Files in road2stat/Rcpi
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS
NEWS.md
R/101-getDrugPubChem.R
R/102-getDrugChEMBL.R
R/103-getDrugCAS.R
R/104-getDrugKEGG.R
R/105-getDrugDrugBank.R
R/106-getDrug.R
R/201-getProtUniProt.R
R/202-getProtKEGG.R
R/203-getProtRCSBPDB.R
R/204-getProt.R
R/300-extractDrugAIO.R
R/301-extractDrugALOGP.R
R/302-extractDrugApol.R
R/304-extractDrugAminoAcidCount.R
R/305-extractDrugAromaticAtomsCount.R
R/306-extractDrugAromaticBondsCount.R
R/307-extractDrugAtomCount.R
R/308-extractDrugAutocorrelationCharge.R
R/309-extractDrugAutocorrelationMass.R
R/310-extractDrugAutocorrelationPolarizability.R
R/311-extractDrugBCUT.R
R/312-extractDrugBPol.R
R/314-extractDrugBondCount.R
R/315-extractDrugCPSA.R
R/316-extractDrugCarbonTypes.R
R/317-extractDrugChiChain.R
R/318-extractDrugChiCluster.R
R/319-extractDrugChiPathCluster.R
R/320-extractDrugChiPath.R
R/321-extractDrugECI.R
R/322-extractDrugFMF.R
R/323-extractDrugFragmentComplexity.R
R/324-extractDrugGravitationalIndex.R
R/325-extractDrugHBondAcceptorCount.R
R/326-extractDrugHBondDonorCount.R
R/327-extractDrugHybridizationRatio.R
R/328-extractDrugIPMolecularLearning.R
R/329-extractDrugKappaShapeIndices.R
R/330-extractDrugKierHallSmarts.R
R/331-extractDrugLargestChain.R
R/332-extractDrugLargestPiSystem.R
R/333-extractDrugLengthOverBreadth.R
R/334-extractDrugLongestAliphaticChain.R
R/335-extractDrugMDE.R
R/336-extractDrugMannholdLogP.R
R/337-extractDrugMomentOfInertia.R
R/338-extractDrugPetitjeanNumber.R
R/339-extractDrugPetitjeanShapeIndex.R
R/340-extractDrugRotatableBondsCount.R
R/341-extractDrugRuleOfFive.R
R/342-extractDrugTPSA.R
R/343-extractDrugVABC.R
R/344-extractDrugVAdjMa.R
R/345-extractDrugWHIM.R
R/346-extractDrugWeight.R
R/347-extractDrugWeightedPath.R
R/348-extractDrugWienerNumbers.R
R/349-extractDrugXLogP.R
R/350-extractDrugZagrebIndex.R
R/371-extractDrugStandard.R
R/372-extractDrugExtended.R
R/373-extractDrugGraph.R
R/374-extractDrugHybridization.R
R/375-extractDrugMACCS.R
R/376-extractDrugEstate.R
R/377-extractDrugPubChem.R
R/378-extractDrugKR.R
R/379-extractDrugShortestPath.R
R/380-extractDrugOBFP2.R
R/381-extractDrugOBFP3.R
R/382-extractDrugOBFP4.R
R/383-extractDrugOBMACCS.R
R/384-extractDrugDescOB.R
R/401-extractProtAAC.R
R/402-extractProtDC.R
R/403-extractProtTC.R
R/404-extractProtMoreauBroto.R
R/405-extractProtMoran.R
R/406-extractProtGeary.R
R/407-extractProtCTDC.R
R/408-extractProtCTDT.R
R/409-extractProtCTDD.R
R/410-extractProtCTriad.R
R/411-extractProtSOCN.R
R/412-extractProtQSO.R
R/413-extractProtPAAC.R
R/414-extractProtAPAAC.R
R/415-extractPCMScales.R
R/416-extractPCMDescScales.R
R/417-extractPCMPropScales.R
R/418-extractPCMFAScales.R
R/419-extractPCMMDSScales.R
R/420-extractPCMBLOSUM.R
R/421-extractProtPSSM.R
R/422-extractProtPSSMFeature.R
R/423-extractProtPSSMAcc.R
R/501-readFASTA.R
R/502-readPDB.R
R/503-readMolFromSDF.R
R/504-readMolFromSmi.R
R/505-convMolFormat.R
R/506-checkProt.R
R/507-segProt.R
R/508-acc.R
R/601-getCPI.R
R/602-getPPI.R
R/701-calcDrugFPSim.R
R/702-calcDrugMCSSim.R
R/703-calcProtGOSim.R
R/704-calcProtSeqSim.R
R/705-searchDrug.R
R/Rcpi-datalist.R
R/Rcpi-package.R
R/rcdk.R
README.md
RELEASE.md
Rcpi.Rproj
_pkgdown.yml
data/AA2DACOR.rda
data/AA3DMoRSE.rda
data/AAACF.rda
data/AABLOSUM100.rda
data/AABLOSUM45.rda
data/AABLOSUM50.rda
data/AABLOSUM62.rda
data/AABLOSUM80.rda
data/AABurden.rda
data/AACPSA.rda
data/AAConn.rda
data/AAConst.rda
data/AADescAll.rda
data/AAEdgeAdj.rda
data/AAEigIdx.rda
data/AAFGC.rda
data/AAGETAWAY.rda
data/AAGeom.rda
data/AAInfo.rda
data/AAMOE2D.rda
data/AAMOE3D.rda
data/AAMetaInfo.rda
data/AAMolProp.rda
data/AAPAM120.rda
data/AAPAM250.rda
data/AAPAM30.rda
data/AAPAM40.rda
data/AAPAM70.rda
data/AARDF.rda
data/AARandic.rda
data/AATopo.rda
data/AATopoChg.rda
data/AAWHIM.rda
data/AAWalk.rda
data/AAindex.rda
inst/CITATION
inst/compseq/DB00530.sdf
inst/compseq/DB00859.sdf
inst/compseq/DB00860.sdf
inst/compseq/tyrphostin.sdf
inst/logo/logo.R
inst/protseq/4HHB.pdb
inst/protseq/P00750.fasta
inst/protseq/P08218.fasta
inst/protseq/P10323.fasta
inst/protseq/P20160.fasta
inst/protseq/Plasminogen.fasta
inst/protseq/Q9NZP8.fasta
inst/sysdata/AAidx.csv
inst/sysdata/CTDict.rda
inst/sysdata/CTIndex.rda
inst/sysdata/Grantham.csv
inst/sysdata/OptAA3d.sdf
inst/sysdata/Schneider-Wrede.csv
inst/sysdata/TCDict.rda
inst/vignettedata/FDAMDD.csv
inst/vignettedata/FDAMDD.smi
inst/vignettedata/GPCR.csv
inst/vignettedata/RI.csv
inst/vignettedata/RI.smi
inst/vignettedata/extracell.fasta
inst/vignettedata/mitochondrion.fasta
man/AA2DACOR.Rd
man/AA3DMoRSE.Rd
man/AAACF.Rd
man/AABLOSUM100.Rd
man/AABLOSUM45.Rd
man/AABLOSUM50.Rd
man/AABLOSUM62.Rd
man/AABLOSUM80.Rd
man/AABurden.Rd
man/AACPSA.Rd
man/AAConn.Rd
man/AAConst.Rd
man/AADescAll.Rd
man/AAEdgeAdj.Rd
man/AAEigIdx.Rd
man/AAFGC.Rd
man/AAGETAWAY.Rd
man/AAGeom.Rd
man/AAInfo.Rd
man/AAMOE2D.Rd
man/AAMOE3D.Rd
man/AAMetaInfo.Rd
man/AAMolProp.Rd
man/AAPAM120.Rd
man/AAPAM250.Rd
man/AAPAM30.Rd
man/AAPAM40.Rd
man/AAPAM70.Rd
man/AARDF.Rd
man/AARandic.Rd
man/AATopo.Rd
man/AATopoChg.Rd
man/AAWHIM.Rd
man/AAWalk.Rd
man/AAindex.Rd
man/OptAA3d.Rd
man/Rcpi-package.Rd
man/acc.Rd
man/calcDrugFPSim.Rd
man/calcDrugMCSSim.Rd
man/calcParProtGOSim.Rd
man/calcParProtSeqSim.Rd
man/calcTwoProtGOSim.Rd
man/calcTwoProtSeqSim.Rd
man/checkProt.Rd
man/convMolFormat.Rd
man/extractDrugAIO.Rd
man/extractDrugALOGP.Rd
man/extractDrugAminoAcidCount.Rd
man/extractDrugApol.Rd
man/extractDrugAromaticAtomsCount.Rd
man/extractDrugAromaticBondsCount.Rd
man/extractDrugAtomCount.Rd
man/extractDrugAutocorrelationCharge.Rd
man/extractDrugAutocorrelationMass.Rd
man/extractDrugAutocorrelationPolarizability.Rd
man/extractDrugBCUT.Rd
man/extractDrugBPol.Rd
man/extractDrugBondCount.Rd
man/extractDrugCPSA.Rd
man/extractDrugCarbonTypes.Rd
man/extractDrugChiChain.Rd
man/extractDrugChiCluster.Rd
man/extractDrugChiPath.Rd
man/extractDrugChiPathCluster.Rd
man/extractDrugDescOB.Rd
man/extractDrugECI.Rd
man/extractDrugEstate.Rd
man/extractDrugEstateComplete.Rd
man/extractDrugExtended.Rd
man/extractDrugExtendedComplete.Rd
man/extractDrugFMF.Rd
man/extractDrugFragmentComplexity.Rd
man/extractDrugGraph.Rd
man/extractDrugGraphComplete.Rd
man/extractDrugGravitationalIndex.Rd
man/extractDrugHBondAcceptorCount.Rd
man/extractDrugHBondDonorCount.Rd
man/extractDrugHybridization.Rd
man/extractDrugHybridizationComplete.Rd
man/extractDrugHybridizationRatio.Rd
man/extractDrugIPMolecularLearning.Rd
man/extractDrugKR.Rd
man/extractDrugKRComplete.Rd
man/extractDrugKappaShapeIndices.Rd
man/extractDrugKierHallSmarts.Rd
man/extractDrugLargestChain.Rd
man/extractDrugLargestPiSystem.Rd
man/extractDrugLengthOverBreadth.Rd
man/extractDrugLongestAliphaticChain.Rd
man/extractDrugMACCS.Rd
man/extractDrugMACCSComplete.Rd
man/extractDrugMDE.Rd
man/extractDrugMannholdLogP.Rd
man/extractDrugMomentOfInertia.Rd
man/extractDrugOBFP2.Rd
man/extractDrugOBFP3.Rd
man/extractDrugOBFP4.Rd
man/extractDrugOBMACCS.Rd
man/extractDrugPetitjeanNumber.Rd
man/extractDrugPetitjeanShapeIndex.Rd
man/extractDrugPubChem.Rd
man/extractDrugPubChemComplete.Rd
man/extractDrugRotatableBondsCount.Rd
man/extractDrugRuleOfFive.Rd
man/extractDrugShortestPath.Rd
man/extractDrugShortestPathComplete.Rd
man/extractDrugStandard.Rd
man/extractDrugStandardComplete.Rd
man/extractDrugTPSA.Rd
man/extractDrugVABC.Rd
man/extractDrugVAdjMa.Rd
man/extractDrugWHIM.Rd
man/extractDrugWeight.Rd
man/extractDrugWeightedPath.Rd
man/extractDrugWienerNumbers.Rd
man/extractDrugXLogP.Rd
man/extractDrugZagrebIndex.Rd
man/extractPCMBLOSUM.Rd
man/extractPCMDescScales.Rd
man/extractPCMFAScales.Rd
man/extractPCMMDSScales.Rd
man/extractPCMPropScales.Rd
man/extractPCMScales.Rd
man/extractProtAAC.Rd
man/extractProtAPAAC.Rd
man/extractProtCTDC.Rd
man/extractProtCTDD.Rd
man/extractProtCTDT.Rd
man/extractProtCTriad.Rd
man/extractProtDC.Rd
man/extractProtGeary.Rd
man/extractProtMoran.Rd
man/extractProtMoreauBroto.Rd
man/extractProtPAAC.Rd
man/extractProtPSSM.Rd
man/extractProtPSSMAcc.Rd
man/extractProtPSSMFeature.Rd
man/extractProtQSO.Rd
man/extractProtSOCN.Rd
man/extractProtTC.Rd
man/figures/logo.png
man/getCPI.Rd
man/getDrug.Rd
man/getFASTAFromKEGG.Rd
man/getFASTAFromUniProt.Rd
man/getMolFromCAS.Rd
man/getMolFromChEMBL.Rd
man/getMolFromDrugBank.Rd
man/getMolFromKEGG.Rd
man/getMolFromPubChem.Rd
man/getPDBFromRCSBPDB.Rd
man/getPPI.Rd
man/getProt.Rd
man/getSeqFromKEGG.Rd
man/getSeqFromRCSBPDB.Rd
man/getSeqFromUniProt.Rd
man/getSmiFromChEMBL.Rd
man/getSmiFromDrugBank.Rd
man/getSmiFromKEGG.Rd
man/getSmiFromPubChem.Rd
man/readFASTA.Rd
man/readMolFromSDF.Rd
man/readMolFromSmi.Rd
man/readPDB.Rd
man/searchDrug.Rd
man/segProt.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/testthat.R
tests/testthat/test_acc.R
tests/testthat/test_checkProt.R
tests/testthat/test_extractDrugALOGP.R
tests/testthat/test_extractDrugECI.R
tests/testthat/test_extractDrugRuleOfFive.R
tests/testthat/test_extractDrugTPSA.R
tests/testthat/test_extractDrugXLogP.R
tests/testthat/test_extractPCMBLOSUM.R
tests/testthat/test_extractProtAAC.R
tests/testthat/test_getCPI.R
tests/testthat/test_getPPI.R
vignettes/Rcpi-quickref.Rmd
vignettes/Rcpi.Rmd
vignettes/Rcpi.bib
vignettes/bioinformatics.csl
vignettes/custom.css
vignettes/figures/ex1-1.png
vignettes/figures/ex2-1.png
vignettes/figures/ex2-2.png
vignettes/figures/ex3-1.png
vignettes/figures/ex4-1.png
vignettes/figures/ex5-1.png
vignettes/figures/ex6-1.png
vignettes/figures/ex6-2.png
