $Id: point.h,v 1.10.16.1 2007-03-25 21:26:10 oliver Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_VIEW_PRIMITIVES_POINT_H │ │ │ │ +8#define BALL_VIEW_PRIMITIVES_POINT_H │ │ │ │ +9 │ │ │ │ +10#ifndef BALL_VIEW_KERNEL_GEOMETRICOBJECT_H │ │ │ │ +11# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_g_e_o_m_e_t_r_i_c_O_b_j_e_c_t_._h> │ │ │ │ +12#endif │ │ │ │ +13 │ │ │ │ +14#ifndef BALL_VIEW_DATATYPE_VERTEX1_H │ │ │ │ +15# include <_B_A_L_L_/_V_I_E_W_/_D_A_T_A_T_Y_P_E_/_v_e_r_t_e_x_1_._h> │ │ │ │ +16#endif │ │ │ │ +17 │ │ │ │ +18namespace _B_A_L_L │ │ │ │ +19{ │ │ │ │ +20 namespace VIEW │ │ │ │ +21 { │ │ │ │ +22 │ │ │ │ +_3_4 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _P_o_i_n_t │ │ │ │ +35 : public _G_e_o_m_e_t_r_i_c_O_b_j_e_c_t, │ │ │ │ +36 public _V_e_r_t_e_x │ │ │ │ +37 { │ │ │ │ +38 public: │ │ │ │ +39 │ │ │ │ +40 _B_A_L_L___C_R_E_A_T_E(_P_o_i_n_t) │ │ │ │ +41 │ │ │ │ +42 │ │ │ │ 45 │ │ │ │ -_5_0 _B_A_L_L___E_X_P_O_R_T char _O_n_e_L_e_t_t_e_r_C_o_d_e(const _S_t_r_i_n_g& aa); │ │ │ │ -51 │ │ │ │ -_5_7 _B_A_L_L___E_X_P_O_R_T _S_t_r_i_n_g _T_h_r_e_e_L_e_t_t_e_r_C_o_d_e(char aa); │ │ │ │ -58 │ │ │ │ -_6_4 _B_A_L_L___E_X_P_O_R_T bool _I_s_O_n_e_L_e_t_t_e_r_C_o_d_e(char aa); │ │ │ │ +46 │ │ │ │ +_5_2 _P_o_i_n_t(); │ │ │ │ +53 │ │ │ │ +_5_6 _P_o_i_n_t(const _P_o_i_n_t& point); │ │ │ │ +57 │ │ │ │ +59 │ │ │ │ +61 │ │ │ │ +_6_4 virtual ~_P_o_i_n_t(); │ │ │ │ 65 │ │ │ │ -_7_1 _B_A_L_L___E_X_P_O_R_T bool _I_s_T_h_r_e_e_L_e_t_t_e_r_C_o_d_e(const _S_t_r_i_n_g& aa); │ │ │ │ -72 │ │ │ │ -_7_6 _B_A_L_L___E_X_P_O_R_T _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e _T_h_r_e_e_L_e_t_t_e_r_T_o_O_n_e_L_e_t_t_e_r(const │ │ │ │ -_T_h_r_e_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e& sequence); │ │ │ │ -77 │ │ │ │ -_8_1 _B_A_L_L___E_X_P_O_R_T _T_h_r_e_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e _O_n_e_L_e_t_t_e_r_T_o_T_h_r_e_e_L_e_t_t_e_r(const │ │ │ │ -_O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e& sequence); │ │ │ │ -82 │ │ │ │ -_8_8 _B_A_L_L___E_X_P_O_R_T _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e _G_e_t_S_e_q_u_e_n_c_e(const _P_r_o_t_e_i_n& protein); │ │ │ │ -89 │ │ │ │ -_9_5 _B_A_L_L___E_X_P_O_R_T _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e _G_e_t_S_e_q_u_e_n_c_e(const _C_h_a_i_n& chain); │ │ │ │ -96 │ │ │ │ -_1_0_2 _B_A_L_L___E_X_P_O_R_T _O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e _G_e_t_S_e_q_u_e_n_c_e(_R_e_s_i_d_u_e_C_o_n_s_t_I_t_e_r_a_t_o_r it); │ │ │ │ -104 │ │ │ │ -106// │ │ │ │ -108 │ │ │ │ -_1_5_0 class _B_A_L_L___E_X_P_O_R_T _N_a_m_e_C_o_n_v_e_r_t_e_r │ │ │ │ -151 : public _E_m_b_e_d_d_a_b_l_e │ │ │ │ -152 { │ │ │ │ -153 public: │ │ │ │ -154 _B_A_L_L___E_M_B_E_D_D_A_B_L_E(_N_a_m_e_C_o_n_v_e_r_t_e_r, _E_m_b_e_d_d_a_b_l_e) │ │ │ │ -155 │ │ │ │ -156 │ │ │ │ -159 │ │ │ │ -_1_6_0 static const _S_t_r_i_n_g VALUE_NA; │ │ │ │ -161 │ │ │ │ -_1_6_3 struct _B_A_L_L___E_X_P_O_R_T _O_p_t_i_o_n │ │ │ │ -164 { │ │ │ │ -_1_6_7 static const char* _I_N_I_F_i_l_e; │ │ │ │ -168 │ │ │ │ -_1_7_1 static const char* _P_S_E_U_D_O___A_T_O_M_S___I_N_I_F_i_l_e; │ │ │ │ -172 │ │ │ │ -173 }; │ │ │ │ -174 │ │ │ │ -_1_7_6 struct _B_A_L_L___E_X_P_O_R_T _D_e_f_a_u_l_t │ │ │ │ -177 { │ │ │ │ -_1_7_8 static const _S_t_r_i_n_g _I_N_I_F_i_l_e; │ │ │ │ -_1_7_9 static const _S_t_r_i_n_g _P_S_E_U_D_O___A_T_O_M_S___I_N_I_F_i_l_e; │ │ │ │ -180 }; │ │ │ │ -181 │ │ │ │ -_1_8_4 _N_a_m_e_C_o_n_v_e_r_t_e_r(); │ │ │ │ -185 │ │ │ │ -_1_8_7 virtual _~_N_a_m_e_C_o_n_v_e_r_t_e_r() {} │ │ │ │ -188 │ │ │ │ -_1_9_1 void _s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s(); │ │ │ │ -192 │ │ │ │ -_1_9_8 bool _s_u_p_p_o_r_t_s_N_a_m_i_n_g_S_c_h_e_m_e(const _S_t_r_i_n_g& scheme_name) const; │ │ │ │ -199 │ │ │ │ -_2_0_5 bool _s_u_p_p_o_r_t_s_P_s_e_u_d_o_A_t_o_m_N_a_m_i_n_g_S_c_h_e_m_e(const _S_t_r_i_n_g& scheme_name) const; │ │ │ │ -206 │ │ │ │ -_2_1_4 _S_t_r_i_n_g _c_o_n_v_e_r_t_N_a_m_e(const _S_t_r_i_n_g& amino_acid, const _S_t_r_i_n_g& old_atom_name, │ │ │ │ -215 const _S_t_r_i_n_g& old_naming_scheme, const _S_t_r_i_n_g& new_naming_scheme) const; │ │ │ │ -216 │ │ │ │ -_2_2_6 bool _m_a_t_c_h_e_s(const _S_t_r_i_n_g& amino_acid, const _S_t_r_i_n_g& old_atom_name, │ │ │ │ -227 const _S_t_r_i_n_g& old_naming_scheme, const _S_t_r_i_n_g& new_atom_name, │ │ │ │ -228 const _S_t_r_i_n_g& new_naming_scheme) const; │ │ │ │ -229 │ │ │ │ -_2_4_1 std::vector _r_e_s_o_l_v_e_P_s_e_u_d_o_A_t_o_m_s(const _S_t_r_i_n_g& amino_acid, const │ │ │ │ -_S_t_r_i_n_g& atom_name, │ │ │ │ -242 const _S_t_r_i_n_g& old_naming_scheme, const _S_t_r_i_n_g& new_naming_scheme) const; │ │ │ │ -243 │ │ │ │ -_2_4_8 _O_p_t_i_o_n_s _o_p_t_i_o_n_s; │ │ │ │ -250 │ │ │ │ -251 protected: │ │ │ │ -252 │ │ │ │ -_2_5_6 void _r_e_a_d_C_o_n_v_e_r_s_i_o_n_T_a_b_l_e__(); │ │ │ │ -257 │ │ │ │ -_2_6_1 void _r_e_a_d_P_s_e_u_d_o_A_t_o_m_s_C_o_n_v_e_r_s_i_o_n_T_a_b_l_e__(); │ │ │ │ -262 │ │ │ │ -_2_6_3 std::vector _c_o_n_v_e_n_t_i_o_n_s__; │ │ │ │ -_2_6_4 std::vector< std::vector > _c_o_n_v_e_r_s_i_o_n___t_a_b_l_e__; │ │ │ │ -265 │ │ │ │ -_2_6_6 std::vector _p_s_e_u_d_o___c_o_n_v_e_n_t_i_o_n_s__; │ │ │ │ -_2_6_7 std::vector< std::vector > > │ │ │ │ -_p_s_e_u_d_o___c_o_n_v_e_r_s_i_o_n___t_a_b_l_e__; │ │ │ │ -268 │ │ │ │ -269 //TODO: unse a StringHashMap of amino acid names to simplify the access │ │ │ │ -270 }; │ │ │ │ -271 │ │ │ │ -272 } // namespace Peptides │ │ │ │ -273 │ │ │ │ -274} // namespace BALL │ │ │ │ -275 │ │ │ │ -276#endif // BALL_STRUCTURE_PEPTIDES_H_ │ │ │ │ -277 │ │ │ │ -278 │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_p_r_o_t_e_i_n_._h │ │ │ │ -_o_p_t_i_o_n_s_._h │ │ │ │ -_e_m_b_e_d_d_a_b_l_e_._h │ │ │ │ -_B_A_L_L___E_M_B_E_D_D_A_B_L_E │ │ │ │ -#define BALL_EMBEDDABLE(TYPE, BASE) │ │ │ │ -DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_3_1 │ │ │ │ +_7_0 virtual void clear(); │ │ │ │ +71 │ │ │ │ +73 │ │ │ │ +76 │ │ │ │ +_7_9 void set(const _P_o_i_n_t& point); │ │ │ │ +80 │ │ │ │ +_8_4 const _P_o_i_n_t& operator = (const _P_o_i_n_t& point); │ │ │ │ +85 │ │ │ │ +_9_0 void swap(_P_o_i_n_t& point); │ │ │ │ +91 │ │ │ │ +93 │ │ │ │ +95 │ │ │ │ +_9_8 virtual bool isValid() const; │ │ │ │ +99 │ │ │ │ +_1_1_0 virtual void dump(_s_t_d::ostream& s = _s_t_d::cout, _S_i_z_e depth = 0) const; │ │ │ │ +111 │ │ │ │ +112 // Method to get all vertices from a geometric object │ │ │ │ +_1_1_3 virtual void getVertices(vector<_V_e_c_t_o_r_3>& vertices) const; │ │ │ │ +114 │ │ │ │ +116 │ │ │ │ +117 }; │ │ │ │ +118 │ │ │ │ +119 } // namespace VIEW │ │ │ │ +120} // namespace BALL │ │ │ │ +121 │ │ │ │ +122#endif // BALL_VIEW_PRIMITIVES_POINT_H │ │ │ │ +_g_e_o_m_e_t_r_i_c_O_b_j_e_c_t_._h │ │ │ │ +_v_e_r_t_e_x_1_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_s_t_d │ │ │ │ +STL namespace. │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_R_e_s_i_d_u_e_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ -ConstBidirectionalIterator< Composite, Residue, Composite::CompositeIterator, │ │ │ │ -ResidueIteratorTraits > ResidueConstIterator │ │ │ │ -DDeeffiinniittiioonn _r_e_s_i_d_u_e_I_t_e_r_a_t_o_r_._h_:_6_7 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_T_h_r_e_e_L_e_t_t_e_r_T_o_O_n_e_L_e_t_t_e_r │ │ │ │ -BALL_EXPORT OneLetterAASequence ThreeLetterToOneLetter(const │ │ │ │ -ThreeLetterAASequence &sequence) │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_G_e_t_S_e_q_u_e_n_c_e │ │ │ │ -BALL_EXPORT OneLetterAASequence GetSequence(const Protein &protein) │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_O_n_e_L_e_t_t_e_r_C_o_d_e │ │ │ │ -BALL_EXPORT char OneLetterCode(const String &aa) │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_I_s_O_n_e_L_e_t_t_e_r_C_o_d_e │ │ │ │ -BALL_EXPORT bool IsOneLetterCode(char aa) │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_T_h_r_e_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e │ │ │ │ -std::list< String > ThreeLetterAASequence │ │ │ │ -An amino acid sequence in three-letter code. │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_O_n_e_L_e_t_t_e_r_T_o_T_h_r_e_e_L_e_t_t_e_r │ │ │ │ -BALL_EXPORT ThreeLetterAASequence OneLetterToThreeLetter(const │ │ │ │ -OneLetterAASequence &sequence) │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_I_s_T_h_r_e_e_L_e_t_t_e_r_C_o_d_e │ │ │ │ -BALL_EXPORT bool IsThreeLetterCode(const String &aa) │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_T_h_r_e_e_L_e_t_t_e_r_C_o_d_e │ │ │ │ -BALL_EXPORT String ThreeLetterCode(char aa) │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_O_n_e_L_e_t_t_e_r_A_A_S_e_q_u_e_n_c_e │ │ │ │ -String OneLetterAASequence │ │ │ │ -An amino acid sequence in one-letter code. │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_3_8 │ │ │ │ -_B_A_L_L_:_:_E_m_b_e_d_d_a_b_l_e │ │ │ │ -DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_8_2 │ │ │ │ -_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ -DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_C_h_a_i_n │ │ │ │ -DDeeffiinniittiioonn _c_h_a_i_n_._h_:_3_2 │ │ │ │ -_B_A_L_L_:_:_P_r_o_t_e_i_n │ │ │ │ -DDeeffiinniittiioonn _p_r_o_t_e_i_n_._h_:_3_0 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r │ │ │ │ -This class provides conversion of atom names between naming schemata. │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_1_5_2 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_~_N_a_m_e_C_o_n_v_e_r_t_e_r │ │ │ │ -virtual ~NameConverter() │ │ │ │ -Destructor. │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_1_8_7 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_p_s_e_u_d_o___c_o_n_v_e_r_s_i_o_n___t_a_b_l_e__ │ │ │ │ -std::vector< std::vector< std::vector< String > > > pseudo_conversion_table_ │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_2_6_7 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_s_u_p_p_o_r_t_s_P_s_e_u_d_o_A_t_o_m_N_a_m_i_n_g_S_c_h_e_m_e │ │ │ │ -bool supportsPseudoAtomNamingScheme(const String &scheme_name) const │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_r_e_a_d_P_s_e_u_d_o_A_t_o_m_s_C_o_n_v_e_r_s_i_o_n_T_a_b_l_e__ │ │ │ │ -void readPseudoAtomsConversionTable_() │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_p_s_e_u_d_o___c_o_n_v_e_n_t_i_o_n_s__ │ │ │ │ -std::vector< String > pseudo_conventions_ │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_2_6_6 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_c_o_n_v_e_r_s_i_o_n___t_a_b_l_e__ │ │ │ │ -std::vector< std::vector< String > > conversion_table_ │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_2_6_4 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_r_e_s_o_l_v_e_P_s_e_u_d_o_A_t_o_m_s │ │ │ │ -std::vector< String > resolvePseudoAtoms(const String &amino_acid, const String │ │ │ │ -&atom_name, const String &old_naming_scheme, const String &new_naming_scheme) │ │ │ │ -const │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_o_p_t_i_o_n_s │ │ │ │ -Options options │ │ │ │ -options │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_2_4_8 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_m_a_t_c_h_e_s │ │ │ │ -bool matches(const String &amino_acid, const String &old_atom_name, const │ │ │ │ -String &old_naming_scheme, const String &new_atom_name, const String │ │ │ │ -&new_naming_scheme) const │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_s_e_t_D_e_f_a_u_l_t_O_p_t_i_o_n_s │ │ │ │ -void setDefaultOptions() │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_s_u_p_p_o_r_t_s_N_a_m_i_n_g_S_c_h_e_m_e │ │ │ │ -bool supportsNamingScheme(const String &scheme_name) const │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_c_o_n_v_e_n_t_i_o_n_s__ │ │ │ │ -std::vector< String > conventions_ │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_2_6_3 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_r_e_a_d_C_o_n_v_e_r_s_i_o_n_T_a_b_l_e__ │ │ │ │ -void readConversionTable_() │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r │ │ │ │ -NameConverter() │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_c_o_n_v_e_r_t_N_a_m_e │ │ │ │ -String convertName(const String &amino_acid, const String &old_atom_name, const │ │ │ │ -String &old_naming_scheme, const String &new_naming_scheme) const │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_O_p_t_i_o_n │ │ │ │ -Option names. │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_1_6_4 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_O_p_t_i_o_n_:_:_P_S_E_U_D_O___A_T_O_M_S___I_N_I_F_i_l_e │ │ │ │ -static const char * PSEUDO_ATOMS_INIFile │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_1_7_1 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_O_p_t_i_o_n_:_:_I_N_I_F_i_l_e │ │ │ │ -static const char * INIFile │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_1_6_7 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_D_e_f_a_u_l_t │ │ │ │ -Default values for options. │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_1_7_7 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_D_e_f_a_u_l_t_:_:_P_S_E_U_D_O___A_T_O_M_S___I_N_I_F_i_l_e │ │ │ │ -static const String PSEUDO_ATOMS_INIFile │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_1_7_9 │ │ │ │ -_B_A_L_L_:_:_P_e_p_t_i_d_e_s_:_:_N_a_m_e_C_o_n_v_e_r_t_e_r_:_:_D_e_f_a_u_l_t_:_:_I_N_I_F_i_l_e │ │ │ │ -static const String INIFile │ │ │ │ -DDeeffiinniittiioonn _p_e_p_t_i_d_e_s_._h_:_1_7_8 │ │ │ │ -_B_A_L_L___E_X_P_O_R_T │ │ │ │ -#define BALL_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_V_e_r_t_e_x │ │ │ │ +DDeeffiinniittiioonn _v_e_r_t_e_x_1_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_O_b_j_e_c_t │ │ │ │ +DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_O_b_j_e_c_t_._h_:_3_7 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_o_i_n_t │ │ │ │ +DDeeffiinniittiioonn _p_o_i_n_t_._h_:_3_7 │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ +#define BALL_VIEW_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d05/a08434.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Slots | │ │ │ Public Member Functions | │ │ │ List of all members │ │ │
    BALL::VIEW::DragLogView Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/WIDGETS/logView.h>

    │ │ │ +

    #include <BALL/VIEW/WIDGETS/logView.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::DragLogView:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ QTextBrowser │ │ │ @@ -106,15 +106,15 @@ │ │ │

    │ │ │ Public Member Functions

    │ │ │  DragLogView (QWidget *parent) │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 20 of file logView.h.

    │ │ │ +

    Definition at line 20 of file logView.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ DragLogView()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d07/a03482.html │ │ │ @@ -76,28 +76,28 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::TreeWidthImplementation< UndirectedGraph >::FillInHeuristic Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/DATATYPE/GRAPH/treeWidth.h>

    │ │ │ +

    #include <BALL/DATATYPE/GRAPH/treeWidth.h>

    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    VertexType & operator() (UndirectedGraph &graph)
     
    Size edgeIncreaseByEliminating (VertexIterator vertex, UndirectedGraph &graph)
     
    │ │ │

    Detailed Description

    │ │ │
    template<class UndirectedGraph>
    │ │ │ struct BALL::TreeWidthImplementation< UndirectedGraph >::FillInHeuristic

    A criterium for GreedyFillIn which search for a vertex with minimum number of additional edges after eliminating

    │ │ │ │ │ │ -

    Definition at line 299 of file treeWidth.h.

    │ │ │ +

    Definition at line 299 of file treeWidth.h.

    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ edgeIncreaseByEliminating()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d09/a00077.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: propertyEditor.h File Reference │ │ │ +BALL: RSEdge.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,63 +65,46 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    propertyEditor.h File Reference
    │ │ │ +
    RSEdge.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/COMMON/global.h>
    │ │ │ -#include <BALL/DATATYPE/hashMap.h>
    │ │ │ -#include <BALL/VIEW/UIC/ui_propertyEditor.h>
    │ │ │ -#include <BALL/VIEW/UIC/ui_propEditorWidget.h>
    │ │ │ -#include <BALL/VIEW/UIC/ui_editorPDBInfoDialog.h>
    │ │ │ -#include <BALL/FORMAT/PDBInfo.h>
    │ │ │ -#include <QtWidgets/QWidget>
    │ │ │ +
    #include <BALL/STRUCTURE/graphEdge.h>
    │ │ │ +#include <BALL/MATHS/angle.h>
    │ │ │ +#include <BALL/MATHS/circle3.h>
    │ │ │ +#include <BALL/MATHS/vector3.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::PropEditorWidget
     
    class  BALL::VIEW::BoolEditorWidget
     
    class  BALL::VIEW::IntEditorWidget
     
    class  BALL::VIEW::UIntEditorWidget
     
    class  BALL::VIEW::FloatEditorWidget
     
    class  BALL::VIEW::DoubleEditorWidget
     
    class  BALL::VIEW::StringEditorWidget
     
    class  BALL::VIEW::PropDeleteWidget
     
    class  BALL::VIEW::PDBInfoEditorWidget
     
    class  BALL::VIEW::PropertyEditor
    class  BALL::RSEdge
     
    │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │ +

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ +Functions

    Storers
    BALL_EXPORT std::ostream & BALL::operator<< (std::ostream &s, const RSEdge &rsedge)
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,46 +1,27 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _W_I_D_G_E_T_S │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -propertyEditor.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include <_B_A_L_L_/_F_O_R_M_A_T_/_P_D_B_I_n_f_o_._h> │ │ │ │ -#include │ │ │ │ +RSEdge.h File Reference │ │ │ │ +#include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_g_r_a_p_h_E_d_g_e_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_a_n_g_l_e_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_c_i_r_c_l_e_3_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_D_e_l_e_t_e_W_i_d_g_e_t │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -  │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r │ │ │ │ +class   _B_A_L_L_:_:_R_S_E_d_g_e │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │ +FFuunnccttiioonnss │ │ │ │ +Storers │ │ │ │ +_B_A_L_L___E_X_P_O_R_T std::ostream &  _B_A_L_L_:_:_o_p_e_r_a_t_o_r_<_< (std::ostream &s, const _R_S_E_d_g_e │ │ │ │ + &rsedge) │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d09/a00077_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: propertyEditor.h Source File │ │ │ +BALL: RSEdge.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,420 +70,275 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    propertyEditor.h
    │ │ │ +
    RSEdge.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1#ifndef BALL_VIEW_WIDGETS_PROPERTYEDITOR_H
    │ │ │ -
    2#define BALL_VIEW_WIDGETS_PROPERTYEDITOR_H
    │ │ │ -
    3
    │ │ │ -
    4#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ -
    5# include <BALL/COMMON/global.h>
    │ │ │ -
    6#endif
    │ │ │ +Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ +
    2// vi: set ts=2:
    │ │ │ +
    3//
    │ │ │ +
    4
    │ │ │ +
    5#ifndef BALL_STRUCTURE_RSEDGE_H
    │ │ │ +
    6#define BALL_STRUCTURE_RSEDGE_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_DATATYPE_HASHMAP_H
    │ │ │ -
    9# include <BALL/DATATYPE/hashMap.h>
    │ │ │ +
    8#ifndef BALL_STRUCTURE_GRAPHEDGE_H
    │ │ │ +
    9# include <BALL/STRUCTURE/graphEdge.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#include <BALL/VIEW/UIC/ui_propertyEditor.h>
    │ │ │ -
    13#include <BALL/VIEW/UIC/ui_propEditorWidget.h>
    │ │ │ -
    14#include <BALL/VIEW/UIC/ui_editorPDBInfoDialog.h>
    │ │ │ +
    12#ifndef BALL_MATHS_ANGLE_H
    │ │ │ +
    13# include <BALL/MATHS/angle.h>
    │ │ │ +
    14#endif
    │ │ │
    15
    │ │ │ -
    16#ifndef BALL_FORMAT_PDBINFO_H
    │ │ │ -
    17# include <BALL/FORMAT/PDBInfo.h>
    │ │ │ +
    16#ifndef BALL_MATHS_CIRCLE3_H
    │ │ │ +
    17# include <BALL/MATHS/circle3.h>
    │ │ │
    18#endif
    │ │ │
    19
    │ │ │ -
    20#include <QtWidgets/QWidget>
    │ │ │ -
    21
    │ │ │ -
    22class QLabel;
    │ │ │ -
    23class QSpinBox;
    │ │ │ -
    24class QLineEdit;
    │ │ │ -
    25class QCheckBox;
    │ │ │ -
    26
    │ │ │ -
    27namespace BALL
    │ │ │ -
    28{
    │ │ │ -
    29 class NamedProperty;
    │ │ │ -
    30 class PropertyManager;
    │ │ │ -
    31
    │ │ │ -
    32 namespace VIEW
    │ │ │ -
    33 {
    │ │ │ -
    │ │ │ -
    38 class PropEditorWidget : public QWidget
    │ │ │ -
    39 {
    │ │ │ -
    40 Q_OBJECT
    │ │ │ -
    41
    │ │ │ -
    42 public:
    │ │ │ -
    46 PropEditorWidget(const std::string& name, QWidget* parent);
    │ │ │ -
    47
    │ │ │ -
    51 virtual const QString& getName() const;
    │ │ │ -
    52
    │ │ │ -
    56 void setEditable(bool mode);
    │ │ │ -
    57
    │ │ │ -
    61 bool isEditable() const;
    │ │ │ -
    62
    │ │ │ -
    70 void apply(PropertyManager* man, bool create = false);
    │ │ │ -
    71
    │ │ │ -
    75 void reset(PropertyManager* man);
    │ │ │ -
    76
    │ │ │ -
    81 virtual PropEditorWidget* clone(const std::string& name, QWidget* parent) = 0;
    │ │ │ -
    82
    │ │ │ -
    83 Q_SIGNALS:
    │ │ │ -
    87 void deleteProperty();
    │ │ │ -
    88
    │ │ │ -
    92 void duplicateProperty();
    │ │ │ -
    93
    │ │ │ -
    97 void valueChanged();
    │ │ │ +
    20#ifndef BALL_MATHS_VECTOR3_H
    │ │ │ +
    21# include <BALL/MATHS/vector3.h>
    │ │ │ +
    22#endif
    │ │ │ +
    23
    │ │ │ +
    24namespace BALL
    │ │ │ +
    25{
    │ │ │ +
    26 class RSFace;
    │ │ │ +
    27 class RSVertex;
    │ │ │ +
    28 class ReducedSurface;
    │ │ │ +
    29 class RSComputer;
    │ │ │ +
    30 class SESEdge;
    │ │ │ +
    31 class SESFace;
    │ │ │ +
    32 class SESVertex;
    │ │ │ +
    33 class SolventExcludedSurface;
    │ │ │ +
    34 class SESComputer;
    │ │ │ +
    35 class SESSingularityCleaner;
    │ │ │ +
    36 class TriangulatedSES;
    │ │ │ +
    37 class SESTriangulator;
    │ │ │ +
    38 class SASEdge;
    │ │ │ +
    39 class SASFace;
    │ │ │ +
    40 class SASVertex;
    │ │ │ +
    41 class SolventAccessibleSurface;
    │ │ │ +
    42 class TriangulatedSAS;
    │ │ │ +
    43 class SASTriangulator;
    │ │ │ +
    44
    │ │ │ +
    │ │ │ +
    48 class BALL_EXPORT RSEdge : public GraphEdge< RSVertex,RSEdge,RSFace >
    │ │ │ +
    49 {
    │ │ │ +
    50 public:
    │ │ │ +
    51
    │ │ │ +
    74 friend class RSFace;
    │ │ │ +
    75 friend class RSVertex;
    │ │ │ +
    76 friend class ReducedSurface;
    │ │ │ +
    77 friend class RSComputer;
    │ │ │ +
    78 friend class SESEdge;
    │ │ │ +
    79 friend class SESFace;
    │ │ │ +
    80 friend class SESVertex;
    │ │ │ +
    81 friend class SolventExcludedSurface;
    │ │ │ +
    82 friend class SESComputer;
    │ │ │ +
    83 friend class SESSingularityCleaner;
    │ │ │ +
    84 friend class TriangulatedSES;
    │ │ │ +
    85 friend class SESTriangulator;
    │ │ │ +
    86 friend class SASEdge;
    │ │ │ +
    87 friend class SASFace;
    │ │ │ +
    88 friend class SolventAccessibleSurface;
    │ │ │ +
    89 friend class SASVertex;
    │ │ │ +
    90 friend class TriangulatedSAS;
    │ │ │ +
    91 friend class SASTriangulator;
    │ │ │ +
    92
    │ │ │ +
    93 BALL_CREATE(RSEdge)
    │ │ │ +
    94
    │ │ │ +
    95
    │ │ │
    98
    │ │ │ -
    99 protected:
    │ │ │ -
    100 void setupUi_();
    │ │ │ -
    101
    │ │ │ -
    105 bool addWidget_(int i, QWidget* w);
    │ │ │ -
    106
    │ │ │ -
    111 virtual void apply_(PropertyManager* man) = 0;
    │ │ │ -
    112
    │ │ │ -
    117 virtual void reset_(const NamedProperty& prop) = 0;
    │ │ │ -
    118
    │ │ │ -
    119 QString name_;
    │ │ │ -
    120 Ui::PropEditorWidget ui_;
    │ │ │ -
    121 };
    │ │ │ -
    │ │ │ -
    122
    │ │ │ -
    │ │ │ -
    123 class BoolEditorWidget : public PropEditorWidget
    │ │ │ -
    124 {
    │ │ │ -
    125 Q_OBJECT
    │ │ │ -
    126
    │ │ │ -
    127 public:
    │ │ │ -
    128 BoolEditorWidget(const NamedProperty& prop, QWidget* parent);
    │ │ │ -
    129 virtual BoolEditorWidget* clone(const std::string& name, QWidget* parent);
    │ │ │ -
    130
    │ │ │ -
    131 protected:
    │ │ │ -
    132 virtual void apply_(PropertyManager* man);
    │ │ │ -
    133 virtual void reset_(const NamedProperty& prop);
    │ │ │ -
    134
    │ │ │ -
    135 private:
    │ │ │ -
    136 QCheckBox* box_;
    │ │ │ -
    137 };
    │ │ │ -
    │ │ │ -
    138
    │ │ │ -
    │ │ │ -
    139 class IntEditorWidget : public PropEditorWidget
    │ │ │ -
    140 {
    │ │ │ -
    141 Q_OBJECT
    │ │ │ -
    142
    │ │ │ -
    143 public:
    │ │ │ -
    144 IntEditorWidget(const NamedProperty& prop, QWidget* parent);
    │ │ │ -
    145 virtual IntEditorWidget* clone(const std::string& name, QWidget* parent);
    │ │ │ -
    146
    │ │ │ -
    147 protected:
    │ │ │ -
    148 virtual void apply_(PropertyManager* man);
    │ │ │ -
    149 virtual void reset_(const NamedProperty& prop);
    │ │ │ -
    150
    │ │ │ -
    151
    │ │ │ -
    152 private:
    │ │ │ -
    153 QSpinBox* box_;
    │ │ │ -
    154 };
    │ │ │ -
    │ │ │ -
    155
    │ │ │ -
    │ │ │ -
    156 class UIntEditorWidget : public PropEditorWidget
    │ │ │ -
    157 {
    │ │ │ -
    158 Q_OBJECT
    │ │ │ +
    99
    │ │ │ +
    102 RSEdge()
    │ │ │ +
    103 ;
    │ │ │ +
    104
    │ │ │ +
    112 RSEdge(const RSEdge& rsedge, bool deep = false)
    │ │ │ +
    113 ;
    │ │ │ +
    114
    │ │ │ +
    133 RSEdge(RSVertex* vertex1,
    │ │ │ +
    134 RSVertex* vertex2,
    │ │ │ +
    135 RSFace* face1,
    │ │ │ +
    136 RSFace* face2,
    │ │ │ +
    137 const TVector3<double>& center_of_torus,
    │ │ │ +
    138 const double& radius_of_torus,
    │ │ │ +
    139 const TAngle<double>& angle,
    │ │ │ +
    140 const TCircle3<double>& circle1,
    │ │ │ +
    141 const TCircle3<double>& circle2,
    │ │ │ +
    142 const TVector3<double>& intersection_point1,
    │ │ │ +
    143 const TVector3<double>& intersection_point2,
    │ │ │ +
    144 bool singular,
    │ │ │ +
    145 Index index)
    │ │ │ +
    146 ;
    │ │ │ +
    147
    │ │ │ +
    152 virtual ~RSEdge()
    │ │ │ +
    153 ;
    │ │ │ +
    154
    │ │ │ +
    156
    │ │ │
    159
    │ │ │ -
    160 public:
    │ │ │ -
    161 UIntEditorWidget(const NamedProperty& prop, QWidget* parent);
    │ │ │ -
    162 virtual UIntEditorWidget* clone(const std::string& name, QWidget* parent);
    │ │ │ -
    163
    │ │ │ -
    164 protected:
    │ │ │ -
    165 virtual void apply_(PropertyManager* man);
    │ │ │ -
    166 virtual void reset_(const NamedProperty& prop);
    │ │ │ -
    167
    │ │ │ -
    168 private:
    │ │ │ -
    169 QSpinBox* box_;
    │ │ │ -
    170 };
    │ │ │ -
    │ │ │ -
    171
    │ │ │ -
    │ │ │ -
    172 class FloatEditorWidget : public PropEditorWidget
    │ │ │ -
    173 {
    │ │ │ -
    174 Q_OBJECT
    │ │ │ -
    175
    │ │ │ -
    176 public:
    │ │ │ -
    177 FloatEditorWidget(const NamedProperty& prop, QWidget* parent);
    │ │ │ -
    178 virtual FloatEditorWidget* clone(const std::string& name, QWidget* parent);
    │ │ │ -
    179
    │ │ │ -
    180 protected:
    │ │ │ -
    181 virtual void apply_(PropertyManager* man);
    │ │ │ -
    182 virtual void reset_(const NamedProperty& prop);
    │ │ │ -
    183
    │ │ │ -
    184 private:
    │ │ │ -
    185 QLineEdit* edit_;
    │ │ │ -
    186 };
    │ │ │ -
    │ │ │ -
    187
    │ │ │ -
    │ │ │ -
    188 class DoubleEditorWidget : public PropEditorWidget
    │ │ │ -
    189 {
    │ │ │ -
    190 Q_OBJECT
    │ │ │ -
    191
    │ │ │ -
    192 public:
    │ │ │ -
    193 DoubleEditorWidget(const NamedProperty& prop, QWidget* parent);
    │ │ │ -
    194 virtual DoubleEditorWidget* clone(const std::string& name, QWidget* parent);
    │ │ │ -
    195
    │ │ │ -
    196 protected:
    │ │ │ -
    197 virtual void apply_(PropertyManager* man);
    │ │ │ -
    198 virtual void reset_(const NamedProperty& prop);
    │ │ │ -
    199
    │ │ │ -
    200 private:
    │ │ │ -
    201 QLineEdit* edit_;
    │ │ │ -
    202 };
    │ │ │ -
    │ │ │ -
    203
    │ │ │ -
    │ │ │ -
    204 class StringEditorWidget : public PropEditorWidget
    │ │ │ -
    205 {
    │ │ │ -
    206 Q_OBJECT
    │ │ │ -
    207
    │ │ │ -
    208 public:
    │ │ │ -
    209 StringEditorWidget(const NamedProperty& prop, QWidget* parent);
    │ │ │ -
    210 virtual StringEditorWidget* clone(const std::string& name, QWidget* parent);
    │ │ │ -
    211
    │ │ │ -
    212 protected:
    │ │ │ -
    213 virtual void apply_(PropertyManager* man);
    │ │ │ -
    214 virtual void reset_(const NamedProperty& prop);
    │ │ │ -
    215
    │ │ │ -
    216 private:
    │ │ │ -
    217 QLineEdit* edit_;
    │ │ │ -
    218 };
    │ │ │ -
    │ │ │ -
    219
    │ │ │ -
    │ │ │ -
    223 class PropDeleteWidget : public PropEditorWidget
    │ │ │ -
    224 {
    │ │ │ -
    225 public:
    │ │ │ -
    │ │ │ -
    226 PropDeleteWidget(const NamedProperty& prop, QWidget* parent)
    │ │ │ -
    227 : PropEditorWidget(prop.getName(), parent)
    │ │ │ -
    228 {
    │ │ │ -
    229 addWidget_(1,new QLabel(tr("(not editable)"),this));
    │ │ │ -
    230 ui_.duplicate_button->setEnabled(false);
    │ │ │ -
    231 }
    │ │ │ -
    │ │ │ -
    │ │ │ -
    232 virtual PropEditorWidget* clone(const std::string&, QWidget*)
    │ │ │ -
    233 {
    │ │ │ -
    234 return NULL;
    │ │ │ -
    235 }
    │ │ │ -
    │ │ │ -
    236 protected:
    │ │ │ -
    237 virtual void apply_(PropertyManager *) {}
    │ │ │ -
    238 virtual void reset_(const NamedProperty &) {}
    │ │ │ -
    239 };
    │ │ │ -
    │ │ │ -
    240
    │ │ │ -
    │ │ │ -
    241 class PDBInfoEditorWidget : public PropEditorWidget
    │ │ │ -
    242 {
    │ │ │ -
    243 Q_OBJECT
    │ │ │ -
    244
    │ │ │ -
    245 public:
    │ │ │ -
    246 PDBInfoEditorWidget(const PDBInfo& info, QWidget* parent);
    │ │ │ -
    247 virtual PDBInfoEditorWidget* clone(const std::string& name, QWidget* parent);
    │ │ │ -
    248
    │ │ │ -
    249 protected Q_SLOTS:
    │ │ │ -
    250 void startEditorDialog();
    │ │ │ -
    251
    │ │ │ -
    252 protected:
    │ │ │ -
    253 virtual void apply_(PropertyManager* man);
    │ │ │ -
    254 virtual void reset_(const NamedProperty& prop);
    │ │ │ -
    255
    │ │ │ -
    256 private:
    │ │ │ -
    257 // TODO: This should maybe become a generic TextEditor and not be as hackish.
    │ │ │ -
    258 class EditorPDBInfoDialog : public QDialog {
    │ │ │ -
    259 public:
    │ │ │ -
    260 EditorPDBInfoDialog(QWidget* parent) : QDialog(parent)
    │ │ │ -
    261 {
    │ │ │ -
    262 ui_.setupUi(this);
    │ │ │ -
    263 QFont mono("Monaco"); mono.setStyleHint(QFont::TypeWriter);
    │ │ │ -
    264 ui_.textEditor->setFont(mono);
    │ │ │ -
    265 }
    │ │ │ -
    266 protected:
    │ │ │ -
    267 friend class PDBInfoEditorWidget;
    │ │ │ -
    268 Ui::editorPDBInfoDialog ui_;
    │ │ │ -
    269 };
    │ │ │ -
    270
    │ │ │ -
    271 PDBInfo localCopy_;
    │ │ │ -
    272 EditorPDBInfoDialog* editorDialog_;
    │ │ │ -
    273 };
    │ │ │ -
    │ │ │ -
    274
    │ │ │ -
    │ │ │ -
    281 class BALL_VIEW_EXPORT PropertyEditor : public QWidget
    │ │ │ -
    282 {
    │ │ │ -
    283 Q_OBJECT
    │ │ │ -
    284
    │ │ │ -
    285 public:
    │ │ │ -
    292 explicit PropertyEditor(QWidget* parent = 0, bool editable = true);
    │ │ │ -
    293
    │ │ │ -
    301 PropertyEditor(PropertyManager* manager, QWidget* parent, bool editable = true);
    │ │ │ +
    166 void set(const RSEdge& rsedge, bool deep = false)
    │ │ │ +
    167 ;
    │ │ │ +
    168
    │ │ │ +
    174 RSEdge& operator = (const RSEdge& rsedge)
    │ │ │ +
    175 ;
    │ │ │ +
    176
    │ │ │ +
    194 void set(RSVertex* vertex0,
    │ │ │ +
    195 RSVertex* vertex1,
    │ │ │ +
    196 RSFace* face0,
    │ │ │ +
    197 RSFace* face1,
    │ │ │ +
    198 const TVector3<double>& center_of_torus,
    │ │ │ +
    199 const double& radius_of_torus,
    │ │ │ +
    200 const TAngle<double>& angle,
    │ │ │ +
    201 const TCircle3<double>& circle0,
    │ │ │ +
    202 const TCircle3<double>& circle1,
    │ │ │ +
    203 const TVector3<double>& intersection_point0,
    │ │ │ +
    204 const TVector3<double>& intersection_point1,
    │ │ │ +
    205 bool singular,
    │ │ │ +
    206 Index index)
    │ │ │ +
    207 ;
    │ │ │ +
    208
    │ │ │ +
    210
    │ │ │ +
    213
    │ │ │ +
    219 void setCenterOfTorus(const TVector3<double>& center)
    │ │ │ +
    220 ;
    │ │ │ +
    221
    │ │ │ +
    227 TVector3<double> getCenterOfTorus() const
    │ │ │ +
    228 ;
    │ │ │ +
    229
    │ │ │ +
    235 void setMajorRadiusOfTorus(const double& radius)
    │ │ │ +
    236 ;
    │ │ │ +
    237
    │ │ │ +
    243 double getMajorRadiusOfTorus() const
    │ │ │ +
    244 ;
    │ │ │ +
    245
    │ │ │ +
    251 void setAngle(const TAngle<double>& angle)
    │ │ │ +
    252 ;
    │ │ │ +
    253
    │ │ │ +
    259 TAngle<double> getAngle() const
    │ │ │ +
    260 ;
    │ │ │ +
    261
    │ │ │ +
    269 void setContactCircle(Position i, const TCircle3<double>& circle)
    │ │ │ +
    270 ;
    │ │ │ +
    271
    │ │ │ +
    280 TCircle3<double> getContactCircle(Position i) const
    │ │ │ +
    281 ;
    │ │ │ +
    282
    │ │ │ +
    289 void setIntersectionPoint(Position i, const TVector3<double>& point)
    │ │ │ +
    290 ;
    │ │ │ +
    291
    │ │ │ +
    301 TVector3<double> getIntersectionPoint(Position i) const;
    │ │ │
    302
    │ │ │ -
    308 void setPropertyManager(PropertyManager* man);
    │ │ │ +
    305 void setSingular(bool singular)
    │ │ │ +
    306 ;
    │ │ │ +
    307
    │ │ │
    309
    │ │ │ -
    313 void setEditable(bool mode);
    │ │ │ +
    310
    │ │ │
    314
    │ │ │ -
    318 bool isEditable() const;
    │ │ │ -
    319
    │ │ │ -
    323 bool hasChanges() const;
    │ │ │ -
    324
    │ │ │ -
    325 public Q_SLOTS:
    │ │ │ -
    329 void apply();
    │ │ │ -
    330
    │ │ │ -
    334 void reset();
    │ │ │ +
    319 virtual bool operator == (const RSEdge& rsedge) const
    │ │ │ +
    320 ;
    │ │ │ +
    321
    │ │ │ +
    326 virtual bool operator != (const RSEdge& rsedge) const
    │ │ │ +
    327 ;
    │ │ │ +
    328
    │ │ │ +
    333 virtual bool operator *=(const RSEdge& rsedge) const
    │ │ │ +
    334 ;
    │ │ │
    335
    │ │ │ -
    336 Q_SIGNALS:
    │ │ │ -
    340 void valueChanged();
    │ │ │ -
    341
    │ │ │ -
    342 protected:
    │ │ │ -
    343 void setupUi_();
    │ │ │ -
    344
    │ │ │ -
    345 PropEditorWidget* addProperty_(const NamedProperty& prop);
    │ │ │ -
    346 PropEditorWidget* addProperty_(PropEditorWidget* editor);
    │ │ │ -
    347 PropEditorWidget* createEditorWidget_(const NamedProperty& prop);
    │ │ │ -
    348 QString chooseName_(const QString& initial);
    │ │ │ -
    349 void deleteProperty_(PropEditorWidget* editor);
    │ │ │ +
    340 bool isSingular() const
    │ │ │ +
    341 ;
    │ │ │ +
    342
    │ │ │ +
    346 bool isFree() const
    │ │ │ +
    347 ;
    │ │ │ +
    348
    │ │ │
    350
    │ │ │ -
    351 protected Q_SLOTS:
    │ │ │ -
    352 void scheduleDelete_();
    │ │ │ -
    353 void scheduleDuplicate_();
    │ │ │ -
    354 void valueChanged_();
    │ │ │ -
    355
    │ │ │ -
    356 void createNewBool_();
    │ │ │ -
    357 void createNewInt_();
    │ │ │ -
    358 void createNewUInt_();
    │ │ │ -
    359 void createNewFloat_();
    │ │ │ -
    360 void createNewDouble_();
    │ │ │ -
    361 void createNewString_();
    │ │ │ -
    362
    │ │ │ -
    363 private:
    │ │ │ -
    364 bool has_changes_;
    │ │ │ -
    365 bool is_editable_;
    │ │ │ -
    366 PropertyManager* manager_;
    │ │ │ -
    367 QList<PropEditorWidget*> new_properties_;
    │ │ │ -
    368 QList<PropEditorWidget*> deleted_properties_;
    │ │ │ -
    369
    │ │ │ -
    370 Ui::PropertyEditor ui_;
    │ │ │ -
    371 };
    │ │ │ -
    │ │ │ -
    372
    │ │ │ -
    373 }
    │ │ │ -
    374}
    │ │ │ -
    375
    │ │ │ -
    376#endif //BALL_VIEW_WIDGETS_PROPERTYEDITOR_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::PropEditorWidget::reset_
    virtual void reset_(const NamedProperty &prop)=0
    │ │ │ -
    BALL::VIEW::PropEditorWidget::clone
    virtual PropEditorWidget * clone(const std::string &name, QWidget *parent)=0
    │ │ │ -
    BALL::VIEW::PropEditorWidget::apply
    void apply(PropertyManager *man, bool create=false)
    │ │ │ -
    BALL::VIEW::PropEditorWidget::PropEditorWidget
    PropEditorWidget(const std::string &name, QWidget *parent)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::PropEditorWidget::reset
    void reset(PropertyManager *man)
    │ │ │ -
    BALL::VIEW::PropEditorWidget::getName
    virtual const QString & getName() const
    │ │ │ -
    BALL::VIEW::PropEditorWidget::apply_
    virtual void apply_(PropertyManager *man)=0
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::PropEditorWidget::addWidget_
    bool addWidget_(int i, QWidget *w)
    │ │ │ - │ │ │ -
    BALL::VIEW::BoolEditorWidget::BoolEditorWidget
    BoolEditorWidget(const NamedProperty &prop, QWidget *parent)
    │ │ │ -
    BALL::VIEW::BoolEditorWidget::apply_
    virtual void apply_(PropertyManager *man)
    │ │ │ -
    BALL::VIEW::BoolEditorWidget::clone
    virtual BoolEditorWidget * clone(const std::string &name, QWidget *parent)
    │ │ │ -
    BALL::VIEW::BoolEditorWidget::reset_
    virtual void reset_(const NamedProperty &prop)
    │ │ │ - │ │ │ -
    BALL::VIEW::IntEditorWidget::reset_
    virtual void reset_(const NamedProperty &prop)
    │ │ │ -
    BALL::VIEW::IntEditorWidget::IntEditorWidget
    IntEditorWidget(const NamedProperty &prop, QWidget *parent)
    │ │ │ -
    BALL::VIEW::IntEditorWidget::apply_
    virtual void apply_(PropertyManager *man)
    │ │ │ -
    BALL::VIEW::IntEditorWidget::clone
    virtual IntEditorWidget * clone(const std::string &name, QWidget *parent)
    │ │ │ - │ │ │ -
    BALL::VIEW::UIntEditorWidget::reset_
    virtual void reset_(const NamedProperty &prop)
    │ │ │ -
    BALL::VIEW::UIntEditorWidget::clone
    virtual UIntEditorWidget * clone(const std::string &name, QWidget *parent)
    │ │ │ -
    BALL::VIEW::UIntEditorWidget::UIntEditorWidget
    UIntEditorWidget(const NamedProperty &prop, QWidget *parent)
    │ │ │ -
    BALL::VIEW::UIntEditorWidget::apply_
    virtual void apply_(PropertyManager *man)
    │ │ │ - │ │ │ -
    BALL::VIEW::FloatEditorWidget::clone
    virtual FloatEditorWidget * clone(const std::string &name, QWidget *parent)
    │ │ │ -
    BALL::VIEW::FloatEditorWidget::reset_
    virtual void reset_(const NamedProperty &prop)
    │ │ │ -
    BALL::VIEW::FloatEditorWidget::apply_
    virtual void apply_(PropertyManager *man)
    │ │ │ -
    BALL::VIEW::FloatEditorWidget::FloatEditorWidget
    FloatEditorWidget(const NamedProperty &prop, QWidget *parent)
    │ │ │ - │ │ │ -
    BALL::VIEW::DoubleEditorWidget::reset_
    virtual void reset_(const NamedProperty &prop)
    │ │ │ -
    BALL::VIEW::DoubleEditorWidget::apply_
    virtual void apply_(PropertyManager *man)
    │ │ │ -
    BALL::VIEW::DoubleEditorWidget::clone
    virtual DoubleEditorWidget * clone(const std::string &name, QWidget *parent)
    │ │ │ -
    BALL::VIEW::DoubleEditorWidget::DoubleEditorWidget
    DoubleEditorWidget(const NamedProperty &prop, QWidget *parent)
    │ │ │ - │ │ │ -
    BALL::VIEW::StringEditorWidget::reset_
    virtual void reset_(const NamedProperty &prop)
    │ │ │ -
    BALL::VIEW::StringEditorWidget::StringEditorWidget
    StringEditorWidget(const NamedProperty &prop, QWidget *parent)
    │ │ │ -
    BALL::VIEW::StringEditorWidget::clone
    virtual StringEditorWidget * clone(const std::string &name, QWidget *parent)
    │ │ │ -
    BALL::VIEW::StringEditorWidget::apply_
    virtual void apply_(PropertyManager *man)
    │ │ │ - │ │ │ -
    BALL::VIEW::PropDeleteWidget::reset_
    virtual void reset_(const NamedProperty &)
    Definition propertyEditor.h:238
    │ │ │ -
    BALL::VIEW::PropDeleteWidget::clone
    virtual PropEditorWidget * clone(const std::string &, QWidget *)
    Definition propertyEditor.h:232
    │ │ │ -
    BALL::VIEW::PropDeleteWidget::apply_
    virtual void apply_(PropertyManager *)
    Definition propertyEditor.h:237
    │ │ │ -
    BALL::VIEW::PropDeleteWidget::PropDeleteWidget
    PropDeleteWidget(const NamedProperty &prop, QWidget *parent)
    Definition propertyEditor.h:226
    │ │ │ - │ │ │ -
    BALL::VIEW::PDBInfoEditorWidget::clone
    virtual PDBInfoEditorWidget * clone(const std::string &name, QWidget *parent)
    │ │ │ -
    BALL::VIEW::PDBInfoEditorWidget::apply_
    virtual void apply_(PropertyManager *man)
    │ │ │ -
    BALL::VIEW::PDBInfoEditorWidget::reset_
    virtual void reset_(const NamedProperty &prop)
    │ │ │ -
    BALL::VIEW::PDBInfoEditorWidget::PDBInfoEditorWidget
    PDBInfoEditorWidget(const PDBInfo &info, QWidget *parent)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::PropertyEditor::setPropertyManager
    void setPropertyManager(PropertyManager *man)
    │ │ │ -
    BALL::VIEW::PropertyEditor::deleteProperty_
    void deleteProperty_(PropEditorWidget *editor)
    │ │ │ -
    BALL::VIEW::PropertyEditor::setEditable
    void setEditable(bool mode)
    │ │ │ -
    BALL::VIEW::PropertyEditor::PropertyEditor
    PropertyEditor(QWidget *parent=0, bool editable=true)
    │ │ │ -
    BALL::VIEW::PropertyEditor::chooseName_
    QString chooseName_(const QString &initial)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::PropertyEditor::createEditorWidget_
    PropEditorWidget * createEditorWidget_(const NamedProperty &prop)
    │ │ │ - │ │ │ -
    BALL::VIEW::PropertyEditor::addProperty_
    PropEditorWidget * addProperty_(PropEditorWidget *editor)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::PropertyEditor::addProperty_
    PropEditorWidget * addProperty_(const NamedProperty &prop)
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::PropertyEditor::PropertyEditor
    PropertyEditor(PropertyManager *manager, QWidget *parent, bool editable=true)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ +
    351 protected:
    │ │ │ +
    352
    │ │ │ +
    353 /*_ @name Attributes
    │ │ │ +
    354 */
    │ │ │ +
    356
    │ │ │ +
    357 /*_ The center of the torus described by the probe when ir rolls over
    │ │ │ +
    358 the RSEdge
    │ │ │ +
    359 */
    │ │ │ +
    360 TVector3<double> center_of_torus_;
    │ │ │ +
    361 /*_ The major radius of the torus described by the probe when ir rolls
    │ │ │ +
    362 over the RSEdge
    │ │ │ +
    363 */
    │ │ │ +
    364 double radius_of_torus_;
    │ │ │ +
    365 /*_ The rotation angle between the starting and ending position of the
    │ │ │ +
    366 probe sphere when it rolls over the RSEdge
    │ │ │ +
    367 */
    │ │ │ +
    368 TAngle<double> angle_;
    │ │ │ +
    369 /*_ The contact circle of the probe sphere with the first RSVertex
    │ │ │ +
    370 */
    │ │ │ +
    371 TCircle3<double> circle0_;
    │ │ │ +
    372 /*_ The contact circle of the probe sphere with the second RSVertex
    │ │ │ +
    373 */
    │ │ │ +
    374 TCircle3<double> circle1_;
    │ │ │ +
    375 /*_ The intersection point of the probe sphere with the RSEdge near to
    │ │ │ +
    376 the first RSVertex (in singular case).
    │ │ │ +
    377 */
    │ │ │ +
    378 TVector3<double> intersection_point0_;
    │ │ │ +
    379 /*_ The intersection point of the probe sphere with the RSEdge near to
    │ │ │ +
    380 the second RSVertex (in singular case).
    │ │ │ +
    381 */
    │ │ │ +
    382 TVector3<double> intersection_point1_;
    │ │ │ +
    383 /*_ singular
    │ │ │ +
    384 */
    │ │ │ +
    385 bool singular_;
    │ │ │ +
    386
    │ │ │ +
    388
    │ │ │ +
    389 };
    │ │ │ +
    │ │ │ +
    390
    │ │ │ +
    394
    │ │ │ +
    397 BALL_EXPORT std::ostream& operator << (std::ostream& s, const RSEdge& rsedge);
    │ │ │ +
    398
    │ │ │ +
    400
    │ │ │ +
    401
    │ │ │ +
    402
    │ │ │ +
    403} // namespace BALL
    │ │ │ +
    404
    │ │ │ +
    405#endif // BALL_STRUCTURE_RSEDGE_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ +
    std
    STL namespace.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,488 +1,293 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _W_I_D_G_E_T_S │ │ │ │ -propertyEditor.h │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ +RSEdge.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1#ifndef BALL_VIEW_WIDGETS_PROPERTYEDITOR_H │ │ │ │ -2#define BALL_VIEW_WIDGETS_PROPERTYEDITOR_H │ │ │ │ -3 │ │ │ │ -4#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ -5# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -6#endif │ │ │ │ +1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ +2// vi: set ts=2: │ │ │ │ +3// │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_STRUCTURE_RSEDGE_H │ │ │ │ +6#define BALL_STRUCTURE_RSEDGE_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_DATATYPE_HASHMAP_H │ │ │ │ -9# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_M_a_p_._h> │ │ │ │ +8#ifndef BALL_STRUCTURE_GRAPHEDGE_H │ │ │ │ +9# include <_B_A_L_L_/_S_T_R_U_C_T_U_R_E_/_g_r_a_p_h_E_d_g_e_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#include │ │ │ │ -13#include │ │ │ │ -14#include │ │ │ │ +12#ifndef BALL_MATHS_ANGLE_H │ │ │ │ +13# include <_B_A_L_L_/_M_A_T_H_S_/_a_n_g_l_e_._h> │ │ │ │ +14#endif │ │ │ │ 15 │ │ │ │ -16#ifndef BALL_FORMAT_PDBINFO_H │ │ │ │ -17# include <_B_A_L_L_/_F_O_R_M_A_T_/_P_D_B_I_n_f_o_._h> │ │ │ │ +16#ifndef BALL_MATHS_CIRCLE3_H │ │ │ │ +17# include <_B_A_L_L_/_M_A_T_H_S_/_c_i_r_c_l_e_3_._h> │ │ │ │ 18#endif │ │ │ │ 19 │ │ │ │ -20#include │ │ │ │ -21 │ │ │ │ -22class QLabel; │ │ │ │ -23class QSpinBox; │ │ │ │ -24class _Q_L_i_n_e_E_d_i_t; │ │ │ │ -25class QCheckBox; │ │ │ │ -26 │ │ │ │ -27namespace _B_A_L_L │ │ │ │ -28{ │ │ │ │ -29 class NamedProperty; │ │ │ │ -30 class PropertyManager; │ │ │ │ -31 │ │ │ │ -32 namespace VIEW │ │ │ │ -33 { │ │ │ │ -_3_8 class _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t : public _Q_W_i_d_g_e_t │ │ │ │ -39 { │ │ │ │ -40 Q_OBJECT │ │ │ │ -41 │ │ │ │ -42 public: │ │ │ │ -_4_6 _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t(const std::string& name, _Q_W_i_d_g_e_t* parent); │ │ │ │ -47 │ │ │ │ -_5_1 virtual const QString& _g_e_t_N_a_m_e() const; │ │ │ │ -52 │ │ │ │ -_5_6 void _s_e_t_E_d_i_t_a_b_l_e(bool mode); │ │ │ │ -57 │ │ │ │ -_6_1 bool _i_s_E_d_i_t_a_b_l_e() const; │ │ │ │ -62 │ │ │ │ -_7_0 void _a_p_p_l_y(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man, bool create = false); │ │ │ │ -71 │ │ │ │ -_7_5 void _r_e_s_e_t(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man); │ │ │ │ -76 │ │ │ │ -_8_1 virtual _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t* _c_l_o_n_e(const std::string& name, _Q_W_i_d_g_e_t* parent) = │ │ │ │ -0; │ │ │ │ -82 │ │ │ │ -83 Q_SIGNALS: │ │ │ │ -_8_7 void _d_e_l_e_t_e_P_r_o_p_e_r_t_y(); │ │ │ │ -88 │ │ │ │ -_9_2 void _d_u_p_l_i_c_a_t_e_P_r_o_p_e_r_t_y(); │ │ │ │ -93 │ │ │ │ -_9_7 void _v_a_l_u_e_C_h_a_n_g_e_d(); │ │ │ │ +20#ifndef BALL_MATHS_VECTOR3_H │ │ │ │ +21# include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +22#endif │ │ │ │ +23 │ │ │ │ +24namespace _B_A_L_L │ │ │ │ +25{ │ │ │ │ +26 class RSFace; │ │ │ │ +27 class RSVertex; │ │ │ │ +28 class ReducedSurface; │ │ │ │ +29 class RSComputer; │ │ │ │ +30 class SESEdge; │ │ │ │ +31 class SESFace; │ │ │ │ +32 class SESVertex; │ │ │ │ +33 class SolventExcludedSurface; │ │ │ │ +34 class SESComputer; │ │ │ │ +35 class SESSingularityCleaner; │ │ │ │ +36 class TriangulatedSES; │ │ │ │ +37 class SESTriangulator; │ │ │ │ +38 class SASEdge; │ │ │ │ +39 class SASFace; │ │ │ │ +40 class SASVertex; │ │ │ │ +41 class SolventAccessibleSurface; │ │ │ │ +42 class TriangulatedSAS; │ │ │ │ +43 class SASTriangulator; │ │ │ │ +44 │ │ │ │ +_4_8 class _B_A_L_L___E_X_P_O_R_T _R_S_E_d_g_e : public _G_r_a_p_h_E_d_g_e< RSVertex,RSEdge,RSFace > │ │ │ │ +49 { │ │ │ │ +50 public: │ │ │ │ +51 │ │ │ │ +_7_4 friend class _R_S_F_a_c_e; │ │ │ │ +_7_5 friend class _R_S_V_e_r_t_e_x; │ │ │ │ +_7_6 friend class _R_e_d_u_c_e_d_S_u_r_f_a_c_e; │ │ │ │ +_7_7 friend class _R_S_C_o_m_p_u_t_e_r; │ │ │ │ +_7_8 friend class _S_E_S_E_d_g_e; │ │ │ │ +_7_9 friend class _S_E_S_F_a_c_e; │ │ │ │ +_8_0 friend class _S_E_S_V_e_r_t_e_x; │ │ │ │ +_8_1 friend class _S_o_l_v_e_n_t_E_x_c_l_u_d_e_d_S_u_r_f_a_c_e; │ │ │ │ +_8_2 friend class _S_E_S_C_o_m_p_u_t_e_r; │ │ │ │ +_8_3 friend class _S_E_S_S_i_n_g_u_l_a_r_i_t_y_C_l_e_a_n_e_r; │ │ │ │ +_8_4 friend class _T_r_i_a_n_g_u_l_a_t_e_d_S_E_S; │ │ │ │ +_8_5 friend class _S_E_S_T_r_i_a_n_g_u_l_a_t_o_r; │ │ │ │ +_8_6 friend class _S_A_S_E_d_g_e; │ │ │ │ +_8_7 friend class _S_A_S_F_a_c_e; │ │ │ │ +_8_8 friend class _S_o_l_v_e_n_t_A_c_c_e_s_s_i_b_l_e_S_u_r_f_a_c_e; │ │ │ │ +_8_9 friend class _S_A_S_V_e_r_t_e_x; │ │ │ │ +_9_0 friend class _T_r_i_a_n_g_u_l_a_t_e_d_S_A_S; │ │ │ │ +_9_1 friend class _S_A_S_T_r_i_a_n_g_u_l_a_t_o_r; │ │ │ │ +92 │ │ │ │ +93 _B_A_L_L___C_R_E_A_T_E(_R_S_E_d_g_e) │ │ │ │ +94 │ │ │ │ +95 │ │ │ │ 98 │ │ │ │ -99 protected: │ │ │ │ -_1_0_0 void _s_e_t_u_p_U_i__(); │ │ │ │ -101 │ │ │ │ -_1_0_5 bool _a_d_d_W_i_d_g_e_t__(int i, _Q_W_i_d_g_e_t* w); │ │ │ │ -106 │ │ │ │ -_1_1_1 virtual void _a_p_p_l_y__(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man) = 0; │ │ │ │ -112 │ │ │ │ -_1_1_7 virtual void _r_e_s_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop) = 0; │ │ │ │ -118 │ │ │ │ -_1_1_9 QString _n_a_m_e__; │ │ │ │ -_1_2_0 Ui::PropEditorWidget _u_i__; │ │ │ │ -121 }; │ │ │ │ -122 │ │ │ │ -_1_2_3 class _B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t : public _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -124 { │ │ │ │ -125 Q_OBJECT │ │ │ │ -126 │ │ │ │ -127 public: │ │ │ │ -_1_2_8 _B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop, _Q_W_i_d_g_e_t* parent); │ │ │ │ -_1_2_9 virtual _B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t* _c_l_o_n_e(const std::string& name, _Q_W_i_d_g_e_t* parent); │ │ │ │ -130 │ │ │ │ -131 protected: │ │ │ │ -_1_3_2 virtual void _a_p_p_l_y__(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man); │ │ │ │ -_1_3_3 virtual void _r_e_s_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop); │ │ │ │ -134 │ │ │ │ -135 private: │ │ │ │ -136 QCheckBox* box_; │ │ │ │ -137 }; │ │ │ │ -138 │ │ │ │ -_1_3_9 class _I_n_t_E_d_i_t_o_r_W_i_d_g_e_t : public _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -140 { │ │ │ │ -141 Q_OBJECT │ │ │ │ -142 │ │ │ │ -143 public: │ │ │ │ -_1_4_4 _I_n_t_E_d_i_t_o_r_W_i_d_g_e_t(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop, _Q_W_i_d_g_e_t* parent); │ │ │ │ -_1_4_5 virtual _I_n_t_E_d_i_t_o_r_W_i_d_g_e_t* _c_l_o_n_e(const std::string& name, _Q_W_i_d_g_e_t* parent); │ │ │ │ -146 │ │ │ │ -147 protected: │ │ │ │ -_1_4_8 virtual void _a_p_p_l_y__(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man); │ │ │ │ -_1_4_9 virtual void _r_e_s_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop); │ │ │ │ -150 │ │ │ │ -151 │ │ │ │ -152 private: │ │ │ │ -153 QSpinBox* box_; │ │ │ │ -154 }; │ │ │ │ -155 │ │ │ │ -_1_5_6 class _U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t : public _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -157 { │ │ │ │ -158 Q_OBJECT │ │ │ │ +99 │ │ │ │ +_1_0_2 _R_S_E_d_g_e() │ │ │ │ +103 ; │ │ │ │ +104 │ │ │ │ +_1_1_2 _R_S_E_d_g_e(const _R_S_E_d_g_e& rsedge, bool deep = false) │ │ │ │ +113 ; │ │ │ │ +114 │ │ │ │ +_1_3_3 _R_S_E_d_g_e(_R_S_V_e_r_t_e_x* vertex1, │ │ │ │ +134 _R_S_V_e_r_t_e_x* vertex2, │ │ │ │ +135 _R_S_F_a_c_e* face1, │ │ │ │ +136 _R_S_F_a_c_e* face2, │ │ │ │ +137 const _T_V_e_c_t_o_r_3& center_of_torus, │ │ │ │ +138 const double& radius_of_torus, │ │ │ │ +139 const _T_A_n_g_l_e& angle, │ │ │ │ +140 const _T_C_i_r_c_l_e_3& circle1, │ │ │ │ +141 const _T_C_i_r_c_l_e_3& circle2, │ │ │ │ +142 const _T_V_e_c_t_o_r_3& intersection_point1, │ │ │ │ +143 const _T_V_e_c_t_o_r_3& intersection_point2, │ │ │ │ +144 bool singular, │ │ │ │ +145 _I_n_d_e_x index) │ │ │ │ +146 ; │ │ │ │ +147 │ │ │ │ +_1_5_2 virtual ~_R_S_E_d_g_e() │ │ │ │ +153 ; │ │ │ │ +154 │ │ │ │ +156 │ │ │ │ 159 │ │ │ │ -160 public: │ │ │ │ -_1_6_1 _U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop, _Q_W_i_d_g_e_t* parent); │ │ │ │ -_1_6_2 virtual _U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t* _c_l_o_n_e(const std::string& name, _Q_W_i_d_g_e_t* parent); │ │ │ │ -163 │ │ │ │ -164 protected: │ │ │ │ -_1_6_5 virtual void _a_p_p_l_y__(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man); │ │ │ │ -_1_6_6 virtual void _r_e_s_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop); │ │ │ │ -167 │ │ │ │ -168 private: │ │ │ │ -169 QSpinBox* box_; │ │ │ │ -170 }; │ │ │ │ -171 │ │ │ │ -_1_7_2 class _F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t : public _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -173 { │ │ │ │ -174 Q_OBJECT │ │ │ │ -175 │ │ │ │ -176 public: │ │ │ │ -_1_7_7 _F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop, _Q_W_i_d_g_e_t* parent); │ │ │ │ -_1_7_8 virtual _F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t* _c_l_o_n_e(const std::string& name, _Q_W_i_d_g_e_t* parent); │ │ │ │ -179 │ │ │ │ -180 protected: │ │ │ │ -_1_8_1 virtual void _a_p_p_l_y__(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man); │ │ │ │ -_1_8_2 virtual void _r_e_s_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop); │ │ │ │ -183 │ │ │ │ -184 private: │ │ │ │ -185 _Q_L_i_n_e_E_d_i_t* edit_; │ │ │ │ -186 }; │ │ │ │ -187 │ │ │ │ -_1_8_8 class _D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t : public _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -189 { │ │ │ │ -190 Q_OBJECT │ │ │ │ -191 │ │ │ │ -192 public: │ │ │ │ -_1_9_3 _D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop, _Q_W_i_d_g_e_t* parent); │ │ │ │ -_1_9_4 virtual _D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t* _c_l_o_n_e(const std::string& name, _Q_W_i_d_g_e_t* │ │ │ │ -parent); │ │ │ │ -195 │ │ │ │ -196 protected: │ │ │ │ -_1_9_7 virtual void _a_p_p_l_y__(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man); │ │ │ │ -_1_9_8 virtual void _r_e_s_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop); │ │ │ │ -199 │ │ │ │ -200 private: │ │ │ │ -201 _Q_L_i_n_e_E_d_i_t* edit_; │ │ │ │ -202 }; │ │ │ │ -203 │ │ │ │ -_2_0_4 class _S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t : public _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -205 { │ │ │ │ -206 Q_OBJECT │ │ │ │ -207 │ │ │ │ -208 public: │ │ │ │ -_2_0_9 _S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop, _Q_W_i_d_g_e_t* parent); │ │ │ │ -_2_1_0 virtual _S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t* _c_l_o_n_e(const std::string& name, _Q_W_i_d_g_e_t* │ │ │ │ -parent); │ │ │ │ -211 │ │ │ │ -212 protected: │ │ │ │ -_2_1_3 virtual void _a_p_p_l_y__(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man); │ │ │ │ -_2_1_4 virtual void _r_e_s_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop); │ │ │ │ -215 │ │ │ │ -216 private: │ │ │ │ -217 _Q_L_i_n_e_E_d_i_t* edit_; │ │ │ │ -218 }; │ │ │ │ -219 │ │ │ │ -_2_2_3 class _P_r_o_p_D_e_l_e_t_e_W_i_d_g_e_t : public _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -224 { │ │ │ │ -225 public: │ │ │ │ -_2_2_6 _P_r_o_p_D_e_l_e_t_e_W_i_d_g_e_t(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop, _Q_W_i_d_g_e_t* parent) │ │ │ │ -227 : _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t(prop._g_e_t_N_a_m_e(), parent) │ │ │ │ -228 { │ │ │ │ -229 _a_d_d_W_i_d_g_e_t__(1,new QLabel(tr("(not editable)"),this)); │ │ │ │ -230 _u_i__.duplicate_button->setEnabled(false); │ │ │ │ -231 } │ │ │ │ -_2_3_2 virtual _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t* _c_l_o_n_e(const std::string&, _Q_W_i_d_g_e_t*) │ │ │ │ -233 { │ │ │ │ -234 return NULL; │ │ │ │ -235 } │ │ │ │ -236 protected: │ │ │ │ -_2_3_7 virtual void _a_p_p_l_y__(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r *) {} │ │ │ │ -_2_3_8 virtual void _r_e_s_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y &) {} │ │ │ │ -239 }; │ │ │ │ -240 │ │ │ │ -_2_4_1 class _P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t : public _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -242 { │ │ │ │ -243 Q_OBJECT │ │ │ │ -244 │ │ │ │ -245 public: │ │ │ │ -_2_4_6 _P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t(const _P_D_B_I_n_f_o& info, _Q_W_i_d_g_e_t* parent); │ │ │ │ -_2_4_7 virtual _P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t* _c_l_o_n_e(const std::string& name, _Q_W_i_d_g_e_t* │ │ │ │ -parent); │ │ │ │ -248 │ │ │ │ -249 protected Q_SLOTS: │ │ │ │ -_2_5_0 void _s_t_a_r_t_E_d_i_t_o_r_D_i_a_l_o_g(); │ │ │ │ -251 │ │ │ │ -252 protected: │ │ │ │ -_2_5_3 virtual void _a_p_p_l_y__(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man); │ │ │ │ -_2_5_4 virtual void _r_e_s_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop); │ │ │ │ -255 │ │ │ │ -256 private: │ │ │ │ -257 // TODO: This should maybe become a generic TextEditor and not be as │ │ │ │ -hackish. │ │ │ │ -258 class EditorPDBInfoDialog : public _Q_D_i_a_l_o_g { │ │ │ │ -259 public: │ │ │ │ -260 EditorPDBInfoDialog(_Q_W_i_d_g_e_t* parent) : _Q_D_i_a_l_o_g(parent) │ │ │ │ -261 { │ │ │ │ -262 ui_.setupUi(this); │ │ │ │ -263 QFont mono("Monaco"); mono.setStyleHint(QFont::TypeWriter); │ │ │ │ -264 ui_.textEditor->setFont(mono); │ │ │ │ -265 } │ │ │ │ -266 protected: │ │ │ │ -267 friend class _P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t; │ │ │ │ -268 Ui::editorPDBInfoDialog ui_; │ │ │ │ -269 }; │ │ │ │ -270 │ │ │ │ -271 _P_D_B_I_n_f_o localCopy_; │ │ │ │ -272 EditorPDBInfoDialog* editorDialog_; │ │ │ │ -273 }; │ │ │ │ -274 │ │ │ │ -_2_8_1 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _P_r_o_p_e_r_t_y_E_d_i_t_o_r : public _Q_W_i_d_g_e_t │ │ │ │ -282 { │ │ │ │ -283 Q_OBJECT │ │ │ │ -284 │ │ │ │ -285 public: │ │ │ │ -_2_9_2 explicit _P_r_o_p_e_r_t_y_E_d_i_t_o_r(_Q_W_i_d_g_e_t* parent = 0, bool editable = true); │ │ │ │ -293 │ │ │ │ -_3_0_1 _P_r_o_p_e_r_t_y_E_d_i_t_o_r(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* manager, _Q_W_i_d_g_e_t* parent, bool editable = │ │ │ │ -true); │ │ │ │ +_1_6_6 void set(const _R_S_E_d_g_e& rsedge, bool deep = false) │ │ │ │ +167 ; │ │ │ │ +168 │ │ │ │ +_1_7_4 _R_S_E_d_g_e& operator = (const _R_S_E_d_g_e& rsedge) │ │ │ │ +175 ; │ │ │ │ +176 │ │ │ │ +_1_9_4 void set(_R_S_V_e_r_t_e_x* vertex0, │ │ │ │ +195 _R_S_V_e_r_t_e_x* vertex1, │ │ │ │ +196 _R_S_F_a_c_e* face0, │ │ │ │ +197 _R_S_F_a_c_e* face1, │ │ │ │ +198 const _T_V_e_c_t_o_r_3& center_of_torus, │ │ │ │ +199 const double& radius_of_torus, │ │ │ │ +200 const _T_A_n_g_l_e& angle, │ │ │ │ +201 const _T_C_i_r_c_l_e_3& circle0, │ │ │ │ +202 const _T_C_i_r_c_l_e_3& circle1, │ │ │ │ +203 const _T_V_e_c_t_o_r_3& intersection_point0, │ │ │ │ +204 const _T_V_e_c_t_o_r_3& intersection_point1, │ │ │ │ +205 bool singular, │ │ │ │ +206 _I_n_d_e_x index) │ │ │ │ +207 ; │ │ │ │ +208 │ │ │ │ +210 │ │ │ │ +213 │ │ │ │ +_2_1_9 void setCenterOfTorus(const _T_V_e_c_t_o_r_3& center) │ │ │ │ +220 ; │ │ │ │ +221 │ │ │ │ +_2_2_7 _T_V_e_c_t_o_r_3 getCenterOfTorus() const │ │ │ │ +228 ; │ │ │ │ +229 │ │ │ │ +_2_3_5 void setMajorRadiusOfTorus(const double& radius) │ │ │ │ +236 ; │ │ │ │ +237 │ │ │ │ +_2_4_3 double getMajorRadiusOfTorus() const │ │ │ │ +244 ; │ │ │ │ +245 │ │ │ │ +_2_5_1 void setAngle(const _T_A_n_g_l_e& angle) │ │ │ │ +252 ; │ │ │ │ +253 │ │ │ │ +_2_5_9 _T_A_n_g_l_e getAngle() const │ │ │ │ +260 ; │ │ │ │ +261 │ │ │ │ +_2_6_9 void setContactCircle(_P_o_s_i_t_i_o_n i, const _T_C_i_r_c_l_e_3& circle) │ │ │ │ +270 ; │ │ │ │ +271 │ │ │ │ +_2_8_0 _T_C_i_r_c_l_e_3 getContactCircle(_P_o_s_i_t_i_o_n i) const │ │ │ │ +281 ; │ │ │ │ +282 │ │ │ │ +_2_8_9 void setIntersectionPoint(_P_o_s_i_t_i_o_n i, const _T_V_e_c_t_o_r_3& point) │ │ │ │ +290 ; │ │ │ │ +291 │ │ │ │ +_3_0_1 _T_V_e_c_t_o_r_3 getIntersectionPoint(_P_o_s_i_t_i_o_n i) const; │ │ │ │ 302 │ │ │ │ -_3_0_8 void _s_e_t_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r(_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* man); │ │ │ │ +_3_0_5 void setSingular(bool singular) │ │ │ │ +306 ; │ │ │ │ +307 │ │ │ │ 309 │ │ │ │ -_3_1_3 void _s_e_t_E_d_i_t_a_b_l_e(bool mode); │ │ │ │ +310 │ │ │ │ 314 │ │ │ │ -_3_1_8 bool _i_s_E_d_i_t_a_b_l_e() const; │ │ │ │ -319 │ │ │ │ -_3_2_3 bool _h_a_s_C_h_a_n_g_e_s() const; │ │ │ │ -324 │ │ │ │ -325 public Q_SLOTS: │ │ │ │ -_3_2_9 void _a_p_p_l_y(); │ │ │ │ -330 │ │ │ │ -_3_3_4 void _r_e_s_e_t(); │ │ │ │ +_3_1_9 virtual bool operator == (const _R_S_E_d_g_e& rsedge) const │ │ │ │ +320 ; │ │ │ │ +321 │ │ │ │ +_3_2_6 virtual bool operator != (const _R_S_E_d_g_e& rsedge) const │ │ │ │ +327 ; │ │ │ │ +328 │ │ │ │ +_3_3_3 virtual bool operator *=(const _R_S_E_d_g_e& rsedge) const │ │ │ │ +334 ; │ │ │ │ 335 │ │ │ │ -336 Q_SIGNALS: │ │ │ │ -_3_4_0 void _v_a_l_u_e_C_h_a_n_g_e_d(); │ │ │ │ -341 │ │ │ │ -342 protected: │ │ │ │ -_3_4_3 void _s_e_t_u_p_U_i__(); │ │ │ │ -344 │ │ │ │ -_3_4_5 _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t* _a_d_d_P_r_o_p_e_r_t_y__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop); │ │ │ │ -_3_4_6 _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t* _a_d_d_P_r_o_p_e_r_t_y__(_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t* editor); │ │ │ │ -_3_4_7 _P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t* _c_r_e_a_t_e_E_d_i_t_o_r_W_i_d_g_e_t__(const _N_a_m_e_d_P_r_o_p_e_r_t_y& prop); │ │ │ │ -_3_4_8 QString _c_h_o_o_s_e_N_a_m_e__(const QString& initial); │ │ │ │ -_3_4_9 void _d_e_l_e_t_e_P_r_o_p_e_r_t_y__(_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t* editor); │ │ │ │ +_3_4_0 bool isSingular() const │ │ │ │ +341 ; │ │ │ │ +342 │ │ │ │ +_3_4_6 bool isFree() const │ │ │ │ +347 ; │ │ │ │ +348 │ │ │ │ 350 │ │ │ │ -351 protected Q_SLOTS: │ │ │ │ -_3_5_2 void _s_c_h_e_d_u_l_e_D_e_l_e_t_e__(); │ │ │ │ -_3_5_3 void _s_c_h_e_d_u_l_e_D_u_p_l_i_c_a_t_e__(); │ │ │ │ -_3_5_4 void _v_a_l_u_e_C_h_a_n_g_e_d__(); │ │ │ │ -355 │ │ │ │ -_3_5_6 void _c_r_e_a_t_e_N_e_w_B_o_o_l__(); │ │ │ │ -_3_5_7 void _c_r_e_a_t_e_N_e_w_I_n_t__(); │ │ │ │ -_3_5_8 void _c_r_e_a_t_e_N_e_w_U_I_n_t__(); │ │ │ │ -_3_5_9 void _c_r_e_a_t_e_N_e_w_F_l_o_a_t__(); │ │ │ │ -_3_6_0 void _c_r_e_a_t_e_N_e_w_D_o_u_b_l_e__(); │ │ │ │ -_3_6_1 void _c_r_e_a_t_e_N_e_w_S_t_r_i_n_g__(); │ │ │ │ -362 │ │ │ │ -363 private: │ │ │ │ -364 bool has_changes_; │ │ │ │ -365 bool is_editable_; │ │ │ │ -366 _P_r_o_p_e_r_t_y_M_a_n_a_g_e_r* manager_; │ │ │ │ -367 QList new_properties_; │ │ │ │ -368 QList deleted_properties_; │ │ │ │ -369 │ │ │ │ -370 Ui::PropertyEditor ui_; │ │ │ │ -371 }; │ │ │ │ -372 │ │ │ │ -373 } │ │ │ │ -374} │ │ │ │ -375 │ │ │ │ -376#endif //BALL_VIEW_WIDGETS_PROPERTYEDITOR_H │ │ │ │ -_P_D_B_I_n_f_o_._h │ │ │ │ -_h_a_s_h_M_a_p_._h │ │ │ │ +351 protected: │ │ │ │ +352 │ │ │ │ +353 /*_ @name Attributes │ │ │ │ +354 */ │ │ │ │ +356 │ │ │ │ +357 /*_ The center of the torus described by the probe when ir rolls over │ │ │ │ +358 the RSEdge │ │ │ │ +359 */ │ │ │ │ +_3_6_0 _T_V_e_c_t_o_r_3 center_of_torus_; │ │ │ │ +361 /*_ The major radius of the torus described by the probe when ir rolls │ │ │ │ +362 over the RSEdge │ │ │ │ +363 */ │ │ │ │ +_3_6_4 double radius_of_torus_; │ │ │ │ +365 /*_ The rotation angle between the starting and ending position of the │ │ │ │ +366 probe sphere when it rolls over the RSEdge │ │ │ │ +367 */ │ │ │ │ +_3_6_8 _T_A_n_g_l_e angle_; │ │ │ │ +369 /*_ The contact circle of the probe sphere with the first RSVertex │ │ │ │ +370 */ │ │ │ │ +_3_7_1 _T_C_i_r_c_l_e_3 circle0_; │ │ │ │ +372 /*_ The contact circle of the probe sphere with the second RSVertex │ │ │ │ +373 */ │ │ │ │ +_3_7_4 _T_C_i_r_c_l_e_3 circle1_; │ │ │ │ +375 /*_ The intersection point of the probe sphere with the RSEdge near to │ │ │ │ +376 the first RSVertex (in singular case). │ │ │ │ +377 */ │ │ │ │ +_3_7_8 _T_V_e_c_t_o_r_3 intersection_point0_; │ │ │ │ +379 /*_ The intersection point of the probe sphere with the RSEdge near to │ │ │ │ +380 the second RSVertex (in singular case). │ │ │ │ +381 */ │ │ │ │ +_3_8_2 _T_V_e_c_t_o_r_3 intersection_point1_; │ │ │ │ +383 /*_ singular │ │ │ │ +384 */ │ │ │ │ +_3_8_5 bool singular_; │ │ │ │ +386 │ │ │ │ +388 │ │ │ │ +389 }; │ │ │ │ +390 │ │ │ │ +394 │ │ │ │ +_3_9_7 _B_A_L_L___E_X_P_O_R_T _s_t_d::ostream& operator << (_s_t_d::ostream& s, const _R_S_E_d_g_e& │ │ │ │ +rsedge); │ │ │ │ +398 │ │ │ │ +400 │ │ │ │ +401 │ │ │ │ +402 │ │ │ │ +403} // namespace BALL │ │ │ │ +404 │ │ │ │ +405#endif // BALL_STRUCTURE_RSEDGE_H │ │ │ │ +_g_r_a_p_h_E_d_g_e_._h │ │ │ │ +_a_n_g_l_e_._h │ │ │ │ +_c_i_r_c_l_e_3_._h │ │ │ │ +_v_e_c_t_o_r_3_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ +_s_t_d │ │ │ │ +STL namespace. │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_N_a_m_e_d_P_r_o_p_e_r_t_y │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_._h_:_4_0 │ │ │ │ -_B_A_L_L_:_:_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_._h_:_3_4_4 │ │ │ │ -_B_A_L_L_:_:_P_D_B_I_n_f_o │ │ │ │ -DDeeffiinniittiioonn _P_D_B_I_n_f_o_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_3_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_r_e_s_e_t__ │ │ │ │ -virtual void reset_(const NamedProperty &prop)=0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_c_l_o_n_e │ │ │ │ -virtual PropEditorWidget * clone(const std::string &name, QWidget *parent)=0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_p_p_l_y │ │ │ │ -void apply(PropertyManager *man, bool create=false) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -PropEditorWidget(const std::string &name, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_i_s_E_d_i_t_a_b_l_e │ │ │ │ -bool isEditable() const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_n_a_m_e__ │ │ │ │ -QString name_ │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_1_1_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_d_u_p_l_i_c_a_t_e_P_r_o_p_e_r_t_y │ │ │ │ -void duplicateProperty() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_d_e_l_e_t_e_P_r_o_p_e_r_t_y │ │ │ │ -void deleteProperty() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_u_i__ │ │ │ │ -Ui::PropEditorWidget ui_ │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_1_2_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_r_e_s_e_t │ │ │ │ -void reset(PropertyManager *man) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_g_e_t_N_a_m_e │ │ │ │ -virtual const QString & getName() const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_p_p_l_y__ │ │ │ │ -virtual void apply_(PropertyManager *man)=0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_s_e_t_E_d_i_t_a_b_l_e │ │ │ │ -void setEditable(bool mode) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_v_a_l_u_e_C_h_a_n_g_e_d │ │ │ │ -void valueChanged() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_s_e_t_u_p_U_i__ │ │ │ │ -void setupUi_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_d_d_W_i_d_g_e_t__ │ │ │ │ -bool addWidget_(int i, QWidget *w) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_1_2_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t_:_:_B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -BoolEditorWidget(const NamedProperty &prop, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_p_p_l_y__ │ │ │ │ -virtual void apply_(PropertyManager *man) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t_:_:_c_l_o_n_e │ │ │ │ -virtual BoolEditorWidget * clone(const std::string &name, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_B_o_o_l_E_d_i_t_o_r_W_i_d_g_e_t_:_:_r_e_s_e_t__ │ │ │ │ -virtual void reset_(const NamedProperty &prop) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_1_4_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_r_e_s_e_t__ │ │ │ │ -virtual void reset_(const NamedProperty &prop) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -IntEditorWidget(const NamedProperty &prop, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_p_p_l_y__ │ │ │ │ -virtual void apply_(PropertyManager *man) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_c_l_o_n_e │ │ │ │ -virtual IntEditorWidget * clone(const std::string &name, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_1_5_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_r_e_s_e_t__ │ │ │ │ -virtual void reset_(const NamedProperty &prop) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_c_l_o_n_e │ │ │ │ -virtual UIntEditorWidget * clone(const std::string &name, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -UIntEditorWidget(const NamedProperty &prop, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_U_I_n_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_p_p_l_y__ │ │ │ │ -virtual void apply_(PropertyManager *man) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_1_7_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_c_l_o_n_e │ │ │ │ -virtual FloatEditorWidget * clone(const std::string &name, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_r_e_s_e_t__ │ │ │ │ -virtual void reset_(const NamedProperty &prop) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_p_p_l_y__ │ │ │ │ -virtual void apply_(PropertyManager *man) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t_:_:_F_l_o_a_t_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -FloatEditorWidget(const NamedProperty &prop, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_1_8_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t_:_:_r_e_s_e_t__ │ │ │ │ -virtual void reset_(const NamedProperty &prop) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_p_p_l_y__ │ │ │ │ -virtual void apply_(PropertyManager *man) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t_:_:_c_l_o_n_e │ │ │ │ -virtual DoubleEditorWidget * clone(const std::string &name, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t_:_:_D_o_u_b_l_e_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -DoubleEditorWidget(const NamedProperty &prop, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_2_0_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t_:_:_r_e_s_e_t__ │ │ │ │ -virtual void reset_(const NamedProperty &prop) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t_:_:_S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -StringEditorWidget(const NamedProperty &prop, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t_:_:_c_l_o_n_e │ │ │ │ -virtual StringEditorWidget * clone(const std::string &name, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_S_t_r_i_n_g_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_p_p_l_y__ │ │ │ │ -virtual void apply_(PropertyManager *man) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_D_e_l_e_t_e_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_2_2_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_D_e_l_e_t_e_W_i_d_g_e_t_:_:_r_e_s_e_t__ │ │ │ │ -virtual void reset_(const NamedProperty &) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_2_3_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_D_e_l_e_t_e_W_i_d_g_e_t_:_:_c_l_o_n_e │ │ │ │ -virtual PropEditorWidget * clone(const std::string &, QWidget *) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_2_3_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_D_e_l_e_t_e_W_i_d_g_e_t_:_:_a_p_p_l_y__ │ │ │ │ -virtual void apply_(PropertyManager *) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_2_3_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_D_e_l_e_t_e_W_i_d_g_e_t_:_:_P_r_o_p_D_e_l_e_t_e_W_i_d_g_e_t │ │ │ │ -PropDeleteWidget(const NamedProperty &prop, QWidget *parent) │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_2_2_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_2_4_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t_:_:_c_l_o_n_e │ │ │ │ -virtual PDBInfoEditorWidget * clone(const std::string &name, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t_:_:_a_p_p_l_y__ │ │ │ │ -virtual void apply_(PropertyManager *man) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t_:_:_r_e_s_e_t__ │ │ │ │ -virtual void reset_(const NamedProperty &prop) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t_:_:_P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t │ │ │ │ -PDBInfoEditorWidget(const PDBInfo &info, QWidget *parent) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_D_B_I_n_f_o_E_d_i_t_o_r_W_i_d_g_e_t_:_:_s_t_a_r_t_E_d_i_t_o_r_D_i_a_l_o_g │ │ │ │ -void startEditorDialog() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r │ │ │ │ -DDeeffiinniittiioonn _p_r_o_p_e_r_t_y_E_d_i_t_o_r_._h_:_2_8_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_a_p_p_l_y │ │ │ │ -void apply() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_s_e_t_P_r_o_p_e_r_t_y_M_a_n_a_g_e_r │ │ │ │ -void setPropertyManager(PropertyManager *man) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_d_e_l_e_t_e_P_r_o_p_e_r_t_y__ │ │ │ │ -void deleteProperty_(PropEditorWidget *editor) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_s_e_t_E_d_i_t_a_b_l_e │ │ │ │ -void setEditable(bool mode) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r │ │ │ │ -PropertyEditor(QWidget *parent=0, bool editable=true) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_c_h_o_o_s_e_N_a_m_e__ │ │ │ │ -QString chooseName_(const QString &initial) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_s_c_h_e_d_u_l_e_D_u_p_l_i_c_a_t_e__ │ │ │ │ -void scheduleDuplicate_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_i_s_E_d_i_t_a_b_l_e │ │ │ │ -bool isEditable() const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_v_a_l_u_e_C_h_a_n_g_e_d__ │ │ │ │ -void valueChanged_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_s_e_t_u_p_U_i__ │ │ │ │ -void setupUi_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_c_r_e_a_t_e_N_e_w_U_I_n_t__ │ │ │ │ -void createNewUInt_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_c_r_e_a_t_e_N_e_w_D_o_u_b_l_e__ │ │ │ │ -void createNewDouble_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_c_r_e_a_t_e_N_e_w_I_n_t__ │ │ │ │ -void createNewInt_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_h_a_s_C_h_a_n_g_e_s │ │ │ │ -bool hasChanges() const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_s_c_h_e_d_u_l_e_D_e_l_e_t_e__ │ │ │ │ -void scheduleDelete_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_c_r_e_a_t_e_E_d_i_t_o_r_W_i_d_g_e_t__ │ │ │ │ -PropEditorWidget * createEditorWidget_(const NamedProperty &prop) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_r_e_s_e_t │ │ │ │ -void reset() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_a_d_d_P_r_o_p_e_r_t_y__ │ │ │ │ -PropEditorWidget * addProperty_(PropEditorWidget *editor) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_v_a_l_u_e_C_h_a_n_g_e_d │ │ │ │ -void valueChanged() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_c_r_e_a_t_e_N_e_w_F_l_o_a_t__ │ │ │ │ -void createNewFloat_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_a_d_d_P_r_o_p_e_r_t_y__ │ │ │ │ -PropEditorWidget * addProperty_(const NamedProperty &prop) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_c_r_e_a_t_e_N_e_w_S_t_r_i_n_g__ │ │ │ │ -void createNewString_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_c_r_e_a_t_e_N_e_w_B_o_o_l__ │ │ │ │ -void createNewBool_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r_:_:_P_r_o_p_e_r_t_y_E_d_i_t_o_r │ │ │ │ -PropertyEditor(PropertyManager *manager, QWidget *parent, bool editable=true) │ │ │ │ -_Q_D_i_a_l_o_g │ │ │ │ -_Q_W_i_d_g_e_t │ │ │ │ -_Q_L_i_n_e_E_d_i_t │ │ │ │ -_g_l_o_b_a_l_._h │ │ │ │ -_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ -#define BALL_VIEW_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ +_B_A_L_L_:_:_T_A_n_g_l_e │ │ │ │ +DDeeffiinniittiioonn _a_n_g_l_e_._h_:_5_3 │ │ │ │ +_B_A_L_L_:_:_T_C_i_r_c_l_e_3 │ │ │ │ +DDeeffiinniittiioonn _c_i_r_c_l_e_3_._h_:_4_6 │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3 │ │ │ │ +DDeeffiinniittiioonn _v_e_c_t_o_r_3_._h_:_7_1 │ │ │ │ +_B_A_L_L_:_:_G_r_a_p_h_E_d_g_e │ │ │ │ +DDeeffiinniittiioonn _g_r_a_p_h_E_d_g_e_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_R_e_d_u_c_e_d_S_u_r_f_a_c_e │ │ │ │ +DDeeffiinniittiioonn _r_e_d_u_c_e_d_S_u_r_f_a_c_e_._h_:_1_9_6 │ │ │ │ +_B_A_L_L_:_:_R_S_C_o_m_p_u_t_e_r │ │ │ │ +DDeeffiinniittiioonn _r_e_d_u_c_e_d_S_u_r_f_a_c_e_._h_:_4_7_6 │ │ │ │ +_B_A_L_L_:_:_R_S_E_d_g_e │ │ │ │ +DDeeffiinniittiioonn _R_S_E_d_g_e_._h_:_4_9 │ │ │ │ +_B_A_L_L_:_:_R_S_F_a_c_e │ │ │ │ +DDeeffiinniittiioonn _R_S_F_a_c_e_._h_:_4_1 │ │ │ │ +_B_A_L_L_:_:_R_S_V_e_r_t_e_x │ │ │ │ +DDeeffiinniittiioonn _R_S_V_e_r_t_e_x_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_S_A_S_E_d_g_e │ │ │ │ +DDeeffiinniittiioonn _S_A_S_E_d_g_e_._h_:_3_4 │ │ │ │ +_B_A_L_L_:_:_S_A_S_F_a_c_e │ │ │ │ +DDeeffiinniittiioonn _S_A_S_F_a_c_e_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_S_A_S_V_e_r_t_e_x │ │ │ │ +DDeeffiinniittiioonn _S_A_S_V_e_r_t_e_x_._h_:_2_9 │ │ │ │ +_B_A_L_L_:_:_S_E_S_E_d_g_e │ │ │ │ +DDeeffiinniittiioonn _S_E_S_E_d_g_e_._h_:_3_4 │ │ │ │ +_B_A_L_L_:_:_S_E_S_F_a_c_e │ │ │ │ +DDeeffiinniittiioonn _S_E_S_F_a_c_e_._h_:_3_8 │ │ │ │ +_B_A_L_L_:_:_S_E_S_V_e_r_t_e_x │ │ │ │ +DDeeffiinniittiioonn _S_E_S_V_e_r_t_e_x_._h_:_3_0 │ │ │ │ +_B_A_L_L_:_:_S_o_l_v_e_n_t_A_c_c_e_s_s_i_b_l_e_S_u_r_f_a_c_e │ │ │ │ +DDeeffiinniittiioonn _s_o_l_v_e_n_t_A_c_c_e_s_s_i_b_l_e_S_u_r_f_a_c_e_._h_:_3_9 │ │ │ │ +_B_A_L_L_:_:_S_o_l_v_e_n_t_E_x_c_l_u_d_e_d_S_u_r_f_a_c_e │ │ │ │ +DDeeffiinniittiioonn _s_o_l_v_e_n_t_E_x_c_l_u_d_e_d_S_u_r_f_a_c_e_._h_:_6_7 │ │ │ │ +_B_A_L_L_:_:_S_E_S_C_o_m_p_u_t_e_r │ │ │ │ +DDeeffiinniittiioonn _s_o_l_v_e_n_t_E_x_c_l_u_d_e_d_S_u_r_f_a_c_e_._h_:_3_1_8 │ │ │ │ +_B_A_L_L_:_:_S_E_S_S_i_n_g_u_l_a_r_i_t_y_C_l_e_a_n_e_r │ │ │ │ +DDeeffiinniittiioonn _s_o_l_v_e_n_t_E_x_c_l_u_d_e_d_S_u_r_f_a_c_e_._h_:_4_5_7 │ │ │ │ +_B_A_L_L_:_:_T_r_i_a_n_g_u_l_a_t_e_d_S_A_S │ │ │ │ +DDeeffiinniittiioonn _t_r_i_a_n_g_u_l_a_t_e_d_S_A_S_._h_:_6_3 │ │ │ │ +_B_A_L_L_:_:_S_A_S_T_r_i_a_n_g_u_l_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _t_r_i_a_n_g_u_l_a_t_e_d_S_A_S_._h_:_1_6_1 │ │ │ │ +_B_A_L_L_:_:_T_r_i_a_n_g_u_l_a_t_e_d_S_E_S │ │ │ │ +DDeeffiinniittiioonn _t_r_i_a_n_g_u_l_a_t_e_d_S_E_S_._h_:_5_5 │ │ │ │ +_B_A_L_L_:_:_S_E_S_T_r_i_a_n_g_u_l_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _t_r_i_a_n_g_u_l_a_t_e_d_S_E_S_._h_:_1_6_4 │ │ │ │ +_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d09/a05054.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::AssignTypeProcessor Class Reference
    Molecular Modeling » Molecular Mechanics » General Force Field Classes.
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/MOLMEC/COMMON/assignTypes.h>

    │ │ │ +

    #include <BALL/MOLMEC/COMMON/assignTypes.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::AssignTypeProcessor:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::AssignBaseProcessor │ │ │ @@ -148,15 +148,15 @@ │ │ │   │ │ │ Size max_number_unassigned_atoms_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Type assignment processor.

    │ │ │ │ │ │ -

    Definition at line 63 of file assignTypes.h.

    │ │ │ +

    Definition at line 63 of file assignTypes.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ AssignTypeProcessor()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -219,15 +219,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 89 of file assignTypes.h.

    │ │ │ +

    Definition at line 89 of file assignTypes.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d0b/a00452.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: networkPreferences.h File Reference │ │ │ +BALL: pluginDialog.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -72,31 +72,37 @@ │ │ │
  • include
  • BALL
  • VIEW
  • DIALOGS
    • │ │ │
    │ │ │
    │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    networkPreferences.h File Reference
    │ │ │ +
    pluginDialog.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/COMMON/global.h>
    │ │ │ -#include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ -#include <BALL/VIEW/UIC/ui_networkPreferences.h>
    │ │ │ -#include <QtWidgets/QWidget>
    │ │ │ +
    #include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ +#include <BALL/VIEW/KERNEL/modularWidget.h>
    │ │ │ +#include <BALL/PLUGIN/pluginHandler.h>
    │ │ │ +#include <QtCore/QModelIndex>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::NetworkPreferences
    class  BALL::VIEW::PluginModel
     
    class  BALL::VIEW::PluginDirectoryModel
     
    class  BALL::VIEW::PluginDialog
     
    │ │ │ │ │ │ + │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  Ui
     
    namespace  BALL
     
    namespace  BALL::VIEW
     
    │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -3,23 +3,29 @@ │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ * _D_I_A_L_O_G_S │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -networkPreferences.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +pluginDialog.h File Reference │ │ │ │ #include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ +#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ +#include <_B_A_L_L_/_P_L_U_G_I_N_/_p_l_u_g_i_n_H_a_n_d_l_e_r_._h> │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_M_o_d_e_l │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_D_i_a_l_o_g │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ +namespace   _U_i │ │ │ │ +  │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d0b/a00452_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: networkPreferences.h Source File │ │ │ +BALL: pluginDialog.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -74,85 +74,165 @@ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -
    networkPreferences.h
    │ │ │ +
    pluginDialog.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ -
    2// vi: set ts=2:
    │ │ │ -
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_VIEW_DIALOGS_NETWORKPREFERENCES_H
    │ │ │ -
    6#define BALL_VIEW_DIALOGS_NETWORKPREFERENCES_H
    │ │ │ +Go to the documentation of this file.
    1#ifndef BALL_VIEW_PLUGINDIALOG_H
    │ │ │ +
    2#define BALL_VIEW_PLUGINDIALOG_H
    │ │ │ +
    3
    │ │ │ +
    4#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY
    │ │ │ +
    5# include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ +
    6#endif
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ -
    9# include <BALL/COMMON/global.h>
    │ │ │ +
    8#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H
    │ │ │ +
    9# include <BALL/VIEW/KERNEL/modularWidget.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY
    │ │ │ -
    13# include <BALL/VIEW/KERNEL/preferencesEntry.h>
    │ │ │ +
    12#ifndef BALL_PLUGIN_PLUGINHANDLER_H
    │ │ │ +
    13# include <BALL/PLUGIN/pluginHandler.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │ -
    16#include <BALL/VIEW/UIC/ui_networkPreferences.h>
    │ │ │ +
    16#include <QtCore/QModelIndex>
    │ │ │
    17
    │ │ │ -
    18#include <QtWidgets/QWidget>
    │ │ │ -
    19
    │ │ │ -
    20namespace BALL
    │ │ │ -
    21{
    │ │ │ -
    22 namespace VIEW
    │ │ │ -
    23 {
    │ │ │ -
    24
    │ │ │ -
    │ │ │ -
    29 class BALL_VIEW_EXPORT NetworkPreferences
    │ │ │ -
    30 : public QWidget,
    │ │ │ -
    31 public Ui_NetworkPreferencesData,
    │ │ │ -
    32 public PreferencesEntry
    │ │ │ -
    33 {
    │ │ │ -
    34 Q_OBJECT
    │ │ │ -
    35
    │ │ │ -
    36 public:
    │ │ │ -
    37
    │ │ │ -
    39 NetworkPreferences(QWidget *parent = NULL, const char *name = "NetworkPreferences", Qt::WindowFlags fl=0);
    │ │ │ -
    40
    │ │ │ -
    42 virtual ~NetworkPreferences();
    │ │ │ -
    43
    │ │ │ -
    45 void applySettings();
    │ │ │ +
    │ │ │ +
    18namespace Ui
    │ │ │ +
    19{
    │ │ │ +
    20 class PluginDialogData;
    │ │ │ +
    21}
    │ │ │ +
    │ │ │ +
    22
    │ │ │ +
    23namespace BALL
    │ │ │ +
    24{
    │ │ │ +
    25 namespace VIEW
    │ │ │ +
    26 {
    │ │ │ +
    27 class VIEWPlugin;
    │ │ │ +
    28
    │ │ │ +
    │ │ │ +
    33 class PluginModel : public QAbstractListModel
    │ │ │ +
    34 {
    │ │ │ +
    35 Q_OBJECT
    │ │ │ +
    36
    │ │ │ +
    37 public:
    │ │ │ +
    38 explicit PluginModel ( QObject* parent = 0 );
    │ │ │ +
    39
    │ │ │ +
    40 int rowCount(const QModelIndex& /* parent */ = QModelIndex()) const;
    │ │ │ +
    41 QVariant data(const QModelIndex& i, int role) const;
    │ │ │ +
    42 void pluginsLoaded();
    │ │ │ +
    43 private:
    │ │ │ +
    44 int num_rows_;
    │ │ │ +
    45 };
    │ │ │ +
    │ │ │
    46
    │ │ │ -
    48 void getSettings();
    │ │ │ -
    49
    │ │ │ -
    51 bool proxyEnabled();
    │ │ │ -
    52
    │ │ │ -
    53 public Q_SLOTS:
    │ │ │ +
    │ │ │ +
    51 class PluginDirectoryModel : public QAbstractListModel
    │ │ │ +
    52 {
    │ │ │ +
    53 Q_OBJECT
    │ │ │
    54
    │ │ │ -
    56 void proxyModeChanged(int proxy_mode);
    │ │ │ +
    55 public:
    │ │ │ +
    56 explicit PluginDirectoryModel ( QObject* parent = 0 );
    │ │ │
    57
    │ │ │ -
    58 };
    │ │ │ -
    │ │ │ -
    59
    │ │ │ -
    60 }
    │ │ │ -
    61} // namespace
    │ │ │ -
    62
    │ │ │ -
    63#endif // BALL_VIEW_DIALOGS_NETWORKPREFERENCES_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::NetworkPreferences::~NetworkPreferences
    virtual ~NetworkPreferences()
    Destructor.
    │ │ │ -
    BALL::VIEW::NetworkPreferences::proxyModeChanged
    void proxyModeChanged(int proxy_mode)
    │ │ │ -
    BALL::VIEW::NetworkPreferences::NetworkPreferences
    NetworkPreferences(QWidget *parent=NULL, const char *name="NetworkPreferences", Qt::WindowFlags fl=0)
    Default Constructor.
    │ │ │ - │ │ │ +
    58 int rowCount(const QModelIndex& /* parent */ = QModelIndex()) const;
    │ │ │ +
    59 QVariant data(const QModelIndex& i, int role) const;
    │ │ │ +
    60
    │ │ │ +
    61 void addDirectory(const QString& dir);
    │ │ │ +
    62 void removeDirectory(const QModelIndex& index);
    │ │ │ +
    63 };
    │ │ │ +
    │ │ │ +
    64
    │ │ │ +
    │ │ │ +
    73 class BALL_VIEW_EXPORT PluginDialog
    │ │ │ +
    74 : public QWidget,
    │ │ │ +
    75 public ModularWidget,
    │ │ │ +
    76 public PreferencesEntry,
    │ │ │ +
    77 public PluginHandler
    │ │ │ +
    78 {
    │ │ │ +
    79 Q_OBJECT
    │ │ │ +
    80
    │ │ │ +
    81 public:
    │ │ │ +
    82 BALL_EMBEDDABLE(PluginDialog, ModularWidget)
    │ │ │ +
    83
    │ │ │ +
    84 PluginDialog(Preferences* preferences, QWidget* parent, const char *name = "PluginDialog");
    │ │ │ +
    85 virtual ~PluginDialog();
    │ │ │ +
    86
    │ │ │ +
    93 virtual void initializeWidget(MainControl& main_control);
    │ │ │ +
    94
    │ │ │ +
    100 virtual void finalizeWidget(MainControl& main_control);
    │ │ │ +
    101
    │ │ │ +
    102 virtual void writePreferenceEntries(INIFile& inifile);
    │ │ │ +
    103 virtual void readPreferenceEntries(const INIFile& inifile);
    │ │ │ +
    104
    │ │ │ +
    105 virtual void registerChildEntry(PreferencesEntry* child);
    │ │ │ +
    106 virtual void unregisterChildEntry(PreferencesEntry* child);
    │ │ │ +
    107
    │ │ │ +
    108 virtual void restoreDefaultValues(bool /* all */ = false);
    │ │ │ +
    109
    │ │ │ +
    110 bool canHandle(BALLPlugin* plugin) const;
    │ │ │ +
    111 bool specificSetup_(BALLPlugin* plugin);
    │ │ │ +
    112 bool specificShutdown_(BALLPlugin* plugin);
    │ │ │ +
    113
    │ │ │ +
    114 protected:
    │ │ │ +
    119 virtual void setDefaultPluginDirectory();
    │ │ │ +
    120
    │ │ │ +
    121 protected Q_SLOTS:
    │ │ │ +
    122 virtual void addPluginDirectory();
    │ │ │ +
    123 virtual void removePluginDirectory();
    │ │ │ +
    124 virtual void directorySelectionChanged(const QModelIndex&, const QModelIndex& /* previous */);
    │ │ │ +
    125 virtual void pluginChanged(QModelIndex current, const QModelIndex& /* previous */);
    │ │ │ +
    126 virtual void togglePluginState();
    │ │ │ +
    127
    │ │ │ +
    128 private:
    │ │ │ +
    129 QModelIndex active_index_;
    │ │ │ +
    130 PluginModel plugin_model_;
    │ │ │ +
    131 PluginDirectoryModel plugin_dir_model_;
    │ │ │ +
    132 Preferences* preferences_;
    │ │ │ +
    133
    │ │ │ +
    134 Ui::PluginDialogData* ui_;
    │ │ │ +
    135 std::list<PreferencesEntry*> child_entries_;
    │ │ │ +
    136 };
    │ │ │ +
    │ │ │ +
    137 }
    │ │ │ +
    138}
    │ │ │ +
    139
    │ │ │ +
    140#endif
    │ │ │ +
    141
    │ │ │ + │ │ │ + │ │ │ +
    BALL_EMBEDDABLE
    #define BALL_EMBEDDABLE(TYPE, BASE)
    Definition embeddable.h:31
    │ │ │ + │ │ │ +
    std
    STL namespace.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::PluginModel::data
    QVariant data(const QModelIndex &i, int role) const
    │ │ │ +
    BALL::VIEW::PluginModel::rowCount
    int rowCount(const QModelIndex &=QModelIndex()) const
    │ │ │ +
    BALL::VIEW::PluginModel::PluginModel
    PluginModel(QObject *parent=0)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::VIEW::PluginDirectoryModel::PluginDirectoryModel
    PluginDirectoryModel(QObject *parent=0)
    │ │ │ +
    BALL::VIEW::PluginDirectoryModel::removeDirectory
    void removeDirectory(const QModelIndex &index)
    │ │ │ +
    BALL::VIEW::PluginDirectoryModel::addDirectory
    void addDirectory(const QString &dir)
    │ │ │ +
    BALL::VIEW::PluginDirectoryModel::data
    QVariant data(const QModelIndex &i, int role) const
    │ │ │ +
    BALL::VIEW::PluginDirectoryModel::rowCount
    int rowCount(const QModelIndex &=QModelIndex()) const
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │ - │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ + │ │ │ +
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -2,92 +2,180 @@ │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ * _V_I_E_W │ │ │ │ * _D_I_A_L_O_G_S │ │ │ │ -networkPreferences.h │ │ │ │ +pluginDialog.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ -2// vi: set ts=2: │ │ │ │ -3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_VIEW_DIALOGS_NETWORKPREFERENCES_H │ │ │ │ -6#define BALL_VIEW_DIALOGS_NETWORKPREFERENCES_H │ │ │ │ +1#ifndef BALL_VIEW_PLUGINDIALOG_H │ │ │ │ +2#define BALL_VIEW_PLUGINDIALOG_H │ │ │ │ +3 │ │ │ │ +4#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY │ │ │ │ +5# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h> │ │ │ │ +6#endif │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ -9# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +8#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H │ │ │ │ +9# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_m_o_d_u_l_a_r_W_i_d_g_e_t_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_VIEW_KERNEL_PREFERENCESENTRY │ │ │ │ -13# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h> │ │ │ │ +12#ifndef BALL_PLUGIN_PLUGINHANDLER_H │ │ │ │ +13# include <_B_A_L_L_/_P_L_U_G_I_N_/_p_l_u_g_i_n_H_a_n_d_l_e_r_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#include │ │ │ │ +16#include │ │ │ │ 17 │ │ │ │ -18#include │ │ │ │ -19 │ │ │ │ -20namespace _B_A_L_L │ │ │ │ -21{ │ │ │ │ -22 namespace VIEW │ │ │ │ -23 { │ │ │ │ -24 │ │ │ │ -_2_9 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ -30 : public _Q_W_i_d_g_e_t, │ │ │ │ -31 public Ui_NetworkPreferencesData, │ │ │ │ -32 public _P_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y │ │ │ │ -33 { │ │ │ │ -34 Q_OBJECT │ │ │ │ -35 │ │ │ │ -36 public: │ │ │ │ -37 │ │ │ │ -_3_9 _N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s(_Q_W_i_d_g_e_t *parent = NULL, const char *name = │ │ │ │ -"NetworkPreferences", Qt::WindowFlags fl=0); │ │ │ │ -40 │ │ │ │ -_4_2 virtual _~_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s(); │ │ │ │ -43 │ │ │ │ -_4_5 void _a_p_p_l_y_S_e_t_t_i_n_g_s(); │ │ │ │ +_1_8namespace _U_i │ │ │ │ +19{ │ │ │ │ +20 class PluginDialogData; │ │ │ │ +21} │ │ │ │ +22 │ │ │ │ +23namespace _B_A_L_L │ │ │ │ +24{ │ │ │ │ +25 namespace VIEW │ │ │ │ +26 { │ │ │ │ +27 class VIEWPlugin; │ │ │ │ +28 │ │ │ │ +_3_3 class _P_l_u_g_i_n_M_o_d_e_l : public _Q_A_b_s_t_r_a_c_t_L_i_s_t_M_o_d_e_l │ │ │ │ +34 { │ │ │ │ +35 Q_OBJECT │ │ │ │ +36 │ │ │ │ +37 public: │ │ │ │ +_3_8 explicit _P_l_u_g_i_n_M_o_d_e_l ( _Q_O_b_j_e_c_t* parent = 0 ); │ │ │ │ +39 │ │ │ │ +_4_0 int _r_o_w_C_o_u_n_t(const QModelIndex& /* parent */ = QModelIndex()) const; │ │ │ │ +_4_1 QVariant _d_a_t_a(const QModelIndex& i, int role) const; │ │ │ │ +_4_2 void _p_l_u_g_i_n_s_L_o_a_d_e_d(); │ │ │ │ +43 private: │ │ │ │ +44 int num_rows_; │ │ │ │ +45 }; │ │ │ │ 46 │ │ │ │ -_4_8 void _g_e_t_S_e_t_t_i_n_g_s(); │ │ │ │ -49 │ │ │ │ -_5_1 bool _p_r_o_x_y_E_n_a_b_l_e_d(); │ │ │ │ -52 │ │ │ │ -53 public Q_SLOTS: │ │ │ │ +_5_1 class _P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l : public _Q_A_b_s_t_r_a_c_t_L_i_s_t_M_o_d_e_l │ │ │ │ +52 { │ │ │ │ +53 Q_OBJECT │ │ │ │ 54 │ │ │ │ -_5_6 void _p_r_o_x_y_M_o_d_e_C_h_a_n_g_e_d(int proxy_mode); │ │ │ │ +55 public: │ │ │ │ +_5_6 explicit _P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l ( _Q_O_b_j_e_c_t* parent = 0 ); │ │ │ │ 57 │ │ │ │ -58 }; │ │ │ │ -59 │ │ │ │ -60 } │ │ │ │ -61} // namespace │ │ │ │ -62 │ │ │ │ -63#endif // BALL_VIEW_DIALOGS_NETWORKPREFERENCES_H │ │ │ │ +_5_8 int _r_o_w_C_o_u_n_t(const QModelIndex& /* parent */ = QModelIndex()) const; │ │ │ │ +_5_9 QVariant _d_a_t_a(const QModelIndex& i, int role) const; │ │ │ │ +60 │ │ │ │ +_6_1 void _a_d_d_D_i_r_e_c_t_o_r_y(const QString& dir); │ │ │ │ +_6_2 void _r_e_m_o_v_e_D_i_r_e_c_t_o_r_y(const QModelIndex& index); │ │ │ │ +63 }; │ │ │ │ +64 │ │ │ │ +_7_3 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _P_l_u_g_i_n_D_i_a_l_o_g │ │ │ │ +74 : public _Q_W_i_d_g_e_t, │ │ │ │ +75 public _M_o_d_u_l_a_r_W_i_d_g_e_t, │ │ │ │ +76 public _P_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y, │ │ │ │ +77 public _P_l_u_g_i_n_H_a_n_d_l_e_r │ │ │ │ +78 { │ │ │ │ +79 Q_OBJECT │ │ │ │ +80 │ │ │ │ +81 public: │ │ │ │ +82 _B_A_L_L___E_M_B_E_D_D_A_B_L_E(_P_l_u_g_i_n_D_i_a_l_o_g, _M_o_d_u_l_a_r_W_i_d_g_e_t) │ │ │ │ +83 │ │ │ │ +_8_4 _P_l_u_g_i_n_D_i_a_l_o_g(_P_r_e_f_e_r_e_n_c_e_s* preferences, _Q_W_i_d_g_e_t* parent, const char *name = │ │ │ │ +"_P_l_u_g_i_n_D_i_a_l_o_g"); │ │ │ │ +_8_5 virtual ~_P_l_u_g_i_n_D_i_a_l_o_g(); │ │ │ │ +86 │ │ │ │ +_9_3 virtual void initializeWidget(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ +94 │ │ │ │ +_1_0_0 virtual void finalizeWidget(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ +101 │ │ │ │ +_1_0_2 virtual void writePreferenceEntries(_I_N_I_F_i_l_e& inifile); │ │ │ │ +_1_0_3 virtual void readPreferenceEntries(const _I_N_I_F_i_l_e& inifile); │ │ │ │ +104 │ │ │ │ +_1_0_5 virtual void registerChildEntry(_P_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y* child); │ │ │ │ +_1_0_6 virtual void unregisterChildEntry(_P_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y* child); │ │ │ │ +107 │ │ │ │ +_1_0_8 virtual void restoreDefaultValues(bool /* all */ = false); │ │ │ │ +109 │ │ │ │ +_1_1_0 bool canHandle(_B_A_L_L_P_l_u_g_i_n* plugin) const; │ │ │ │ +_1_1_1 bool specificSetup_(_B_A_L_L_P_l_u_g_i_n* plugin); │ │ │ │ +_1_1_2 bool specificShutdown_(_B_A_L_L_P_l_u_g_i_n* plugin); │ │ │ │ +113 │ │ │ │ +114 protected: │ │ │ │ +_1_1_9 virtual void setDefaultPluginDirectory(); │ │ │ │ +120 │ │ │ │ +121 protected Q_SLOTS: │ │ │ │ +_1_2_2 virtual void addPluginDirectory(); │ │ │ │ +_1_2_3 virtual void removePluginDirectory(); │ │ │ │ +_1_2_4 virtual void directorySelectionChanged(const QModelIndex&, const │ │ │ │ +QModelIndex& /* previous */); │ │ │ │ +_1_2_5 virtual void pluginChanged(QModelIndex current, const QModelIndex& / │ │ │ │ +* previous */); │ │ │ │ +_1_2_6 virtual void togglePluginState(); │ │ │ │ +127 │ │ │ │ +128 private: │ │ │ │ +129 QModelIndex active_index_; │ │ │ │ +130 _P_l_u_g_i_n_M_o_d_e_l plugin_model_; │ │ │ │ +131 _P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l plugin_dir_model_; │ │ │ │ +132 _P_r_e_f_e_r_e_n_c_e_s* preferences_; │ │ │ │ +133 │ │ │ │ +134 _U_i::PluginDialogData* ui_; │ │ │ │ +135 _s_t_d::list<_P_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y*> child_entries_; │ │ │ │ +136 }; │ │ │ │ +137 } │ │ │ │ +138} │ │ │ │ +139 │ │ │ │ +140#endif │ │ │ │ +141 │ │ │ │ +_m_o_d_u_l_a_r_W_i_d_g_e_t_._h │ │ │ │ _p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h │ │ │ │ +_B_A_L_L___E_M_B_E_D_D_A_B_L_E │ │ │ │ +#define BALL_EMBEDDABLE(TYPE, BASE) │ │ │ │ +DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_3_1 │ │ │ │ +_p_l_u_g_i_n_H_a_n_d_l_e_r_._h │ │ │ │ +_s_t_d │ │ │ │ +STL namespace. │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ -DDeeffiinniittiioonn _n_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s_:_:_p_r_o_x_y_E_n_a_b_l_e_d │ │ │ │ -bool proxyEnabled() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s_:_:_a_p_p_l_y_S_e_t_t_i_n_g_s │ │ │ │ -void applySettings() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s_:_:_g_e_t_S_e_t_t_i_n_g_s │ │ │ │ -void getSettings() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s_:_:_~_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ -virtual ~NetworkPreferences() │ │ │ │ -Destructor. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s_:_:_p_r_o_x_y_M_o_d_e_C_h_a_n_g_e_d │ │ │ │ -void proxyModeChanged(int proxy_mode) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s_:_:_N_e_t_w_o_r_k_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ -NetworkPreferences(QWidget *parent=NULL, const char *name="NetworkPreferences", │ │ │ │ -Qt::WindowFlags fl=0) │ │ │ │ -Default Constructor. │ │ │ │ +_U_i │ │ │ │ +DDeeffiinniittiioonn _p_l_u_g_i_n_D_i_a_l_o_g_._h_:_1_9 │ │ │ │ +_B_A_L_L_:_:_I_N_I_F_i_l_e │ │ │ │ +DDeeffiinniittiioonn _I_N_I_F_i_l_e_._h_:_2_9 │ │ │ │ +_B_A_L_L_:_:_B_A_L_L_P_l_u_g_i_n │ │ │ │ +DDeeffiinniittiioonn _B_A_L_L_P_l_u_g_i_n_._h_:_2_1 │ │ │ │ +_B_A_L_L_:_:_P_l_u_g_i_n_H_a_n_d_l_e_r │ │ │ │ +DDeeffiinniittiioonn _p_l_u_g_i_n_H_a_n_d_l_e_r_._h_:_2_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_M_o_d_e_l │ │ │ │ +DDeeffiinniittiioonn _p_l_u_g_i_n_D_i_a_l_o_g_._h_:_3_4 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_M_o_d_e_l_:_:_d_a_t_a │ │ │ │ +QVariant data(const QModelIndex &i, int role) const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_M_o_d_e_l_:_:_r_o_w_C_o_u_n_t │ │ │ │ +int rowCount(const QModelIndex &=QModelIndex()) const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_M_o_d_e_l_:_:_P_l_u_g_i_n_M_o_d_e_l │ │ │ │ +PluginModel(QObject *parent=0) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_M_o_d_e_l_:_:_p_l_u_g_i_n_s_L_o_a_d_e_d │ │ │ │ +void pluginsLoaded() │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l │ │ │ │ +DDeeffiinniittiioonn _p_l_u_g_i_n_D_i_a_l_o_g_._h_:_5_2 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l_:_:_P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l │ │ │ │ +PluginDirectoryModel(QObject *parent=0) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l_:_:_r_e_m_o_v_e_D_i_r_e_c_t_o_r_y │ │ │ │ +void removeDirectory(const QModelIndex &index) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l_:_:_a_d_d_D_i_r_e_c_t_o_r_y │ │ │ │ +void addDirectory(const QString &dir) │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l_:_:_d_a_t_a │ │ │ │ +QVariant data(const QModelIndex &i, int role) const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_D_i_r_e_c_t_o_r_y_M_o_d_e_l_:_:_r_o_w_C_o_u_n_t │ │ │ │ +int rowCount(const QModelIndex &=QModelIndex()) const │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_l_u_g_i_n_D_i_a_l_o_g │ │ │ │ +DDeeffiinniittiioonn _p_l_u_g_i_n_D_i_a_l_o_g_._h_:_7_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_P_r_e_f_e_r_e_n_c_e_s │ │ │ │ +DDeeffiinniittiioonn _p_r_e_f_e_r_e_n_c_e_s_._h_:_4_3 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ +DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ +_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_u_l_a_r_W_i_d_g_e_t │ │ │ │ +DDeeffiinniittiioonn _m_o_d_u_l_a_r_W_i_d_g_e_t_._h_:_6_3 │ │ │ │ _B_A_L_L_:_:_V_I_E_W_:_:_P_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y │ │ │ │ DDeeffiinniittiioonn _p_r_e_f_e_r_e_n_c_e_s_E_n_t_r_y_._h_:_6_9 │ │ │ │ +_Q_O_b_j_e_c_t │ │ │ │ _Q_W_i_d_g_e_t │ │ │ │ -_g_l_o_b_a_l_._h │ │ │ │ +_Q_A_b_s_t_r_a_c_t_L_i_s_t_M_o_d_e_l │ │ │ │ _B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ #define BALL_VIEW_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d0b/a04890.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::TQuaternion< T > Class Template Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/MATHS/quaternion.h>

    │ │ │ +

    #include <BALL/MATHS/quaternion.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::TQuaternion< T >:
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ │ │ │ @@ -166,15 +166,15 @@ │ │ │ │ │ │
     
    │ │ │

    Detailed Description

    │ │ │
    template<typename T>
    │ │ │ class BALL::TQuaternion< T >

    Generic Quaternion Class.

    │ │ │

    Representing a rotation in three dimensional space.

    │ │ │ │ │ │ -

    Definition at line 23 of file quaternion.h.

    │ │ │ +

    Definition at line 23 of file quaternion.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ TQuaternion() [1/5]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ @@ -186,15 +186,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Default constructor. This method creates a new TQuaternion object. The quaternion is set to an identity quaternion.

    │ │ │ │ │ │ -

    Definition at line 294 of file quaternion.h.

    │ │ │ +

    Definition at line 294 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ TQuaternion() [2/5]

    │ │ │ │ │ │
    │ │ │ @@ -214,15 +214,15 @@ │ │ │

    Copy constructor. Create a new TQuaternion object from another.

    Parameters
    │ │ │ │ │ │ │ │ │
    TQuaternionthe TQuaternion object to be copied
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 301 of file quaternion.h.

    │ │ │ +

    Definition at line 301 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ TQuaternion() [3/5]

    │ │ │ │ │ │
    │ │ │ @@ -242,15 +242,15 @@ │ │ │

    Detailed constructor. Create a new TQuaternion object from an Eigen::Quaternion<T>.

    Parameters
    │ │ │ │ │ │ │ │ │
    Eigen::Quaternion<T>
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 307 of file quaternion.h.

    │ │ │ +

    Definition at line 307 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ TQuaternion() [4/5]

    │ │ │ │ │ │
    │ │ │ @@ -295,15 +295,15 @@ │ │ │ iassigned to the vector component i │ │ │ jassigned to the vector component j │ │ │ kassigned to the vector component k │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 313 of file quaternion.h.

    │ │ │ +

    Definition at line 313 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ TQuaternion() [5/5]

    │ │ │ │ │ │
    │ │ │ @@ -334,15 +334,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    axisassigned to the axis
    angleassigned to the angle
    │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 319 of file quaternion.h.

    │ │ │ +

    Definition at line 319 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ ~TQuaternion()

    │ │ │ │ │ │
    │ │ │ @@ -356,15 +356,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Destructor. Destructs the TQuaternion object. As there are no dynamic data structures, nothing happens.

    │ │ │ │ │ │ -

    Definition at line 326 of file quaternion.h.

    │ │ │ +

    Definition at line 326 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ clear()

    │ │ │ │ │ │ @@ -379,15 +379,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Clear method. The values are set to the identity quaternion.

    │ │ │ │ │ │ -

    Definition at line 331 of file quaternion.h.

    │ │ │ +

    Definition at line 331 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ dump()

    │ │ │ │ │ │
    │ │ │ @@ -418,15 +418,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    s- output stream where to output the internal state of {*this}
    depth- the dumping depth
    │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 605 of file quaternion.h.

    │ │ │ +

    Definition at line 605 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ fromAxisAngle()

    │ │ │ │ │ │
    │ │ │ @@ -457,15 +457,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    axisthe rotation axis
    anglethe rotation angle
    │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 407 of file quaternion.h.

    │ │ │ +

    Definition at line 407 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ fromEulerAngles()

    │ │ │ │ │ │
    │ │ │ @@ -503,43 +503,43 @@ │ │ │ yawthe rotation about the yaw axis z-axis() │ │ │ pitchthe rotation about the pitch axis (y-axis) │ │ │ rollthe nrotation about the roll axis (x-axis) │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 419 of file quaternion.h.

    │ │ │ +

    Definition at line 419 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ get()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TQuaternion< T >::get BALL_INLINE void BALL::TQuaternion< T >::get (TQuaternion< T > & q) const
    │ │ │
    │ │ │

    Assign to another TQuaternion. Assigns the components to another TQuaternion.

    Parameters
    │ │ │ │ │ │ │ │ │
    qthe TQuaternion to be assigned to
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 488 of file quaternion.h.

    │ │ │ +

    Definition at line 488 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getAngle()

    │ │ │ │ │ │
    │ │ │ @@ -553,15 +553,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Get the positive angle rotation.

    Returns
    T the angle value
    │ │ │ │ │ │ -

    Definition at line 494 of file quaternion.h.

    │ │ │ +

    Definition at line 494 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getAxis()

    │ │ │ │ │ │
    │ │ │ @@ -575,59 +575,59 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Get the normalized direction vector of the rotation axis.

    Returns
    TVector3 the axis
    │ │ │ │ │ │ -

    Definition at line 502 of file quaternion.h.

    │ │ │ +

    Definition at line 502 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ getConjugate()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE TQuaternion< T > BALL::TQuaternion< T >::getConjugate BALL_INLINE TQuaternion< T > BALL::TQuaternion< T >::getConjugate () const
    │ │ │
    │ │ │

    Return the conjugate TQuaternion. (The axis components are negated.)

    Returns
    TQuaternion the conjugate TQuaternion
    │ │ │ │ │ │ -

    Definition at line 534 of file quaternion.h.

    │ │ │ +

    Definition at line 534 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getInverse()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE TQuaternion< T > BALL::TQuaternion< T >::getInverse BALL_INLINE TQuaternion< T > BALL::TQuaternion< T >::getInverse () const
    │ │ │
    │ │ │

    Get the inverse TQuaternion.

    Returns
    TQuaternion the inverse TQuaternion
    │ │ │ │ │ │ -

    Definition at line 527 of file quaternion.h.

    │ │ │ +

    Definition at line 527 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getRotationMatrix()

    │ │ │ │ │ │
    │ │ │ @@ -648,15 +648,15 @@ │ │ │ │ │ │ │ │ │
    mthe matrix to compute from
    │ │ │ │ │ │ │ │ │
    Returns
    TMatrix4x4 the rotation matrix
    │ │ │ │ │ │ -

    Definition at line 511 of file quaternion.h.

    │ │ │ +

    Definition at line 511 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ i() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -670,15 +670,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Get the axis component i.

    Returns
    get a reference to the axis component i
    │ │ │ │ │ │ -

    Definition at line 558 of file quaternion.h.

    │ │ │ +

    Definition at line 558 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ i() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -692,15 +692,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Get the constant axis component i.

    Returns
    get a const reference to the axis component i
    │ │ │ │ │ │ -

    Definition at line 552 of file quaternion.h.

    │ │ │ +

    Definition at line 552 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ j() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -714,15 +714,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Get the axis component j.

    Returns
    get a reference to the axis component j
    │ │ │ │ │ │ -

    Definition at line 570 of file quaternion.h.

    │ │ │ +

    Definition at line 570 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ j() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -736,15 +736,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Get the constant axis component j.

    Returns
    get a const reference to the axis component j
    │ │ │ │ │ │ -

    Definition at line 564 of file quaternion.h.

    │ │ │ +

    Definition at line 564 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ k() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -758,15 +758,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Get the axis component k.

    Returns
    get a reference to the axis component k
    │ │ │ │ │ │ -

    Definition at line 582 of file quaternion.h.

    │ │ │ +

    Definition at line 582 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ k() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -780,107 +780,107 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Get the constant axis component k.

    Returns
    get a const reference to the axis component k
    │ │ │ │ │ │ -

    Definition at line 576 of file quaternion.h.

    │ │ │ +

    Definition at line 576 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ normalize()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE TQuaternion< T > & BALL::TQuaternion< T >::normalize BALL_INLINE TQuaternion< T > & BALL::TQuaternion< T >::normalize ()
    │ │ │
    │ │ │

    Normalize the quaternion. The quaternion is scaled with its norm:

    Returns
    TQuaternion&, a reference to the normalized quaternion
    │ │ │ │ │ │ -

    Definition at line 390 of file quaternion.h.

    │ │ │ +

    Definition at line 390 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ operator=() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE TQuaternion< T > & BALL::TQuaternion< T >::operator= BALL_INLINE TQuaternion< T > & BALL::TQuaternion< T >::operator= (const Eigen::Quaternion< T > & q)
    │ │ │
    │ │ │

    Assignment operator Assign the TQuaternion components from an Eigen::Quaternion.

    │ │ │ │ │ │ -

    Definition at line 360 of file quaternion.h.

    │ │ │ +

    Definition at line 360 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ operator=() [2/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE TQuaternion< T > & BALL::TQuaternion< T >::operator= BALL_INLINE TQuaternion< T > & BALL::TQuaternion< T >::operator= (const TQuaternion< T > & q)
    │ │ │
    │ │ │

    Assignment operator. Assign the TQuaternion components form another TQuaternion.

    │ │ │ │ │ │ -

    Definition at line 368 of file quaternion.h.

    │ │ │ +

    Definition at line 368 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ operator==()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE bool BALL::TQuaternion< T >::operator== BALL_INLINE bool BALL::TQuaternion< T >::operator== (const TQuaternion< T > & q)
    │ │ │
    │ │ │ │ │ │

    Equality operator Returns true if the given Quaternion q is equal to this.

    │ │ │ │ │ │ -

    Definition at line 376 of file quaternion.h.

    │ │ │ +

    Definition at line 376 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ set() [1/3]

    │ │ │ │ │ │
    │ │ │ @@ -900,28 +900,28 @@ │ │ │

    Assign coefficients of q to this quaternion

    Parameters
    │ │ │ │ │ │ │ │ │
    qthe Eigen::Quaternion<T> to copy coefficients from
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 343 of file quaternion.h.

    │ │ │ +

    Definition at line 343 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ set() [2/3]

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -953,15 +953,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TQuaternion< T >::set BALL_INLINE void BALL::TQuaternion< T >::set (const T & a,
    iassigned to the vector component i
    jassigned to the vector component j
    kassigned to the vector component k
    │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 350 of file quaternion.h.

    │ │ │ +

    Definition at line 350 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ set() [3/3]

    │ │ │ │ │ │
    │ │ │ @@ -981,37 +981,37 @@ │ │ │

    Assign coefficients of q to this quaternion

    Parameters
    │ │ │ │ │ │ │ │ │
    qthe Quaternion to copy coefficients from
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 337 of file quaternion.h.

    │ │ │ +

    Definition at line 337 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setIdentity()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ template<typename T >
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE void BALL::TQuaternion< T >::setIdentity BALL_INLINE void BALL::TQuaternion< T >::setIdentity ()
    │ │ │
    │ │ │

    Set to an identity matrix. angular component w = 1; axis components i,j,k are set to 0;

    │ │ │ │ │ │ -

    Definition at line 383 of file quaternion.h.

    │ │ │ +

    Definition at line 383 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ swap()

    │ │ │ │ │ │
    │ │ │ @@ -1031,15 +1031,15 @@ │ │ │

    Swap the contents of two TQuaternion.

    Parameters
    │ │ │ │ │ │ │ │ │
    qthe TQuaternion to swap contents with
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 398 of file quaternion.h.

    │ │ │ +

    Definition at line 398 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ toAxisAngle()

    │ │ │ │ │ │
    │ │ │ @@ -1070,15 +1070,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    axisthe rotation axis
    anglethe rotation angle
    │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 441 of file quaternion.h.

    │ │ │ +

    Definition at line 441 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ toEulerAngles()

    │ │ │ │ │ │
    │ │ │ @@ -1116,15 +1116,15 @@ │ │ │ yawthe rotation about the yaw axis z-axis() │ │ │ pitchthe rotation about the pitch axis (y-axis) │ │ │ rollthe nrotation about the roll axis (x-axis) │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -

    Definition at line 452 of file quaternion.h.

    │ │ │ +

    Definition at line 452 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ w() [1/2]

    │ │ │ │ │ │
    │ │ │ @@ -1138,15 +1138,15 @@ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │

    Get the angular component w.

    Returns
    get a reference to the angular component w
    │ │ │ │ │ │ -

    Definition at line 546 of file quaternion.h.

    │ │ │ +

    Definition at line 546 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ w() [2/2]

    │ │ │ │ │ │
    │ │ │ @@ -1160,15 +1160,15 @@ │ │ │ ) │ │ │ const │ │ │ │ │ │ │ │ │
    │ │ │

    Get the constant angular component w.

    Returns
    get a const reference to the angular component w
    │ │ │ │ │ │ -

    Definition at line 540 of file quaternion.h.

    │ │ │ +

    Definition at line 540 of file quaternion.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d0b/a06458.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Static Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::SLICKScore::Default Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SCORING/FUNCTIONS/slickScore.h>

    │ │ │ +

    #include <BALL/SCORING/FUNCTIONS/slickScore.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -94,15 +94,15 @@ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Static Public Attributes

    static const float CONST
     
    static const float CHPI
     
     
    static const float POLAR
     
    │ │ │

    Detailed Description

    │ │ │

    Default values for SLICKEnergy options.

    │ │ │ │ │ │ -

    Definition at line 64 of file slickScore.h.

    │ │ │ +

    Definition at line 64 of file slickScore.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ CHPI

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -116,15 +116,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ static
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 73 of file slickScore.h.

    │ │ │ +

    Definition at line 73 of file slickScore.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ CONST

    │ │ │ │ │ │
    │ │ │ @@ -141,15 +141,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │

    The additive constant (

    See also
    Default::CONST)
    │ │ │ │ │ │ -

    Definition at line 69 of file slickScore.h.

    │ │ │ +

    Definition at line 69 of file slickScore.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ HB

    │ │ │ │ │ │
    │ │ │ @@ -165,15 +165,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 77 of file slickScore.h.

    │ │ │ +

    Definition at line 77 of file slickScore.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ POLAR

    │ │ │ │ │ │
    │ │ │ @@ -189,15 +189,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 85 of file slickScore.h.

    │ │ │ +

    Definition at line 85 of file slickScore.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ VDW

    │ │ │ │ │ │
    │ │ │ @@ -213,15 +213,15 @@ │ │ │ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 81 of file slickScore.h.

    │ │ │ +

    Definition at line 81 of file slickScore.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d13/a04714.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::SingleBondsPredicate Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/KERNEL/standardPredicates.h>

    │ │ │ +

    #include <BALL/KERNEL/standardPredicates.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::SingleBondsPredicate:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::NumberOfBondsPredicate │ │ │ @@ -134,15 +134,15 @@ │ │ │ - Protected Attributes inherited from BALL::ExpressionPredicate │ │ │ String argument_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Predicate class for atoms bearing single bonds. Arguments of this class are required to consist of an relational operator and a number between 1 and 8.

    │ │ │ │ │ │ -

    Definition at line 378 of file standardPredicates.h.

    │ │ │ +

    Definition at line 378 of file standardPredicates.h.

    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ operator()()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d15/a07522.html │ │ │ @@ -79,15 +79,15 @@ │ │ │ Protected Slots | │ │ │ Friends | │ │ │ List of all members │ │ │
    BALL::VIEW::AssignBondOrderConfigurationDialog Class Reference
    Visualisation » QT Dialogs
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/DIALOGS/assignBondOrderConfigurationDialog.h>

    │ │ │ +

    #include <BALL/VIEW/DIALOGS/assignBondOrderConfigurationDialog.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::AssignBondOrderConfigurationDialog:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ QDialog │ │ │ @@ -128,17 +128,17 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -169,15 +169,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -303,15 +303,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -352,15 +352,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
     
    virtual void clear ()
     
    virtual void checkMenu (MainControl &main_control)
     
    QAction * insertMenuEntry (Position parent_id, const QString &name, const QObject *receiver=0, const char *slot=0, const String &description="", QKeySequence accel=QKeySequence(), const QString &menu_hint=QString(""), UIOperationMode::OperationMode minimal_mode=UIOperationMode::MODE_ALL)
     
    BALL_DEPRECATED void setMenuHelp (QAction *, const String &)
    BALL_DEPRECATED void setMenuHelp (QAction *, const String &)
     
    virtual BALL_DEPRECATED void registerForHelpSystem (const QObject *, const String &)
    virtual BALL_DEPRECATED void registerForHelpSystem (const QObject *, const String &)
     
    virtual void addToolBarEntries (QToolBar *main_tb)
     
    void setIcon (QAction *action, const String &filename, bool add_to_main_toolbar=true)
     
    virtual void initializePreferencesTab (Preferences &preferences)
     
     
    FragmentDB & getFragmentDB () const
     
    virtual void dump (std::ostream &s=std::cout, Size depth=0) const
     
    void setWorkingDirFromFilename_ (String filename)
     
    virtual BALL_DEPRECATED void showHelp (const String &)
    virtual BALL_DEPRECATED void showHelp (const String &)
     
    virtual void finalizeWidget (MainControl &main_control)
     
    virtual bool canHandle (const String &) const
     
    virtual bool openFile (const String &)
     
    - Protected Member Functions inherited from BALL::VIEW::PreferencesEntry
    void registerWidgets_ ()
     
    void registerObject_ (QObject *widget)
     
    void unregisterObject_ (QObject *widget)
     
    BALL_DEPRECATED void registerWidgetForHelpSystem_ (const QWidget *, const String &)
    BALL_DEPRECATED void registerWidgetForHelpSystem_ (const QWidget *, const String &)
     
    void restoreValues_ (bool all, const ValueMap &map)
     
    void insertStackEntry_ (QWidget *, const String &name)
     
    bool isSupported_ (QObject &widget)
     
     
    StackPages stack_pages_
     
    │ │ │

    Detailed Description

    │ │ │

    Dialog for changing the options of the assignBondOrderProcessor

    │ │ │ │ │ │ -

    Definition at line 35 of file assignBondOrderConfigurationDialog.h.

    │ │ │ +

    Definition at line 35 of file assignBondOrderConfigurationDialog.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ AssignBondOrderConfigurationDialog()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -669,15 +669,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ friend
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 41 of file assignBondOrderConfigurationDialog.h.

    │ │ │ +

    Definition at line 41 of file assignBondOrderConfigurationDialog.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d19/a03526.html │ │ │ @@ -76,25 +76,25 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    boost::hash< BALL::Quadruple< T1, T2, T3, T4 > > Struct Template Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/DATATYPE/hashMap.h>

    │ │ │ +

    #include <BALL/DATATYPE/hashMap.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    size_t operator() (const BALL::Quadruple< T1, T2, T3, T4 > &s) const
     
    │ │ │

    Detailed Description

    │ │ │
    template<typename T1, typename T2, typename T3, typename T4>
    │ │ │ struct boost::hash< BALL::Quadruple< T1, T2, T3, T4 > >
    │ │ │ -

    Definition at line 50 of file hashMap.h.

    │ │ │ +

    Definition at line 50 of file hashMap.h.

    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ operator()()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ @@ -114,15 +114,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 52 of file hashMap.h.

    │ │ │ +

    Definition at line 52 of file hashMap.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d1a/a07130.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::SASEdge Class Reference
    Molecular Modeling » Molecular Structure » Molecular Surface Computation
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/STRUCTURE/SASEdge.h>

    │ │ │ +

    #include <BALL/STRUCTURE/SASEdge.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::SASEdge:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::GraphEdge< SASVertex, SASEdge, SASFace > │ │ │ @@ -209,15 +209,15 @@ │ │ │   │ │ │ Index index_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Generic SASEdge Class. <>

    │ │ │ │ │ │ -

    Definition at line 33 of file SASEdge.h.

    │ │ │ +

    Definition at line 33 of file SASEdge.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ SASEdge() [1/3]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -702,15 +702,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ friend
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 47 of file SASEdge.h.

    │ │ │ +

    Definition at line 47 of file SASEdge.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ SASTriangulator

    │ │ │ │ │ │
    │ │ │ @@ -726,15 +726,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 50 of file SASEdge.h.

    │ │ │ +

    Definition at line 50 of file SASEdge.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ SASVertex

    │ │ │ │ │ │
    │ │ │ @@ -750,15 +750,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 46 of file SASEdge.h.

    │ │ │ +

    Definition at line 46 of file SASEdge.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ SolventAccessibleSurface

    │ │ │ │ │ │
    │ │ │ @@ -774,15 +774,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 48 of file SASEdge.h.

    │ │ │ +

    Definition at line 48 of file SASEdge.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ TriangulatedSAS

    │ │ │ │ │ │
    │ │ │ @@ -798,15 +798,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 49 of file SASEdge.h.

    │ │ │ +

    Definition at line 49 of file SASEdge.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ angle_

    │ │ │ │ │ │ @@ -823,15 +823,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 211 of file SASEdge.h.

    │ │ │ +

    Definition at line 211 of file SASEdge.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ circle_

    │ │ │ │ │ │
    │ │ │ @@ -847,15 +847,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 208 of file SASEdge.h.

    │ │ │ +

    Definition at line 208 of file SASEdge.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d1b/a06326.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members │ │ │
    BALL::PB Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SCORING/COMPONENTS/PB.h>

    │ │ │ +

    #include <BALL/SCORING/COMPONENTS/PB.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::PB:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::ScoringComponent │ │ │ @@ -195,15 +195,15 @@ │ │ │ - Protected Member Functions inherited from BALL::ScoringComponent │ │ │ double scaleScore (double score) const │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Poisson-Boltzmann scoring term

    │ │ │ │ │ │ -

    Definition at line 15 of file PB.h.

    │ │ │ +

    Definition at line 15 of file PB.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ PB()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -342,15 +342,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 33 of file PB.h.

    │ │ │ +

    Definition at line 33 of file PB.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ ligand_atoms_

    │ │ │ │ │ │
    │ │ │ @@ -366,15 +366,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 32 of file PB.h.

    │ │ │ +

    Definition at line 32 of file PB.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ pb_solver_

    │ │ │ │ │ │
    │ │ │ @@ -390,15 +390,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 29 of file PB.h.

    │ │ │ +

    Definition at line 29 of file PB.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ receptor_atoms_

    │ │ │ │ │ │
    │ │ │ @@ -414,15 +414,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 31 of file PB.h.

    │ │ │ +

    Definition at line 31 of file PB.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d1e/a07378.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::TReadWriteLock< ReadWriteLockType > Class Template Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SYSTEM/mutex.h>

    │ │ │ +

    #include <BALL/SYSTEM/mutex.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::TReadWriteLock< ReadWriteLockType >:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ ReadWriteLockType │ │ │ @@ -97,15 +97,15 @@ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │
    template<class ReadWriteLockType>
    │ │ │ class BALL::TReadWriteLock< ReadWriteLockType >

    This class provides a very thin wrapper around different read-write mutex types. As default, BALL supports QReadWriteLock, but if it has been configured with boost::thread support enabled, boost::mutex can also be used. Similarly, we can simply provide instantiations using, e.g, Intel thread building blocks.

    │ │ │

    A BALL-mutex needs to provide the functions void lockForRead(), void lockForWrite(), void unlock(), bool tryLockForRead(), and bool tryLockForWrite().

    │ │ │ │ │ │ -

    Definition at line 90 of file mutex.h.

    │ │ │ +

    Definition at line 90 of file mutex.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ TReadWriteLock()

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ @@ -125,15 +125,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 94 of file mutex.h.

    │ │ │ +

    Definition at line 94 of file mutex.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d1f/a05078.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Friends | │ │ │ List of all members
    │ │ │
    BALL::ForceFieldComponent Class Reference
    Molecular Modeling » Molecular Mechanics » General Force Field Classes.
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/MOLMEC/COMMON/forceFieldComponent.h>

    │ │ │ +

    #include <BALL/MOLMEC/COMMON/forceFieldComponent.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::ForceFieldComponent:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::ScoringComponent │ │ │ @@ -233,15 +233,15 @@ │ │ │   │ │ │ String type_name_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Generic force field component class.

    │ │ │ │ │ │ -

    Definition at line 34 of file forceFieldComponent.h.

    │ │ │ +

    Definition at line 34 of file forceFieldComponent.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ForceFieldComponent() [1/3]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -403,15 +403,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inline
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 100 of file forceFieldComponent.h.

    │ │ │ +

    Definition at line 100 of file forceFieldComponent.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ setEnabled()

    │ │ │ │ │ │
    │ │ │ @@ -431,15 +431,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 103 of file forceFieldComponent.h.

    │ │ │ +

    Definition at line 103 of file forceFieldComponent.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ setForceField()

    │ │ │ │ │ │
    │ │ │ @@ -641,15 +641,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 37 of file forceFieldComponent.h.

    │ │ │ +

    Definition at line 37 of file forceFieldComponent.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ energy_

    │ │ │ │ │ │ @@ -666,15 +666,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 156 of file forceFieldComponent.h.

    │ │ │ +

    Definition at line 156 of file forceFieldComponent.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ force_field_

    │ │ │ │ │ │
    │ │ │ @@ -690,15 +690,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 152 of file forceFieldComponent.h.

    │ │ │ +

    Definition at line 152 of file forceFieldComponent.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d20/a07698.html │ │ │ @@ -79,15 +79,15 @@ │ │ │ Protected Slots | │ │ │ Protected Member Functions | │ │ │ List of all members │ │ │
    BALL::VIEW::PTEDialog Class Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/DIALOGS/PTEDialog.h>

    │ │ │ +

    #include <BALL/VIEW/DIALOGS/PTEDialog.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::PTEDialog:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ QDialog │ │ │ @@ -119,15 +119,15 @@ │ │ │   │ │ │ void connectChilds_ (QObject *o) │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Dialog for choosing the element type for the edit mode of scene. \ingroups ViewDialogs

    │ │ │ │ │ │ -

    Definition at line 24 of file PTEDialog.h.

    │ │ │ +

    Definition at line 24 of file PTEDialog.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ PTEDialog()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d21/a08062.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Types | │ │ │ List of all members
    │ │ │
    BALL::VIEW::LabelModel Class Reference
    Visualisation » Model Processors
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/MODELS/labelModel.h>

    │ │ │ +

    #include <BALL/VIEW/MODELS/labelModel.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::LabelModel:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::ModelProcessor │ │ │ @@ -179,18 +179,18 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -300,15 +300,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    virtual ~UnaryProcessor ()
     
    virtual bool start ()
     
    virtual bool finish ()
     
    - Public Member Functions inherited from BALL::PropertyManager
    BALL_INLINE PropertyManager ()
    BALL_INLINE PropertyManager ()
     Default constructor.
     
    BALL_INLINE PropertyManager (const PropertyManager &property_manager)
    BALL_INLINE PropertyManager (const PropertyManager &property_manager)
     Copy constructor.
     
    virtual ~PropertyManager ()
     Destructor.
     
    virtual void destroy ()
     Clears all properties.
     
    float surface_drawing_precision_
     
    │ │ │

    Detailed Description

    │ │ │

    LabelModel class. The LabelModel is a model processor that is responsible for creating and updateing Labels. It supports special text tags, that allows for automaticaly created labels, see the documentation for the Label class.

    See also
    Label
    │ │ │ │ │ │ -

    Definition at line 36 of file labelModel.h.

    │ │ │ +

    Definition at line 36 of file labelModel.h.

    │ │ │

    Member Enumeration Documentation

    │ │ │ │ │ │

    ◆ Mode

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -320,15 +320,15 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Enumerator
    ALL_ITEMS 
    ALL_ATOMS 
    ALL_RESIDUES 
    ONE_LABEL 
    │ │ │ │ │ │ -

    Definition at line 43 of file labelModel.h.

    │ │ │ +

    Definition at line 43 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ LabelModel() [1/2]

    │ │ │ │ │ │ @@ -440,15 +440,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 82 of file labelModel.h.

    │ │ │ +

    Definition at line 82 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getFont()

    │ │ │ │ │ │
    │ │ │ @@ -467,15 +467,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 76 of file labelModel.h.

    │ │ │ +

    Definition at line 76 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getText()

    │ │ │ │ │ │
    │ │ │ @@ -494,15 +494,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 94 of file labelModel.h.

    │ │ │ +

    Definition at line 94 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ getType()

    │ │ │ │ │ │
    │ │ │ @@ -521,15 +521,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 88 of file labelModel.h.

    │ │ │ +

    Definition at line 88 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ operator()()

    │ │ │ │ │ │
    │ │ │ @@ -578,15 +578,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 79 of file labelModel.h.

    │ │ │ +

    Definition at line 79 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setFont()

    │ │ │ │ │ │
    │ │ │ @@ -606,15 +606,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 73 of file labelModel.h.

    │ │ │ +

    Definition at line 73 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setMode()

    │ │ │ │ │ │
    │ │ │ @@ -634,15 +634,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 85 of file labelModel.h.

    │ │ │ +

    Definition at line 85 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ setText()

    │ │ │ │ │ │
    │ │ │ @@ -662,15 +662,15 @@ │ │ │ │ │ │ │ │ │ inline │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 91 of file labelModel.h.

    │ │ │ +

    Definition at line 91 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ center_

    │ │ │ │ │ │ @@ -687,15 +687,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 117 of file labelModel.h.

    │ │ │ +

    Definition at line 117 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ center_processor_

    │ │ │ │ │ │
    │ │ │ @@ -711,15 +711,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 118 of file labelModel.h.

    │ │ │ +

    Definition at line 118 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ color_

    │ │ │ │ │ │
    │ │ │ @@ -735,15 +735,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 113 of file labelModel.h.

    │ │ │ +

    Definition at line 113 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ font_

    │ │ │ │ │ │
    │ │ │ @@ -759,15 +759,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 112 of file labelModel.h.

    │ │ │ +

    Definition at line 112 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ mode_

    │ │ │ │ │ │
    │ │ │ @@ -783,15 +783,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 114 of file labelModel.h.

    │ │ │ +

    Definition at line 114 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ nr_objects_

    │ │ │ │ │ │
    │ │ │ @@ -807,15 +807,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 116 of file labelModel.h.

    │ │ │ +

    Definition at line 116 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ text_

    │ │ │ │ │ │
    │ │ │ @@ -831,15 +831,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 115 of file labelModel.h.

    │ │ │ +

    Definition at line 115 of file labelModel.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d22/a05546.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Member Functions | │ │ │ List of all members
    │ │ │
    BALL::BALLPlugin Class Referenceabstract
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/PLUGIN/BALLPlugin.h>

    │ │ │ +

    #include <BALL/PLUGIN/BALLPlugin.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -95,15 +95,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    virtual ~BALLPlugin ()
     
    virtual QString getName () const =0
     
    virtual bool activate ()=0
     
    virtual bool deactivate ()=0
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 20 of file BALLPlugin.h.

    │ │ │ +

    Definition at line 20 of file BALLPlugin.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ~BALLPlugin()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -120,15 +120,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ inlinevirtual
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 23 of file BALLPlugin.h.

    │ │ │ +

    Definition at line 23 of file BALLPlugin.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ activate()

    │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d24/a04514.html │ │ │ @@ -76,44 +76,44 @@ │ │ │
    │ │ │ Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::ExpressionParser::State Struct Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/KERNEL/expressionParser.h>

    │ │ │ +

    #include <BALL/KERNEL/expressionParser.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Attributes

    Size char_count
     
    ExpressionParser * current_parser
     
    const char * buffer
     
    SyntaxTree * tree
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 172 of file expressionParser.h.

    │ │ │ +

    Definition at line 172 of file expressionParser.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ buffer

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    const char* BALL::ExpressionParser::State::buffer
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 176 of file expressionParser.h.

    │ │ │ +

    Definition at line 176 of file expressionParser.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ char_count

    │ │ │ │ │ │
    │ │ │ @@ -121,15 +121,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Size BALL::ExpressionParser::State::char_count
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 174 of file expressionParser.h.

    │ │ │ +

    Definition at line 174 of file expressionParser.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ current_parser

    │ │ │ │ │ │
    │ │ │ @@ -137,15 +137,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    ExpressionParser* BALL::ExpressionParser::State::current_parser
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 175 of file expressionParser.h.

    │ │ │ +

    Definition at line 175 of file expressionParser.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ tree

    │ │ │ │ │ │
    │ │ │ @@ -153,15 +153,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    SyntaxTree* BALL::ExpressionParser::State::tree
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 177 of file expressionParser.h.

    │ │ │ +

    Definition at line 177 of file expressionParser.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d27/a06878.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::FragmentDB::BuildBondsProcessor::Connection Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/STRUCTURE/fragmentDB.h>

    │ │ │ +

    #include <BALL/STRUCTURE/fragmentDB.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -95,29 +95,29 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Attributes

    Atom * atom
     
    String type_name
     
    float dist
     
    float delta
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 348 of file fragmentDB.h.

    │ │ │ +

    Definition at line 348 of file fragmentDB.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ atom

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Atom* BALL::FragmentDB::BuildBondsProcessor::Connection::atom
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 350 of file fragmentDB.h.

    │ │ │ +

    Definition at line 350 of file fragmentDB.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ connect_to

    │ │ │ │ │ │
    │ │ │ @@ -125,15 +125,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    String BALL::FragmentDB::BuildBondsProcessor::Connection::connect_to
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 352 of file fragmentDB.h.

    │ │ │ +

    Definition at line 352 of file fragmentDB.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ delta

    │ │ │ │ │ │
    │ │ │ @@ -141,15 +141,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    float BALL::FragmentDB::BuildBondsProcessor::Connection::delta
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 355 of file fragmentDB.h.

    │ │ │ +

    Definition at line 355 of file fragmentDB.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ dist

    │ │ │ │ │ │
    │ │ │ @@ -157,15 +157,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    float BALL::FragmentDB::BuildBondsProcessor::Connection::dist
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 354 of file fragmentDB.h.

    │ │ │ +

    Definition at line 354 of file fragmentDB.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ order

    │ │ │ │ │ │
    │ │ │ @@ -173,15 +173,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Bond::Order BALL::FragmentDB::BuildBondsProcessor::Connection::order
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 353 of file fragmentDB.h.

    │ │ │ +

    Definition at line 353 of file fragmentDB.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ type_name

    │ │ │ │ │ │
    │ │ │ @@ -189,15 +189,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    String BALL::FragmentDB::BuildBondsProcessor::Connection::type_name
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 351 of file fragmentDB.h.

    │ │ │ +

    Definition at line 351 of file fragmentDB.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d2a/a04566.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Friends | │ │ │ List of all members
    │ │ │
    BALL::PDBAtom Class Reference
    Kernel Classes » Molecular Datastructures
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/KERNEL/PDBAtom.h>

    │ │ │ +

    #include <BALL/KERNEL/PDBAtom.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::PDBAtom:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::Atom │ │ │ @@ -203,15 +203,15 @@ │ │ │   │ │ │  PDBAtom (const PDBAtom &pdb_atom, bool deep=true) │ │ │  Copy constructor.
    │ │ │   │ │ │  PDBAtom (const String &name) │ │ │  Constructor.
    │ │ │   │ │ │ - PDBAtom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Atom::Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, char branch_designator=BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR, char remoteness_indicator=BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, char alternate_location_indicator=BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR, float occupancy=BALL_PDBATOM_DEFAULT_OCCUPANCY, float temperature_factor=BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR) │ │ │ + PDBAtom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Atom::Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, char branch_designator=BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR, char remoteness_indicator=BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, char alternate_location_indicator=BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR, float occupancy=BALL_PDBATOM_DEFAULT_OCCUPANCY, float temperature_factor=BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR) │ │ │  Detailed constructor.
    │ │ │   │ │ │ virtual ~PDBAtom () │ │ │  Destructor.
    │ │ │   │ │ │ virtual void destroy () │ │ │   │ │ │ @@ -270,15 +270,15 @@ │ │ │ float getTemperatureFactor () const │ │ │   │ │ │ - Public Member Functions inherited from BALL::Atom │ │ │  Atom () │ │ │   │ │ │  Atom (const Atom &atom, bool deep=true) │ │ │   │ │ │ - Atom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, Index formal_charge=BALL_ATOM_DEFAULT_FORMAL_CHARGE) │ │ │ + Atom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, Index formal_charge=BALL_ATOM_DEFAULT_FORMAL_CHARGE) │ │ │   │ │ │ virtual ~Atom () │ │ │   │ │ │ void set (const Atom &atom, bool deep=true) │ │ │   │ │ │ void get (Atom &atom, bool deep=true) const │ │ │   │ │ │ @@ -451,39 +451,39 @@ │ │ │   │ │ │ void disableStoreInteractions () │ │ │   │ │ │ void enableStoreInteractions () │ │ │   │ │ │ - Public Member Functions inherited from BALL::Composite │ │ │ template<typename T > │ │ │ -BALL_INLINE bool apply (UnaryProcessor< T > &processor) │ │ │ +BALL_INLINE bool apply (UnaryProcessor< T > &processor) │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE bool apply (ConstUnaryProcessor< T > &processor) const │ │ │ +BALL_INLINE bool apply (ConstUnaryProcessor< T > &processor) const │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE T * getAncestor (const T &) │ │ │ +BALL_INLINE T * getAncestor (const T &) │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE const T * getAncestor (const T &) const │ │ │ +BALL_INLINE const T * getAncestor (const T &) const │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE T * getPrevious (const T &) │ │ │ +BALL_INLINE T * getPrevious (const T &) │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE const T * getPrevious (const T &dummy) const │ │ │ +BALL_INLINE const T * getPrevious (const T &dummy) const │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE T * getNext (const T &) │ │ │ +BALL_INLINE T * getNext (const T &) │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE const T * getNext (const T &dummy) const │ │ │ +BALL_INLINE const T * getNext (const T &dummy) const │ │ │   │ │ │ template<typename T > │ │ │ -BALL_INLINE bool hasAncestor (const T &dummy) const │ │ │ +BALL_INLINE bool hasAncestor (const T &dummy) const │ │ │   │ │ │  Composite () │ │ │   │ │ │  Composite (const Composite &composite, bool deep=true) │ │ │   │ │ │ virtual ~Composite () │ │ │   │ │ │ @@ -830,18 +830,18 @@ │ │ │ void write (PersistenceManager &pm) const │ │ │   │ │ │ bool read (PersistenceManager &pm) │ │ │   │ │ │ virtual void dump (::std::ostream &s=std::cout, Size depth=0) const │ │ │   │ │ │ - Public Member Functions inherited from BALL::PropertyManager │ │ │ -BALL_INLINE PropertyManager () │ │ │ +BALL_INLINE PropertyManager () │ │ │  Default constructor.
    │ │ │   │ │ │ -BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │ +BALL_INLINE PropertyManager (const PropertyManager &property_manager) │ │ │  Copy constructor.
    │ │ │   │ │ │ virtual ~PropertyManager () │ │ │  Destructor.
    │ │ │   │ │ │ void set (const PropertyManager &property_manager) │ │ │   │ │ │ @@ -988,15 +988,15 @@ │ │ │ static AtomIndexList free_list_ │ │ │   │ │ │ │ │ │

    Detailed Description

    │ │ │

    Atom class with additional attributes. This class represents atoms read from PDB files. It contains additional attributes to hold the crystallographic properties of atoms from a PDB file (e.g., temperature factor, occupancy). For details on the PDB format and the detailed meaning of those fields, please refer to the PDB documentation at http://www.rcsb.org

    │ │ │
    See also
    PDBFile
    │ │ │ │ │ │ -

    Definition at line 38 of file PDBAtom.h.

    │ │ │ +

    Definition at line 38 of file PDBAtom.h.

    │ │ │

    Member Enumeration Documentation

    │ │ │ │ │ │

    ◆ Property

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -1009,15 +1009,15 @@ │ │ │
    │ │ │ │ │ │ │ │ │
    Enumerator
    PROPERTY__HETATM 

    Property which indicates whether the current atom is a HETATM.

    │ │ │
    NUMBER_OF_PROPERTIES 

    The number of properties in PDBAtom.

    │ │ │
    │ │ │ │ │ │ -

    Definition at line 76 of file PDBAtom.h.

    │ │ │ +

    Definition at line 76 of file PDBAtom.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ RemotenessIndicator

    │ │ │ │ │ │
    │ │ │ @@ -1044,15 +1044,15 @@ │ │ │ REMOTENESS_INDICATOR__ZETA  │ │ │ REMOTENESS_INDICATOR__zeta  │ │ │ REMOTENESS_INDICATOR__ETA  │ │ │ REMOTENESS_INDICATOR__eta  │ │ │ NUMBER_OF_REMOTENESS_INDICATORS  │ │ │ │ │ │ │ │ │ -

    Definition at line 53 of file PDBAtom.h.

    │ │ │ +

    Definition at line 53 of file PDBAtom.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ PDBAtom() [1/4]

    │ │ │ │ │ │ @@ -1140,81 +1140,81 @@ │ │ │ const String &  │ │ │ name, │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ const String &  │ │ │ - type_name = BALL_ATOM_DEFAULT_TYPE_NAME, │ │ │ + type_name = BALL_ATOM_DEFAULT_TYPE_NAME, │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ Atom::Type  │ │ │ - atom_type = BALL_ATOM_DEFAULT_TYPE, │ │ │ + atom_type = BALL_ATOM_DEFAULT_TYPE, │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ const Vector3 &  │ │ │ - position = Vector3(BALL_ATOM_DEFAULT_POSITION), │ │ │ + position = Vector3(BALL_ATOM_DEFAULT_POSITION), │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ const Vector3 &  │ │ │ - velocity = Vector3(BALL_ATOM_DEFAULT_VELOCITY), │ │ │ + velocity = Vector3(BALL_ATOM_DEFAULT_VELOCITY), │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ const Vector3 &  │ │ │ - force = Vector3(BALL_ATOM_DEFAULT_FORCE), │ │ │ + force = Vector3(BALL_ATOM_DEFAULT_FORCE), │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ float  │ │ │ - charge = BALL_ATOM_DEFAULT_CHARGE, │ │ │ + charge = BALL_ATOM_DEFAULT_CHARGE, │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ float  │ │ │ - radius = BALL_ATOM_DEFAULT_RADIUS, │ │ │ + radius = BALL_ATOM_DEFAULT_RADIUS, │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ char  │ │ │ - branch_designator = BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR, │ │ │ + branch_designator = BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR, │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ char  │ │ │ - remoteness_indicator = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, │ │ │ + remoteness_indicator = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ char  │ │ │ - alternate_location_indicator = BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR, │ │ │ + alternate_location_indicator = BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR, │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ float  │ │ │ - occupancy = BALL_PDBATOM_DEFAULT_OCCUPANCY, │ │ │ + occupancy = BALL_PDBATOM_DEFAULT_OCCUPANCY, │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ float  │ │ │ - temperature_factor = BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR  │ │ │ + temperature_factor = BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR  │ │ │ │ │ │ │ │ │ │ │ │ ) │ │ │ │ │ │ │ │ │ │ │ │ @@ -1923,15 +1923,15 @@ │ │ │ │ │ │ │ │ │ friend │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 43 of file PDBAtom.h.

    │ │ │ +

    Definition at line 43 of file PDBAtom.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d31/a06574.html │ │ │ @@ -76,15 +76,15 @@ │ │ │
    │ │ │ Static Public Attributes | │ │ │ List of all members
    │ │ │
    BALL::FDPB::Boundary Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/SOLVATION/poissonBoltzmann.h>

    │ │ │ +

    #include <BALL/SOLVATION/poissonBoltzmann.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -94,15 +94,15 @@ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Static Public Attributes

    static const String ZERO
     
    static const String DEBYE
     
     
    static const String FOCUSING
     
    │ │ │

    Detailed Description

    │ │ │

    This struct contains symbols for the available boundary conditions.

    │ │ │ │ │ │ -

    Definition at line 411 of file poissonBoltzmann.h.

    │ │ │ +

    Definition at line 411 of file poissonBoltzmann.h.

    │ │ │

    Member Data Documentation

    │ │ │ │ │ │

    ◆ COULOMB

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -117,15 +117,15 @@ │ │ │ │ │ │ │ │ │
    │ │ │ static
    │ │ │
    │ │ │

    Boundary condition Coulomb: potential at boundary points is estimated using coulomb's law.

    │ │ │ │ │ │ -

    Definition at line 436 of file poissonBoltzmann.h.

    │ │ │ +

    Definition at line 436 of file poissonBoltzmann.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ DEBYE

    │ │ │ │ │ │
    │ │ │ @@ -148,15 +148,15 @@ │ │ │ \[ │ │ │ \phi_{x,y,z} = \sum_i \frac{1}{4 \pi \varepsilon \varepsilon_0} │ │ │ \frac{q_i}{r} e^{-\frac{r}{d}} │ │ │ \] │ │ │

    │ │ │ This options tends to become very slow for large grids. │ │ │ │ │ │ -

    Definition at line 431 of file poissonBoltzmann.h.

    │ │ │ +

    Definition at line 431 of file poissonBoltzmann.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ DIPOLE

    │ │ │ │ │ │
    │ │ │ @@ -173,15 +173,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │

    Boundary condition Dipole: potential is estimated via dipole potentials

    │ │ │ │ │ │ -

    Definition at line 440 of file poissonBoltzmann.h.

    │ │ │ +

    Definition at line 440 of file poissonBoltzmann.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ FOCUSING

    │ │ │ │ │ │
    │ │ │ @@ -198,15 +198,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │

    Boundary condition Focusing: potential is estimated via a larger but coarser grid. Focusing calculates a larger grid (double extension in each direction) centered on the final grid with a four times the spacing of the final grid. Focusing also assigns an estimate of the electrostatic potential to each grid point in the final grid, thus acceleratingthe convergence.

    │ │ │ │ │ │ -

    Definition at line 448 of file poissonBoltzmann.h.

    │ │ │ +

    Definition at line 448 of file poissonBoltzmann.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ZERO

    │ │ │ │ │ │
    │ │ │ @@ -223,15 +223,15 @@ │ │ │ │ │ │ static │ │ │ │ │ │ │ │ │
    │ │ │

    Boundary condition zero: boundary points have zero potential. A Potential of zero is assigned to all points on the grid boundary. This is the simplest and least accurate method. It's use is not recommended.

    │ │ │ │ │ │ -

    Definition at line 419 of file poissonBoltzmann.h.

    │ │ │ +

    Definition at line 419 of file poissonBoltzmann.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d33/a20356.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: predicate.h File Reference │ │ │ +BALL: exception.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,40 +65,119 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces
    │ │ │ -
    predicate.h File Reference
    │ │ │ +Namespaces | │ │ │ +Functions | │ │ │ +Variables
    │ │ │ +
    exception.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/COMMON/global.h>
    │ │ │ -#include <functional>
    │ │ │ +
    #include <BALL/CONFIG/config.h>
    │ │ │ +#include <BALL/COMMON/global.h>
    │ │ │ +#include <new>
    │ │ │ +#include <string>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::UnaryPredicate< T >
    class  BALL::Exception::GeneralException
     
    class  BALL::BinaryPredicate< T1, T2 >
    class  BALL::Exception::IndexUnderflow
     
    class  BALL::Exception::SizeUnderflow
     
    class  BALL::Exception::IndexOverflow
     
    class  BALL::Exception::InvalidArgument
     
    class  BALL::Exception::InvalidRange
     
    class  BALL::Exception::InvalidSize
     
    class  BALL::Exception::OutOfRange
     
    class  BALL::Exception::InvalidFormat
     
    class  BALL::Exception::IllegalSelfOperation
     
    class  BALL::Exception::NullPointer
     
    class  BALL::Exception::InvalidIterator
     
    class  BALL::Exception::IncompatibleIterators
     
    class  BALL::Exception::NotImplemented
     
    class  BALL::Exception::IllegalTreeOperation
     
    class  BALL::Exception::OutOfMemory
     
    class  BALL::Exception::BufferOverflow
     
    class  BALL::Exception::DivisionByZero
     
    class  BALL::Exception::OutOfGrid
     
    class  BALL::Exception::FileNotFound
     
    class  BALL::Exception::IllegalPosition
     
    class  BALL::Exception::ParseError
     
    class  BALL::Exception::Precondition
     
    class  BALL::Exception::Postcondition
     
    class  BALL::Exception::InvalidOption
     Exception to be thrown if an invalid option is given. More...
     
    class  BALL::Exception::TooManyErrors
     Exception to be thrown if too many errors occur, e.g. in ForceField. More...
     
    class  BALL::Exception::TooManyBonds
     Exception to be thrown if too many bonds for one atom. More...
     
    class  BALL::Exception::CUDAError
     
    class  BALL::Exception::NoBufferAvailable
     
    class  BALL::Exception::FormatUnsupported
     
    class  BALL::Exception::NotInitialized
     
    class  BALL::Exception::GlobalExceptionHandler
     
    │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ + │ │ │ +

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::Exception
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +

    │ │ │ +Functions

    BALL_EXPORT std::ostream & BALL::operator<< (std::ostream &os, const Exception::GeneralException &e)
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ +Variables

    BALL_EXPORT GlobalExceptionHandler BALL::Exception::globalHandler
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,22 +1,97 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _C_O_N_C_E_P_T │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -predicate.h File Reference │ │ │ │ + * _C_O_M_M_O_N │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _F_u_n_c_t_i_o_n_s | _V_a_r_i_a_b_l_e_s │ │ │ │ +exception.h File Reference │ │ │ │ +#include │ │ │ │ #include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -#include │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_U_n_a_r_y_P_r_e_d_i_c_a_t_e_<_ _T_ _> │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │   │ │ │ │ -class   _B_A_L_L_:_:_B_i_n_a_r_y_P_r_e_d_i_c_a_t_e_<_ _T_1_,_ _T_2_ _> │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_U_n_d_e_r_f_l_o_w │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_S_i_z_e_U_n_d_e_r_f_l_o_w │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_O_v_e_r_f_l_o_w │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_A_r_g_u_m_e_n_t │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_R_a_n_g_e │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_S_i_z_e │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_R_a_n_g_e │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_F_o_r_m_a_t │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_l_l_e_g_a_l_S_e_l_f_O_p_e_r_a_t_i_o_n │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_u_l_l_P_o_i_n_t_e_r │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_I_t_e_r_a_t_o_r │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_c_o_m_p_a_t_i_b_l_e_I_t_e_r_a_t_o_r_s │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_o_t_I_m_p_l_e_m_e_n_t_e_d │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_l_l_e_g_a_l_T_r_e_e_O_p_e_r_a_t_i_o_n │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_M_e_m_o_r_y │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_B_u_f_f_e_r_O_v_e_r_f_l_o_w │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_D_i_v_i_s_i_o_n_B_y_Z_e_r_o │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_G_r_i_d │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_F_i_l_e_N_o_t_F_o_u_n_d │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_l_l_e_g_a_l_P_o_s_i_t_i_o_n │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_P_a_r_s_e_E_r_r_o_r │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_P_r_e_c_o_n_d_i_t_i_o_n │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_P_o_s_t_c_o_n_d_i_t_i_o_n │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_O_p_t_i_o_n │ │ │ │ +  _E_x_c_e_p_t_i_o_n to be thrown if an invalid option is given. _M_o_r_e_._._. │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_T_o_o_M_a_n_y_E_r_r_o_r_s │ │ │ │ +  _E_x_c_e_p_t_i_o_n to be thrown if too many errors occur, e.g. in _F_o_r_c_e_F_i_e_l_d. │ │ │ │ + _M_o_r_e_._._. │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_T_o_o_M_a_n_y_B_o_n_d_s │ │ │ │ +  _E_x_c_e_p_t_i_o_n to be thrown if too many bonds for one atom. _M_o_r_e_._._. │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_C_U_D_A_E_r_r_o_r │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_o_B_u_f_f_e_r_A_v_a_i_l_a_b_l_e │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_F_o_r_m_a_t_U_n_s_u_p_p_o_r_t_e_d │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_o_t_I_n_i_t_i_a_l_i_z_e_d │ │ │ │ +  │ │ │ │ +class   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +namespace   _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n │ │ │ │ +  │ │ │ │ +FFuunnccttiioonnss │ │ │ │ +_B_A_L_L___E_X_P_O_R_T std::ostream &  _B_A_L_L_:_:_o_p_e_r_a_t_o_r_<_< (std::ostream &os, const │ │ │ │ + _E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n &e) │ │ │ │ +  │ │ │ │ +VVaarriiaabblleess │ │ │ │ +_B_A_L_L___E_X_P_O_R_T _G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r  _B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_g_l_o_b_a_l_H_a_n_d_l_e_r │ │ │ │ +  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d33/a20356_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: predicate.h Source File │ │ │ +BALL: exception.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,98 +70,547 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    CONCEPT/predicate.h
    │ │ │ +
    COMMON/exception.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_CONCEPT_PREDICATE_H
    │ │ │ -
    6#define BALL_CONCEPT_PREDICATE_H
    │ │ │ +
    4
    │ │ │ +
    5#ifndef BALL_COMMON_EXCEPTION_H
    │ │ │ +
    6#define BALL_COMMON_EXCEPTION_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ -
    9# include <BALL/COMMON/global.h>
    │ │ │ +
    8#ifndef BALL_CONFIG_CONFIG_H
    │ │ │ +
    9# include <BALL/CONFIG/config.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#include <functional>
    │ │ │ -
    13
    │ │ │ -
    14namespace BALL
    │ │ │ -
    15{
    │ │ │ -
    16 using std::unary_function;
    │ │ │ -
    17 using std::binary_function;
    │ │ │ -
    18
    │ │ │ -
    24
    │ │ │ -
    27 template <typename T>
    │ │ │ -
    │ │ │ -
    28 class UnaryPredicate
    │ │ │ -
    29 : public unary_function<T, bool>
    │ │ │ -
    30 {
    │ │ │ -
    31 public:
    │ │ │ -
    33 virtual ~UnaryPredicate() {}
    │ │ │ -
    34
    │ │ │ -
    │ │ │ -
    36 virtual bool operator() (const T& /* x */) const
    │ │ │ -
    37 ;
    │ │ │ -
    38 };
    │ │ │ -
    39
    │ │ │ -
    42 template <typename T1, typename T2>
    │ │ │ -
    │ │ │ -
    43 class BinaryPredicate
    │ │ │ -
    44 : public binary_function<T1, T2, bool>
    │ │ │ -
    45 {
    │ │ │ -
    46 public:
    │ │ │ -
    47
    │ │ │ -
    49 virtual bool operator() (const T1& x, const T2& y) const
    │ │ │ -
    50 ;
    │ │ │ -
    51
    │ │ │ -
    53 virtual ~BinaryPredicate() {}
    │ │ │ -
    54 };
    │ │ │ -
    │ │ │ -
    55
    │ │ │ -
    56 template <typename T>
    │ │ │ -
    │ │ │ -
    57 bool UnaryPredicate<T>::operator() (const T& /* x */) const
    │ │ │ -
    58
    │ │ │ -
    59 {
    │ │ │ -
    60 return true;
    │ │ │ -
    61 }
    │ │ │ -
    │ │ │ -
    │ │ │ -
    62
    │ │ │ -
    63 template <typename T1, typename T2>
    │ │ │ -
    │ │ │ -
    64 bool BinaryPredicate<T1, T2>::operator() (const T1&, const T2&) const
    │ │ │ -
    65
    │ │ │ -
    66 {
    │ │ │ -
    67 return true;
    │ │ │ -
    68 }
    │ │ │ -
    │ │ │ -
    70} // namespace BALL
    │ │ │ -
    71
    │ │ │ -
    72
    │ │ │ -
    73#endif // BALL_CONCEPT_PREDICATE_H
    │ │ │ -
    │ │ │ - │ │ │ - │ │ │ -
    BALL::UnaryPredicate::operator()
    virtual bool operator()(const T &) const
    Definition CONCEPT/predicate.h:57
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::BinaryPredicate::operator()
    virtual bool operator()(const T1 &x, const T2 &y) const
    Definition CONCEPT/predicate.h:64
    │ │ │ - │ │ │ +
    12#ifndef BALL_COMMON_GLOBAL_H
    │ │ │ +
    13# include <BALL/COMMON/global.h>
    │ │ │ +
    14#endif
    │ │ │ +
    15
    │ │ │ +
    16#ifdef BALL_COMPILER_MSVC
    │ │ │ +
    17 #pragma warning(push)
    │ │ │ +
    18 #pragma warning( disable : 4251 ) //disable needs to have dll-interface to be used by clients of class 'std::string'
    │ │ │ +
    19#endif
    │ │ │ +
    20
    │ │ │ +
    21#include <new>
    │ │ │ +
    22#include <string>
    │ │ │ +
    23
    │ │ │ +
    24namespace BALL
    │ │ │ +
    25{
    │ │ │ +
    26
    │ │ │ +
    27 class String;
    │ │ │ +
    28
    │ │ │ +
    │ │ │ +
    32 namespace Exception
    │ │ │ +
    33 {
    │ │ │ +
    34
    │ │ │ +
    │ │ │ +
    59 class BALL_EXPORT GeneralException
    │ │ │ +
    60 : public std::exception
    │ │ │ +
    61 {
    │ │ │ +
    62 public:
    │ │ │ +
    63
    │ │ │ +
    67
    │ │ │ +
    69 GeneralException();
    │ │ │ +
    70
    │ │ │ +
    72 GeneralException(const char* file, int line);
    │ │ │ +
    73
    │ │ │ +
    75 GeneralException
    │ │ │ +
    76 (const char* file, int line,
    │ │ │ +
    77 const String& name , const String& message);
    │ │ │ +
    78
    │ │ │ +
    80 GeneralException(const GeneralException& exception);
    │ │ │ +
    81
    │ │ │ +
    83 virtual ~GeneralException() throw();
    │ │ │ +
    85
    │ │ │ +
    89
    │ │ │ +
    91 const char* getName() const;
    │ │ │ +
    92
    │ │ │ +
    94 const char* getMessage() const;
    │ │ │ +
    95
    │ │ │ +
    97 void setMessage(const std::string& message);
    │ │ │ +
    98
    │ │ │ +
    100 int getLine() const;
    │ │ │ +
    101
    │ │ │ +
    103 const char* getFile() const;
    │ │ │ +
    105
    │ │ │ +
    106 protected:
    │ │ │ +
    107 const char* file_;
    │ │ │ +
    108 int line_;
    │ │ │ +
    109
    │ │ │ +
    110 std::string name_;
    │ │ │ +
    111 std::string message_;
    │ │ │ +
    112 };
    │ │ │ +
    │ │ │ +
    113
    │ │ │ +
    │ │ │ +
    122 class BALL_EXPORT IndexUnderflow
    │ │ │ +
    123 : public GeneralException
    │ │ │ +
    124 {
    │ │ │ +
    125 public:
    │ │ │ +
    126
    │ │ │ +
    127 IndexUnderflow(const char* file, int line, Index index = 0, Size size = 0);
    │ │ │ +
    128
    │ │ │ +
    129
    │ │ │ +
    130 protected:
    │ │ │ +
    131
    │ │ │ +
    132 Size size_;
    │ │ │ +
    133 Index index_;
    │ │ │ +
    134 };
    │ │ │ +
    │ │ │ +
    135
    │ │ │ +
    │ │ │ +
    143 class BALL_EXPORT SizeUnderflow
    │ │ │ +
    144 : public GeneralException
    │ │ │ +
    145 {
    │ │ │ +
    146 public:
    │ │ │ +
    147
    │ │ │ +
    148 SizeUnderflow(const char* file, int line, Size size = 0);
    │ │ │ +
    149
    │ │ │ +
    150 protected:
    │ │ │ +
    151 Size size_;
    │ │ │ +
    152 };
    │ │ │ +
    │ │ │ +
    153
    │ │ │ +
    │ │ │ +
    162 class BALL_EXPORT IndexOverflow
    │ │ │ +
    163 : public GeneralException
    │ │ │ +
    164 {
    │ │ │ +
    165 public:
    │ │ │ +
    166 IndexOverflow(const char* file, int line, Index index = 0, Size size = 0);
    │ │ │ +
    167
    │ │ │ +
    168 protected:
    │ │ │ +
    169
    │ │ │ +
    170 Size size_;
    │ │ │ +
    171 Index index_;
    │ │ │ +
    172 };
    │ │ │ +
    │ │ │ +
    173
    │ │ │ +
    │ │ │ +
    177 class BALL_EXPORT InvalidArgument
    │ │ │ +
    178 : public GeneralException
    │ │ │ +
    179 {
    │ │ │ +
    180 public:
    │ │ │ +
    181 InvalidArgument(const char* file, int line, const String& arg);
    │ │ │ +
    182 };
    │ │ │ +
    │ │ │ +
    183
    │ │ │ +
    │ │ │ +
    187 class BALL_EXPORT InvalidRange
    │ │ │ +
    188 : public GeneralException
    │ │ │ +
    189 {
    │ │ │ +
    190 public:
    │ │ │ +
    191 InvalidRange(const char* file, int line, float value);
    │ │ │ +
    192 };
    │ │ │ +
    │ │ │ +
    193
    │ │ │ +
    194
    │ │ │ +
    │ │ │ +
    201 class BALL_EXPORT InvalidSize
    │ │ │ +
    202 : public GeneralException
    │ │ │ +
    203 {
    │ │ │ +
    204 public:
    │ │ │ +
    205
    │ │ │ +
    206 InvalidSize(const char* file, int line, Size size = 0);
    │ │ │ +
    207
    │ │ │ +
    208 protected:
    │ │ │ +
    209 Size size_;
    │ │ │ +
    210 };
    │ │ │ +
    │ │ │ +
    211
    │ │ │ +
    212
    │ │ │ +
    │ │ │ +
    217 class BALL_EXPORT OutOfRange
    │ │ │ +
    218 : public GeneralException
    │ │ │ +
    219 {
    │ │ │ +
    220 public:
    │ │ │ +
    221 OutOfRange(const char* file, int line);
    │ │ │ +
    222 };
    │ │ │ +
    │ │ │ +
    223
    │ │ │ +
    │ │ │ +
    229 class BALL_EXPORT InvalidFormat
    │ │ │ +
    230 : public GeneralException
    │ │ │ +
    231 {
    │ │ │ +
    232 public:
    │ │ │ +
    233 InvalidFormat(const char* file, int line, const String& s);
    │ │ │ +
    234
    │ │ │ +
    235 ~InvalidFormat() throw();
    │ │ │ +
    236
    │ │ │ +
    237 protected:
    │ │ │ +
    238
    │ │ │ +
    239 std::string format_;
    │ │ │ +
    240 };
    │ │ │ +
    │ │ │ +
    241
    │ │ │ +
    │ │ │ +
    247 class BALL_EXPORT IllegalSelfOperation
    │ │ │ +
    248 : public GeneralException
    │ │ │ +
    249 {
    │ │ │ +
    250 public:
    │ │ │ +
    251 IllegalSelfOperation(const char* file, int line);
    │ │ │ +
    252 };
    │ │ │ +
    │ │ │ +
    253
    │ │ │ +
    │ │ │ +
    258 class BALL_EXPORT NullPointer
    │ │ │ +
    259 : public GeneralException
    │ │ │ +
    260 {
    │ │ │ +
    261 public:
    │ │ │ +
    262 NullPointer(const char* file, int line);
    │ │ │ +
    263 };
    │ │ │ +
    │ │ │ +
    264
    │ │ │ +
    │ │ │ +
    268 class BALL_EXPORT InvalidIterator
    │ │ │ +
    269 : public GeneralException
    │ │ │ +
    270 {
    │ │ │ +
    271 public:
    │ │ │ +
    272 InvalidIterator(const char* file, int line);
    │ │ │ +
    273 };
    │ │ │ +
    │ │ │ +
    274
    │ │ │ +
    │ │ │ +
    279 class BALL_EXPORT IncompatibleIterators
    │ │ │ +
    280 : public GeneralException
    │ │ │ +
    281 {
    │ │ │ +
    282 public:
    │ │ │ +
    283 IncompatibleIterators(const char* file, int line);
    │ │ │ +
    284 };
    │ │ │ +
    │ │ │ +
    285
    │ │ │ +
    │ │ │ +
    292 class BALL_EXPORT NotImplemented
    │ │ │ +
    293 : public GeneralException
    │ │ │ +
    294 {
    │ │ │ +
    295 public:
    │ │ │ +
    296 NotImplemented(const char* file, int line);
    │ │ │ +
    297 };
    │ │ │ +
    │ │ │ +
    298
    │ │ │ +
    │ │ │ +
    303 class BALL_EXPORT IllegalTreeOperation
    │ │ │ +
    304 : public GeneralException
    │ │ │ +
    305 {
    │ │ │ +
    306 public:
    │ │ │ +
    307 IllegalTreeOperation(const char* file, int line);
    │ │ │ +
    308 };
    │ │ │ +
    │ │ │ +
    309
    │ │ │ +
    │ │ │ +
    316 class BALL_EXPORT OutOfMemory
    │ │ │ +
    317 : public GeneralException, public std::bad_alloc
    │ │ │ +
    318 {
    │ │ │ +
    319 public:
    │ │ │ +
    320 OutOfMemory(const char* file, int line, Size size = 0);
    │ │ │ +
    321
    │ │ │ +
    322 virtual ~OutOfMemory()
    │ │ │ +
    323 throw();
    │ │ │ +
    324
    │ │ │ +
    325 protected:
    │ │ │ +
    326 Size size_;
    │ │ │ +
    327 };
    │ │ │ +
    │ │ │ +
    328
    │ │ │ +
    │ │ │ +
    331 class BALL_EXPORT BufferOverflow
    │ │ │ +
    332 : public GeneralException
    │ │ │ +
    333 {
    │ │ │ +
    334 public:
    │ │ │ +
    335 BufferOverflow(const char* file, int line);
    │ │ │ +
    336 };
    │ │ │ +
    │ │ │ +
    337
    │ │ │ +
    │ │ │ +
    340 class BALL_EXPORT DivisionByZero
    │ │ │ +
    341 : public GeneralException
    │ │ │ +
    342 {
    │ │ │ +
    343 public:
    │ │ │ +
    344 DivisionByZero(const char* file, int line);
    │ │ │ +
    345 };
    │ │ │ +
    │ │ │ +
    346
    │ │ │ +
    │ │ │ +
    349 class BALL_EXPORT OutOfGrid
    │ │ │ +
    350 : public GeneralException
    │ │ │ +
    351 {
    │ │ │ +
    352 public:
    │ │ │ +
    353 OutOfGrid(const char* file, int line);
    │ │ │ +
    354 };
    │ │ │ +
    │ │ │ +
    355
    │ │ │ +
    │ │ │ +
    359 class BALL_EXPORT FileNotFound
    │ │ │ +
    360 : public GeneralException
    │ │ │ +
    361 {
    │ │ │ +
    362 public:
    │ │ │ +
    363 FileNotFound(const char* file, int line, const String& filename);
    │ │ │ +
    364
    │ │ │ +
    365 ~FileNotFound()
    │ │ │ +
    366 throw();
    │ │ │ +
    367 String getFilename() const;
    │ │ │ +
    368
    │ │ │ +
    369 protected:
    │ │ │ +
    370 std::string filename_;
    │ │ │ +
    371 };
    │ │ │ +
    │ │ │ +
    372
    │ │ │ +
    │ │ │ +
    376 class BALL_EXPORT IllegalPosition
    │ │ │ +
    377 : public GeneralException
    │ │ │ +
    378 {
    │ │ │ +
    379 public:
    │ │ │ +
    380 IllegalPosition(const char* file, int line, float x, float y, float z);
    │ │ │ +
    381 };
    │ │ │ +
    │ │ │ +
    382
    │ │ │ +
    │ │ │ +
    386 class BALL_EXPORT ParseError
    │ │ │ +
    387 : public GeneralException
    │ │ │ +
    388 {
    │ │ │ +
    389 public:
    │ │ │ +
    391 ParseError(const char* file, int line, const String& expression,
    │ │ │ +
    392 const String& message);
    │ │ │ +
    393 };
    │ │ │ +
    │ │ │ +
    394
    │ │ │ +
    │ │ │ +
    398 class BALL_EXPORT Precondition
    │ │ │ +
    399 : public GeneralException
    │ │ │ +
    400 {
    │ │ │ +
    401 public:
    │ │ │ +
    403 Precondition(const char* file, int line, const char* condition);
    │ │ │ +
    404 };
    │ │ │ +
    │ │ │ +
    405
    │ │ │ +
    │ │ │ +
    409 class BALL_EXPORT Postcondition
    │ │ │ +
    410 : public GeneralException
    │ │ │ +
    411 {
    │ │ │ +
    412 public:
    │ │ │ +
    414 Postcondition(const char* file, int line, const char* condition);
    │ │ │ +
    415 };
    │ │ │ +
    │ │ │ +
    416
    │ │ │ +
    │ │ │ +
    418 class BALL_EXPORT InvalidOption: public Exception::GeneralException
    │ │ │ +
    419 {
    │ │ │ +
    420 public:
    │ │ │ +
    421
    │ │ │ +
    423 InvalidOption(const char* file, int line, String option);
    │ │ │ +
    424 };
    │ │ │ +
    │ │ │ +
    425
    │ │ │ +
    │ │ │ +
    427 class BALL_EXPORT TooManyErrors
    │ │ │ +
    428 : public Exception::GeneralException
    │ │ │ +
    429 {
    │ │ │ +
    430 public:
    │ │ │ +
    432 TooManyErrors(const char* file, int line);
    │ │ │ +
    433 };
    │ │ │ +
    │ │ │ +
    434
    │ │ │ +
    │ │ │ +
    436 class BALL_EXPORT TooManyBonds
    │ │ │ +
    437 : public Exception::GeneralException
    │ │ │ +
    438 {
    │ │ │ +
    439 public:
    │ │ │ +
    441 TooManyBonds(const char* file, int line, const String& error);
    │ │ │ +
    442 };
    │ │ │ +
    │ │ │ +
    443
    │ │ │ +
    │ │ │ +
    447 class BALL_DEPRECATED BALL_EXPORT CUDAError
    │ │ │ +
    448 : public Exception::GeneralException
    │ │ │ +
    449 {
    │ │ │ +
    450 public:
    │ │ │ +
    451 CUDAError(const char* file, int line, const String& error);
    │ │ │ +
    452 };
    │ │ │ +
    │ │ │ +
    453
    │ │ │ +
    │ │ │ +
    461 class BALL_EXPORT NoBufferAvailable
    │ │ │ +
    462 : public Exception::GeneralException
    │ │ │ +
    463 {
    │ │ │ +
    464 public:
    │ │ │ +
    465 NoBufferAvailable(const char* file, int line, const String& reason);
    │ │ │ +
    466 };
    │ │ │ +
    │ │ │ +
    467
    │ │ │ +
    │ │ │ +
    473 class BALL_EXPORT FormatUnsupported
    │ │ │ +
    474 : public Exception::GeneralException
    │ │ │ +
    475 {
    │ │ │ +
    476 public:
    │ │ │ +
    477 FormatUnsupported(const char* file, int line);
    │ │ │ +
    478 };
    │ │ │ +
    │ │ │ +
    479
    │ │ │ +
    │ │ │ +
    485 class BALL_EXPORT NotInitialized : public Exception::GeneralException
    │ │ │ +
    486 {
    │ │ │ +
    487 public:
    │ │ │ +
    488 NotInitialized(const char* file, int line, const String& reason);
    │ │ │ +
    489 };
    │ │ │ +
    │ │ │ +
    490
    │ │ │ +
    │ │ │ +
    493 class BALL_EXPORT GlobalExceptionHandler
    │ │ │ +
    494 {
    │ │ │ +
    495 public:
    │ │ │ +
    499
    │ │ │ +
    516 GlobalExceptionHandler();
    │ │ │ +
    518
    │ │ │ +
    522
    │ │ │ +
    524 static void setName(const String& name);
    │ │ │ +
    525
    │ │ │ +
    527 static void setMessage(const String& message);
    │ │ │ +
    528
    │ │ │ +
    530 static void setLine(int line);
    │ │ │ +
    531
    │ │ │ +
    533 static void setFile(const String& file);
    │ │ │ +
    534
    │ │ │ +
    536 static void set
    │ │ │ +
    537 (const String& file, int line,
    │ │ │ +
    538 const String& name, const String& message);
    │ │ │ +
    540
    │ │ │ +
    541 protected:
    │ │ │ +
    542
    │ │ │ +
    544 static void terminate();
    │ │ │ +
    545
    │ │ │ +
    549 static void newHandler();
    │ │ │ +
    550
    │ │ │ +
    551 static std::string file_;
    │ │ │ +
    552 static int line_;
    │ │ │ +
    553 static std::string name_;
    │ │ │ +
    554 static std::string message_;
    │ │ │ +
    555 };
    │ │ │ +
    │ │ │ +
    556
    │ │ │ +
    559 BALL_EXPORT extern GlobalExceptionHandler globalHandler;
    │ │ │ +
    560
    │ │ │ +
    561 }
    │ │ │ +
    │ │ │ +
    580 BALL_EXPORT
    │ │ │ +
    581 std::ostream& operator << (std::ostream& os, const Exception::GeneralException& e);
    │ │ │ +
    582
    │ │ │ +
    583} // namespace BALL
    │ │ │ +
    584
    │ │ │ +
    585#ifdef BALL_COMPILER_MSVC
    │ │ │ +
    586 #pragma warning(pop)
    │ │ │ +
    587#endif
    │ │ │ +
    588
    │ │ │ +
    589#endif // BALL_COMMON_EXCEPTION_H
    │ │ │ +
    std
    STL namespace.
    │ │ │ + │ │ │ +
    BALL::Exception::globalHandler
    BALL_EXPORT GlobalExceptionHandler globalHandler
    │ │ │ + │ │ │ +
    BALL::Exception::GeneralException::~GeneralException
    virtual ~GeneralException()
    Destructor.
    │ │ │ +
    BALL::Exception::GeneralException::GeneralException
    GeneralException()
    Default constructor.
    │ │ │ +
    BALL::Exception::GeneralException::GeneralException
    GeneralException(const char *file, int line, const String &name, const String &message)
    Constructor.
    │ │ │ +
    BALL::Exception::GeneralException::GeneralException
    GeneralException(const char *file, int line)
    Constructor.
    │ │ │ +
    BALL::Exception::GeneralException::GeneralException
    GeneralException(const GeneralException &exception)
    Copy constructor.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Exception::IndexUnderflow::IndexUnderflow
    IndexUnderflow(const char *file, int line, Index index=0, Size size=0)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Exception::SizeUnderflow::SizeUnderflow
    SizeUnderflow(const char *file, int line, Size size=0)
    │ │ │ + │ │ │ +
    BALL::Exception::IndexOverflow::IndexOverflow
    IndexOverflow(const char *file, int line, Index index=0, Size size=0)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Exception::InvalidArgument::InvalidArgument
    InvalidArgument(const char *file, int line, const String &arg)
    │ │ │ + │ │ │ +
    BALL::Exception::InvalidRange::InvalidRange
    InvalidRange(const char *file, int line, float value)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Exception::InvalidSize::InvalidSize
    InvalidSize(const char *file, int line, Size size=0)
    │ │ │ + │ │ │ +
    BALL::Exception::OutOfRange::OutOfRange
    OutOfRange(const char *file, int line)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Exception::InvalidFormat::InvalidFormat
    InvalidFormat(const char *file, int line, const String &s)
    │ │ │ + │ │ │ +
    BALL::Exception::IllegalSelfOperation::IllegalSelfOperation
    IllegalSelfOperation(const char *file, int line)
    │ │ │ + │ │ │ +
    BALL::Exception::NullPointer::NullPointer
    NullPointer(const char *file, int line)
    │ │ │ + │ │ │ +
    BALL::Exception::InvalidIterator::InvalidIterator
    InvalidIterator(const char *file, int line)
    │ │ │ + │ │ │ +
    BALL::Exception::IncompatibleIterators::IncompatibleIterators
    IncompatibleIterators(const char *file, int line)
    │ │ │ + │ │ │ +
    BALL::Exception::NotImplemented::NotImplemented
    NotImplemented(const char *file, int line)
    │ │ │ + │ │ │ +
    BALL::Exception::IllegalTreeOperation::IllegalTreeOperation
    IllegalTreeOperation(const char *file, int line)
    │ │ │ + │ │ │ +
    BALL::Exception::OutOfMemory::OutOfMemory
    OutOfMemory(const char *file, int line, Size size=0)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Exception::BufferOverflow::BufferOverflow
    BufferOverflow(const char *file, int line)
    │ │ │ + │ │ │ +
    BALL::Exception::DivisionByZero::DivisionByZero
    DivisionByZero(const char *file, int line)
    │ │ │ + │ │ │ +
    BALL::Exception::OutOfGrid::OutOfGrid
    OutOfGrid(const char *file, int line)
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Exception::FileNotFound::FileNotFound
    FileNotFound(const char *file, int line, const String &filename)
    │ │ │ + │ │ │ +
    BALL::Exception::IllegalPosition::IllegalPosition
    IllegalPosition(const char *file, int line, float x, float y, float z)
    │ │ │ + │ │ │ +
    BALL::Exception::ParseError::ParseError
    ParseError(const char *file, int line, const String &expression, const String &message)
    │ │ │ + │ │ │ +
    BALL::Exception::Precondition::Precondition
    Precondition(const char *file, int line, const char *condition)
    │ │ │ + │ │ │ +
    BALL::Exception::Postcondition::Postcondition
    Postcondition(const char *file, int line, const char *condition)
    │ │ │ +
    BALL::Exception::InvalidOption
    Exception to be thrown if an invalid option is given.
    Definition COMMON/exception.h:419
    │ │ │ +
    BALL::Exception::InvalidOption::InvalidOption
    InvalidOption(const char *file, int line, String option)
    │ │ │ +
    BALL::Exception::TooManyErrors
    Exception to be thrown if too many errors occur, e.g. in ForceField.
    Definition COMMON/exception.h:429
    │ │ │ +
    BALL::Exception::TooManyErrors::TooManyErrors
    TooManyErrors(const char *file, int line)
    │ │ │ +
    BALL::Exception::TooManyBonds
    Exception to be thrown if too many bonds for one atom.
    Definition COMMON/exception.h:438
    │ │ │ +
    BALL::Exception::TooManyBonds::TooManyBonds
    TooManyBonds(const char *file, int line, const String &error)
    │ │ │ + │ │ │ +
    BALL::Exception::CUDAError::CUDAError
    CUDAError(const char *file, int line, const String &error)
    │ │ │ + │ │ │ +
    BALL::Exception::NoBufferAvailable::NoBufferAvailable
    NoBufferAvailable(const char *file, int line, const String &reason)
    │ │ │ + │ │ │ +
    BALL::Exception::FormatUnsupported::FormatUnsupported
    FormatUnsupported(const char *file, int line)
    │ │ │ + │ │ │ +
    BALL::Exception::NotInitialized::NotInitialized
    NotInitialized(const char *file, int line, const String &reason)
    │ │ │ + │ │ │ +
    BALL::Exception::GlobalExceptionHandler::set
    static void set(const String &file, int line, const String &name, const String &message)
    Set all exception attributes.
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Exception::GlobalExceptionHandler::setFile
    static void setFile(const String &file)
    The source file name where the exception was thrown.
    │ │ │ +
    BALL::Exception::GlobalExceptionHandler::setName
    static void setName(const String &name)
    Assign the name of the exception. This should agree with the class name.
    │ │ │ +
    BALL::Exception::GlobalExceptionHandler::setLine
    static void setLine(int line)
    Set the line number the exception was thrown. Should be set to LINE in most cases.
    │ │ │ +
    BALL::Exception::GlobalExceptionHandler::terminate
    static void terminate()
    The BALL replacement for terminate.
    │ │ │ +
    BALL::Exception::GlobalExceptionHandler::setMessage
    static void setMessage(const String &message)
    Set the error message.
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_DEPRECATED
    #define BALL_DEPRECATED
    Definition COMMON/global.h:64
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,89 +1,597 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _C_O_N_C_E_P_T │ │ │ │ -CONCEPT/predicate.h │ │ │ │ + * _C_O_M_M_O_N │ │ │ │ +COMMON/exception.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_CONCEPT_PREDICATE_H │ │ │ │ -6#define BALL_CONCEPT_PREDICATE_H │ │ │ │ +5#ifndef BALL_COMMON_EXCEPTION_H │ │ │ │ +6#define BALL_COMMON_EXCEPTION_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ -9# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +8#ifndef BALL_CONFIG_CONFIG_H │ │ │ │ +9# include │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#include │ │ │ │ -13 │ │ │ │ -14namespace _B_A_L_L │ │ │ │ -15{ │ │ │ │ -16 using std::unary_function; │ │ │ │ -17 using std::binary_function; │ │ │ │ -18 │ │ │ │ -24 │ │ │ │ -27 template │ │ │ │ -_2_8 class _U_n_a_r_y_P_r_e_d_i_c_a_t_e │ │ │ │ -29 : public unary_function │ │ │ │ -30 { │ │ │ │ -31 public: │ │ │ │ -_3_3 virtual _~_U_n_a_r_y_P_r_e_d_i_c_a_t_e() {} │ │ │ │ +12#ifndef BALL_COMMON_GLOBAL_H │ │ │ │ +13# include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifdef BALL_COMPILER_MSVC │ │ │ │ +17 #pragma warning(push) │ │ │ │ +18 #pragma warning( disable : 4251 ) //disable needs to have dll-interface to │ │ │ │ +be used by clients of class 'std::string' │ │ │ │ +19#endif │ │ │ │ +20 │ │ │ │ +21#include │ │ │ │ +22#include │ │ │ │ +23 │ │ │ │ +24namespace _B_A_L_L │ │ │ │ +25{ │ │ │ │ +26 │ │ │ │ +27 class String; │ │ │ │ +28 │ │ │ │ +_3_2 namespace Exception │ │ │ │ +33 { │ │ │ │ 34 │ │ │ │ -_3_6 virtual bool _o_p_e_r_a_t_o_r_(_)_ (const T& /* x */) const │ │ │ │ -37 ; │ │ │ │ -38 }; │ │ │ │ -39 │ │ │ │ -42 template │ │ │ │ -_4_3 class _B_i_n_a_r_y_P_r_e_d_i_c_a_t_e │ │ │ │ -44 : public binary_function │ │ │ │ -45 { │ │ │ │ -46 public: │ │ │ │ -47 │ │ │ │ -49 virtual bool _o_p_e_r_a_t_o_r_(_)_ (const T1& x, const T2& y) const │ │ │ │ -50 ; │ │ │ │ -51 │ │ │ │ -_5_3 virtual _~_B_i_n_a_r_y_P_r_e_d_i_c_a_t_e() {} │ │ │ │ -54 }; │ │ │ │ -55 │ │ │ │ -56 template │ │ │ │ -_5_7 bool _U_n_a_r_y_P_r_e_d_i_c_a_t_e_<_T_>_:_:_o_p_e_r_a_t_o_r_(_)_ (const T& /* x */) const │ │ │ │ -58 │ │ │ │ -59 { │ │ │ │ -60 return true; │ │ │ │ -61 } │ │ │ │ -62 │ │ │ │ -63 template │ │ │ │ -_6_4 bool _B_i_n_a_r_y_P_r_e_d_i_c_a_t_e_<_T_1_,_ _T_2_>_:_:_o_p_e_r_a_t_o_r_(_)_ (const T1&, const T2&) const │ │ │ │ -65 │ │ │ │ -66 { │ │ │ │ -67 return true; │ │ │ │ -68 } │ │ │ │ -70} // namespace BALL │ │ │ │ -71 │ │ │ │ -72 │ │ │ │ -73#endif // BALL_CONCEPT_PREDICATE_H │ │ │ │ +_5_9 class _B_A_L_L___E_X_P_O_R_T _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +60 : public std::exception │ │ │ │ +61 { │ │ │ │ +62 public: │ │ │ │ +63 │ │ │ │ +67 │ │ │ │ +_6_9 _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n(); │ │ │ │ +70 │ │ │ │ +_7_2 _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n(const char* file, int line); │ │ │ │ +73 │ │ │ │ +_7_5 _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +76 (const char* file, int line, │ │ │ │ +77 const _S_t_r_i_n_g& name , const _S_t_r_i_n_g& message); │ │ │ │ +78 │ │ │ │ +_8_0 _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n(const _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n& exception); │ │ │ │ +81 │ │ │ │ +_8_3 virtual _~_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n() throw(); │ │ │ │ +85 │ │ │ │ +89 │ │ │ │ +_9_1 const char* getName() const; │ │ │ │ +92 │ │ │ │ +_9_4 const char* getMessage() const; │ │ │ │ +95 │ │ │ │ +_9_7 void setMessage(const _s_t_d::string& message); │ │ │ │ +98 │ │ │ │ +_1_0_0 int getLine() const; │ │ │ │ +101 │ │ │ │ +_1_0_3 const char* getFile() const; │ │ │ │ +105 │ │ │ │ +106 protected: │ │ │ │ +_1_0_7 const char* file_; │ │ │ │ +_1_0_8 int line_; │ │ │ │ +109 │ │ │ │ +_1_1_0 _s_t_d::string name_; │ │ │ │ +_1_1_1 _s_t_d::string message_; │ │ │ │ +112 }; │ │ │ │ +113 │ │ │ │ +_1_2_2 class _B_A_L_L___E_X_P_O_R_T _I_n_d_e_x_U_n_d_e_r_f_l_o_w │ │ │ │ +123 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +124 { │ │ │ │ +125 public: │ │ │ │ +126 │ │ │ │ +_1_2_7 _I_n_d_e_x_U_n_d_e_r_f_l_o_w(const char* file, int line, _I_n_d_e_x index = 0, _S_i_z_e size = 0); │ │ │ │ +128 │ │ │ │ +129 │ │ │ │ +130 protected: │ │ │ │ +131 │ │ │ │ +_1_3_2 _S_i_z_e _s_i_z_e__; │ │ │ │ +_1_3_3 _I_n_d_e_x _i_n_d_e_x__; │ │ │ │ +134 }; │ │ │ │ +135 │ │ │ │ +_1_4_3 class _B_A_L_L___E_X_P_O_R_T _S_i_z_e_U_n_d_e_r_f_l_o_w │ │ │ │ +144 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +145 { │ │ │ │ +146 public: │ │ │ │ +147 │ │ │ │ +_1_4_8 _S_i_z_e_U_n_d_e_r_f_l_o_w(const char* file, int line, _S_i_z_e size = 0); │ │ │ │ +149 │ │ │ │ +150 protected: │ │ │ │ +_1_5_1 _S_i_z_e _s_i_z_e__; │ │ │ │ +152 }; │ │ │ │ +153 │ │ │ │ +_1_6_2 class _B_A_L_L___E_X_P_O_R_T _I_n_d_e_x_O_v_e_r_f_l_o_w │ │ │ │ +163 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +164 { │ │ │ │ +165 public: │ │ │ │ +_1_6_6 _I_n_d_e_x_O_v_e_r_f_l_o_w(const char* file, int line, _I_n_d_e_x index = 0, _S_i_z_e size = 0); │ │ │ │ +167 │ │ │ │ +168 protected: │ │ │ │ +169 │ │ │ │ +_1_7_0 _S_i_z_e _s_i_z_e__; │ │ │ │ +_1_7_1 _I_n_d_e_x _i_n_d_e_x__; │ │ │ │ +172 }; │ │ │ │ +173 │ │ │ │ +_1_7_7 class _B_A_L_L___E_X_P_O_R_T _I_n_v_a_l_i_d_A_r_g_u_m_e_n_t │ │ │ │ +178 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +179 { │ │ │ │ +180 public: │ │ │ │ +_1_8_1 _I_n_v_a_l_i_d_A_r_g_u_m_e_n_t(const char* file, int line, const _S_t_r_i_n_g& arg); │ │ │ │ +182 }; │ │ │ │ +183 │ │ │ │ +_1_8_7 class _B_A_L_L___E_X_P_O_R_T _I_n_v_a_l_i_d_R_a_n_g_e │ │ │ │ +188 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +189 { │ │ │ │ +190 public: │ │ │ │ +_1_9_1 _I_n_v_a_l_i_d_R_a_n_g_e(const char* file, int line, float value); │ │ │ │ +192 }; │ │ │ │ +193 │ │ │ │ +194 │ │ │ │ +_2_0_1 class _B_A_L_L___E_X_P_O_R_T _I_n_v_a_l_i_d_S_i_z_e │ │ │ │ +202 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +203 { │ │ │ │ +204 public: │ │ │ │ +205 │ │ │ │ +_2_0_6 _I_n_v_a_l_i_d_S_i_z_e(const char* file, int line, _S_i_z_e size = 0); │ │ │ │ +207 │ │ │ │ +208 protected: │ │ │ │ +_2_0_9 _S_i_z_e _s_i_z_e__; │ │ │ │ +210 }; │ │ │ │ +211 │ │ │ │ +212 │ │ │ │ +_2_1_7 class _B_A_L_L___E_X_P_O_R_T _O_u_t_O_f_R_a_n_g_e │ │ │ │ +218 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +219 { │ │ │ │ +220 public: │ │ │ │ +_2_2_1 _O_u_t_O_f_R_a_n_g_e(const char* file, int line); │ │ │ │ +222 }; │ │ │ │ +223 │ │ │ │ +_2_2_9 class _B_A_L_L___E_X_P_O_R_T _I_n_v_a_l_i_d_F_o_r_m_a_t │ │ │ │ +230 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +231 { │ │ │ │ +232 public: │ │ │ │ +_2_3_3 _I_n_v_a_l_i_d_F_o_r_m_a_t(const char* file, int line, const _S_t_r_i_n_g& s); │ │ │ │ +234 │ │ │ │ +_2_3_5 _~_I_n_v_a_l_i_d_F_o_r_m_a_t() throw(); │ │ │ │ +236 │ │ │ │ +237 protected: │ │ │ │ +238 │ │ │ │ +_2_3_9 _s_t_d::string format_; │ │ │ │ +240 }; │ │ │ │ +241 │ │ │ │ +_2_4_7 class _B_A_L_L___E_X_P_O_R_T _I_l_l_e_g_a_l_S_e_l_f_O_p_e_r_a_t_i_o_n │ │ │ │ +248 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +249 { │ │ │ │ +250 public: │ │ │ │ +_2_5_1 _I_l_l_e_g_a_l_S_e_l_f_O_p_e_r_a_t_i_o_n(const char* file, int line); │ │ │ │ +252 }; │ │ │ │ +253 │ │ │ │ +_2_5_8 class _B_A_L_L___E_X_P_O_R_T _N_u_l_l_P_o_i_n_t_e_r │ │ │ │ +259 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +260 { │ │ │ │ +261 public: │ │ │ │ +_2_6_2 _N_u_l_l_P_o_i_n_t_e_r(const char* file, int line); │ │ │ │ +263 }; │ │ │ │ +264 │ │ │ │ +_2_6_8 class _B_A_L_L___E_X_P_O_R_T _I_n_v_a_l_i_d_I_t_e_r_a_t_o_r │ │ │ │ +269 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +270 { │ │ │ │ +271 public: │ │ │ │ +_2_7_2 _I_n_v_a_l_i_d_I_t_e_r_a_t_o_r(const char* file, int line); │ │ │ │ +273 }; │ │ │ │ +274 │ │ │ │ +_2_7_9 class _B_A_L_L___E_X_P_O_R_T _I_n_c_o_m_p_a_t_i_b_l_e_I_t_e_r_a_t_o_r_s │ │ │ │ +280 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +281 { │ │ │ │ +282 public: │ │ │ │ +_2_8_3 _I_n_c_o_m_p_a_t_i_b_l_e_I_t_e_r_a_t_o_r_s(const char* file, int line); │ │ │ │ +284 }; │ │ │ │ +285 │ │ │ │ +_2_9_2 class _B_A_L_L___E_X_P_O_R_T _N_o_t_I_m_p_l_e_m_e_n_t_e_d │ │ │ │ +293 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +294 { │ │ │ │ +295 public: │ │ │ │ +_2_9_6 _N_o_t_I_m_p_l_e_m_e_n_t_e_d(const char* file, int line); │ │ │ │ +297 }; │ │ │ │ +298 │ │ │ │ +_3_0_3 class _B_A_L_L___E_X_P_O_R_T _I_l_l_e_g_a_l_T_r_e_e_O_p_e_r_a_t_i_o_n │ │ │ │ +304 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +305 { │ │ │ │ +306 public: │ │ │ │ +_3_0_7 _I_l_l_e_g_a_l_T_r_e_e_O_p_e_r_a_t_i_o_n(const char* file, int line); │ │ │ │ +308 }; │ │ │ │ +309 │ │ │ │ +_3_1_6 class _B_A_L_L___E_X_P_O_R_T _O_u_t_O_f_M_e_m_o_r_y │ │ │ │ +317 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n, public std::bad_alloc │ │ │ │ +318 { │ │ │ │ +319 public: │ │ │ │ +_3_2_0 _O_u_t_O_f_M_e_m_o_r_y(const char* file, int line, _S_i_z_e size = 0); │ │ │ │ +321 │ │ │ │ +_3_2_2 virtual _~_O_u_t_O_f_M_e_m_o_r_y() │ │ │ │ +323 throw(); │ │ │ │ +324 │ │ │ │ +325 protected: │ │ │ │ +_3_2_6 _S_i_z_e size_; │ │ │ │ +327 }; │ │ │ │ +328 │ │ │ │ +_3_3_1 class _B_A_L_L___E_X_P_O_R_T _B_u_f_f_e_r_O_v_e_r_f_l_o_w │ │ │ │ +332 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +333 { │ │ │ │ +334 public: │ │ │ │ +_3_3_5 _B_u_f_f_e_r_O_v_e_r_f_l_o_w(const char* file, int line); │ │ │ │ +336 }; │ │ │ │ +337 │ │ │ │ +_3_4_0 class _B_A_L_L___E_X_P_O_R_T _D_i_v_i_s_i_o_n_B_y_Z_e_r_o │ │ │ │ +341 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +342 { │ │ │ │ +343 public: │ │ │ │ +_3_4_4 _D_i_v_i_s_i_o_n_B_y_Z_e_r_o(const char* file, int line); │ │ │ │ +345 }; │ │ │ │ +346 │ │ │ │ +_3_4_9 class _B_A_L_L___E_X_P_O_R_T _O_u_t_O_f_G_r_i_d │ │ │ │ +350 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +351 { │ │ │ │ +352 public: │ │ │ │ +_3_5_3 _O_u_t_O_f_G_r_i_d(const char* file, int line); │ │ │ │ +354 }; │ │ │ │ +355 │ │ │ │ +_3_5_9 class _B_A_L_L___E_X_P_O_R_T _F_i_l_e_N_o_t_F_o_u_n_d │ │ │ │ +360 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +361 { │ │ │ │ +362 public: │ │ │ │ +_3_6_3 _F_i_l_e_N_o_t_F_o_u_n_d(const char* file, int line, const _S_t_r_i_n_g& filename); │ │ │ │ +364 │ │ │ │ +_3_6_5 _~_F_i_l_e_N_o_t_F_o_u_n_d() │ │ │ │ +366 throw(); │ │ │ │ +_3_6_7 _S_t_r_i_n_g getFilename() const; │ │ │ │ +368 │ │ │ │ +369 protected: │ │ │ │ +_3_7_0 _s_t_d::string filename_; │ │ │ │ +371 }; │ │ │ │ +372 │ │ │ │ +_3_7_6 class _B_A_L_L___E_X_P_O_R_T _I_l_l_e_g_a_l_P_o_s_i_t_i_o_n │ │ │ │ +377 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +378 { │ │ │ │ +379 public: │ │ │ │ +_3_8_0 _I_l_l_e_g_a_l_P_o_s_i_t_i_o_n(const char* file, int line, float x, float y, float z); │ │ │ │ +381 }; │ │ │ │ +382 │ │ │ │ +_3_8_6 class _B_A_L_L___E_X_P_O_R_T _P_a_r_s_e_E_r_r_o_r │ │ │ │ +387 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +388 { │ │ │ │ +389 public: │ │ │ │ +_3_9_1 _P_a_r_s_e_E_r_r_o_r(const char* file, int line, const _S_t_r_i_n_g& expression, │ │ │ │ +392 const _S_t_r_i_n_g& message); │ │ │ │ +393 }; │ │ │ │ +394 │ │ │ │ +_3_9_8 class _B_A_L_L___E_X_P_O_R_T _P_r_e_c_o_n_d_i_t_i_o_n │ │ │ │ +399 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +400 { │ │ │ │ +401 public: │ │ │ │ +_4_0_3 _P_r_e_c_o_n_d_i_t_i_o_n(const char* file, int line, const char* condition); │ │ │ │ +404 }; │ │ │ │ +405 │ │ │ │ +_4_0_9 class _B_A_L_L___E_X_P_O_R_T _P_o_s_t_c_o_n_d_i_t_i_o_n │ │ │ │ +410 : public _G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +411 { │ │ │ │ +412 public: │ │ │ │ +_4_1_4 _P_o_s_t_c_o_n_d_i_t_i_o_n(const char* file, int line, const char* condition); │ │ │ │ +415 }; │ │ │ │ +416 │ │ │ │ +_4_1_8 class _B_A_L_L___E_X_P_O_R_T _I_n_v_a_l_i_d_O_p_t_i_o_n: public _E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +419 { │ │ │ │ +420 public: │ │ │ │ +421 │ │ │ │ +_4_2_3 _I_n_v_a_l_i_d_O_p_t_i_o_n(const char* file, int line, _S_t_r_i_n_g option); │ │ │ │ +424 }; │ │ │ │ +425 │ │ │ │ +_4_2_7 class _B_A_L_L___E_X_P_O_R_T _T_o_o_M_a_n_y_E_r_r_o_r_s │ │ │ │ +428 : public _E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +429 { │ │ │ │ +430 public: │ │ │ │ +_4_3_2 _T_o_o_M_a_n_y_E_r_r_o_r_s(const char* file, int line); │ │ │ │ +433 }; │ │ │ │ +434 │ │ │ │ +_4_3_6 class _B_A_L_L___E_X_P_O_R_T _T_o_o_M_a_n_y_B_o_n_d_s │ │ │ │ +437 : public _E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +438 { │ │ │ │ +439 public: │ │ │ │ +_4_4_1 _T_o_o_M_a_n_y_B_o_n_d_s(const char* file, int line, const _S_t_r_i_n_g& error); │ │ │ │ +442 }; │ │ │ │ +443 │ │ │ │ +_4_4_7 class _B_A_L_L___D_E_P_R_E_C_A_T_E_D _B_A_L_L___E_X_P_O_R_T _C_U_D_A_E_r_r_o_r │ │ │ │ +448 : public _E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +449 { │ │ │ │ +450 public: │ │ │ │ +_4_5_1 _C_U_D_A_E_r_r_o_r(const char* file, int line, const _S_t_r_i_n_g& error); │ │ │ │ +452 }; │ │ │ │ +453 │ │ │ │ +_4_6_1 class _B_A_L_L___E_X_P_O_R_T _N_o_B_u_f_f_e_r_A_v_a_i_l_a_b_l_e │ │ │ │ +462 : public _E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +463 { │ │ │ │ +464 public: │ │ │ │ +_4_6_5 _N_o_B_u_f_f_e_r_A_v_a_i_l_a_b_l_e(const char* file, int line, const _S_t_r_i_n_g& reason); │ │ │ │ +466 }; │ │ │ │ +467 │ │ │ │ +_4_7_3 class _B_A_L_L___E_X_P_O_R_T _F_o_r_m_a_t_U_n_s_u_p_p_o_r_t_e_d │ │ │ │ +474 : public _E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +475 { │ │ │ │ +476 public: │ │ │ │ +_4_7_7 _F_o_r_m_a_t_U_n_s_u_p_p_o_r_t_e_d(const char* file, int line); │ │ │ │ +478 }; │ │ │ │ +479 │ │ │ │ +_4_8_5 class _B_A_L_L___E_X_P_O_R_T _N_o_t_I_n_i_t_i_a_l_i_z_e_d : public _E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +486 { │ │ │ │ +487 public: │ │ │ │ +_4_8_8 _N_o_t_I_n_i_t_i_a_l_i_z_e_d(const char* file, int line, const _S_t_r_i_n_g& reason); │ │ │ │ +489 }; │ │ │ │ +490 │ │ │ │ +_4_9_3 class _B_A_L_L___E_X_P_O_R_T _G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r │ │ │ │ +494 { │ │ │ │ +495 public: │ │ │ │ +499 │ │ │ │ +_5_1_6 _G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r(); │ │ │ │ +518 │ │ │ │ +522 │ │ │ │ +_5_2_4 static void _s_e_t_N_a_m_e(const _S_t_r_i_n_g& name); │ │ │ │ +525 │ │ │ │ +_5_2_7 static void _s_e_t_M_e_s_s_a_g_e(const _S_t_r_i_n_g& message); │ │ │ │ +528 │ │ │ │ +_5_3_0 static void _s_e_t_L_i_n_e(int line); │ │ │ │ +531 │ │ │ │ +_5_3_3 static void _s_e_t_F_i_l_e(const _S_t_r_i_n_g& file); │ │ │ │ +534 │ │ │ │ +_5_3_6 static void _s_e_t │ │ │ │ +537 (const _S_t_r_i_n_g& file, int line, │ │ │ │ +538 const _S_t_r_i_n_g& name, const _S_t_r_i_n_g& message); │ │ │ │ +540 │ │ │ │ +541 protected: │ │ │ │ +542 │ │ │ │ +_5_4_4 static void _t_e_r_m_i_n_a_t_e(); │ │ │ │ +545 │ │ │ │ +_5_4_9 static void _n_e_w_H_a_n_d_l_e_r(); │ │ │ │ +550 │ │ │ │ +_5_5_1 static std::string _f_i_l_e__; │ │ │ │ +_5_5_2 static int _l_i_n_e__; │ │ │ │ +_5_5_3 static std::string _n_a_m_e__; │ │ │ │ +_5_5_4 static std::string _m_e_s_s_a_g_e__; │ │ │ │ +555 }; │ │ │ │ +556 │ │ │ │ +559 _B_A_L_L___E_X_P_O_R_T extern _G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r _g_l_o_b_a_l_H_a_n_d_l_e_r; │ │ │ │ +560 │ │ │ │ +561 } │ │ │ │ +580 _B_A_L_L___E_X_P_O_R_T │ │ │ │ +_5_8_1 std::ostream& operator << (std::ostream& os, const _E_x_c_e_p_t_i_o_n_:_: │ │ │ │ +_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n& e); │ │ │ │ +582 │ │ │ │ +583} // namespace BALL │ │ │ │ +584 │ │ │ │ +585#ifdef BALL_COMPILER_MSVC │ │ │ │ +586 #pragma warning(pop) │ │ │ │ +587#endif │ │ │ │ +588 │ │ │ │ +589#endif // BALL_COMMON_EXCEPTION_H │ │ │ │ +_s_t_d │ │ │ │ +STL namespace. │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_e_d_i_c_a_t_e │ │ │ │ -DDeeffiinniittiioonn _C_O_N_C_E_P_T_/_p_r_e_d_i_c_a_t_e_._h_:_3_0 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_e_d_i_c_a_t_e_:_:_o_p_e_r_a_t_o_r_(_) │ │ │ │ -virtual bool operator()(const T &) const │ │ │ │ -DDeeffiinniittiioonn _C_O_N_C_E_P_T_/_p_r_e_d_i_c_a_t_e_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_U_n_a_r_y_P_r_e_d_i_c_a_t_e_:_:_~_U_n_a_r_y_P_r_e_d_i_c_a_t_e │ │ │ │ -virtual ~UnaryPredicate() │ │ │ │ -DDeeffiinniittiioonn _C_O_N_C_E_P_T_/_p_r_e_d_i_c_a_t_e_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_P_r_e_d_i_c_a_t_e │ │ │ │ -DDeeffiinniittiioonn _C_O_N_C_E_P_T_/_p_r_e_d_i_c_a_t_e_._h_:_4_5 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_P_r_e_d_i_c_a_t_e_:_:_~_B_i_n_a_r_y_P_r_e_d_i_c_a_t_e │ │ │ │ -virtual ~BinaryPredicate() │ │ │ │ -DDeeffiinniittiioonn _C_O_N_C_E_P_T_/_p_r_e_d_i_c_a_t_e_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_B_i_n_a_r_y_P_r_e_d_i_c_a_t_e_:_:_o_p_e_r_a_t_o_r_(_) │ │ │ │ -virtual bool operator()(const T1 &x, const T2 &y) const │ │ │ │ -DDeeffiinniittiioonn _C_O_N_C_E_P_T_/_p_r_e_d_i_c_a_t_e_._h_:_6_4 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_g_l_o_b_a_l_H_a_n_d_l_e_r │ │ │ │ +BALL_EXPORT GlobalExceptionHandler globalHandler │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_6_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n_:_:_~_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +virtual ~GeneralException() │ │ │ │ +Destructor. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +GeneralException() │ │ │ │ +Default constructor. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +GeneralException(const char *file, int line, const String &name, const String │ │ │ │ +&message) │ │ │ │ +Constructor. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +GeneralException(const char *file, int line) │ │ │ │ +Constructor. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n_:_:_G_e_n_e_r_a_l_E_x_c_e_p_t_i_o_n │ │ │ │ +GeneralException(const GeneralException &exception) │ │ │ │ +Copy constructor. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_U_n_d_e_r_f_l_o_w │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_2_4 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_U_n_d_e_r_f_l_o_w_:_:_s_i_z_e__ │ │ │ │ +Size size_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_3_2 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_U_n_d_e_r_f_l_o_w_:_:_i_n_d_e_x__ │ │ │ │ +Index index_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_3_3 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_U_n_d_e_r_f_l_o_w_:_:_I_n_d_e_x_U_n_d_e_r_f_l_o_w │ │ │ │ +IndexUnderflow(const char *file, int line, Index index=0, Size size=0) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_S_i_z_e_U_n_d_e_r_f_l_o_w │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_4_5 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_S_i_z_e_U_n_d_e_r_f_l_o_w_:_:_s_i_z_e__ │ │ │ │ +Size size_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_5_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_S_i_z_e_U_n_d_e_r_f_l_o_w_:_:_S_i_z_e_U_n_d_e_r_f_l_o_w │ │ │ │ +SizeUnderflow(const char *file, int line, Size size=0) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_O_v_e_r_f_l_o_w │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_6_4 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_O_v_e_r_f_l_o_w_:_:_I_n_d_e_x_O_v_e_r_f_l_o_w │ │ │ │ +IndexOverflow(const char *file, int line, Index index=0, Size size=0) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_O_v_e_r_f_l_o_w_:_:_s_i_z_e__ │ │ │ │ +Size size_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_7_0 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_d_e_x_O_v_e_r_f_l_o_w_:_:_i_n_d_e_x__ │ │ │ │ +Index index_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_7_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_A_r_g_u_m_e_n_t │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_7_9 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_A_r_g_u_m_e_n_t_:_:_I_n_v_a_l_i_d_A_r_g_u_m_e_n_t │ │ │ │ +InvalidArgument(const char *file, int line, const String &arg) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_R_a_n_g_e │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_1_8_9 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_R_a_n_g_e_:_:_I_n_v_a_l_i_d_R_a_n_g_e │ │ │ │ +InvalidRange(const char *file, int line, float value) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_S_i_z_e │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_0_3 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_S_i_z_e_:_:_s_i_z_e__ │ │ │ │ +Size size_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_0_9 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_S_i_z_e_:_:_I_n_v_a_l_i_d_S_i_z_e │ │ │ │ +InvalidSize(const char *file, int line, Size size=0) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_R_a_n_g_e │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_1_9 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_R_a_n_g_e_:_:_O_u_t_O_f_R_a_n_g_e │ │ │ │ +OutOfRange(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_F_o_r_m_a_t │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_3_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_F_o_r_m_a_t_:_:_~_I_n_v_a_l_i_d_F_o_r_m_a_t │ │ │ │ +~InvalidFormat() │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_F_o_r_m_a_t_:_:_I_n_v_a_l_i_d_F_o_r_m_a_t │ │ │ │ +InvalidFormat(const char *file, int line, const String &s) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_l_l_e_g_a_l_S_e_l_f_O_p_e_r_a_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_4_9 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_l_l_e_g_a_l_S_e_l_f_O_p_e_r_a_t_i_o_n_:_:_I_l_l_e_g_a_l_S_e_l_f_O_p_e_r_a_t_i_o_n │ │ │ │ +IllegalSelfOperation(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_u_l_l_P_o_i_n_t_e_r │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_6_0 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_u_l_l_P_o_i_n_t_e_r_:_:_N_u_l_l_P_o_i_n_t_e_r │ │ │ │ +NullPointer(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_I_t_e_r_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_7_0 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_I_t_e_r_a_t_o_r_:_:_I_n_v_a_l_i_d_I_t_e_r_a_t_o_r │ │ │ │ +InvalidIterator(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_c_o_m_p_a_t_i_b_l_e_I_t_e_r_a_t_o_r_s │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_8_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_c_o_m_p_a_t_i_b_l_e_I_t_e_r_a_t_o_r_s_:_:_I_n_c_o_m_p_a_t_i_b_l_e_I_t_e_r_a_t_o_r_s │ │ │ │ +IncompatibleIterators(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_o_t_I_m_p_l_e_m_e_n_t_e_d │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_2_9_4 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_o_t_I_m_p_l_e_m_e_n_t_e_d_:_:_N_o_t_I_m_p_l_e_m_e_n_t_e_d │ │ │ │ +NotImplemented(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_l_l_e_g_a_l_T_r_e_e_O_p_e_r_a_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_3_0_5 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_l_l_e_g_a_l_T_r_e_e_O_p_e_r_a_t_i_o_n_:_:_I_l_l_e_g_a_l_T_r_e_e_O_p_e_r_a_t_i_o_n │ │ │ │ +IllegalTreeOperation(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_M_e_m_o_r_y │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_3_1_8 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_M_e_m_o_r_y_:_:_O_u_t_O_f_M_e_m_o_r_y │ │ │ │ +OutOfMemory(const char *file, int line, Size size=0) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_M_e_m_o_r_y_:_:_~_O_u_t_O_f_M_e_m_o_r_y │ │ │ │ +virtual ~OutOfMemory() │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_B_u_f_f_e_r_O_v_e_r_f_l_o_w │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_3_3_3 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_B_u_f_f_e_r_O_v_e_r_f_l_o_w_:_:_B_u_f_f_e_r_O_v_e_r_f_l_o_w │ │ │ │ +BufferOverflow(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_D_i_v_i_s_i_o_n_B_y_Z_e_r_o │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_3_4_2 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_D_i_v_i_s_i_o_n_B_y_Z_e_r_o_:_:_D_i_v_i_s_i_o_n_B_y_Z_e_r_o │ │ │ │ +DivisionByZero(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_G_r_i_d │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_3_5_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_O_u_t_O_f_G_r_i_d_:_:_O_u_t_O_f_G_r_i_d │ │ │ │ +OutOfGrid(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_F_i_l_e_N_o_t_F_o_u_n_d │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_3_6_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_F_i_l_e_N_o_t_F_o_u_n_d_:_:_~_F_i_l_e_N_o_t_F_o_u_n_d │ │ │ │ +~FileNotFound() │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_F_i_l_e_N_o_t_F_o_u_n_d_:_:_F_i_l_e_N_o_t_F_o_u_n_d │ │ │ │ +FileNotFound(const char *file, int line, const String &filename) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_l_l_e_g_a_l_P_o_s_i_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_3_7_8 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_l_l_e_g_a_l_P_o_s_i_t_i_o_n_:_:_I_l_l_e_g_a_l_P_o_s_i_t_i_o_n │ │ │ │ +IllegalPosition(const char *file, int line, float x, float y, float z) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_P_a_r_s_e_E_r_r_o_r │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_3_8_8 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_P_a_r_s_e_E_r_r_o_r_:_:_P_a_r_s_e_E_r_r_o_r │ │ │ │ +ParseError(const char *file, int line, const String &expression, const String │ │ │ │ +&message) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_P_r_e_c_o_n_d_i_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_0_0 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_P_r_e_c_o_n_d_i_t_i_o_n_:_:_P_r_e_c_o_n_d_i_t_i_o_n │ │ │ │ +Precondition(const char *file, int line, const char *condition) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_P_o_s_t_c_o_n_d_i_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_1_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_P_o_s_t_c_o_n_d_i_t_i_o_n_:_:_P_o_s_t_c_o_n_d_i_t_i_o_n │ │ │ │ +Postcondition(const char *file, int line, const char *condition) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_O_p_t_i_o_n │ │ │ │ +Exception to be thrown if an invalid option is given. │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_1_9 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_I_n_v_a_l_i_d_O_p_t_i_o_n_:_:_I_n_v_a_l_i_d_O_p_t_i_o_n │ │ │ │ +InvalidOption(const char *file, int line, String option) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_T_o_o_M_a_n_y_E_r_r_o_r_s │ │ │ │ +Exception to be thrown if too many errors occur, e.g. in ForceField. │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_2_9 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_T_o_o_M_a_n_y_E_r_r_o_r_s_:_:_T_o_o_M_a_n_y_E_r_r_o_r_s │ │ │ │ +TooManyErrors(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_T_o_o_M_a_n_y_B_o_n_d_s │ │ │ │ +Exception to be thrown if too many bonds for one atom. │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_3_8 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_T_o_o_M_a_n_y_B_o_n_d_s_:_:_T_o_o_M_a_n_y_B_o_n_d_s │ │ │ │ +TooManyBonds(const char *file, int line, const String &error) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_C_U_D_A_E_r_r_o_r │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_4_9 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_C_U_D_A_E_r_r_o_r_:_:_C_U_D_A_E_r_r_o_r │ │ │ │ +CUDAError(const char *file, int line, const String &error) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_o_B_u_f_f_e_r_A_v_a_i_l_a_b_l_e │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_6_3 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_o_B_u_f_f_e_r_A_v_a_i_l_a_b_l_e_:_:_N_o_B_u_f_f_e_r_A_v_a_i_l_a_b_l_e │ │ │ │ +NoBufferAvailable(const char *file, int line, const String &reason) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_F_o_r_m_a_t_U_n_s_u_p_p_o_r_t_e_d │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_7_5 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_F_o_r_m_a_t_U_n_s_u_p_p_o_r_t_e_d_:_:_F_o_r_m_a_t_U_n_s_u_p_p_o_r_t_e_d │ │ │ │ +FormatUnsupported(const char *file, int line) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_o_t_I_n_i_t_i_a_l_i_z_e_d │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_8_6 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_N_o_t_I_n_i_t_i_a_l_i_z_e_d_:_:_N_o_t_I_n_i_t_i_a_l_i_z_e_d │ │ │ │ +NotInitialized(const char *file, int line, const String &reason) │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_4_9_4 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_s_e_t │ │ │ │ +static void set(const String &file, int line, const String &name, const String │ │ │ │ +&message) │ │ │ │ +Set all exception attributes. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r │ │ │ │ +GlobalExceptionHandler() │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_f_i_l_e__ │ │ │ │ +static std::string file_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_5_5_1 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_s_e_t_F_i_l_e │ │ │ │ +static void setFile(const String &file) │ │ │ │ +The source file name where the exception was thrown. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_s_e_t_N_a_m_e │ │ │ │ +static void setName(const String &name) │ │ │ │ +Assign the name of the exception. This should agree with the class name. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_s_e_t_L_i_n_e │ │ │ │ +static void setLine(int line) │ │ │ │ +Set the line number the exception was thrown. Should be set to LINE in most │ │ │ │ +cases. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_t_e_r_m_i_n_a_t_e │ │ │ │ +static void terminate() │ │ │ │ +The BALL replacement for terminate. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_s_e_t_M_e_s_s_a_g_e │ │ │ │ +static void setMessage(const String &message) │ │ │ │ +Set the error message. │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_n_e_w_H_a_n_d_l_e_r │ │ │ │ +static void newHandler() │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_n_a_m_e__ │ │ │ │ +static std::string name_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_5_5_3 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_m_e_s_s_a_g_e__ │ │ │ │ +static std::string message_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_5_5_4 │ │ │ │ +_B_A_L_L_:_:_E_x_c_e_p_t_i_o_n_:_:_G_l_o_b_a_l_E_x_c_e_p_t_i_o_n_H_a_n_d_l_e_r_:_:_l_i_n_e__ │ │ │ │ +static int line_ │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_e_x_c_e_p_t_i_o_n_._h_:_5_5_2 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L___I_N_D_E_X___T_Y_P_E │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _g_l_o_b_a_l_._h │ │ │ │ +_B_A_L_L___D_E_P_R_E_C_A_T_E_D │ │ │ │ +#define BALL_DEPRECATED │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_6_4 │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d34/a01211.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: pyKernel.h File Reference │ │ │ +BALL: nucleotideIterator.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,41 +65,51 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces
    │ │ │ -
    pyKernel.h File Reference
    │ │ │ +Namespaces | │ │ │ +Typedefs
    │ │ │ +
    nucleotideIterator.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/COMMON/global.h>
    │ │ │ -#include <Python.h>
    │ │ │ -#include <map>
    │ │ │ -#include <string>
    │ │ │ -#include <utility>
    │ │ │ +
    #include <BALL/KERNEL/iterator.h>
    │ │ │ +#include <BALL/KERNEL/predicate.h>
    │ │ │ +#include <BALL/CONCEPT/stdIteratorWrapper.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::PyKernel
    class  BALL::NucleotideIteratorTraits
     
    │ │ │ │ │ │ │ │ │ │ │ │ +

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ +Typedefs

    typedef BidirectionalIterator< Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits > BALL::NucleotideIterator
     
    typedef ConstBidirectionalIterator< Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits > BALL::NucleotideConstIterator
     
    typedef std::reverse_iterator< NucleotideIterator > BALL::NucleotideReverseIterator
     
    typedef std::reverse_iterator< NucleotideConstIterator > BALL::NucleotideConstReverseIterator
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,23 +1,37 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _P_Y_T_H_O_N │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -pyKernel.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _T_y_p_e_d_e_f_s │ │ │ │ +nucleotideIterator.h File Reference │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_i_t_e_r_a_t_o_r_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_e_d_i_c_a_t_e_._h> │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_P_y_K_e_r_n_e_l │ │ │ │ +class   _B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ +TTyyppeeddeeffss │ │ │ │ +typedef _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r< _C_o_m_p_o_s_i_t_e, │ │ │ │ +_N_u_c_l_e_o_t_i_d_e, _C_o_m_p_o_s_i_t_e_:_:_C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r, │ │ │ │ + _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s >  _B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r │ │ │ │ +  │ │ │ │ + typedef _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r< │ │ │ │ + _C_o_m_p_o_s_i_t_e, _N_u_c_l_e_o_t_i_d_e, _C_o_m_p_o_s_i_t_e_:_: │ │ │ │ + _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r, │ │ │ │ + _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s >  _B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ +  │ │ │ │ + typedef std::reverse_iterator< │ │ │ │ + _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r >  _B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ +  │ │ │ │ + typedef std::reverse_iterator< │ │ │ │ + _N_u_c_l_e_o_t_i_d_e_C_o_n_s_t_I_t_e_r_a_t_o_r >  _B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ +  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d34/a01211_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: pyKernel.h Source File │ │ │ +BALL: nucleotideIterator.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,74 +70,132 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    pyKernel.h
    │ │ │ +
    nucleotideIterator.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1#ifndef BALL_PYTHON_PYKERNEL_H
    │ │ │ -
    2#define BALL_PYTHON_PYKERNEL_H
    │ │ │ -
    3
    │ │ │ -
    4#include <BALL/COMMON/global.h>
    │ │ │ -
    5
    │ │ │ -
    6#include <Python.h>
    │ │ │ -
    7
    │ │ │ -
    8#include <map>
    │ │ │ -
    9#include <string>
    │ │ │ -
    10#include <utility>
    │ │ │ -
    11
    │ │ │ -
    12namespace BALL
    │ │ │ -
    13{
    │ │ │ -
    │ │ │ -
    14 class PyKernel
    │ │ │ -
    15 {
    │ │ │ -
    16 public:
    │ │ │ -
    17 using KeyValArgs = std::map<std::string, std::string>;
    │ │ │ -
    18
    │ │ │ -
    19 PyKernel() = default;
    │ │ │ -
    20 virtual ~PyKernel() = default;
    │ │ │ +Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ +
    2// vi: set ts=2:
    │ │ │ +
    3//
    │ │ │ +
    4// $Id: nucleotideIterator.h,v 1.13 2005/10/23 12:02:19 oliver Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_KERNEL_NUCLEOTIDEITERATOR_H
    │ │ │ +
    8#define BALL_KERNEL_NUCLEOTIDEITERATOR_H
    │ │ │ +
    9
    │ │ │ +
    10#ifndef BALL_KERNEL_ITERATOR_H
    │ │ │ +
    11# include <BALL/KERNEL/iterator.h>
    │ │ │ +
    12#endif
    │ │ │ +
    13
    │ │ │ +
    14#ifndef BALL_KERNEL_PREDICATE_H
    │ │ │ +
    15# include <BALL/KERNEL/predicate.h>
    │ │ │ +
    16#endif
    │ │ │ +
    17
    │ │ │ +
    18#ifndef BALL_CONCEPT_STDITERATORWRAPPER_H
    │ │ │ +
    19# include <BALL/CONCEPT/stdIteratorWrapper.h>
    │ │ │ +
    20#endif
    │ │ │
    21
    │ │ │ -
    27 virtual bool isStarted() const = 0;
    │ │ │ -
    28
    │ │ │ -
    34 virtual std::string getErrorMessage() const = 0;
    │ │ │ -
    35
    │ │ │ -
    43 virtual std::pair<bool, std::string> run(std::string str) = 0;
    │ │ │ -
    44
    │ │ │ -
    53 BALL_DEPRECATED virtual bool runFile(std::string filename) = 0;
    │ │ │ -
    54
    │ │ │ -
    63 virtual bool execute(const std::string& module, const std::string& func, const KeyValArgs& args) = 0;
    │ │ │ -
    64
    │ │ │ -
    65 protected:
    │ │ │ -
    66
    │ │ │ -
    73 virtual void loadScriptDir();
    │ │ │ -
    74 };
    │ │ │ +
    22namespace BALL
    │ │ │ +
    23{
    │ │ │ +
    24 class Nucleotide;
    │ │ │ +
    25
    │ │ │ +
    │ │ │ +
    29 class BALL_EXPORT NucleotideIteratorTraits
    │ │ │ +
    30 : public CompositeIteratorTraits
    │ │ │ +
    31 {
    │ │ │ +
    32 public:
    │ │ │ +
    33
    │ │ │ +
    │ │ │ +
    34 NucleotideIteratorTraits()
    │ │ │ +
    35 : CompositeIteratorTraits()
    │ │ │ +
    36 {
    │ │ │ +
    37 predicate_ = &RTTI::getDefault<KernelPredicate<Nucleotide> >();
    │ │ │ +
    38 }
    │ │ │ +
    │ │ │ +
    39
    │ │ │ +
    │ │ │ +
    40 NucleotideIteratorTraits(const Composite& composite)
    │ │ │ +
    41 : CompositeIteratorTraits(composite)
    │ │ │ +
    42 {
    │ │ │ +
    43 predicate_ = &RTTI::getDefault<KernelPredicate<Nucleotide> >();
    │ │ │ +
    44 }
    │ │ │ +
    │ │ │ +
    45
    │ │ │ +
    │ │ │ +
    46 NucleotideIteratorTraits(const NucleotideIteratorTraits& traits, bool /* deep */ = true)
    │ │ │ +
    47 : CompositeIteratorTraits(traits)
    │ │ │ +
    48 {
    │ │ │ +
    49 }
    │ │ │ +
    │ │ │ +
    50
    │ │ │ +
    │ │ │ +
    51 NucleotideIteratorTraits& operator =(const NucleotideIteratorTraits& traits)
    │ │ │ +
    52 {
    │ │ │ +
    53 CompositeIteratorTraits::operator=(traits);
    │ │ │ +
    54 return *this;
    │ │ │ +
    55 }
    │ │ │ +
    │ │ │ +
    56
    │ │ │ +
    │ │ │ +
    57 void resetPredicate()
    │ │ │ +
    58 {
    │ │ │ +
    59 predicate_ = &RTTI::getDefault<KernelPredicate<Nucleotide> >();
    │ │ │ +
    60 }
    │ │ │ +
    │ │ │ +
    61 };
    │ │ │
    │ │ │ -
    75}
    │ │ │ +
    62
    │ │ │ +
    63
    │ │ │ +
    64
    │ │ │ +
    65 typedef BidirectionalIterator
    │ │ │ +
    66 <Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits>
    │ │ │ +
    67 NucleotideIterator;
    │ │ │ +
    68
    │ │ │ +
    69 typedef ConstBidirectionalIterator
    │ │ │ +
    70 <Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits>
    │ │ │ +
    71 NucleotideConstIterator;
    │ │ │ +
    72
    │ │ │ +
    73 typedef std::reverse_iterator<NucleotideIterator> NucleotideReverseIterator;
    │ │ │ +
    74
    │ │ │ +
    75 typedef std::reverse_iterator<NucleotideConstIterator> NucleotideConstReverseIterator;
    │ │ │
    76
    │ │ │ -
    77#endif // BALL_PYTHON_PYKERNEL_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL::PyKernel::runFile
    virtual BALL_DEPRECATED bool runFile(std::string filename)=0
    │ │ │ -
    BALL::PyKernel::~PyKernel
    virtual ~PyKernel()=default
    │ │ │ -
    BALL::PyKernel::KeyValArgs
    std::map< std::string, std::string > KeyValArgs
    Definition pyKernel.h:17
    │ │ │ -
    BALL::PyKernel::execute
    virtual bool execute(const std::string &module, const std::string &func, const KeyValArgs &args)=0
    │ │ │ -
    BALL::PyKernel::isStarted
    virtual bool isStarted() const =0
    │ │ │ -
    BALL::PyKernel::loadScriptDir
    virtual void loadScriptDir()
    │ │ │ -
    BALL::PyKernel::PyKernel
    PyKernel()=default
    │ │ │ -
    BALL::PyKernel::run
    virtual std::pair< bool, std::string > run(std::string str)=0
    │ │ │ -
    BALL::PyKernel::getErrorMessage
    virtual std::string getErrorMessage() const =0
    │ │ │ - │ │ │ -
    BALL_DEPRECATED
    #define BALL_DEPRECATED
    Definition COMMON/global.h:64
    │ │ │ +
    77 IteratorWrapper(Nucleotide)
    │ │ │ +
    78 ConstIteratorWrapper(Nucleotide)
    │ │ │ +
    79} // namespace BALL
    │ │ │ +
    80
    │ │ │ +
    81#endif // BALL_KERNEL_NUCLEOTIDEITERATOR_H
    │ │ │ + │ │ │ +
    ConstIteratorWrapper
    #define ConstIteratorWrapper(type)
    Definition stdIteratorWrapper.h:17
    │ │ │ +
    IteratorWrapper
    #define IteratorWrapper(type)
    Definition stdIteratorWrapper.h:4
    │ │ │ + │ │ │ + │ │ │ +
    BALL::NucleotideConstIterator
    ConstBidirectionalIterator< Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits > NucleotideConstIterator
    Definition nucleotideIterator.h:71
    │ │ │ +
    BALL::NucleotideIterator
    BidirectionalIterator< Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits > NucleotideIterator
    Definition nucleotideIterator.h:67
    │ │ │ +
    BALL::NucleotideConstReverseIterator
    std::reverse_iterator< NucleotideConstIterator > NucleotideConstReverseIterator
    Definition nucleotideIterator.h:75
    │ │ │ +
    BALL::NucleotideReverseIterator
    std::reverse_iterator< NucleotideIterator > NucleotideReverseIterator
    Definition nucleotideIterator.h:73
    │ │ │ + │ │ │ + │ │ │ +
    BALL::Composite::CompositeIterator
    BidirectionalIterator< Composite, Composite, Composite *, CompositeIteratorTraits > CompositeIterator
    Definition composite.h:1468
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::NucleotideIteratorTraits::NucleotideIteratorTraits
    NucleotideIteratorTraits(const Composite &composite)
    Definition nucleotideIterator.h:40
    │ │ │ + │ │ │ +
    BALL::NucleotideIteratorTraits::NucleotideIteratorTraits
    NucleotideIteratorTraits(const NucleotideIteratorTraits &traits, bool=true)
    Definition nucleotideIterator.h:46
    │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,78 +1,147 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _P_Y_T_H_O_N │ │ │ │ -pyKernel.h │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ +nucleotideIterator.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1#ifndef BALL_PYTHON_PYKERNEL_H │ │ │ │ -2#define BALL_PYTHON_PYKERNEL_H │ │ │ │ -3 │ │ │ │ -4#include <_B_A_L_L_/_C_O_M_M_O_N_/_g_l_o_b_a_l_._h> │ │ │ │ -5 │ │ │ │ -6#include │ │ │ │ -7 │ │ │ │ -8#include │ │ │ │ -9#include │ │ │ │ -10#include │ │ │ │ -11 │ │ │ │ -12namespace _B_A_L_L │ │ │ │ -13{ │ │ │ │ -_1_4 class _P_y_K_e_r_n_e_l │ │ │ │ -15 { │ │ │ │ -16 public: │ │ │ │ -_1_7 using _K_e_y_V_a_l_A_r_g_s = std::map; │ │ │ │ -18 │ │ │ │ -_1_9 _P_y_K_e_r_n_e_l() = default; │ │ │ │ -_2_0 virtual _~_P_y_K_e_r_n_e_l() = default; │ │ │ │ +1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ +2// vi: set ts=2: │ │ │ │ +3// │ │ │ │ +4// $Id: nucleotideIterator.h,v 1.13 2005/10/23 12:02:19 oliver Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_KERNEL_NUCLEOTIDEITERATOR_H │ │ │ │ +8#define BALL_KERNEL_NUCLEOTIDEITERATOR_H │ │ │ │ +9 │ │ │ │ +10#ifndef BALL_KERNEL_ITERATOR_H │ │ │ │ +11# include <_B_A_L_L_/_K_E_R_N_E_L_/_i_t_e_r_a_t_o_r_._h> │ │ │ │ +12#endif │ │ │ │ +13 │ │ │ │ +14#ifndef BALL_KERNEL_PREDICATE_H │ │ │ │ +15# include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_e_d_i_c_a_t_e_._h> │ │ │ │ +16#endif │ │ │ │ +17 │ │ │ │ +18#ifndef BALL_CONCEPT_STDITERATORWRAPPER_H │ │ │ │ +19# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h> │ │ │ │ +20#endif │ │ │ │ 21 │ │ │ │ -_2_7 virtual bool _i_s_S_t_a_r_t_e_d() const = 0; │ │ │ │ -28 │ │ │ │ -_3_4 virtual std::string _g_e_t_E_r_r_o_r_M_e_s_s_a_g_e() const = 0; │ │ │ │ -35 │ │ │ │ -_4_3 virtual std::pair _r_u_n(std::string str) = 0; │ │ │ │ -44 │ │ │ │ -_5_3 _B_A_L_L___D_E_P_R_E_C_A_T_E_D virtual bool _r_u_n_F_i_l_e(std::string filename) = 0; │ │ │ │ -54 │ │ │ │ -_6_3 virtual bool _e_x_e_c_u_t_e(const std::string& module, const std::string& func, │ │ │ │ -const _K_e_y_V_a_l_A_r_g_s& args) = 0; │ │ │ │ +22namespace _B_A_L_L │ │ │ │ +23{ │ │ │ │ +24 class Nucleotide; │ │ │ │ +25 │ │ │ │ +_2_9 class _B_A_L_L___E_X_P_O_R_T _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +30 : public _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +31 { │ │ │ │ +32 public: │ │ │ │ +33 │ │ │ │ +_3_4 _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s() │ │ │ │ +35 : _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s() │ │ │ │ +36 { │ │ │ │ +37 predicate_ = &RTTI::getDefault >(); │ │ │ │ +38 } │ │ │ │ +39 │ │ │ │ +_4_0 _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s(const _C_o_m_p_o_s_i_t_e& composite) │ │ │ │ +41 : _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s(composite) │ │ │ │ +42 { │ │ │ │ +43 predicate_ = &RTTI::getDefault >(); │ │ │ │ +44 } │ │ │ │ +45 │ │ │ │ +_4_6 _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s(const _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits, bool / │ │ │ │ +* deep */ = true) │ │ │ │ +47 : _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s(traits) │ │ │ │ +48 { │ │ │ │ +49 } │ │ │ │ +50 │ │ │ │ +_5_1 _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s& operator =(const _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits) │ │ │ │ +52 { │ │ │ │ +53 CompositeIteratorTraits::operator=(traits); │ │ │ │ +54 return *this; │ │ │ │ +55 } │ │ │ │ +56 │ │ │ │ +_5_7 void _r_e_s_e_t_P_r_e_d_i_c_a_t_e() │ │ │ │ +58 { │ │ │ │ +59 predicate_ = &RTTI::getDefault >(); │ │ │ │ +60 } │ │ │ │ +61 }; │ │ │ │ +62 │ │ │ │ +63 │ │ │ │ 64 │ │ │ │ -65 protected: │ │ │ │ -66 │ │ │ │ -_7_3 virtual void _l_o_a_d_S_c_r_i_p_t_D_i_r(); │ │ │ │ -74 }; │ │ │ │ -75} │ │ │ │ +65 typedef BidirectionalIterator │ │ │ │ +66 │ │ │ │ +_6_7 _N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r; │ │ │ │ +68 │ │ │ │ +69 typedef _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ +70 <_C_o_m_p_o_s_i_t_e, _N_u_c_l_e_o_t_i_d_e, _C_o_m_p_o_s_i_t_e_:_:_C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r, │ │ │ │ +_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s> │ │ │ │ +_7_1 _N_u_c_l_e_o_t_i_d_e_C_o_n_s_t_I_t_e_r_a_t_o_r; │ │ │ │ +72 │ │ │ │ +_7_3 typedef std::reverse_iterator _N_u_c_l_e_o_t_i_d_e_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r; │ │ │ │ +74 │ │ │ │ +_7_5 typedef std::reverse_iterator │ │ │ │ +_N_u_c_l_e_o_t_i_d_e_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r; │ │ │ │ 76 │ │ │ │ -77#endif // BALL_PYTHON_PYKERNEL_H │ │ │ │ +77 _I_t_e_r_a_t_o_r_W_r_a_p_p_e_r(_N_u_c_l_e_o_t_i_d_e) │ │ │ │ +78 _C_o_n_s_t_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r(_N_u_c_l_e_o_t_i_d_e) │ │ │ │ +79} // namespace BALL │ │ │ │ +80 │ │ │ │ +81#endif // BALL_KERNEL_NUCLEOTIDEITERATOR_H │ │ │ │ +_s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h │ │ │ │ +_C_o_n_s_t_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r │ │ │ │ +#define ConstIteratorWrapper(type) │ │ │ │ +DDeeffiinniittiioonn _s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h_:_1_7 │ │ │ │ +_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r │ │ │ │ +#define IteratorWrapper(type) │ │ │ │ +DDeeffiinniittiioonn _s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h_:_4 │ │ │ │ +_i_t_e_r_a_t_o_r_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l │ │ │ │ -DDeeffiinniittiioonn _p_y_K_e_r_n_e_l_._h_:_1_5 │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l_:_:_r_u_n_F_i_l_e │ │ │ │ -virtual BALL_DEPRECATED bool runFile(std::string filename)=0 │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l_:_:_~_P_y_K_e_r_n_e_l │ │ │ │ -virtual ~PyKernel()=default │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l_:_:_K_e_y_V_a_l_A_r_g_s │ │ │ │ -std::map< std::string, std::string > KeyValArgs │ │ │ │ -DDeeffiinniittiioonn _p_y_K_e_r_n_e_l_._h_:_1_7 │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l_:_:_e_x_e_c_u_t_e │ │ │ │ -virtual bool execute(const std::string &module, const std::string &func, const │ │ │ │ -KeyValArgs &args)=0 │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l_:_:_i_s_S_t_a_r_t_e_d │ │ │ │ -virtual bool isStarted() const =0 │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l_:_:_l_o_a_d_S_c_r_i_p_t_D_i_r │ │ │ │ -virtual void loadScriptDir() │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l_:_:_P_y_K_e_r_n_e_l │ │ │ │ -PyKernel()=default │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l_:_:_r_u_n │ │ │ │ -virtual std::pair< bool, std::string > run(std::string str)=0 │ │ │ │ -_B_A_L_L_:_:_P_y_K_e_r_n_e_l_:_:_g_e_t_E_r_r_o_r_M_e_s_s_a_g_e │ │ │ │ -virtual std::string getErrorMessage() const =0 │ │ │ │ -_g_l_o_b_a_l_._h │ │ │ │ -_B_A_L_L___D_E_P_R_E_C_A_T_E_D │ │ │ │ -#define BALL_DEPRECATED │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_6_4 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ +ConstBidirectionalIterator< Composite, Nucleotide, Composite:: │ │ │ │ +CompositeIterator, NucleotideIteratorTraits > NucleotideConstIterator │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_._h_:_7_1 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r │ │ │ │ +BidirectionalIterator< Composite, Nucleotide, Composite::CompositeIterator, │ │ │ │ +NucleotideIteratorTraits > NucleotideIterator │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_._h_:_6_7 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ +std::reverse_iterator< NucleotideConstIterator > NucleotideConstReverseIterator │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_._h_:_7_5 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ +std::reverse_iterator< NucleotideIterator > NucleotideReverseIterator │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ +DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_5 │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e_:_:_C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r │ │ │ │ +BidirectionalIterator< Composite, Composite, Composite *, │ │ │ │ +CompositeIteratorTraits > CompositeIterator │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_1_4_6_8 │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +DDeeffiinniittiioonn _i_t_e_r_a_t_o_r_._h_:_8_4 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_._h_:_3_7 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_r_e_s_e_t_P_r_e_d_i_c_a_t_e │ │ │ │ +void resetPredicate() │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +NucleotideIteratorTraits(const Composite &composite) │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_._h_:_4_0 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +NucleotideIteratorTraits() │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_._h_:_3_4 │ │ │ │ +_B_A_L_L_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_N_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +NucleotideIteratorTraits(const NucleotideIteratorTraits &traits, bool=true) │ │ │ │ +DDeeffiinniittiioonn _n_u_c_l_e_o_t_i_d_e_I_t_e_r_a_t_o_r_._h_:_4_6 │ │ │ │ +_p_r_e_d_i_c_a_t_e_._h │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d35/a01184.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: bayesModel.h File Reference │ │ │ +BALL: molecule.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,39 +65,39 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    bayesModel.h File Reference
    │ │ │ +
    molecule.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/QSAR/classificationModel.h>
    │ │ │ +
    #include <BALL/KERNEL/atomContainer.h>
    │ │ │ +#include <BALL/KERNEL/fragment.h>
    │ │ │ +#include <BALL/KERNEL/fragmentIterator.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::QSAR::BayesModel
    class  BALL::Molecule
     
    │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::QSAR
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,21 +1,21 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -bayesModel.h File Reference │ │ │ │ -#include <_B_A_L_L_/_Q_S_A_R_/_c_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l_._h> │ │ │ │ +molecule.h File Reference │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_f_r_a_g_m_e_n_t_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_f_r_a_g_m_e_n_t_I_t_e_r_a_t_o_r_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_Q_S_A_R_:_:_B_a_y_e_s_M_o_d_e_l │ │ │ │ +class   _B_A_L_L_:_:_M_o_l_e_c_u_l_e │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_Q_S_A_R │ │ │ │ -  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d35/a01184_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: bayesModel.h Source File │ │ │ +BALL: molecule.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,74 +70,229 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    bayesModel.h
    │ │ │ +
    molecule.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4//
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    5
    │ │ │ -
    6#ifndef BALL_QSAR_BAYESMODEL_H
    │ │ │ -
    7#define BALL_QSAR_BAYESMODEL_H
    │ │ │ -
    8
    │ │ │ -
    9#ifndef BALL_QSAR_CLASSIFICATIONMODEL_H
    │ │ │ -
    10#include <BALL/QSAR/classificationModel.h>
    │ │ │ -
    11#endif
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    12
    │ │ │ -
    13namespace BALL
    │ │ │ -
    14{
    │ │ │ -
    15 namespace QSAR
    │ │ │ -
    16 {
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    18 class BALL_EXPORT BayesModel : public ClassificationModel
    │ │ │ -
    19 {
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    20 public:
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    21
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    22 BayesModel(const QSARData& q);
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    4
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    5#ifndef BALL_KERNEL_MOLECULE_H
    │ │ │ +
    6#define BALL_KERNEL_MOLECULE_H
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    7
    │ │ │ +
    8#ifndef BALL_KERNEL_ATOMCONTAINER_H
    │ │ │ +
    9# include <BALL/KERNEL/atomContainer.h>
    │ │ │ +
    10#endif
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    11
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    12#ifndef BALL_KERNEL_FRAGMENT_H
    │ │ │ +
    13# include <BALL/KERNEL/fragment.h>
    │ │ │ +
    14#endif
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    15
    │ │ │ +
    16#ifndef BALL_KERNEL_FRAGMENTITERATOR_H
    │ │ │ +
    17# include <BALL/KERNEL/fragmentIterator.h>
    │ │ │ +
    18#endif
    │ │ │ +
    19
    │ │ │ +
    20namespace BALL
    │ │ │ +
    21{
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    22 class System;
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    23
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    24 virtual bool isTrained() = 0;
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    25
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    28 virtual vector<double> calculateProbabilities(int activitiy_index, int feature_index, double feature_value) = 0;
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    29
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    31 virtual int getNoResponseVariables() = 0;
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    32
    │ │ │ +
    │ │ │ +
    29 class BALL_EXPORT Molecule
    │ │ │ +
    30 : public AtomContainer
    │ │ │ +
    31 {
    │ │ │ +
    32 public:
    │ │ │
    33
    │ │ │ -
    34 protected:
    │ │ │ -
    36 double min_prob_diff_;
    │ │ │ -
    37
    │ │ │ -
    39 double undef_act_class_id_;
    │ │ │ -
    40
    │ │ │ -
    41 };
    │ │ │ -
    │ │ │ -
    42 }
    │ │ │ -
    43}
    │ │ │ -
    44
    │ │ │ -
    45#endif //BAYESMODEL_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::QSAR::BayesModel::getNoResponseVariables
    virtual int getNoResponseVariables()=0
    │ │ │ -
    BALL::QSAR::BayesModel::calculateProbabilities
    virtual vector< double > calculateProbabilities(int activitiy_index, int feature_index, double feature_value)=0
    │ │ │ - │ │ │ -
    BALL::QSAR::BayesModel::BayesModel
    BayesModel(const QSARData &q)
    │ │ │ -
    BALL::QSAR::BayesModel::isTrained
    virtual bool isTrained()=0
    │ │ │ - │ │ │ - │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    34 BALL_CREATE_DEEP(Molecule)
    │ │ │ +
    35
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    36
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    39
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    40
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    │ │ │ +
    42 enum Property
    │ │ │ +
    43 {
    │ │ │ +
    44 IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES,
    │ │ │ +
    45 NUMBER_OF_PROPERTIES
    │ │ │ +
    46 };
    │ │ │ +
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    47
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    49
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    52
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    55 Molecule();
    │ │ │ +
    56
    │ │ │ +
    59 Molecule(const Molecule& molecule, bool deep = true);
    │ │ │ +
    60
    │ │ │ +
    63 Molecule(const AtomContainer& atomContainer, bool deep = true);
    │ │ │ +
    64
    │ │ │ +
    67 Molecule(const String& name);
    │ │ │ +
    68
    │ │ │ +
    71 virtual ~Molecule();
    │ │ │ +
    72
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    74
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    77
    │ │ │ +
    81 void persistentWrite(PersistenceManager& pm, const char* name = 0) const;
    │ │ │ +
    82
    │ │ │ +
    86 void persistentRead(PersistenceManager& pm);
    │ │ │ +
    87
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    89
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    92
    │ │ │ +
    97 void set(const Molecule& molecule, bool deep = true);
    │ │ │ +
    98
    │ │ │ +
    102 Molecule& operator = (const Molecule& molecule);
    │ │ │ +
    103
    │ │ │ +
    108 void get(Molecule& molecule, bool deep = true) const;
    │ │ │ +
    109
    │ │ │ +
    113 void swap(Molecule& molecule);
    │ │ │ +
    114
    │ │ │ +
    116
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    119
    │ │ │ +
    123 System* getSystem();
    │ │ │ +
    124
    │ │ │ +
    128 const System* getSystem() const;
    │ │ │ +
    129
    │ │ │ +
    133 void prepend(Atom& atom);
    │ │ │ +
    134
    │ │ │ +
    138 void append(Atom& atom);
    │ │ │ +
    139
    │ │ │ +
    143 void insert(Atom& atom);
    │ │ │ +
    144
    │ │ │ +
    149 void insertBefore(Atom& atom, Composite& before);
    │ │ │ +
    150
    │ │ │ +
    155 void insertAfter(Atom& atom, Composite& after);
    │ │ │ +
    156
    │ │ │ +
    160 bool remove(Atom& atom);
    │ │ │ +
    161
    │ │ │ +
    165 void prepend(AtomContainer& atom_container);
    │ │ │ +
    166
    │ │ │ +
    170 void append(AtomContainer& atom_container);
    │ │ │ +
    171
    │ │ │ +
    175 void insert(AtomContainer& atom_container);
    │ │ │ +
    176
    │ │ │ +
    181 void insertBefore(AtomContainer& atom_container, Composite& before);
    │ │ │ +
    182
    │ │ │ +
    187 void insertAfter(AtomContainer& atom_container, Composite& after);
    │ │ │ +
    188
    │ │ │ +
    192 void spliceBefore(AtomContainer& atom_container);
    │ │ │ +
    193
    │ │ │ +
    197 void spliceAfter(AtomContainer& atom_container);
    │ │ │ +
    198
    │ │ │ +
    204 void splice(AtomContainer& atom_container);
    │ │ │ +
    205
    │ │ │ +
    209 bool remove(AtomContainer& atom_container);
    │ │ │ +
    210
    │ │ │ +
    212
    │ │ │ +
    216 virtual bool isMolecule() const { return true; }
    │ │ │ +
    218
    │ │ │ +
    222
    │ │ │ +
    229 virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
    │ │ │ +
    230
    │ │ │ +
    232
    │ │ │ +
    237 bool operator == (const Molecule& molecule) const;
    │ │ │ +
    238
    │ │ │ +
    242 bool operator != (const Molecule& molecule) const;
    │ │ │ +
    243
    │ │ │ +
    244
    │ │ │ +
    245 BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Fragment)
    │ │ │ +
    246 BALL_DECLARE_STD_ITERATOR_WRAPPER(Molecule, Fragment, fragments)
    │ │ │ +
    247
    │ │ │ +
    248
    │ │ │ +
    249 protected:
    │ │ │ +
    250
    │ │ │ +
    251 Molecule* getMolecule();
    │ │ │ +
    252
    │ │ │ +
    253 const Molecule* getMolecule() const;
    │ │ │ +
    254
    │ │ │ +
    255 AtomContainer* getSuperAtomContainer();
    │ │ │ +
    256
    │ │ │ +
    257 const AtomContainer* getSuperAtomContainer() const;
    │ │ │ +
    258
    │ │ │ +
    259 void prepend(Molecule& molecule);
    │ │ │ +
    260
    │ │ │ +
    261 void append(Molecule& molecule);
    │ │ │ +
    262
    │ │ │ +
    263 void insert(Molecule& molecule);
    │ │ │ +
    264
    │ │ │ +
    265 void insertBefore(Molecule& molecule, Composite& composite);
    │ │ │ +
    266
    │ │ │ +
    267 void insertAfter(Molecule& molecule, Composite& composite);
    │ │ │ +
    268
    │ │ │ +
    269 bool remove(Molecule& molecule);
    │ │ │ +
    270
    │ │ │ +
    271 bool isSubAtomContainerOf(const AtomContainer& atom_container) const;
    │ │ │ +
    272 };
    │ │ │ +
    │ │ │ +
    273} // namespace BALL
    │ │ │ +
    274
    │ │ │ +
    275#endif // BALL_KERNEL_MOLECULE_H
    │ │ │ +
    BALL_DECLARE_STD_ITERATOR_WRAPPER
    #define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name)
    Definition stdIteratorWrapper.h:30
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_KERNEL_DEFINE_ITERATOR_CREATORS
    #define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type)
    Definition iterator.h:25
    │ │ │ +
    BALL_CREATE_DEEP
    #define BALL_CREATE_DEEP(name)
    Definition create.h:26
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::Molecule::persistentRead
    void persistentRead(PersistenceManager &pm)
    │ │ │ +
    BALL::Molecule::dump
    virtual void dump(std::ostream &s=std::cout, Size depth=0) const
    │ │ │ +
    BALL::Molecule::persistentWrite
    void persistentWrite(PersistenceManager &pm, const char *name=0) const
    │ │ │ +
    BALL::Molecule::getMolecule
    Molecule * getMolecule()
    │ │ │ +
    BALL::Molecule::~Molecule
    virtual ~Molecule()
    │ │ │ +
    BALL::Molecule::insertBefore
    void insertBefore(Molecule &molecule, Composite &composite)
    │ │ │ +
    BALL::Molecule::getSystem
    const System * getSystem() const
    │ │ │ +
    BALL::Molecule::insert
    void insert(AtomContainer &atom_container)
    │ │ │ +
    BALL::Molecule::remove
    bool remove(Atom &atom)
    │ │ │ +
    BALL::Molecule::insertBefore
    void insertBefore(AtomContainer &atom_container, Composite &before)
    │ │ │ +
    BALL::Molecule::splice
    void splice(AtomContainer &atom_container)
    │ │ │ +
    BALL::Molecule::prepend
    void prepend(Atom &atom)
    │ │ │ +
    BALL::Molecule::swap
    void swap(Molecule &molecule)
    │ │ │ +
    BALL::Molecule::prepend
    void prepend(AtomContainer &atom_container)
    │ │ │ +
    BALL::Molecule::remove
    bool remove(Molecule &molecule)
    │ │ │ +
    BALL::Molecule::set
    void set(const Molecule &molecule, bool deep=true)
    │ │ │ +
    BALL::Molecule::insert
    void insert(Atom &atom)
    │ │ │ +
    BALL::Molecule::get
    void get(Molecule &molecule, bool deep=true) const
    │ │ │ +
    BALL::Molecule::append
    void append(Atom &atom)
    │ │ │ +
    BALL::Molecule::Molecule
    Molecule(const String &name)
    │ │ │ +
    BALL::Molecule::append
    void append(Molecule &molecule)
    │ │ │ +
    BALL::Molecule::Molecule
    Molecule(const AtomContainer &atomContainer, bool deep=true)
    │ │ │ +
    BALL::Molecule::insertAfter
    void insertAfter(AtomContainer &atom_container, Composite &after)
    │ │ │ +
    BALL::Molecule::getSystem
    System * getSystem()
    │ │ │ +
    BALL::Molecule::insertAfter
    void insertAfter(Molecule &molecule, Composite &composite)
    │ │ │ +
    BALL::Molecule::insertBefore
    void insertBefore(Atom &atom, Composite &before)
    │ │ │ +
    BALL::Molecule::spliceBefore
    void spliceBefore(AtomContainer &atom_container)
    │ │ │ +
    BALL::Molecule::insert
    void insert(Molecule &molecule)
    │ │ │ +
    BALL::Molecule::isMolecule
    virtual bool isMolecule() const
    Definition molecule.h:216
    │ │ │ +
    BALL::Molecule::Molecule
    Molecule(const Molecule &molecule, bool deep=true)
    │ │ │ +
    BALL::Molecule::getMolecule
    const Molecule * getMolecule() const
    │ │ │ +
    BALL::Molecule::remove
    bool remove(AtomContainer &atom_container)
    │ │ │ +
    BALL::Molecule::append
    void append(AtomContainer &atom_container)
    │ │ │ +
    BALL::Molecule::getSuperAtomContainer
    const AtomContainer * getSuperAtomContainer() const
    │ │ │ +
    BALL::Molecule::prepend
    void prepend(Molecule &molecule)
    │ │ │ +
    BALL::Molecule::insertAfter
    void insertAfter(Atom &atom, Composite &after)
    │ │ │ +
    BALL::Molecule::spliceAfter
    void spliceAfter(AtomContainer &atom_container)
    │ │ │ +
    BALL::Molecule::getSuperAtomContainer
    AtomContainer * getSuperAtomContainer()
    │ │ │ + │ │ │ +
    BALL::Molecule::isSubAtomContainerOf
    bool isSubAtomContainerOf(const AtomContainer &atom_container) const
    │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,78 +1,275 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _Q_S_A_R │ │ │ │ -bayesModel.h │ │ │ │ + * _K_E_R_N_E_L │ │ │ │ +molecule.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// │ │ │ │ -5 │ │ │ │ -6#ifndef BALL_QSAR_BAYESMODEL_H │ │ │ │ -7#define BALL_QSAR_BAYESMODEL_H │ │ │ │ -8 │ │ │ │ -9#ifndef BALL_QSAR_CLASSIFICATIONMODEL_H │ │ │ │ -10#include <_B_A_L_L_/_Q_S_A_R_/_c_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l_._h> │ │ │ │ -11#endif │ │ │ │ -12 │ │ │ │ -13namespace _B_A_L_L │ │ │ │ -14{ │ │ │ │ -15 namespace QSAR │ │ │ │ -16 { │ │ │ │ -_1_8 class _B_A_L_L___E_X_P_O_R_T _B_a_y_e_s_M_o_d_e_l : public _C_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l │ │ │ │ -19 { │ │ │ │ -20 public: │ │ │ │ -21 │ │ │ │ -_2_2 _B_a_y_e_s_M_o_d_e_l(const _Q_S_A_R_D_a_t_a& q); │ │ │ │ +4 │ │ │ │ +5#ifndef BALL_KERNEL_MOLECULE_H │ │ │ │ +6#define BALL_KERNEL_MOLECULE_H │ │ │ │ +7 │ │ │ │ +8#ifndef BALL_KERNEL_ATOMCONTAINER_H │ │ │ │ +9# include <_B_A_L_L_/_K_E_R_N_E_L_/_a_t_o_m_C_o_n_t_a_i_n_e_r_._h> │ │ │ │ +10#endif │ │ │ │ +11 │ │ │ │ +12#ifndef BALL_KERNEL_FRAGMENT_H │ │ │ │ +13# include <_B_A_L_L_/_K_E_R_N_E_L_/_f_r_a_g_m_e_n_t_._h> │ │ │ │ +14#endif │ │ │ │ +15 │ │ │ │ +16#ifndef BALL_KERNEL_FRAGMENTITERATOR_H │ │ │ │ +17# include <_B_A_L_L_/_K_E_R_N_E_L_/_f_r_a_g_m_e_n_t_I_t_e_r_a_t_o_r_._h> │ │ │ │ +18#endif │ │ │ │ +19 │ │ │ │ +20namespace _B_A_L_L │ │ │ │ +21{ │ │ │ │ +22 class System; │ │ │ │ 23 │ │ │ │ -_2_4 virtual bool _i_s_T_r_a_i_n_e_d() = 0; │ │ │ │ -25 │ │ │ │ -_2_8 virtual vector _c_a_l_c_u_l_a_t_e_P_r_o_b_a_b_i_l_i_t_i_e_s(int activitiy_index, int │ │ │ │ -feature_index, double feature_value) = 0; │ │ │ │ -29 │ │ │ │ -_3_1 virtual int _g_e_t_N_o_R_e_s_p_o_n_s_e_V_a_r_i_a_b_l_e_s() = 0; │ │ │ │ -32 │ │ │ │ +_2_9 class _B_A_L_L___E_X_P_O_R_T _M_o_l_e_c_u_l_e │ │ │ │ +30 : public _A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ +31 { │ │ │ │ +32 public: │ │ │ │ 33 │ │ │ │ -34 protected: │ │ │ │ -_3_6 double _m_i_n___p_r_o_b___d_i_f_f__; │ │ │ │ -37 │ │ │ │ -_3_9 double _u_n_d_e_f___a_c_t___c_l_a_s_s___i_d__; │ │ │ │ +34 _B_A_L_L___C_R_E_A_T_E___D_E_E_P(_M_o_l_e_c_u_l_e) │ │ │ │ +35 │ │ │ │ +36 │ │ │ │ +39 │ │ │ │ 40 │ │ │ │ -41 }; │ │ │ │ -42 } │ │ │ │ -43} │ │ │ │ -44 │ │ │ │ -45#endif //BAYESMODEL_H │ │ │ │ -_c_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l_._h │ │ │ │ +_4_2 enum _P_r_o_p_e_r_t_y │ │ │ │ +43 { │ │ │ │ +_4_4 IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES, │ │ │ │ +45 NUMBER_OF_PROPERTIES │ │ │ │ +_4_6 }; │ │ │ │ +47 │ │ │ │ +49 │ │ │ │ +52 │ │ │ │ +_5_5 _M_o_l_e_c_u_l_e(); │ │ │ │ +56 │ │ │ │ +_5_9 _M_o_l_e_c_u_l_e(const _M_o_l_e_c_u_l_e& molecule, bool deep = true); │ │ │ │ +60 │ │ │ │ +_6_3 _M_o_l_e_c_u_l_e(const _A_t_o_m_C_o_n_t_a_i_n_e_r& atomContainer, bool deep = true); │ │ │ │ +64 │ │ │ │ +_6_7 _M_o_l_e_c_u_l_e(const _S_t_r_i_n_g& name); │ │ │ │ +68 │ │ │ │ +_7_1 virtual _~_M_o_l_e_c_u_l_e(); │ │ │ │ +72 │ │ │ │ +74 │ │ │ │ +77 │ │ │ │ +_8_1 void _p_e_r_s_i_s_t_e_n_t_W_r_i_t_e(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm, const char* name = 0) const; │ │ │ │ +82 │ │ │ │ +_8_6 void _p_e_r_s_i_s_t_e_n_t_R_e_a_d(_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r& pm); │ │ │ │ +87 │ │ │ │ +89 │ │ │ │ +92 │ │ │ │ +_9_7 void _s_e_t(const _M_o_l_e_c_u_l_e& molecule, bool deep = true); │ │ │ │ +98 │ │ │ │ +_1_0_2 _M_o_l_e_c_u_l_e& operator = (const _M_o_l_e_c_u_l_e& molecule); │ │ │ │ +103 │ │ │ │ +_1_0_8 void _g_e_t(_M_o_l_e_c_u_l_e& molecule, bool deep = true) const; │ │ │ │ +109 │ │ │ │ +_1_1_3 void _s_w_a_p(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ +114 │ │ │ │ +116 │ │ │ │ +119 │ │ │ │ +_1_2_3 _S_y_s_t_e_m* _g_e_t_S_y_s_t_e_m(); │ │ │ │ +124 │ │ │ │ +_1_2_8 const _S_y_s_t_e_m* _g_e_t_S_y_s_t_e_m() const; │ │ │ │ +129 │ │ │ │ +_1_3_3 void _p_r_e_p_e_n_d(_A_t_o_m& atom); │ │ │ │ +134 │ │ │ │ +_1_3_8 void _a_p_p_e_n_d(_A_t_o_m& atom); │ │ │ │ +139 │ │ │ │ +_1_4_3 void _i_n_s_e_r_t(_A_t_o_m& atom); │ │ │ │ +144 │ │ │ │ +_1_4_9 void _i_n_s_e_r_t_B_e_f_o_r_e(_A_t_o_m& atom, _C_o_m_p_o_s_i_t_e& before); │ │ │ │ +150 │ │ │ │ +_1_5_5 void _i_n_s_e_r_t_A_f_t_e_r(_A_t_o_m& atom, _C_o_m_p_o_s_i_t_e& after); │ │ │ │ +156 │ │ │ │ +_1_6_0 bool _r_e_m_o_v_e(_A_t_o_m& atom); │ │ │ │ +161 │ │ │ │ +_1_6_5 void _p_r_e_p_e_n_d(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +166 │ │ │ │ +_1_7_0 void _a_p_p_e_n_d(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +171 │ │ │ │ +_1_7_5 void _i_n_s_e_r_t(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +176 │ │ │ │ +_1_8_1 void _i_n_s_e_r_t_B_e_f_o_r_e(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container, _C_o_m_p_o_s_i_t_e& before); │ │ │ │ +182 │ │ │ │ +_1_8_7 void _i_n_s_e_r_t_A_f_t_e_r(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container, _C_o_m_p_o_s_i_t_e& after); │ │ │ │ +188 │ │ │ │ +_1_9_2 void _s_p_l_i_c_e_B_e_f_o_r_e(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +193 │ │ │ │ +_1_9_7 void _s_p_l_i_c_e_A_f_t_e_r(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +198 │ │ │ │ +_2_0_4 void _s_p_l_i_c_e(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +205 │ │ │ │ +_2_0_9 bool _r_e_m_o_v_e(_A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container); │ │ │ │ +210 │ │ │ │ +212 │ │ │ │ +_2_1_6 virtual bool _i_s_M_o_l_e_c_u_l_e() const { return true; } │ │ │ │ +218 │ │ │ │ +222 │ │ │ │ +_2_2_9 virtual void _d_u_m_p(std::ostream& s = std::cout, _S_i_z_e depth = 0) const; │ │ │ │ +230 │ │ │ │ +232 │ │ │ │ +_2_3_7 bool operator == (const _M_o_l_e_c_u_l_e& molecule) const; │ │ │ │ +238 │ │ │ │ +_2_4_2 bool operator != (const _M_o_l_e_c_u_l_e& molecule) const; │ │ │ │ +243 │ │ │ │ +244 │ │ │ │ +245 _B_A_L_L___K_E_R_N_E_L___D_E_F_I_N_E___I_T_E_R_A_T_O_R___C_R_E_A_T_O_R_S(_F_r_a_g_m_e_n_t) │ │ │ │ +246 _B_A_L_L___D_E_C_L_A_R_E___S_T_D___I_T_E_R_A_T_O_R___W_R_A_P_P_E_R(_M_o_l_e_c_u_l_e, _F_r_a_g_m_e_n_t, fragments) │ │ │ │ +247 │ │ │ │ +248 │ │ │ │ +249 protected: │ │ │ │ +250 │ │ │ │ +_2_5_1 _M_o_l_e_c_u_l_e* _g_e_t_M_o_l_e_c_u_l_e(); │ │ │ │ +252 │ │ │ │ +_2_5_3 const _M_o_l_e_c_u_l_e* _g_e_t_M_o_l_e_c_u_l_e() const; │ │ │ │ +254 │ │ │ │ +_2_5_5 _A_t_o_m_C_o_n_t_a_i_n_e_r* _g_e_t_S_u_p_e_r_A_t_o_m_C_o_n_t_a_i_n_e_r(); │ │ │ │ +256 │ │ │ │ +_2_5_7 const _A_t_o_m_C_o_n_t_a_i_n_e_r* _g_e_t_S_u_p_e_r_A_t_o_m_C_o_n_t_a_i_n_e_r() const; │ │ │ │ +258 │ │ │ │ +_2_5_9 void _p_r_e_p_e_n_d(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ +260 │ │ │ │ +_2_6_1 void _a_p_p_e_n_d(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ +262 │ │ │ │ +_2_6_3 void _i_n_s_e_r_t(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ +264 │ │ │ │ +_2_6_5 void _i_n_s_e_r_t_B_e_f_o_r_e(_M_o_l_e_c_u_l_e& molecule, _C_o_m_p_o_s_i_t_e& composite); │ │ │ │ +266 │ │ │ │ +_2_6_7 void _i_n_s_e_r_t_A_f_t_e_r(_M_o_l_e_c_u_l_e& molecule, _C_o_m_p_o_s_i_t_e& composite); │ │ │ │ +268 │ │ │ │ +_2_6_9 bool _r_e_m_o_v_e(_M_o_l_e_c_u_l_e& molecule); │ │ │ │ +270 │ │ │ │ +_2_7_1 bool _i_s_S_u_b_A_t_o_m_C_o_n_t_a_i_n_e_r_O_f(const _A_t_o_m_C_o_n_t_a_i_n_e_r& atom_container) const; │ │ │ │ +272 }; │ │ │ │ +273} // namespace BALL │ │ │ │ +274 │ │ │ │ +275#endif // BALL_KERNEL_MOLECULE_H │ │ │ │ +_B_A_L_L___D_E_C_L_A_R_E___S_T_D___I_T_E_R_A_T_O_R___W_R_A_P_P_E_R │ │ │ │ +#define BALL_DECLARE_STD_ITERATOR_WRAPPER(container, type, method_name) │ │ │ │ +DDeeffiinniittiioonn _s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h_:_3_0 │ │ │ │ +_f_r_a_g_m_e_n_t_._h │ │ │ │ +_f_r_a_g_m_e_n_t_I_t_e_r_a_t_o_r_._h │ │ │ │ +_a_t_o_m_C_o_n_t_a_i_n_e_r_._h │ │ │ │ +_B_A_L_L___K_E_R_N_E_L___D_E_F_I_N_E___I_T_E_R_A_T_O_R___C_R_E_A_T_O_R_S │ │ │ │ +#define BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Type) │ │ │ │ +DDeeffiinniittiioonn _i_t_e_r_a_t_o_r_._h_:_2_5 │ │ │ │ +_B_A_L_L___C_R_E_A_T_E___D_E_E_P │ │ │ │ +#define BALL_CREATE_DEEP(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_2_6 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_B_a_y_e_s_M_o_d_e_l │ │ │ │ -DDeeffiinniittiioonn _b_a_y_e_s_M_o_d_e_l_._h_:_1_9 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_B_a_y_e_s_M_o_d_e_l_:_:_u_n_d_e_f___a_c_t___c_l_a_s_s___i_d__ │ │ │ │ -double undef_act_class_id_ │ │ │ │ -DDeeffiinniittiioonn _b_a_y_e_s_M_o_d_e_l_._h_:_3_9 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_B_a_y_e_s_M_o_d_e_l_:_:_g_e_t_N_o_R_e_s_p_o_n_s_e_V_a_r_i_a_b_l_e_s │ │ │ │ -virtual int getNoResponseVariables()=0 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_B_a_y_e_s_M_o_d_e_l_:_:_c_a_l_c_u_l_a_t_e_P_r_o_b_a_b_i_l_i_t_i_e_s │ │ │ │ -virtual vector< double > calculateProbabilities(int activitiy_index, int │ │ │ │ -feature_index, double feature_value)=0 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_B_a_y_e_s_M_o_d_e_l_:_:_m_i_n___p_r_o_b___d_i_f_f__ │ │ │ │ -double min_prob_diff_ │ │ │ │ -DDeeffiinniittiioonn _b_a_y_e_s_M_o_d_e_l_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_B_a_y_e_s_M_o_d_e_l_:_:_B_a_y_e_s_M_o_d_e_l │ │ │ │ -BayesModel(const QSARData &q) │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_B_a_y_e_s_M_o_d_e_l_:_:_i_s_T_r_a_i_n_e_d │ │ │ │ -virtual bool isTrained()=0 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_C_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l │ │ │ │ -DDeeffiinniittiioonn _c_l_a_s_s_i_f_i_c_a_t_i_o_n_M_o_d_e_l_._h_:_2_8 │ │ │ │ -_B_A_L_L_:_:_Q_S_A_R_:_:_Q_S_A_R_D_a_t_a │ │ │ │ -DDeeffiinniittiioonn _Q_S_A_R_D_a_t_a_._h_:_5_6 │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_P_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r │ │ │ │ +DDeeffiinniittiioonn _p_e_r_s_i_s_t_e_n_c_e_M_a_n_a_g_e_r_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_._h_:_9_0 │ │ │ │ +_B_A_L_L_:_:_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ +DDeeffiinniittiioonn _a_t_o_m_C_o_n_t_a_i_n_e_r_._h_:_3_2 │ │ │ │ +_B_A_L_L_:_:_F_r_a_g_m_e_n_t │ │ │ │ +DDeeffiinniittiioonn _f_r_a_g_m_e_n_t_._h_:_2_2 │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e │ │ │ │ +DDeeffiinniittiioonn _m_o_l_e_c_u_l_e_._h_:_3_1 │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_M_o_l_e_c_u_l_e │ │ │ │ +Molecule() │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_e_r_s_i_s_t_e_n_t_R_e_a_d │ │ │ │ +void persistentRead(PersistenceManager &pm) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_d_u_m_p │ │ │ │ +virtual void dump(std::ostream &s=std::cout, Size depth=0) const │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_e_r_s_i_s_t_e_n_t_W_r_i_t_e │ │ │ │ +void persistentWrite(PersistenceManager &pm, const char *name=0) const │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_M_o_l_e_c_u_l_e │ │ │ │ +Molecule * getMolecule() │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_~_M_o_l_e_c_u_l_e │ │ │ │ +virtual ~Molecule() │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_B_e_f_o_r_e │ │ │ │ +void insertBefore(Molecule &molecule, Composite &composite) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_S_y_s_t_e_m │ │ │ │ +const System * getSystem() const │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t │ │ │ │ +void insert(AtomContainer &atom_container) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_r_e_m_o_v_e │ │ │ │ +bool remove(Atom &atom) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_B_e_f_o_r_e │ │ │ │ +void insertBefore(AtomContainer &atom_container, Composite &before) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_p_l_i_c_e │ │ │ │ +void splice(AtomContainer &atom_container) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_r_e_p_e_n_d │ │ │ │ +void prepend(Atom &atom) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_w_a_p │ │ │ │ +void swap(Molecule &molecule) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_r_e_p_e_n_d │ │ │ │ +void prepend(AtomContainer &atom_container) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_r_e_m_o_v_e │ │ │ │ +bool remove(Molecule &molecule) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_e_t │ │ │ │ +void set(const Molecule &molecule, bool deep=true) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t │ │ │ │ +void insert(Atom &atom) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t │ │ │ │ +void get(Molecule &molecule, bool deep=true) const │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_a_p_p_e_n_d │ │ │ │ +void append(Atom &atom) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_M_o_l_e_c_u_l_e │ │ │ │ +Molecule(const String &name) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_a_p_p_e_n_d │ │ │ │ +void append(Molecule &molecule) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_M_o_l_e_c_u_l_e │ │ │ │ +Molecule(const AtomContainer &atomContainer, bool deep=true) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_A_f_t_e_r │ │ │ │ +void insertAfter(AtomContainer &atom_container, Composite &after) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_S_y_s_t_e_m │ │ │ │ +System * getSystem() │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_A_f_t_e_r │ │ │ │ +void insertAfter(Molecule &molecule, Composite &composite) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_B_e_f_o_r_e │ │ │ │ +void insertBefore(Atom &atom, Composite &before) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_p_l_i_c_e_B_e_f_o_r_e │ │ │ │ +void spliceBefore(AtomContainer &atom_container) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t │ │ │ │ +void insert(Molecule &molecule) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_s_M_o_l_e_c_u_l_e │ │ │ │ +virtual bool isMolecule() const │ │ │ │ +DDeeffiinniittiioonn _m_o_l_e_c_u_l_e_._h_:_2_1_6 │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_M_o_l_e_c_u_l_e │ │ │ │ +Molecule(const Molecule &molecule, bool deep=true) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_M_o_l_e_c_u_l_e │ │ │ │ +const Molecule * getMolecule() const │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_r_e_m_o_v_e │ │ │ │ +bool remove(AtomContainer &atom_container) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_a_p_p_e_n_d │ │ │ │ +void append(AtomContainer &atom_container) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_S_u_p_e_r_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ +const AtomContainer * getSuperAtomContainer() const │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_p_r_e_p_e_n_d │ │ │ │ +void prepend(Molecule &molecule) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_n_s_e_r_t_A_f_t_e_r │ │ │ │ +void insertAfter(Atom &atom, Composite &after) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_s_p_l_i_c_e_A_f_t_e_r │ │ │ │ +void spliceAfter(AtomContainer &atom_container) │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_g_e_t_S_u_p_e_r_A_t_o_m_C_o_n_t_a_i_n_e_r │ │ │ │ +AtomContainer * getSuperAtomContainer() │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_P_r_o_p_e_r_t_y │ │ │ │ +Property │ │ │ │ +DDeeffiinniittiioonn _m_o_l_e_c_u_l_e_._h_:_4_3 │ │ │ │ +_B_A_L_L_:_:_M_o_l_e_c_u_l_e_:_:_i_s_S_u_b_A_t_o_m_C_o_n_t_a_i_n_e_r_O_f │ │ │ │ +bool isSubAtomContainerOf(const AtomContainer &atom_container) const │ │ │ │ +_B_A_L_L_:_:_S_y_s_t_e_m │ │ │ │ +DDeeffiinniittiioonn _K_E_R_N_E_L_/_s_y_s_t_e_m_._h_:_4_0 │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d35/a03398.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::BitVector Class Reference
    Foundation Classes » General datastructures » Miscellaneous
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/DATATYPE/bitVector.h>

    │ │ │ +

    #include <BALL/DATATYPE/bitVector.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -202,43 +202,43 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    Constructors and Destructors
     BitVector ()
     
     BitVector (Size size)
     
    virtual void write (std::ostream &s) const
     
    virtual void write (PersistenceManager &pm) const
     
    virtual bool read (PersistenceManager &pm)
     
    BALL_EXPORT friend std::istream & operator>> (std::istream &s, BitVector &bit_vector)
    BALL_EXPORT friend std::istream & operator>> (std::istream &s, BitVector &bit_vector)
     
    BALL_EXPORT friend std::ostream & operator<< (std::ostream &s, const BitVector &bit_vector)
    BALL_EXPORT friend std::ostream & operator<< (std::ostream &s, const BitVector &bit_vector)
     
    void validateIndex_ (Index &index)
     
    void validateIndex_ (Index &index) const
     
    void validateRange_ (Index &first, Index &last) const
     
    │ │ │

    Detailed Description

    │ │ │

    Bit vector class. Indices may be given as negative arguments: start from the end -1 therefore means the last bit. Some functions resize the instance if a index greater than the size of the instance is given. Other functions throw exception in this case.

    │ │ │ │ │ │ -

    Definition at line 176 of file bitVector.h.

    │ │ │ +

    Definition at line 176 of file bitVector.h.

    │ │ │

    Member Typedef Documentation

    │ │ │ │ │ │

    ◆ BlockType

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef unsigned char BALL::BitVector::BlockType
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 188 of file bitVector.h.

    │ │ │ +

    Definition at line 188 of file bitVector.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ VectorType

    │ │ │ │ │ │
    │ │ │ @@ -246,15 +246,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef std::vector<BlockType> BALL::BitVector::VectorType
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 190 of file bitVector.h.

    │ │ │ +

    Definition at line 190 of file bitVector.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ BitVector() [1/4]

    │ │ │ │ │ │ @@ -1714,15 +1714,15 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -1751,15 +1751,15 @@ │ │ │
    │ │ │
    │ │ │
    BALL_EXPORT friend std::ostream & operator<< BALL_EXPORT friend std::ostream & operator<< (std::ostream & s,
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -1804,15 +1804,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_EXPORT friend std::istream & operator>> BALL_EXPORT friend std::istream & operator>> (std::istream & s,
    │ │ │ static
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 192 of file bitVector.h.

    │ │ │ +

    Definition at line 192 of file bitVector.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ CharBits

    │ │ │ │ │ │
    │ │ │ @@ -1828,15 +1828,15 @@ │ │ │
    		│ │ │ static
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 194 of file bitVector.h.

    │ │ │ +

    Definition at line 194 of file bitVector.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d39/a02048.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: bidirectionalIterator.h File Reference │ │ │ +BALL: create.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,41 +65,108 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ -Classes | │ │ │ -Namespaces
    │ │ │ -
    bidirectionalIterator.h File Reference
    │ │ │ +Macros
    │ │ │ +
    create.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/CONCEPT/forwardIterator.h>
    │ │ │ -
    │ │ │ + │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -

    │ │ │ -Classes

    class  BALL::ConstBidirectionalIterator< Container, DataType, Position, Traits >
     
    class  BALL::BidirectionalIterator< Container, DataType, Position, Traits >
     Mutable bidirectional iterator. More...
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │

    │ │ │ -Namespaces

    namespace  BALL
     

    │ │ │ +Macros

    #define BALL_CREATE_DEEP(name)
     
    #define BALL_CREATE(name)
     
    #define BALL_DEFINE_CREATE(name)
     
    │ │ │ +

    Macro Definition Documentation

    │ │ │ + │ │ │ +

    ◆ BALL_CREATE

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_CREATE( name)
    │ │ │ +
    │ │ │ +Value:
    \
    │ │ │ +
    virtual void* create(bool /* deep */ = true, bool empty = false) const\
    │ │ │ +
    {\
    │ │ │ +
    void* ptr;\
    │ │ │ +
    if (empty == true)\
    │ │ │ +
    {\
    │ │ │ +
    ptr = (void*)new name;\
    │ │ │ +
    }\
    │ │ │ +
    else\
    │ │ │ +
    {\
    │ │ │ +
    ptr = (void*)new name(*this);\
    │ │ │ +
    }\
    │ │ │ +
    \
    │ │ │ +
    return ptr;\
    │ │ │ +
    }\
    │ │ │ +
    \
    │ │ │ +
    static void* createDefault()\
    │ │ │ +
    {\
    │ │ │ +
    return static_cast<void*>(new name);\
    │ │ │ +
    }
    │ │ │ +

    Virtual construction macro. This macro is used to define the virtual create method for classes that do not define a copy constructor taking a second argument (boolean, deep or shallow copy). On inclusion of this macro in the public interface of a class, the virtual creation method becomes available. The create method's signature is as follows: virtual void* create(bool deep = true, bool empty = false) const

    The create method either creates an empty default object of the class (empty == true) or a copy of the object. The use of the create method requires a (public) default constructor (when creating an empty copy) and a copy constructor taking a reference to an object. The macro also implements a static method createDefault that returns a void pointer to a new instance of name.
    │ │ │ +
    Parameters
    │ │ │ + │ │ │ + │ │ │ +
    namethe class name
    │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    Definition at line 62 of file create.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ +

    ◆ BALL_DEFINE_CREATE

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    #define BALL_DEFINE_CREATE( name)
    │ │ │ +
    │ │ │ +Value:
    \
    │ │ │ +
    virtual void* create(bool deep = true, bool empty = false) const;\
    │ │ │ +
    static void* createDefault();
    │ │ │ +

    Virtual cloning method definition macro. If the create method has to be implemented by the user, this macro just defines the create method and the createDefault method. The function signatures are: 

      virtual void* create(bool deep = true, bool empty = false) const;
│ │ │ +  static void* createDefault();
│ │ │ +
    │ │ │ +

    Definition at line 93 of file create.h.

    │ │ │ + │ │ │ +
    │ │ │ +
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,23 +1,70 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _C_O_N_C_E_P_T │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -bidirectionalIterator.h File Reference │ │ │ │ -#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h> │ │ │ │ + * _C_O_M_M_O_N │ │ │ │ +_M_a_c_r_o_s │ │ │ │ +create.h File Reference │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_ _C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s │ │ │ │ - _> │ │ │ │ +MMaaccrrooss │ │ │ │ +#define  _B_A_L_L___C_R_E_A_T_E___D_E_E_P(name) │ │ │ │   │ │ │ │ -class   _B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_ _C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_ _> │ │ │ │ -  Mutable bidirectional iterator. _M_o_r_e_._._. │ │ │ │ +#define  _B_A_L_L___C_R_E_A_T_E(name) │ │ │ │   │ │ │ │ -NNaammeessppaacceess │ │ │ │ -namespace   _B_A_L_L │ │ │ │ +#define  _B_A_L_L___D_E_F_I_N_E___C_R_E_A_T_E(name) │ │ │ │   │ │ │ │ +********** MMaaccrroo DDeeffiinniittiioonn DDooccuummeennttaattiioonn ********** │ │ │ │ +********** _?◆_? BBAALLLL__CCRREEAATTEE ********** │ │ │ │ +#define BALL_CREATE (   name ) │ │ │ │ +VVaalluuee:: │ │ │ │ +\ │ │ │ │ +virtual void* create(bool /* deep */ = true, bool empty = false) const\ │ │ │ │ +{\ │ │ │ │ +void* ptr;\ │ │ │ │ +if (empty == true)\ │ │ │ │ +{\ │ │ │ │ +ptr = (void*)new name;\ │ │ │ │ +}\ │ │ │ │ +else\ │ │ │ │ +{\ │ │ │ │ +ptr = (void*)new name(*this);\ │ │ │ │ +}\ │ │ │ │ +\ │ │ │ │ +return ptr;\ │ │ │ │ +}\ │ │ │ │ +\ │ │ │ │ +static void* createDefault()\ │ │ │ │ +{\ │ │ │ │ +return static_cast(new name);\ │ │ │ │ +} │ │ │ │ +Virtual construction macro. This macro is used to define the virtual ccrreeaattee │ │ │ │ +method for classes that do not define a copy constructor taking a second │ │ │ │ +argument (boolean, deep or shallow copy). On inclusion of this macro in the │ │ │ │ +public interface of a class, the virtual creation method becomes available. The │ │ │ │ +create method's signature is as follows: virtual void* ccrreeaattee(bool deep = true, │ │ │ │ +bool empty = false) const │ │ │ │ + The create method either creates an empty default object of the class │ │ │ │ + (empty == ttrruuee) or a copy of the object. The use of the create method │ │ │ │ + requires a (public) default constructor (when creating an empty copy) and │ │ │ │ + a copy constructor taking a reference to an object. The macro also │ │ │ │ + implements a static method createDefault that returns a void pointer to a │ │ │ │ + new instance of name. │ │ │ │ + Parameters │ │ │ │ + name the class name │ │ │ │ +Definition at line _6_2 of file _c_r_e_a_t_e_._h. │ │ │ │ +********** _?◆_? BBAALLLL__DDEEFFIINNEE__CCRREEAATTEE ********** │ │ │ │ +#define BALL_DEFINE_CREATE (   name ) │ │ │ │ +VVaalluuee:: │ │ │ │ +\ │ │ │ │ +virtual void* create(bool deep = true, bool empty = false) const;\ │ │ │ │ +static void* createDefault(); │ │ │ │ +Virtual cloning method definition macro. If the create method has to be │ │ │ │ +implemented by the user, this macro just defines the create method and the │ │ │ │ +createDefault method. The function signatures are: │ │ │ │ + virtual void* create(bool deep = true, bool empty = false) const; │ │ │ │ + static void* createDefault(); │ │ │ │ +Definition at line _9_3 of file _c_r_e_a_t_e_._h. │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d39/a02048_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: bidirectionalIterator.h Source File │ │ │ +BALL: create.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,490 +70,86 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    bidirectionalIterator.h
    │ │ │ +
    create.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │
    4
    │ │ │ -
    5#ifndef BALL_CONCEPT_BIDIRECTIONALITERATOR_H
    │ │ │ -
    6#define BALL_CONCEPT_BIDIRECTIONALITERATOR_H
    │ │ │ +
    5#ifndef BALL_COMMON_CREATE_H
    │ │ │ +
    6#define BALL_COMMON_CREATE_H
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_CONCEPT_FORWARDITERATOR_H
    │ │ │ -
    9# include <BALL/CONCEPT/forwardIterator.h>
    │ │ │ -
    10#endif
    │ │ │ -
    11
    │ │ │ -
    12namespace BALL
    │ │ │ -
    13{
    │ │ │ -
    14
    │ │ │ -
    19
    │ │ │ -
    22 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    │ │ │ -
    23 class ConstBidirectionalIterator
    │ │ │ -
    24 : public ConstForwardIterator<Container, DataType, Position, Traits>
    │ │ │ -
    25 {
    │ │ │ -
    26 public:
    │ │ │ -
    27
    │ │ │ -
    31
    │ │ │ -
    33 typedef std::bidirectional_iterator_tag iterator_category;
    │ │ │ -
    34 // convenience typedef
    │ │ │ -
    35 typedef ConstForwardIterator<Container, DataType, Position, Traits> Base;
    │ │ │ -
    37
    │ │ │ -
    41
    │ │ │ -
    43 BALL_INLINE ConstBidirectionalIterator() {}
    │ │ │ -
    44
    │ │ │ -
    │ │ │ -
    46 BALL_INLINE ConstBidirectionalIterator(const ConstBidirectionalIterator& iterator)
    │ │ │ -
    47 : Base(iterator)
    │ │ │ -
    48 {
    │ │ │ -
    49 }
    │ │ │ -
    │ │ │ -
    50
    │ │ │ -
    52 BALL_INLINE ~ConstBidirectionalIterator() {}
    │ │ │ -
    54
    │ │ │ -
    58
    │ │ │ -
    │ │ │ -
    62 BALL_INLINE void toBegin();
    │ │ │ -
    63
    │ │ │ -
    65 BALL_INLINE bool isBegin() const { return Base::getTraits().isBegin(); }
    │ │ │ -
    66
    │ │ │ -
    │ │ │ -
    70 void toEnd();
    │ │ │ -
    71
    │ │ │ -
    73 BALL_INLINE bool isEnd() const { return Base::getTraits().isEnd(); }
    │ │ │ -
    74
    │ │ │ -
    │ │ │ -
    78 void toRBegin();
    │ │ │ -
    79
    │ │ │ -
    81 BALL_INLINE bool isRBegin() const { return Base::getTraits().isRBegin(); }
    │ │ │ -
    82
    │ │ │ -
    │ │ │ -
    86 void toREnd();
    │ │ │ -
    87
    │ │ │ -
    89 BALL_INLINE bool isREnd() const { return Base::getTraits().isREnd(); }
    │ │ │ -
    90
    │ │ │ -
    │ │ │ -
    94 BALL_INLINE ConstBidirectionalIterator& operator ++ ();
    │ │ │ -
    95
    │ │ │ -
    │ │ │ -
    99 BALL_INLINE ConstBidirectionalIterator operator ++ (int);
    │ │ │ -
    100
    │ │ │ -
    │ │ │ -
    104 BALL_INLINE ConstBidirectionalIterator& operator -- ();
    │ │ │ -
    105
    │ │ │ -
    │ │ │ -
    109 BALL_INLINE ConstBidirectionalIterator operator -- (int);
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    110
    │ │ │ -
    │ │ │ -
    114 static ConstBidirectionalIterator begin(const Container& container);
    │ │ │ -
    115
    │ │ │ -
    │ │ │ -
    119 static ConstBidirectionalIterator end(const Container& container);
    │ │ │ -
    120
    │ │ │ -
    │ │ │ -
    124 static ConstBidirectionalIterator rbegin(const Container& container);
    │ │ │ -
    125
    │ │ │ -
    │ │ │ -
    129 static ConstBidirectionalIterator rend(const Container& container);
    │ │ │ -
    131
    │ │ │ -
    132 protected:
    │ │ │ -
    133
    │ │ │ -
    │ │ │ -
    135 BALL_INLINE ConstBidirectionalIterator(const Container& container)
    │ │ │ -
    136 : Base(container)
    │ │ │ -
    137 {
    │ │ │ -
    138 }
    │ │ │ -
    │ │ │ -
    139 };
    │ │ │ -
    141
    │ │ │ -
    142 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    143 BALL_INLINE
    │ │ │ -
    │ │ │ -
    144 void ConstBidirectionalIterator<Container, DataType, Position, Traits>::toBegin()
    │ │ │ -
    145 {
    │ │ │ -
    146 BALL_PRECONDITION_EXCEPTION(!Base::getTraits().isSingular(), "cannot set unbound iterator to begin")
    │ │ │ -
    147 Base::getTraits().toBegin();
    │ │ │ -
    148 }
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    149
    │ │ │ -
    150 template <typename Container, typename DataType, typename Position, typename Traits>
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    151 BALL_INLINE
    │ │ │ -
    │ │ │ -
    152 void ConstBidirectionalIterator<Container, DataType, Position, Traits>::toEnd()
    │ │ │ -
    153 {
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    154 BALL_PRECONDITION_EXCEPTION(!Base::getTraits().isSingular(), "cannot set unbound iterator to end")
    │ │ │ -
    155 Base::getTraits().toEnd();
    │ │ │ -
    156 }
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    157
    │ │ │ -
    158 template <typename Container, typename DataType, typename Position, typename Traits>
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    159 BALL_INLINE
    │ │ │ -
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    160 void ConstBidirectionalIterator<Container, DataType, Position, Traits>::toRBegin()
    │ │ │ -
    161 {
    │ │ │ -
    162 BALL_PRECONDITION_EXCEPTION(!Base::getTraits().isSingular(), "cannot set unbound iterator to reverse begin")
    │ │ │ -
    163 Base::getTraits().toRBegin();
    │ │ │ -
    164 }
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    165
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    166 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    167 BALL_INLINE
    │ │ │ -
    │ │ │ -
    168 void ConstBidirectionalIterator<Container, DataType, Position, Traits>::toREnd()
    │ │ │ -
    169 {
    │ │ │ -
    170 BALL_PRECONDITION_EXCEPTION(!Base::getTraits().isSingular(), "cannot set unbound iterator to reverse end")
    │ │ │ -
    171 Base::getTraits().toREnd();
    │ │ │ -
    172 }
    │ │ │ -
    │ │ │ -
    173
    │ │ │ -
    174 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    175 BALL_INLINE
    │ │ │ -
    176 ConstBidirectionalIterator<Container, DataType, Position, Traits>&
    │ │ │ -
    │ │ │ -
    177 ConstBidirectionalIterator<Container, DataType, Position, Traits>::operator ++ ()
    │ │ │ -
    178 {
    │ │ │ -
    179 BALL_PRECONDITION_EXCEPTION(Base::getTraits().isValid(), "cannot increment an invalid iterator")
    │ │ │ -
    180 Base::getTraits().forward();
    │ │ │ -
    181 return *this;
    │ │ │ -
    182 }
    │ │ │ -
    │ │ │ -
    183
    │ │ │ -
    184 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    185 BALL_INLINE
    │ │ │ -
    186 ConstBidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    187 ConstBidirectionalIterator<Container, DataType, Position, Traits>::operator ++ (int)
    │ │ │ -
    188 {
    │ │ │ -
    189 BALL_PRECONDITION_EXCEPTION(Base::getTraits().isValid(), "cannot increment an invalid iterator")
    │ │ │ -
    190 ConstBidirectionalIterator iterator(*this);
    │ │ │ -
    191 ++(*this);
    │ │ │ -
    192 return iterator;
    │ │ │ -
    193 }
    │ │ │ -
    │ │ │ -
    194
    │ │ │ -
    195 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    196 BALL_INLINE
    │ │ │ -
    197 ConstBidirectionalIterator<Container, DataType, Position, Traits>&
    │ │ │ -
    │ │ │ -
    198 ConstBidirectionalIterator<Container, DataType, Position, Traits>::operator -- ()
    │ │ │ -
    199 {
    │ │ │ -
    200 BALL_PRECONDITION_EXCEPTION(!Base::getTraits().isSingular(), "cannot decrement unbound iterator")
    │ │ │ -
    201 Base::getTraits().backward();
    │ │ │ -
    202 return *this;
    │ │ │ -
    203 }
    │ │ │ -
    │ │ │ -
    204
    │ │ │ -
    205 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    206 BALL_INLINE
    │ │ │ -
    207 ConstBidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    208 ConstBidirectionalIterator<Container, DataType, Position, Traits>::operator -- (int)
    │ │ │ -
    209 {
    │ │ │ -
    210 BALL_PRECONDITION_EXCEPTION(!Base::getTraits().isSingular(), "cannot decrement an unbound iterator")
    │ │ │ -
    211 ConstBidirectionalIterator iterator(*this);
    │ │ │ -
    212 --(*this);
    │ │ │ -
    213 return iterator;
    │ │ │ -
    214 }
    │ │ │ -
    │ │ │ -
    215
    │ │ │ -
    216 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    217 BALL_INLINE
    │ │ │ -
    218 ConstBidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    219 ConstBidirectionalIterator<Container, DataType, Position, Traits>::begin(const Container& container)
    │ │ │ -
    220 {
    │ │ │ -
    221 ConstBidirectionalIterator iterator(container);
    │ │ │ -
    222 iterator.toBegin();
    │ │ │ -
    223 return iterator;
    │ │ │ -
    224 }
    │ │ │ -
    │ │ │ -
    225
    │ │ │ -
    226 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    227 BALL_INLINE
    │ │ │ -
    228 ConstBidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    229 ConstBidirectionalIterator<Container, DataType, Position, Traits>::end(const Container& container)
    │ │ │ -
    230 {
    │ │ │ -
    231 ConstBidirectionalIterator iterator(container);
    │ │ │ -
    232 iterator.toEnd();
    │ │ │ -
    233 return iterator;
    │ │ │ -
    234 }
    │ │ │ -
    │ │ │ -
    235
    │ │ │ -
    236 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    237 BALL_INLINE
    │ │ │ -
    238 ConstBidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    239 ConstBidirectionalIterator<Container, DataType, Position, Traits>::rbegin(const Container& container)
    │ │ │ -
    240 {
    │ │ │ -
    241 ConstBidirectionalIterator iterator(container);
    │ │ │ -
    242 iterator.toRBegin();
    │ │ │ -
    243 return iterator;
    │ │ │ -
    244 }
    │ │ │ -
    │ │ │ -
    245
    │ │ │ -
    246 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    247 BALL_INLINE
    │ │ │ -
    248 ConstBidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    249 ConstBidirectionalIterator<Container, DataType, Position, Traits>::rend(const Container& container)
    │ │ │ -
    250 {
    │ │ │ -
    251 ConstBidirectionalIterator iterator(container);
    │ │ │ -
    252 iterator.toREnd();
    │ │ │ -
    253 return iterator;
    │ │ │ -
    254 }
    │ │ │ -
    │ │ │ -
    │ │ │ -
    255
    │ │ │ -
    257 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    │ │ │ -
    258 class BidirectionalIterator
    │ │ │ -
    259 : public ConstBidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    260 {
    │ │ │ -
    261 public:
    │ │ │ -
    262
    │ │ │ -
    266
    │ │ │ -
    268 typedef DataType& reference;
    │ │ │ -
    270 typedef DataType* pointer;
    │ │ │ -
    271 // convenience typedef
    │ │ │ -
    272 typedef ConstBidirectionalIterator<Container, DataType, Position, Traits> Base;
    │ │ │ -
    274
    │ │ │ -
    278
    │ │ │ -
    280 BALL_INLINE BidirectionalIterator() {}
    │ │ │ -
    281
    │ │ │ -
    │ │ │ -
    283 BALL_INLINE BidirectionalIterator(const BidirectionalIterator& iterator)
    │ │ │ -
    284
    │ │ │ -
    285 : ConstBidirectionalIterator<Container, DataType, Position, Traits>(iterator)
    │ │ │ -
    286 {
    │ │ │ -
    287 }
    │ │ │ -
    │ │ │ -
    288
    │ │ │ -
    290 BALL_INLINE ~BidirectionalIterator() {}
    │ │ │ -
    291
    │ │ │ -
    293
    │ │ │ -
    297
    │ │ │ -
    299 BALL_INLINE reference operator * () const { return (reference)Base::getTraits().getData(); }
    │ │ │ -
    300
    │ │ │ -
    302 BALL_INLINE pointer operator -> () const { return (pointer)&Base::getTraits().getData(); }
    │ │ │ -
    303
    │ │ │ -
    │ │ │ -
    307 BALL_INLINE BidirectionalIterator& operator ++ ();
    │ │ │ -
    308
    │ │ │ -
    │ │ │ -
    312 BALL_INLINE BidirectionalIterator operator ++ (int);
    │ │ │ -
    313
    │ │ │ -
    │ │ │ -
    317 BALL_INLINE BidirectionalIterator& operator -- ();
    │ │ │ -
    318
    │ │ │ -
    │ │ │ -
    322 BALL_INLINE BidirectionalIterator operator -- (int);
    │ │ │ -
    323
    │ │ │ -
    │ │ │ -
    327 static BidirectionalIterator begin(const Container& container);
    │ │ │ -
    328
    │ │ │ -
    │ │ │ -
    332 static BidirectionalIterator end(const Container& container);
    │ │ │ -
    333
    │ │ │ -
    │ │ │ -
    337 static BidirectionalIterator rbegin(const Container& container);
    │ │ │ -
    338
    │ │ │ -
    │ │ │ -
    342 static BidirectionalIterator rend(const Container& container);
    │ │ │ -
    344
    │ │ │ -
    345 protected:
    │ │ │ -
    346
    │ │ │ -
    │ │ │ -
    348 BALL_INLINE BidirectionalIterator(const Container& container) ;
    │ │ │ -
    349 };
    │ │ │ -
    350
    │ │ │ -
    351
    │ │ │ -
    352 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    353 BALL_INLINE
    │ │ │ -
    354 BidirectionalIterator<Container, DataType, Position, Traits>&
    │ │ │ -
    │ │ │ -
    355 BidirectionalIterator<Container, DataType, Position, Traits>::operator ++ ()
    │ │ │ -
    356 {
    │ │ │ -
    357 Base::operator ++ ();
    │ │ │ -
    358 return *this;
    │ │ │ -
    359 }
    │ │ │ -
    │ │ │ -
    360
    │ │ │ -
    361 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    362 BALL_INLINE
    │ │ │ -
    363 BidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    364 BidirectionalIterator<Container, DataType, Position, Traits>::operator ++ (int)
    │ │ │ -
    365 {
    │ │ │ -
    366 BidirectionalIterator iterator(*this);
    │ │ │ -
    367 this->operator ++ ();
    │ │ │ -
    368 return iterator;
    │ │ │ -
    369 }
    │ │ │ -
    │ │ │ -
    370
    │ │ │ -
    371 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    372 BALL_INLINE
    │ │ │ -
    373 BidirectionalIterator<Container, DataType, Position, Traits>&
    │ │ │ -
    │ │ │ -
    374 BidirectionalIterator<Container, DataType, Position, Traits>::operator -- ()
    │ │ │ -
    375 {
    │ │ │ -
    376 Base::operator -- ();
    │ │ │ -
    377 return *this;
    │ │ │ -
    378 }
    │ │ │ -
    │ │ │ -
    379
    │ │ │ -
    380 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    381 BALL_INLINE
    │ │ │ -
    382 BidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    383 BidirectionalIterator<Container, DataType, Position, Traits>::operator -- (int)
    │ │ │ -
    384 {
    │ │ │ -
    385 BidirectionalIterator iterator(*this);
    │ │ │ -
    386 this->operator -- ();
    │ │ │ -
    387 return iterator;
    │ │ │ -
    388 }
    │ │ │ -
    │ │ │ -
    389
    │ │ │ -
    390 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    391 BALL_INLINE
    │ │ │ -
    392 BidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    393 BidirectionalIterator<Container, DataType, Position, Traits>::begin(const Container& container)
    │ │ │ -
    394 {
    │ │ │ -
    395 BidirectionalIterator iterator(container);
    │ │ │ -
    396 iterator.toBegin();
    │ │ │ -
    397 return iterator;
    │ │ │ -
    398 }
    │ │ │ -
    │ │ │ -
    399
    │ │ │ -
    400 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    401 BALL_INLINE
    │ │ │ -
    402 BidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    403 BidirectionalIterator<Container, DataType, Position, Traits>::end(const Container& container)
    │ │ │ -
    404 {
    │ │ │ -
    405 BidirectionalIterator iterator(container);
    │ │ │ -
    406 iterator.toEnd();
    │ │ │ -
    407 return iterator;
    │ │ │ -
    408 }
    │ │ │ -
    │ │ │ -
    409
    │ │ │ -
    410 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    411 BALL_INLINE
    │ │ │ -
    412 BidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    413 BidirectionalIterator<Container, DataType, Position, Traits>::rbegin(const Container& container)
    │ │ │ -
    414 {
    │ │ │ -
    415 BidirectionalIterator iterator(container);
    │ │ │ -
    416 iterator.toRBegin();
    │ │ │ -
    417 return iterator;
    │ │ │ -
    418 }
    │ │ │ -
    │ │ │ -
    419
    │ │ │ -
    420 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    421 BALL_INLINE
    │ │ │ -
    422 BidirectionalIterator<Container, DataType, Position, Traits>
    │ │ │ -
    │ │ │ -
    423 BidirectionalIterator<Container, DataType, Position, Traits>::rend(const Container& container)
    │ │ │ -
    424 {
    │ │ │ -
    425 BidirectionalIterator iterator(container);
    │ │ │ -
    426 iterator.toREnd();
    │ │ │ -
    427 return iterator;
    │ │ │ -
    428 }
    │ │ │ -
    │ │ │ -
    429
    │ │ │ -
    430 template <typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ -
    431 BALL_INLINE
    │ │ │ -
    │ │ │ -
    432 BidirectionalIterator<Container, DataType, Position, Traits>::BidirectionalIterator(const Container& container)
    │ │ │ -
    433
    │ │ │ -
    434 : ConstBidirectionalIterator<Container, DataType, Position, Traits>(container)
    │ │ │ -
    435 {
    │ │ │ -
    436 }
    │ │ │ -
    │ │ │ -
    │ │ │ -
    437
    │ │ │ -
    438
    │ │ │ -
    439} // namespace BALL
    │ │ │ -
    440
    │ │ │ -
    441#endif // BALL_CONCEPT_BIDIRECTIONALITERATOR_H
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ -
    │ │ │ - │ │ │ -
    BALL_INLINE
    #define BALL_INLINE
    Definition debug.h:15
    │ │ │ -
    BALL_PRECONDITION_EXCEPTION
    #define BALL_PRECONDITION_EXCEPTION(condition, message)
    Definition debug.h:89
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::ConstBidirectionalIterator::begin
    static ConstBidirectionalIterator begin(const Container &container)
    Definition bidirectionalIterator.h:219
    │ │ │ -
    BALL::ConstBidirectionalIterator::end
    static ConstBidirectionalIterator end(const Container &container)
    Definition bidirectionalIterator.h:229
    │ │ │ -
    BALL::ConstBidirectionalIterator::operator--
    BALL_INLINE ConstBidirectionalIterator & operator--()
    Definition bidirectionalIterator.h:198
    │ │ │ -
    BALL::ConstBidirectionalIterator::iterator_category
    std::bidirectional_iterator_tag iterator_category
    Definition bidirectionalIterator.h:33
    │ │ │ -
    BALL::ConstBidirectionalIterator::isEnd
    BALL_INLINE bool isEnd() const
    Check whether the iterator points to the position after the last item of the container.
    Definition bidirectionalIterator.h:73
    │ │ │ -
    BALL::ConstBidirectionalIterator::isRBegin
    BALL_INLINE bool isRBegin() const
    Test whether the iterator points to the "reverse" first element of the container.
    Definition bidirectionalIterator.h:81
    │ │ │ - │ │ │ -
    BALL::ConstBidirectionalIterator::ConstBidirectionalIterator
    BALL_INLINE ConstBidirectionalIterator(const ConstBidirectionalIterator &iterator)
    Definition bidirectionalIterator.h:46
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ConstBidirectionalIterator::rend
    static ConstBidirectionalIterator rend(const Container &container)
    Definition bidirectionalIterator.h:249
    │ │ │ - │ │ │ - │ │ │ -
    BALL::ConstBidirectionalIterator::rbegin
    static ConstBidirectionalIterator rbegin(const Container &container)
    Definition bidirectionalIterator.h:239
    │ │ │ -
    BALL::ConstBidirectionalIterator::isBegin
    BALL_INLINE bool isBegin() const
    Check whether the iterator points to the item at the beginning of the container.
    Definition bidirectionalIterator.h:65
    │ │ │ -
    BALL::ConstBidirectionalIterator::isREnd
    BALL_INLINE bool isREnd() const
    Test wheter the iterator points to the position before the first element.
    Definition bidirectionalIterator.h:89
    │ │ │ -
    BALL::ConstBidirectionalIterator::ConstBidirectionalIterator
    BALL_INLINE ConstBidirectionalIterator(const Container &container)
    Construct an iterator bound to a specific container.
    Definition bidirectionalIterator.h:135
    │ │ │ -
    BALL::ConstBidirectionalIterator::operator++
    BALL_INLINE ConstBidirectionalIterator & operator++()
    Definition bidirectionalIterator.h:177
    │ │ │ -
    BALL::ConstBidirectionalIterator::Base
    ConstForwardIterator< Container, DataType, Position, Traits > Base
    Definition bidirectionalIterator.h:35
    │ │ │ -
    BALL::BidirectionalIterator
    Mutable bidirectional iterator.
    Definition bidirectionalIterator.h:260
    │ │ │ -
    BALL::BidirectionalIterator::~BidirectionalIterator
    BALL_INLINE ~BidirectionalIterator()
    Destructor.
    Definition bidirectionalIterator.h:290
    │ │ │ -
    BALL::BidirectionalIterator::operator++
    BALL_INLINE BidirectionalIterator & operator++()
    Definition bidirectionalIterator.h:355
    │ │ │ -
    BALL::BidirectionalIterator::end
    static BidirectionalIterator end(const Container &container)
    Definition bidirectionalIterator.h:403
    │ │ │ - │ │ │ -
    BALL::BidirectionalIterator::rbegin
    static BidirectionalIterator rbegin(const Container &container)
    Definition bidirectionalIterator.h:413
    │ │ │ -
    BALL::BidirectionalIterator::Base
    ConstBidirectionalIterator< Container, DataType, Position, Traits > Base
    Definition bidirectionalIterator.h:272
    │ │ │ -
    BALL::BidirectionalIterator::operator--
    BALL_INLINE BidirectionalIterator & operator--()
    Definition bidirectionalIterator.h:374
    │ │ │ -
    BALL::BidirectionalIterator::rend
    static BidirectionalIterator rend(const Container &container)
    Definition bidirectionalIterator.h:423
    │ │ │ -
    BALL::BidirectionalIterator::BidirectionalIterator
    BALL_INLINE BidirectionalIterator(const Container &container)
    Construct an iterator bound to a specific container.
    Definition bidirectionalIterator.h:432
    │ │ │ - │ │ │ -
    BALL::BidirectionalIterator::operator*
    BALL_INLINE reference operator*() const
    Dereferentiation.
    Definition bidirectionalIterator.h:299
    │ │ │ -
    BALL::BidirectionalIterator::operator->
    BALL_INLINE pointer operator->() const
    Pointer dereferentiation.
    Definition bidirectionalIterator.h:302
    │ │ │ -
    BALL::BidirectionalIterator::begin
    static BidirectionalIterator begin(const Container &container)
    Definition bidirectionalIterator.h:393
    │ │ │ -
    BALL::BidirectionalIterator::BidirectionalIterator
    BALL_INLINE BidirectionalIterator()
    Default constructor.
    Definition bidirectionalIterator.h:280
    │ │ │ -
    BALL::BidirectionalIterator::BidirectionalIterator
    BALL_INLINE BidirectionalIterator(const BidirectionalIterator &iterator)
    Copy constructor.
    Definition bidirectionalIterator.h:283
    │ │ │ - │ │ │ - │ │ │ +
    9
    │ │ │ +
    │ │ │ +
    26#define BALL_CREATE_DEEP(name)\
    │ │ │ +
    27\
    │ │ │ +
    28 virtual void* create(bool deep = true, bool empty = false) const\
    │ │ │ +
    29 {\
    │ │ │ +
    30 void* ptr;\
    │ │ │ +
    31 if (empty == true)\
    │ │ │ +
    32 {\
    │ │ │ +
    33 ptr = (void*)new name;\
    │ │ │ +
    34 }\
    │ │ │ +
    35 else\
    │ │ │ +
    36 {\
    │ │ │ +
    37 ptr = (void*)new name(*this, deep);\
    │ │ │ +
    38 }\
    │ │ │ +
    39 \
    │ │ │ +
    40 return ptr;\
    │ │ │ +
    41 }\
    │ │ │ +
    42 \
    │ │ │ +
    43 static void* createDefault()\
    │ │ │ +
    44 {\
    │ │ │ +
    45 return static_cast<void*>(new name);\
    │ │ │ +
    46 }
    │ │ │ +
    │ │ │ +
    47
    │ │ │ +
    │ │ │ +
    62#define BALL_CREATE(name)\
    │ │ │ +
    63\
    │ │ │ +
    64 virtual void* create(bool /* deep */ = true, bool empty = false) const\
    │ │ │ +
    65 {\
    │ │ │ +
    66 void* ptr;\
    │ │ │ +
    67 if (empty == true)\
    │ │ │ +
    68 {\
    │ │ │ +
    69 ptr = (void*)new name;\
    │ │ │ +
    70 }\
    │ │ │ +
    71 else\
    │ │ │ +
    72 {\
    │ │ │ +
    73 ptr = (void*)new name(*this);\
    │ │ │ +
    74 }\
    │ │ │ +
    75 \
    │ │ │ +
    76 return ptr;\
    │ │ │ +
    77 }\
    │ │ │ +
    78 \
    │ │ │ +
    79 static void* createDefault()\
    │ │ │ +
    80 {\
    │ │ │ +
    81 return static_cast<void*>(new name);\
    │ │ │ +
    82 }
    │ │ │ +
    │ │ │ +
    83
    │ │ │ +
    │ │ │ +
    93#define BALL_DEFINE_CREATE(name)\
    │ │ │ +
    94\
    │ │ │ +
    95 virtual void* create(bool deep = true, bool empty = false) const;\
    │ │ │ +
    96 static void* createDefault();
    │ │ │ +
    │ │ │ +
    97
    │ │ │ +
    99
    │ │ │ +
    100#endif // BALL_COMMON_CREATE_H
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,538 +1,70 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _C_O_N_C_E_P_T │ │ │ │ -bidirectionalIterator.h │ │ │ │ + * _C_O_M_M_O_N │ │ │ │ +create.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ 4 │ │ │ │ -5#ifndef BALL_CONCEPT_BIDIRECTIONALITERATOR_H │ │ │ │ -6#define BALL_CONCEPT_BIDIRECTIONALITERATOR_H │ │ │ │ +5#ifndef BALL_COMMON_CREATE_H │ │ │ │ +6#define BALL_COMMON_CREATE_H │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_CONCEPT_FORWARDITERATOR_H │ │ │ │ -9# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12namespace _B_A_L_L │ │ │ │ -13{ │ │ │ │ -14 │ │ │ │ -19 │ │ │ │ -22 template │ │ │ │ -_2_3 class _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -24 : public _C_o_n_s_t_F_o_r_w_a_r_d_I_t_e_r_a_t_o_r │ │ │ │ -25 { │ │ │ │ -26 public: │ │ │ │ -27 │ │ │ │ -31 │ │ │ │ -_3_3 typedef std::bidirectional_iterator_tag _i_t_e_r_a_t_o_r___c_a_t_e_g_o_r_y; │ │ │ │ -34 // convenience typedef │ │ │ │ -_3_5 typedef _C_o_n_s_t_F_o_r_w_a_r_d_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> _B_a_s_e; │ │ │ │ -37 │ │ │ │ -41 │ │ │ │ -_4_3 _B_A_L_L___I_N_L_I_N_E _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r() {} │ │ │ │ -44 │ │ │ │ -_4_6 _B_A_L_L___I_N_L_I_N_E _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r(const _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r& │ │ │ │ -iterator) │ │ │ │ -47 : _B_a_s_e(iterator) │ │ │ │ -48 { │ │ │ │ -49 } │ │ │ │ -50 │ │ │ │ -_5_2 _B_A_L_L___I_N_L_I_N_E _~_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r() {} │ │ │ │ -54 │ │ │ │ -58 │ │ │ │ -_6_2 _B_A_L_L___I_N_L_I_N_E void _t_o_B_e_g_i_n(); │ │ │ │ -63 │ │ │ │ -_6_5 _B_A_L_L___I_N_L_I_N_E bool _i_s_B_e_g_i_n() const { return Base::getTraits().isBegin(); } │ │ │ │ -66 │ │ │ │ -_7_0 void _t_o_E_n_d(); │ │ │ │ -71 │ │ │ │ -_7_3 _B_A_L_L___I_N_L_I_N_E bool _i_s_E_n_d() const { return Base::getTraits().isEnd(); } │ │ │ │ -74 │ │ │ │ -_7_8 void _t_o_R_B_e_g_i_n(); │ │ │ │ -79 │ │ │ │ -_8_1 _B_A_L_L___I_N_L_I_N_E bool _i_s_R_B_e_g_i_n() const { return Base::getTraits().isRBegin(); } │ │ │ │ -82 │ │ │ │ -_8_6 void _t_o_R_E_n_d(); │ │ │ │ -87 │ │ │ │ -_8_9 _B_A_L_L___I_N_L_I_N_E bool _i_s_R_E_n_d() const { return Base::getTraits().isREnd(); } │ │ │ │ -90 │ │ │ │ -_9_4 _B_A_L_L___I_N_L_I_N_E _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r& _o_p_e_r_a_t_o_r_ _+_+_ (); │ │ │ │ -95 │ │ │ │ -_9_9 _B_A_L_L___I_N_L_I_N_E _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _o_p_e_r_a_t_o_r_ _+_+_ (int); │ │ │ │ -100 │ │ │ │ -_1_0_4 _B_A_L_L___I_N_L_I_N_E _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r& _o_p_e_r_a_t_o_r_ _-_-_ (); │ │ │ │ -105 │ │ │ │ -_1_0_9 _B_A_L_L___I_N_L_I_N_E _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _o_p_e_r_a_t_o_r_ _-_-_ (int); │ │ │ │ -110 │ │ │ │ -_1_1_4 static _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _b_e_g_i_n(const Container& container); │ │ │ │ -115 │ │ │ │ -_1_1_9 static _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _e_n_d(const Container& container); │ │ │ │ -120 │ │ │ │ -_1_2_4 static _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _r_b_e_g_i_n(const Container& container); │ │ │ │ -125 │ │ │ │ -_1_2_9 static _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _r_e_n_d(const Container& container); │ │ │ │ -131 │ │ │ │ -132 protected: │ │ │ │ -133 │ │ │ │ -_1_3_5 _B_A_L_L___I_N_L_I_N_E _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r(const Container& container) │ │ │ │ -136 : _B_a_s_e(container) │ │ │ │ -137 { │ │ │ │ -138 } │ │ │ │ -139 }; │ │ │ │ -141 │ │ │ │ -142 template │ │ │ │ -143 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_4_4 void _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_: │ │ │ │ -_t_o_B_e_g_i_n() │ │ │ │ -145 { │ │ │ │ -146 _B_A_L_L___P_R_E_C_O_N_D_I_T_I_O_N___E_X_C_E_P_T_I_O_N(!Base::getTraits().isSingular(), "cannot set │ │ │ │ -unbound iterator to begin") │ │ │ │ -147 Base::getTraits().toBegin(); │ │ │ │ -148 } │ │ │ │ -149 │ │ │ │ -150 template │ │ │ │ -151 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_5_2 void _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_: │ │ │ │ -_t_o_E_n_d() │ │ │ │ -153 { │ │ │ │ -154 _B_A_L_L___P_R_E_C_O_N_D_I_T_I_O_N___E_X_C_E_P_T_I_O_N(!Base::getTraits().isSingular(), "cannot set │ │ │ │ -unbound iterator to end") │ │ │ │ -155 Base::getTraits().toEnd(); │ │ │ │ -156 } │ │ │ │ -157 │ │ │ │ -158 template │ │ │ │ -159 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_6_0 void _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_: │ │ │ │ -_t_o_R_B_e_g_i_n() │ │ │ │ -161 { │ │ │ │ -162 _B_A_L_L___P_R_E_C_O_N_D_I_T_I_O_N___E_X_C_E_P_T_I_O_N(!Base::getTraits().isSingular(), "cannot set │ │ │ │ -unbound iterator to reverse begin") │ │ │ │ -163 Base::getTraits().toRBegin(); │ │ │ │ -164 } │ │ │ │ -165 │ │ │ │ -166 template │ │ │ │ -167 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_1_6_8 void _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_: │ │ │ │ -_t_o_R_E_n_d() │ │ │ │ -169 { │ │ │ │ -170 _B_A_L_L___P_R_E_C_O_N_D_I_T_I_O_N___E_X_C_E_P_T_I_O_N(!Base::getTraits().isSingular(), "cannot set │ │ │ │ -unbound iterator to reverse end") │ │ │ │ -171 Base::getTraits().toREnd(); │ │ │ │ -172 } │ │ │ │ -173 │ │ │ │ -174 template │ │ │ │ -175 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -176 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>& │ │ │ │ -_1_7_7 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_o_p_e_r_a_t_o_r │ │ │ │ -_+_+_ () │ │ │ │ -178 { │ │ │ │ -179 _B_A_L_L___P_R_E_C_O_N_D_I_T_I_O_N___E_X_C_E_P_T_I_O_N(Base::getTraits().isValid(), "cannot increment │ │ │ │ -an invalid iterator") │ │ │ │ -180 Base::getTraits().forward(); │ │ │ │ -181 return *this; │ │ │ │ -182 } │ │ │ │ -183 │ │ │ │ -184 template │ │ │ │ -185 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -186 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_1_8_7 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_o_p_e_r_a_t_o_r │ │ │ │ -_+_+_ (int) │ │ │ │ -188 { │ │ │ │ -189 _B_A_L_L___P_R_E_C_O_N_D_I_T_I_O_N___E_X_C_E_P_T_I_O_N(Base::getTraits().isValid(), "cannot increment │ │ │ │ -an invalid iterator") │ │ │ │ -190 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(*this); │ │ │ │ -191 ++(*this); │ │ │ │ -192 return iterator; │ │ │ │ -193 } │ │ │ │ -194 │ │ │ │ -195 template │ │ │ │ -196 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -197 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>& │ │ │ │ -_1_9_8 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_o_p_e_r_a_t_o_r │ │ │ │ -_-_-_ () │ │ │ │ -199 { │ │ │ │ -200 _B_A_L_L___P_R_E_C_O_N_D_I_T_I_O_N___E_X_C_E_P_T_I_O_N(!Base::getTraits().isSingular(), "cannot │ │ │ │ -decrement unbound iterator") │ │ │ │ -201 Base::getTraits().backward(); │ │ │ │ -202 return *this; │ │ │ │ -203 } │ │ │ │ -204 │ │ │ │ -205 template │ │ │ │ -206 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -207 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_2_0_8 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_o_p_e_r_a_t_o_r │ │ │ │ -_-_-_ (int) │ │ │ │ -209 { │ │ │ │ -210 _B_A_L_L___P_R_E_C_O_N_D_I_T_I_O_N___E_X_C_E_P_T_I_O_N(!Base::getTraits().isSingular(), "cannot │ │ │ │ -decrement an unbound iterator") │ │ │ │ -211 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(*this); │ │ │ │ -212 --(*this); │ │ │ │ -213 return iterator; │ │ │ │ -214 } │ │ │ │ -215 │ │ │ │ -216 template │ │ │ │ -217 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -218 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_2_1_9 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_b_e_g_i_n │ │ │ │ -(const Container& container) │ │ │ │ -220 { │ │ │ │ -221 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(container); │ │ │ │ -222 iterator._t_o_B_e_g_i_n(); │ │ │ │ -223 return iterator; │ │ │ │ -224 } │ │ │ │ -225 │ │ │ │ -226 template │ │ │ │ -227 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -228 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_2_2_9 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_e_n_d │ │ │ │ -(const Container& container) │ │ │ │ -230 { │ │ │ │ -231 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(container); │ │ │ │ -232 iterator._t_o_E_n_d(); │ │ │ │ -233 return iterator; │ │ │ │ -234 } │ │ │ │ -235 │ │ │ │ -236 template │ │ │ │ -237 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -238 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_2_3_9 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_r_b_e_g_i_n │ │ │ │ -(const Container& container) │ │ │ │ -240 { │ │ │ │ -241 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(container); │ │ │ │ -242 iterator._t_o_R_B_e_g_i_n(); │ │ │ │ -243 return iterator; │ │ │ │ -244 } │ │ │ │ -245 │ │ │ │ -246 template │ │ │ │ -247 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -248 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_2_4_9 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_r_e_n_d │ │ │ │ -(const Container& container) │ │ │ │ -250 { │ │ │ │ -251 _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(container); │ │ │ │ -252 iterator._t_o_R_E_n_d(); │ │ │ │ -253 return iterator; │ │ │ │ -254 } │ │ │ │ -255 │ │ │ │ -257 template │ │ │ │ -_2_5_8 class _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -259 : public _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -260 { │ │ │ │ -261 public: │ │ │ │ -262 │ │ │ │ -266 │ │ │ │ -_2_6_8 typedef DataType& _r_e_f_e_r_e_n_c_e; │ │ │ │ -_2_7_0 typedef DataType* _p_o_i_n_t_e_r; │ │ │ │ -271 // convenience typedef │ │ │ │ -_2_7_2 typedef _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_B_a_s_e; │ │ │ │ -274 │ │ │ │ -278 │ │ │ │ -_2_8_0 _B_A_L_L___I_N_L_I_N_E _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r() {} │ │ │ │ -281 │ │ │ │ -_2_8_3 _B_A_L_L___I_N_L_I_N_E _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r(const _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r& iterator) │ │ │ │ -284 │ │ │ │ -285 : _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -(iterator) │ │ │ │ -286 { │ │ │ │ -287 } │ │ │ │ -288 │ │ │ │ -_2_9_0 _B_A_L_L___I_N_L_I_N_E _~_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r() {} │ │ │ │ -291 │ │ │ │ -293 │ │ │ │ -297 │ │ │ │ -_2_9_9 _B_A_L_L___I_N_L_I_N_E _r_e_f_e_r_e_n_c_e _o_p_e_r_a_t_o_r_ _*_ () const { return (_r_e_f_e_r_e_n_c_e)Base:: │ │ │ │ -getTraits().getData(); } │ │ │ │ -300 │ │ │ │ -_3_0_2 _B_A_L_L___I_N_L_I_N_E _p_o_i_n_t_e_r _o_p_e_r_a_t_o_r_ _-_>_ () const { return (_p_o_i_n_t_e_r)&Base::getTraits │ │ │ │ -().getData(); } │ │ │ │ -303 │ │ │ │ -_3_0_7 _B_A_L_L___I_N_L_I_N_E _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r& _o_p_e_r_a_t_o_r_ _+_+_ (); │ │ │ │ -308 │ │ │ │ -_3_1_2 _B_A_L_L___I_N_L_I_N_E _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _o_p_e_r_a_t_o_r_ _+_+_ (int); │ │ │ │ -313 │ │ │ │ -_3_1_7 _B_A_L_L___I_N_L_I_N_E _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r& _o_p_e_r_a_t_o_r_ _-_-_ (); │ │ │ │ -318 │ │ │ │ -_3_2_2 _B_A_L_L___I_N_L_I_N_E _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _o_p_e_r_a_t_o_r_ _-_-_ (int); │ │ │ │ -323 │ │ │ │ -_3_2_7 static _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _b_e_g_i_n(const Container& container); │ │ │ │ -328 │ │ │ │ -_3_3_2 static _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _e_n_d(const Container& container); │ │ │ │ -333 │ │ │ │ -_3_3_7 static _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _r_b_e_g_i_n(const Container& container); │ │ │ │ -338 │ │ │ │ -_3_4_2 static _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r _r_e_n_d(const Container& container); │ │ │ │ -344 │ │ │ │ -345 protected: │ │ │ │ -346 │ │ │ │ -_3_4_8 _B_A_L_L___I_N_L_I_N_E _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r(const Container& container) ; │ │ │ │ -349 }; │ │ │ │ -350 │ │ │ │ -351 │ │ │ │ -352 template │ │ │ │ -353 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -354 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>& │ │ │ │ -_3_5_5 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_o_p_e_r_a_t_o_r_ _+_+_ │ │ │ │ -() │ │ │ │ -356 { │ │ │ │ -357 Base::operator ++ (); │ │ │ │ -358 return *this; │ │ │ │ -359 } │ │ │ │ -360 │ │ │ │ -361 template │ │ │ │ -362 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -363 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_3_6_4 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_o_p_e_r_a_t_o_r_ _+_+_ │ │ │ │ -(int) │ │ │ │ -365 { │ │ │ │ -366 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(*this); │ │ │ │ -367 this->operator ++ (); │ │ │ │ -368 return iterator; │ │ │ │ -369 } │ │ │ │ -370 │ │ │ │ -371 template │ │ │ │ -372 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -373 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>& │ │ │ │ -_3_7_4 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_o_p_e_r_a_t_o_r_ _-_-_ │ │ │ │ -() │ │ │ │ -375 { │ │ │ │ -376 Base::operator -- (); │ │ │ │ -377 return *this; │ │ │ │ -378 } │ │ │ │ -379 │ │ │ │ -380 template │ │ │ │ -381 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -382 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_3_8_3 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_o_p_e_r_a_t_o_r_ _-_-_ │ │ │ │ -(int) │ │ │ │ -384 { │ │ │ │ -385 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(*this); │ │ │ │ -386 this->operator -- (); │ │ │ │ -387 return iterator; │ │ │ │ -388 } │ │ │ │ -389 │ │ │ │ -390 template │ │ │ │ -391 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -392 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_3_9_3 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_b_e_g_i_n(const │ │ │ │ -Container& container) │ │ │ │ -394 { │ │ │ │ -395 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(container); │ │ │ │ -396 iterator._t_o_B_e_g_i_n(); │ │ │ │ -397 return iterator; │ │ │ │ -398 } │ │ │ │ -399 │ │ │ │ -400 template │ │ │ │ -401 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -402 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_4_0_3 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_e_n_d(const │ │ │ │ -Container& container) │ │ │ │ -404 { │ │ │ │ -405 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(container); │ │ │ │ -406 iterator._t_o_E_n_d(); │ │ │ │ -407 return iterator; │ │ │ │ -408 } │ │ │ │ -409 │ │ │ │ -410 template │ │ │ │ -411 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -412 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_4_1_3 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_r_b_e_g_i_n(const │ │ │ │ -Container& container) │ │ │ │ -414 { │ │ │ │ -415 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(container); │ │ │ │ -416 iterator._t_o_R_B_e_g_i_n(); │ │ │ │ -417 return iterator; │ │ │ │ -418 } │ │ │ │ -419 │ │ │ │ -420 template │ │ │ │ -421 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -422 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_> │ │ │ │ -_4_2_3 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_:_r_e_n_d(const │ │ │ │ -Container& container) │ │ │ │ -424 { │ │ │ │ -425 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r iterator(container); │ │ │ │ -426 iterator._t_o_R_E_n_d(); │ │ │ │ -427 return iterator; │ │ │ │ -428 } │ │ │ │ -429 │ │ │ │ -430 template │ │ │ │ -431 _B_A_L_L___I_N_L_I_N_E │ │ │ │ -_4_3_2 _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_<_C_o_n_t_a_i_n_e_r_,_ _D_a_t_a_T_y_p_e_,_ _P_o_s_i_t_i_o_n_,_ _T_r_a_i_t_s_>_:_: │ │ │ │ -_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r(const Container& container) │ │ │ │ -433 │ │ │ │ -434 : _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -(container) │ │ │ │ -435 { │ │ │ │ -436 } │ │ │ │ -437 │ │ │ │ -438 │ │ │ │ -439} // namespace BALL │ │ │ │ -440 │ │ │ │ -441#endif // BALL_CONCEPT_BIDIRECTIONALITERATOR_H │ │ │ │ -_f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h │ │ │ │ -_B_A_L_L___I_N_L_I_N_E │ │ │ │ -#define BALL_INLINE │ │ │ │ -DDeeffiinniittiioonn _d_e_b_u_g_._h_:_1_5 │ │ │ │ -_B_A_L_L___P_R_E_C_O_N_D_I_T_I_O_N___E_X_C_E_P_T_I_O_N │ │ │ │ -#define BALL_PRECONDITION_EXCEPTION(condition, message) │ │ │ │ -DDeeffiinniittiioonn _d_e_b_u_g_._h_:_8_9 │ │ │ │ -_B_A_L_L │ │ │ │ -DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_5 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_~_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -BALL_INLINE ~ConstBidirectionalIterator() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_5_2 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_b_e_g_i_n │ │ │ │ -static ConstBidirectionalIterator begin(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_1_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_e_n_d │ │ │ │ -static ConstBidirectionalIterator end(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_2_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_o_p_e_r_a_t_o_r_-_- │ │ │ │ -BALL_INLINE ConstBidirectionalIterator & operator--() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_1_9_8 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_i_t_e_r_a_t_o_r___c_a_t_e_g_o_r_y │ │ │ │ -std::bidirectional_iterator_tag iterator_category │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_3_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_i_s_E_n_d │ │ │ │ -BALL_INLINE bool isEnd() const │ │ │ │ -Check whether the iterator points to the position after the last item of the │ │ │ │ -container. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_7_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_i_s_R_B_e_g_i_n │ │ │ │ -BALL_INLINE bool isRBegin() const │ │ │ │ -Test whether the iterator points to the "reverse" first element of the │ │ │ │ -container. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_8_1 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_t_o_B_e_g_i_n │ │ │ │ -BALL_INLINE void toBegin() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_1_4_4 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -BALL_INLINE ConstBidirectionalIterator(const ConstBidirectionalIterator │ │ │ │ -&iterator) │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_4_6 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_t_o_E_n_d │ │ │ │ -void toEnd() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_1_5_2 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -BALL_INLINE ConstBidirectionalIterator() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_r_e_n_d │ │ │ │ -static ConstBidirectionalIterator rend(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_4_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_t_o_R_B_e_g_i_n │ │ │ │ -void toRBegin() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_1_6_0 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_t_o_R_E_n_d │ │ │ │ -void toREnd() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_1_6_8 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_r_b_e_g_i_n │ │ │ │ -static ConstBidirectionalIterator rbegin(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_3_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_i_s_B_e_g_i_n │ │ │ │ -BALL_INLINE bool isBegin() const │ │ │ │ -Check whether the iterator points to the item at the beginning of the │ │ │ │ -container. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_6_5 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_i_s_R_E_n_d │ │ │ │ -BALL_INLINE bool isREnd() const │ │ │ │ -Test wheter the iterator points to the position before the first element. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_8_9 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -BALL_INLINE ConstBidirectionalIterator(const Container &container) │ │ │ │ -Construct an iterator bound to a specific container. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_1_3_5 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_o_p_e_r_a_t_o_r_+_+ │ │ │ │ -BALL_INLINE ConstBidirectionalIterator & operator++() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_1_7_7 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_B_a_s_e │ │ │ │ -ConstForwardIterator< Container, DataType, Position, Traits > Base │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_3_5 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -Mutable bidirectional iterator. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_6_0 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_~_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -BALL_INLINE ~BidirectionalIterator() │ │ │ │ -Destructor. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_9_0 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_o_p_e_r_a_t_o_r_+_+ │ │ │ │ -BALL_INLINE BidirectionalIterator & operator++() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_3_5_5 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_e_n_d │ │ │ │ -static BidirectionalIterator end(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_4_0_3 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_p_o_i_n_t_e_r │ │ │ │ -DataType * pointer │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_7_0 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_r_b_e_g_i_n │ │ │ │ -static BidirectionalIterator rbegin(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_4_1_3 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_B_a_s_e │ │ │ │ -ConstBidirectionalIterator< Container, DataType, Position, Traits > Base │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_7_2 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_o_p_e_r_a_t_o_r_-_- │ │ │ │ -BALL_INLINE BidirectionalIterator & operator--() │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_3_7_4 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_r_e_n_d │ │ │ │ -static BidirectionalIterator rend(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_4_2_3 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -BALL_INLINE BidirectionalIterator(const Container &container) │ │ │ │ -Construct an iterator bound to a specific container. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_4_3_2 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_r_e_f_e_r_e_n_c_e │ │ │ │ -DataType & reference │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_6_8 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_o_p_e_r_a_t_o_r_* │ │ │ │ -BALL_INLINE reference operator*() const │ │ │ │ -Dereferentiation. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_9_9 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_o_p_e_r_a_t_o_r_-_> │ │ │ │ -BALL_INLINE pointer operator->() const │ │ │ │ -Pointer dereferentiation. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_3_0_2 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_b_e_g_i_n │ │ │ │ -static BidirectionalIterator begin(const Container &container) │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_3_9_3 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -BALL_INLINE BidirectionalIterator() │ │ │ │ -Default constructor. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_8_0 │ │ │ │ -_B_A_L_L_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_:_:_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -BALL_INLINE BidirectionalIterator(const BidirectionalIterator &iterator) │ │ │ │ -Copy constructor. │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_8_3 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_F_o_r_w_a_r_d_I_t_e_r_a_t_o_r │ │ │ │ -DDeeffiinniittiioonn _f_o_r_w_a_r_d_I_t_e_r_a_t_o_r_._h_:_2_6 │ │ │ │ -_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +9 │ │ │ │ +_2_6#define BALL_CREATE_DEEP(name)\ │ │ │ │ +27\ │ │ │ │ +28 virtual void* create(bool deep = true, bool empty = false) const\ │ │ │ │ +29 {\ │ │ │ │ +30 void* ptr;\ │ │ │ │ +31 if (empty == true)\ │ │ │ │ +32 {\ │ │ │ │ +33 ptr = (void*)new name;\ │ │ │ │ +34 }\ │ │ │ │ +35 else\ │ │ │ │ +36 {\ │ │ │ │ +37 ptr = (void*)new name(*this, deep);\ │ │ │ │ +38 }\ │ │ │ │ +39 \ │ │ │ │ +40 return ptr;\ │ │ │ │ +41 }\ │ │ │ │ +42 \ │ │ │ │ +43 static void* createDefault()\ │ │ │ │ +44 {\ │ │ │ │ +45 return static_cast(new name);\ │ │ │ │ +46 } │ │ │ │ +47 │ │ │ │ +_6_2#define BALL_CREATE(name)\ │ │ │ │ +63\ │ │ │ │ +64 virtual void* create(bool /* deep */ = true, bool empty = false) const\ │ │ │ │ +65 {\ │ │ │ │ +66 void* ptr;\ │ │ │ │ +67 if (empty == true)\ │ │ │ │ +68 {\ │ │ │ │ +69 ptr = (void*)new name;\ │ │ │ │ +70 }\ │ │ │ │ +71 else\ │ │ │ │ +72 {\ │ │ │ │ +73 ptr = (void*)new name(*this);\ │ │ │ │ +74 }\ │ │ │ │ +75 \ │ │ │ │ +76 return ptr;\ │ │ │ │ +77 }\ │ │ │ │ +78 \ │ │ │ │ +79 static void* createDefault()\ │ │ │ │ +80 {\ │ │ │ │ +81 return static_cast(new name);\ │ │ │ │ +82 } │ │ │ │ +83 │ │ │ │ +_9_3#define BALL_DEFINE_CREATE(name)\ │ │ │ │ +94\ │ │ │ │ +95 virtual void* create(bool deep = true, bool empty = false) const;\ │ │ │ │ +96 static void* createDefault(); │ │ │ │ +97 │ │ │ │ +99 │ │ │ │ +100#endif // BALL_COMMON_CREATE_H │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d3a/a01622.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: nucleicAcidIterator.h File Reference │ │ │ +BALL: gpModel.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,52 +65,40 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ -Namespaces | │ │ │ -Typedefs
    │ │ │ -
    nucleicAcidIterator.h File Reference
    │ │ │ +Namespaces
    │ │ │ +
    gpModel.h File Reference
    │ │ │ │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/KERNEL/nucleicAcid.h>
    │ │ │ -#include <BALL/KERNEL/iterator.h>
    │ │ │ -#include <BALL/KERNEL/predicate.h>
    │ │ │ +
    #include <BALL/QSAR/kernelModel.h>
    │ │ │ +#include <BALL/QSAR/nonlinearModel.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::NucleicAcidIteratorTraits
    class  BALL::QSAR::GPModel
     
    │ │ │ │ │ │ │ │ │ │ │ │ -

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ + │ │ │ + │ │ │

    │ │ │ -Typedefs

    typedef BidirectionalIterator< Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits > BALL::NucleicAcidIterator
     
    typedef ConstBidirectionalIterator< Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits > BALL::NucleicAcidConstIterator
     
    typedef std::reverse_iterator< NucleicAcidIterator > BALL::NucleicAcidReverseIterator
     
    typedef std::reverse_iterator< NucleicAcidConstIterator > BALL::NucleicAcidConstReverseIterator
     
    namespace  BALL::QSAR
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,39 +1,22 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ -_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s | _T_y_p_e_d_e_f_s │ │ │ │ -nucleicAcidIterator.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_n_u_c_l_e_i_c_A_c_i_d_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_i_t_e_r_a_t_o_r_._h> │ │ │ │ -#include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_e_d_i_c_a_t_e_._h> │ │ │ │ + * _Q_S_A_R │ │ │ │ +_C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ +gpModel.h File Reference │ │ │ │ +#include <_B_A_L_L_/_Q_S_A_R_/_k_e_r_n_e_l_M_o_d_e_l_._h> │ │ │ │ +#include <_B_A_L_L_/_Q_S_A_R_/_n_o_n_l_i_n_e_a_r_M_o_d_e_l_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ +class   _B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -TTyyppeeddeeffss │ │ │ │ -typedef _B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r< _C_o_m_p_o_s_i_t_e, │ │ │ │ - _N_u_c_l_e_i_c_A_c_i_d, _C_o_m_p_o_s_i_t_e_:_: │ │ │ │ - _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r, │ │ │ │ - _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s >  _B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r │ │ │ │ -  │ │ │ │ - typedef _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r< │ │ │ │ - _C_o_m_p_o_s_i_t_e, _N_u_c_l_e_i_c_A_c_i_d, _C_o_m_p_o_s_i_t_e_:_: │ │ │ │ - _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r, │ │ │ │ - _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s >  _B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ -  │ │ │ │ - typedef std::reverse_iterator< │ │ │ │ - _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r >  _B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ -  │ │ │ │ - typedef std::reverse_iterator< │ │ │ │ - _N_u_c_l_e_i_c_A_c_i_d_C_o_n_s_t_I_t_e_r_a_t_o_r >  _B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ +namespace   _B_A_L_L_:_:_Q_S_A_R │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d3a/a01622_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: nucleicAcidIterator.h Source File │ │ │ +BALL: gpModel.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,137 +70,100 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    nucleicAcidIterator.h
    │ │ │ +
    gpModel.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4// $Id: nucleicAcidIterator.h,v 1.11 2005/10/23 12:02:19 oliver Exp $
    │ │ │ -
    5//
    │ │ │ -
    6
    │ │ │ -
    7#ifndef BALL_KERNEL_NUCLEICACIDITERATOR_H
    │ │ │ -
    8#define BALL_KERNEL_NUCLEICACIDITERATOR_H
    │ │ │ -
    9
    │ │ │ -
    10#ifndef BALL_COMMON_H
    │ │ │ -
    11# include <BALL/common.h>
    │ │ │ -
    12#endif
    │ │ │ -
    13
    │ │ │ -
    14#ifndef BALL_KERNEL_NUCLEOTIDE_H
    │ │ │ -
    15# include <BALL/KERNEL/nucleicAcid.h>
    │ │ │ -
    16#endif
    │ │ │ -
    17
    │ │ │ -
    18#ifndef BALL_KERNEL_ITERATOR_H
    │ │ │ -
    19# include <BALL/KERNEL/iterator.h>
    │ │ │ -
    20#endif
    │ │ │ -
    21
    │ │ │ -
    22#ifndef BALL_KERNEL_PREDICATE_H
    │ │ │ -
    23# include <BALL/KERNEL/predicate.h>
    │ │ │ -
    24#endif
    │ │ │ -
    25
    │ │ │ -
    26namespace BALL
    │ │ │ -
    27{
    │ │ │ -
    28 class NucleicAcid;
    │ │ │ -
    29
    │ │ │ -
    │ │ │ -
    34 class BALL_EXPORT NucleicAcidIteratorTraits
    │ │ │ -
    35 : public CompositeIteratorTraits
    │ │ │ -
    36 {
    │ │ │ -
    37 public:
    │ │ │ -
    38
    │ │ │ -
    │ │ │ -
    39 NucleicAcidIteratorTraits()
    │ │ │ -
    40 : CompositeIteratorTraits()
    │ │ │ -
    41 {
    │ │ │ -
    42 predicate_ = &RTTI::getDefault<KernelPredicate<NucleicAcid> >();
    │ │ │ -
    43 }
    │ │ │ -
    │ │ │ -
    44
    │ │ │ -
    │ │ │ -
    45 NucleicAcidIteratorTraits(const Composite& composite)
    │ │ │ -
    46 : CompositeIteratorTraits(composite)
    │ │ │ -
    47 {
    │ │ │ -
    48 predicate_ = &RTTI::getDefault<KernelPredicate<NucleicAcid> >();
    │ │ │ -
    49 }
    │ │ │ -
    │ │ │ -
    50
    │ │ │ -
    │ │ │ -
    51 NucleicAcidIteratorTraits(const NucleicAcidIteratorTraits& traits, bool /* deep */ = true)
    │ │ │ -
    52 : CompositeIteratorTraits(traits)
    │ │ │ -
    53 {
    │ │ │ -
    54 }
    │ │ │ -
    │ │ │ -
    55
    │ │ │ -
    │ │ │ -
    56 NucleicAcidIteratorTraits& operator =(const NucleicAcidIteratorTraits& traits)
    │ │ │ -
    57 {
    │ │ │ -
    58 CompositeIteratorTraits::operator=(traits);
    │ │ │ -
    59 return *this;
    │ │ │ -
    60 }
    │ │ │ -
    │ │ │ -
    61
    │ │ │ -
    │ │ │ -
    62 void resetPredicate()
    │ │ │ -
    63 {
    │ │ │ -
    64 predicate_ = &RTTI::getDefault<KernelPredicate<NucleicAcid> >();
    │ │ │ -
    65 }
    │ │ │ -
    │ │ │ -
    66 };
    │ │ │ -
    │ │ │ -
    67
    │ │ │ -
    68
    │ │ │ -
    69
    │ │ │ -
    70 typedef BidirectionalIterator
    │ │ │ -
    71 <Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits>
    │ │ │ -
    72 NucleicAcidIterator;
    │ │ │ -
    73
    │ │ │ -
    74 typedef ConstBidirectionalIterator
    │ │ │ -
    75 <Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits>
    │ │ │ -
    76 NucleicAcidConstIterator;
    │ │ │ -
    77
    │ │ │ -
    78 typedef std::reverse_iterator<NucleicAcidIterator> NucleicAcidReverseIterator;
    │ │ │ -
    79
    │ │ │ -
    80 typedef std::reverse_iterator<NucleicAcidConstIterator> NucleicAcidConstReverseIterator;
    │ │ │ -
    81
    │ │ │ -
    82 IteratorWrapper(NucleicAcid)
    │ │ │ -
    83 ConstIteratorWrapper(NucleicAcid)
    │ │ │ -
    84} // namespace BALL
    │ │ │ -
    85
    │ │ │ -
    86#endif // BALL_KERNEL_NUCLEICACIDITERATOR_H
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    ConstIteratorWrapper
    #define ConstIteratorWrapper(type)
    Definition stdIteratorWrapper.h:17
    │ │ │ -
    IteratorWrapper
    #define IteratorWrapper(type)
    Definition stdIteratorWrapper.h:4
    │ │ │ - │ │ │ -
    BALL::NucleicAcidReverseIterator
    std::reverse_iterator< NucleicAcidIterator > NucleicAcidReverseIterator
    Definition nucleicAcidIterator.h:78
    │ │ │ -
    BALL::NucleicAcidConstReverseIterator
    std::reverse_iterator< NucleicAcidConstIterator > NucleicAcidConstReverseIterator
    Definition nucleicAcidIterator.h:80
    │ │ │ -
    BALL::NucleicAcidConstIterator
    ConstBidirectionalIterator< Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits > NucleicAcidConstIterator
    Definition nucleicAcidIterator.h:76
    │ │ │ -
    BALL::NucleicAcidIterator
    BidirectionalIterator< Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits > NucleicAcidIterator
    Definition nucleicAcidIterator.h:72
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Composite::CompositeIterator
    BidirectionalIterator< Composite, Composite, Composite *, CompositeIteratorTraits > CompositeIterator
    Definition composite.h:1468
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::NucleicAcidIteratorTraits::NucleicAcidIteratorTraits
    NucleicAcidIteratorTraits(const NucleicAcidIteratorTraits &traits, bool=true)
    Definition nucleicAcidIterator.h:51
    │ │ │ - │ │ │ -
    BALL::NucleicAcidIteratorTraits::NucleicAcidIteratorTraits
    NucleicAcidIteratorTraits(const Composite &composite)
    Definition nucleicAcidIterator.h:45
    │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ - │ │ │ +
    4//
    │ │ │ +
    5
    │ │ │ +
    6#ifndef BALL_QSAR_GPMODEL_H
    │ │ │ +
    7#define BALL_QSAR_GPMODEL_H
    │ │ │ +
    8
    │ │ │ +
    9#ifndef BALL_QSAR_KERNELMODEL_H
    │ │ │ +
    10#include <BALL/QSAR/kernelModel.h>
    │ │ │ +
    11#endif
    │ │ │ +
    12
    │ │ │ +
    13#ifndef BALL_QSAR_NONLINEARMODEL_H
    │ │ │ +
    14#include <BALL/QSAR/nonlinearModel.h>
    │ │ │ +
    15#endif
    │ │ │ +
    16
    │ │ │ +
    17namespace BALL
    │ │ │ +
    18{
    │ │ │ +
    19 namespace QSAR
    │ │ │ +
    20 {
    │ │ │ +
    │ │ │ +
    21 class BALL_EXPORT GPModel : public KernelModel
    │ │ │ +
    22 {
    │ │ │ +
    23 public:
    │ │ │ +
    27 GPModel(const QSARData& q, int k_type, double p1, double p2=-1);
    │ │ │ +
    28
    │ │ │ +
    29 GPModel(const QSARData& q, Eigen::VectorXd& w);
    │ │ │ +
    30
    │ │ │ +
    32 GPModel(const QSARData& q, String s1, String s2);
    │ │ │ +
    33
    │ │ │ +
    34 GPModel(const QSARData& q, const LinearModel& lm, int column);
    │ │ │ +
    35
    │ │ │ +
    36 ~GPModel();
    │ │ │ +
    37
    │ │ │ +
    38 EIGEN_MAKE_ALIGNED_OPERATOR_NEW
    │ │ │ +
    40
    │ │ │ +
    44 void train();
    │ │ │ +
    45
    │ │ │ +
    46 Eigen::VectorXd predict(const vector<double>& substance, bool transform=1);
    │ │ │ +
    47
    │ │ │ +
    49 double calculateStdErr();
    │ │ │ +
    50
    │ │ │ +
    51 void setParameters(vector<double>& v);
    │ │ │ +
    52
    │ │ │ +
    53 vector<double> getParameters() const;
    │ │ │ +
    55
    │ │ │ +
    56 private:
    │ │ │ +
    60 Eigen::MatrixXd L_;
    │ │ │ +
    61
    │ │ │ +
    63 Eigen::VectorXd input_;
    │ │ │ +
    64
    │ │ │ +
    65 Eigen::RowVectorXd K_t_;
    │ │ │ +
    66
    │ │ │ +
    67 double lambda_;
    │ │ │ +
    69 };
    │ │ │ +
    │ │ │ +
    70 }
    │ │ │ +
    71}
    │ │ │ +
    72
    │ │ │ +
    73#endif // GPMODEL
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::QSAR::GPModel::GPModel
    GPModel(const QSARData &q, Eigen::VectorXd &w)
    │ │ │ +
    BALL::QSAR::GPModel::setParameters
    void setParameters(vector< double > &v)
    │ │ │ +
    BALL::QSAR::GPModel::GPModel
    GPModel(const QSARData &q, String s1, String s2)
    │ │ │ +
    BALL::QSAR::GPModel::predict
    Eigen::VectorXd predict(const vector< double > &substance, bool transform=1)
    │ │ │ +
    BALL::QSAR::GPModel::GPModel
    GPModel(const QSARData &q, const LinearModel &lm, int column)
    │ │ │ +
    BALL::QSAR::GPModel::calculateStdErr
    double calculateStdErr()
    │ │ │ +
    BALL::QSAR::GPModel::GPModel
    GPModel(const QSARData &q, int k_type, double p1, double p2=-1)
    │ │ │ +
    BALL::QSAR::GPModel::getParameters
    vector< double > getParameters() const
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,155 +1,106 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _K_E_R_N_E_L │ │ │ │ -nucleicAcidIterator.h │ │ │ │ + * _Q_S_A_R │ │ │ │ +gpModel.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4// $Id: nucleicAcidIterator.h,v 1.11 2005/10/23 12:02:19 oliver Exp $ │ │ │ │ -5// │ │ │ │ -6 │ │ │ │ -7#ifndef BALL_KERNEL_NUCLEICACIDITERATOR_H │ │ │ │ -8#define BALL_KERNEL_NUCLEICACIDITERATOR_H │ │ │ │ -9 │ │ │ │ -10#ifndef BALL_COMMON_H │ │ │ │ -11# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -12#endif │ │ │ │ -13 │ │ │ │ -14#ifndef BALL_KERNEL_NUCLEOTIDE_H │ │ │ │ -15# include <_B_A_L_L_/_K_E_R_N_E_L_/_n_u_c_l_e_i_c_A_c_i_d_._h> │ │ │ │ -16#endif │ │ │ │ -17 │ │ │ │ -18#ifndef BALL_KERNEL_ITERATOR_H │ │ │ │ -19# include <_B_A_L_L_/_K_E_R_N_E_L_/_i_t_e_r_a_t_o_r_._h> │ │ │ │ -20#endif │ │ │ │ -21 │ │ │ │ -22#ifndef BALL_KERNEL_PREDICATE_H │ │ │ │ -23# include <_B_A_L_L_/_K_E_R_N_E_L_/_p_r_e_d_i_c_a_t_e_._h> │ │ │ │ -24#endif │ │ │ │ -25 │ │ │ │ -26namespace _B_A_L_L │ │ │ │ -27{ │ │ │ │ -28 class NucleicAcid; │ │ │ │ -29 │ │ │ │ -_3_4 class _B_A_L_L___E_X_P_O_R_T _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ -35 : public _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ -36 { │ │ │ │ -37 public: │ │ │ │ -38 │ │ │ │ -_3_9 _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s() │ │ │ │ -40 : _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s() │ │ │ │ -41 { │ │ │ │ -42 predicate_ = &RTTI::getDefault >(); │ │ │ │ -43 } │ │ │ │ -44 │ │ │ │ -_4_5 _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s(const _C_o_m_p_o_s_i_t_e& composite) │ │ │ │ -46 : _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s(composite) │ │ │ │ -47 { │ │ │ │ -48 predicate_ = &RTTI::getDefault >(); │ │ │ │ -49 } │ │ │ │ +4// │ │ │ │ +5 │ │ │ │ +6#ifndef BALL_QSAR_GPMODEL_H │ │ │ │ +7#define BALL_QSAR_GPMODEL_H │ │ │ │ +8 │ │ │ │ +9#ifndef BALL_QSAR_KERNELMODEL_H │ │ │ │ +10#include <_B_A_L_L_/_Q_S_A_R_/_k_e_r_n_e_l_M_o_d_e_l_._h> │ │ │ │ +11#endif │ │ │ │ +12 │ │ │ │ +13#ifndef BALL_QSAR_NONLINEARMODEL_H │ │ │ │ +14#include <_B_A_L_L_/_Q_S_A_R_/_n_o_n_l_i_n_e_a_r_M_o_d_e_l_._h> │ │ │ │ +15#endif │ │ │ │ +16 │ │ │ │ +17namespace _B_A_L_L │ │ │ │ +18{ │ │ │ │ +19 namespace QSAR │ │ │ │ +20 { │ │ │ │ +_2_1 class _B_A_L_L___E_X_P_O_R_T _G_P_M_o_d_e_l : public _K_e_r_n_e_l_M_o_d_e_l │ │ │ │ +22 { │ │ │ │ +23 public: │ │ │ │ +_2_7 _G_P_M_o_d_e_l(const _Q_S_A_R_D_a_t_a& q, int k_type, double p1, double p2=-1); │ │ │ │ +28 │ │ │ │ +_2_9 _G_P_M_o_d_e_l(const _Q_S_A_R_D_a_t_a& q, Eigen::VectorXd& w); │ │ │ │ +30 │ │ │ │ +_3_2 _G_P_M_o_d_e_l(const _Q_S_A_R_D_a_t_a& q, _S_t_r_i_n_g s1, _S_t_r_i_n_g s2); │ │ │ │ +33 │ │ │ │ +_3_4 _G_P_M_o_d_e_l(const _Q_S_A_R_D_a_t_a& q, const _L_i_n_e_a_r_M_o_d_e_l& lm, int column); │ │ │ │ +35 │ │ │ │ +_3_6 _~_G_P_M_o_d_e_l(); │ │ │ │ +37 │ │ │ │ +38 EIGEN_MAKE_ALIGNED_OPERATOR_NEW │ │ │ │ +40 │ │ │ │ +_4_4 void _t_r_a_i_n(); │ │ │ │ +45 │ │ │ │ +_4_6 Eigen::VectorXd _p_r_e_d_i_c_t(const vector& substance, bool transform=1); │ │ │ │ +47 │ │ │ │ +_4_9 double _c_a_l_c_u_l_a_t_e_S_t_d_E_r_r(); │ │ │ │ 50 │ │ │ │ -_5_1 _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s(const _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& traits, bool / │ │ │ │ -* deep */ = true) │ │ │ │ -52 : _C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s(traits) │ │ │ │ -53 { │ │ │ │ -54 } │ │ │ │ +_5_1 void _s_e_t_P_a_r_a_m_e_t_e_r_s(vector& v); │ │ │ │ +52 │ │ │ │ +_5_3 vector _g_e_t_P_a_r_a_m_e_t_e_r_s() const; │ │ │ │ 55 │ │ │ │ -_5_6 _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& operator =(const _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s& │ │ │ │ -traits) │ │ │ │ -57 { │ │ │ │ -58 CompositeIteratorTraits::operator=(traits); │ │ │ │ -59 return *this; │ │ │ │ -60 } │ │ │ │ +56 private: │ │ │ │ +60 Eigen::MatrixXd L_; │ │ │ │ 61 │ │ │ │ -_6_2 void _r_e_s_e_t_P_r_e_d_i_c_a_t_e() │ │ │ │ -63 { │ │ │ │ -64 predicate_ = &RTTI::getDefault >(); │ │ │ │ -65 } │ │ │ │ -66 }; │ │ │ │ -67 │ │ │ │ -68 │ │ │ │ -69 │ │ │ │ -70 typedef BidirectionalIterator │ │ │ │ -71 │ │ │ │ -_7_2 _N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r; │ │ │ │ -73 │ │ │ │ -74 typedef _C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -75 <_C_o_m_p_o_s_i_t_e, _N_u_c_l_e_i_c_A_c_i_d, _C_o_m_p_o_s_i_t_e_:_:_C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r, │ │ │ │ -_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s> │ │ │ │ -_7_6 _N_u_c_l_e_i_c_A_c_i_d_C_o_n_s_t_I_t_e_r_a_t_o_r; │ │ │ │ -77 │ │ │ │ -_7_8 typedef std::reverse_iterator │ │ │ │ -_N_u_c_l_e_i_c_A_c_i_d_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r; │ │ │ │ -79 │ │ │ │ -_8_0 typedef std::reverse_iterator │ │ │ │ -_N_u_c_l_e_i_c_A_c_i_d_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r; │ │ │ │ -81 │ │ │ │ -82 _I_t_e_r_a_t_o_r_W_r_a_p_p_e_r(_N_u_c_l_e_i_c_A_c_i_d) │ │ │ │ -83 _C_o_n_s_t_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r(_N_u_c_l_e_i_c_A_c_i_d) │ │ │ │ -84} // namespace BALL │ │ │ │ -85 │ │ │ │ -86#endif // BALL_KERNEL_NUCLEICACIDITERATOR_H │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_n_u_c_l_e_i_c_A_c_i_d_._h │ │ │ │ -_i_t_e_r_a_t_o_r_._h │ │ │ │ -_C_o_n_s_t_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r │ │ │ │ -#define ConstIteratorWrapper(type) │ │ │ │ -DDeeffiinniittiioonn _s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h_:_1_7 │ │ │ │ -_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r │ │ │ │ -#define IteratorWrapper(type) │ │ │ │ -DDeeffiinniittiioonn _s_t_d_I_t_e_r_a_t_o_r_W_r_a_p_p_e_r_._h_:_4 │ │ │ │ +63 Eigen::VectorXd input_; │ │ │ │ +64 │ │ │ │ +65 Eigen::RowVectorXd K_t_; │ │ │ │ +66 │ │ │ │ +67 double lambda_; │ │ │ │ +69 }; │ │ │ │ +70 } │ │ │ │ +71} │ │ │ │ +72 │ │ │ │ +73#endif // GPMODEL │ │ │ │ +_n_o_n_l_i_n_e_a_r_M_o_d_e_l_._h │ │ │ │ +_k_e_r_n_e_l_M_o_d_e_l_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ -std::reverse_iterator< NucleicAcidIterator > NucleicAcidReverseIterator │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_._h_:_7_8 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_C_o_n_s_t_R_e_v_e_r_s_e_I_t_e_r_a_t_o_r │ │ │ │ -std::reverse_iterator< NucleicAcidConstIterator > │ │ │ │ -NucleicAcidConstReverseIterator │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_._h_:_8_0 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_C_o_n_s_t_I_t_e_r_a_t_o_r │ │ │ │ -ConstBidirectionalIterator< Composite, NucleicAcid, Composite:: │ │ │ │ -CompositeIterator, NucleicAcidIteratorTraits > NucleicAcidConstIterator │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_._h_:_7_6 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r │ │ │ │ -BidirectionalIterator< Composite, NucleicAcid, Composite::CompositeIterator, │ │ │ │ -NucleicAcidIteratorTraits > NucleicAcidIterator │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_._h_:_7_2 │ │ │ │ -_B_A_L_L_:_:_C_o_n_s_t_B_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r │ │ │ │ -DDeeffiinniittiioonn _b_i_d_i_r_e_c_t_i_o_n_a_l_I_t_e_r_a_t_o_r_._h_:_2_5 │ │ │ │ -_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ -DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ -_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e_:_:_C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r │ │ │ │ -BidirectionalIterator< Composite, Composite, Composite *, │ │ │ │ -CompositeIteratorTraits > CompositeIterator │ │ │ │ -DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_1_4_6_8 │ │ │ │ -_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ -DDeeffiinniittiioonn _i_t_e_r_a_t_o_r_._h_:_8_4 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_._h_:_2_9 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_._h_:_3_6 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_r_e_s_e_t_P_r_e_d_i_c_a_t_e │ │ │ │ -void resetPredicate() │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_._h_:_6_2 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ -NucleicAcidIteratorTraits(const NucleicAcidIteratorTraits &traits, bool=true) │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_._h_:_5_1 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ -NucleicAcidIteratorTraits() │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_._h_:_3_9 │ │ │ │ -_B_A_L_L_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s_:_:_N_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_T_r_a_i_t_s │ │ │ │ -NucleicAcidIteratorTraits(const Composite &composite) │ │ │ │ -DDeeffiinniittiioonn _n_u_c_l_e_i_c_A_c_i_d_I_t_e_r_a_t_o_r_._h_:_4_5 │ │ │ │ +_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ +DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l │ │ │ │ +DDeeffiinniittiioonn _g_p_M_o_d_e_l_._h_:_2_2 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_t_r_a_i_n │ │ │ │ +void train() │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_G_P_M_o_d_e_l │ │ │ │ +GPModel(const QSARData &q, Eigen::VectorXd &w) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_s_e_t_P_a_r_a_m_e_t_e_r_s │ │ │ │ +void setParameters(vector< double > &v) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_G_P_M_o_d_e_l │ │ │ │ +GPModel(const QSARData &q, String s1, String s2) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_p_r_e_d_i_c_t │ │ │ │ +Eigen::VectorXd predict(const vector< double > &substance, bool transform=1) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_G_P_M_o_d_e_l │ │ │ │ +GPModel(const QSARData &q, const LinearModel &lm, int column) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_c_a_l_c_u_l_a_t_e_S_t_d_E_r_r │ │ │ │ +double calculateStdErr() │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_G_P_M_o_d_e_l │ │ │ │ +GPModel(const QSARData &q, int k_type, double p1, double p2=-1) │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_g_e_t_P_a_r_a_m_e_t_e_r_s │ │ │ │ +vector< double > getParameters() const │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_G_P_M_o_d_e_l_:_:_~_G_P_M_o_d_e_l │ │ │ │ +~GPModel() │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_K_e_r_n_e_l_M_o_d_e_l │ │ │ │ +DDeeffiinniittiioonn _k_e_r_n_e_l_M_o_d_e_l_._h_:_2_8 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_L_i_n_e_a_r_M_o_d_e_l │ │ │ │ +DDeeffiinniittiioonn _l_i_n_e_a_r_M_o_d_e_l_._h_:_1_8 │ │ │ │ +_B_A_L_L_:_:_Q_S_A_R_:_:_Q_S_A_R_D_a_t_a │ │ │ │ +DDeeffiinniittiioonn _Q_S_A_R_D_a_t_a_._h_:_5_6 │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ -_p_r_e_d_i_c_a_t_e_._h │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d3b/a08510.html │ │ │ @@ -78,15 +78,15 @@ │ │ │ Static Public Member Functions | │ │ │ Public Attributes | │ │ │ List of all members │ │ │
    BALL::VIEW::Hotkey Struct Reference
    │ │ │ │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/WIDGETS/pyWidget.h>

    │ │ │ +

    #include <BALL/VIEW/WIDGETS/pyWidget.h>

    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -114,15 +114,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    bool operator== (const Hotkey &hotkey) const
     
    bool operator== (const QKeyEvent &e) const
     
    Qt::KeyboardModifiers button_state
     
    Qt::Key key
     
    │ │ │

    Detailed Description

    │ │ │
    │ │ │ -

    Definition at line 101 of file pyWidget.h.

    │ │ │ +

    Definition at line 101 of file pyWidget.h.

    │ │ │

    Member Function Documentation

    │ │ │ │ │ │

    ◆ createHotkey()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -214,15 +214,15 @@ │ │ │ inline │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    Needed for MSVC.

    │ │ │ │ │ │ -

    Definition at line 119 of file pyWidget.h.

    │ │ │ +

    Definition at line 119 of file pyWidget.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ operator=()

    │ │ │ │ │ │
    │ │ │ @@ -303,15 +303,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    String BALL::VIEW::Hotkey::action
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 128 of file pyWidget.h.

    │ │ │ +

    Definition at line 128 of file pyWidget.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ button_state

    │ │ │ │ │ │
    │ │ │ @@ -319,15 +319,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Qt::KeyboardModifiers BALL::VIEW::Hotkey::button_state
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 129 of file pyWidget.h.

    │ │ │ +

    Definition at line 129 of file pyWidget.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ comment

    │ │ │ │ │ │
    │ │ │ @@ -335,15 +335,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    String BALL::VIEW::Hotkey::comment
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 127 of file pyWidget.h.

    │ │ │ +

    Definition at line 127 of file pyWidget.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ key

    │ │ │ │ │ │
    │ │ │ @@ -351,15 +351,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    Qt::Key BALL::VIEW::Hotkey::key
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 130 of file pyWidget.h.

    │ │ │ +

    Definition at line 130 of file pyWidget.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d40/a07158.html │ │ │ @@ -78,15 +78,15 @@ │ │ │
    BALL::SecondaryStructureProcessor Class Reference
    Molecular Modeling » Molecular Structure » Miscellaneous
    │ │ │ │ │ │
    │ │ │ │ │ │

    Secondary structure extraction from 3D structure. │ │ │ More...

    │ │ │ │ │ │ -

    #include <BALL/STRUCTURE/secondaryStructureProcessor.h>

    │ │ │ +

    #include <BALL/STRUCTURE/secondaryStructureProcessor.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::SecondaryStructureProcessor:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::UnaryProcessor< Composite > │ │ │ @@ -165,15 +165,15 @@ │ │ │

    Secondary Structure Processor.

    │ │ │

    This class implements the DSSP algorithm described in "Kabsch W & Sander C (1983). │ │ │ Dictionary of protein secondary structure: │ │ │ pattern recognition of hydrogen-bonded and geometrical features. │ │ │ Biopolymers, 22, 2577-2637."

    │ │ │

    When applied to a protein, it removes the instances of SecondaryStructure from the protein, predicts the secondary structure elements based (mostly) on H-bond patterns and backbone torsions and reinserts the appropriate secondary structure elements at the predicted positions.

    │ │ │ │ │ │ -

    Definition at line 38 of file secondaryStructureProcessor.h.

    │ │ │ +

    Definition at line 38 of file secondaryStructureProcessor.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ SecondaryStructureProcessor()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -496,15 +496,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
    │ │ │
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    Definition at line 77 of file secondaryStructureProcessor.h.

    │ │ │ +

    Definition at line 77 of file secondaryStructureProcessor.h.

    │ │ │ │ │ │
    │ │ │
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    ◆ fourturn_

    │ │ │ │ │ │
    │ │ │ @@ -520,15 +520,15 @@ │ │ │
    		│ │ │ protected
    │ │ │
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    Definition at line 78 of file secondaryStructureProcessor.h.

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    Definition at line 78 of file secondaryStructureProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ HBonds_

    │ │ │ │ │ │
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    Definition at line 71 of file secondaryStructureProcessor.h.

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    Definition at line 71 of file secondaryStructureProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ posbridges_

    │ │ │ │ │ │
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    Definition at line 74 of file secondaryStructureProcessor.h.

    │ │ │ +

    Definition at line 74 of file secondaryStructureProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ sheet_

    │ │ │ │ │ │
    │ │ │ @@ -592,15 +592,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 76 of file secondaryStructureProcessor.h.

    │ │ │ +

    Definition at line 76 of file secondaryStructureProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ summary_

    │ │ │ │ │ │
    │ │ │ @@ -616,15 +616,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 80 of file secondaryStructureProcessor.h.

    │ │ │ +

    Definition at line 80 of file secondaryStructureProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ threeturn_

    │ │ │ │ │ │
    │ │ │ @@ -640,15 +640,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
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    Definition at line 79 of file secondaryStructureProcessor.h.

    │ │ │ +

    Definition at line 79 of file secondaryStructureProcessor.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d41/a08186.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::VIEW::Point Class Reference
    Visualisation » Geometric Objects
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/VIEW/PRIMITIVES/point.h>

    │ │ │ +

    #include <BALL/VIEW/PRIMITIVES/point.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::VIEW::Point:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::VIEW::GeometricObject │ │ │ @@ -191,15 +191,15 @@ │ │ │

    Point class. An instance of Point represents an instance of the geometric representation "point". A point has the following properties.

      │ │ │
    • color - the color of the point
      • │ │ │
    • vertex - the position of the point
      The class Point is derived from the classes GeometricObject and Vertex. See these classes for further information concerning interface and additional methods.
      │ │ │
      │ │ │
      • │ │ │
    │ │ │ │ │ │ -

    Definition at line 34 of file point.h.

    │ │ │ +

    Definition at line 34 of file point.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ Point() [1/2]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d43/a07042.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::ReconstructFragmentProcessor Class Reference
    Molecular Modeling » Molecular Structure » Miscellaneous
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/STRUCTURE/reconstructFragmentProcessor.h>

    │ │ │ +

    #include <BALL/STRUCTURE/reconstructFragmentProcessor.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::ReconstructFragmentProcessor:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::UnaryProcessor< Fragment > │ │ │ @@ -92,17 +92,17 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -153,15 +153,15 @@ │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    Constructors and Destructors
     ReconstructFragmentProcessor ()
     
     ReconstructFragmentProcessor (const FragmentDB &db)
     ReconstructFragmentProcessor (const FragmentDB &db)
     
     ReconstructFragmentProcessor (const ReconstructFragmentProcessor &db)
     ReconstructFragmentProcessor (const ReconstructFragmentProcessor &db)
     
    virtual ~ReconstructFragmentProcessor ()
     
    Processor-related methods
    virtual bool start ()
     
    virtual bool finish ()
     
    typedef const ArgumentType * const_argument_pointer
     
    │ │ │

    Detailed Description

    │ │ │

    ReconstructFragmentProcessor. <>

    │ │ │ │ │ │ -

    Definition at line 33 of file reconstructFragmentProcessor.h.

    │ │ │ +

    Definition at line 33 of file reconstructFragmentProcessor.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ ReconstructFragmentProcessor() [1/3]

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -551,15 +551,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
    │ │ │
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    Definition at line 151 of file reconstructFragmentProcessor.h.

    │ │ │ +

    Definition at line 151 of file reconstructFragmentProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ inserted_atoms_

    │ │ │ │ │ │
    │ │ │ @@ -575,15 +575,15 @@ │ │ │ │ │ │ │ │ │ protected │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ -

    Definition at line 155 of file reconstructFragmentProcessor.h.

    │ │ │ +

    Definition at line 155 of file reconstructFragmentProcessor.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d44/a00098.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: geometricControl.h File Reference │ │ │ +BALL: bindingPocketProcessor.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,43 +65,49 @@ │ │ │
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │
    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    geometricControl.h File Reference
    │ │ │ +
    bindingPocketProcessor.h File Reference
    │ │ │
    │ │ │
    │ │ │ -
    #include <BALL/common.h>
    │ │ │ -#include <BALL/VIEW/WIDGETS/genericControl.h>
    │ │ │ -#include <BALL/VIEW/KERNEL/common.h>
    │ │ │ -#include <QtCore/QPoint>
    │ │ │ -#include <QtWidgets/QMenu>
    │ │ │ +
    #include <BALL/CONCEPT/processor.h>
    │ │ │ +#include <BALL/KERNEL/residue.h>
    │ │ │ +#include <BALL/MATHS/vector3.h>
    │ │ │ +#include <BALL/KERNEL/system.h>
    │ │ │ +#include <BALL/DATATYPE/hashGrid.h>
    │ │ │ +#include <BALL/DATATYPE/options.h>
    │ │ │ +#include <vector>
    │ │ │ +#include <string>
    │ │ │ +#include <fstream>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::VIEW::GeometricControl
    class  BALL::BindingPocketProcessor
     
    struct  BALL::BindingPocketProcessor::Option
     
    struct  BALL::BindingPocketProcessor::Default
     
    │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ - │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    namespace  BALL::VIEW
     
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,26 +1,31 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _W_I_D_G_E_T_S │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -geometricControl.h File Reference │ │ │ │ -#include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_W_I_D_G_E_T_S_/_g_e_n_e_r_i_c_C_o_n_t_r_o_l_._h> │ │ │ │ -#include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_c_o_m_m_o_n_._h> │ │ │ │ -#include │ │ │ │ -#include │ │ │ │ +bindingPocketProcessor.h File Reference │ │ │ │ +#include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_r_e_s_i_d_u_e_._h> │ │ │ │ +#include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ +#include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_G_r_i_d_._h> │ │ │ │ +#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ +#include │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l │ │ │ │ + class   _B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ -namespace   _B_A_L_L_:_:_V_I_E_W │ │ │ │ -  │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d44/a00098_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: geometricControl.h Source File │ │ │ +BALL: bindingPocketProcessor.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,266 +70,331 @@ │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    geometricControl.h
    │ │ │ +
    bindingPocketProcessor.h
    │ │ │
    │ │ │
    │ │ │ -Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │ -
    2// vi: set ts=2:
    │ │ │ -
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_VIEW_WIDGETS_GEOMETRICCONTROL_H
    │ │ │ -
    6#define BALL_VIEW_WIDGETS_GEOMETRICCONTROL_H
    │ │ │ +Go to the documentation of this file.
    1#ifndef BALL_STRUCTURE_BINDINGPOCKETPROCESSOR_H
    │ │ │ +
    2#define BALL_STRUCTURE_BINDINGPOCKETPROCESSOR_H
    │ │ │ +
    3
    │ │ │ +
    4#ifndef BALL_CONCEPT_PROCESSOR_H
    │ │ │ +
    5# include <BALL/CONCEPT/processor.h>
    │ │ │ +
    6#endif
    │ │ │
    7
    │ │ │ -
    8#ifndef BALL_COMMON_H
    │ │ │ -
    9# include <BALL/common.h>
    │ │ │ +
    8#ifndef BALL_KERNEL_RESIDUE_H
    │ │ │ +
    9# include <BALL/KERNEL/residue.h>
    │ │ │
    10#endif
    │ │ │
    11
    │ │ │ -
    12#ifndef BALL_VIEW_WIDGETS_GENERICCONTROL_H
    │ │ │ -
    13# include <BALL/VIEW/WIDGETS/genericControl.h>
    │ │ │ +
    12#ifndef BALL_MATHS_VECTOR3_H
    │ │ │ +
    13# include <BALL/MATHS/vector3.h>
    │ │ │
    14#endif
    │ │ │
    15
    │ │ │ -
    16#ifndef BALL_VIEW_KERNEL_COMMON_H
    │ │ │ -
    17# include <BALL/VIEW/KERNEL/common.h>
    │ │ │ -
    18#endif
    │ │ │ +
    16#ifndef BALL_KERNEL_SYSTEM_H
    │ │ │ +
    17# include <BALL/KERNEL/system.h>
    │ │ │ +
    18#endif
    │ │ │
    19
    │ │ │ -
    20#include <QtCore/QPoint>
    │ │ │ -
    21#include <QtWidgets/QMenu>
    │ │ │ -
    22
    │ │ │ -
    23namespace BALL
    │ │ │ -
    24{
    │ │ │ -
    25 namespace VIEW
    │ │ │ -
    26 {
    │ │ │ -
    27 class Representation;
    │ │ │ -
    28 class ModifyRepresentationDialog;
    │ │ │ -
    29 class ClippingPlane;
    │ │ │ -
    30 class TransformationMessage;
    │ │ │ -
    31
    │ │ │ -
    │ │ │ -
    41 class BALL_VIEW_EXPORT GeometricControl
    │ │ │ -
    42 : public GenericControl
    │ │ │ -
    43 {
    │ │ │ -
    44 Q_OBJECT
    │ │ │ -
    45
    │ │ │ -
    46 public:
    │ │ │ -
    47
    │ │ │ -
    48 BALL_EMBEDDABLE(GeometricControl, GenericControl)
    │ │ │ -
    49
    │ │ │ -
    50
    │ │ │ -
    53
    │ │ │ -
    54
    │ │ │ -
    69 GeometricControl(QWidget* parent = 0, const char* name = 0);
    │ │ │ -
    70
    │ │ │ -
    72 virtual ~GeometricControl();
    │ │ │ -
    73
    │ │ │ -
    77 virtual void clear(){};
    │ │ │ -
    78
    │ │ │ -
    80 virtual void initializeWidget(MainControl& main_control);
    │ │ │ -
    81
    │ │ │ -
    83
    │ │ │ -
    84
    │ │ │ -
    87 virtual void addRepresentation(Representation& rep);
    │ │ │ -
    88
    │ │ │ -
    91 virtual void removeRepresentation(Representation& rep);
    │ │ │ -
    92
    │ │ │ -
    95 virtual void updateRepresentation(Representation& rep, bool force=false);
    │ │ │ -
    96
    │ │ │ -
    102 std::list<Representation*> getHighlightedRepresentations() const;
    │ │ │ -
    103
    │ │ │ -
    107 virtual void onNotify(Message *message);
    │ │ │ -
    108
    │ │ │ -
    115 virtual void buildContextMenu();
    │ │ │ -
    116
    │ │ │ -
    118 virtual void checkMenu(MainControl& main_control);
    │ │ │ -
    119
    │ │ │ -
    121 void moveItems(const TransformationMessage& msg);
    │ │ │ -
    122
    │ │ │ -
    123 void updateClippingPlanes();
    │ │ │ -
    124
    │ │ │ -
    125 public Q_SLOTS:
    │ │ │ -
    126
    │ │ │ -
    128
    │ │ │ -
    131
    │ │ │ -
    133 virtual void renameRepresentation();
    │ │ │ -
    134
    │ │ │ -
    136 virtual void selectAtoms();
    │ │ │ -
    137
    │ │ │ -
    139 virtual void selectedRepresentation(Representation& representation, bool state);
    │ │ │ +
    20#ifndef BALL_DATATYPE_HASHGRID_H
    │ │ │ +
    21# include <BALL/DATATYPE/hashGrid.h>
    │ │ │ +
    22#endif
    │ │ │ +
    23
    │ │ │ +
    24#ifndef BALL_DATATYPE_OPTIONS_H
    │ │ │ +
    25# include <BALL/DATATYPE/options.h>
    │ │ │ +
    26#endif
    │ │ │ +
    27
    │ │ │ +
    28#include <vector>
    │ │ │ +
    29#include <string>
    │ │ │ +
    30
    │ │ │ +
    31#include <fstream>
    │ │ │ +
    32
    │ │ │ +
    33namespace BALL
    │ │ │ +
    34{
    │ │ │ +
    35
    │ │ │ +
    │ │ │ +
    40 class BALL_EXPORT BindingPocketProcessor
    │ │ │ +
    41 : public UnaryProcessor<Composite>
    │ │ │ +
    42 {
    │ │ │ +
    43
    │ │ │ +
    44 public:
    │ │ │ +
    45
    │ │ │ +
    │ │ │ +
    48 struct Option
    │ │ │ +
    49 {
    │ │ │ +
    51 static const String HEAVY_ONLY;
    │ │ │ +
    53 static const String PARSE_INI_FILE;
    │ │ │ +
    55 static const String INI_FILE_NAME;
    │ │ │ +
    56
    │ │ │ +
    58 static const String RADIUS_HYDROGEN;
    │ │ │ +
    59 static const String RADIUS_OXYGEN;
    │ │ │ +
    60 static const String RADIUS_NITROGEN;
    │ │ │ +
    61 static const String RADIUS_CARBON;
    │ │ │ +
    62 static const String RADIUS_SULFUR;
    │ │ │ +
    63
    │ │ │ +
    65 static const String PROBE_SPHERE_RADIUS;
    │ │ │ +
    67 static const String PROBE_SPHERE_RADIUS_HYDROGEN_FREE;
    │ │ │ +
    69 static const String PROBE_LAYER_RADIUS;
    │ │ │ +
    71 static const String BURIAL_COUNT_THRESHOLD;
    │ │ │ +
    73 static const String BURIAL_COUNT_THRESHOLD_HYDROGEN_FREE;
    │ │ │ +
    75 static const String BURIAL_COUNT_RADIUS;
    │ │ │ +
    77 static const String PW_SQUARE_WELL;
    │ │ │ +
    78 static const String PW_GAUSSIAN_WIDTH;
    │ │ │ +
    79 static const String PW_MAX_DISTANCE;
    │ │ │ +
    81 static const String MAX_ASPS;
    │ │ │ +
    82 // additional factor for the computation of the collision of two spheres
    │ │ │ +
    83 static const String CLASH_FACTOR;
    │ │ │ +
    85 static const String ASP_SEPERATION;
    │ │ │ +
    86 };
    │ │ │ +
    │ │ │ +
    87
    │ │ │ +
    │ │ │ +
    90 struct Default
    │ │ │ +
    91 {
    │ │ │ +
    92 static const bool HEAVY_ONLY;
    │ │ │ +
    93 static const bool PARSE_INI_FILE;
    │ │ │ +
    94 static const String INI_FILE_NAME;
    │ │ │ +
    95
    │ │ │ +
    96 static const double RADIUS_HYDROGEN;
    │ │ │ +
    97 static const double RADIUS_OXYGEN;
    │ │ │ +
    98 static const double RADIUS_NITROGEN;
    │ │ │ +
    99 static const double RADIUS_CARBON;
    │ │ │ +
    100 static const double RADIUS_SULFUR;
    │ │ │ +
    101
    │ │ │ +
    102 static const double PROBE_SPHERE_RADIUS;
    │ │ │ +
    103 static const double PROBE_SPHERE_RADIUS_HYDROGEN_FREE;
    │ │ │ +
    104 static const double PROBE_LAYER_RADIUS;
    │ │ │ +
    105 static const Position BURIAL_COUNT_THRESHOLD;
    │ │ │ +
    106 static const Position BURIAL_COUNT_THRESHOLD_HYDROGEN_FREE;
    │ │ │ +
    107 static const double BURIAL_COUNT_RADIUS;
    │ │ │ +
    108 static const double PW_SQUARE_WELL;
    │ │ │ +
    109 static const double PW_GAUSSIAN_WIDTH;
    │ │ │ +
    110 static const double PW_MAX_DISTANCE;
    │ │ │ +
    111 static const Position MAX_ASPS;
    │ │ │ +
    112 static const double CLASH_FACTOR;
    │ │ │ +
    113 static const double ASP_SEPERATION;
    │ │ │ +
    114 };
    │ │ │ +
    │ │ │ +
    115
    │ │ │ +
    118 BindingPocketProcessor();
    │ │ │ +
    119
    │ │ │ +
    122 BindingPocketProcessor(Options& new_options);
    │ │ │ +
    123
    │ │ │ +
    126 BindingPocketProcessor(const BindingPocketProcessor& pp);
    │ │ │ +
    127
    │ │ │ +
    130 virtual ~BindingPocketProcessor();
    │ │ │ +
    131
    │ │ │ +
    134 const BindingPocketProcessor& operator=(const BindingPocketProcessor& pp);
    │ │ │ +
    135
    │ │ │ +
    137 virtual bool finish();
    │ │ │ +
    138
    │ │ │ +
    139 virtual Processor::Result operator() (Composite &composite);
    │ │ │
    140
    │ │ │ -
    142 virtual void updateSelection();
    │ │ │ -
    143
    │ │ │ -
    145 virtual void focus();
    │ │ │ -
    146
    │ │ │ -
    148 virtual void enterMoveMode();
    │ │ │ -
    149
    │ │ │ -
    151 virtual void flipClippingCapping();
    │ │ │ +
    143 const vector<std::pair<Vector3,double> >& getActiveSitePoints() const;
    │ │ │ +
    144
    │ │ │ +
    147 const vector<vector<std::pair<Vector3,double> > >& getLayers() const;
    │ │ │ +
    148
    │ │ │ +
    151 Options options;
    │ │ │
    152
    │ │ │ -
    154 virtual void flipClippingPlane();
    │ │ │ -
    155
    │ │ │ -
    157 virtual void setClippingPosition();
    │ │ │ -
    158
    │ │ │ -
    160 virtual void setClippingPlaneX();
    │ │ │ -
    161
    │ │ │ -
    163 virtual void setClippingPlaneY();
    │ │ │ -
    164
    │ │ │ -
    166 virtual void setClippingPlaneZ();
    │ │ │ -
    167
    │ │ │ -
    169 void hideShowClippingPlane();
    │ │ │ -
    170
    │ │ │ -
    172 virtual void selectClipRepresentations();
    │ │ │ -
    173
    │ │ │ -
    175 void createNewClippingPlane();
    │ │ │ -
    176
    │ │ │ -
    178 void duplicate();
    │ │ │ -
    179
    │ │ │ -
    181 void saveSurface();
    │ │ │ -
    182
    │ │ │ -
    184 void loadSurface();
    │ │ │ -
    185
    │ │ │ -
    187 ModifyRepresentationDialog* getModifySurfaceDialog();
    │ │ │ -
    188
    │ │ │ -
    189 protected Q_SLOTS:
    │ │ │ -
    190
    │ │ │ -
    192
    │ │ │ -
    194
    │ │ │ -
    196 virtual void modifyRepresentation_();
    │ │ │ -
    197
    │ │ │ -
    200 virtual void generateListViewItem_(Representation& rep);
    │ │ │ -
    201
    │ │ │ -
    203 virtual void deleteCurrentItems();
    │ │ │ -
    204
    │ │ │ -
    206 virtual void setupProximityLight();
    │ │ │ -
    207
    │ │ │ -
    209
    │ │ │ -
    210 protected Q_SLOTS:
    │ │ │ -
    211
    │ │ │ -
    212 virtual void onItemClicked(QTreeWidgetItem* item, int col);
    │ │ │ -
    213 void showGuestContextMenu(const QPoint& pos);
    │ │ │ -
    214
    │ │ │ -
    215 protected:
    │ │ │ -
    216
    │ │ │ -
    217 void addItem_(const String& text, const char* member, QWidget* widget = 0);
    │ │ │ -
    218
    │ │ │ -
    219 // only for Python Interface
    │ │ │ -
    220 GeometricControl(const GeometricControl& control);
    │ │ │ -
    221
    │ │ │ -
    │ │ │ -
    222 enum ColumnID
    │ │ │ -
    223 {
    │ │ │ -
    224 COLUMN_ID__TYPE = 0,
    │ │ │ -
    225 COLUMN_ID__Properties
    │ │ │ -
    226 };
    │ │ │ -
    │ │ │ -
    227
    │ │ │ -
    228 void setClippingPlane_(const Vector3& n);
    │ │ │ -
    229
    │ │ │ -
    230 // the context menu
    │ │ │ -
    231 QMenu context_menu_;
    │ │ │ -
    232 QMenu clipping_plane_context_menu_;
    │ │ │ -
    233
    │ │ │ -
    234 Representation* context_representation_;
    │ │ │ -
    235 ClippingPlane* context_plane_;
    │ │ │ -
    236
    │ │ │ -
    237 HashMap<Representation*, QTreeWidgetItem*> representation_to_item_;
    │ │ │ -
    238 HashMap<ClippingPlane*, QTreeWidgetItem*> plane_to_item_;
    │ │ │ -
    239 HashMap<QTreeWidgetItem*, Representation*> item_to_representation_;
    │ │ │ -
    240 HashMap<QTreeWidgetItem*, ClippingPlane*> item_to_plane_;
    │ │ │ -
    241
    │ │ │ -
    242 ModifyRepresentationDialog* modify_rep_dialog_;
    │ │ │ -
    243
    │ │ │ -
    244 bool creating_representations_;
    │ │ │ -
    245 bool ignore_change_;
    │ │ │ -
    246
    │ │ │ -
    247 QAction* menu_clipping_plane_, *menu_load_surface_, *modify_surface_;
    │ │ │ -
    248 vector<QAction*> context_menu_actions_;
    │ │ │ -
    249 };
    │ │ │ +
    153 private:
    │ │ │ +
    154
    │ │ │ +
    158 class Sphere_
    │ │ │ +
    159 {
    │ │ │ +
    160 public:
    │ │ │ +
    162 Sphere_();
    │ │ │ +
    163
    │ │ │ +
    166 BALL::Vector3 position;
    │ │ │ +
    167
    │ │ │ +
    170 float radius;
    │ │ │ +
    171
    │ │ │ +
    174 Position b_count;
    │ │ │ +
    175
    │ │ │ +
    178 float probe_weight;
    │ │ │ +
    179
    │ │ │ +
    182 Position layer;
    │ │ │ +
    183
    │ │ │ +
    186 inline bool operator<(const Sphere_& sp) const {return probe_weight > sp.probe_weight;};
    │ │ │ +
    187
    │ │ │ +
    190 int id;
    │ │ │ +
    191 static int global_id;
    │ │ │ +
    192 Position a,b,c,d;
    │ │ │ +
    193
    │ │ │ +
    196 inline bool operator==(const Sphere_& sp) const {return a == sp.a && b == sp.b && c == sp.c && d == sp.d;};
    │ │ │ +
    197 };
    │ │ │ +
    198
    │ │ │ +
    201 class SphereComparator_
    │ │ │ +
    202 {
    │ │ │ +
    203 public:
    │ │ │ +
    204 int operator()(const Sphere_& sp1, const Sphere_& sp2) const
    │ │ │ +
    205 {
    │ │ │ +
    206 if (sp1.a != sp2.a)
    │ │ │ +
    207 return sp1.a < sp2.a;
    │ │ │ +
    208 if (sp1.b != sp2.b)
    │ │ │ +
    209 return sp1.b < sp2.b;
    │ │ │ +
    210 if (sp1.c != sp2.c)
    │ │ │ +
    211 return sp1.c < sp2.c;
    │ │ │ +
    212 if (sp1.d != sp2.d)
    │ │ │ +
    213 return sp1.d < sp2.d;
    │ │ │ +
    214 return 0;
    │ │ │ +
    215 };
    │ │ │ +
    216 };
    │ │ │ +
    217
    │ │ │ +
    220 Position layer_;
    │ │ │ +
    221
    │ │ │ +
    225 friend std::ostream& operator<<(std::ostream& os, const BindingPocketProcessor::Sphere_& /*sp*/) {return os;};
    │ │ │ +
    226
    │ │ │ +
    229 HashGrid3<Sphere_> sphere_grid_;
    │ │ │ +
    230
    │ │ │ +
    233 HashGrid3<Sphere_> protein_grid_;
    │ │ │ +
    234
    │ │ │ +
    237 HashGrid3<Sphere_> layer_grid_;
    │ │ │ +
    238
    │ │ │ +
    241 HashGrid3<Sphere_> clayer_grid_;
    │ │ │ +
    242
    │ │ │ +
    245 HashGrid3<Sphere_> BC_grid_;
    │ │ │ +
    246
    │ │ │ +
    249 HashGrid3<Sphere_> pw_grid_;
    │ │ │ +
    250
    │ │ │ +
    253 HashGrid3<Sphere_> candidates_grid_;
    │ │ │ +
    254
    │ │ │ +
    255 std::vector<Sphere_> sorted_spheres_;
    │ │ │ +
    256
    │ │ │ +
    259 double sphere_rad_;
    │ │ │ +
    260
    │ │ │ +
    263 double second_layer_rad_;
    │ │ │ +
    264
    │ │ │ +
    267 double protein_clash_rad_;
    │ │ │ +
    268
    │ │ │ +
    271 double BC_threshold_;
    │ │ │ +
    272
    │ │ │ +
    275 Position found_new_;
    │ │ │ +
    276
    │ │ │ +
    277 double c_factor_;
    │ │ │ +
    278
    │ │ │ +
    281 std::vector<Sphere_> candidates;
    │ │ │ +
    282
    │ │ │ +
    283 std::vector<std::pair<Vector3,double> > asps_;
    │ │ │ +
    284
    │ │ │ +
    285 std::vector<std::vector<std::pair<Vector3,double> > > layers_;
    │ │ │ +
    286
    │ │ │ +
    293 double radius_(const String& element);
    │ │ │ +
    294
    │ │ │ +
    297 void trySphere__(HashGridBox3<Sphere_>::DataIterator data_it,
    │ │ │ +
    298 HashGridBox3<Sphere_>::DataIterator data_it2,
    │ │ │ +
    299 HashGridBox3<Sphere_>::DataIterator data_it3);
    │ │ │ +
    300
    │ │ │ +
    303 void addSphere_s_();
    │ │ │ +
    304
    │ │ │ +
    307 Vector3 calculateT_(HashGridBox3<Sphere_>::DataIterator data_it,
    │ │ │ +
    308 HashGridBox3<Sphere_>::DataIterator data_it2);
    │ │ │ +
    309
    │ │ │ +
    312 void testFirst_(HashGrid3<Sphere_>& hg,HashGridBox3<Sphere_>::DataIterator data_it,
    │ │ │ +
    313 Position x, Position y, Position z);
    │ │ │ +
    314
    │ │ │ +
    315 void testSecond_(HashGrid3<Sphere_>& hg,HashGridBox3<Sphere_>::DataIterator data_it,
    │ │ │ +
    316 HashGridBox3<Sphere_>::DataIterator data_it2,
    │ │ │ +
    317 Position x, Position y, Position z,Position step);
    │ │ │ +
    318
    │ │ │ +
    321 bool testSphereClash_(Vector3& v);
    │ │ │ +
    322
    │ │ │ +
    325 bool testProteinClash_(Vector3& v);
    │ │ │ +
    326
    │ │ │ +
    329 bool testBC_(Sphere_& sp);
    │ │ │ +
    330
    │ │ │ +
    333 void weedCandidates_();
    │ │ │ +
    334
    │ │ │ +
    337 bool parse_();
    │ │ │ +
    338
    │ │ │ +
    339
    │ │ │ +
    340 bool second_it_;
    │ │ │ +
    341
    │ │ │ +
    342 };
    │ │ │
    │ │ │ -
    250
    │ │ │ -
    251} } // namespaces
    │ │ │ -
    252
    │ │ │ -
    253#endif // BALL_VIEW_WIDGETS_GEOMETRICCONTROL_H
    │ │ │ - │ │ │ - │ │ │ -
    BALL_EMBEDDABLE
    #define BALL_EMBEDDABLE(TYPE, BASE)
    Definition embeddable.h:31
    │ │ │ - │ │ │ -
    BALL::HashMap
    HashMap class based on the STL map (containing serveral convenience functions)
    Definition hashMap.h:74
    │ │ │ - │ │ │ +
    343
    │ │ │ +
    344} //namesspace BALL
    │ │ │ +
    345
    │ │ │ +
    346#endif // BALL_STRUCTURE_BINDINGPOCKETPROCESSOR_H
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::operator<
    BALL_EXPORT bool operator<(const String &s1, const String &s2)
    │ │ │ +
    BALL::Position
    BALL_SIZE_TYPE Position
    Definition COMMON/global.h:140
    │ │ │ +
    BALL::operator==
    BALL_EXPORT bool operator==(const String &s1, const String &s2)
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::HashGrid3
    Three-dimensional Hash Grid Class.
    Definition hashGrid.h:755
    │ │ │ +
    BALL::HashGridBox3::DataIterator
    ForwardIterator< HashGridBox3< Item >, Item, DataIteratorPosition, DataIteratorTraits > DataIterator
    Definition hashGrid.h:492
    │ │ │ + │ │ │ + │ │ │ │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::initializeWidget
    virtual void initializeWidget(MainControl &main_control)
    │ │ │ -
    BALL::VIEW::GeometricControl::onNotify
    virtual void onNotify(Message *message)
    │ │ │ -
    BALL::VIEW::GeometricControl::representation_to_item_
    HashMap< Representation *, QTreeWidgetItem * > representation_to_item_
    Definition geometricControl.h:237
    │ │ │ -
    BALL::VIEW::GeometricControl::setClippingPlaneX
    virtual void setClippingPlaneX()
    │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::setClippingPosition
    virtual void setClippingPosition()
    │ │ │ -
    BALL::VIEW::GeometricControl::addRepresentation
    virtual void addRepresentation(Representation &rep)
    │ │ │ -
    BALL::VIEW::GeometricControl::setClippingPlaneY
    virtual void setClippingPlaneY()
    │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::item_to_plane_
    HashMap< QTreeWidgetItem *, ClippingPlane * > item_to_plane_
    Definition geometricControl.h:240
    │ │ │ -
    BALL::VIEW::GeometricControl::getModifySurfaceDialog
    ModifyRepresentationDialog * getModifySurfaceDialog()
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::buildContextMenu
    virtual void buildContextMenu()
    │ │ │ -
    BALL::VIEW::GeometricControl::renameRepresentation
    virtual void renameRepresentation()
    │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::setupProximityLight
    virtual void setupProximityLight()
    │ │ │ -
    BALL::VIEW::GeometricControl::updateSelection
    virtual void updateSelection()
    │ │ │ -
    BALL::VIEW::GeometricControl::moveItems
    void moveItems(const TransformationMessage &msg)
    │ │ │ -
    BALL::VIEW::GeometricControl::context_representation_
    Representation * context_representation_
    Definition geometricControl.h:234
    │ │ │ -
    BALL::VIEW::GeometricControl::checkMenu
    virtual void checkMenu(MainControl &main_control)
    Overloaded from ModularWidget.
    │ │ │ -
    BALL::VIEW::GeometricControl::setClippingPlaneZ
    virtual void setClippingPlaneZ()
    │ │ │ -
    BALL::VIEW::GeometricControl::removeRepresentation
    virtual void removeRepresentation(Representation &rep)
    │ │ │ -
    BALL::VIEW::GeometricControl::generateListViewItem_
    virtual void generateListViewItem_(Representation &rep)
    │ │ │ -
    BALL::VIEW::GeometricControl::item_to_representation_
    HashMap< QTreeWidgetItem *, Representation * > item_to_representation_
    Definition geometricControl.h:239
    │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::showGuestContextMenu
    void showGuestContextMenu(const QPoint &pos)
    │ │ │ -
    BALL::VIEW::GeometricControl::selectClipRepresentations
    virtual void selectClipRepresentations()
    │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::flipClippingPlane
    virtual void flipClippingPlane()
    │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::flipClippingCapping
    virtual void flipClippingCapping()
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::onItemClicked
    virtual void onItemClicked(QTreeWidgetItem *item, int col)
    │ │ │ -
    BALL::VIEW::GeometricControl::addItem_
    void addItem_(const String &text, const char *member, QWidget *widget=0)
    │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::selectedRepresentation
    virtual void selectedRepresentation(Representation &representation, bool state)
    │ │ │ -
    BALL::VIEW::GeometricControl::plane_to_item_
    HashMap< ClippingPlane *, QTreeWidgetItem * > plane_to_item_
    Definition geometricControl.h:238
    │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::context_menu_actions_
    vector< QAction * > context_menu_actions_
    Definition geometricControl.h:248
    │ │ │ -
    BALL::VIEW::GeometricControl::deleteCurrentItems
    virtual void deleteCurrentItems()
    Overloaded from GenericControl.
    │ │ │ -
    BALL::VIEW::GeometricControl::GeometricControl
    GeometricControl(const GeometricControl &control)
    │ │ │ -
    BALL::VIEW::GeometricControl::modify_rep_dialog_
    ModifyRepresentationDialog * modify_rep_dialog_
    Definition geometricControl.h:242
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::modifyRepresentation_
    virtual void modifyRepresentation_()
    │ │ │ - │ │ │ - │ │ │ -
    BALL::VIEW::GeometricControl::setClippingPlane_
    void setClippingPlane_(const Vector3 &n)
    │ │ │ -
    BALL::VIEW::GeometricControl::getHighlightedRepresentations
    std::list< Representation * > getHighlightedRepresentations() const
    │ │ │ -
    BALL::VIEW::GeometricControl::updateRepresentation
    virtual void updateRepresentation(Representation &rep, bool force=false)
    │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL_VIEW_EXPORT
    #define BALL_VIEW_EXPORT
    Definition COMMON/global.h:52
    │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::operator=
    const BindingPocketProcessor & operator=(const BindingPocketProcessor &pp)
    │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::operator<<
    friend std::ostream & operator<<(std::ostream &os, const BindingPocketProcessor::Sphere_ &)
    Definition bindingPocketProcessor.h:225
    │ │ │ +
    BALL::BindingPocketProcessor::getActiveSitePoints
    const vector< std::pair< Vector3, double > > & getActiveSitePoints() const
    │ │ │ +
    BALL::BindingPocketProcessor::finish
    virtual bool finish()
    Finish .
    │ │ │ +
    BALL::BindingPocketProcessor::BindingPocketProcessor
    BindingPocketProcessor(const BindingPocketProcessor &pp)
    │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::BindingPocketProcessor
    BindingPocketProcessor(Options &new_options)
    │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::getLayers
    const vector< vector< std::pair< Vector3, double > > > & getLayers() const
    │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::Option::INI_FILE_NAME
    static const String INI_FILE_NAME
    name of the ini-file
    Definition bindingPocketProcessor.h:55
    │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::Option::PROBE_SPHERE_RADIUS_HYDROGEN_FREE
    static const String PROBE_SPHERE_RADIUS_HYDROGEN_FREE
    probe sphere radius for heavy atoms only
    Definition bindingPocketProcessor.h:67
    │ │ │ +
    BALL::BindingPocketProcessor::Option::PROBE_SPHERE_RADIUS
    static const String PROBE_SPHERE_RADIUS
    probe sphere radius for computation with hydrogen atoms
    Definition bindingPocketProcessor.h:65
    │ │ │ +
    BALL::BindingPocketProcessor::Option::BURIAL_COUNT_THRESHOLD
    static const String BURIAL_COUNT_THRESHOLD
    burial count threshold for computation with hydrogen atoms
    Definition bindingPocketProcessor.h:71
    │ │ │ +
    BALL::BindingPocketProcessor::Option::PW_SQUARE_WELL
    static const String PW_SQUARE_WELL
    options for the computation of the probe weight
    Definition bindingPocketProcessor.h:77
    │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::Option::BURIAL_COUNT_RADIUS
    static const String BURIAL_COUNT_RADIUS
    radius for the computation of the burial count
    Definition bindingPocketProcessor.h:75
    │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::Option::BURIAL_COUNT_THRESHOLD_HYDROGEN_FREE
    static const String BURIAL_COUNT_THRESHOLD_HYDROGEN_FREE
    burial count threshold for heavy atoms only
    Definition bindingPocketProcessor.h:73
    │ │ │ +
    BALL::BindingPocketProcessor::Option::RADIUS_HYDROGEN
    static const String RADIUS_HYDROGEN
    atom radius of individual elements
    Definition bindingPocketProcessor.h:58
    │ │ │ +
    BALL::BindingPocketProcessor::Option::PROBE_LAYER_RADIUS
    static const String PROBE_LAYER_RADIUS
    probe radius for colision of probes in one layer
    Definition bindingPocketProcessor.h:69
    │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::Option::MAX_ASPS
    static const String MAX_ASPS
    maximum number of active site points
    Definition bindingPocketProcessor.h:81
    │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::Option::PARSE_INI_FILE
    static const String PARSE_INI_FILE
    try to parse ini-file
    Definition bindingPocketProcessor.h:53
    │ │ │ +
    BALL::BindingPocketProcessor::Option::HEAVY_ONLY
    static const String HEAVY_ONLY
    use only heavy atoms for computation
    Definition bindingPocketProcessor.h:51
    │ │ │ +
    BALL::BindingPocketProcessor::Option::ASP_SEPERATION
    static const String ASP_SEPERATION
    minumum distance between two active site points
    Definition bindingPocketProcessor.h:85
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL::BindingPocketProcessor::Default::BURIAL_COUNT_THRESHOLD_HYDROGEN_FREE
    static const Position BURIAL_COUNT_THRESHOLD_HYDROGEN_FREE
    Definition bindingPocketProcessor.h:106
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ + │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,338 +1,448 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _V_I_E_W │ │ │ │ - * _W_I_D_G_E_T_S │ │ │ │ -geometricControl.h │ │ │ │ + * _S_T_R_U_C_T_U_R_E │ │ │ │ +bindingPocketProcessor.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ -1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ -2// vi: set ts=2: │ │ │ │ -3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_VIEW_WIDGETS_GEOMETRICCONTROL_H │ │ │ │ -6#define BALL_VIEW_WIDGETS_GEOMETRICCONTROL_H │ │ │ │ +1#ifndef BALL_STRUCTURE_BINDINGPOCKETPROCESSOR_H │ │ │ │ +2#define BALL_STRUCTURE_BINDINGPOCKETPROCESSOR_H │ │ │ │ +3 │ │ │ │ +4#ifndef BALL_CONCEPT_PROCESSOR_H │ │ │ │ +5# include <_B_A_L_L_/_C_O_N_C_E_P_T_/_p_r_o_c_e_s_s_o_r_._h> │ │ │ │ +6#endif │ │ │ │ 7 │ │ │ │ -8#ifndef BALL_COMMON_H │ │ │ │ -9# include <_B_A_L_L_/_c_o_m_m_o_n_._h> │ │ │ │ +8#ifndef BALL_KERNEL_RESIDUE_H │ │ │ │ +9# include <_B_A_L_L_/_K_E_R_N_E_L_/_r_e_s_i_d_u_e_._h> │ │ │ │ 10#endif │ │ │ │ 11 │ │ │ │ -12#ifndef BALL_VIEW_WIDGETS_GENERICCONTROL_H │ │ │ │ -13# include <_B_A_L_L_/_V_I_E_W_/_W_I_D_G_E_T_S_/_g_e_n_e_r_i_c_C_o_n_t_r_o_l_._h> │ │ │ │ +12#ifndef BALL_MATHS_VECTOR3_H │ │ │ │ +13# include <_B_A_L_L_/_M_A_T_H_S_/_v_e_c_t_o_r_3_._h> │ │ │ │ 14#endif │ │ │ │ 15 │ │ │ │ -16#ifndef BALL_VIEW_KERNEL_COMMON_H │ │ │ │ -17# include <_B_A_L_L_/_V_I_E_W_/_K_E_R_N_E_L_/_c_o_m_m_o_n_._h> │ │ │ │ +16#ifndef BALL_KERNEL_SYSTEM_H │ │ │ │ +17# include <_B_A_L_L_/_K_E_R_N_E_L_/_s_y_s_t_e_m_._h> │ │ │ │ 18#endif │ │ │ │ 19 │ │ │ │ -20#include │ │ │ │ -21#include │ │ │ │ -22 │ │ │ │ -23namespace _B_A_L_L │ │ │ │ -24{ │ │ │ │ -25 namespace VIEW │ │ │ │ -26 { │ │ │ │ -27 class Representation; │ │ │ │ -28 class ModifyRepresentationDialog; │ │ │ │ -29 class ClippingPlane; │ │ │ │ -30 class TransformationMessage; │ │ │ │ -31 │ │ │ │ -_4_1 class _B_A_L_L___V_I_E_W___E_X_P_O_R_T _G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l │ │ │ │ -42 : public _G_e_n_e_r_i_c_C_o_n_t_r_o_l │ │ │ │ -43 { │ │ │ │ -44 Q_OBJECT │ │ │ │ +20#ifndef BALL_DATATYPE_HASHGRID_H │ │ │ │ +21# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_h_a_s_h_G_r_i_d_._h> │ │ │ │ +22#endif │ │ │ │ +23 │ │ │ │ +24#ifndef BALL_DATATYPE_OPTIONS_H │ │ │ │ +25# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_o_p_t_i_o_n_s_._h> │ │ │ │ +26#endif │ │ │ │ +27 │ │ │ │ +28#include │ │ │ │ +29#include │ │ │ │ +30 │ │ │ │ +31#include │ │ │ │ +32 │ │ │ │ +33namespace _B_A_L_L │ │ │ │ +34{ │ │ │ │ +35 │ │ │ │ +_4_0 class _B_A_L_L___E_X_P_O_R_T _B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r │ │ │ │ +41 : public _U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ +42 { │ │ │ │ +43 │ │ │ │ +44 public: │ │ │ │ 45 │ │ │ │ -46 public: │ │ │ │ -47 │ │ │ │ -48 _B_A_L_L___E_M_B_E_D_D_A_B_L_E(_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l, _G_e_n_e_r_i_c_C_o_n_t_r_o_l) │ │ │ │ -49 │ │ │ │ -50 │ │ │ │ -53 │ │ │ │ -54 │ │ │ │ -_6_9 _G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l(_Q_W_i_d_g_e_t* parent = 0, const char* name = 0); │ │ │ │ -70 │ │ │ │ -_7_2 virtual ~_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l(); │ │ │ │ -73 │ │ │ │ -_7_7 virtual void clear(){}; │ │ │ │ -78 │ │ │ │ -_8_0 virtual void _i_n_i_t_i_a_l_i_z_e_W_i_d_g_e_t(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ -81 │ │ │ │ -83 │ │ │ │ -84 │ │ │ │ -_8_7 virtual void _a_d_d_R_e_p_r_e_s_e_n_t_a_t_i_o_n(_R_e_p_r_e_s_e_n_t_a_t_i_o_n& rep); │ │ │ │ -88 │ │ │ │ -_9_1 virtual void _r_e_m_o_v_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n(_R_e_p_r_e_s_e_n_t_a_t_i_o_n& rep); │ │ │ │ -92 │ │ │ │ -_9_5 virtual void _u_p_d_a_t_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n(_R_e_p_r_e_s_e_n_t_a_t_i_o_n& rep, bool force=false); │ │ │ │ -96 │ │ │ │ -_1_0_2 std::list _g_e_t_H_i_g_h_l_i_g_h_t_e_d_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s() const; │ │ │ │ -103 │ │ │ │ -_1_0_7 virtual void _o_n_N_o_t_i_f_y(_M_e_s_s_a_g_e *message); │ │ │ │ -108 │ │ │ │ -_1_1_5 virtual void _b_u_i_l_d_C_o_n_t_e_x_t_M_e_n_u(); │ │ │ │ -116 │ │ │ │ -_1_1_8 virtual void _c_h_e_c_k_M_e_n_u(_M_a_i_n_C_o_n_t_r_o_l& main_control); │ │ │ │ +_4_8 struct _O_p_t_i_o_n │ │ │ │ +49 { │ │ │ │ +_5_1 static const _S_t_r_i_n_g _H_E_A_V_Y___O_N_L_Y; │ │ │ │ +_5_3 static const _S_t_r_i_n_g _P_A_R_S_E___I_N_I___F_I_L_E; │ │ │ │ +_5_5 static const _S_t_r_i_n_g _I_N_I___F_I_L_E___N_A_M_E; │ │ │ │ +56 │ │ │ │ +_5_8 static const _S_t_r_i_n_g _R_A_D_I_U_S___H_Y_D_R_O_G_E_N; │ │ │ │ +_5_9 static const _S_t_r_i_n_g _R_A_D_I_U_S___O_X_Y_G_E_N; │ │ │ │ +_6_0 static const _S_t_r_i_n_g _R_A_D_I_U_S___N_I_T_R_O_G_E_N; │ │ │ │ +_6_1 static const _S_t_r_i_n_g _R_A_D_I_U_S___C_A_R_B_O_N; │ │ │ │ +_6_2 static const _S_t_r_i_n_g _R_A_D_I_U_S___S_U_L_F_U_R; │ │ │ │ +63 │ │ │ │ +_6_5 static const _S_t_r_i_n_g _P_R_O_B_E___S_P_H_E_R_E___R_A_D_I_U_S; │ │ │ │ +_6_7 static const _S_t_r_i_n_g _P_R_O_B_E___S_P_H_E_R_E___R_A_D_I_U_S___H_Y_D_R_O_G_E_N___F_R_E_E; │ │ │ │ +_6_9 static const _S_t_r_i_n_g _P_R_O_B_E___L_A_Y_E_R___R_A_D_I_U_S; │ │ │ │ +_7_1 static const _S_t_r_i_n_g _B_U_R_I_A_L___C_O_U_N_T___T_H_R_E_S_H_O_L_D; │ │ │ │ +_7_3 static const _S_t_r_i_n_g _B_U_R_I_A_L___C_O_U_N_T___T_H_R_E_S_H_O_L_D___H_Y_D_R_O_G_E_N___F_R_E_E; │ │ │ │ +_7_5 static const _S_t_r_i_n_g _B_U_R_I_A_L___C_O_U_N_T___R_A_D_I_U_S; │ │ │ │ +_7_7 static const _S_t_r_i_n_g _P_W___S_Q_U_A_R_E___W_E_L_L; │ │ │ │ +_7_8 static const _S_t_r_i_n_g _P_W___G_A_U_S_S_I_A_N___W_I_D_T_H; │ │ │ │ +_7_9 static const _S_t_r_i_n_g _P_W___M_A_X___D_I_S_T_A_N_C_E; │ │ │ │ +_8_1 static const _S_t_r_i_n_g _M_A_X___A_S_P_S; │ │ │ │ +82 // additional factor for the computation of the collision of two spheres │ │ │ │ +_8_3 static const _S_t_r_i_n_g _C_L_A_S_H___F_A_C_T_O_R; │ │ │ │ +_8_5 static const _S_t_r_i_n_g _A_S_P___S_E_P_E_R_A_T_I_O_N; │ │ │ │ +86 }; │ │ │ │ +87 │ │ │ │ +_9_0 struct _D_e_f_a_u_l_t │ │ │ │ +91 { │ │ │ │ +_9_2 static const bool _H_E_A_V_Y___O_N_L_Y; │ │ │ │ +_9_3 static const bool _P_A_R_S_E___I_N_I___F_I_L_E; │ │ │ │ +_9_4 static const _S_t_r_i_n_g _I_N_I___F_I_L_E___N_A_M_E; │ │ │ │ +95 │ │ │ │ +_9_6 static const double _R_A_D_I_U_S___H_Y_D_R_O_G_E_N; │ │ │ │ +_9_7 static const double _R_A_D_I_U_S___O_X_Y_G_E_N; │ │ │ │ +_9_8 static const double _R_A_D_I_U_S___N_I_T_R_O_G_E_N; │ │ │ │ +_9_9 static const double _R_A_D_I_U_S___C_A_R_B_O_N; │ │ │ │ +_1_0_0 static const double _R_A_D_I_U_S___S_U_L_F_U_R; │ │ │ │ +101 │ │ │ │ +_1_0_2 static const double _P_R_O_B_E___S_P_H_E_R_E___R_A_D_I_U_S; │ │ │ │ +_1_0_3 static const double _P_R_O_B_E___S_P_H_E_R_E___R_A_D_I_U_S___H_Y_D_R_O_G_E_N___F_R_E_E; │ │ │ │ +_1_0_4 static const double _P_R_O_B_E___L_A_Y_E_R___R_A_D_I_U_S; │ │ │ │ +_1_0_5 static const _P_o_s_i_t_i_o_n _B_U_R_I_A_L___C_O_U_N_T___T_H_R_E_S_H_O_L_D; │ │ │ │ +_1_0_6 static const _P_o_s_i_t_i_o_n _B_U_R_I_A_L___C_O_U_N_T___T_H_R_E_S_H_O_L_D___H_Y_D_R_O_G_E_N___F_R_E_E; │ │ │ │ +_1_0_7 static const double _B_U_R_I_A_L___C_O_U_N_T___R_A_D_I_U_S; │ │ │ │ +_1_0_8 static const double _P_W___S_Q_U_A_R_E___W_E_L_L; │ │ │ │ +_1_0_9 static const double _P_W___G_A_U_S_S_I_A_N___W_I_D_T_H; │ │ │ │ +_1_1_0 static const double _P_W___M_A_X___D_I_S_T_A_N_C_E; │ │ │ │ +_1_1_1 static const _P_o_s_i_t_i_o_n _M_A_X___A_S_P_S; │ │ │ │ +_1_1_2 static const double _C_L_A_S_H___F_A_C_T_O_R; │ │ │ │ +_1_1_3 static const double _A_S_P___S_E_P_E_R_A_T_I_O_N; │ │ │ │ +114 }; │ │ │ │ +115 │ │ │ │ +_1_1_8 _B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r(); │ │ │ │ 119 │ │ │ │ -_1_2_1 void _m_o_v_e_I_t_e_m_s(const _T_r_a_n_s_f_o_r_m_a_t_i_o_n_M_e_s_s_a_g_e& msg); │ │ │ │ -122 │ │ │ │ -_1_2_3 void _u_p_d_a_t_e_C_l_i_p_p_i_n_g_P_l_a_n_e_s(); │ │ │ │ -124 │ │ │ │ -125 public Q_SLOTS: │ │ │ │ -126 │ │ │ │ -128 │ │ │ │ +_1_2_2 _B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r(_O_p_t_i_o_n_s& new_options); │ │ │ │ +123 │ │ │ │ +_1_2_6 _B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r(const _B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r& pp); │ │ │ │ +127 │ │ │ │ +_1_3_0 virtual _~_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r(); │ │ │ │ 131 │ │ │ │ -_1_3_3 virtual void _r_e_n_a_m_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n(); │ │ │ │ -134 │ │ │ │ -_1_3_6 virtual void _s_e_l_e_c_t_A_t_o_m_s(); │ │ │ │ -137 │ │ │ │ -_1_3_9 virtual void _s_e_l_e_c_t_e_d_R_e_p_r_e_s_e_n_t_a_t_i_o_n(_R_e_p_r_e_s_e_n_t_a_t_i_o_n& representation, bool │ │ │ │ -state); │ │ │ │ +_1_3_4 const _B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r& _o_p_e_r_a_t_o_r_=(const _B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r& pp); │ │ │ │ +135 │ │ │ │ +_1_3_7 virtual bool _f_i_n_i_s_h(); │ │ │ │ +138 │ │ │ │ +_1_3_9 virtual _P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t operator() (_C_o_m_p_o_s_i_t_e &composite); │ │ │ │ 140 │ │ │ │ -_1_4_2 virtual void _u_p_d_a_t_e_S_e_l_e_c_t_i_o_n(); │ │ │ │ -143 │ │ │ │ -_1_4_5 virtual void _f_o_c_u_s(); │ │ │ │ -146 │ │ │ │ -_1_4_8 virtual void _e_n_t_e_r_M_o_v_e_M_o_d_e(); │ │ │ │ -149 │ │ │ │ -_1_5_1 virtual void _f_l_i_p_C_l_i_p_p_i_n_g_C_a_p_p_i_n_g(); │ │ │ │ +_1_4_3 const vector >& _g_e_t_A_c_t_i_v_e_S_i_t_e_P_o_i_n_t_s() const; │ │ │ │ +144 │ │ │ │ +_1_4_7 const vector > >& _g_e_t_L_a_y_e_r_s() const; │ │ │ │ +148 │ │ │ │ +_1_5_1 _O_p_t_i_o_n_s _o_p_t_i_o_n_s; │ │ │ │ 152 │ │ │ │ -_1_5_4 virtual void _f_l_i_p_C_l_i_p_p_i_n_g_P_l_a_n_e(); │ │ │ │ -155 │ │ │ │ -_1_5_7 virtual void _s_e_t_C_l_i_p_p_i_n_g_P_o_s_i_t_i_o_n(); │ │ │ │ -158 │ │ │ │ -_1_6_0 virtual void _s_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e_X(); │ │ │ │ -161 │ │ │ │ -_1_6_3 virtual void _s_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e_Y(); │ │ │ │ -164 │ │ │ │ -_1_6_6 virtual void _s_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e_Z(); │ │ │ │ +153 private: │ │ │ │ +154 │ │ │ │ +158 class Sphere_ │ │ │ │ +159 { │ │ │ │ +160 public: │ │ │ │ +162 Sphere_(); │ │ │ │ +163 │ │ │ │ +166 _B_A_L_L_:_:_V_e_c_t_o_r_3 position; │ │ │ │ 167 │ │ │ │ -_1_6_9 void _h_i_d_e_S_h_o_w_C_l_i_p_p_i_n_g_P_l_a_n_e(); │ │ │ │ -170 │ │ │ │ -_1_7_2 virtual void _s_e_l_e_c_t_C_l_i_p_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s(); │ │ │ │ -173 │ │ │ │ -_1_7_5 void _c_r_e_a_t_e_N_e_w_C_l_i_p_p_i_n_g_P_l_a_n_e(); │ │ │ │ -176 │ │ │ │ -_1_7_8 void _d_u_p_l_i_c_a_t_e(); │ │ │ │ +170 float radius; │ │ │ │ +171 │ │ │ │ +174 _P_o_s_i_t_i_o_n b_count; │ │ │ │ +175 │ │ │ │ +178 float probe_weight; │ │ │ │ 179 │ │ │ │ -_1_8_1 void _s_a_v_e_S_u_r_f_a_c_e(); │ │ │ │ -182 │ │ │ │ -_1_8_4 void _l_o_a_d_S_u_r_f_a_c_e(); │ │ │ │ -185 │ │ │ │ -_1_8_7 _M_o_d_i_f_y_R_e_p_r_e_s_e_n_t_a_t_i_o_n_D_i_a_l_o_g* _g_e_t_M_o_d_i_f_y_S_u_r_f_a_c_e_D_i_a_l_o_g(); │ │ │ │ -188 │ │ │ │ -189 protected Q_SLOTS: │ │ │ │ -190 │ │ │ │ -192 │ │ │ │ -194 │ │ │ │ -_1_9_6 virtual void _m_o_d_i_f_y_R_e_p_r_e_s_e_n_t_a_t_i_o_n__(); │ │ │ │ -197 │ │ │ │ -_2_0_0 virtual void _g_e_n_e_r_a_t_e_L_i_s_t_V_i_e_w_I_t_e_m__(_R_e_p_r_e_s_e_n_t_a_t_i_o_n& rep); │ │ │ │ -201 │ │ │ │ -_2_0_3 virtual void _d_e_l_e_t_e_C_u_r_r_e_n_t_I_t_e_m_s(); │ │ │ │ -204 │ │ │ │ -_2_0_6 virtual void _s_e_t_u_p_P_r_o_x_i_m_i_t_y_L_i_g_h_t(); │ │ │ │ -207 │ │ │ │ -209 │ │ │ │ -210 protected Q_SLOTS: │ │ │ │ -211 │ │ │ │ -_2_1_2 virtual void _o_n_I_t_e_m_C_l_i_c_k_e_d(_Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m* item, int col); │ │ │ │ -_2_1_3 void _s_h_o_w_G_u_e_s_t_C_o_n_t_e_x_t_M_e_n_u(const QPoint& pos); │ │ │ │ -214 │ │ │ │ -215 protected: │ │ │ │ -216 │ │ │ │ -_2_1_7 void _a_d_d_I_t_e_m__(const _S_t_r_i_n_g& text, const char* member, _Q_W_i_d_g_e_t* widget = 0); │ │ │ │ -218 │ │ │ │ -219 // only for Python Interface │ │ │ │ -_2_2_0 _G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l(const _G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l& control); │ │ │ │ +182 _P_o_s_i_t_i_o_n layer; │ │ │ │ +183 │ │ │ │ +186 inline bool _o_p_e_r_a_t_o_r_<(const Sphere_& sp) const {return probe_weight > │ │ │ │ +sp.probe_weight;}; │ │ │ │ +187 │ │ │ │ +190 int id; │ │ │ │ +191 static int global_id; │ │ │ │ +192 _P_o_s_i_t_i_o_n a,b,c,d; │ │ │ │ +193 │ │ │ │ +196 inline bool _o_p_e_r_a_t_o_r_=_=(const Sphere_& sp) const {return a == sp.a && b == │ │ │ │ +sp.b && c == sp.c && d == sp.d;}; │ │ │ │ +197 }; │ │ │ │ +198 │ │ │ │ +201 class SphereComparator_ │ │ │ │ +202 { │ │ │ │ +203 public: │ │ │ │ +204 int operator()(const Sphere_& sp1, const Sphere_& sp2) const │ │ │ │ +205 { │ │ │ │ +206 if (sp1.a != sp2.a) │ │ │ │ +207 return sp1.a < sp2.a; │ │ │ │ +208 if (sp1.b != sp2.b) │ │ │ │ +209 return sp1.b < sp2.b; │ │ │ │ +210 if (sp1.c != sp2.c) │ │ │ │ +211 return sp1.c < sp2.c; │ │ │ │ +212 if (sp1.d != sp2.d) │ │ │ │ +213 return sp1.d < sp2.d; │ │ │ │ +214 return 0; │ │ │ │ +215 }; │ │ │ │ +216 }; │ │ │ │ +217 │ │ │ │ +220 _P_o_s_i_t_i_o_n layer_; │ │ │ │ 221 │ │ │ │ -_2_2_2 enum _C_o_l_u_m_n_I_D │ │ │ │ -223 { │ │ │ │ -_2_2_4 COLUMN_ID__TYPE = 0, │ │ │ │ -225 COLUMN_ID__Properties │ │ │ │ -_2_2_6 }; │ │ │ │ -227 │ │ │ │ -_2_2_8 void _s_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e__(const _V_e_c_t_o_r_3& n); │ │ │ │ -229 │ │ │ │ -230 // the context menu │ │ │ │ -_2_3_1 QMenu _c_o_n_t_e_x_t___m_e_n_u__; │ │ │ │ -_2_3_2 QMenu _c_l_i_p_p_i_n_g___p_l_a_n_e___c_o_n_t_e_x_t___m_e_n_u__; │ │ │ │ -233 │ │ │ │ -_2_3_4 _R_e_p_r_e_s_e_n_t_a_t_i_o_n* _c_o_n_t_e_x_t___r_e_p_r_e_s_e_n_t_a_t_i_o_n__; │ │ │ │ -_2_3_5 _C_l_i_p_p_i_n_g_P_l_a_n_e* _c_o_n_t_e_x_t___p_l_a_n_e__; │ │ │ │ -236 │ │ │ │ -_2_3_7 _H_a_s_h_M_a_p_<_R_e_p_r_e_s_e_n_t_a_t_i_o_n_*_,_ _Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m_*_> _r_e_p_r_e_s_e_n_t_a_t_i_o_n___t_o___i_t_e_m__; │ │ │ │ -_2_3_8 _H_a_s_h_M_a_p_<_C_l_i_p_p_i_n_g_P_l_a_n_e_*_,_ _Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m_*_> _p_l_a_n_e___t_o___i_t_e_m__; │ │ │ │ -_2_3_9 _H_a_s_h_M_a_p_<_Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m_*_,_ _R_e_p_r_e_s_e_n_t_a_t_i_o_n_*_> _i_t_e_m___t_o___r_e_p_r_e_s_e_n_t_a_t_i_o_n__; │ │ │ │ -_2_4_0 _H_a_s_h_M_a_p_<_Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m_*_,_ _C_l_i_p_p_i_n_g_P_l_a_n_e_*_> _i_t_e_m___t_o___p_l_a_n_e__; │ │ │ │ -241 │ │ │ │ -_2_4_2 _M_o_d_i_f_y_R_e_p_r_e_s_e_n_t_a_t_i_o_n_D_i_a_l_o_g* _m_o_d_i_f_y___r_e_p___d_i_a_l_o_g__; │ │ │ │ -243 │ │ │ │ -_2_4_4 bool _c_r_e_a_t_i_n_g___r_e_p_r_e_s_e_n_t_a_t_i_o_n_s__; │ │ │ │ -_2_4_5 bool _i_g_n_o_r_e___c_h_a_n_g_e__; │ │ │ │ +_2_2_5 friend std::ostream& _o_p_e_r_a_t_o_r_<_<(std::ostream& os, const │ │ │ │ +BindingPocketProcessor::Sphere_& /*sp*/) {return os;}; │ │ │ │ +226 │ │ │ │ +229 _H_a_s_h_G_r_i_d_3_<_S_p_h_e_r_e___> sphere_grid_; │ │ │ │ +230 │ │ │ │ +233 _H_a_s_h_G_r_i_d_3_<_S_p_h_e_r_e___> protein_grid_; │ │ │ │ +234 │ │ │ │ +237 _H_a_s_h_G_r_i_d_3_<_S_p_h_e_r_e___> layer_grid_; │ │ │ │ +238 │ │ │ │ +241 _H_a_s_h_G_r_i_d_3_<_S_p_h_e_r_e___> clayer_grid_; │ │ │ │ +242 │ │ │ │ +245 _H_a_s_h_G_r_i_d_3_<_S_p_h_e_r_e___> BC_grid_; │ │ │ │ 246 │ │ │ │ -_2_4_7 QAction* _m_e_n_u___c_l_i_p_p_i_n_g___p_l_a_n_e__, *menu_load_surface_, *modify_surface_; │ │ │ │ -_2_4_8 vector _c_o_n_t_e_x_t___m_e_n_u___a_c_t_i_o_n_s__; │ │ │ │ -249 }; │ │ │ │ +249 _H_a_s_h_G_r_i_d_3_<_S_p_h_e_r_e___> pw_grid_; │ │ │ │ 250 │ │ │ │ -251} } // namespaces │ │ │ │ -252 │ │ │ │ -253#endif // BALL_VIEW_WIDGETS_GEOMETRICCONTROL_H │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_g_e_n_e_r_i_c_C_o_n_t_r_o_l_._h │ │ │ │ -_B_A_L_L___E_M_B_E_D_D_A_B_L_E │ │ │ │ -#define BALL_EMBEDDABLE(TYPE, BASE) │ │ │ │ -DDeeffiinniittiioonn _e_m_b_e_d_d_a_b_l_e_._h_:_3_1 │ │ │ │ +253 _H_a_s_h_G_r_i_d_3_<_S_p_h_e_r_e___> candidates_grid_; │ │ │ │ +254 │ │ │ │ +255 std::vector sorted_spheres_; │ │ │ │ +256 │ │ │ │ +259 double sphere_rad_; │ │ │ │ +260 │ │ │ │ +263 double second_layer_rad_; │ │ │ │ +264 │ │ │ │ +267 double protein_clash_rad_; │ │ │ │ +268 │ │ │ │ +271 double BC_threshold_; │ │ │ │ +272 │ │ │ │ +275 _P_o_s_i_t_i_o_n found_new_; │ │ │ │ +276 │ │ │ │ +277 double c_factor_; │ │ │ │ +278 │ │ │ │ +281 std::vector candidates; │ │ │ │ +282 │ │ │ │ +283 std::vector > asps_; │ │ │ │ +284 │ │ │ │ +285 std::vector > > layers_; │ │ │ │ +286 │ │ │ │ +293 double radius_(const _S_t_r_i_n_g& element); │ │ │ │ +294 │ │ │ │ +297 void trySphere__(_H_a_s_h_G_r_i_d_B_o_x_3_<_S_p_h_e_r_e___>_:_:_D_a_t_a_I_t_e_r_a_t_o_r data_it, │ │ │ │ +298 _H_a_s_h_G_r_i_d_B_o_x_3_<_S_p_h_e_r_e___>_:_:_D_a_t_a_I_t_e_r_a_t_o_r data_it2, │ │ │ │ +299 _H_a_s_h_G_r_i_d_B_o_x_3_<_S_p_h_e_r_e___>_:_:_D_a_t_a_I_t_e_r_a_t_o_r data_it3); │ │ │ │ +300 │ │ │ │ +303 void addSphere_s_(); │ │ │ │ +304 │ │ │ │ +307 _V_e_c_t_o_r_3 calculateT_(_H_a_s_h_G_r_i_d_B_o_x_3_<_S_p_h_e_r_e___>_:_:_D_a_t_a_I_t_e_r_a_t_o_r data_it, │ │ │ │ +308 _H_a_s_h_G_r_i_d_B_o_x_3_<_S_p_h_e_r_e___>_:_:_D_a_t_a_I_t_e_r_a_t_o_r data_it2); │ │ │ │ +309 │ │ │ │ +312 void testFirst_(_H_a_s_h_G_r_i_d_3_<_S_p_h_e_r_e___>& hg,_H_a_s_h_G_r_i_d_B_o_x_3_<_S_p_h_e_r_e___>_:_:_D_a_t_a_I_t_e_r_a_t_o_r │ │ │ │ +data_it, │ │ │ │ +313 _P_o_s_i_t_i_o_n x, _P_o_s_i_t_i_o_n y, _P_o_s_i_t_i_o_n z); │ │ │ │ +314 │ │ │ │ +315 void testSecond_(_H_a_s_h_G_r_i_d_3_<_S_p_h_e_r_e___>& hg,_H_a_s_h_G_r_i_d_B_o_x_3_<_S_p_h_e_r_e___>_:_:_D_a_t_a_I_t_e_r_a_t_o_r │ │ │ │ +data_it, │ │ │ │ +316 _H_a_s_h_G_r_i_d_B_o_x_3_<_S_p_h_e_r_e___>_:_:_D_a_t_a_I_t_e_r_a_t_o_r data_it2, │ │ │ │ +317 _P_o_s_i_t_i_o_n x, _P_o_s_i_t_i_o_n y, _P_o_s_i_t_i_o_n z,_P_o_s_i_t_i_o_n step); │ │ │ │ +318 │ │ │ │ +321 bool testSphereClash_(_V_e_c_t_o_r_3& v); │ │ │ │ +322 │ │ │ │ +325 bool testProteinClash_(_V_e_c_t_o_r_3& v); │ │ │ │ +326 │ │ │ │ +329 bool testBC_(Sphere_& sp); │ │ │ │ +330 │ │ │ │ +333 void weedCandidates_(); │ │ │ │ +334 │ │ │ │ +337 bool parse_(); │ │ │ │ +338 │ │ │ │ +339 │ │ │ │ +340 bool second_it_; │ │ │ │ +341 │ │ │ │ +342 }; │ │ │ │ +343 │ │ │ │ +344} //namesspace BALL │ │ │ │ +345 │ │ │ │ +346#endif // BALL_STRUCTURE_BINDINGPOCKETPROCESSOR_H │ │ │ │ +_p_r_o_c_e_s_s_o_r_._h │ │ │ │ +_r_e_s_i_d_u_e_._h │ │ │ │ +_v_e_c_t_o_r_3_._h │ │ │ │ +_o_p_t_i_o_n_s_._h │ │ │ │ +_h_a_s_h_G_r_i_d_._h │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_H_a_s_h_M_a_p │ │ │ │ -HashMap class based on the STL map (containing serveral convenience functions) │ │ │ │ -DDeeffiinniittiioonn _h_a_s_h_M_a_p_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_o_p_e_r_a_t_o_r_< │ │ │ │ +BALL_EXPORT bool operator<(const String &s1, const String &s2) │ │ │ │ +_B_A_L_L_:_:_P_o_s_i_t_i_o_n │ │ │ │ +BALL_SIZE_TYPE Position │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_1_4_0 │ │ │ │ +_B_A_L_L_:_:_o_p_e_r_a_t_o_r_=_= │ │ │ │ +BALL_EXPORT bool operator==(const String &s1, const String &s2) │ │ │ │ +_B_A_L_L_:_:_C_o_m_p_o_s_i_t_e │ │ │ │ +DDeeffiinniittiioonn _c_o_m_p_o_s_i_t_e_._h_:_7_4 │ │ │ │ +_B_A_L_L_:_:_P_r_o_c_e_s_s_o_r_:_:_R_e_s_u_l_t │ │ │ │ +int Result │ │ │ │ +DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_3_6 │ │ │ │ +_B_A_L_L_:_:_U_n_a_r_y_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _p_r_o_c_e_s_s_o_r_._h_:_6_0 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_G_r_i_d_3 │ │ │ │ +Three-dimensional Hash Grid Class. │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_G_r_i_d_._h_:_7_5_5 │ │ │ │ +_B_A_L_L_:_:_H_a_s_h_G_r_i_d_B_o_x_3_:_:_D_a_t_a_I_t_e_r_a_t_o_r │ │ │ │ +ForwardIterator< HashGridBox3< Item >, Item, DataIteratorPosition, │ │ │ │ +DataIteratorTraits > DataIterator │ │ │ │ +DDeeffiinniittiioonn _h_a_s_h_G_r_i_d_._h_:_4_9_2 │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ _B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ _B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_o_d_i_f_y_R_e_p_r_e_s_e_n_t_a_t_i_o_n_D_i_a_l_o_g │ │ │ │ -DDeeffiinniittiioonn _m_o_d_i_f_y_R_e_p_r_e_s_e_n_t_a_t_i_o_n_D_i_a_l_o_g_._h_:_5_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_C_l_i_p_p_i_n_g_P_l_a_n_e │ │ │ │ -DDeeffiinniittiioonn _c_l_i_p_p_i_n_g_P_l_a_n_e_._h_:_2_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_a_i_n_C_o_n_t_r_o_l │ │ │ │ -DDeeffiinniittiioonn _m_a_i_n_C_o_n_t_r_o_l_._h_:_1_1_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_M_e_s_s_a_g_e │ │ │ │ -DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_5_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_T_r_a_n_s_f_o_r_m_a_t_i_o_n_M_e_s_s_a_g_e │ │ │ │ -DDeeffiinniittiioonn _m_e_s_s_a_g_e_._h_:_7_3_6 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -DDeeffiinniittiioonn _r_e_p_r_e_s_e_n_t_a_t_i_o_n_._h_:_5_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_n_e_r_i_c_C_o_n_t_r_o_l │ │ │ │ -DDeeffiinniittiioonn _g_e_n_e_r_i_c_C_o_n_t_r_o_l_._h_:_5_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_4_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_i_n_i_t_i_a_l_i_z_e_W_i_d_g_e_t │ │ │ │ -virtual void initializeWidget(MainControl &main_control) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_o_n_N_o_t_i_f_y │ │ │ │ -virtual void onNotify(Message *message) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_r_e_p_r_e_s_e_n_t_a_t_i_o_n___t_o___i_t_e_m__ │ │ │ │ -HashMap< Representation *, QTreeWidgetItem * > representation_to_item_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_3_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e_X │ │ │ │ -virtual void setClippingPlaneX() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_C_o_l_u_m_n_I_D │ │ │ │ -ColumnID │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_2_3 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_e_t_C_l_i_p_p_i_n_g_P_o_s_i_t_i_o_n │ │ │ │ -virtual void setClippingPosition() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_a_d_d_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -virtual void addRepresentation(Representation &rep) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e_Y │ │ │ │ -virtual void setClippingPlaneY() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_a_v_e_S_u_r_f_a_c_e │ │ │ │ -void saveSurface() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_i_t_e_m___t_o___p_l_a_n_e__ │ │ │ │ -HashMap< QTreeWidgetItem *, ClippingPlane * > item_to_plane_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_4_0 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_g_e_t_M_o_d_i_f_y_S_u_r_f_a_c_e_D_i_a_l_o_g │ │ │ │ -ModifyRepresentationDialog * getModifySurfaceDialog() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_c_o_n_t_e_x_t___p_l_a_n_e__ │ │ │ │ -ClippingPlane * context_plane_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_3_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_h_i_d_e_S_h_o_w_C_l_i_p_p_i_n_g_P_l_a_n_e │ │ │ │ -void hideShowClippingPlane() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_b_u_i_l_d_C_o_n_t_e_x_t_M_e_n_u │ │ │ │ -virtual void buildContextMenu() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_r_e_n_a_m_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -virtual void renameRepresentation() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_u_p_d_a_t_e_C_l_i_p_p_i_n_g_P_l_a_n_e_s │ │ │ │ -void updateClippingPlanes() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_e_t_u_p_P_r_o_x_i_m_i_t_y_L_i_g_h_t │ │ │ │ -virtual void setupProximityLight() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_u_p_d_a_t_e_S_e_l_e_c_t_i_o_n │ │ │ │ -virtual void updateSelection() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_m_o_v_e_I_t_e_m_s │ │ │ │ -void moveItems(const TransformationMessage &msg) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_c_o_n_t_e_x_t___r_e_p_r_e_s_e_n_t_a_t_i_o_n__ │ │ │ │ -Representation * context_representation_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_3_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_c_h_e_c_k_M_e_n_u │ │ │ │ -virtual void checkMenu(MainControl &main_control) │ │ │ │ -Overloaded from ModularWidget. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e_Z │ │ │ │ -virtual void setClippingPlaneZ() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_r_e_m_o_v_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -virtual void removeRepresentation(Representation &rep) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_g_e_n_e_r_a_t_e_L_i_s_t_V_i_e_w_I_t_e_m__ │ │ │ │ -virtual void generateListViewItem_(Representation &rep) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_i_t_e_m___t_o___r_e_p_r_e_s_e_n_t_a_t_i_o_n__ │ │ │ │ -HashMap< QTreeWidgetItem *, Representation * > item_to_representation_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_3_9 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_c_o_n_t_e_x_t___m_e_n_u__ │ │ │ │ -QMenu context_menu_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_3_1 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_h_o_w_G_u_e_s_t_C_o_n_t_e_x_t_M_e_n_u │ │ │ │ -void showGuestContextMenu(const QPoint &pos) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_e_l_e_c_t_C_l_i_p_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s │ │ │ │ -virtual void selectClipRepresentations() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_e_l_e_c_t_A_t_o_m_s │ │ │ │ -virtual void selectAtoms() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_f_l_i_p_C_l_i_p_p_i_n_g_P_l_a_n_e │ │ │ │ -virtual void flipClippingPlane() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_i_g_n_o_r_e___c_h_a_n_g_e__ │ │ │ │ -bool ignore_change_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_4_5 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_f_l_i_p_C_l_i_p_p_i_n_g_C_a_p_p_i_n_g │ │ │ │ -virtual void flipClippingCapping() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_d_u_p_l_i_c_a_t_e │ │ │ │ -void duplicate() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_e_n_t_e_r_M_o_v_e_M_o_d_e │ │ │ │ -virtual void enterMoveMode() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_o_n_I_t_e_m_C_l_i_c_k_e_d │ │ │ │ -virtual void onItemClicked(QTreeWidgetItem *item, int col) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_a_d_d_I_t_e_m__ │ │ │ │ -void addItem_(const String &text, const char *member, QWidget *widget=0) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_c_l_i_p_p_i_n_g___p_l_a_n_e___c_o_n_t_e_x_t___m_e_n_u__ │ │ │ │ -QMenu clipping_plane_context_menu_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_3_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_e_l_e_c_t_e_d_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -virtual void selectedRepresentation(Representation &representation, bool state) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_p_l_a_n_e___t_o___i_t_e_m__ │ │ │ │ -HashMap< ClippingPlane *, QTreeWidgetItem * > plane_to_item_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_3_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_c_r_e_a_t_i_n_g___r_e_p_r_e_s_e_n_t_a_t_i_o_n_s__ │ │ │ │ -bool creating_representations_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_4_4 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_c_o_n_t_e_x_t___m_e_n_u___a_c_t_i_o_n_s__ │ │ │ │ -vector< QAction * > context_menu_actions_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_4_8 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_d_e_l_e_t_e_C_u_r_r_e_n_t_I_t_e_m_s │ │ │ │ -virtual void deleteCurrentItems() │ │ │ │ -Overloaded from GenericControl. │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l │ │ │ │ -GeometricControl(const GeometricControl &control) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_m_o_d_i_f_y___r_e_p___d_i_a_l_o_g__ │ │ │ │ -ModifyRepresentationDialog * modify_rep_dialog_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_4_2 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_f_o_c_u_s │ │ │ │ -virtual void focus() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_l_o_a_d_S_u_r_f_a_c_e │ │ │ │ -void loadSurface() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_m_o_d_i_f_y_R_e_p_r_e_s_e_n_t_a_t_i_o_n__ │ │ │ │ -virtual void modifyRepresentation_() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_m_e_n_u___c_l_i_p_p_i_n_g___p_l_a_n_e__ │ │ │ │ -QAction * menu_clipping_plane_ │ │ │ │ -DDeeffiinniittiioonn _g_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_._h_:_2_4_7 │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_c_r_e_a_t_e_N_e_w_C_l_i_p_p_i_n_g_P_l_a_n_e │ │ │ │ -void createNewClippingPlane() │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_s_e_t_C_l_i_p_p_i_n_g_P_l_a_n_e__ │ │ │ │ -void setClippingPlane_(const Vector3 &n) │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_g_e_t_H_i_g_h_l_i_g_h_t_e_d_R_e_p_r_e_s_e_n_t_a_t_i_o_n_s │ │ │ │ -std::list< Representation * > getHighlightedRepresentations() const │ │ │ │ -_B_A_L_L_:_:_V_I_E_W_:_:_G_e_o_m_e_t_r_i_c_C_o_n_t_r_o_l_:_:_u_p_d_a_t_e_R_e_p_r_e_s_e_n_t_a_t_i_o_n │ │ │ │ -virtual void updateRepresentation(Representation &rep, bool force=false) │ │ │ │ -_Q_W_i_d_g_e_t │ │ │ │ -_Q_T_r_e_e_W_i_d_g_e_t_I_t_e_m │ │ │ │ -_c_o_m_m_o_n_._h │ │ │ │ -_B_A_L_L___V_I_E_W___E_X_P_O_R_T │ │ │ │ -#define BALL_VIEW_EXPORT │ │ │ │ -DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_2 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_4_2 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ +const BindingPocketProcessor & operator=(const BindingPocketProcessor &pp) │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r │ │ │ │ +BindingPocketProcessor() │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_o_p_e_r_a_t_o_r_<_< │ │ │ │ +friend std::ostream & operator<<(std::ostream &os, const │ │ │ │ +BindingPocketProcessor::Sphere_ &) │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_2_2_5 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_g_e_t_A_c_t_i_v_e_S_i_t_e_P_o_i_n_t_s │ │ │ │ +const vector< std::pair< Vector3, double > > & getActiveSitePoints() const │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_f_i_n_i_s_h │ │ │ │ +virtual bool finish() │ │ │ │ +Finish . │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r │ │ │ │ +BindingPocketProcessor(const BindingPocketProcessor &pp) │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_o_p_t_i_o_n_s │ │ │ │ +Options options │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_5_1 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r │ │ │ │ +BindingPocketProcessor(Options &new_options) │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_~_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r │ │ │ │ +virtual ~BindingPocketProcessor() │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_g_e_t_L_a_y_e_r_s │ │ │ │ +const vector< vector< std::pair< Vector3, double > > > & getLayers() const │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_4_9 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_I_N_I___F_I_L_E___N_A_M_E │ │ │ │ +static const String INI_FILE_NAME │ │ │ │ +name of the ini-file │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_5_5 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_R_A_D_I_U_S___N_I_T_R_O_G_E_N │ │ │ │ +static const String RADIUS_NITROGEN │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_6_0 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_R_O_B_E___S_P_H_E_R_E___R_A_D_I_U_S___H_Y_D_R_O_G_E_N___F_R_E_E │ │ │ │ +static const String PROBE_SPHERE_RADIUS_HYDROGEN_FREE │ │ │ │ +probe sphere radius for heavy atoms only │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_6_7 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_R_O_B_E___S_P_H_E_R_E___R_A_D_I_U_S │ │ │ │ +static const String PROBE_SPHERE_RADIUS │ │ │ │ +probe sphere radius for computation with hydrogen atoms │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_6_5 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_B_U_R_I_A_L___C_O_U_N_T___T_H_R_E_S_H_O_L_D │ │ │ │ +static const String BURIAL_COUNT_THRESHOLD │ │ │ │ +burial count threshold for computation with hydrogen atoms │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_7_1 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_W___S_Q_U_A_R_E___W_E_L_L │ │ │ │ +static const String PW_SQUARE_WELL │ │ │ │ +options for the computation of the probe weight │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_7_7 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_R_A_D_I_U_S___C_A_R_B_O_N │ │ │ │ +static const String RADIUS_CARBON │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_6_1 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_B_U_R_I_A_L___C_O_U_N_T___R_A_D_I_U_S │ │ │ │ +static const String BURIAL_COUNT_RADIUS │ │ │ │ +radius for the computation of the burial count │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_7_5 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_W___G_A_U_S_S_I_A_N___W_I_D_T_H │ │ │ │ +static const String PW_GAUSSIAN_WIDTH │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_7_8 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_B_U_R_I_A_L___C_O_U_N_T___T_H_R_E_S_H_O_L_D___H_Y_D_R_O_G_E_N___F_R_E_E │ │ │ │ +static const String BURIAL_COUNT_THRESHOLD_HYDROGEN_FREE │ │ │ │ +burial count threshold for heavy atoms only │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_7_3 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_R_A_D_I_U_S___H_Y_D_R_O_G_E_N │ │ │ │ +static const String RADIUS_HYDROGEN │ │ │ │ +atom radius of individual elements │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_5_8 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_R_O_B_E___L_A_Y_E_R___R_A_D_I_U_S │ │ │ │ +static const String PROBE_LAYER_RADIUS │ │ │ │ +probe radius for colision of probes in one layer │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_6_9 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_W___M_A_X___D_I_S_T_A_N_C_E │ │ │ │ +static const String PW_MAX_DISTANCE │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_7_9 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_M_A_X___A_S_P_S │ │ │ │ +static const String MAX_ASPS │ │ │ │ +maximum number of active site points │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_8_1 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_C_L_A_S_H___F_A_C_T_O_R │ │ │ │ +static const String CLASH_FACTOR │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_8_3 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_R_A_D_I_U_S___S_U_L_F_U_R │ │ │ │ +static const String RADIUS_SULFUR │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_6_2 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_R_A_D_I_U_S___O_X_Y_G_E_N │ │ │ │ +static const String RADIUS_OXYGEN │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_5_9 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_P_A_R_S_E___I_N_I___F_I_L_E │ │ │ │ +static const String PARSE_INI_FILE │ │ │ │ +try to parse ini-file │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_5_3 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_H_E_A_V_Y___O_N_L_Y │ │ │ │ +static const String HEAVY_ONLY │ │ │ │ +use only heavy atoms for computation │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_5_1 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_O_p_t_i_o_n_:_:_A_S_P___S_E_P_E_R_A_T_I_O_N │ │ │ │ +static const String ASP_SEPERATION │ │ │ │ +minumum distance between two active site points │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_8_5 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_9_1 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_W___M_A_X___D_I_S_T_A_N_C_E │ │ │ │ +static const double PW_MAX_DISTANCE │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_1_0 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_M_A_X___A_S_P_S │ │ │ │ +static const Position MAX_ASPS │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_1_1 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_R_O_B_E___S_P_H_E_R_E___R_A_D_I_U_S │ │ │ │ +static const double PROBE_SPHERE_RADIUS │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_0_2 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_R_A_D_I_U_S___O_X_Y_G_E_N │ │ │ │ +static const double RADIUS_OXYGEN │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_9_7 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_B_U_R_I_A_L___C_O_U_N_T___T_H_R_E_S_H_O_L_D___H_Y_D_R_O_G_E_N___F_R_E_E │ │ │ │ +static const Position BURIAL_COUNT_THRESHOLD_HYDROGEN_FREE │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_0_6 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_R_A_D_I_U_S___N_I_T_R_O_G_E_N │ │ │ │ +static const double RADIUS_NITROGEN │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_9_8 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_C_L_A_S_H___F_A_C_T_O_R │ │ │ │ +static const double CLASH_FACTOR │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_1_2 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_I_N_I___F_I_L_E___N_A_M_E │ │ │ │ +static const String INI_FILE_NAME │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_9_4 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_A_R_S_E___I_N_I___F_I_L_E │ │ │ │ +static const bool PARSE_INI_FILE │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_9_3 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_A_S_P___S_E_P_E_R_A_T_I_O_N │ │ │ │ +static const double ASP_SEPERATION │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_1_3 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_B_U_R_I_A_L___C_O_U_N_T___T_H_R_E_S_H_O_L_D │ │ │ │ +static const Position BURIAL_COUNT_THRESHOLD │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_0_5 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_R_O_B_E___L_A_Y_E_R___R_A_D_I_U_S │ │ │ │ +static const double PROBE_LAYER_RADIUS │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_0_4 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_R_A_D_I_U_S___C_A_R_B_O_N │ │ │ │ +static const double RADIUS_CARBON │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_9_9 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_R_A_D_I_U_S___S_U_L_F_U_R │ │ │ │ +static const double RADIUS_SULFUR │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_0_0 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_W___G_A_U_S_S_I_A_N___W_I_D_T_H │ │ │ │ +static const double PW_GAUSSIAN_WIDTH │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_0_9 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_W___S_Q_U_A_R_E___W_E_L_L │ │ │ │ +static const double PW_SQUARE_WELL │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_0_8 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_B_U_R_I_A_L___C_O_U_N_T___R_A_D_I_U_S │ │ │ │ +static const double BURIAL_COUNT_RADIUS │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_0_7 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_R_A_D_I_U_S___H_Y_D_R_O_G_E_N │ │ │ │ +static const double RADIUS_HYDROGEN │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_9_6 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_H_E_A_V_Y___O_N_L_Y │ │ │ │ +static const bool HEAVY_ONLY │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_9_2 │ │ │ │ +_B_A_L_L_:_:_B_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_:_:_D_e_f_a_u_l_t_:_:_P_R_O_B_E___S_P_H_E_R_E___R_A_D_I_U_S___H_Y_D_R_O_G_E_N___F_R_E_E │ │ │ │ +static const double PROBE_SPHERE_RADIUS_HYDROGEN_FREE │ │ │ │ +DDeeffiinniittiioonn _b_i_n_d_i_n_g_P_o_c_k_e_t_P_r_o_c_e_s_s_o_r_._h_:_1_0_3 │ │ │ │ +_B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ +_B_A_L_L___E_X_P_O_R_T │ │ │ │ +#define BALL_EXPORT │ │ │ │ +DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ +_s_y_s_t_e_m_._h │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d44/a03074.html │ │ │ @@ -77,15 +77,15 @@ │ │ │ Public Member Functions | │ │ │ Protected Attributes | │ │ │ List of all members
    │ │ │
    BALL::Exception::InvalidSize Class Reference
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/COMMON/exception.h>

    │ │ │ +

    #include <BALL/COMMON/exception.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::Exception::InvalidSize:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::Exception::GeneralException │ │ │ @@ -146,15 +146,15 @@ │ │ │

    Invalid Size Throw this exception to indicate that a size was unexpected. The constructor has an additional argument: the value of of the requested size.

    Parameters
    │ │ │ │ │ │ │ │ │
    sizethe size causing the problem
    │ │ │
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    Definition at line 201 of file COMMON/exception.h.

    │ │ │ +

    Definition at line 201 of file COMMON/exception.h.

    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ InvalidSize()

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │ @@ -203,15 +203,15 @@ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ protected
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    Definition at line 209 of file COMMON/exception.h.

    │ │ │ +

    Definition at line 209 of file COMMON/exception.h.

    │ │ │ │ │ │
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    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d46/a01739.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: bruker2DFile.h File Reference │ │ │ +BALL: conjugateGradient.h File Reference │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -65,32 +65,36 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
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    │ │ │ Classes | │ │ │ Namespaces
    │ │ │ -
    bruker2DFile.h File Reference
    │ │ │ +
    conjugateGradient.h File Reference
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    │ │ │
    │ │ │ -
    #include <BALL/FORMAT/JCAMPFile.h>
    │ │ │ -#include <BALL/DATATYPE/regularData2D.h>
    │ │ │ +
    #include <BALL/MOLMEC/MINIMIZATION/energyMinimizer.h>
    │ │ │ +#include <BALL/MOLMEC/MINIMIZATION/lineSearch.h>
    │ │ │
    │ │ │

    Go to the source code of this file.

    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │

    │ │ │ Classes

    class  BALL::Bruker2DFile
    class  BALL::ConjugateGradientMinimizer
     
    struct  BALL::ConjugateGradientMinimizer::Option
     
    struct  BALL::ConjugateGradientMinimizer::Default
     
    │ │ │ │ │ │ │ │ │ │ │ │

    │ │ │ Namespaces

    namespace  BALL
     
    │ │ │ ├── html2text {} │ │ │ │ @@ -1,20 +1,25 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _F_O_R_M_A_T │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _M_I_N_I_M_I_Z_A_T_I_O_N │ │ │ │ _C_l_a_s_s_e_s | _N_a_m_e_s_p_a_c_e_s │ │ │ │ -bruker2DFile.h File Reference │ │ │ │ -#include <_B_A_L_L_/_F_O_R_M_A_T_/_J_C_A_M_P_F_i_l_e_._h> │ │ │ │ -#include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_r_e_g_u_l_a_r_D_a_t_a_2_D_._h> │ │ │ │ +conjugateGradient.h File Reference │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h> │ │ │ │ +#include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_l_i_n_e_S_e_a_r_c_h_._h> │ │ │ │ _G_o_ _t_o_ _t_h_e_ _s_o_u_r_c_e_ _c_o_d_e_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ CCllaasssseess │ │ │ │ -class   _B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e │ │ │ │ + class   _B_A_L_L_:_:_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n │ │ │ │ +  │ │ │ │ +struct   _B_A_L_L_:_:_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t │ │ │ │   │ │ │ │ NNaammeessppaacceess │ │ │ │ namespace   _B_A_L_L │ │ │ │   │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d46/a01739_source.html │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ -BALL: bruker2DFile.h Source File │ │ │ +BALL: conjugateGradient.h Source File │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -70,132 +70,175 @@ │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ -
    bruker2DFile.h
    │ │ │ +
    conjugateGradient.h
    │ │ │
    │ │ │
    │ │ │ Go to the documentation of this file.
    1// -*- Mode: C++; tab-width: 2; -*-
    │ │ │
    2// vi: set ts=2:
    │ │ │
    3//
    │ │ │ -
    4
    │ │ │ -
    5#ifndef BALL_FORMAT_BRUKER2DFILE_H
    │ │ │ -
    6#define BALL_FORMAT_BRUKER2DFILE_H
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    7
    │ │ │ -
    8#ifndef BALL_FORMAT_JCAMPFILE_H
    │ │ │ -
    9# include <BALL/FORMAT/JCAMPFile.h>
    │ │ │ -
    10#endif
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    11
    │ │ │ -
    12#ifndef BALL_DATATYPE_REGULARDATA2D_H
    │ │ │ -
    13# include <BALL/DATATYPE/regularData2D.h>
    │ │ │ -
    14#endif
    │ │ │ -
    15
    │ │ │ -
    16namespace BALL
    │ │ │ -
    17{
    │ │ │ -
    │ │ │ -
    24 class BALL_EXPORT Bruker2DFile
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    25 : public File
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    26 {
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    27 public:
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    28
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    31 Bruker2DFile();
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    32
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    37 Bruker2DFile(const String& name, OpenMode open_mode = std::ios::in | std::ios::binary);
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    38
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    41 virtual ~Bruker2DFile();
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    42
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    46 void read();
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    47
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    51 void read(const String &name);
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    52
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    54 const RegularData2D& getData() const { return spectrum_; }
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    56 RegularData2D& getData() { return spectrum_; }
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    57
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    60 std::list<std::pair<int, int> > getPeakList() const;
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    61
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    64 std::pair<double, double> getShift(Position x, Position y);
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    65
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    68 std::pair<Position, Position> getPosition(double x, double y);
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    69
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    72 void setShiftRange(double offsetf1, double offsetf2, double swidthf1, double swidthf2,
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    73 double bfreqf1, double bfreqf2, double spointnumf1, double spointnumf2);
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    74
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    75 private:
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    76 const Bruker2DFile& operator = (const Bruker2DFile& file);
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    77
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    78 protected:
    │ │ │ -
    80 JCAMPFile parsf1_;
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    81 JCAMPFile parsf2_;
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    82
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    83 Size minx_;
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    84 Size maxx_;
    │ │ │ -
    85 Size miny_;
    │ │ │ -
    86 Size maxy_;
    │ │ │ -
    87
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    88 // To be replaced by regularData2D
    │ │ │ -
    89 RegularData2D dat_;
    │ │ │ -
    90 double soffsetf1_;
    │ │ │ -
    91 double soffsetf2_;
    │ │ │ -
    92 double swidthf1_;
    │ │ │ -
    93 double swidthf2_;
    │ │ │ -
    94 double bfreqf1_;
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    95 double bfreqf2_;
    │ │ │ -
    96 Size spointnumf1_;
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    97 Size spointnumf2_;
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    98 RegularData2D spectrum_;
    │ │ │ -
    99 };
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    │ │ │ -
    100}
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    101
    │ │ │ -
    102#endif
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Bruker2DFile::getData
    const RegularData2D & getData() const
    Return a reference to the spectrum.
    Definition bruker2DFile.h:54
    │ │ │ -
    BALL::Bruker2DFile::read
    void read(const String &name)
    │ │ │ - │ │ │ -
    BALL::Bruker2DFile::Bruker2DFile
    Bruker2DFile(const String &name, OpenMode open_mode=std::ios::in|std::ios::binary)
    │ │ │ - │ │ │ -
    BALL::Bruker2DFile::setShiftRange
    void setShiftRange(double offsetf1, double offsetf2, double swidthf1, double swidthf2, double bfreqf1, double bfreqf2, double spointnumf1, double spointnumf2)
    │ │ │ -
    BALL::Bruker2DFile::getData
    RegularData2D & getData()
    Definition bruker2DFile.h:56
    │ │ │ -
    BALL::Bruker2DFile::getShift
    std::pair< double, double > getShift(Position x, Position y)
    │ │ │ - │ │ │ -
    BALL::Bruker2DFile::~Bruker2DFile
    virtual ~Bruker2DFile()
    │ │ │ -
    BALL::Bruker2DFile::parsf1_
    JCAMPFile parsf1_
    These classes give access to the parameters used in aqcuiring the spectrum.
    Definition bruker2DFile.h:80
    │ │ │ -
    BALL::Bruker2DFile::dat_
    RegularData2D dat_
    Definition bruker2DFile.h:89
    │ │ │ - │ │ │ - │ │ │ -
    BALL::Bruker2DFile::getPosition
    std::pair< Position, Position > getPosition(double x, double y)
    │ │ │ - │ │ │ -
    BALL::Bruker2DFile::getPeakList
    std::list< std::pair< int, int > > getPeakList() const
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::Bruker2DFile::spectrum_
    RegularData2D spectrum_
    Definition bruker2DFile.h:98
    │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
    BALL::File::OpenMode
    std::ios::openmode OpenMode
    Definition file.h:165
    │ │ │ +
    4// $Id: conjugateGradient.h,v 1.29.20.6 2007/08/07 09:12:33 aleru Exp $
    │ │ │ +
    5//
    │ │ │ +
    6
    │ │ │ +
    7#ifndef BALL_MOLMEC_MINIMIZATION_CONJUGATEGRADIENT_H
    │ │ │ +
    8#define BALL_MOLMEC_MINIMIZATION_CONJUGATEGRADIENT_H
    │ │ │ +
    9
    │ │ │ +
    10#ifndef BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H
    │ │ │ +
    11# include <BALL/MOLMEC/MINIMIZATION/energyMinimizer.h>
    │ │ │ +
    12#endif
    │ │ │ +
    13
    │ │ │ +
    14#ifndef BALL_MOLMEC_MINIMIZATION_LINESEARCH_H
    │ │ │ +
    15# include <BALL/MOLMEC/MINIMIZATION/lineSearch.h>
    │ │ │ +
    16#endif
    │ │ │ +
    17
    │ │ │ +
    18namespace BALL
    │ │ │ +
    19{
    │ │ │ +
    │ │ │ +
    40 class BALL_EXPORT ConjugateGradientMinimizer
    │ │ │ +
    41 : public EnergyMinimizer
    │ │ │ +
    42 {
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    43 public:
    │ │ │ +
    44
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    48
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    │ │ │ +
    52 enum UpdateMethod
    │ │ │ +
    53 {
    │ │ │ +
    56 POLAK_RIBIERE = 1,
    │ │ │ +
    57
    │ │ │ +
    60 FLETCHER_REEVES = 2,
    │ │ │ +
    61
    │ │ │ +
    64 SHANNO = 3
    │ │ │ +
    65 };
    │ │ │ +
    │ │ │ +
    66
    │ │ │ +
    68
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    71
    │ │ │ +
    │ │ │ +
    74 struct Option
    │ │ │ +
    75 {
    │ │ │ +
    78 static const char* UPDATE_METHOD;
    │ │ │ +
    79 };
    │ │ │ +
    │ │ │ +
    80
    │ │ │ +
    │ │ │ +
    83 struct BALL_EXPORT Default
    │ │ │ +
    84 {
    │ │ │ +
    87 static const Size UPDATE_METHOD;
    │ │ │ +
    88 };
    │ │ │ +
    │ │ │ +
    89
    │ │ │ +
    91
    │ │ │ +
    94
    │ │ │ +
    95 BALL_CREATE(ConjugateGradientMinimizer)
    │ │ │ +
    96
    │ │ │ +
    97
    │ │ │ +
    99 ConjugateGradientMinimizer();
    │ │ │ +
    100
    │ │ │ +
    103 ConjugateGradientMinimizer(ForceField& force_field);
    │ │ │ +
    104
    │ │ │ +
    107 ConjugateGradientMinimizer(ForceField& force_field,SnapShotManager *ssm);
    │ │ │ +
    108
    │ │ │ +
    111 ConjugateGradientMinimizer(ForceField& force_field,
    │ │ │ +
    112 SnapShotManager* ssm, const Options& options);
    │ │ │ +
    113
    │ │ │ +
    116 ConjugateGradientMinimizer(ForceField& force_field, const Options& options);
    │ │ │ +
    117
    │ │ │ +
    120 ConjugateGradientMinimizer(const ConjugateGradientMinimizer& rhs);
    │ │ │ +
    121
    │ │ │ +
    124 virtual ~ConjugateGradientMinimizer();
    │ │ │ +
    125
    │ │ │ +
    127
    │ │ │ +
    130
    │ │ │ +
    133 const ConjugateGradientMinimizer& operator = (const ConjugateGradientMinimizer& rhs);
    │ │ │ +
    134
    │ │ │ +
    136
    │ │ │ +
    139
    │ │ │ +
    142 virtual bool specificSetup();
    │ │ │ +
    143
    │ │ │ +
    145
    │ │ │ +
    148
    │ │ │ +
    152 void setUpdateMethod(UpdateMethod method);
    │ │ │ +
    153
    │ │ │ +
    156 UpdateMethod getUpdateMethod() const;
    │ │ │ +
    157
    │ │ │ +
    164 virtual double findStep();
    │ │ │ +
    165
    │ │ │ +
    171 virtual void updateDirection();
    │ │ │ +
    172
    │ │ │ +
    181 virtual bool minimize(Size iterations = 0, bool resume = false);
    │ │ │ +
    182
    │ │ │ +
    183 protected:
    │ │ │ +
    184
    │ │ │ +
    186
    │ │ │ +
    189
    │ │ │ +
    192 LineSearch line_search_;
    │ │ │ +
    193
    │ │ │ +
    196 Gradient unscaled_direction_;
    │ │ │ +
    197
    │ │ │ +
    200 Size number_of_atoms_;
    │ │ │ +
    201
    │ │ │ +
    204 Size updt_method_;
    │ │ │ +
    205
    │ │ │ +
    208 bool first_iter_;
    │ │ │ +
    209
    │ │ │ +
    212 double old_gtg_;
    │ │ │ +
    213
    │ │ │ +
    216 vector<Vector3> a_i_;
    │ │ │ +
    217
    │ │ │ +
    220 vector<Vector3> b_i_;
    │ │ │ +
    221
    │ │ │ +
    224 vector<Vector3> p_t_;
    │ │ │ +
    225
    │ │ │ +
    228 vector<Vector3> y_t_;
    │ │ │ +
    229
    │ │ │ +
    232 vector<Vector3> p_i_;
    │ │ │ +
    233
    │ │ │ +
    236 vector<Vector3> y_i_;
    │ │ │ +
    237
    │ │ │ +
    240 double D_1_;
    │ │ │ +
    241
    │ │ │ +
    244 double D_4_;
    │ │ │ +
    245
    │ │ │ +
    248 Size restart_frequency_;
    │ │ │ +
    249
    │ │ │ +
    255 Size last_restart_iter_;
    │ │ │ +
    256
    │ │ │ +
    258
    │ │ │ +
    259 };
    │ │ │ +
    │ │ │ +
    260} // end of namespace BALL
    │ │ │ +
    261
    │ │ │ +
    262#endif // BALL_MOLMEC_MINIMIZATION_CONJUGATEGRADIENT_H
    │ │ │ + │ │ │ + │ │ │ +
    BALL_CREATE
    #define BALL_CREATE(name)
    Definition create.h:62
    │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │ -
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │ +
    BALL_EXPORT
    #define BALL_EXPORT
    Definition COMMON/global.h:50
    │ │ │
    │ │ │ │ │ │
    │ │ │ Generated by doxygen 1.9.8 │ │ │
    │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,181 +1,180 @@ │ │ │ │ BALL 1.5.0 │ │ │ │ Loading... │ │ │ │ Searching... │ │ │ │ No Matches │ │ │ │ * _i_n_c_l_u_d_e │ │ │ │ * _B_A_L_L │ │ │ │ - * _F_O_R_M_A_T │ │ │ │ -bruker2DFile.h │ │ │ │ + * _M_O_L_M_E_C │ │ │ │ + * _M_I_N_I_M_I_Z_A_T_I_O_N │ │ │ │ +conjugateGradient.h │ │ │ │ _G_o_ _t_o_ _t_h_e_ _d_o_c_u_m_e_n_t_a_t_i_o_n_ _o_f_ _t_h_i_s_ _f_i_l_e_. │ │ │ │ 1// -*- Mode: C++; tab-width: 2; -*- │ │ │ │ 2// vi: set ts=2: │ │ │ │ 3// │ │ │ │ -4 │ │ │ │ -5#ifndef BALL_FORMAT_BRUKER2DFILE_H │ │ │ │ -6#define BALL_FORMAT_BRUKER2DFILE_H │ │ │ │ -7 │ │ │ │ -8#ifndef BALL_FORMAT_JCAMPFILE_H │ │ │ │ -9# include <_B_A_L_L_/_F_O_R_M_A_T_/_J_C_A_M_P_F_i_l_e_._h> │ │ │ │ -10#endif │ │ │ │ -11 │ │ │ │ -12#ifndef BALL_DATATYPE_REGULARDATA2D_H │ │ │ │ -13# include <_B_A_L_L_/_D_A_T_A_T_Y_P_E_/_r_e_g_u_l_a_r_D_a_t_a_2_D_._h> │ │ │ │ -14#endif │ │ │ │ -15 │ │ │ │ -16namespace _B_A_L_L │ │ │ │ -17{ │ │ │ │ -_2_4 class _B_A_L_L___E_X_P_O_R_T _B_r_u_k_e_r_2_D_F_i_l_e │ │ │ │ -25 : public _F_i_l_e │ │ │ │ -26 { │ │ │ │ -27 public: │ │ │ │ -28 │ │ │ │ -_3_1 _B_r_u_k_e_r_2_D_F_i_l_e(); │ │ │ │ -32 │ │ │ │ -_3_7 _B_r_u_k_e_r_2_D_F_i_l_e(const _S_t_r_i_n_g& name, _O_p_e_n_M_o_d_e open_mode = std::ios::in | std:: │ │ │ │ -ios::binary); │ │ │ │ -38 │ │ │ │ -_4_1 virtual _~_B_r_u_k_e_r_2_D_F_i_l_e(); │ │ │ │ -42 │ │ │ │ -_4_6 void _r_e_a_d(); │ │ │ │ -47 │ │ │ │ -_5_1 void _r_e_a_d(const _S_t_r_i_n_g &name); │ │ │ │ -52 │ │ │ │ -_5_4 const _R_e_g_u_l_a_r_D_a_t_a_2_D& _g_e_t_D_a_t_a() const { return spectrum_; } │ │ │ │ -_5_6 _R_e_g_u_l_a_r_D_a_t_a_2_D& _g_e_t_D_a_t_a() { return spectrum_; } │ │ │ │ +4// $Id: conjugateGradient.h,v 1.29.20.6 2007/08/07 09:12:33 aleru Exp $ │ │ │ │ +5// │ │ │ │ +6 │ │ │ │ +7#ifndef BALL_MOLMEC_MINIMIZATION_CONJUGATEGRADIENT_H │ │ │ │ +8#define BALL_MOLMEC_MINIMIZATION_CONJUGATEGRADIENT_H │ │ │ │ +9 │ │ │ │ +10#ifndef BALL_MOLMEC_MINIMIZATION_ENERGYMINIMIZER_H │ │ │ │ +11# include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h> │ │ │ │ +12#endif │ │ │ │ +13 │ │ │ │ +14#ifndef BALL_MOLMEC_MINIMIZATION_LINESEARCH_H │ │ │ │ +15# include <_B_A_L_L_/_M_O_L_M_E_C_/_M_I_N_I_M_I_Z_A_T_I_O_N_/_l_i_n_e_S_e_a_r_c_h_._h> │ │ │ │ +16#endif │ │ │ │ +17 │ │ │ │ +18namespace _B_A_L_L │ │ │ │ +19{ │ │ │ │ +_4_0 class _B_A_L_L___E_X_P_O_R_T _C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r │ │ │ │ +41 : public _E_n_e_r_g_y_M_i_n_i_m_i_z_e_r │ │ │ │ +42 { │ │ │ │ +43 public: │ │ │ │ +44 │ │ │ │ +48 │ │ │ │ +_5_2 enum _U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ +53 { │ │ │ │ +_5_6 POLAK_RIBIERE = 1, │ │ │ │ 57 │ │ │ │ -_6_0 std::list > _g_e_t_P_e_a_k_L_i_s_t() const; │ │ │ │ +_6_0 FLETCHER_REEVES = 2, │ │ │ │ 61 │ │ │ │ -_6_4 std::pair _g_e_t_S_h_i_f_t(_P_o_s_i_t_i_o_n x, _P_o_s_i_t_i_o_n y); │ │ │ │ -65 │ │ │ │ -_6_8 std::pair _g_e_t_P_o_s_i_t_i_o_n(double x, double y); │ │ │ │ -69 │ │ │ │ -_7_2 void _s_e_t_S_h_i_f_t_R_a_n_g_e(double offsetf1, double offsetf2, double swidthf1, double │ │ │ │ -swidthf2, │ │ │ │ -73 double bfreqf1, double bfreqf2, double spointnumf1, double spointnumf2); │ │ │ │ -74 │ │ │ │ -75 private: │ │ │ │ -76 const _B_r_u_k_e_r_2_D_F_i_l_e& operator = (const _B_r_u_k_e_r_2_D_F_i_l_e& file); │ │ │ │ -77 │ │ │ │ -78 protected: │ │ │ │ -_8_0 _J_C_A_M_P_F_i_l_e _p_a_r_s_f_1__; │ │ │ │ -_8_1 _J_C_A_M_P_F_i_l_e _p_a_r_s_f_2__; │ │ │ │ -82 │ │ │ │ -_8_3 _S_i_z_e _m_i_n_x__; │ │ │ │ -_8_4 _S_i_z_e _m_a_x_x__; │ │ │ │ -_8_5 _S_i_z_e _m_i_n_y__; │ │ │ │ -_8_6 _S_i_z_e _m_a_x_y__; │ │ │ │ -87 │ │ │ │ -88 // To be replaced by regularData2D │ │ │ │ -_8_9 _R_e_g_u_l_a_r_D_a_t_a_2_D _d_a_t__; │ │ │ │ -_9_0 double _s_o_f_f_s_e_t_f_1__; │ │ │ │ -_9_1 double _s_o_f_f_s_e_t_f_2__; │ │ │ │ -_9_2 double _s_w_i_d_t_h_f_1__; │ │ │ │ -_9_3 double _s_w_i_d_t_h_f_2__; │ │ │ │ -_9_4 double _b_f_r_e_q_f_1__; │ │ │ │ -_9_5 double _b_f_r_e_q_f_2__; │ │ │ │ -_9_6 _S_i_z_e _s_p_o_i_n_t_n_u_m_f_1__; │ │ │ │ -_9_7 _S_i_z_e _s_p_o_i_n_t_n_u_m_f_2__; │ │ │ │ -_9_8 _R_e_g_u_l_a_r_D_a_t_a_2_D _s_p_e_c_t_r_u_m__; │ │ │ │ -99 }; │ │ │ │ -100} │ │ │ │ -101 │ │ │ │ -102#endif │ │ │ │ -_J_C_A_M_P_F_i_l_e_._h │ │ │ │ -_r_e_g_u_l_a_r_D_a_t_a_2_D_._h │ │ │ │ +64 SHANNO = 3 │ │ │ │ +_6_5 }; │ │ │ │ +66 │ │ │ │ +68 │ │ │ │ +71 │ │ │ │ +_7_4 struct _O_p_t_i_o_n │ │ │ │ +75 { │ │ │ │ +_7_8 static const char* _U_P_D_A_T_E___M_E_T_H_O_D; │ │ │ │ +79 }; │ │ │ │ +80 │ │ │ │ +_8_3 struct _B_A_L_L___E_X_P_O_R_T _D_e_f_a_u_l_t │ │ │ │ +84 { │ │ │ │ +_8_7 static const _S_i_z_e _U_P_D_A_T_E___M_E_T_H_O_D; │ │ │ │ +88 }; │ │ │ │ +89 │ │ │ │ +91 │ │ │ │ +94 │ │ │ │ +95 _B_A_L_L___C_R_E_A_T_E(_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r) │ │ │ │ +96 │ │ │ │ +97 │ │ │ │ +_9_9 _C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r(); │ │ │ │ +100 │ │ │ │ +_1_0_3 _C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field); │ │ │ │ +104 │ │ │ │ +_1_0_7 _C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field,_S_n_a_p_S_h_o_t_M_a_n_a_g_e_r *ssm); │ │ │ │ +108 │ │ │ │ +_1_1_1 _C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field, │ │ │ │ +112 _S_n_a_p_S_h_o_t_M_a_n_a_g_e_r* ssm, const _O_p_t_i_o_n_s& options); │ │ │ │ +113 │ │ │ │ +_1_1_6 _C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r(_F_o_r_c_e_F_i_e_l_d& force_field, const _O_p_t_i_o_n_s& │ │ │ │ +options); │ │ │ │ +117 │ │ │ │ +_1_2_0 _C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r(const _C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r& rhs); │ │ │ │ +121 │ │ │ │ +_1_2_4 virtual ~_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r(); │ │ │ │ +125 │ │ │ │ +127 │ │ │ │ +130 │ │ │ │ +_1_3_3 const _C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r& operator = (const │ │ │ │ +_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r& rhs); │ │ │ │ +134 │ │ │ │ +136 │ │ │ │ +139 │ │ │ │ +_1_4_2 virtual bool specificSetup(); │ │ │ │ +143 │ │ │ │ +145 │ │ │ │ +148 │ │ │ │ +_1_5_2 void setUpdateMethod(_U_p_d_a_t_e_M_e_t_h_o_d method); │ │ │ │ +153 │ │ │ │ +_1_5_6 _U_p_d_a_t_e_M_e_t_h_o_d getUpdateMethod() const; │ │ │ │ +157 │ │ │ │ +_1_6_4 virtual double findStep(); │ │ │ │ +165 │ │ │ │ +_1_7_1 virtual void updateDirection(); │ │ │ │ +172 │ │ │ │ +_1_8_1 virtual bool minimize(_S_i_z_e iterations = 0, bool resume = false); │ │ │ │ +182 │ │ │ │ +183 protected: │ │ │ │ +184 │ │ │ │ +186 │ │ │ │ +189 │ │ │ │ +_1_9_2 _L_i_n_e_S_e_a_r_c_h line_search_; │ │ │ │ +193 │ │ │ │ +_1_9_6 _G_r_a_d_i_e_n_t unscaled_direction_; │ │ │ │ +197 │ │ │ │ +_2_0_0 _S_i_z_e number_of_atoms_; │ │ │ │ +201 │ │ │ │ +_2_0_4 _S_i_z_e updt_method_; │ │ │ │ +205 │ │ │ │ +_2_0_8 bool first_iter_; │ │ │ │ +209 │ │ │ │ +_2_1_2 double old_gtg_; │ │ │ │ +213 │ │ │ │ +_2_1_6 vector<_V_e_c_t_o_r_3> a_i_; │ │ │ │ +217 │ │ │ │ +_2_2_0 vector<_V_e_c_t_o_r_3> b_i_; │ │ │ │ +221 │ │ │ │ +_2_2_4 vector<_V_e_c_t_o_r_3> p_t_; │ │ │ │ +225 │ │ │ │ +_2_2_8 vector<_V_e_c_t_o_r_3> y_t_; │ │ │ │ +229 │ │ │ │ +_2_3_2 vector<_V_e_c_t_o_r_3> p_i_; │ │ │ │ +233 │ │ │ │ +_2_3_6 vector<_V_e_c_t_o_r_3> y_i_; │ │ │ │ +237 │ │ │ │ +_2_4_0 double D_1_; │ │ │ │ +241 │ │ │ │ +_2_4_4 double D_4_; │ │ │ │ +245 │ │ │ │ +_2_4_8 _S_i_z_e restart_frequency_; │ │ │ │ +249 │ │ │ │ +_2_5_5 _S_i_z_e last_restart_iter_; │ │ │ │ +256 │ │ │ │ +258 │ │ │ │ +259 }; │ │ │ │ +260} // end of namespace BALL │ │ │ │ +261 │ │ │ │ +262#endif // BALL_MOLMEC_MINIMIZATION_CONJUGATEGRADIENT_H │ │ │ │ +_l_i_n_e_S_e_a_r_c_h_._h │ │ │ │ +_e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h │ │ │ │ +_B_A_L_L___C_R_E_A_T_E │ │ │ │ +#define BALL_CREATE(name) │ │ │ │ +DDeeffiinniittiioonn _c_r_e_a_t_e_._h_:_6_2 │ │ │ │ _B_A_L_L │ │ │ │ DDeeffiinniittiioonn _c_o_n_s_t_a_n_t_s_._h_:_1_3 │ │ │ │ -_B_A_L_L_:_:_T_R_e_g_u_l_a_r_D_a_t_a_2_D_<_ _f_l_o_a_t_ _> │ │ │ │ -_B_A_L_L_:_:_S_t_r_i_n_g │ │ │ │ -DDeeffiinniittiioonn _s_t_r_i_n_g_._h_:_5_7 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_2_6 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_b_f_r_e_q_f_2__ │ │ │ │ -double bfreqf2_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_9_5 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_g_e_t_D_a_t_a │ │ │ │ -const RegularData2D & getData() const │ │ │ │ -Return a reference to the spectrum. │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_5_4 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_r_e_a_d │ │ │ │ -void read(const String &name) │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_b_f_r_e_q_f_1__ │ │ │ │ -double bfreqf1_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_9_4 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_B_r_u_k_e_r_2_D_F_i_l_e │ │ │ │ -Bruker2DFile(const String &name, OpenMode open_mode=std::ios::in|std::ios:: │ │ │ │ -binary) │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_s_o_f_f_s_e_t_f_1__ │ │ │ │ -double soffsetf1_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_9_0 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_s_e_t_S_h_i_f_t_R_a_n_g_e │ │ │ │ -void setShiftRange(double offsetf1, double offsetf2, double swidthf1, double │ │ │ │ -swidthf2, double bfreqf1, double bfreqf2, double spointnumf1, double │ │ │ │ -spointnumf2) │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_g_e_t_D_a_t_a │ │ │ │ -RegularData2D & getData() │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_5_6 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_g_e_t_S_h_i_f_t │ │ │ │ -std::pair< double, double > getShift(Position x, Position y) │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_s_p_o_i_n_t_n_u_m_f_2__ │ │ │ │ -Size spointnumf2_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_9_7 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_~_B_r_u_k_e_r_2_D_F_i_l_e │ │ │ │ -virtual ~Bruker2DFile() │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_p_a_r_s_f_1__ │ │ │ │ -JCAMPFile parsf1_ │ │ │ │ -These classes give access to the parameters used in aqcuiring the spectrum. │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_8_0 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_d_a_t__ │ │ │ │ -RegularData2D dat_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_8_9 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_s_w_i_d_t_h_f_1__ │ │ │ │ -double swidthf1_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_9_2 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_m_i_n_x__ │ │ │ │ -Size minx_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_8_3 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_g_e_t_P_o_s_i_t_i_o_n │ │ │ │ -std::pair< Position, Position > getPosition(double x, double y) │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_s_p_o_i_n_t_n_u_m_f_1__ │ │ │ │ -Size spointnumf1_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_9_6 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_g_e_t_P_e_a_k_L_i_s_t │ │ │ │ -std::list< std::pair< int, int > > getPeakList() const │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_B_r_u_k_e_r_2_D_F_i_l_e │ │ │ │ -Bruker2DFile() │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_p_a_r_s_f_2__ │ │ │ │ -JCAMPFile parsf2_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_8_1 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_r_e_a_d │ │ │ │ -void read() │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_m_a_x_x__ │ │ │ │ -Size maxx_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_8_4 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_m_a_x_y__ │ │ │ │ -Size maxy_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_8_6 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_s_p_e_c_t_r_u_m__ │ │ │ │ -RegularData2D spectrum_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_9_8 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_s_w_i_d_t_h_f_2__ │ │ │ │ -double swidthf2_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_9_3 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_m_i_n_y__ │ │ │ │ -Size miny_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_8_5 │ │ │ │ -_B_A_L_L_:_:_B_r_u_k_e_r_2_D_F_i_l_e_:_:_s_o_f_f_s_e_t_f_2__ │ │ │ │ -double soffsetf2_ │ │ │ │ -DDeeffiinniittiioonn _b_r_u_k_e_r_2_D_F_i_l_e_._h_:_9_1 │ │ │ │ -_B_A_L_L_:_:_J_C_A_M_P_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _J_C_A_M_P_F_i_l_e_._h_:_3_0 │ │ │ │ -_B_A_L_L_:_:_F_i_l_e │ │ │ │ -DDeeffiinniittiioonn _f_i_l_e_._h_:_1_3_6 │ │ │ │ -_B_A_L_L_:_:_F_i_l_e_:_:_O_p_e_n_M_o_d_e │ │ │ │ -std::ios::openmode OpenMode │ │ │ │ -DDeeffiinniittiioonn _f_i_l_e_._h_:_1_6_5 │ │ │ │ +_B_A_L_L_:_:_O_p_t_i_o_n_s │ │ │ │ +DDeeffiinniittiioonn _o_p_t_i_o_n_s_._h_:_4_8 │ │ │ │ +_B_A_L_L_:_:_T_V_e_c_t_o_r_3_<_ _f_l_o_a_t_ _> │ │ │ │ +_B_A_L_L_:_:_F_o_r_c_e_F_i_e_l_d │ │ │ │ +DDeeffiinniittiioonn _f_o_r_c_e_F_i_e_l_d_._h_:_8_6 │ │ │ │ +_B_A_L_L_:_:_G_r_a_d_i_e_n_t │ │ │ │ +DDeeffiinniittiioonn _g_r_a_d_i_e_n_t_._h_:_4_5 │ │ │ │ +_B_A_L_L_:_:_S_n_a_p_S_h_o_t_M_a_n_a_g_e_r │ │ │ │ +DDeeffiinniittiioonn _s_n_a_p_S_h_o_t_M_a_n_a_g_e_r_._h_:_3_4 │ │ │ │ +_B_A_L_L_:_:_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r │ │ │ │ +DDeeffiinniittiioonn _c_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_._h_:_4_2 │ │ │ │ +_B_A_L_L_:_:_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r_:_:_U_p_d_a_t_e_M_e_t_h_o_d │ │ │ │ +UpdateMethod │ │ │ │ +DDeeffiinniittiioonn _c_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_._h_:_5_3 │ │ │ │ +_B_A_L_L_:_:_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n │ │ │ │ +DDeeffiinniittiioonn _c_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_._h_:_7_5 │ │ │ │ +_B_A_L_L_:_:_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r_:_:_O_p_t_i_o_n_:_:_U_P_D_A_T_E___M_E_T_H_O_D │ │ │ │ +static const char * UPDATE_METHOD │ │ │ │ +DDeeffiinniittiioonn _c_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_._h_:_7_8 │ │ │ │ +_B_A_L_L_:_:_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t │ │ │ │ +DDeeffiinniittiioonn _c_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_._h_:_8_4 │ │ │ │ +_B_A_L_L_:_:_C_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_M_i_n_i_m_i_z_e_r_:_:_D_e_f_a_u_l_t_:_:_U_P_D_A_T_E___M_E_T_H_O_D │ │ │ │ +static const Size UPDATE_METHOD │ │ │ │ +DDeeffiinniittiioonn _c_o_n_j_u_g_a_t_e_G_r_a_d_i_e_n_t_._h_:_8_7 │ │ │ │ +_B_A_L_L_:_:_E_n_e_r_g_y_M_i_n_i_m_i_z_e_r │ │ │ │ +DDeeffiinniittiioonn _e_n_e_r_g_y_M_i_n_i_m_i_z_e_r_._h_:_3_0 │ │ │ │ +_B_A_L_L_:_:_L_i_n_e_S_e_a_r_c_h │ │ │ │ +DDeeffiinniittiioonn _l_i_n_e_S_e_a_r_c_h_._h_:_3_3 │ │ │ │ _B_A_L_L___S_I_Z_E___T_Y_P_E │ │ │ │ _B_A_L_L___E_X_P_O_R_T │ │ │ │ #define BALL_EXPORT │ │ │ │ DDeeffiinniittiioonn _C_O_M_M_O_N_/_g_l_o_b_a_l_._h_:_5_0 │ │ │ │ =============================================================================== │ │ │ │ Generated by _[_d_o_x_y_g_e_n_] 1.9.8 │ │ ├── ./usr/share/doc/libball1.5/html/BALL/d1/d48/a03218.html │ │ │ @@ -75,15 +75,15 @@ │ │ │
    │ │ │
    │ │ │ List of all members
    │ │ │
    BALL::BaseIterator< Container, DataType, Position, Traits > Class Template Reference
    Foundation Classes » Concepts » Iterators
    │ │ │
    │ │ │
    │ │ │ │ │ │ -

    #include <BALL/CONCEPT/baseIterator.h>

    │ │ │ +

    #include <BALL/CONCEPT/baseIterator.h>

    │ │ │
    │ │ │ Inheritance diagram for BALL::BaseIterator< Container, DataType, Position, Traits >:
    │ │ │
    │ │ │
    │ │ │ │ │ │ │ │ │ BALL::ConstForwardIterator< Composite, Composite, Composite *, CompositeIteratorTraits > │ │ │ @@ -113,89 +113,89 @@ │ │ │   │ │ │ typedef std::input_iterator_tag iterator_category │ │ │   │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │

    │ │ │ Public Member Functions

    Constructors and Destructors
    BALL_INLINE BaseIterator ()
    BALL_INLINE BaseIterator ()
     Default constructor.
     
    BALL_INLINE BaseIterator (const BaseIterator &iterator)
    BALL_INLINE BaseIterator (const BaseIterator &iterator)
     Copy constructor.
     
    BALL_INLINE ~BaseIterator ()
    BALL_INLINE ~BaseIterator ()
     Destructor.
     
    Assignment
    BALL_INLINE BaseIterator & operator= (const BaseIterator &iterator)
    BALL_INLINE BaseIterator & operator= (const BaseIterator &iterator)
     
    BALL_INLINE void swap (BaseIterator &iterator)
    BALL_INLINE void swap (BaseIterator &iterator)
     Swap two iterators.
     
    Accessors
    BALL_INLINE void invalidate ()
    BALL_INLINE void invalidate ()
     Invalidate the iterator.
     
    BALL_INLINE void setTraits (const Traits &traits)
    BALL_INLINE void setTraits (const Traits &traits)
     Set the traits.
     
    BALL_INLINE const Traits & getTraits () const
    BALL_INLINE const Traits & getTraits () const
     Get a constant reference to the traits of this iterator.
     
    BALL_INLINE Traits & getTraits ()
    BALL_INLINE Traits & getTraits ()
     Get a constant reference to the traits of this iterator.
     
    BALL_INLINE const Container * getContainer () const
    BALL_INLINE const Container * getContainer () const
     Get a constant pointer to the container of this iterator.
     
    Converters
    BALL_INLINE operator const Position & () const
    BALL_INLINE operator const Position & () const
     
    BALL_INLINE reference operator* () const
    BALL_INLINE reference operator* () const
     Convert an iterator to its Datatype by returning a reference to the current data.
     
    BALL_INLINE pointer operator-> () const
    BALL_INLINE pointer operator-> () const
     Return a pointer to the current data.
     
    │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │

    Predicates

    BALL_INLINE bool operator== (const BaseIterator &iterator) const
    BALL_INLINE bool operator== (const BaseIterator &iterator) const
     Equality operator.
     
    BALL_INLINE bool operator!= (const BaseIterator &iterator) const
    BALL_INLINE bool operator!= (const BaseIterator &iterator) const
     Inequality operator.
     
    BALL_INLINE bool isSingular () const
    BALL_INLINE bool isSingular () const
     
    BALL_INLINE bool isValid () const
    BALL_INLINE bool isValid () const
     
    BALL_INLINE bool operator+ () const
    BALL_INLINE bool operator+ () const
     Validity predicate.
     
    BALL_INLINE bool operator- () const
    BALL_INLINE bool operator- () const
     Invalidity perdicate.
     
    BALL_INLINE BaseIterator (const Container &container)
    BALL_INLINE BaseIterator (const Container &container)
     
    │ │ │

    Detailed Description

    │ │ │
    template<typename Container, typename DataType, typename Position, typename Traits>
    │ │ │ class BALL::BaseIterator< Container, DataType, Position, Traits >

    Generic Iterator Class. This template class implements the basic behaviour of an iterator. Iterators are basically STL-like iterators. They provide the full STL iterator interface, but also offer additional features.

    │ │ │

    BaseIterator itself is a base class to the other iterator classes only and should not be used by itself.

    │ │ │

    An important difference exists for the iterators of the kernel objects. For most kernel objects, multiple iterators exist. Therefore, we could not simply use begin() and end() like in STL, but we introduced specialized methods like AtomContainer::beginAtom and AtomContainer::endAtom . For similar reasons, the iterators for kernel classes are not implemented as nested classes of the respective kernel classes, but as independent classes to avoid code replication. An exception is Atom::BondIterator , which is relevant to Atom alone.

    │ │ │

    Each BALL iterator can be bound to a container, so once the iteration has started, it "knows" about the end() of the container. Therefore, BALL iterators additionally implement the unary plus operator to check for the validity of the iterator. this allows the convenient implementation of for loops, e.g. as follows:

    │ │ │
    AtomIterator atom_it = system.beginAtom();
    │ │ │
    for (; +atom_it; ++atom_it)
    │ │ │
    {
    │ │ │
    ....
    │ │ │
    }
    │ │ │ -
    BALL::AtomIterator
    BidirectionalIterator< Composite, Atom, Composite::CompositeIterator, AtomIteratorTraits > AtomIterator
    Definition atomIterator.h:84
    │ │ │ +
    BALL::AtomIterator
    BidirectionalIterator< Composite, Atom, Composite::CompositeIterator, AtomIteratorTraits > AtomIterator
    Definition atomIterator.h:84
    │ │ │
    │ │ │ -

    Definition at line 64 of file baseIterator.h.

    │ │ │ +

    Definition at line 64 of file baseIterator.h.

    │ │ │

    Member Typedef Documentation

    │ │ │ │ │ │

    ◆ difference_type

    │ │ │ │ │ │
    │ │ │
    │ │ │
    │ │ │ @@ -203,15 +203,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef Position BALL::BaseIterator< Container, DataType, Position, Traits >::difference_type
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 76 of file baseIterator.h.

    │ │ │ +

    Definition at line 76 of file baseIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ iterator_category

    │ │ │ │ │ │
    │ │ │ @@ -221,15 +221,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef std::input_iterator_tag BALL::BaseIterator< Container, DataType, Position, Traits >::iterator_category
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 82 of file baseIterator.h.

    │ │ │ +

    Definition at line 82 of file baseIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ pointer

    │ │ │ │ │ │
    │ │ │ @@ -239,15 +239,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef const DataType* BALL::BaseIterator< Container, DataType, Position, Traits >::pointer
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 78 of file baseIterator.h.

    │ │ │ +

    Definition at line 78 of file baseIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ reference

    │ │ │ │ │ │
    │ │ │ @@ -257,15 +257,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef const DataType& BALL::BaseIterator< Container, DataType, Position, Traits >::reference
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 80 of file baseIterator.h.

    │ │ │ +

    Definition at line 80 of file baseIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │ │ │ │

    ◆ value_type

    │ │ │ │ │ │
    │ │ │ @@ -275,15 +275,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    typedef DataType BALL::BaseIterator< Container, DataType, Position, Traits >::value_type
    │ │ │
    │ │ │ │ │ │ -

    Definition at line 74 of file baseIterator.h.

    │ │ │ +

    Definition at line 74 of file baseIterator.h.

    │ │ │ │ │ │
    │ │ │
    │ │ │

    Constructor & Destructor Documentation

    │ │ │ │ │ │

    ◆ BaseIterator() [1/3]

    │ │ │ │ │ │ @@ -292,30 +292,30 @@ │ │ │
    │ │ │ template<typename Container , typename DataType , typename Position , typename Traits >
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE BALL::BaseIterator< Container, DataType, Position, Traits >::BaseIterator BALL_INLINE BALL::BaseIterator< Container, DataType, Position, Traits >::BaseIterator ()
    │ │ │     		│ │ │ inline
    │ │ │
    │ │ │ │ │ │

    Default constructor.

    │ │ │ │ │ │ -

    Definition at line 89 of file baseIterator.h.

    │ │ │ +

    Definition at line 89 of file baseIterator.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ BaseIterator() [2/3]

    │ │ │ │ │ │
    │ │ │ @@ -323,15 +323,15 @@ │ │ │
    │ │ │ template<typename Container , typename DataType , typename Position , typename Traits >
    │ │ │ │ │ │ │ │ │ │ │ │ @@ -339,15 +339,15 @@ │ │ │ inline │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE BALL::BaseIterator< Container, DataType, Position, Traits >::BaseIterator BALL_INLINE BALL::BaseIterator< Container, DataType, Position, Traits >::BaseIterator (const BaseIterator< Container, DataType, Position, Traits > & iterator)
    │ │ │
    │ │ │
    │ │ │ │ │ │

    Copy constructor.

    │ │ │ │ │ │ -

    Definition at line 92 of file baseIterator.h.

    │ │ │ +

    Definition at line 92 of file baseIterator.h.

    │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │

    ◆ ~BaseIterator()

    │ │ │ │ │ │
    │ │ │ @@ -355,30 +355,30 @@ │ │ │
    │ │ │ template<typename Container , typename DataType , typename Position , typename Traits >
    │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    │ │ │ │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
    BALL_INLINE BALL::BaseIterator< Container, DataType, Position, Traits >::~BaseIterator BALL_INLINE BALL::BaseIterator< Container, DataType, Position, Traits >::~BaseIterator ()
    │ │ │     		│ │ │ inline
    │ │ │
    │ │ │ │ │ │

    Destructor.

    │ │ │ │ │ │ -

    Definition at line 98 of file baseIterator.h.

    │ │ │ +

    Definition at line 98 o TRUNCATED DUE TO SIZE LIMIT: 10485760 bytes