--- /srv/rebuilderd/tmp/rebuilderdttM9CN/inputs/r-bioc-rcpi_1.48.0+ds-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdttM9CN/out/r-bioc-rcpi_1.48.0+ds-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-11 20:58:51.000000 debian-binary │ --rw-r--r-- 0 0 0 2364 2026-08-11 20:58:51.000000 control.tar.xz │ --rw-r--r-- 0 0 0 1133840 2026-08-11 20:58:51.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 2304 2026-08-11 20:58:51.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 1139192 2026-08-11 20:58:51.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 754 2026-08-11 20:58:51.000000 ./control │ │ │ --rw-r--r-- 0 root (0) root (0) 4744 2026-08-11 20:58:51.000000 ./md5sums │ │ │ +-rw-r--r-- 0 root (0) root (0) 685 2026-08-11 20:58:51.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 4664 2026-08-11 20:58:51.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,13 @@ │ │ │ Package: r-bioc-rcpi │ │ │ Version: 1.48.0+ds-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 2496 │ │ │ +Installed-Size: 2499 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-biostrings, r-bioc-gosemsim, r-cran-curl, r-cran-doparallel, r-cran-foreach, r-cran-httr2, r-cran-jsonlite, r-cran-rlang, pkgconf, r-bioc-pwalign, r-pkg-team-core-architecture │ │ │ -Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat (>= 3.0.0) │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/Rcpi/ │ │ │ Description: molecular informatics toolkit for compound-protein interaction │ │ │ Rcpi offers a molecular informatics toolkit with a │ │ │ comprehensive integration of bioinformatics and │ │ │ chemoinformatics tools for drug discovery. │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -4,15 +4,14 @@ │ │ │ │ usr/lib/R/site-library/Rcpi/Meta/Rd.rds │ │ │ │ usr/lib/R/site-library/Rcpi/Meta/data.rds │ │ │ │ usr/lib/R/site-library/Rcpi/Meta/features.rds │ │ │ │ usr/lib/R/site-library/Rcpi/Meta/hsearch.rds │ │ │ │ usr/lib/R/site-library/Rcpi/Meta/links.rds │ │ │ │ usr/lib/R/site-library/Rcpi/Meta/nsInfo.rds │ │ │ │ usr/lib/R/site-library/Rcpi/Meta/package.rds │ │ │ │ -usr/lib/R/site-library/Rcpi/Meta/vignette.rds │ │ │ │ usr/lib/R/site-library/Rcpi/NAMESPACE │ │ │ │ usr/lib/R/site-library/Rcpi/NEWS │ │ │ │ usr/lib/R/site-library/Rcpi/R/Rcpi │ │ │ │ usr/lib/R/site-library/Rcpi/R/Rcpi.rdb │ │ │ │ usr/lib/R/site-library/Rcpi/R/Rcpi.rdx │ │ │ │ usr/lib/R/site-library/Rcpi/README.md │ │ │ │ usr/lib/R/site-library/Rcpi/compseq/DB00530.sdf ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -11,44 +11,43 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 5636 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/Meta/Rd.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 706 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/Meta/data.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 123 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/Meta/features.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 4726 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/Meta/hsearch.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 2204 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1401 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1436 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/Meta/package.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 282 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 4150 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 4784 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/NEWS │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/R/Rcpi │ │ │ --rw-r--r-- 0 root (0) root (0) 173568 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/R/Rcpi.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 2359 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/R/Rcpi.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 173575 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/R/Rcpi.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 2363 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/R/Rcpi.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 5411 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/compseq/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3818 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/compseq/DB00530.sdf │ │ │ -rw-r--r-- 0 root (0) root (0) 2118 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/compseq/DB00859.sdf │ │ │ -rw-r--r-- 0 root (0) root (0) 5496 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/compseq/DB00860.sdf │ │ │ -rw-r--r-- 0 root (0) root (0) 517450 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/compseq/tyrphostin.sdf │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 229580 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/data/Rdata.rdb │ │ │ -rw-r--r-- 0 root (0) root (0) 381 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/data/Rdata.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 603 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/data/Rdata.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 19209 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/doc/Rcpi-quickref.Rmd │ │ │ -rw-r--r-- 0 root (0) root (0) 14103 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/doc/Rcpi.R │ │ │ -rw-r--r-- 0 root (0) root (0) 37130 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/doc/Rcpi.Rmd │ │ │ --rw-r--r-- 0 root (0) root (0) 1980 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/doc/index.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 1295 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/doc/index.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 5784 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/AnIndex │ │ │ --rw-r--r-- 0 root (0) root (0) 361051 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/Rcpi.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 3659 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/Rcpi.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 365249 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/Rcpi.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 3671 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/Rcpi.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 1351 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/aliases.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/figures/ │ │ │ -rw-r--r-- 0 root (0) root (0) 37248 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/figures/logo.png │ │ │ --rw-r--r-- 0 root (0) root (0) 1430 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 1445 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 28658 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/logo/ │ │ │ -rw-r--r-- 0 root (0) root (0) 459 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/logo/logo.R │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/protseq/ │ │ │ -rw-r--r-- 0 root (0) root (0) 478224 2026-08-11 20:58:51.000000 ./usr/lib/R/site-library/Rcpi/protseq/4HHB.pdb │ │ ├── ./usr/lib/R/site-library/Rcpi/R/Rcpi.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -256,15 +256,15 @@ │ │ │ │ "imports" = " methods = c(as = "as"), stats = c(cmdscale = "cmdscale"), " │ │ │ │ "imports" = " stats = c(dist = "dist"), stats = c(factanal = "factanal"), " │ │ │ │ "imports" = " stats = c(na.omit = "na.omit"), stats = c(prcomp = "prcomp"), " │ │ │ │ "imports" = " stats = c(predict = "predict"), stats = c(sd = "sd"), utils = c(capture.output = "capture.output"), " │ │ │ │ "imports" = " utils = c(combn = "combn"), utils = c(getFromNamespace = "getFromNamespace"), " │ │ │ │ "imports" = " utils = c(read.csv = "read.csv"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-rcpi/debian/r-bioc-rcpi/usr/lib/R/site-library/Rcpi"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/debian/r-bioc-rcpi/usr/lib/R/site-library/Rcpi"" │ │ │ │ "spec" = "c(name = "Rcpi", version = "1.48.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/Rcpi/R/Rcpi.rdx │ │ │ ├── Rcpi.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,478 +1,478 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 4535 52 │ │ │ │ │ +[1] 4542 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 4718 52 │ │ │ │ │ +[1] 4725 52 │ │ │ │ │ │ │ │ │ │ $variables$.calcSeqPairSim │ │ │ │ │ -[1] 4770 1709 │ │ │ │ │ +[1] 4777 1709 │ │ │ │ │ │ │ │ │ │ $variables$.calcgoPairSim │ │ │ │ │ -[1] 6479 1304 │ │ │ │ │ +[1] 6486 1304 │ │ │ │ │ │ │ │ │ │ $variables$.getCPICombine │ │ │ │ │ -[1] 7783 261 │ │ │ │ │ +[1] 7790 261 │ │ │ │ │ │ │ │ │ │ $variables$.getCPITensor │ │ │ │ │ -[1] 8044 433 │ │ │ │ │ +[1] 8051 433 │ │ │ │ │ │ │ │ │ │ $variables$.getPPICombine │ │ │ │ │ -[1] 8477 261 │ │ │ │ │ +[1] 8484 261 │ │ │ │ │ │ │ │ │ │ $variables$.getPPIEntry │ │ │ │ │ -[1] 8738 315 │ │ │ │ │ +[1] 8745 315 │ │ │ │ │ │ │ │ │ │ $variables$.getPPITensor │ │ │ │ │ -[1] 9053 437 │ │ │ │ │ +[1] 9060 437 │ │ │ │ │ │ │ │ │ │ $variables$.inner │ │ │ │ │ -[1] 9490 506 │ │ │ │ │ +[1] 9497 506 │ │ │ │ │ │ │ │ │ │ $variables$.orgdb │ │ │ │ │ -[1] 9996 322 │ │ │ │ │ +[1] 10003 322 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 10318 49 │ │ │ │ │ +[1] 10325 49 │ │ │ │ │ │ │ │ │ │ $variables$acc │ │ │ │ │ -[1] 10367 2415 │ │ │ │ │ +[1] 10374 2415 │ │ │ │ │ │ │ │ │ │ $variables$calcDrugFPSim │ │ │ │ │ -[1] 12782 2822 │ │ │ │ │ +[1] 12789 2822 │ │ │ │ │ │ │ │ │ │ $variables$calcDrugMCSSim │ │ │ │ │ -[1] 15604 1634 │ │ │ │ │ +[1] 15611 1634 │ │ │ │ │ │ │ │ │ │ $variables$calcParProtGOSim │ │ │ │ │ -[1] 17238 2121 │ │ │ │ │ +[1] 17245 2121 │ │ │ │ │ │ │ │ │ │ $variables$calcParProtSeqSim │ │ │ │ │ -[1] 19359 1743 │ │ │ │ │ +[1] 19366 1743 │ │ │ │ │ │ │ │ │ │ $variables$calcTwoProtGOSim │ │ │ │ │ -[1] 21102 1172 │ │ │ │ │ +[1] 21109 1172 │ │ │ │ │ │ │ │ │ │ $variables$calcTwoProtSeqSim │ │ │ │ │ -[1] 22274 686 │ │ │ │ │ +[1] 22281 686 │ │ │ │ │ │ │ │ │ │ $variables$checkProt │ │ │ │ │ -[1] 22960 607 │ │ │ │ │ +[1] 22967 607 │ │ │ │ │ │ │ │ │ │ $variables$check_ob │ │ │ │ │ -[1] 23567 373 │ │ │ │ │ +[1] 23574 373 │ │ │ │ │ │ │ │ │ │ $variables$convMolFormat │ │ │ │ │ -[1] 23940 395 │ │ │ │ │ +[1] 23947 395 │ │ │ │ │ │ │ │ │ │ $variables$evaluateDescriptor │ │ │ │ │ -[1] 24335 695 │ │ │ │ │ +[1] 24342 695 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAIO │ │ │ │ │ -[1] 25030 1383 │ │ │ │ │ +[1] 25037 1383 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugALOGP │ │ │ │ │ -[1] 26413 302 │ │ │ │ │ +[1] 26420 302 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAminoAcidCount │ │ │ │ │ -[1] 26715 309 │ │ │ │ │ +[1] 26722 309 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugApol │ │ │ │ │ -[1] 27024 300 │ │ │ │ │ +[1] 27031 300 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAromaticAtomsCount │ │ │ │ │ -[1] 27324 312 │ │ │ │ │ +[1] 27331 312 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAromaticBondsCount │ │ │ │ │ -[1] 27636 312 │ │ │ │ │ +[1] 27643 312 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAtomCount │ │ │ │ │ -[1] 27948 303 │ │ │ │ │ +[1] 27955 303 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAutocorrelationCharge │ │ │ │ │ -[1] 28251 315 │ │ │ │ │ +[1] 28258 315 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAutocorrelationMass │ │ │ │ │ -[1] 28566 313 │ │ │ │ │ +[1] 28573 313 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAutocorrelationPolarizability │ │ │ │ │ -[1] 28879 323 │ │ │ │ │ +[1] 28886 323 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugBCUT │ │ │ │ │ -[1] 29202 300 │ │ │ │ │ +[1] 29209 300 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugBPol │ │ │ │ │ -[1] 29502 300 │ │ │ │ │ +[1] 29509 300 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugBondCount │ │ │ │ │ -[1] 29802 303 │ │ │ │ │ +[1] 29809 303 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugCPSA │ │ │ │ │ -[1] 30105 301 │ │ │ │ │ +[1] 30112 301 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugCarbonTypes │ │ │ │ │ -[1] 30406 304 │ │ │ │ │ +[1] 30413 304 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugChiChain │ │ │ │ │ -[1] 30710 301 │ │ │ │ │ +[1] 30717 301 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugChiCluster │ │ │ │ │ -[1] 31011 303 │ │ │ │ │ +[1] 31018 303 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugChiPath │ │ │ │ │ -[1] 31314 302 │ │ │ │ │ +[1] 31321 302 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugChiPathCluster │ │ │ │ │ -[1] 31616 308 │ │ │ │ │ +[1] 31623 308 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugDescOB │ │ │ │ │ -[1] 31924 1831 │ │ │ │ │ +[1] 31931 1831 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugECI │ │ │ │ │ -[1] 33755 315 │ │ │ │ │ +[1] 33762 315 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugEstate │ │ │ │ │ -[1] 34070 1118 │ │ │ │ │ +[1] 34077 1118 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugEstateComplete │ │ │ │ │ -[1] 35188 981 │ │ │ │ │ +[1] 35195 981 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugExtended │ │ │ │ │ -[1] 36169 1198 │ │ │ │ │ +[1] 36176 1198 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugExtendedComplete │ │ │ │ │ -[1] 37367 1094 │ │ │ │ │ +[1] 37374 1094 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugFMF │ │ │ │ │ -[1] 38461 299 │ │ │ │ │ +[1] 38468 299 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugFragmentComplexity │ │ │ │ │ -[1] 38760 311 │ │ │ │ │ +[1] 38767 311 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugGraph │ │ │ │ │ -[1] 39071 1194 │ │ │ │ │ +[1] 39078 1194 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugGraphComplete │ │ │ │ │ -[1] 40265 1090 │ │ │ │ │ +[1] 40272 1090 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugGravitationalIndex │ │ │ │ │ -[1] 41355 309 │ │ │ │ │ +[1] 41362 309 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHBondAcceptorCount │ │ │ │ │ -[1] 41664 311 │ │ │ │ │ +[1] 41671 311 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHBondDonorCount │ │ │ │ │ -[1] 41975 310 │ │ │ │ │ +[1] 41982 310 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHybridization │ │ │ │ │ -[1] 42285 1204 │ │ │ │ │ +[1] 42292 1204 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHybridizationComplete │ │ │ │ │ -[1] 43489 1100 │ │ │ │ │ +[1] 43496 1100 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHybridizationRatio │ │ │ │ │ -[1] 44589 310 │ │ │ │ │ +[1] 44596 310 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugIPMolecularLearning │ │ │ │ │ -[1] 44899 311 │ │ │ │ │ +[1] 44906 311 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugKR │ │ │ │ │ -[1] 45210 1114 │ │ │ │ │ +[1] 45217 1114 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugKRComplete │ │ │ │ │ -[1] 46324 978 │ │ │ │ │ +[1] 46331 978 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugKappaShapeIndices │ │ │ │ │ -[1] 47302 312 │ │ │ │ │ +[1] 47309 312 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugKierHallSmarts │ │ │ │ │ -[1] 47614 309 │ │ │ │ │ +[1] 47621 309 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugLargestChain │ │ │ │ │ -[1] 47923 306 │ │ │ │ │ +[1] 47930 306 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugLargestPiSystem │ │ │ │ │ -[1] 48229 311 │ │ │ │ │ +[1] 48236 311 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugLengthOverBreadth │ │ │ │ │ -[1] 48540 313 │ │ │ │ │ +[1] 48547 313 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugLongestAliphaticChain │ │ │ │ │ -[1] 48853 315 │ │ │ │ │ +[1] 48860 315 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMACCS │ │ │ │ │ -[1] 49168 1117 │ │ │ │ │ +[1] 49175 1117 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMACCSComplete │ │ │ │ │ -[1] 50285 981 │ │ │ │ │ +[1] 50292 981 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMDE │ │ │ │ │ -[1] 51266 300 │ │ │ │ │ +[1] 51273 300 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMannholdLogP │ │ │ │ │ -[1] 51566 308 │ │ │ │ │ +[1] 51573 308 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMomentOfInertia │ │ │ │ │ -[1] 51874 311 │ │ │ │ │ +[1] 51881 311 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugOBFP2 │ │ │ │ │ -[1] 52185 1821 │ │ │ │ │ +[1] 52192 1821 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugOBFP3 │ │ │ │ │ -[1] 54006 1818 │ │ │ │ │ +[1] 54013 1818 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugOBFP4 │ │ │ │ │ -[1] 55824 1820 │ │ │ │ │ +[1] 55831 1820 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugOBMACCS │ │ │ │ │ -[1] 57644 1818 │ │ │ │ │ +[1] 57651 1818 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugPetitjeanNumber │ │ │ │ │ -[1] 59462 310 │ │ │ │ │ +[1] 59469 310 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugPetitjeanShapeIndex │ │ │ │ │ -[1] 59772 310 │ │ │ │ │ +[1] 59779 310 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugPubChem │ │ │ │ │ -[1] 60082 1120 │ │ │ │ │ +[1] 60089 1120 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugPubChemComplete │ │ │ │ │ -[1] 61202 984 │ │ │ │ │ +[1] 61209 984 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugRotatableBondsCount │ │ │ │ │ -[1] 62186 312 │ │ │ │ │ +[1] 62193 312 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugRuleOfFive │ │ │ │ │ -[1] 62498 305 │ │ │ │ │ +[1] 62505 305 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugShortestPath │ │ │ │ │ -[1] 62803 1201 │ │ │ │ │ +[1] 62810 1201 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugShortestPathComplete │ │ │ │ │ -[1] 64004 1098 │ │ │ │ │ +[1] 64011 1098 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugStandard │ │ │ │ │ -[1] 65102 1199 │ │ │ │ │ +[1] 65109 1199 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugStandardComplete │ │ │ │ │ -[1] 66301 1095 │ │ │ │ │ +[1] 66308 1095 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugTPSA │ │ │ │ │ -[1] 67396 301 │ │ │ │ │ +[1] 67403 301 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugVABC │ │ │ │ │ -[1] 67697 301 │ │ │ │ │ +[1] 67704 301 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugVAdjMa │ │ │ │ │ -[1] 67998 302 │ │ │ │ │ +[1] 68005 302 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugWHIM │ │ │ │ │ -[1] 68300 302 │ │ │ │ │ +[1] 68307 302 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugWeight │ │ │ │ │ -[1] 68602 299 │ │ │ │ │ +[1] 68609 299 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugWeightedPath │ │ │ │ │ -[1] 68901 307 │ │ │ │ │ +[1] 68908 307 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugWienerNumbers │ │ │ │ │ -[1] 69208 307 │ │ │ │ │ +[1] 69215 307 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugXLogP │ │ │ │ │ -[1] 69515 302 │ │ │ │ │ +[1] 69522 302 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugZagrebIndex │ │ │ │ │ -[1] 69817 302 │ │ │ │ │ +[1] 69824 302 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMBLOSUM │ │ │ │ │ -[1] 70119 1636 │ │ │ │ │ +[1] 70126 1636 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMDescScales │ │ │ │ │ -[1] 71755 588 │ │ │ │ │ +[1] 71762 588 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMFAScales │ │ │ │ │ -[1] 72343 1519 │ │ │ │ │ +[1] 72350 1519 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMMDSScales │ │ │ │ │ -[1] 73862 1621 │ │ │ │ │ +[1] 73869 1621 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMPropScales │ │ │ │ │ -[1] 75483 740 │ │ │ │ │ +[1] 75490 740 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMScales │ │ │ │ │ -[1] 76223 1552 │ │ │ │ │ +[1] 76230 1552 │ │ │ │ │ │ │ │ │ │ $variables$extractProtAAC │ │ │ │ │ -[1] 77775 904 │ │ │ │ │ +[1] 77782 904 │ │ │ │ │ │ │ │ │ │ $variables$extractProtAPAAC │ │ │ │ │ -[1] 78679 5025 │ │ │ │ │ +[1] 78686 5025 │ │ │ │ │ │ │ │ │ │ $variables$extractProtCTDC │ │ │ │ │ -[1] 83704 2970 │ │ │ │ │ +[1] 83711 2970 │ │ │ │ │ │ │ │ │ │ $variables$extractProtCTDD │ │ │ │ │ -[1] 86674 4200 │ │ │ │ │ +[1] 86681 4200 │ │ │ │ │ │ │ │ │ │ $variables$extractProtCTDT │ │ │ │ │ -[1] 90874 4283 │ │ │ │ │ +[1] 90881 4283 │ │ │ │ │ │ │ │ │ │ $variables$extractProtCTriad │ │ │ │ │ -[1] 95157 6089 │ │ │ │ │ +[1] 95164 6089 │ │ │ │ │ │ │ │ │ │ $variables$extractProtDC │ │ │ │ │ -[1] 101246 1279 │ │ │ │ │ +[1] 101253 1279 │ │ │ │ │ │ │ │ │ │ $variables$extractProtGeary │ │ │ │ │ -[1] 102525 4169 │ │ │ │ │ +[1] 102532 4169 │ │ │ │ │ │ │ │ │ │ $variables$extractProtMoran │ │ │ │ │ -[1] 106694 4167 │ │ │ │ │ +[1] 106701 4167 │ │ │ │ │ │ │ │ │ │ $variables$extractProtMoreauBroto │ │ │ │ │ -[1] 110861 3914 │ │ │ │ │ +[1] 110868 3914 │ │ │ │ │ │ │ │ │ │ $variables$extractProtPAAC │ │ │ │ │ -[1] 114775 4695 │ │ │ │ │ +[1] 114782 4695 │ │ │ │ │ │ │ │ │ │ $variables$extractProtPSSM │ │ │ │ │ -[1] 119470 6419 │ │ │ │ │ +[1] 119477 6419 │ │ │ │ │ │ │ │ │ │ $variables$extractProtPSSMAcc │ │ │ │ │ -[1] 125889 3281 │ │ │ │ │ +[1] 125896 3281 │ │ │ │ │ │ │ │ │ │ $variables$extractProtPSSMFeature │ │ │ │ │ -[1] 129170 828 │ │ │ │ │ +[1] 129177 828 │ │ │ │ │ │ │ │ │ │ $variables$extractProtQSO │ │ │ │ │ -[1] 129998 3521 │ │ │ │ │ +[1] 130005 3521 │ │ │ │ │ │ │ │ │ │ $variables$extractProtSOCN │ │ │ │ │ -[1] 133519 2560 │ │ │ │ │ +[1] 133526 2560 │ │ │ │ │ │ │ │ │ │ $variables$extractProtTC │ │ │ │ │ -[1] 136079 1522 │ │ │ │ │ +[1] 136086 1522 │ │ │ │ │ │ │ │ │ │ $variables$getCPI │ │ │ │ │ -[1] 137601 1629 │ │ │ │ │ +[1] 137608 1629 │ │ │ │ │ │ │ │ │ │ $variables$getDrug │ │ │ │ │ -[1] 139230 1437 │ │ │ │ │ +[1] 139237 1437 │ │ │ │ │ │ │ │ │ │ $variables$getFASTAFromKEGG │ │ │ │ │ -[1] 140667 451 │ │ │ │ │ +[1] 140674 451 │ │ │ │ │ │ │ │ │ │ $variables$getFASTAFromUniProt │ │ │ │ │ -[1] 141118 452 │ │ │ │ │ +[1] 141125 452 │ │ │ │ │ │ │ │ │ │ $variables$getFingerprint │ │ │ │ │ -[1] 141570 654 │ │ │ │ │ +[1] 141577 654 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromCAS │ │ │ │ │ -[1] 142224 1182 │ │ │ │ │ +[1] 142231 1182 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromChEMBL │ │ │ │ │ -[1] 143406 1273 │ │ │ │ │ +[1] 143413 1273 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromDrugBank │ │ │ │ │ -[1] 144679 477 │ │ │ │ │ +[1] 144686 477 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromKEGG │ │ │ │ │ -[1] 145156 447 │ │ │ │ │ +[1] 145163 447 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromPubChem │ │ │ │ │ -[1] 145603 499 │ │ │ │ │ +[1] 145610 499 │ │ │ │ │ │ │ │ │ │ $variables$getPDBFromRCSBPDB │ │ │ │ │ -[1] 146102 453 │ │ │ │ │ +[1] 146109 453 │ │ │ │ │ │ │ │ │ │ $variables$getPPI │ │ │ │ │ -[1] 146555 2202 │ │ │ │ │ +[1] 146562 2202 │ │ │ │ │ │ │ │ │ │ $variables$getProt │ │ │ │ │ -[1] 148757 1609 │ │ │ │ │ +[1] 148764 1609 │ │ │ │ │ │ │ │ │ │ $variables$getSeqFromKEGG │ │ │ │ │ -[1] 150366 806 │ │ │ │ │ +[1] 150373 806 │ │ │ │ │ │ │ │ │ │ $variables$getSeqFromRCSBPDB │ │ │ │ │ -[1] 151172 934 │ │ │ │ │ +[1] 151179 934 │ │ │ │ │ │ │ │ │ │ $variables$getSeqFromUniProt │ │ │ │ │ -[1] 152106 808 │ │ │ │ │ +[1] 152113 808 │ │ │ │ │ │ │ │ │ │ $variables$getSmiFromChEMBL │ │ │ │ │ -[1] 152914 950 │ │ │ │ │ +[1] 152921 950 │ │ │ │ │ │ │ │ │ │ $variables$getSmiFromDrugBank │ │ │ │ │ -[1] 153864 875 │ │ │ │ │ +[1] 153871 875 │ │ │ │ │ │ │ │ │ │ $variables$getSmiFromKEGG │ │ │ │ │ -[1] 154739 870 │ │ │ │ │ +[1] 154746 870 │ │ │ │ │ │ │ │ │ │ $variables$getSmiFromPubChem │ │ │ │ │ -[1] 155609 875 │ │ │ │ │ +[1] 155616 875 │ │ │ │ │ │ │ │ │ │ $variables$getSmiles │ │ │ │ │ -[1] 156484 536 │ │ │ │ │ +[1] 156491 536 │ │ │ │ │ │ │ │ │ │ $variables$get_pwa │ │ │ │ │ -[1] 157020 265 │ │ │ │ │ +[1] 157027 265 │ │ │ │ │ │ │ │ │ │ $variables$get_url_parallel │ │ │ │ │ -[1] 157285 1051 │ │ │ │ │ +[1] 157292 1051 │ │ │ │ │ │ │ │ │ │ $variables$is_pkg_available │ │ │ │ │ -[1] 158336 240 │ │ │ │ │ +[1] 158343 240 │ │ │ │ │ │ │ │ │ │ $variables$is_pwalign_installed │ │ │ │ │ -[1] 158576 243 │ │ │ │ │ +[1] 158583 243 │ │ │ │ │ │ │ │ │ │ $variables$is_pwalign_needed │ │ │ │ │ -[1] 158819 277 │ │ │ │ │ +[1] 158826 277 │ │ │ │ │ │ │ │ │ │ $variables$loadMolecules │ │ │ │ │ -[1] 159096 529 │ │ │ │ │ +[1] 159103 529 │ │ │ │ │ │ │ │ │ │ $variables$parseSmiles │ │ │ │ │ -[1] 159625 517 │ │ │ │ │ +[1] 159632 517 │ │ │ │ │ │ │ │ │ │ $variables$readFASTA │ │ │ │ │ -[1] 160142 1997 │ │ │ │ │ +[1] 160149 1997 │ │ │ │ │ │ │ │ │ │ $variables$readMolFromSDF │ │ │ │ │ -[1] 162139 323 │ │ │ │ │ +[1] 162146 323 │ │ │ │ │ │ │ │ │ │ $variables$readMolFromSmi │ │ │ │ │ -[1] 162462 702 │ │ │ │ │ +[1] 162469 702 │ │ │ │ │ │ │ │ │ │ $variables$readPDB │ │ │ │ │ -[1] 163164 3288 │ │ │ │ │ +[1] 163171 3288 │ │ │ │ │ │ │ │ │ │ $variables$resolve_pwa │ │ │ │ │ -[1] 166452 505 │ │ │ │ │ +[1] 166459 505 │ │ │ │ │ │ │ │ │ │ $variables$searchDrug │ │ │ │ │ -[1] 166957 4903 │ │ │ │ │ +[1] 166964 4903 │ │ │ │ │ │ │ │ │ │ $variables$segProt │ │ │ │ │ -[1] 171860 1708 │ │ │ │ │ +[1] 171867 1708 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 288 4247 │ │ │ │ │ +[1] 288 4254 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 0 131 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 131 157 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 4587 131 │ │ │ │ │ +[1] 4594 131 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/Rcpi/doc/index.html │ │ │ @@ -10,33 +10,18 @@ │ │ │ │ │ │
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│ │ │

Vignettes from package 'Rcpi'

│ │ │ - │ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
Rcpi::Rcpi Quick Reference Cardsource
Rcpi::Rcpi: R/Bioconductor Package as an Integrated Informatics Platform for Drug Discoverysource
│ │ │ +The package contains no vignette meta-information. │ │ │

Other files in the doc directory

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ │ + │ │ │
Rcpi-quickref.Rmd
Rcpi.R
Rcpi.Rmd
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,9 +1,9 @@ │ │ │ │ ************ VViiggnneetttteess aanndd ootthheerr ddooccuummeennttaattiioonn[[[[RR llooggoo]]]] ************ │ │ │ │ =============================================================================== │ │ │ │ _[_[_U_p_]_]_[_[_T_o_p_]_] │ │ │ │ ********** VViiggnneetttteess ffrroomm ppaacckkaaggee ''RRccppii'' ********** │ │ │ │ -_R_c_p_i_:_: Rcpi Quick Reference Card _s_o_u_r_c_e │ │ │ │ -_R_c_p_i_:_: Rcpi: R/Bioconductor Package as an Integrated Informatics _s_o_u_r_c_e │ │ │ │ - Platform for Drug Discovery │ │ │ │ +The package contains no vignette meta-information. │ │ │ │ ********** OOtthheerr ffiilleess iinn tthhee ddoocc ddiirreeccttoorryy ********** │ │ │ │ + _R_c_p_i_-_q_u_i_c_k_r_e_f_._R_m_d │ │ │ │ _R_c_p_i_._R │ │ │ │ + _R_c_p_i_._R_m_d │ │ ├── ./usr/lib/R/site-library/Rcpi/help/Rcpi.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -3,111 +3,111 @@ │ │ │ │ structure(list(structure("AA2DACOR", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("2D Autocorrelations Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the 2D autocorrelations descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AA2DACOR data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AA2DACOR)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AA2DACOR.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AA2DACOR.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AA3DMoRSE (list) = structure(list(structure(list(structure("3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AA3DMoRSE", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AA3DMoRSE", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the 3D-MoRSE descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AA3DMoRSE data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AA3DMoRSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AA3DMoRSE.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AA3DMoRSE.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAACF (list) = structure(list(structure(list(structure("Atom-Centred Fragments Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAACF", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAACF", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Atom-Centred Fragments Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the atom-centred fragments descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAACF data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAACF)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAACF.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAACF.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AABLOSUM100 (list) = structure(list(structure(list(structure("BLOSUM100 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AABLOSUM100", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AABLOSUM100", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM100 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM100 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AABLOSUM100 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AABLOSUM100)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM100.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM100.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AABLOSUM45 (list) = structure(list(structure(list(structure("BLOSUM45 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AABLOSUM45", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AABLOSUM45", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM45 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM45 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AABLOSUM45 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AABLOSUM45)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM45.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM45.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AABLOSUM50 (list) = structure(list(structure(list(structure("BLOSUM50 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AABLOSUM50", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AABLOSUM50", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM50 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM50 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AABLOSUM50 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AABLOSUM50)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM50.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM50.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AABLOSUM62 (list) = structure(list(structure(list(structure("BLOSUM62 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AABLOSUM62", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AABLOSUM62", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM62 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM62 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AABLOSUM62 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AABLOSUM62)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM62.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM62.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AABLOSUM80 (list) = structure(list(structure(list(structure("BLOSUM80 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AABLOSUM80", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AABLOSUM80", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM80 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BLOSUM80 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AABLOSUM80 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AABLOSUM80)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM80.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM80.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AABurden (list) = structure(list(structure(list(structure("Burden Eigenvalues Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AABurden", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AABurden", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Burden Eigenvalues Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the Burden eigenvalues descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AABurden data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AABurden)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AABurden.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABurden.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AACPSA (list) = structure(list(structure(list(structure("CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AACPSA", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AACPSA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the CPSA descriptors of the 20 amino acids\n", Rd_tag = "TEXT"), │ │ │ │ @@ -117,135 +117,135 @@ │ │ │ │ structure("before calculating these CPSA descriptors.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The SDF file containing the information of the optimized amino acid molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("is included in this package. See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("OptAA3d", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for more information.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AACPSA data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AACPSA)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AACPSA.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AACPSA.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAConn (list) = structure(list(structure(list(structure("Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAConn", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAConn", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the connectivity indices descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAConn data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAConn)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAConn.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAConn.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAConst (list) = structure(list(structure(list(structure("Constitutional Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAConst", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAConst", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Constitutional Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the constitutional descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAConst data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAConst)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAConst.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAConst.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AADescAll (list) = structure(list(structure(list(structure("All 2D Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AADescAll", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AADescAll", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("All 2D Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes all the 2D descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AADescAll data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AADescAll)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AADescAll.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AADescAll.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAEdgeAdj (list) = structure(list(structure(list(structure("Edge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAEdgeAdj", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAEdgeAdj", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Edge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the edge adjacency indices descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAEdgeAdj data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAEdgeAdj)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAEdgeAdj.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAEdgeAdj.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAEigIdx (list) = structure(list(structure(list(structure("Eigenvalue-Based Indices Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAEigIdx", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAEigIdx", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Eigenvalue-Based Indices Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the eigenvalue-based indices descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAEigIdx data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAEigIdx)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAEigIdx.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAEigIdx.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAFGC (list) = structure(list(structure(list(structure("Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAFGC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAFGC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the functional group counts descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAFGC data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAFGC)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAFGC.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAFGC.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAGETAWAY (list) = structure(list(structure(list(structure("GETAWAY Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAGETAWAY", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAGETAWAY", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("GETAWAY Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the GETAWAY descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAGETAWAY data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAGETAWAY)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAGETAWAY.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAGETAWAY.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAGeom (list) = structure(list(structure(list(structure("Geometrical Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAGeom", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAGeom", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Geometrical Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the geometrical descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAGeom data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAGeom)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAGeom.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAGeom.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAInfo (list) = structure(list(structure(list(structure("Information Indices Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAInfo", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAInfo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Information Indices Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the information indices descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAInfo data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAInfo)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAInfo.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAInfo.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAMOE2D (list) = structure(list(structure(list(structure("2D Descriptors for 20 Amino Acids calculated by MOE 2011.10", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAMOE2D", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAMOE2D", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("2D Descriptors for 20 Amino Acids calculated by MOE 2011.10\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the 2D descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by MOE 2011.10\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAMOE2D data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAMOE2D)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAMOE2D.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAMOE2D.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAMOE3D (list) = structure(list(structure(list(structure("3D Descriptors for 20 Amino Acids calculated by MOE 2011.10", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAMOE3D", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAMOE3D", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("3D Descriptors for 20 Amino Acids calculated by MOE 2011.10\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the 3D descriptors of the 20 amino acids\n", Rd_tag = "TEXT"), │ │ │ │ @@ -254,15 +254,15 @@ │ │ │ │ structure("before calculating these 3D descriptors.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The SDF file containing the information of the optimized amino acid molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("is included in this package. See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("OptAA3d", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for more information.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAMOE3D data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAMOE3D)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAMOE3D.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAMOE3D.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAMetaInfo (list) = structure(list(structure(list(structure("Meta Information for the 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAMetaInfo", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAMetaInfo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Meta Information for the 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the meta information of\n", Rd_tag = "TEXT"), │ │ │ │ @@ -285,161 +285,161 @@ │ │ │ │ list(structure("PubChem CID for the amino acid", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure(list(structure("PUBCHEM_LINK", Rd_tag = "RCODE")), Rd_tag = "\\code")), │ │ │ │ list(structure("PubChem link for the amino acid", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAMetaInfo data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAMetaInfo)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAMetaInfo.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAMetaInfo)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAMetaInfo.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAMolProp (list) = structure(list(structure(list(structure("Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAMolProp", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAMolProp", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the molecular properties descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAMolProp data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAMolProp)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAMolProp.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAMolProp.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAPAM120 (list) = structure(list(structure(list(structure("PAM120 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAPAM120", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAPAM120", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM120 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM120 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAPAM120 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAPAM120)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM120.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM120.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAPAM250 (list) = structure(list(structure(list(structure("PAM250 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAPAM250", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAPAM250", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM250 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM250 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAPAM250 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAPAM250)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM250.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM250.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAPAM30 (list) = structure(list(structure(list(structure("PAM30 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAPAM30", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAPAM30", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM30 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM30 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAPAM30 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAPAM30)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM30.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM30.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAPAM40 (list) = structure(list(structure(list(structure("PAM40 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAPAM40", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAPAM40", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM40 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM40 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAPAM40 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAPAM40)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM40.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM40.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAPAM70 (list) = structure(list(structure(list(structure("PAM70 Matrix for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAPAM70", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAPAM70", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM70 Matrix for 20 Amino Acids\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PAM70 Matrix for the 20 amino acids. The matrix was extracted from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostrings", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package of Bioconductor.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAPAM70 data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAPAM70)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM70.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM70.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AARDF (list) = structure(list(structure(list(structure("RDF Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AARDF", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AARDF", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("RDF Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the RDF descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AARDF data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AARDF)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AARDF.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AARDF.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AARandic (list) = structure(list(structure(list(structure("Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AARandic", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AARandic", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the Randic molecular profiles descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AARandic data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AARandic)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AARandic.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AARandic.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AATopo (list) = structure(list(structure(list(structure("Topological Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AATopo", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AATopo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Topological Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the topological descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AATopo data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AATopo)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AATopo.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AATopo.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AATopoChg (list) = structure(list(structure(list(structure("Topological Charge Indices Descriptors for 20 Amino Acids\n", Rd_tag = "TEXT"), │ │ │ │ structure("calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AATopoChg", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AATopoChg", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Topological Charge Indices Descriptors for 20 Amino Acids\n", Rd_tag = "TEXT"), │ │ │ │ structure("calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the topological charge indices descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AATopoChg data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AATopoChg)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AATopoChg.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AATopoChg.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAWHIM (list) = structure(list(structure(list(structure("WHIM Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAWHIM", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAWHIM", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("WHIM Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the WHIM descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAWHIM data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAWHIM)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAWHIM.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAWHIM.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAWalk (list) = structure(list(structure(list(structure("Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAWalk", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAWalk", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This dataset includes the walk and path counts descriptors of\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 20 amino acids calculated by Dragon (version 5.4)\n", Rd_tag = "TEXT"), │ │ │ │ structure("used for scales extraction in this package.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAWalk data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAWalk)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAWalk.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAWalk.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ AAindex (list) = structure(list(structure(list(structure("AAindex Data of 544 Physicochemical and Biological Properties\n", Rd_tag = "TEXT"), │ │ │ │ structure("for 20 Amino Acids", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("AAindex", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("AAindex", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAindex Data of 544 Physicochemical and Biological Properties\n", Rd_tag = "TEXT"), │ │ │ │ @@ -449,26 +449,26 @@ │ │ │ │ structure(") as of\n", Rd_tag = "TEXT"), structure("November 2012 (Data Last Modified 2006-08-14).\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("With this data, users could investigate each property's accession number\n", Rd_tag = "TEXT"), │ │ │ │ structure("and other details. Visit ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("https://www.genome.jp/dbget/aaindex.html", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("for more information.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("AAindex data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(AAindex)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/AAindex.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAindex.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ OptAA3d (list) = structure(list(structure(list(structure("OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("OptAA3d", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("OptAA3d", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("OptAA3d data\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# This example requires the rcdk package\n", Rd_tag = "RCODE"), │ │ │ │ structure("# library('rcdk')\n", Rd_tag = "RCODE"), structure("# optaa3d = load.molecules(system.file('sysdata/OptAA3d.sdf', package = 'Rcpi'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# view.molecule.2d(optaa3d[[1]]) # view the first amino acid\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/OptAA3d.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# view.molecule.2d(optaa3d[[1]]) # view the first amino acid\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/OptAA3d.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ Rcpi-package (list) = structure(list(structure(list(structure("Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("Rcpi-package", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("Rcpi", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Rcpi-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -501,15 +501,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("https://github.com/nanxstats/Rcpi", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" Report bugs at ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("https://github.com/nanxstats/Rcpi/issues", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ - structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/Rcpi-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/Rcpi-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ acc (list) = structure(list(structure(list(structure("Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors\n", Rd_tag = "TEXT"), │ │ │ │ structure("of the Same Length", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("acc", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("acc", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates auto covariance and auto cross covariance\n", Rd_tag = "TEXT"), │ │ │ │ @@ -555,15 +555,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("and ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractPCMPropScales", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("p = 8 # p is the scales number\n", Rd_tag = "RCODE"), │ │ │ │ structure("n = 200 # n is the amino acid number\n", Rd_tag = "RCODE"), │ │ │ │ structure("lag = 7 # lag parameter\n", Rd_tag = "RCODE"), │ │ │ │ structure("mat = matrix(rnorm(p * n), nrow = p, ncol = n)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("acc(mat, lag)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/acc.Rd", class = "Rd", meta = list( │ │ │ │ + structure("acc(mat, lag)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/acc.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcDrugFPSim (list) = structure(list(structure(list(structure("Calculate Drug Molecule Similarity Derived by Molecular Fingerprints", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcDrugFPSim", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcDrugFPSim", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate Drug Molecule Similarity Derived by Molecular Fingerprints\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("calcDrugFPSim(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -643,15 +643,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("fp3 = extractDrugEstateComplete(mols[[1]])\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp4 = extractDrugEstateComplete(mols[[2]])\n", Rd_tag = "RCODE"), │ │ │ │ structure("calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'tanimoto')\n", Rd_tag = "RCODE"), │ │ │ │ structure("calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'euclidean')\n", Rd_tag = "RCODE"), │ │ │ │ structure("calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'cosine')\n", Rd_tag = "RCODE"), │ │ │ │ structure("calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'dice')\n", Rd_tag = "RCODE"), │ │ │ │ structure("calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'hamming')", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/calcDrugFPSim.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcDrugFPSim.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcDrugMCSSim (list) = structure(list(structure(list(structure("Calculate Drug Molecule Similarity Derived by\n", Rd_tag = "TEXT"), │ │ │ │ structure("Maximum Common Substructure Search", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcDrugMCSSim", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcDrugMCSSim", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate Drug Molecule Similarity Derived by\n", Rd_tag = "TEXT"), │ │ │ │ @@ -717,15 +717,15 @@ │ │ │ │ structure("mol2 = 'O=C(NCc1cc(OC)c(O)cc1)CCCC/C=C/C(C)C'\n", Rd_tag = "RCODE"), │ │ │ │ structure("mol3 = readChar(system.file('compseq/DB00859.sdf', package = 'Rcpi'), nchars = 1e+6)\n", Rd_tag = "RCODE"), │ │ │ │ structure("mol4 = readChar(system.file('compseq/DB00860.sdf', package = 'Rcpi'), nchars = 1e+6)\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "VERB"), structure("sim1 = calcDrugMCSSim(mol1, mol2, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("sim2 = calcDrugMCSSim(mol3, mol4, type = 'sdf', plot = TRUE)\n", Rd_tag = "VERB"), │ │ │ │ structure("print(sim1[[2]]) # Tanimoto Coefficient\n", Rd_tag = "VERB"), │ │ │ │ structure("print(sim2[[3]]) # Overlap Coefficient\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/calcDrugMCSSim.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcDrugMCSSim.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcParProtGOSim (list) = structure(list(structure(list(structure("Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcParProtGOSim", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcParProtGOSim", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("calcParProtGOSim(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -853,15 +853,15 @@ │ │ │ │ structure("go3 = c('GO:0003735', 'GO:0005622', 'GO:0005840', 'GO:0006412') # PDE4DIP\n", Rd_tag = "RCODE"), │ │ │ │ structure("glist = list(go1, go2, go3)\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("calcParProtGOSim(glist, type = 'go', ont = 'CC', measure = 'Wang')", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# By Entrez gene id\n", Rd_tag = "RCODE"), │ │ │ │ structure("genelist = list(c('150', '151', '152', '1814', '1815', '1816'))\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("calcParProtGOSim(genelist, type = 'gene', ont = 'BP', measure = 'Wang')", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/calcParProtGOSim.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcParProtGOSim.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcParProtSeqSim (list) = structure(list(structure(list(structure("Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcParProtSeqSim", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcParProtSeqSim", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("calcParProtSeqSim(protlist, cores = 2, type = \"local\", submat = \"BLOSUM62\")\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -942,15 +942,15 @@ │ │ │ │ structure("s3 = readFASTA(system.file('protseq/P10323.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("s4 = readFASTA(system.file('protseq/P20160.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("s5 = readFASTA(system.file('protseq/Q9NZP8.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("plist = list(s1, s2, s3, s4, s5)\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("psimmat = calcParProtSeqSim(plist, cores = 2, type = 'local',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" submat = 'BLOSUM62')\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(psimmat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/calcParProtSeqSim.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcParProtSeqSim.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcTwoProtGOSim (list) = structure(list(structure(list(structure("Protein Similarity Calculation based on Gene Ontology (GO) Similarity", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcTwoProtGOSim", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcTwoProtGOSim", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Protein Similarity Calculation based on Gene Ontology (GO) Similarity\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("calcTwoProtGOSim(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1076,15 +1076,15 @@ │ │ │ │ structure("go1 = c(\"GO:0004022\", \"GO:0004024\", \"GO:0004023\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("go2 = c(\"GO:0009055\", \"GO:0020037\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("calcTwoProtGOSim(go1, go2, type = 'go', ont = 'MF', measure = 'Wang')", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# By Entrez gene id\n", Rd_tag = "RCODE"), │ │ │ │ structure("gene1 = '241'\n", Rd_tag = "RCODE"), structure("gene2 = '251'\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("calcTwoProtGOSim(gene1, gene2, type = 'gene', ont = 'CC', measure = 'Lin')", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/calcTwoProtGOSim.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcTwoProtGOSim.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcTwoProtSeqSim (list) = structure(list(structure(list(structure("Protein Sequence Alignment for Two Protein Sequences", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcTwoProtSeqSim", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcTwoProtSeqSim", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Protein Sequence Alignment for Two Protein Sequences\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("calcTwoProtSeqSim(seq1, seq2, type = \"local\", submat = \"BLOSUM62\")\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1143,15 +1143,15 @@ │ │ │ │ structure("calcTwoProtGOSim", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for calculating the\n", Rd_tag = "TEXT"), │ │ │ │ structure("GO semantic similarity between two groups of GO terms or two Entrez gene IDs.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("s1 = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("s2 = readFASTA(system.file('protseq/P10323.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("seqalign = calcTwoProtSeqSim(s1, s2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("seqalign\n", Rd_tag = "RCODE"), structure("slot(seqalign, \"score\")", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/calcTwoProtSeqSim.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcTwoProtSeqSim.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ checkProt (list) = structure(list(structure(list(structure("Check if the protein sequence's amino acid types are the 20 default types", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("checkProt", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("checkProt", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Check if the protein sequence's amino acid types are the 20 default types\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("checkProt(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1162,15 +1162,15 @@ │ │ │ │ structure("the 20 default types.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Logical. ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("TRUE", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" if all of the amino acid types of the sequence\n", Rd_tag = "TEXT"), │ │ │ │ structure(" are within the 20 default types.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("checkProt(x) # TRUE\n", Rd_tag = "RCODE"), │ │ │ │ - structure("checkProt(paste(x, 'Z', sep = '')) # FALSE\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/checkProt.Rd", class = "Rd", meta = list( │ │ │ │ + structure("checkProt(paste(x, 'Z', sep = '')) # FALSE\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/checkProt.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ convMolFormat (list) = structure(list(structure(list(structure("Chemical File Formats Conversion", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("convMolFormat", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("convMolFormat", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Chemical File Formats Conversion\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("convMolFormat(infile, outfile, from, to)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1520,15 +1520,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure("# SDF to SMILES\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ structure("\n", Rd_tag = "VERB"), structure("convMolFormat(infile = sdf, outfile = 'aa.smi',\n", Rd_tag = "VERB"), │ │ │ │ structure(" from = 'sdf', to = 'smiles')", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# SMILES to MOPAC Cartesian format\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "VERB"), structure("convMolFormat(infile = 'aa.smi', outfile = 'aa.mop',\n", Rd_tag = "VERB"), │ │ │ │ structure(" from = 'smiles', to = 'mop')", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/convMolFormat.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/convMolFormat.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugAIO (list) = structure(list(structure(list(structure("Calculate All Molecular Descriptors in Rcpi at Once", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugAIO", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugAIO", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate All Molecular Descriptors in Rcpi at Once\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugAIO(molecules, silent = TRUE, warn = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1559,15 +1559,15 @@ │ │ │ │ structure("values will be ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("NA", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# Load 20 small molecules that have 3D coordinates\n", Rd_tag = "RCODE"), │ │ │ │ structure("sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSDF(sdf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugAIO(mol, warn = FALSE)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAIO.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAIO.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugALOGP (list) = structure(list(structure(list(structure("Calculate Atom Additive logP and Molar Refractivity Values Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugALOGP", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugALOGP", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate Atom Additive logP and Molar Refractivity Values Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugALOGP(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1606,15 +1606,15 @@ │ │ │ │ structure("quantitative structure-activity relationships.\n", Rd_tag = "TEXT"), │ │ │ │ structure("2. Modeling dispersive and hydrophobic interactions,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of Chemical Information and Computer Science, 1987, 27:21-35.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugALOGP(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugALOGP.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugALOGP.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugAminoAcidCount (list) = structure(list(structure(list(structure("Calculate the Number of Amino Acids Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugAminoAcidCount", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugAminoAcidCount", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Number of Amino Acids Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugAminoAcidCount(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1653,15 +1653,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("nV", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure("nW", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugAminoAcidCount(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAminoAcidCount.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAminoAcidCount.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugApol (list) = structure(list(structure(list(structure("Calculate the Sum of the Atomic Polarizabilities Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugApol", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugApol", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Sum of the Atomic Polarizabilities Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugApol(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1684,15 +1684,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("apol", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugApol(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugApol.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugApol.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugAromaticAtomsCount (list) = structure(list(structure(list(structure("Calculate the Number of Aromatic Atoms Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugAromaticAtomsCount", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugAromaticAtomsCount", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Number of Aromatic Atoms Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugAromaticAtomsCount(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1711,15 +1711,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("naAromAtom", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugAromaticAtomsCount(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAromaticAtomsCount.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAromaticAtomsCount.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugAromaticBondsCount (list) = structure(list(structure(list(structure("Calculate the Number of Aromatic Bonds Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugAromaticBondsCount", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugAromaticBondsCount", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Number of Aromatic Bonds Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugAromaticBondsCount(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1738,15 +1738,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("nAromBond", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugAromaticBondsCount(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAromaticBondsCount.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAromaticBondsCount.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugAtomCount (list) = structure(list(structure(list(structure("Calculate the Number of Atom Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugAtomCount", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugAtomCount", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Number of Atom Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugAtomCount(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1766,15 +1766,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("nAtom", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugAtomCount(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAtomCount.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAtomCount.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugAutocorrelationCharge (list) = structure(list(structure(list(structure("Calculate the Moreau-Broto Autocorrelation Descriptors using Partial Charges", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugAutocorrelationCharge", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugAutocorrelationCharge", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Moreau-Broto Autocorrelation Descriptors using Partial Charges\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugAutocorrelationCharge(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1798,15 +1798,15 @@ │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure("ATSc4", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure("ATSc5", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugAutocorrelationCharge(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAutocorrelationCharge.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAutocorrelationCharge.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugAutocorrelationMass (list) = structure(list(structure(list(structure("Calculate the Moreau-Broto Autocorrelation Descriptors using Atomic Weight", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugAutocorrelationMass", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugAutocorrelationMass", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Moreau-Broto Autocorrelation Descriptors using Atomic Weight\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugAutocorrelationMass(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1832,15 +1832,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Moreau, Gilles, and Pierre Broto.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The autocorrelation of a topological structure: a new molecular descriptor.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Nouv. J. Chim 4 (1980): 359-360.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugAutocorrelationMass(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAutocorrelationMass.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAutocorrelationMass.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugAutocorrelationPolarizability (list) = structure(list(structure(list(structure("Calculate the Moreau-Broto Autocorrelation Descriptors using Polarizability", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugAutocorrelationPolarizability", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugAutocorrelationPolarizability", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Moreau-Broto Autocorrelation Descriptors using Polarizability\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugAutocorrelationPolarizability(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1862,15 +1862,15 @@ │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure("ATSp4", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure("ATSp5", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugAutocorrelationPolarizability(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAutocorrelationPolarizability.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAutocorrelationPolarizability.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugBCUT (list) = structure(list(structure(list(structure("BCUT -- Eigenvalue Based Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugBCUT", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugBCUT", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("BCUT -- Eigenvalue Based Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugBCUT(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1946,15 +1946,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Kang, Y.K. and Jhon, M.S.,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Additivity of Atomic Static Polarizabilities and Dispersion Coefficients,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Theoretica Chimica Acta, 1982, 61:41-48\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugBCUT(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugBCUT.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugBCUT.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugBPol (list) = structure(list(structure(list(structure("Calculate the Descriptor that Describes the Sum of the Absolute\n", Rd_tag = "TEXT"), │ │ │ │ structure("Value of the Difference between Atomic Polarizabilities of\n", Rd_tag = "TEXT"), │ │ │ │ structure("All Bonded Atoms in the Molecule", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugBPol", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugBPol", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1982,15 +1982,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("bpol", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugBPol(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugBPol.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugBPol.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugBondCount (list) = structure(list(structure(list(structure("Calculate the Descriptor Based on the Number of Bonds of a\n", Rd_tag = "TEXT"), │ │ │ │ structure("Certain Bond Order", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugBondCount", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugBondCount", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Descriptor Based on the Number of Bonds of a\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2012,15 +2012,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("nB", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugBondCount(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugBondCount.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugBondCount.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugCPSA (list) = structure(list(structure(list(structure("A Variety of Descriptors Combining Surface Area and Partial Charge Information", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugCPSA", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugCPSA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A Variety of Descriptors Combining Surface Area and Partial Charge Information\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugCPSA(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2140,15 +2140,15 @@ │ │ │ │ structure("Area Structural Descriptors in Computer Assissted\n", Rd_tag = "TEXT"), │ │ │ │ structure("Quantitative Structure Property Relationship Studies,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Analytical Chemistry, 1990, 62:2323.2329.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSDF(sdf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugCPSA(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugCPSA.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugCPSA.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugCarbonTypes (list) = structure(list(structure(list(structure("Topological Descriptor Characterizing the Carbon Connectivity\n", Rd_tag = "TEXT"), │ │ │ │ structure("in Terms of Hybridization", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugCarbonTypes", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugCarbonTypes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Topological Descriptor Characterizing the Carbon Connectivity\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2207,15 +2207,15 @@ │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure("C3SP3", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure("C4SP3", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugCarbonTypes(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugCarbonTypes.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugCarbonTypes.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugChiChain (list) = structure(list(structure(list(structure("Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugChiChain", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugChiChain", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugChiChain(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2272,15 +2272,15 @@ │ │ │ │ structure("recent versions of Molconn-Z use simplified fragment definitions\n", Rd_tag = "TEXT"), │ │ │ │ structure("(i.e., rings without branches etc.) whereas these descriptors use\n", Rd_tag = "TEXT"), │ │ │ │ structure("the older more complex fragment definitions.\n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugChiChain(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugChiChain.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugChiChain.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugChiCluster (list) = structure(list(structure(list(structure("Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugChiCluster", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugChiCluster", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugChiCluster(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2316,15 +2316,15 @@ │ │ │ │ structure("In addition, recent versions of Molconn-Z use simplified fragment\n", Rd_tag = "TEXT"), │ │ │ │ structure("definitions (i.e., rings without branches etc.)\n", Rd_tag = "TEXT"), │ │ │ │ structure("whereas these descriptors use the older more complex fragment definitions.\n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugChiCluster(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugChiCluster.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugChiCluster.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugChiPath (list) = structure(list(structure(list(structure("Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugChiPath", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugChiPath", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugChiPath(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2356,15 +2356,15 @@ │ │ │ │ structure("In addition, recent versions of Molconn-Z use simplified fragment definitions\n", Rd_tag = "TEXT"), │ │ │ │ structure("(i.e., rings without branches etc.) whereas these descriptors use the older\n", Rd_tag = "TEXT"), │ │ │ │ structure("more complex fragment definitions.\n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugChiPath(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugChiPath.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugChiPath.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugChiPathCluster (list) = structure(list(structure(list(structure("Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugChiPathCluster", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugChiPathCluster", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugChiPathCluster(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2418,15 +2418,15 @@ │ │ │ │ structure(" fragment definitions (i.e., rings without branches etc.)\n", Rd_tag = "TEXT"), │ │ │ │ structure(" whereas these descriptors use the older more complex\n", Rd_tag = "TEXT"), │ │ │ │ structure(" fragment definitions.\n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugChiPathCluster(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugChiPathCluster.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugChiPathCluster.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugDescOB (list) = structure(list(structure(list(structure("Calculate Molecular Descriptors Provided by OpenBabel", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugDescOB", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugDescOB", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate Molecular Descriptors Provided by OpenBabel\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugDescOB(molecules, type = c(\"smile\", \"sdf\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2515,15 +2515,15 @@ │ │ │ │ structure("mol4 = readChar(system.file('sysdata/OptAA3d.sdf', package = 'Rcpi'),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" nchars = 1e+6) # multiple molecules in a sdf file\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(list(structure("\n", Rd_tag = "VERB"), │ │ │ │ structure("smidesc0 = extractDrugDescOB(mol1, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("smidesc1 = extractDrugDescOB(mol2, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdfdesc0 = extractDrugDescOB(mol3, type = 'sdf')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdfdesc1 = extractDrugDescOB(mol4, type = 'sdf')", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugDescOB.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugDescOB.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugECI (list) = structure(list(structure(list(structure("Calculate the Eccentric Connectivity Index Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugECI", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugECI", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Eccentric Connectivity Index Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugECI(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2555,15 +2555,15 @@ │ │ │ │ structure("Eccentric Connectivity Index: A Novel Highly Discriminating\n", Rd_tag = "TEXT"), │ │ │ │ structure("Topological Descriptor for Structure-Property and Structure-Activity Studies,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of Chemical Information and Computer Sciences, 37:273-282\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugECI(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugECI.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugECI.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugEstate (list) = structure(list(structure(list(structure("Calculate the E-State Molecular Fingerprints (in Compact Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugEstate", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugEstate", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the E-State Molecular Fingerprints (in Compact Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugEstate(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2584,15 +2584,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugEstateComplete", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugEstate(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugEstate.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugEstate.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugEstateComplete (list) = structure(list(structure(list(structure("Calculate the E-State Molecular Fingerprints (in Complete Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugEstateComplete", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugEstateComplete", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the E-State Molecular Fingerprints (in Complete Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugEstateComplete(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2612,15 +2612,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugEstate", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugEstateComplete(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugEstateComplete.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugEstateComplete.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugExtended (list) = structure(list(structure(list(structure("Calculate the Extended Molecular Fingerprints (in Compact Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugExtended", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugExtended", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Extended Molecular Fingerprints (in Compact Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugExtended(molecules, depth = 6, size = 1024, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2654,15 +2654,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugExtendedComplete", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugExtended(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugExtended.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugExtended.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugExtendedComplete (list) = structure(list(structure(list(structure("Calculate the Extended Molecular Fingerprints (in Complete Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugExtendedComplete", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugExtendedComplete", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Extended Molecular Fingerprints (in Complete Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugExtendedComplete(molecules, depth = 6, size = 1024, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2694,15 +2694,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugExtended", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugExtendedComplete(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugExtendedComplete.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugExtendedComplete.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugFMF (list) = structure(list(structure(list(structure("Calculate the FMF Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugFMF", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugFMF", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the FMF Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugFMF(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2730,15 +2730,15 @@ │ │ │ │ structure("Investigation of the relationship between topology and selectivity\n", Rd_tag = "TEXT"), │ │ │ │ structure("for druglike molecules. Journal of medicinal chemistry,\n", Rd_tag = "TEXT"), │ │ │ │ structure("53(21), 7709-7714.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugFMF(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugFMF.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugFMF.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugFragmentComplexity (list) = structure(list(structure(list(structure("Calculate Complexity of a System", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugFragmentComplexity", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugFragmentComplexity", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate Complexity of a System\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugFragmentComplexity(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2767,15 +2767,15 @@ │ │ │ │ structure("for use in structure-activity studies:\n", Rd_tag = "TEXT"), │ │ │ │ structure("database mining and recursive partitioning.,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of chemical information and modeling, 2006, 46:1069-1077\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugFragmentComplexity(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugFragmentComplexity.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugFragmentComplexity.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugGraph (list) = structure(list(structure(list(structure("Calculate the Graph Molecular Fingerprints (in Compact Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugGraph", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugGraph", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Graph Molecular Fingerprints (in Compact Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugGraph(molecules, depth = 6, size = 1024, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2807,15 +2807,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugGraphComplete", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugGraph(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugGraph.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugGraph.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugGraphComplete (list) = structure(list(structure(list(structure("Calculate the Graph Molecular Fingerprints (in Complete Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugGraphComplete", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugGraphComplete", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Graph Molecular Fingerprints (in Complete Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugGraphComplete(molecules, depth = 6, size = 1024, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2846,15 +2846,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugGraph", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugGraphComplete(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugGraphComplete.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugGraphComplete.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugGravitationalIndex (list) = structure(list(structure(list(structure("Descriptor Characterizing the Mass Distribution of the Molecule.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugGravitationalIndex", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugGravitationalIndex", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor Characterizing the Mass Distribution of the Molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugGravitationalIndex(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2912,15 +2912,15 @@ │ │ │ │ structure("Prediction of Human Intestinal Absorption of Drug Compounds\n", Rd_tag = "TEXT"), │ │ │ │ structure("From Molecular Structure,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of Chemical Information and Computer Sciences, 1998, 38:726-735.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSDF(sdf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugGravitationalIndex(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugGravitationalIndex.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugGravitationalIndex.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugHBondAcceptorCount (list) = structure(list(structure(list(structure("Number of Hydrogen Bond Acceptors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugHBondAcceptorCount", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugHBondAcceptorCount", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Number of Hydrogen Bond Acceptors\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugHBondAcceptorCount(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2950,15 +2950,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("nHBAcc", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugHBondAcceptorCount(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHBondAcceptorCount.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHBondAcceptorCount.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugHBondDonorCount (list) = structure(list(structure(list(structure("Number of Hydrogen Bond Donors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugHBondDonorCount", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugHBondDonorCount", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Number of Hydrogen Bond Donors\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugHBondDonorCount(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2986,15 +2986,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("nHBDon", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugHBondDonorCount(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHBondDonorCount.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHBondDonorCount.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugHybridization (list) = structure(list(structure(list(structure("Calculate the Hybridization Molecular Fingerprints (in Compact Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugHybridization", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugHybridization", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Hybridization Molecular Fingerprints (in Compact Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugHybridization(molecules, depth = 6, size = 1024, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3026,15 +3026,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugHybridizationComplete", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugHybridization(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHybridization.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHybridization.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugHybridizationComplete (list) = structure(list(structure(list(structure("Calculate the Hybridization Molecular Fingerprints (in Complete Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugHybridizationComplete", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugHybridizationComplete", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Hybridization Molecular Fingerprints (in Complete Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugHybridizationComplete(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -3068,15 +3068,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugHybridization", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugHybridizationComplete(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHybridizationComplete.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHybridizationComplete.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugHybridizationRatio (list) = structure(list(structure(list(structure("Descriptor that Characterizing Molecular Complexity\n", Rd_tag = "TEXT"), │ │ │ │ structure("in Terms of Carbon Hybridization States", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugHybridizationRatio", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugHybridizationRatio", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Characterizing Molecular Complexity\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3103,15 +3103,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("HybRatio", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugHybridizationRatio(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHybridizationRatio.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHybridizationRatio.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugIPMolecularLearning (list) = structure(list(structure(list(structure("Calculate the Descriptor that Evaluates the Ionization Potential", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugIPMolecularLearning", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugIPMolecularLearning", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Descriptor that Evaluates the Ionization Potential\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugIPMolecularLearning(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3131,15 +3131,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("MolIP", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugIPMolecularLearning(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugIPMolecularLearning.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugIPMolecularLearning.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugKR (list) = structure(list(structure(list(structure("Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugKR", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugKR", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugKR(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3159,15 +3159,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugKRComplete", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugKR(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugKR.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugKR.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugKRComplete (list) = structure(list(structure(list(structure("Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugKRComplete", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugKRComplete", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugKRComplete(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3186,15 +3186,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugKR", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugKRComplete(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugKRComplete.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugKRComplete.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugKappaShapeIndices (list) = structure(list(structure(list(structure("Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugKappaShapeIndices", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugKappaShapeIndices", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugKappaShapeIndices(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3233,15 +3233,15 @@ │ │ │ │ structure(list(structure("Kier3", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" - Third kappa shape index\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugKappaShapeIndices(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugKappaShapeIndices.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugKappaShapeIndices.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugKierHallSmarts (list) = structure(list(structure(list(structure("Descriptor that Counts the Number of Occurrences of the E-State Fragments", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugKierHallSmarts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugKierHallSmarts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Counts the Number of Occurrences of the E-State Fragments\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugKierHallSmarts(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3916,15 +3916,15 @@ │ │ │ │ structure("A Novel Combination of Electronic, Topological,\n", Rd_tag = "TEXT"), │ │ │ │ structure("and Valence State Information,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of Chemical Information and Computer Science, 1995, 35:1039-1045.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugKierHallSmarts(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugKierHallSmarts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugKierHallSmarts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugLargestChain (list) = structure(list(structure(list(structure("Descriptor that Calculates the Number of Atoms in the Largest Chain", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugLargestChain", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugLargestChain", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Number of Atoms in the Largest Chain\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugLargestChain(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3947,15 +3947,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("nAtomLC", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugLargestChain(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugLargestChain.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugLargestChain.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugLargestPiSystem (list) = structure(list(structure(list(structure("Descriptor that Calculates the Number of Atoms in the Largest Pi Chain", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugLargestPiSystem", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugLargestPiSystem", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Number of Atoms in the Largest Pi Chain\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugLargestPiSystem(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3974,15 +3974,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("nAtomP", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugLargestPiSystem(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugLargestPiSystem.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugLargestPiSystem.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugLengthOverBreadth (list) = structure(list(structure(list(structure("Calculate the Ratio of Length to Breadth Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugLengthOverBreadth", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugLengthOverBreadth", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Ratio of Length to Breadth Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugLengthOverBreadth(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4014,15 +4014,15 @@ │ │ │ │ structure("minimum area (defined by the product of the X & Y extents for that orientation).\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The descriptor assumes that the atoms have been configured.\n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSDF(sdf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugLengthOverBreadth(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugLengthOverBreadth.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugLengthOverBreadth.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugLongestAliphaticChain (list) = structure(list(structure(list(structure("Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugLongestAliphaticChain", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugLongestAliphaticChain", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugLongestAliphaticChain(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4041,15 +4041,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("nAtomLAC", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugLongestAliphaticChain(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugLongestAliphaticChain.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugLongestAliphaticChain.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugMACCS (list) = structure(list(structure(list(structure("Calculate the MACCS Molecular Fingerprints (in Compact Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugMACCS", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugMACCS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the MACCS Molecular Fingerprints (in Compact Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugMACCS(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4069,15 +4069,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugMACCSComplete", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugMACCS(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMACCS.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMACCS.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugMACCSComplete (list) = structure(list(structure(list(structure("Calculate the MACCS Molecular Fingerprints (in Complete Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugMACCSComplete", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugMACCSComplete", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the MACCS Molecular Fingerprints (in Complete Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugMACCSComplete(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4096,15 +4096,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugMACCS", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugMACCSComplete(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMACCSComplete.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMACCSComplete.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugMDE (list) = structure(list(structure(list(structure("Calculate Molecular Distance Edge (MDE) Descriptors for C, N and O", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugMDE", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugMDE", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate Molecular Distance Edge (MDE) Descriptors for C, N and O\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugMDE(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4129,15 +4129,15 @@ │ │ │ │ structure("Approach to estimation and prediction for normal boiling point (NBP)\n", Rd_tag = "TEXT"), │ │ │ │ structure("of alkanes based on a novel molecular distance-edge (MDE) vector, lambda.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of chemical information and computer sciences, 38(3), 387-394.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugMDE(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMDE.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMDE.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugMannholdLogP (list) = structure(list(structure(list(structure("Descriptor that Calculates the LogP Based on a Simple Equation\n", Rd_tag = "TEXT"), │ │ │ │ structure("Using the Number of Carbons and Hetero Atoms", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugMannholdLogP", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugMannholdLogP", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the LogP Based on a Simple Equation\n", Rd_tag = "TEXT"), │ │ │ │ @@ -4164,15 +4164,15 @@ │ │ │ │ structure("Calculation of molecular lipophilicity: State-of-the-art and\n", Rd_tag = "TEXT"), │ │ │ │ structure("comparison of log P methods on more than 96,000 compounds.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of pharmaceutical sciences, 98(3), 861-893.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugMannholdLogP(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMannholdLogP.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMannholdLogP.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugMomentOfInertia (list) = structure(list(structure(list(structure("Descriptor that Calculates the Principal Moments of\n", Rd_tag = "TEXT"), │ │ │ │ structure("Inertia and Ratios of the Principal Moments", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugMomentOfInertia", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugMomentOfInertia", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Principal Moments of\n", Rd_tag = "TEXT"), │ │ │ │ @@ -4228,15 +4228,15 @@ │ │ │ │ structure("of the MI tensor are below ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("1e-3", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure("then the ratio's are set to a default of 1000.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSDF(sdf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugMomentOfInertia(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMomentOfInertia.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMomentOfInertia.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugOBFP2 (list) = structure(list(structure(list(structure("Calculate the FP2 Molecular Fingerprints", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugOBFP2", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugOBFP2", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the FP2 Molecular Fingerprints\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugOBFP2(molecules, type = c(\"smile\", \"sdf\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4261,15 +4261,15 @@ │ │ │ │ structure("mol4 = readChar(system.file('sysdata/OptAA3d.sdf', package = 'Rcpi'),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" nchars = 1e+6) # multiple molecules in a sdf file\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(list(structure("\n", Rd_tag = "VERB"), │ │ │ │ structure("smifp0 = extractDrugOBFP2(mol1, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("smifp1 = extractDrugOBFP2(mol2, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdffp0 = extractDrugOBFP2(mol3, type = 'sdf')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdffp1 = extractDrugOBFP2(mol4, type = 'sdf')", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugOBFP2.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugOBFP2.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugOBFP3 (list) = structure(list(structure(list(structure("Calculate the FP3 Molecular Fingerprints", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugOBFP3", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugOBFP3", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the FP3 Molecular Fingerprints\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugOBFP3(molecules, type = c(\"smile\", \"sdf\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4293,15 +4293,15 @@ │ │ │ │ structure(" nchars = 1e+6) # single molecule in a sdf file\n", Rd_tag = "RCODE"), │ │ │ │ structure("mol4 = readChar(system.file('sysdata/OptAA3d.sdf', package = 'Rcpi'),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" nchars = 1e+6) # multiple molecules in a sdf file\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "VERB"), structure("smifp0 = extractDrugOBFP3(mol1, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("smifp1 = extractDrugOBFP3(mol2, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdffp0 = extractDrugOBFP3(mol3, type = 'sdf')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdffp1 = extractDrugOBFP3(mol4, type = 'sdf')", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugOBFP3.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugOBFP3.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugOBFP4 (list) = structure(list(structure(list(structure("Calculate the FP4 Molecular Fingerprints", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugOBFP4", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugOBFP4", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the FP4 Molecular Fingerprints\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugOBFP4(molecules, type = c(\"smile\", \"sdf\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4326,15 +4326,15 @@ │ │ │ │ structure("mol4 = readChar(system.file('sysdata/OptAA3d.sdf', package = 'Rcpi'),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" nchars = 1e+6) # multiple molecules in a sdf file\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(list(structure("\n", Rd_tag = "VERB"), │ │ │ │ structure("smifp0 = extractDrugOBFP4(mol1, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("smifp1 = extractDrugOBFP4(mol2, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdffp0 = extractDrugOBFP4(mol3, type = 'sdf')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdffp1 = extractDrugOBFP4(mol4, type = 'sdf')", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugOBFP4.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugOBFP4.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugOBMACCS (list) = structure(list(structure(list(structure("Calculate the MACCS Molecular Fingerprints", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugOBMACCS", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugOBMACCS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the MACCS Molecular Fingerprints\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugOBMACCS(molecules, type = c(\"smile\", \"sdf\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4360,15 +4360,15 @@ │ │ │ │ structure(" nchars = 1e+6) # multiple molecules in a sdf file\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(list(structure("\n", Rd_tag = "VERB"), │ │ │ │ structure("# MACCS may not be available in current version of ChemmineOB\n", Rd_tag = "VERB"), │ │ │ │ structure("smifp0 = extractDrugOBMACCS(mol1, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("smifp1 = extractDrugOBMACCS(mol2, type = 'smile')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdffp0 = extractDrugOBMACCS(mol3, type = 'sdf')\n", Rd_tag = "VERB"), │ │ │ │ structure("sdffp1 = extractDrugOBMACCS(mol4, type = 'sdf')", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugOBMACCS.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugOBMACCS.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugPetitjeanNumber (list) = structure(list(structure(list(structure("Descriptor that Calculates the Petitjean Number of a Molecule", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugPetitjeanNumber", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugPetitjeanNumber", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Petitjean Number of a Molecule\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugPetitjeanNumber(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4405,15 +4405,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("PetitjeanNumber", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugPetitjeanNumber(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugPetitjeanNumber.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugPetitjeanNumber.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugPetitjeanShapeIndex (list) = structure(list(structure(list(structure("Descriptor that Calculates the Petitjean Shape Indices", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugPetitjeanShapeIndex", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugPetitjeanShapeIndex", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Petitjean Shape Indices\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugPetitjeanShapeIndex(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4444,15 +4444,15 @@ │ │ │ │ structure("The Extent of the Relationship between the Graph-Theoretical\n", Rd_tag = "TEXT"), │ │ │ │ structure("and the Geometrical Shape Coefficients of Chemical Compounds,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of Chemical Information and Computer Science, 1995, 35:714-716.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSDF(sdf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugPetitjeanShapeIndex(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugPetitjeanShapeIndex.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugPetitjeanShapeIndex.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugPubChem (list) = structure(list(structure(list(structure("Calculate the PubChem Molecular Fingerprints (in Compact Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugPubChem", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugPubChem", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the PubChem Molecular Fingerprints (in Compact Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugPubChem(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4472,15 +4472,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugPubChemComplete", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugPubChem(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugPubChem.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugPubChem.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugPubChemComplete (list) = structure(list(structure(list(structure("Calculate the PubChem Molecular Fingerprints (in Complete Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugPubChemComplete", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugPubChemComplete", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the PubChem Molecular Fingerprints (in Complete Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugPubChemComplete(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4499,15 +4499,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugPubChem", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugPubChemComplete(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugPubChemComplete.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugPubChemComplete.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugRotatableBondsCount (list) = structure(list(structure(list(structure("Descriptor that Calculates the Number of Nonrotatable Bonds on A Molecule", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugRotatableBondsCount", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugRotatableBondsCount", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Number of Nonrotatable Bonds on A Molecule\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugRotatableBondsCount(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4529,15 +4529,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("nRotB", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugRotatableBondsCount(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugRotatableBondsCount.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugRotatableBondsCount.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugRuleOfFive (list) = structure(list(structure(list(structure("Descriptor that Calculates the Number Failures of the Lipinski's Rule Of Five", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugRuleOfFive", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugRuleOfFive", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Number Failures of the Lipinski's Rule Of Five\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugRuleOfFive(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4558,15 +4558,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("LipinskiFailures", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugRuleOfFive(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugRuleOfFive.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugRuleOfFive.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugShortestPath (list) = structure(list(structure(list(structure("Calculate the Shortest Path Molecular Fingerprints (in Compact Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugShortestPath", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugShortestPath", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Shortest Path Molecular Fingerprints (in Compact Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugShortestPath(molecules, depth = 6, size = 1024, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4597,15 +4597,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugShortestPathComplete", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugShortestPath(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugShortestPath.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugShortestPath.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugShortestPathComplete (list) = structure(list(structure(list(structure("Calculate the Shortest Path Molecular Fingerprints (in Complete Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugShortestPathComplete", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugShortestPathComplete", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Shortest Path Molecular Fingerprints (in Complete Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugShortestPathComplete(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -4638,15 +4638,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugShortestPath", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugShortestPathComplete(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugShortestPathComplete.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugShortestPathComplete.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugStandard (list) = structure(list(structure(list(structure("Calculate the Standard Molecular Fingerprints (in Compact Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugStandard", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugStandard", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Standard Molecular Fingerprints (in Compact Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugStandard(molecules, depth = 6, size = 1024, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4678,15 +4678,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugStandardComplete", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugStandard(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugStandard.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugStandard.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugStandardComplete (list) = structure(list(structure(list(structure("Calculate the Standard Molecular Fingerprints (in Complete Format)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugStandardComplete", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugStandardComplete", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the Standard Molecular Fingerprints (in Complete Format)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugStandardComplete(molecules, depth = 6, size = 1024, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4717,15 +4717,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("extractDrugStandard", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("fp = extractDrugStandardComplete(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(fp)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugStandardComplete.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugStandardComplete.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugTPSA (list) = structure(list(structure(list(structure("Descriptor of Topological Polar Surface Area Based on\n", Rd_tag = "TEXT"), │ │ │ │ structure("Fragment Contributions (TPSA)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugTPSA", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugTPSA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor of Topological Polar Surface Area Based on\n", Rd_tag = "TEXT"), │ │ │ │ @@ -4752,15 +4752,15 @@ │ │ │ │ structure("fragment-based contributions and its application to the prediction\n", Rd_tag = "TEXT"), │ │ │ │ structure("of drug transport properties.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of medicinal chemistry, 43(20), 3714-3717.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugTPSA(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugTPSA.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugTPSA.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugVABC (list) = structure(list(structure(list(structure("Descriptor that Calculates the Volume of A Molecule", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugVABC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugVABC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Volume of A Molecule\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugVABC(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4779,15 +4779,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("VABC", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugVABC(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugVABC.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugVABC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugVAdjMa (list) = structure(list(structure(list(structure("Descriptor that Calculates the Vertex Adjacency Information of A Molecule", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugVAdjMa", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugVAdjMa", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Vertex Adjacency Information of A Molecule\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugVAdjMa(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4815,15 +4815,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("VAdjMat", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugVAdjMa(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugVAdjMa.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugVAdjMa.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugWHIM (list) = structure(list(structure(list(structure("Calculate Holistic Descriptors Described by Todeschini et al.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugWHIM", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugWHIM", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate Holistic Descriptors Described by Todeschini et al.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugWHIM(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4895,15 +4895,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Todeschini, R. and Gramatica, P.,\n", Rd_tag = "TEXT"), │ │ │ │ structure("New 3D Molecular Descriptors: The WHIM theory and QAR Applications,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Persepectives in Drug Discovery and Design, 1998, ?:355-380.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSDF(sdf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugWHIM(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugWHIM.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugWHIM.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugWeight (list) = structure(list(structure(list(structure("Descriptor that Calculates the Total Weight of Atoms", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugWeight", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugWeight", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Total Weight of Atoms\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugWeight(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4922,15 +4922,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("MW", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugWeight(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugWeight.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugWeight.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugWeightedPath (list) = structure(list(structure(list(structure("Descriptor that Calculates the Weighted Path (Molecular ID)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugWeightedPath", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugWeightedPath", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Weighted Path (Molecular ID)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugWeightedPath(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -4976,15 +4976,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Randic, M., On molecular identification numbers (1984).\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of Chemical Information and Computer Science, 24:164-175.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugWeightedPath(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugWeightedPath.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugWeightedPath.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugWienerNumbers (list) = structure(list(structure(list(structure("Descriptor that Calculates Wiener Path Number and Wiener Polarity Number", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugWienerNumbers", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugWienerNumbers", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates Wiener Path Number and Wiener Polarity Number\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractDrugWienerNumbers(molecules, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5011,15 +5011,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Wiener, H. (1947).\n", Rd_tag = "TEXT"), │ │ │ │ structure("Structural determination of paraffin boiling points.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of the American Chemical Society, 69(1), 17-20.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugWienerNumbers(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugWienerNumbers.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugWienerNumbers.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugXLogP (list) = structure(list(structure(list(structure("Descriptor that Calculates the Prediction of logP\n", Rd_tag = "TEXT"), │ │ │ │ structure("Based on the Atom-Type Method Called XLogP", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugXLogP", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugXLogP", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Prediction of logP\n", Rd_tag = "TEXT"), │ │ │ │ @@ -5046,15 +5046,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Wang, R., Gao, Y., and Lai, L.,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Calculating partition coefficient by atom-additive method,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Perspectives in Drug Discovery and Design, 2000, 19:47-66.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugXLogP(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugXLogP.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugXLogP.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractDrugZagrebIndex (list) = structure(list(structure(list(structure("Descriptor that Calculates the Sum of the Squared Atom Degrees\n", Rd_tag = "TEXT"), │ │ │ │ structure("of All Heavy Atoms", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractDrugZagrebIndex", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractDrugZagrebIndex", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Descriptor that Calculates the Sum of the Squared Atom Degrees\n", Rd_tag = "TEXT"), │ │ │ │ @@ -5078,15 +5078,15 @@ │ │ │ │ structure("This function returns one column named ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Zagreb", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("dat = extractDrugZagrebIndex(mol)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(dat)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugZagrebIndex.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugZagrebIndex.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractPCMBLOSUM (list) = structure(list(structure(list(structure("Generalized BLOSUM and PAM Matrix-Derived Descriptors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractPCMBLOSUM", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractPCMBLOSUM", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Generalized BLOSUM and PAM Matrix-Derived Descriptors\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractPCMBLOSUM(x, submat = \"AABLOSUM62\", k, lag, scale = TRUE, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5155,15 +5155,15 @@ │ │ │ │ structure(list(structure("p", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is the number of scales selected.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Georgiev, A. G. (2009).\n", Rd_tag = "TEXT"), │ │ │ │ structure("Interpretable numerical descriptors of amino acid space.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Journal of Computational Biology, 16(5), 703--723.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("blosum = extractPCMBLOSUM(x, submat = 'AABLOSUM62', k = 5, lag = 7, scale = TRUE, silent = FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMBLOSUM.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractPCMBLOSUM.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractPCMDescScales (list) = structure(list(structure(list(structure("Scales-Based Descriptors with 20+ classes of Molecular Descriptors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractPCMDescScales", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractPCMDescScales", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Scales-Based Descriptors with 20+ classes of Molecular Descriptors\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractPCMDescScales(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -5271,15 +5271,15 @@ │ │ │ │ structure(" is the number of scales selected.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractPCMScales", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for generalized\n", Rd_tag = "TEXT"), structure("AA-descriptor based scales descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("descscales = extractPCMDescScales(x, propmat = 'AATopo', index = c(37:41, 43:47),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" pc = 5, lag = 7, silent = FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMDescScales.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractPCMDescScales.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractPCMFAScales (list) = structure(list(structure(list(structure("Generalized Scales-Based Descriptors derived by Factor Analysis", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractPCMFAScales", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractPCMFAScales", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Generalized Scales-Based Descriptors derived by Factor Analysis\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractPCMFAScales(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -5340,15 +5340,15 @@ │ │ │ │ structure("Solving the protein sequence metric problem.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Proceedings of the National Academy of Sciences of the\n", Rd_tag = "TEXT"), │ │ │ │ structure("United States of America,\n", Rd_tag = "TEXT"), │ │ │ │ structure("102(18), 6395-6400.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(AATopo)\n", Rd_tag = "RCODE"), structure("tprops = AATopo[, c(37:41, 43:47)] # select a set of topological descriptors\n", Rd_tag = "RCODE"), │ │ │ │ structure("fa = extractPCMFAScales(x, propmat = tprops, factors = 5, lag = 7, silent = FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMFAScales.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractPCMFAScales.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractPCMMDSScales (list) = structure(list(structure(list(structure("Generalized Scales-Based Descriptors derived by Multidimensional Scaling", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractPCMMDSScales", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractPCMMDSScales", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Generalized Scales-Based Descriptors derived by Multidimensional Scaling\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractPCMMDSScales(x, propmat, k, lag, scale = TRUE, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5402,15 +5402,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractPCMScales", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for generalized scales-based\n", Rd_tag = "TEXT"), │ │ │ │ structure("descriptors derived by Principal Components Analysis.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(AATopo)\n", Rd_tag = "RCODE"), structure("tprops = AATopo[, c(37:41, 43:47)] # select a set of topological descriptors\n", Rd_tag = "RCODE"), │ │ │ │ structure("mds = extractPCMMDSScales(x, propmat = tprops, k = 5, lag = 7, silent = FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMMDSScales.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractPCMMDSScales.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractPCMPropScales (list) = structure(list(structure(list(structure("Generalized AA-Properties Based Scales Descriptors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractPCMPropScales", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractPCMPropScales", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Generalized AA-Properties Based Scales Descriptors\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractPCMPropScales(x, index = NULL, pc, lag, scale = TRUE, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5459,15 +5459,15 @@ │ │ │ │ structure(list(structure("p", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is the number of scales (principal components) selected.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractPCMScales", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for\n", Rd_tag = "TEXT"), structure("generalized scales-based descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("propscales = extractPCMPropScales(x, index = c(160:165, 258:296), pc = 5, lag = 7, silent = FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMPropScales.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractPCMPropScales.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractPCMScales (list) = structure(list(structure(list(structure("Generalized Scales-Based Descriptors derived by Principal Components Analysis", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractPCMScales", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractPCMScales", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Generalized Scales-Based Descriptors derived by Principal Components Analysis\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractPCMScales(x, propmat, pc, lag, scale = TRUE, silent = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5519,15 +5519,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractPCMDescScales", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for generalized\n", Rd_tag = "TEXT"), structure("AA property based scales descriptors, and ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractPCMPropScales", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("for (19 classes) AA descriptor based scales descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(AAindex)\n", Rd_tag = "RCODE"), structure("AAidxmat = t(na.omit(as.matrix(AAindex[, 7:26])))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("scales = extractPCMScales(x, propmat = AAidxmat, pc = 5, lag = 7, silent = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMScales.Rd", class = "Rd", meta = list( │ │ │ │ + structure("scales = extractPCMScales(x, propmat = AAidxmat, pc = 5, lag = 7, silent = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractPCMScales.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtAAC (list) = structure(list(structure(list(structure("Amino Acid Composition Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtAAC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtAAC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Amino Acid Composition Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtAAC(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5543,15 +5543,15 @@ │ │ │ │ structure(", 2004, 279, 23262.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractProtDC", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("extractProtTC", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" for Dipeptide Composition and Tripeptide Composition descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ - structure("extractProtAAC(x)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtAAC.Rd", class = "Rd", meta = list( │ │ │ │ + structure("extractProtAAC(x)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtAAC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtAPAAC (list) = structure(list(structure(list(structure("Amphiphilic Pseudo Amino Acid Composition Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtAPAAC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtAPAAC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Amphiphilic Pseudo Amino Acid Composition Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtAPAAC(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -5698,15 +5698,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Use 2 default properties, 4 properties in the AAindex database,\n", Rd_tag = "RCODE"), │ │ │ │ structure("# and 3 cutomized properties\n", Rd_tag = "RCODE"), │ │ │ │ structure("extractProtAPAAC(x, customprops = myprops,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" props = c('Hydrophobicity', 'Hydrophilicity',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'CIDH920105', 'BHAR880101',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'CHAM820101', 'CHAM820102',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'MyProp1', 'MyProp2', 'MyProp3'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtAPAAC.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtAPAAC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtCTDC (list) = structure(list(structure(list(structure("CTD Descriptors - Composition", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtCTDC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtCTDC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("CTD Descriptors - Composition\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtCTDC(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5727,15 +5727,15 @@ │ │ │ │ structure(", 1999, 35, 401-407.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractProtCTDT", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("extractProtCTDD", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("for the Transition and Distribution descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ - structure("extractProtCTDC(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtCTDC.Rd", class = "Rd", meta = list( │ │ │ │ + structure("extractProtCTDC(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtCTDC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtCTDD (list) = structure(list(structure(list(structure("CTD Descriptors - Distribution", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtCTDD", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtCTDD", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("CTD Descriptors - Distribution\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtCTDD(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5756,15 +5756,15 @@ │ │ │ │ structure(", 1999, 35, 401-407.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractProtCTDC", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("extractProtCTDT", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("for the Composition and Transition descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ - structure("extractProtCTDD(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtCTDD.Rd", class = "Rd", meta = list( │ │ │ │ + structure("extractProtCTDD(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtCTDD.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtCTDT (list) = structure(list(structure(list(structure("CTD Descriptors - Transition", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtCTDT", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtCTDT", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("CTD Descriptors - Transition\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtCTDT(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5785,15 +5785,15 @@ │ │ │ │ structure(", 1999, 35, 401-407.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractProtCTDC", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("extractProtCTDD", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("for the Composition and Distribution descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ - structure("extractProtCTDT(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtCTDT.Rd", class = "Rd", meta = list( │ │ │ │ + structure("extractProtCTDT(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtCTDT.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtCTriad (list) = structure(list(structure(list(structure("Conjoint Triad Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtCTriad", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtCTriad", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Conjoint Triad Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtCTriad(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5804,15 +5804,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A length 343 named vector\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("J.W. Shen, J. Zhang, X.M. Luo, W.L. Zhu,\n", Rd_tag = "TEXT"), │ │ │ │ structure("K.Q. Yu, K.X. Chen, Y.X. Li, H.L. Jiang.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Predicting Protein-protein Interactions Based Only on Sequences Information.\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Proceedings of the National Academy of Sciences", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(". 007, 104, 4337--4341.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ - structure("extractProtCTriad(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtCTriad.Rd", class = "Rd", meta = list( │ │ │ │ + structure("extractProtCTriad(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtCTriad.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtDC (list) = structure(list(structure(list(structure("Dipeptide Composition Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtDC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtDC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Dipeptide Composition Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtDC(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -5828,15 +5828,15 @@ │ │ │ │ structure(", 2004, 279, 23262.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractProtAAC", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("extractProtTC", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" for Amino Acid Composition and Tripeptide Composition descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ - structure("extractProtDC(x)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtDC.Rd", class = "Rd", meta = list( │ │ │ │ + structure("extractProtDC(x)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtDC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtGeary (list) = structure(list(structure(list(structure("Geary Autocorrelation Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtGeary", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtGeary", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Geary Autocorrelation Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtGeary(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -5989,15 +5989,15 @@ │ │ │ │ structure(" T = c(-0.05, -0.4, 45), W = c(0.81, -3.4, 130),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" Y = c(0.26, -2.3, 107), V = c(1.08, -1.5, 43))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Use 4 properties in the AAindex database, and 3 cutomized properties\n", Rd_tag = "RCODE"), │ │ │ │ structure("extractProtGeary(x, customprops = myprops,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" props = c('CIDH920105', 'BHAR880101',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'CHAM820101', 'CHAM820102',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'MyProp1', 'MyProp2', 'MyProp3'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtGeary.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtGeary.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtMoran (list) = structure(list(structure(list(structure("Moran Autocorrelation Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtMoran", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtMoran", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Moran Autocorrelation Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtMoran(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -6150,15 +6150,15 @@ │ │ │ │ structure(" T = c(-0.05, -0.4, 45), W = c(0.81, -3.4, 130),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" Y = c(0.26, -2.3, 107), V = c(1.08, -1.5, 43))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Use 4 properties in the AAindex database, and 3 cutomized properties\n", Rd_tag = "RCODE"), │ │ │ │ structure("extractProtMoran(x, customprops = myprops,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" props = c('CIDH920105', 'BHAR880101',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'CHAM820101', 'CHAM820102',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'MyProp1', 'MyProp2', 'MyProp3'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtMoran.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtMoran.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtMoreauBroto (list) = structure(list(structure(list(structure("Normalized Moreau-Broto Autocorrelation Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtMoreauBroto", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtMoreauBroto", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Normalized Moreau-Broto Autocorrelation Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtMoreauBroto(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -6311,15 +6311,15 @@ │ │ │ │ structure(" T = c(-0.05, -0.4, 45), W = c(0.81, -3.4, 130),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" Y = c(0.26, -2.3, 107), V = c(1.08, -1.5, 43))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Use 4 properties in the AAindex database, and 3 cutomized properties\n", Rd_tag = "RCODE"), │ │ │ │ structure("extractProtMoreauBroto(x, customprops = myprops,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" props = c('CIDH920105', 'BHAR880101',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'CHAM820101', 'CHAM820102',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'MyProp1', 'MyProp2', 'MyProp3'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtMoreauBroto.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtMoreauBroto.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtPAAC (list) = structure(list(structure(list(structure("Pseudo Amino Acid Composition Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtPAAC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtPAAC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Pseudo Amino Acid Composition Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtPAAC(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -6472,15 +6472,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Use 3 default properties, 4 properties in the AAindex database,\n", Rd_tag = "RCODE"), │ │ │ │ structure("# and 3 cutomized properties\n", Rd_tag = "RCODE"), │ │ │ │ structure("extractProtPAAC(x, customprops = myprops,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" props = c('Hydrophobicity', 'Hydrophilicity', 'SideChainMass',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'CIDH920105', 'BHAR880101',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'CHAM820101', 'CHAM820102',\n", Rd_tag = "RCODE"), │ │ │ │ structure(" 'MyProp1', 'MyProp2', 'MyProp3'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtPAAC.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtPAAC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtPSSM (list) = structure(list(structure(list(structure("Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtPSSM", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtPSSM", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtPSSM(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -6698,15 +6698,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("extractProtPSSMAcc", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("dbpath = tempfile('tempdb', fileext = '.fasta')\n", Rd_tag = "RCODE"), │ │ │ │ structure("invisible(file.copy(from = system.file('protseq/Plasminogen.fasta', package = 'Rcpi'), to = dbpath))\n", Rd_tag = "RCODE"), │ │ │ │ structure("pssmmat = extractProtPSSM(seq = x, database.path = dbpath)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(pssmmat) # 20 x 562 (P00750: length 562, 20 Amino Acids)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtPSSM.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtPSSM.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtPSSMAcc (list) = structure(list(structure(list(structure("Profile-based protein representation derived by PSSM\n", Rd_tag = "TEXT"), │ │ │ │ structure("(Position-Specific Scoring Matrix) and auto cross covariance", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtPSSMAcc", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtPSSMAcc", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Profile-based protein representation derived by PSSM\n", Rd_tag = "TEXT"), │ │ │ │ @@ -6740,15 +6740,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("dbpath = tempfile('tempdb', fileext = '.fasta')\n", Rd_tag = "RCODE"), │ │ │ │ structure("invisible(file.copy(from = system.file('protseq/Plasminogen.fasta', package = 'Rcpi'), to = dbpath))\n", Rd_tag = "RCODE"), │ │ │ │ structure("pssmmat = extractProtPSSM(seq = x, database.path = dbpath)\n", Rd_tag = "RCODE"), │ │ │ │ structure("pssmacc = extractProtPSSMAcc(pssmmat, lag = 3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("tail(pssmacc)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtPSSMAcc.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtPSSMAcc.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtPSSMFeature (list) = structure(list(structure(list(structure("Profile-based protein representation derived by PSSM\n", Rd_tag = "TEXT"), │ │ │ │ structure("(Position-Specific Scoring Matrix)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtPSSMFeature", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtPSSMFeature", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Profile-based protein representation derived by PSSM\n", Rd_tag = "TEXT"), │ │ │ │ @@ -6787,15 +6787,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("dbpath = tempfile('tempdb', fileext = '.fasta')\n", Rd_tag = "RCODE"), │ │ │ │ structure("invisible(file.copy(from = system.file('protseq/Plasminogen.fasta', package = 'Rcpi'), to = dbpath))\n", Rd_tag = "RCODE"), │ │ │ │ structure("pssmmat = extractProtPSSM(seq = x, database.path = dbpath)\n", Rd_tag = "RCODE"), │ │ │ │ structure("pssmfeature = extractProtPSSMFeature(pssmmat)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(pssmfeature)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtPSSMFeature.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtPSSMFeature.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtQSO (list) = structure(list(structure(list(structure("Quasi-Sequence-Order (QSO) Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtQSO", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtQSO", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Quasi-Sequence-Order (QSO) Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtQSO(x, nlag = 30, w = 0.1)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -6828,15 +6828,15 @@ │ │ │ │ structure("Molecular Evolution: Do Novo Design of an Idealized Leader Cleavge Site.\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biophys Journal", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 1994, 66, 335-344.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractProtSOCN", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("for sequence-order-coupling numbers.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ - structure("extractProtQSO(x)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtQSO.Rd", class = "Rd", meta = list( │ │ │ │ + structure("extractProtQSO(x)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtQSO.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtSOCN (list) = structure(list(structure(list(structure("Sequence-Order-Coupling Numbers", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtSOCN", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtSOCN", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sequence-Order-Coupling Numbers\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtSOCN(x, nlag = 30)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -6867,15 +6867,15 @@ │ │ │ │ structure(list(structure("Biophys Journal", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 1994, 66, 335-344.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractProtQSO", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for\n", Rd_tag = "TEXT"), structure("quasi-sequence-order descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("extractProtSOCN(x)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtSOCN.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtSOCN.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractProtTC (list) = structure(list(structure(list(structure("Tripeptide Composition Descriptor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractProtTC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractProtTC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Tripeptide Composition Descriptor\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractProtTC(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -6891,15 +6891,15 @@ │ │ │ │ structure(", 2004, 279, 23262.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractProtAAC", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("extractProtDC", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" for Amino Acid Composition and Dipeptide Composition descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ - structure("extractProtTC(x)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtTC.Rd", class = "Rd", meta = list( │ │ │ │ + structure("extractProtTC(x)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractProtTC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getCPI (list) = structure(list(structure(list(structure("Generating Compound-Protein Interaction Descriptors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getCPI", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getCPI", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Generating Compound-Protein Interaction Descriptors\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getCPI(drugmat, protmat, type = c(\"combine\", \"tensorprod\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -6936,15 +6936,15 @@ │ │ │ │ structure(" for generating\n", Rd_tag = "TEXT"), structure("protein-protein interaction descriptors.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = matrix(1:10, ncol = 2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y = matrix(1:15, ncol = 3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("getCPI(x, y, 'combine')\n", Rd_tag = "RCODE"), │ │ │ │ structure("getCPI(x, y, 'tensorprod')\n", Rd_tag = "RCODE"), │ │ │ │ structure("getCPI(x, y, type = c('combine', 'tensorprod'))\n", Rd_tag = "RCODE"), │ │ │ │ structure("getCPI(x, y, type = c('tensorprod', 'combine'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getCPI.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getCPI.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getDrug (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in MOL and SMILES Format from Databases", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getDrug", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getDrug", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in MOL and SMILES Format from Databases\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getDrug(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -6990,15 +6990,15 @@ │ │ │ │ structure(" character vector,\n", Rd_tag = "TEXT"), structure("each element containing the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getProt", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving protein sequences\n", Rd_tag = "TEXT"), │ │ │ │ structure("from three databases.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('DB00859', 'DB00860')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getDrug(id, 'drugbank', 'smile')", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getDrug.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getDrug.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getFASTAFromKEGG (list) = structure(list(structure(list(structure("Retrieve Protein Sequence in FASTA Format from the KEGG Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getFASTAFromKEGG", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getFASTAFromKEGG", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Protein Sequence in FASTA Format from the KEGG Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getFASTAFromKEGG(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7023,15 +7023,15 @@ │ │ │ │ structure(" for retrieving protein\n", Rd_tag = "TEXT"), │ │ │ │ structure("represented by amino acid sequence from the KEGG database.\n", Rd_tag = "TEXT"), │ │ │ │ structure("See ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("readFASTA", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for reading FASTA format files.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('hsa:10161', 'hsa:10162')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getFASTAFromKEGG(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getFASTAFromKEGG.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getFASTAFromKEGG.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getFASTAFromUniProt (list) = structure(list(structure(list(structure("Retrieve Protein Sequence in FASTA Format from the UniProt Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getFASTAFromUniProt", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getFASTAFromUniProt", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Protein Sequence in FASTA Format from the UniProt Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getFASTAFromUniProt(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7062,15 +7062,15 @@ │ │ │ │ structure(" for retrieving protein\n", Rd_tag = "TEXT"), │ │ │ │ structure("represented by amino acid sequence from the UniProt database.\n", Rd_tag = "TEXT"), │ │ │ │ structure("See ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("readFASTA", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for reading FASTA format files.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('P00750', 'P00751', 'P00752')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getFASTAFromUniProt(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getFASTAFromUniProt.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getFASTAFromUniProt.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getMolFromCAS (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in InChI Format from the CAS Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getMolFromCAS", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getMolFromCAS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in InChI Format from the CAS Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromCAS(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7095,15 +7095,15 @@ │ │ │ │ structure(" character vector,\n", Rd_tag = "TEXT"), structure("each element containing the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getDrug", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("in MOL and SMILES Format from other databases.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = '52-67-5' # Penicillamine\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromCAS(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromCAS.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getMolFromCAS.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getMolFromChEMBL (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in MOL Format from the ChEMBL Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getMolFromChEMBL", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getMolFromChEMBL", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in MOL Format from the ChEMBL Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromChEMBL(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7126,15 +7126,15 @@ │ │ │ │ structure(" character vector,\n", Rd_tag = "TEXT"), structure("each element containing the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getSmiFromChEMBL", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("in SMILES format from the ChEMBL database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = 'CHEMBL1430' # Penicillamine\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromChEMBL(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromChEMBL.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getMolFromChEMBL.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getMolFromDrugBank (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in MOL Format from the DrugBank Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getMolFromDrugBank", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getMolFromDrugBank", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in MOL Format from the DrugBank Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromDrugBank(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7157,15 +7157,15 @@ │ │ │ │ structure(" character vector,\n", Rd_tag = "TEXT"), structure("each element containing the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getSmiFromDrugBank", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("in SMILES format from the DrugBank database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = 'DB00859' # Penicillamine\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromDrugBank(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromDrugBank.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getMolFromDrugBank.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getMolFromKEGG (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in MOL Format from the KEGG Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getMolFromKEGG", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getMolFromKEGG", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in MOL Format from the KEGG Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromKEGG(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7187,15 +7187,15 @@ │ │ │ │ structure(" character vector,\n", Rd_tag = "TEXT"), structure("each element containing the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getSmiFromKEGG", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("in SMILES format from the KEGG database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = 'D00496' # Penicillamine\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromKEGG(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromKEGG.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getMolFromKEGG.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getMolFromPubChem (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in MOL Format from the PubChem Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getMolFromPubChem", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getMolFromPubChem", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in MOL Format from the PubChem Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromPubChem(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7218,15 +7218,15 @@ │ │ │ │ structure(" character vector,\n", Rd_tag = "TEXT"), structure("each element containing the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getSmiFromPubChem", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("in SMILES format from the PubChem database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('7847562', '7847563') # Penicillamine\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getMolFromPubChem(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromPubChem.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getMolFromPubChem.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getPDBFromRCSBPDB (list) = structure(list(structure(list(structure("Retrieve Protein Sequence in PDB Format from RCSB PDB", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getPDBFromRCSBPDB", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getPDBFromRCSBPDB", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Protein Sequence in PDB Format from RCSB PDB\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getPDBFromRCSBPDB(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7247,15 +7247,15 @@ │ │ │ │ structure("in PDB format.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getSeqFromRCSBPDB", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving protein\n", Rd_tag = "TEXT"), │ │ │ │ structure("represented by amino acid sequence from the RCSB PDB database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('4HHB', '4FF9')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getPDBFromRCSBPDB(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getPDBFromRCSBPDB.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getPDBFromRCSBPDB.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getPPI (list) = structure(list(structure(list(structure("Generating Protein-Protein Interaction Descriptors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getPPI", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getPPI", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Generating Protein-Protein Interaction Descriptors\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getPPI(protmat1, protmat2, type = c(\"combine\", \"tensorprod\", \"entrywise\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7309,15 +7309,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("getPPI(x, y, type = 'combine')\n", Rd_tag = "RCODE"), │ │ │ │ structure("getPPI(x, y, type = 'tensorprod')\n", Rd_tag = "RCODE"), │ │ │ │ structure("getPPI(x, y, type = 'entrywise')\n", Rd_tag = "RCODE"), │ │ │ │ structure("getPPI(x, y, type = c('combine', 'tensorprod'))\n", Rd_tag = "RCODE"), │ │ │ │ structure("getPPI(x, y, type = c('combine', 'entrywise'))\n", Rd_tag = "RCODE"), │ │ │ │ structure("getPPI(x, y, type = c('entrywise', 'tensorprod'))\n", Rd_tag = "RCODE"), │ │ │ │ structure("getPPI(x, y, type = c('combine', 'entrywise', 'tensorprod'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getPPI.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getPPI.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getProt (list) = structure(list(structure(list(structure("Retrieve Protein Sequence in various Formats from Databases", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getProt", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getProt", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Protein Sequence in various Formats from Databases\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getProt(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -7362,15 +7362,15 @@ │ │ │ │ structure("containing the corresponding protein sequence(s) or file(s).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getDrug", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("from five databases.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('P00750', 'P00751', 'P00752')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getProt(id, from = 'uniprot', type = 'aaseq')", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getProt.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getProt.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getSeqFromKEGG (list) = structure(list(structure(list(structure("Retrieve Protein Sequence from the KEGG Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getSeqFromKEGG", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getSeqFromKEGG", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Protein Sequence from the KEGG Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSeqFromKEGG(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7392,15 +7392,15 @@ │ │ │ │ structure("amino acid sequence(s).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getFASTAFromKEGG", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving protein sequence\n", Rd_tag = "TEXT"), │ │ │ │ structure("in FASTA format from the KEGG database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('hsa:10161', 'hsa:10162')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSeqFromKEGG(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getSeqFromKEGG.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getSeqFromKEGG.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getSeqFromRCSBPDB (list) = structure(list(structure(list(structure("Retrieve Protein Sequence from RCSB PDB", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getSeqFromRCSBPDB", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getSeqFromRCSBPDB", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Protein Sequence from RCSB PDB\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSeqFromRCSBPDB(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7421,15 +7421,15 @@ │ │ │ │ structure("amino acid sequence(s).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getPDBFromRCSBPDB", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving protein\n", Rd_tag = "TEXT"), │ │ │ │ structure("in PDB format from the RCSB PDB database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('4HHB', '4FF9')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSeqFromRCSBPDB(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getSeqFromRCSBPDB.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getSeqFromRCSBPDB.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getSeqFromUniProt (list) = structure(list(structure(list(structure("Retrieve Protein Sequence from the UniProt Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getSeqFromUniProt", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getSeqFromUniProt", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Protein Sequence from the UniProt Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSeqFromUniProt(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7457,15 +7457,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getFASTAFromUniProt", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving protein\n", Rd_tag = "TEXT"), │ │ │ │ structure("sequences in FASTA format from the UniProt database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('P00750', 'P00751', 'P00752')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSeqFromUniProt(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getSeqFromUniProt.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getSeqFromUniProt.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getSmiFromChEMBL (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in SMILES Format from the ChEMBL Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getSmiFromChEMBL", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getSmiFromChEMBL", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in SMILES Format from the ChEMBL Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSmiFromChEMBL(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7488,15 +7488,15 @@ │ │ │ │ structure(" character vector,\n", Rd_tag = "TEXT"), structure("each element containing the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getMolFromChEMBL", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("in MOL format from the ChEMBL database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = 'CHEMBL1430' # Penicillamine\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSmiFromChEMBL(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getSmiFromChEMBL.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getSmiFromChEMBL.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getSmiFromDrugBank (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in SMILES Format from the DrugBank Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getSmiFromDrugBank", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getSmiFromDrugBank", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in SMILES Format from the DrugBank Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSmiFromDrugBank(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7520,15 +7520,15 @@ │ │ │ │ structure("the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getMolFromDrugBank", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("in MOL format from the DrugBank database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = 'DB00859' # Penicillamine\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSmiFromDrugBank(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getSmiFromDrugBank.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getSmiFromDrugBank.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getSmiFromKEGG (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in SMILES Format from the KEGG Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getSmiFromKEGG", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getSmiFromKEGG", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in SMILES Format from the KEGG Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSmiFromKEGG(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7551,15 +7551,15 @@ │ │ │ │ structure(" character vector,\n", Rd_tag = "TEXT"), structure("each element containing the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getMolFromKEGG", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("in MOL format from the KEGG database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = 'D00496' # Penicillamine\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSmiFromKEGG(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getSmiFromKEGG.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getSmiFromKEGG.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getSmiFromPubChem (list) = structure(list(structure(list(structure("Retrieve Drug Molecules in SMILES Format from the PubChem Database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getSmiFromPubChem", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getSmiFromPubChem", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Retrieve Drug Molecules in SMILES Format from the PubChem Database\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSmiFromPubChem(id, parallel = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7582,15 +7582,15 @@ │ │ │ │ structure(" character vector,\n", Rd_tag = "TEXT"), structure("each element containing the corresponding drug molecule.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getMolFromPubChem", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for retrieving drug molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("in MOL format from the PubChem database.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("id = c('7847562', '7847563') # Penicillamine\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getSmiFromPubChem(id)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/getSmiFromPubChem.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/getSmiFromPubChem.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ readFASTA (list) = structure(list(structure(list(structure("Read Protein Sequences in FASTA Format", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("readFASTA", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("readFASTA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -7636,15 +7636,15 @@ │ │ │ │ structure("of the United States of America", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 85: 2444-2448.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("readPDB", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for reading protein sequences\n", Rd_tag = "TEXT"), │ │ │ │ structure("in PDB format.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("P00750 = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("P00750\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/readFASTA.Rd", class = "Rd", meta = list( │ │ │ │ + structure("P00750\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/readFASTA.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ readMolFromSDF (list) = structure(list(structure(list(structure("Read Molecules from SDF Files and Return Parsed Java Molecular Object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("readMolFromSDF", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("readMolFromSDF", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Read Molecules from SDF Files and Return Parsed Java Molecular Object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("readMolFromSDF(sdffile)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7661,15 +7661,15 @@ │ │ │ │ structure(" for reading molecules by SMILES\n", Rd_tag = "TEXT"), │ │ │ │ structure("string and returning parsed Java molecular object.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("sdf = system.file('compseq/DB00859.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure("sdfs = c(system.file('compseq/DB00859.sdf', package = 'Rcpi'),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" system.file('compseq/DB00860.sdf', package = 'Rcpi'))\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = readMolFromSDF(sdf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("mols = readMolFromSDF(sdfs)", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/readMolFromSDF.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/readMolFromSDF.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ readMolFromSmi (list) = structure(list(structure(list(structure("Read Molecules from SMILES Files and Return Parsed Java\n", Rd_tag = "TEXT"), │ │ │ │ structure("Molecular Object or Plain Text List", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("readMolFromSmi", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("readMolFromSmi", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Read Molecules from SMILES Files and Return Parsed Java\n", Rd_tag = "TEXT"), │ │ │ │ @@ -7707,15 +7707,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("readMolFromSDF", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for reading molecules\n", Rd_tag = "TEXT"), │ │ │ │ structure("from SDF files and returning parsed Java molecular object.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol1 = readMolFromSmi(smi, type = 'mol')\n", Rd_tag = "RCODE"), │ │ │ │ structure("mol2 = readMolFromSmi(smi, type = 'text')", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/readMolFromSmi.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/readMolFromSmi.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ readPDB (list) = structure(list(structure(list(structure("Read Protein Sequences in PDB Format", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("readPDB", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("readPDB", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Read Protein Sequences in PDB Format\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("readPDB(file = system.file(\"protseq/4HHB.pdb\", package = \"Rcpi\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -7740,15 +7740,15 @@ │ │ │ │ structure(list(structure("https://files.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("readFASTA", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for reading protein sequences\n", Rd_tag = "TEXT"), │ │ │ │ structure("in FASTA format.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("Seq4HHB = readPDB(system.file('protseq/4HHB.pdb', package = 'Rcpi'))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("Seq4HHB\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/readPDB.Rd", class = "Rd", meta = list( │ │ │ │ + structure("Seq4HHB\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/readPDB.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -7871,15 +7871,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mol = system.file('compseq/DB00530.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure("# DrugBank ID DB00530: Erlotinib\n", Rd_tag = "RCODE"), │ │ │ │ structure("moldb = system.file('compseq/tyrphostin.sdf', package = 'Rcpi')\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Database composed by searching 'tyrphostin' in PubChem and filtered by Lipinski's Rule of Five\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("searchDrug(mol, moldb, cores = 4, method = 'fp', fptype = 'maccs', fpsim = 'hamming')\n", Rd_tag = "RCODE"), │ │ │ │ structure("searchDrug(mol, moldb, cores = 4, method = 'fp', fptype = 'fp2', fpsim = 'tanimoto')\n", Rd_tag = "RCODE"), │ │ │ │ structure("searchDrug(mol, moldb, cores = 4, method = 'mcs', mcssim = 'tanimoto')", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/searchDrug.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/searchDrug.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ segProt (list) = structure(list(structure(list(structure("Protein Sequence Segmentation", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("segProt", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("segProt", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Protein Sequence Segmentation\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("segProt(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -7938,10 +7938,10 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function extracts the segmentations from the protein sequence.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A named list, each component contains one of the\n", Rd_tag = "TEXT"), │ │ │ │ structure(" segmentations (a character string), names of the list components\n", Rd_tag = "TEXT"), │ │ │ │ structure(" are the positions of the specified amino acid in the sequence.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure("segProt(x, aa = 'R', k = 5)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-rcpi/man/segProt.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/segProt.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/Rcpi/help/Rcpi.rdx │ │ │ ├── Rcpi.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,1003 +1,1003 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$AA2DACOR │ │ │ │ │ -[1] 279 790 │ │ │ │ │ +[1] 292 804 │ │ │ │ │ │ │ │ │ │ $variables$AA3DMoRSE │ │ │ │ │ -[1] 1348 783 │ │ │ │ │ +[1] 1389 797 │ │ │ │ │ │ │ │ │ │ $variables$AAACF │ │ │ │ │ -[1] 2405 794 │ │ │ │ │ +[1] 2474 809 │ │ │ │ │ │ │ │ │ │ $variables$AABLOSUM100 │ │ │ │ │ -[1] 3482 773 │ │ │ │ │ +[1] 3578 787 │ │ │ │ │ │ │ │ │ │ $variables$AABLOSUM45 │ │ │ │ │ -[1] 4537 766 │ │ │ │ │ +[1] 4659 780 │ │ │ │ │ │ │ │ │ │ $variables$AABLOSUM50 │ │ │ │ │ -[1] 5585 766 │ │ │ │ │ +[1] 5734 781 │ │ │ │ │ │ │ │ │ │ $variables$AABLOSUM62 │ │ │ │ │ -[1] 6633 766 │ │ │ │ │ +[1] 6810 781 │ │ │ │ │ │ │ │ │ │ $variables$AABLOSUM80 │ │ │ │ │ -[1] 7681 765 │ │ │ │ │ +[1] 7885 780 │ │ │ │ │ │ │ │ │ │ $variables$AABurden │ │ │ │ │ -[1] 8722 783 │ │ │ │ │ +[1] 8955 799 │ │ │ │ │ │ │ │ │ │ $variables$AACPSA │ │ │ │ │ -[1] 9780 1050 │ │ │ │ │ +[1] 10043 1064 │ │ │ │ │ │ │ │ │ │ $variables$AAConn │ │ │ │ │ -[1] 11104 787 │ │ │ │ │ +[1] 11396 800 │ │ │ │ │ │ │ │ │ │ $variables$AAConst │ │ │ │ │ -[1] 12166 779 │ │ │ │ │ +[1] 12486 794 │ │ │ │ │ │ │ │ │ │ $variables$AADescAll │ │ │ │ │ -[1] 13222 781 │ │ │ │ │ +[1] 13570 795 │ │ │ │ │ │ │ │ │ │ $variables$AAEdgeAdj │ │ │ │ │ -[1] 14281 801 │ │ │ │ │ +[1] 14656 815 │ │ │ │ │ │ │ │ │ │ $variables$AAEigIdx │ │ │ │ │ -[1] 15358 795 │ │ │ │ │ +[1] 15763 810 │ │ │ │ │ │ │ │ │ │ $variables$AAFGC │ │ │ │ │ -[1] 16428 793 │ │ │ │ │ +[1] 16862 809 │ │ │ │ │ │ │ │ │ │ $variables$AAGETAWAY │ │ │ │ │ -[1] 17500 780 │ │ │ │ │ +[1] 17963 794 │ │ │ │ │ │ │ │ │ │ $variables$AAGeom │ │ │ │ │ -[1] 18554 776 │ │ │ │ │ +[1] 19046 790 │ │ │ │ │ │ │ │ │ │ $variables$AAInfo │ │ │ │ │ -[1] 19604 784 │ │ │ │ │ +[1] 20125 797 │ │ │ │ │ │ │ │ │ │ $variables$AAMOE2D │ │ │ │ │ -[1] 20665 756 │ │ │ │ │ +[1] 21214 770 │ │ │ │ │ │ │ │ │ │ $variables$AAMOE3D │ │ │ │ │ -[1] 21698 997 │ │ │ │ │ +[1] 22276 1012 │ │ │ │ │ │ │ │ │ │ $variables$AAMetaInfo │ │ │ │ │ -[1] 22975 1366 │ │ │ │ │ +[1] 23580 1380 │ │ │ │ │ │ │ │ │ │ $variables$AAMolProp │ │ │ │ │ -[1] 24619 795 │ │ │ │ │ +[1] 25251 809 │ │ │ │ │ │ │ │ │ │ $variables$AAPAM120 │ │ │ │ │ -[1] 25692 771 │ │ │ │ │ +[1] 26353 786 │ │ │ │ │ │ │ │ │ │ $variables$AAPAM250 │ │ │ │ │ -[1] 26741 772 │ │ │ │ │ +[1] 27432 788 │ │ │ │ │ │ │ │ │ │ $variables$AAPAM30 │ │ │ │ │ -[1] 27790 767 │ │ │ │ │ +[1] 28511 782 │ │ │ │ │ │ │ │ │ │ $variables$AAPAM40 │ │ │ │ │ -[1] 28834 767 │ │ │ │ │ +[1] 29584 782 │ │ │ │ │ │ │ │ │ │ $variables$AAPAM70 │ │ │ │ │ -[1] 29878 766 │ │ │ │ │ +[1] 30657 782 │ │ │ │ │ │ │ │ │ │ $variables$AARDF │ │ │ │ │ -[1] 30919 771 │ │ │ │ │ +[1] 31728 787 │ │ │ │ │ │ │ │ │ │ $variables$AARandic │ │ │ │ │ -[1] 31965 790 │ │ │ │ │ +[1] 32805 806 │ │ │ │ │ │ │ │ │ │ $variables$AATopo │ │ │ │ │ -[1] 33028 776 │ │ │ │ │ +[1] 33900 791 │ │ │ │ │ │ │ │ │ │ $variables$AATopoChg │ │ │ │ │ -[1] 34083 828 │ │ │ │ │ +[1] 34983 845 │ │ │ │ │ │ │ │ │ │ $variables$AAWHIM │ │ │ │ │ -[1] 35187 775 │ │ │ │ │ +[1] 36119 790 │ │ │ │ │ │ │ │ │ │ $variables$AAWalk │ │ │ │ │ -[1] 36236 792 │ │ │ │ │ +[1] 37198 805 │ │ │ │ │ │ │ │ │ │ $variables$AAindex │ │ │ │ │ -[1] 37303 1112 │ │ │ │ │ +[1] 38293 1125 │ │ │ │ │ │ │ │ │ │ $variables$OptAA3d │ │ │ │ │ -[1] 38690 833 │ │ │ │ │ +[1] 39708 847 │ │ │ │ │ │ │ │ │ │ $variables$`Rcpi-package` │ │ │ │ │ -[1] 39802 1640 │ │ │ │ │ +[1] 40846 1654 │ │ │ │ │ │ │ │ │ │ $variables$acc │ │ │ │ │ -[1] 41713 2411 │ │ │ │ │ +[1] 42785 2425 │ │ │ │ │ │ │ │ │ │ $variables$calcDrugFPSim │ │ │ │ │ -[1] 44405 2949 │ │ │ │ │ +[1] 45504 2961 │ │ │ │ │ │ │ │ │ │ $variables$calcDrugMCSSim │ │ │ │ │ -[1] 47636 2708 │ │ │ │ │ +[1] 48760 2723 │ │ │ │ │ │ │ │ │ │ $variables$calcParProtGOSim │ │ │ │ │ -[1] 50626 3896 │ │ │ │ │ +[1] 51778 3910 │ │ │ │ │ │ │ │ │ │ $variables$calcParProtSeqSim │ │ │ │ │ -[1] 54804 3028 │ │ │ │ │ +[1] 55984 3043 │ │ │ │ │ │ │ │ │ │ $variables$calcTwoProtGOSim │ │ │ │ │ -[1] 58115 3754 │ │ │ │ │ +[1] 59323 3767 │ │ │ │ │ │ │ │ │ │ $variables$calcTwoProtSeqSim │ │ │ │ │ -[1] 62152 2464 │ │ │ │ │ +[1] 63386 2478 │ │ │ │ │ │ │ │ │ │ $variables$checkProt │ │ │ │ │ -[1] 64893 1084 │ │ │ │ │ +[1] 66155 1099 │ │ │ │ │ │ │ │ │ │ $variables$convMolFormat │ │ │ │ │ -[1] 66257 7520 │ │ │ │ │ +[1] 67548 7534 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAIO │ │ │ │ │ -[1] 74060 1741 │ │ │ │ │ +[1] 75378 1754 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugALOGP │ │ │ │ │ -[1] 76087 2179 │ │ │ │ │ +[1] 77430 2191 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAminoAcidCount │ │ │ │ │ -[1] 78556 1941 │ │ │ │ │ +[1] 79923 1954 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugApol │ │ │ │ │ -[1] 80780 1499 │ │ │ │ │ +[1] 82172 1512 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAromaticAtomsCount │ │ │ │ │ -[1] 82571 1371 │ │ │ │ │ +[1] 83989 1385 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAromaticBondsCount │ │ │ │ │ -[1] 84234 1374 │ │ │ │ │ +[1] 85679 1388 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAtomCount │ │ │ │ │ -[1] 85895 1399 │ │ │ │ │ +[1] 87366 1412 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAutocorrelationCharge │ │ │ │ │ -[1] 87589 1570 │ │ │ │ │ +[1] 89086 1584 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAutocorrelationMass │ │ │ │ │ -[1] 89452 1730 │ │ │ │ │ +[1] 90976 1743 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugAutocorrelationPolarizability │ │ │ │ │ -[1] 91483 1528 │ │ │ │ │ +[1] 93033 1541 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugBCUT │ │ │ │ │ -[1] 93295 3402 │ │ │ │ │ +[1] 94871 3413 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugBPol │ │ │ │ │ -[1] 96980 1678 │ │ │ │ │ +[1] 98579 1690 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugBondCount │ │ │ │ │ -[1] 98946 1433 │ │ │ │ │ +[1] 100568 1448 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugCPSA │ │ │ │ │ -[1] 100662 3302 │ │ │ │ │ +[1] 102312 3316 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugCarbonTypes │ │ │ │ │ -[1] 104253 2279 │ │ │ │ │ +[1] 105928 2292 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugChiChain │ │ │ │ │ -[1] 106819 2303 │ │ │ │ │ +[1] 108519 2316 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugChiCluster │ │ │ │ │ -[1] 109410 1983 │ │ │ │ │ +[1] 111136 1995 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugChiPath │ │ │ │ │ -[1] 111679 1941 │ │ │ │ │ +[1] 113429 1952 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugChiPathCluster │ │ │ │ │ -[1] 113911 2382 │ │ │ │ │ +[1] 115684 2395 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugDescOB │ │ │ │ │ -[1] 116578 3261 │ │ │ │ │ +[1] 118376 3275 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugECI │ │ │ │ │ -[1] 120122 2022 │ │ │ │ │ +[1] 121946 2034 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugEstate │ │ │ │ │ -[1] 122428 1465 │ │ │ │ │ +[1] 124276 1479 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugEstateComplete │ │ │ │ │ -[1] 124182 1411 │ │ │ │ │ +[1] 126057 1424 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugExtended │ │ │ │ │ -[1] 125880 1844 │ │ │ │ │ +[1] 127779 1856 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugExtendedComplete │ │ │ │ │ -[1] 128016 1775 │ │ │ │ │ +[1] 129939 1789 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugFMF │ │ │ │ │ -[1] 130076 1829 │ │ │ │ │ +[1] 132024 1841 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugFragmentComplexity │ │ │ │ │ -[1] 132199 1863 │ │ │ │ │ +[1] 134171 1876 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugGraph │ │ │ │ │ -[1] 134347 1765 │ │ │ │ │ +[1] 136343 1777 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugGraphComplete │ │ │ │ │ -[1] 136403 1723 │ │ │ │ │ +[1] 138422 1737 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugGravitationalIndex │ │ │ │ │ -[1] 138420 2512 │ │ │ │ │ +[1] 140465 2525 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHBondAcceptorCount │ │ │ │ │ -[1] 141226 1768 │ │ │ │ │ +[1] 143296 1780 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHBondDonorCount │ │ │ │ │ -[1] 143286 1737 │ │ │ │ │ +[1] 145379 1750 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHybridization │ │ │ │ │ -[1] 145315 1761 │ │ │ │ │ +[1] 147432 1775 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHybridizationComplete │ │ │ │ │ -[1] 147373 1793 │ │ │ │ │ +[1] 149515 1805 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugHybridizationRatio │ │ │ │ │ -[1] 149461 1692 │ │ │ │ │ +[1] 151626 1705 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugIPMolecularLearning │ │ │ │ │ -[1] 151449 1445 │ │ │ │ │ +[1] 153639 1459 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugKR │ │ │ │ │ -[1] 153178 1437 │ │ │ │ │ +[1] 155392 1450 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugKRComplete │ │ │ │ │ -[1] 154904 1383 │ │ │ │ │ +[1] 157143 1396 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugKappaShapeIndices │ │ │ │ │ -[1] 156581 2051 │ │ │ │ │ +[1] 158845 2063 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugKierHallSmarts │ │ │ │ │ -[1] 158924 12573 │ │ │ │ │ +[1] 161211 12587 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugLargestChain │ │ │ │ │ -[1] 171788 1497 │ │ │ │ │ +[1] 174100 1509 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugLargestPiSystem │ │ │ │ │ -[1] 173578 1393 │ │ │ │ │ +[1] 175912 1406 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugLengthOverBreadth │ │ │ │ │ -[1] 175266 1858 │ │ │ │ │ +[1] 177625 1870 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugLongestAliphaticChain │ │ │ │ │ -[1] 177422 1390 │ │ │ │ │ +[1] 179804 1403 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMACCS │ │ │ │ │ -[1] 179099 1432 │ │ │ │ │ +[1] 181505 1445 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMACCSComplete │ │ │ │ │ -[1] 180823 1382 │ │ │ │ │ +[1] 183253 1396 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMDE │ │ │ │ │ -[1] 182490 1698 │ │ │ │ │ +[1] 184945 1711 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMannholdLogP │ │ │ │ │ -[1] 184479 1765 │ │ │ │ │ +[1] 186958 1776 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugMomentOfInertia │ │ │ │ │ -[1] 186536 2478 │ │ │ │ │ +[1] 189038 2493 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugOBFP2 │ │ │ │ │ -[1] 189301 1535 │ │ │ │ │ +[1] 191828 1547 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugOBFP3 │ │ │ │ │ -[1] 191123 1526 │ │ │ │ │ +[1] 193672 1538 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugOBFP4 │ │ │ │ │ -[1] 192935 1535 │ │ │ │ │ +[1] 195507 1546 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugOBMACCS │ │ │ │ │ -[1] 194759 1588 │ │ │ │ │ +[1] 197353 1601 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugPetitjeanNumber │ │ │ │ │ -[1] 196639 1984 │ │ │ │ │ +[1] 199257 1996 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugPetitjeanShapeIndex │ │ │ │ │ -[1] 198918 1899 │ │ │ │ │ +[1] 201560 1911 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugPubChem │ │ │ │ │ -[1] 201104 1430 │ │ │ │ │ +[1] 203768 1444 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugPubChemComplete │ │ │ │ │ -[1] 202826 1378 │ │ │ │ │ +[1] 205516 1391 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugRotatableBondsCount │ │ │ │ │ -[1] 204499 1554 │ │ │ │ │ +[1] 207213 1568 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugRuleOfFive │ │ │ │ │ -[1] 206342 1465 │ │ │ │ │ +[1] 209083 1479 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugShortestPath │ │ │ │ │ -[1] 208097 1746 │ │ │ │ │ +[1] 210864 1757 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugShortestPathComplete │ │ │ │ │ -[1] 210138 1773 │ │ │ │ │ +[1] 212928 1785 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugStandard │ │ │ │ │ -[1] 212198 1755 │ │ │ │ │ +[1] 215010 1767 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugStandardComplete │ │ │ │ │ -[1] 214245 1710 │ │ │ │ │ +[1] 217081 1723 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugTPSA │ │ │ │ │ -[1] 216240 1698 │ │ │ │ │ +[1] 219100 1710 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugVABC │ │ │ │ │ -[1] 218223 1357 │ │ │ │ │ +[1] 221106 1370 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugVAdjMa │ │ │ │ │ -[1] 219867 1616 │ │ │ │ │ +[1] 222774 1629 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugWHIM │ │ │ │ │ -[1] 221769 2913 │ │ │ │ │ +[1] 224700 2925 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugWeight │ │ │ │ │ -[1] 224967 1362 │ │ │ │ │ +[1] 227922 1376 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugWeightedPath │ │ │ │ │ -[1] 226619 2260 │ │ │ │ │ +[1] 229600 2272 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugWienerNumbers │ │ │ │ │ -[1] 229169 1716 │ │ │ │ │ +[1] 232173 1729 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugXLogP │ │ │ │ │ -[1] 231171 1718 │ │ │ │ │ +[1] 234199 1731 │ │ │ │ │ │ │ │ │ │ $variables$extractDrugZagrebIndex │ │ │ │ │ -[1] 233179 1498 │ │ │ │ │ +[1] 236232 1511 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMBLOSUM │ │ │ │ │ -[1] 234964 2780 │ │ │ │ │ +[1] 238041 2794 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMDescScales │ │ │ │ │ -[1] 238033 3616 │ │ │ │ │ +[1] 241134 3629 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMFAScales │ │ │ │ │ -[1] 241937 2838 │ │ │ │ │ +[1] 245062 2851 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMMDSScales │ │ │ │ │ -[1] 245064 2636 │ │ │ │ │ +[1] 248213 2649 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMPropScales │ │ │ │ │ -[1] 247989 2323 │ │ │ │ │ +[1] 251161 2336 │ │ │ │ │ │ │ │ │ │ $variables$extractPCMScales │ │ │ │ │ -[1] 250597 2613 │ │ │ │ │ +[1] 253794 2627 │ │ │ │ │ │ │ │ │ │ $variables$extractProtAAC │ │ │ │ │ -[1] 253494 1372 │ │ │ │ │ +[1] 256715 1386 │ │ │ │ │ │ │ │ │ │ $variables$extractProtAPAAC │ │ │ │ │ -[1] 255151 4913 │ │ │ │ │ +[1] 258397 4926 │ │ │ │ │ │ │ │ │ │ $variables$extractProtCTDC │ │ │ │ │ -[1] 260349 1628 │ │ │ │ │ +[1] 263618 1640 │ │ │ │ │ │ │ │ │ │ $variables$extractProtCTDD │ │ │ │ │ -[1] 262262 1621 │ │ │ │ │ +[1] 265553 1633 │ │ │ │ │ │ │ │ │ │ $variables$extractProtCTDT │ │ │ │ │ -[1] 264168 1629 │ │ │ │ │ +[1] 267481 1641 │ │ │ │ │ │ │ │ │ │ $variables$extractProtCTriad │ │ │ │ │ -[1] 266082 1210 │ │ │ │ │ +[1] 269418 1223 │ │ │ │ │ │ │ │ │ │ $variables$extractProtDC │ │ │ │ │ -[1] 267575 1372 │ │ │ │ │ +[1] 270935 1385 │ │ │ │ │ │ │ │ │ │ $variables$extractProtGeary │ │ │ │ │ -[1] 269232 5043 │ │ │ │ │ +[1] 272616 5056 │ │ │ │ │ │ │ │ │ │ $variables$extractProtMoran │ │ │ │ │ -[1] 274560 5043 │ │ │ │ │ +[1] 277968 5056 │ │ │ │ │ │ │ │ │ │ $variables$extractProtMoreauBroto │ │ │ │ │ -[1] 279894 5055 │ │ │ │ │ +[1] 283324 5068 │ │ │ │ │ │ │ │ │ │ $variables$extractProtPAAC │ │ │ │ │ -[1] 285233 5137 │ │ │ │ │ +[1] 288687 5153 │ │ │ │ │ │ │ │ │ │ $variables$extractProtPSSM │ │ │ │ │ -[1] 290655 7358 │ │ │ │ │ +[1] 294135 7369 │ │ │ │ │ │ │ │ │ │ $variables$extractProtPSSMAcc │ │ │ │ │ -[1] 298300 2085 │ │ │ │ │ +[1] 301802 2095 │ │ │ │ │ │ │ │ │ │ $variables$extractProtPSSMFeature │ │ │ │ │ -[1] 300676 2247 │ │ │ │ │ +[1] 304198 2260 │ │ │ │ │ │ │ │ │ │ $variables$extractProtQSO │ │ │ │ │ -[1] 303206 2006 │ │ │ │ │ +[1] 306752 2018 │ │ │ │ │ │ │ │ │ │ $variables$extractProtSOCN │ │ │ │ │ -[1] 305497 1919 │ │ │ │ │ +[1] 309066 1930 │ │ │ │ │ │ │ │ │ │ $variables$extractProtTC │ │ │ │ │ -[1] 307699 1368 │ │ │ │ │ +[1] 311290 1382 │ │ │ │ │ │ │ │ │ │ $variables$getCPI │ │ │ │ │ -[1] 309344 1779 │ │ │ │ │ +[1] 312962 1791 │ │ │ │ │ │ │ │ │ │ $variables$getDrug │ │ │ │ │ -[1] 311401 2151 │ │ │ │ │ +[1] 315043 2164 │ │ │ │ │ │ │ │ │ │ $variables$getFASTAFromKEGG │ │ │ │ │ -[1] 313839 1598 │ │ │ │ │ +[1] 317505 1610 │ │ │ │ │ │ │ │ │ │ $variables$getFASTAFromUniProt │ │ │ │ │ -[1] 315725 1801 │ │ │ │ │ +[1] 319413 1814 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromCAS │ │ │ │ │ -[1] 317810 1675 │ │ │ │ │ +[1] 321521 1688 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromChEMBL │ │ │ │ │ -[1] 319772 1552 │ │ │ │ │ +[1] 323506 1563 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromDrugBank │ │ │ │ │ -[1] 321612 1554 │ │ │ │ │ +[1] 325368 1567 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromKEGG │ │ │ │ │ -[1] 323451 1531 │ │ │ │ │ +[1] 327231 1543 │ │ │ │ │ │ │ │ │ │ $variables$getMolFromPubChem │ │ │ │ │ -[1] 325269 1568 │ │ │ │ │ +[1] 329071 1579 │ │ │ │ │ │ │ │ │ │ $variables$getPDBFromRCSBPDB │ │ │ │ │ -[1] 327124 1497 │ │ │ │ │ +[1] 330948 1510 │ │ │ │ │ │ │ │ │ │ $variables$getPPI │ │ │ │ │ -[1] 328897 2156 │ │ │ │ │ +[1] 332747 2168 │ │ │ │ │ │ │ │ │ │ $variables$getProt │ │ │ │ │ -[1] 331329 2098 │ │ │ │ │ +[1] 335204 2110 │ │ │ │ │ │ │ │ │ │ $variables$getSeqFromKEGG │ │ │ │ │ -[1] 333711 1494 │ │ │ │ │ +[1] 337610 1506 │ │ │ │ │ │ │ │ │ │ $variables$getSeqFromRCSBPDB │ │ │ │ │ -[1] 335491 1487 │ │ │ │ │ +[1] 339414 1499 │ │ │ │ │ │ │ │ │ │ $variables$getSeqFromUniProt │ │ │ │ │ -[1] 337262 1718 │ │ │ │ │ +[1] 341209 1729 │ │ │ │ │ │ │ │ │ │ $variables$getSmiFromChEMBL │ │ │ │ │ -[1] 339266 1553 │ │ │ │ │ +[1] 343235 1565 │ │ │ │ │ │ │ │ │ │ $variables$getSmiFromDrugBank │ │ │ │ │ -[1] 341105 1558 │ │ │ │ │ +[1] 345097 1571 │ │ │ │ │ │ │ │ │ │ $variables$getSmiFromKEGG │ │ │ │ │ -[1] 342947 1554 │ │ │ │ │ +[1] 346963 1566 │ │ │ │ │ │ │ │ │ │ $variables$getSmiFromPubChem │ │ │ │ │ -[1] 344787 1572 │ │ │ │ │ +[1] 348825 1584 │ │ │ │ │ │ │ │ │ │ $variables$readFASTA │ │ │ │ │ -[1] 346638 2212 │ │ │ │ │ +[1] 350699 2225 │ │ │ │ │ │ │ │ │ │ $variables$readMolFromSDF │ │ │ │ │ -[1] 349133 1299 │ │ │ │ │ +[1] 353218 1313 │ │ │ │ │ │ │ │ │ │ $variables$readMolFromSmi │ │ │ │ │ -[1] 350714 1899 │ │ │ │ │ +[1] 354825 1913 │ │ │ │ │ │ │ │ │ │ $variables$readPDB │ │ │ │ │ -[1] 352890 1750 │ │ │ │ │ +[1] 357028 1763 │ │ │ │ │ │ │ │ │ │ $variables$searchDrug │ │ │ │ │ -[1] 354920 3890 │ │ │ │ │ +[1] 359082 3899 │ │ │ │ │ │ │ │ │ │ $variables$segProt │ │ │ │ │ -[1] 359086 1965 │ │ │ │ │ +[1] 363270 1979 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 279 │ │ │ │ │ +[1] 0 292 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 9505 275 │ │ │ │ │ +[1] 9754 289 │ │ │ │ │ │ │ │ │ │ $references$`env::100` │ │ │ │ │ -[1] 196347 292 │ │ │ │ │ +[1] 198954 303 │ │ │ │ │ │ │ │ │ │ $references$`env::101` │ │ │ │ │ -[1] 198623 295 │ │ │ │ │ +[1] 201253 307 │ │ │ │ │ │ │ │ │ │ $references$`env::102` │ │ │ │ │ -[1] 200817 287 │ │ │ │ │ +[1] 203471 297 │ │ │ │ │ │ │ │ │ │ $references$`env::103` │ │ │ │ │ -[1] 202534 292 │ │ │ │ │ +[1] 205212 304 │ │ │ │ │ │ │ │ │ │ $references$`env::104` │ │ │ │ │ -[1] 204204 295 │ │ │ │ │ +[1] 206907 306 │ │ │ │ │ │ │ │ │ │ $references$`env::105` │ │ │ │ │ -[1] 206053 289 │ │ │ │ │ +[1] 208781 302 │ │ │ │ │ │ │ │ │ │ $references$`env::106` │ │ │ │ │ -[1] 207807 290 │ │ │ │ │ +[1] 210562 302 │ │ │ │ │ │ │ │ │ │ $references$`env::107` │ │ │ │ │ -[1] 209843 295 │ │ │ │ │ +[1] 212621 307 │ │ │ │ │ │ │ │ │ │ $references$`env::108` │ │ │ │ │ -[1] 211911 287 │ │ │ │ │ +[1] 214713 297 │ │ │ │ │ │ │ │ │ │ $references$`env::109` │ │ │ │ │ -[1] 213953 292 │ │ │ │ │ +[1] 216777 304 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 10830 274 │ │ │ │ │ +[1] 11107 289 │ │ │ │ │ │ │ │ │ │ $references$`env::110` │ │ │ │ │ -[1] 215955 285 │ │ │ │ │ +[1] 218804 296 │ │ │ │ │ │ │ │ │ │ $references$`env::111` │ │ │ │ │ -[1] 217938 285 │ │ │ │ │ +[1] 220810 296 │ │ │ │ │ │ │ │ │ │ $references$`env::112` │ │ │ │ │ -[1] 219580 287 │ │ │ │ │ +[1] 222476 298 │ │ │ │ │ │ │ │ │ │ $references$`env::113` │ │ │ │ │ -[1] 221483 286 │ │ │ │ │ +[1] 224403 297 │ │ │ │ │ │ │ │ │ │ $references$`env::114` │ │ │ │ │ -[1] 224682 285 │ │ │ │ │ +[1] 227625 297 │ │ │ │ │ │ │ │ │ │ $references$`env::115` │ │ │ │ │ -[1] 226329 290 │ │ │ │ │ +[1] 229298 302 │ │ │ │ │ │ │ │ │ │ $references$`env::116` │ │ │ │ │ -[1] 228879 290 │ │ │ │ │ +[1] 231872 301 │ │ │ │ │ │ │ │ │ │ $references$`env::117` │ │ │ │ │ -[1] 230885 286 │ │ │ │ │ +[1] 233902 297 │ │ │ │ │ │ │ │ │ │ $references$`env::118` │ │ │ │ │ -[1] 232889 290 │ │ │ │ │ +[1] 235930 302 │ │ │ │ │ │ │ │ │ │ $references$`env::119` │ │ │ │ │ -[1] 234677 287 │ │ │ │ │ +[1] 237743 298 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 11891 275 │ │ │ │ │ +[1] 12196 290 │ │ │ │ │ │ │ │ │ │ $references$`env::120` │ │ │ │ │ -[1] 237744 289 │ │ │ │ │ +[1] 240835 299 │ │ │ │ │ │ │ │ │ │ $references$`env::121` │ │ │ │ │ -[1] 241649 288 │ │ │ │ │ +[1] 244763 299 │ │ │ │ │ │ │ │ │ │ $references$`env::122` │ │ │ │ │ -[1] 244775 289 │ │ │ │ │ +[1] 247913 300 │ │ │ │ │ │ │ │ │ │ $references$`env::123` │ │ │ │ │ -[1] 247700 289 │ │ │ │ │ +[1] 250862 299 │ │ │ │ │ │ │ │ │ │ $references$`env::124` │ │ │ │ │ -[1] 250312 285 │ │ │ │ │ +[1] 253497 297 │ │ │ │ │ │ │ │ │ │ $references$`env::125` │ │ │ │ │ -[1] 253210 284 │ │ │ │ │ +[1] 256421 294 │ │ │ │ │ │ │ │ │ │ $references$`env::126` │ │ │ │ │ -[1] 254866 285 │ │ │ │ │ +[1] 258101 296 │ │ │ │ │ │ │ │ │ │ $references$`env::127` │ │ │ │ │ -[1] 260064 285 │ │ │ │ │ +[1] 263323 295 │ │ │ │ │ │ │ │ │ │ $references$`env::128` │ │ │ │ │ -[1] 261977 285 │ │ │ │ │ +[1] 265258 295 │ │ │ │ │ │ │ │ │ │ $references$`env::129` │ │ │ │ │ -[1] 263883 285 │ │ │ │ │ +[1] 267186 295 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 12945 277 │ │ │ │ │ +[1] 13280 290 │ │ │ │ │ │ │ │ │ │ $references$`env::130` │ │ │ │ │ -[1] 265797 285 │ │ │ │ │ +[1] 269122 296 │ │ │ │ │ │ │ │ │ │ $references$`env::131` │ │ │ │ │ -[1] 267292 283 │ │ │ │ │ +[1] 270641 294 │ │ │ │ │ │ │ │ │ │ $references$`env::132` │ │ │ │ │ -[1] 268947 285 │ │ │ │ │ +[1] 272320 296 │ │ │ │ │ │ │ │ │ │ $references$`env::133` │ │ │ │ │ -[1] 274275 285 │ │ │ │ │ +[1] 277672 296 │ │ │ │ │ │ │ │ │ │ $references$`env::134` │ │ │ │ │ -[1] 279603 291 │ │ │ │ │ +[1] 283024 300 │ │ │ │ │ │ │ │ │ │ $references$`env::135` │ │ │ │ │ -[1] 284949 284 │ │ │ │ │ +[1] 288392 295 │ │ │ │ │ │ │ │ │ │ $references$`env::136` │ │ │ │ │ -[1] 290370 285 │ │ │ │ │ +[1] 293840 295 │ │ │ │ │ │ │ │ │ │ $references$`env::137` │ │ │ │ │ -[1] 298013 287 │ │ │ │ │ +[1] 301504 298 │ │ │ │ │ │ │ │ │ │ $references$`env::138` │ │ │ │ │ -[1] 300385 291 │ │ │ │ │ +[1] 303897 301 │ │ │ │ │ │ │ │ │ │ $references$`env::139` │ │ │ │ │ -[1] 302923 283 │ │ │ │ │ +[1] 306458 294 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 14003 278 │ │ │ │ │ +[1] 14365 291 │ │ │ │ │ │ │ │ │ │ $references$`env::140` │ │ │ │ │ -[1] 305212 285 │ │ │ │ │ +[1] 308770 296 │ │ │ │ │ │ │ │ │ │ $references$`env::141` │ │ │ │ │ -[1] 307416 283 │ │ │ │ │ +[1] 310996 294 │ │ │ │ │ │ │ │ │ │ $references$`env::142` │ │ │ │ │ -[1] 309067 277 │ │ │ │ │ +[1] 312672 290 │ │ │ │ │ │ │ │ │ │ $references$`env::143` │ │ │ │ │ -[1] 311123 278 │ │ │ │ │ +[1] 314753 290 │ │ │ │ │ │ │ │ │ │ $references$`env::144` │ │ │ │ │ -[1] 313552 287 │ │ │ │ │ +[1] 317207 298 │ │ │ │ │ │ │ │ │ │ $references$`env::145` │ │ │ │ │ -[1] 315437 288 │ │ │ │ │ +[1] 319115 298 │ │ │ │ │ │ │ │ │ │ $references$`env::146` │ │ │ │ │ -[1] 317526 284 │ │ │ │ │ +[1] 321227 294 │ │ │ │ │ │ │ │ │ │ $references$`env::147` │ │ │ │ │ -[1] 319485 287 │ │ │ │ │ +[1] 323209 297 │ │ │ │ │ │ │ │ │ │ $references$`env::148` │ │ │ │ │ -[1] 321324 288 │ │ │ │ │ +[1] 325069 299 │ │ │ │ │ │ │ │ │ │ $references$`env::149` │ │ │ │ │ -[1] 323166 285 │ │ │ │ │ +[1] 326935 296 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 15082 276 │ │ │ │ │ +[1] 15471 292 │ │ │ │ │ │ │ │ │ │ $references$`env::150` │ │ │ │ │ -[1] 324982 287 │ │ │ │ │ +[1] 328774 297 │ │ │ │ │ │ │ │ │ │ $references$`env::151` │ │ │ │ │ -[1] 326837 287 │ │ │ │ │ +[1] 330650 298 │ │ │ │ │ │ │ │ │ │ $references$`env::152` │ │ │ │ │ -[1] 328621 276 │ │ │ │ │ +[1] 332458 289 │ │ │ │ │ │ │ │ │ │ $references$`env::153` │ │ │ │ │ -[1] 331053 276 │ │ │ │ │ +[1] 334915 289 │ │ │ │ │ │ │ │ │ │ $references$`env::154` │ │ │ │ │ -[1] 333427 284 │ │ │ │ │ +[1] 337314 296 │ │ │ │ │ │ │ │ │ │ $references$`env::155` │ │ │ │ │ -[1] 335205 286 │ │ │ │ │ +[1] 339116 298 │ │ │ │ │ │ │ │ │ │ $references$`env::156` │ │ │ │ │ -[1] 336978 284 │ │ │ │ │ +[1] 340913 296 │ │ │ │ │ │ │ │ │ │ $references$`env::157` │ │ │ │ │ -[1] 338980 286 │ │ │ │ │ +[1] 342938 297 │ │ │ │ │ │ │ │ │ │ $references$`env::158` │ │ │ │ │ -[1] 340819 286 │ │ │ │ │ +[1] 344800 297 │ │ │ │ │ │ │ │ │ │ $references$`env::159` │ │ │ │ │ -[1] 342663 284 │ │ │ │ │ +[1] 346668 295 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 16153 275 │ │ │ │ │ +[1] 16573 289 │ │ │ │ │ │ │ │ │ │ $references$`env::160` │ │ │ │ │ -[1] 344501 286 │ │ │ │ │ +[1] 348529 296 │ │ │ │ │ │ │ │ │ │ $references$`env::161` │ │ │ │ │ -[1] 346359 279 │ │ │ │ │ +[1] 350409 290 │ │ │ │ │ │ │ │ │ │ $references$`env::162` │ │ │ │ │ -[1] 348850 283 │ │ │ │ │ +[1] 352924 294 │ │ │ │ │ │ │ │ │ │ $references$`env::163` │ │ │ │ │ -[1] 350432 282 │ │ │ │ │ +[1] 354531 294 │ │ │ │ │ │ │ │ │ │ $references$`env::164` │ │ │ │ │ -[1] 352613 277 │ │ │ │ │ +[1] 356738 290 │ │ │ │ │ │ │ │ │ │ $references$`env::165` │ │ │ │ │ -[1] 354640 280 │ │ │ │ │ +[1] 358791 291 │ │ │ │ │ │ │ │ │ │ $references$`env::166` │ │ │ │ │ -[1] 358810 276 │ │ │ │ │ +[1] 362981 289 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 17221 279 │ │ │ │ │ +[1] 17671 292 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 18280 274 │ │ │ │ │ +[1] 18757 289 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 19330 274 │ │ │ │ │ +[1] 19836 289 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 1069 279 │ │ │ │ │ +[1] 1096 293 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 20388 277 │ │ │ │ │ +[1] 20922 292 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 21421 277 │ │ │ │ │ +[1] 21984 292 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 22695 280 │ │ │ │ │ +[1] 23288 292 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 24341 278 │ │ │ │ │ +[1] 24960 291 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 25414 278 │ │ │ │ │ +[1] 26060 293 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 26463 278 │ │ │ │ │ +[1] 27139 293 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 27513 277 │ │ │ │ │ +[1] 28220 291 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 28557 277 │ │ │ │ │ +[1] 29293 291 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 29601 277 │ │ │ │ │ +[1] 30366 291 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 30644 275 │ │ │ │ │ +[1] 31439 289 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 2131 274 │ │ │ │ │ +[1] 2186 288 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 31690 275 │ │ │ │ │ +[1] 32515 290 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 32755 273 │ │ │ │ │ +[1] 33611 289 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 33804 279 │ │ │ │ │ +[1] 34691 292 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 34911 276 │ │ │ │ │ +[1] 35828 291 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 35962 274 │ │ │ │ │ +[1] 36909 289 │ │ │ │ │ │ │ │ │ │ $references$`env::35` │ │ │ │ │ -[1] 37028 275 │ │ │ │ │ +[1] 38003 290 │ │ │ │ │ │ │ │ │ │ $references$`env::36` │ │ │ │ │ -[1] 38415 275 │ │ │ │ │ +[1] 39418 290 │ │ │ │ │ │ │ │ │ │ $references$`env::37` │ │ │ │ │ -[1] 39523 279 │ │ │ │ │ +[1] 40555 291 │ │ │ │ │ │ │ │ │ │ $references$`env::38` │ │ │ │ │ -[1] 41442 271 │ │ │ │ │ +[1] 42500 285 │ │ │ │ │ │ │ │ │ │ $references$`env::39` │ │ │ │ │ -[1] 44124 281 │ │ │ │ │ +[1] 45210 294 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 3199 283 │ │ │ │ │ +[1] 3283 295 │ │ │ │ │ │ │ │ │ │ $references$`env::40` │ │ │ │ │ -[1] 47354 282 │ │ │ │ │ +[1] 48465 295 │ │ │ │ │ │ │ │ │ │ $references$`env::41` │ │ │ │ │ -[1] 50344 282 │ │ │ │ │ +[1] 51483 295 │ │ │ │ │ │ │ │ │ │ $references$`env::42` │ │ │ │ │ -[1] 54522 282 │ │ │ │ │ +[1] 55688 296 │ │ │ │ │ │ │ │ │ │ $references$`env::43` │ │ │ │ │ -[1] 57832 283 │ │ │ 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"/home/moeller/Salsa/r-bioc-rcpi/man/AA2DACOR.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-rcpi/man/AA3DMoRSE.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-rcpi/man/AAACF.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM100.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM45.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM50.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM62.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-rcpi/man/AABLOSUM80.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-rcpi/man/AABurden.Rd" │ │ │ │ │ - [10] "/home/moeller/Salsa/r-bioc-rcpi/man/AACPSA.Rd" │ │ │ │ │ - [11] "/home/moeller/Salsa/r-bioc-rcpi/man/AAConn.Rd" │ │ │ │ │ - [12] "/home/moeller/Salsa/r-bioc-rcpi/man/AAConst.Rd" │ │ │ │ │ - [13] "/home/moeller/Salsa/r-bioc-rcpi/man/AADescAll.Rd" │ │ │ │ │ - [14] "/home/moeller/Salsa/r-bioc-rcpi/man/AAEdgeAdj.Rd" │ │ │ │ │ - [15] "/home/moeller/Salsa/r-bioc-rcpi/man/AAEigIdx.Rd" │ │ │ │ │ - [16] "/home/moeller/Salsa/r-bioc-rcpi/man/AAFGC.Rd" │ │ │ │ │ - [17] "/home/moeller/Salsa/r-bioc-rcpi/man/AAGETAWAY.Rd" │ │ │ │ │ - [18] "/home/moeller/Salsa/r-bioc-rcpi/man/AAGeom.Rd" │ │ │ │ │ - [19] "/home/moeller/Salsa/r-bioc-rcpi/man/AAInfo.Rd" │ │ │ │ │ - [20] "/home/moeller/Salsa/r-bioc-rcpi/man/AAMOE2D.Rd" │ │ │ │ │ - [21] "/home/moeller/Salsa/r-bioc-rcpi/man/AAMOE3D.Rd" │ │ │ │ │ - [22] "/home/moeller/Salsa/r-bioc-rcpi/man/AAMetaInfo.Rd" │ │ │ │ │ - [23] "/home/moeller/Salsa/r-bioc-rcpi/man/AAMolProp.Rd" │ │ │ │ │ - [24] "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM120.Rd" │ │ │ │ │ - [25] "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM250.Rd" │ │ │ │ │ - [26] "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM30.Rd" │ │ │ │ │ - [27] "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM40.Rd" │ │ │ │ │ - [28] "/home/moeller/Salsa/r-bioc-rcpi/man/AAPAM70.Rd" │ │ │ │ │ - [29] "/home/moeller/Salsa/r-bioc-rcpi/man/AARDF.Rd" │ │ │ │ │ - [30] "/home/moeller/Salsa/r-bioc-rcpi/man/AARandic.Rd" │ │ │ │ │ - [31] "/home/moeller/Salsa/r-bioc-rcpi/man/AATopo.Rd" │ │ │ │ │ - [32] "/home/moeller/Salsa/r-bioc-rcpi/man/AATopoChg.Rd" │ │ │ │ │ - [33] "/home/moeller/Salsa/r-bioc-rcpi/man/AAWHIM.Rd" │ │ │ │ │ - [34] "/home/moeller/Salsa/r-bioc-rcpi/man/AAWalk.Rd" │ │ │ │ │ - [35] "/home/moeller/Salsa/r-bioc-rcpi/man/AAindex.Rd" │ │ │ │ │ - [36] "/home/moeller/Salsa/r-bioc-rcpi/man/OptAA3d.Rd" │ │ │ │ │ - [37] "/home/moeller/Salsa/r-bioc-rcpi/man/Rcpi-package.Rd" │ │ │ │ │ - [38] "/home/moeller/Salsa/r-bioc-rcpi/man/acc.Rd" │ │ │ │ │ - [39] "/home/moeller/Salsa/r-bioc-rcpi/man/calcDrugFPSim.Rd" │ │ │ │ │ - [40] "/home/moeller/Salsa/r-bioc-rcpi/man/calcDrugMCSSim.Rd" │ │ │ │ │ - [41] "/home/moeller/Salsa/r-bioc-rcpi/man/calcParProtGOSim.Rd" │ │ │ │ │ - [42] "/home/moeller/Salsa/r-bioc-rcpi/man/calcParProtSeqSim.Rd" │ │ │ │ │ - [43] "/home/moeller/Salsa/r-bioc-rcpi/man/calcTwoProtGOSim.Rd" │ │ │ │ │ - [44] "/home/moeller/Salsa/r-bioc-rcpi/man/calcTwoProtSeqSim.Rd" │ │ │ │ │ - [45] "/home/moeller/Salsa/r-bioc-rcpi/man/checkProt.Rd" │ │ │ │ │ - [46] "/home/moeller/Salsa/r-bioc-rcpi/man/convMolFormat.Rd" │ │ │ │ │ - [47] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAIO.Rd" │ │ │ │ │ - [48] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugALOGP.Rd" │ │ │ │ │ - [49] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAminoAcidCount.Rd" │ │ │ │ │ - [50] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugApol.Rd" │ │ │ │ │ - [51] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAromaticAtomsCount.Rd" │ │ │ │ │ - [52] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAromaticBondsCount.Rd" │ │ │ │ │ - [53] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAtomCount.Rd" │ │ │ │ │ - [54] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAutocorrelationCharge.Rd" │ │ │ │ │ - [55] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAutocorrelationMass.Rd" │ │ │ │ │ - [56] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugAutocorrelationPolarizability.Rd" │ │ │ │ │ - [57] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugBCUT.Rd" │ │ │ │ │ - [58] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugBPol.Rd" │ │ │ │ │ - [59] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugBondCount.Rd" │ │ │ │ │ - [60] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugCPSA.Rd" │ │ │ │ │ - [61] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugCarbonTypes.Rd" │ │ │ │ │ - [62] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugChiChain.Rd" │ │ │ │ │ - [63] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugChiCluster.Rd" │ │ │ │ │ - [64] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugChiPath.Rd" │ │ │ │ │ - [65] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugChiPathCluster.Rd" │ │ │ │ │ - [66] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugDescOB.Rd" │ │ │ │ │ - [67] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugECI.Rd" │ │ │ │ │ - [68] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugEstate.Rd" │ │ │ │ │ - [69] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugEstateComplete.Rd" │ │ │ │ │ - [70] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugExtended.Rd" │ │ │ │ │ - [71] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugExtendedComplete.Rd" │ │ │ │ │ - [72] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugFMF.Rd" │ │ │ │ │ - [73] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugFragmentComplexity.Rd" │ │ │ │ │ - [74] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugGraph.Rd" │ │ │ │ │ - [75] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugGraphComplete.Rd" │ │ │ │ │ - [76] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugGravitationalIndex.Rd" │ │ │ │ │ - [77] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHBondAcceptorCount.Rd" │ │ │ │ │ - [78] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHBondDonorCount.Rd" │ │ │ │ │ - [79] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHybridization.Rd" │ │ │ │ │ - [80] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHybridizationComplete.Rd" │ │ │ │ │ - [81] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugHybridizationRatio.Rd" │ │ │ │ │ - [82] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugIPMolecularLearning.Rd" │ │ │ │ │ - [83] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugKR.Rd" │ │ │ │ │ - [84] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugKRComplete.Rd" │ │ │ │ │ - [85] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugKappaShapeIndices.Rd" │ │ │ │ │ - [86] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugKierHallSmarts.Rd" │ │ │ │ │ - [87] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugLargestChain.Rd" │ │ │ │ │ - [88] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugLargestPiSystem.Rd" │ │ │ │ │ - [89] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugLengthOverBreadth.Rd" │ │ │ │ │ - [90] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugLongestAliphaticChain.Rd" │ │ │ │ │ - [91] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMACCS.Rd" │ │ │ │ │ - [92] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMACCSComplete.Rd" │ │ │ │ │ - [93] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMDE.Rd" │ │ │ │ │ - [94] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMannholdLogP.Rd" │ │ │ │ │ - [95] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugMomentOfInertia.Rd" │ │ │ │ │ - [96] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugOBFP2.Rd" │ │ │ │ │ - [97] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugOBFP3.Rd" │ │ │ │ │ - [98] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugOBFP4.Rd" │ │ │ │ │ - [99] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugOBMACCS.Rd" │ │ │ │ │ -[100] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugPetitjeanNumber.Rd" │ │ │ │ │ -[101] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugPetitjeanShapeIndex.Rd" │ │ │ │ │ -[102] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugPubChem.Rd" │ │ │ │ │ -[103] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugPubChemComplete.Rd" │ │ │ │ │ -[104] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugRotatableBondsCount.Rd" │ │ │ │ │ -[105] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugRuleOfFive.Rd" │ │ │ │ │ -[106] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugShortestPath.Rd" │ │ │ │ │ -[107] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugShortestPathComplete.Rd" │ │ │ │ │ -[108] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugStandard.Rd" │ │ │ │ │ -[109] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugStandardComplete.Rd" │ │ │ │ │ -[110] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugTPSA.Rd" │ │ │ │ │ -[111] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugVABC.Rd" │ │ │ │ │ -[112] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugVAdjMa.Rd" │ │ │ │ │ -[113] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugWHIM.Rd" │ │ │ │ │ -[114] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugWeight.Rd" │ │ │ │ │ -[115] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugWeightedPath.Rd" │ │ │ │ │ -[116] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugWienerNumbers.Rd" │ │ │ │ │ -[117] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugXLogP.Rd" │ │ │ │ │ -[118] "/home/moeller/Salsa/r-bioc-rcpi/man/extractDrugZagrebIndex.Rd" │ │ │ │ │ -[119] "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMBLOSUM.Rd" │ │ │ │ │ -[120] "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMDescScales.Rd" │ │ │ │ │ -[121] "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMFAScales.Rd" │ │ │ │ │ -[122] "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMMDSScales.Rd" │ │ │ │ │ -[123] "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMPropScales.Rd" │ │ │ │ │ -[124] "/home/moeller/Salsa/r-bioc-rcpi/man/extractPCMScales.Rd" │ │ │ │ │ -[125] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtAAC.Rd" │ │ │ │ │ -[126] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtAPAAC.Rd" │ │ │ │ │ -[127] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtCTDC.Rd" │ │ │ │ │ -[128] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtCTDD.Rd" │ │ │ │ │ -[129] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtCTDT.Rd" │ │ │ │ │ -[130] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtCTriad.Rd" │ │ │ │ │ -[131] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtDC.Rd" │ │ │ │ │ -[132] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtGeary.Rd" │ │ │ │ │ -[133] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtMoran.Rd" │ │ │ │ │ -[134] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtMoreauBroto.Rd" │ │ │ │ │ -[135] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtPAAC.Rd" │ │ │ │ │ -[136] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtPSSM.Rd" │ │ │ │ │ -[137] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtPSSMAcc.Rd" │ │ │ │ │ -[138] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtPSSMFeature.Rd" │ │ │ │ │ -[139] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtQSO.Rd" │ │ │ │ │ -[140] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtSOCN.Rd" │ │ │ │ │ -[141] "/home/moeller/Salsa/r-bioc-rcpi/man/extractProtTC.Rd" │ │ │ │ │ -[142] "/home/moeller/Salsa/r-bioc-rcpi/man/getCPI.Rd" │ │ │ │ │ -[143] "/home/moeller/Salsa/r-bioc-rcpi/man/getDrug.Rd" │ │ │ │ │ -[144] "/home/moeller/Salsa/r-bioc-rcpi/man/getFASTAFromKEGG.Rd" │ │ │ │ │ -[145] "/home/moeller/Salsa/r-bioc-rcpi/man/getFASTAFromUniProt.Rd" │ │ │ │ │ -[146] "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromCAS.Rd" │ │ │ │ │ -[147] "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromChEMBL.Rd" │ │ │ │ │ -[148] "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromDrugBank.Rd" │ │ │ │ │ -[149] "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromKEGG.Rd" │ │ │ │ │ -[150] "/home/moeller/Salsa/r-bioc-rcpi/man/getMolFromPubChem.Rd" │ │ │ │ │ -[151] "/home/moeller/Salsa/r-bioc-rcpi/man/getPDBFromRCSBPDB.Rd" │ │ │ │ │ -[152] "/home/moeller/Salsa/r-bioc-rcpi/man/getPPI.Rd" │ │ │ │ │ -[153] "/home/moeller/Salsa/r-bioc-rcpi/man/getProt.Rd" │ │ │ │ │ -[154] "/home/moeller/Salsa/r-bioc-rcpi/man/getSeqFromKEGG.Rd" │ │ │ │ │ -[155] "/home/moeller/Salsa/r-bioc-rcpi/man/getSeqFromRCSBPDB.Rd" │ │ │ │ │ -[156] "/home/moeller/Salsa/r-bioc-rcpi/man/getSeqFromUniProt.Rd" │ │ │ │ │ -[157] "/home/moeller/Salsa/r-bioc-rcpi/man/getSmiFromChEMBL.Rd" │ │ │ │ │ -[158] "/home/moeller/Salsa/r-bioc-rcpi/man/getSmiFromDrugBank.Rd" │ │ │ │ │ -[159] "/home/moeller/Salsa/r-bioc-rcpi/man/getSmiFromKEGG.Rd" │ │ │ │ │ -[160] "/home/moeller/Salsa/r-bioc-rcpi/man/getSmiFromPubChem.Rd" │ │ │ │ │ -[161] "/home/moeller/Salsa/r-bioc-rcpi/man/readFASTA.Rd" │ │ │ │ │ -[162] "/home/moeller/Salsa/r-bioc-rcpi/man/readMolFromSDF.Rd" │ │ │ │ │ -[163] "/home/moeller/Salsa/r-bioc-rcpi/man/readMolFromSmi.Rd" │ │ │ │ │ -[164] "/home/moeller/Salsa/r-bioc-rcpi/man/readPDB.Rd" │ │ │ │ │ -[165] "/home/moeller/Salsa/r-bioc-rcpi/man/searchDrug.Rd" │ │ │ │ │ -[166] "/home/moeller/Salsa/r-bioc-rcpi/man/segProt.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AA2DACOR.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AA3DMoRSE.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAACF.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM100.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM45.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM50.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM62.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABLOSUM80.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AABurden.Rd" │ │ │ │ │ + [10] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AACPSA.Rd" │ │ │ │ │ + [11] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAConn.Rd" │ │ │ │ │ + [12] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAConst.Rd" │ │ │ │ │ + [13] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AADescAll.Rd" │ │ │ │ │ + [14] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAEdgeAdj.Rd" │ │ │ │ │ + [15] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAEigIdx.Rd" │ │ │ │ │ + [16] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAFGC.Rd" │ │ │ │ │ + [17] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAGETAWAY.Rd" │ │ │ │ │ + [18] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAGeom.Rd" │ │ │ │ │ + [19] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAInfo.Rd" │ │ │ │ │ + [20] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAMOE2D.Rd" │ │ │ │ │ + [21] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAMOE3D.Rd" │ │ │ │ │ + [22] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAMetaInfo.Rd" │ │ │ │ │ + [23] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAMolProp.Rd" │ │ │ │ │ + [24] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM120.Rd" │ │ │ │ │ + [25] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM250.Rd" │ │ │ │ │ + [26] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM30.Rd" │ │ │ │ │ + [27] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM40.Rd" │ │ │ │ │ + [28] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAPAM70.Rd" │ │ │ │ │ + [29] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AARDF.Rd" │ │ │ │ │ + [30] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AARandic.Rd" │ │ │ │ │ + [31] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AATopo.Rd" │ │ │ │ │ + [32] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AATopoChg.Rd" │ │ │ │ │ + [33] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAWHIM.Rd" │ │ │ │ │ + [34] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAWalk.Rd" │ │ │ │ │ + [35] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/AAindex.Rd" │ │ │ │ │ + [36] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/OptAA3d.Rd" │ │ │ │ │ + [37] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/Rcpi-package.Rd" │ │ │ │ │ + [38] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/acc.Rd" │ │ │ │ │ + [39] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcDrugFPSim.Rd" │ │ │ │ │ + [40] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcDrugMCSSim.Rd" │ │ │ │ │ + [41] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcParProtGOSim.Rd" │ │ │ │ │ + [42] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcParProtSeqSim.Rd" │ │ │ │ │ + [43] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcTwoProtGOSim.Rd" │ │ │ │ │ + [44] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/calcTwoProtSeqSim.Rd" │ │ │ │ │ + [45] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/checkProt.Rd" │ │ │ │ │ + [46] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/convMolFormat.Rd" │ │ │ │ │ + [47] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAIO.Rd" │ │ │ │ │ + [48] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugALOGP.Rd" │ │ │ │ │ + [49] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAminoAcidCount.Rd" │ │ │ │ │ + [50] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugApol.Rd" │ │ │ │ │ + [51] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAromaticAtomsCount.Rd" │ │ │ │ │ + [52] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAromaticBondsCount.Rd" │ │ │ │ │ + [53] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAtomCount.Rd" │ │ │ │ │ + [54] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAutocorrelationCharge.Rd" │ │ │ │ │ + [55] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAutocorrelationMass.Rd" │ │ │ │ │ + [56] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugAutocorrelationPolarizability.Rd" │ │ │ │ │ + [57] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugBCUT.Rd" │ │ │ │ │ + [58] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugBPol.Rd" │ │ │ │ │ + [59] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugBondCount.Rd" │ │ │ │ │ + [60] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugCPSA.Rd" │ │ │ │ │ + [61] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugCarbonTypes.Rd" │ │ │ │ │ + [62] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugChiChain.Rd" │ │ │ │ │ + [63] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugChiCluster.Rd" │ │ │ │ │ + [64] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugChiPath.Rd" │ │ │ │ │ + [65] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugChiPathCluster.Rd" │ │ │ │ │ + [66] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugDescOB.Rd" │ │ │ │ │ + [67] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugECI.Rd" │ │ │ │ │ + [68] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugEstate.Rd" │ │ │ │ │ + [69] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugEstateComplete.Rd" │ │ │ │ │ + [70] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugExtended.Rd" │ │ │ │ │ + [71] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugExtendedComplete.Rd" │ │ │ │ │ + [72] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugFMF.Rd" │ │ │ │ │ + [73] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugFragmentComplexity.Rd" │ │ │ │ │ + [74] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugGraph.Rd" │ │ │ │ │ + [75] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugGraphComplete.Rd" │ │ │ │ │ + [76] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugGravitationalIndex.Rd" │ │ │ │ │ + [77] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHBondAcceptorCount.Rd" │ │ │ │ │ + [78] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHBondDonorCount.Rd" │ │ │ │ │ + [79] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHybridization.Rd" │ │ │ │ │ + [80] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHybridizationComplete.Rd" │ │ │ │ │ + [81] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugHybridizationRatio.Rd" │ │ │ │ │ + [82] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugIPMolecularLearning.Rd" │ │ │ │ │ + [83] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugKR.Rd" │ │ │ │ │ + [84] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugKRComplete.Rd" │ │ │ │ │ + [85] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugKappaShapeIndices.Rd" │ │ │ │ │ + [86] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugKierHallSmarts.Rd" │ │ │ │ │ + [87] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugLargestChain.Rd" │ │ │ │ │ + [88] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugLargestPiSystem.Rd" │ │ │ │ │ + [89] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugLengthOverBreadth.Rd" │ │ │ │ │ + [90] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugLongestAliphaticChain.Rd" │ │ │ │ │ + [91] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMACCS.Rd" │ │ │ │ │ + [92] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMACCSComplete.Rd" │ │ │ │ │ + [93] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMDE.Rd" │ │ │ │ │ + [94] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMannholdLogP.Rd" │ │ │ │ │ + [95] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugMomentOfInertia.Rd" │ │ │ │ │ + [96] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugOBFP2.Rd" │ │ │ │ │ + [97] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugOBFP3.Rd" │ │ │ │ │ + [98] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugOBFP4.Rd" │ │ │ │ │ + [99] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugOBMACCS.Rd" │ │ │ │ │ +[100] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugPetitjeanNumber.Rd" │ │ │ │ │ +[101] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugPetitjeanShapeIndex.Rd" │ │ │ │ │ +[102] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugPubChem.Rd" │ │ │ │ │ +[103] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugPubChemComplete.Rd" │ │ │ │ │ +[104] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugRotatableBondsCount.Rd" │ │ │ │ │ +[105] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugRuleOfFive.Rd" │ │ │ │ │ +[106] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugShortestPath.Rd" │ │ │ │ │ +[107] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugShortestPathComplete.Rd" │ │ │ │ │ +[108] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugStandard.Rd" │ │ │ │ │ +[109] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugStandardComplete.Rd" │ │ │ │ │ +[110] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugTPSA.Rd" │ │ │ │ │ +[111] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugVABC.Rd" │ │ │ │ │ +[112] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugVAdjMa.Rd" │ │ │ │ │ +[113] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugWHIM.Rd" │ │ │ │ │ +[114] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugWeight.Rd" │ │ │ │ │ +[115] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugWeightedPath.Rd" │ │ │ │ │ +[116] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugWienerNumbers.Rd" │ │ │ │ │ +[117] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugXLogP.Rd" │ │ │ │ │ +[118] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractDrugZagrebIndex.Rd" │ │ │ │ │ +[119] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractPCMBLOSUM.Rd" │ │ │ │ │ +[120] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractPCMDescScales.Rd" │ │ │ │ │ +[121] "/build/reproducible-path/r-bioc-rcpi-1.48.0+ds/man/extractPCMFAScales.Rd" 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