Rcpi: Toolkit for Compound-Protein Interaction in Drug Discovery

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Rcpi offers a molecular informatics toolkit with a comprehensive integration of bioinformatics and chemoinformatics tools for drug discovery.

Author
Nan Xiao <me@nanx.me>, Dongsheng Cao, Qingsong Xu <qsxu@csu.edu.cn>
Date of publication
None
Maintainer
Nan Xiao <me@nanx.me>
License
Artistic-2.0
Version
1.10.4
URLs

View on Bioconductor

Man pages

AA2DACOR
2D Autocorrelations Descriptors for 20 Amino Acids calculated...
AA3DMoRSE
3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon
AAACF
Atom-Centred Fragments Descriptors for 20 Amino Acids...
AABLOSUM100
BLOSUM100 Matrix for 20 Amino Acids
AABLOSUM45
BLOSUM45 Matrix for 20 Amino Acids
AABLOSUM50
BLOSUM50 Matrix for 20 Amino Acids
AABLOSUM62
BLOSUM62 Matrix for 20 Amino Acids
AABLOSUM80
BLOSUM80 Matrix for 20 Amino Acids
AABurden
Burden Eigenvalues Descriptors for 20 Amino Acids calculated...
AAConn
Connectivity Indices Descriptors for 20 Amino Acids...
AAConst
Constitutional Descriptors for 20 Amino Acids calculated by...
AACPSA
CPSA Descriptors for 20 Amino Acids calculated by Discovery...
AADescAll
All 2D Descriptors for 20 Amino Acids calculated by Dragon
AAEdgeAdj
Edge Adjacency Indices Descriptors for 20 Amino Acids...
AAEigIdx
Eigenvalue-Based Indices Descriptors for 20 Amino Acids...
AAFGC
Functional Group Counts Descriptors for 20 Amino Acids...
AAGeom
Geometrical Descriptors for 20 Amino Acids calculated by...
AAGETAWAY
GETAWAY Descriptors for 20 Amino Acids calculated by Dragon
AAindex
AAindex Data of 544 Physicochemical and Biological Properties...
AAInfo
Information Indices Descriptors for 20 Amino Acids calculated...
AAMetaInfo
Meta Information for the 20 Amino Acids
AAMOE2D
2D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMOE3D
3D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMolProp
Molecular Properties Descriptors for 20 Amino Acids...
AAPAM120
PAM120 Matrix for 20 Amino Acids
AAPAM250
PAM250 Matrix for 20 Amino Acids
AAPAM30
PAM30 Matrix for 20 Amino Acids
AAPAM40
PAM40 Matrix for 20 Amino Acids
AAPAM70
PAM70 Matrix for 20 Amino Acids
AARandic
Randic Molecular Profiles Descriptors for 20 Amino Acids...
AARDF
RDF Descriptors for 20 Amino Acids calculated by Dragon
AATopo
Topological Descriptors for 20 Amino Acids calculated by...
AATopoChg
Topological Charge Indices Descriptors for 20 Amino Acids...
AAWalk
Walk and Path Counts Descriptors for 20 Amino Acids...
AAWHIM
WHIM Descriptors for 20 Amino Acids calculated by Dragon
acc
Auto Cross Covariance (ACC) for Generating Scales-Based...
calcDrugFPSim
Calculate Drug Molecule Similarity Derived by Molecular...
calcDrugMCSSim
Calculate Drug Molecule Similarity Derived by Maximum Common...
calcParProtGOSim
Protein Sequence Similarity Calculation based on Gene...
calcParProtSeqSim
Parallellized Protein Sequence Similarity Calculation based...
calcTwoProtGOSim
Protein Similarity Calculation based on Gene Ontology (GO)...
calcTwoProtSeqSim
Protein Sequence Alignment for Two Protein Sequences
checkProt
Check if the protein sequence's amino acid types are the 20...
convMolFormat
Chemical File Formats Conversion
extractDrugAIO
Calculates All the Molecular Descriptors in the Rcpi Package...
extractDrugALOGP
Calculates Atom Additive logP and Molar Refractivity Values...
extractDrugAminoAcidCount
Calculates the Number of Amino Acids Descriptor
extractDrugApol
Calculates the Sum of the Atomic Polarizabilities Descriptor
extractDrugAromaticAtomsCount
Calculates the Number of Aromatic Atoms Descriptor
extractDrugAromaticBondsCount
Calculates the Number of Aromatic Bonds Descriptor
extractDrugAtomCount
Calculates the Number of Atom Descriptor
extractDrugAutocorrelationCharge
Calculates the Moreau-Broto Autocorrelation Descriptors using...
extractDrugAutocorrelationMass
Calculates the Moreau-Broto Autocorrelation Descriptors using...
extractDrugAutocorrelationPolarizability
Calculates the Moreau-Broto Autocorrelation Descriptors using...
extractDrugBCUT
BCUT - Eigenvalue Based Descriptor
extractDrugBondCount
Calculates the Descriptor Based on the Number of Bonds of a...
extractDrugBPol
Calculates the Descriptor that Describes the Sum of the...
extractDrugCarbonTypes
Topological Descriptor Characterizing the Carbon Connectivity...
extractDrugChiChain
Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4,...
extractDrugChiCluster
Evaluates the Kier and Hall Chi cluster indices of orders 3,...
extractDrugChiPath
Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7
extractDrugChiPathCluster
Calculate the Kier and Hall Chi Path Cluster Indices of...
extractDrugCPSA
A Variety of Descriptors Combining Surface Area and Partial...
extractDrugDescOB
Calculate Molecular Descriptors Provided by OpenBabel
extractDrugECI
Calculates the Eccentric Connectivity Index Descriptor
extractDrugEstate
Calculate the E-State Molecular Fingerprints (in Compact...
extractDrugEstateComplete
Calculate the E-State Molecular Fingerprints (in Complete...
extractDrugExtended
Calculate the Extended Molecular Fingerprints (in Compact...
extractDrugExtendedComplete
Calculate the Extended Molecular Fingerprints (in Complete...
extractDrugFMF
Calculates the FMF Descriptor
extractDrugFragmentComplexity
Calculate Complexity of a System
extractDrugGraph
Calculate the Graph Molecular Fingerprints (in Compact...
extractDrugGraphComplete
Calculate the Graph Molecular Fingerprints (in Complete...
extractDrugGravitationalIndex
Descriptor Characterizing the Mass Distribution of the...
extractDrugHBondAcceptorCount
Descriptor that Calculates the Number of Hydrogen Bond...
extractDrugHBondDonorCount
Descriptor that Calculates the Number of Hydrogen Bond Donors
extractDrugHybridization
Calculate the Hybridization Molecular Fingerprints (in...
extractDrugHybridizationComplete
Calculate the Hybridization Molecular Fingerprints (in...
extractDrugHybridizationRatio
Descriptor that Characterizing Molecular Complexity in Terms...
extractDrugIPMolecularLearning
Calculates the Descriptor that Evaluates the Ionization...
extractDrugKappaShapeIndices
Descriptor that Calculates Kier and Hall Kappa Molecular...
extractDrugKierHallSmarts
Descriptor that Counts the Number of Occurrences of the...
extractDrugKR
Calculate the KR (Klekota and Roth) Molecular Fingerprints...
extractDrugKRComplete
Calculate the KR (Klekota and Roth) Molecular Fingerprints...
extractDrugLargestChain
Descriptor that Calculates the Number of Atoms in the Largest...
extractDrugLargestPiSystem
Descriptor that Calculates the Number of Atoms in the Largest...
extractDrugLengthOverBreadth
Calculates the Ratio of Length to Breadth Descriptor
extractDrugLongestAliphaticChain
Descriptor that Calculates the Number of Atoms in the Longest...
extractDrugMACCS
Calculate the MACCS Molecular Fingerprints (in Compact...
extractDrugMACCSComplete
Calculate the MACCS Molecular Fingerprints (in Complete...
extractDrugMannholdLogP
Descriptor that Calculates the LogP Based on a Simple...
extractDrugMDE
Calculate Molecular Distance Edge (MDE) Descriptors for C, N...
extractDrugMomentOfInertia
Descriptor that Calculates the Principal Moments of Inertia...
extractDrugOBFP2
Calculate the FP2 Molecular Fingerprints
extractDrugOBFP3
Calculate the FP3 Molecular Fingerprints
extractDrugOBFP4
Calculate the FP4 Molecular Fingerprints
extractDrugOBMACCS
Calculate the MACCS Molecular Fingerprints
extractDrugPetitjeanNumber
Descriptor that Calculates the Petitjean Number of a Molecule
extractDrugPetitjeanShapeIndex
Descriptor that Calculates the Petitjean Shape Indices
extractDrugPubChem
Calculate the PubChem Molecular Fingerprints (in Compact...
extractDrugPubChemComplete
Calculate the PubChem Molecular Fingerprints (in Complete...
extractDrugRotatableBondsCount
Descriptor that Calculates the Number of Nonrotatable Bonds...
extractDrugRuleOfFive
Descriptor that Calculates the Number Failures of the...
extractDrugShortestPath
Calculate the Shortest Path Molecular Fingerprints (in...
extractDrugShortestPathComplete
Calculate the Shortest Path Molecular Fingerprints (in...
extractDrugStandard
Calculate the Standard Molecular Fingerprints (in Compact...
extractDrugStandardComplete
Calculate the Standard Molecular Fingerprints (in Complete...
extractDrugTPSA
Descriptor of Topological Polar Surface Area Based on...
extractDrugVABC
Descriptor that Calculates the Volume of A Molecule
extractDrugVAdjMa
Descriptor that Calculates the Vertex Adjacency Information...
extractDrugWeight
Descriptor that Calculates the Total Weight of Atoms
extractDrugWeightedPath
Descriptor that Calculates the Weighted Path (Molecular ID)
extractDrugWHIM
Calculate Holistic Descriptors Described by Todeschini et al.
extractDrugWienerNumbers
Descriptor that Calculates Wiener Path Number and Wiener...
extractDrugXLogP
Descriptor that Calculates the Prediction of logP Based on...
extractDrugZagrebIndex
Descriptor that Calculates the Sum of the Squared Atom...
extractPCMBLOSUM
Generalized BLOSUM and PAM Matrix-Derived Descriptors
extractPCMDescScales
Scales-Based Descriptors with 20+ classes of Molecular...
extractPCMFAScales
Generalized Scales-Based Descriptors derived by Factor...
extractPCMMDSScales
Generalized Scales-Based Descriptors derived by...
extractPCMPropScales
Generalized AA-Properties Based Scales Descriptors
extractPCMScales
Generalized Scales-Based Descriptors derived by Principal...
extractProtAAC
Amino Acid Composition Descriptor
extractProtAPAAC
Amphiphilic Pseudo Amino Acid Composition Descriptor
extractProtCTDC
CTD Descriptors - Composition
extractProtCTDD
CTD Descriptors - Distribution
extractProtCTDT
CTD Descriptors - Transition
extractProtCTriad
Conjoint Triad Descriptor
extractProtDC
Dipeptide Composition Descriptor
extractProtGeary
Geary Autocorrelation Descriptor
extractProtMoran
Moran Autocorrelation Descriptor
extractProtMoreauBroto
Normalized Moreau-Broto Autocorrelation Descriptor
extractProtPAAC
Pseudo Amino Acid Composition Descriptor
extractProtPSSM
Compute PSSM (Position-Specific Scoring Matrix) for given...
extractProtPSSMAcc
Profile-based protein representation derived by PSSM...
extractProtPSSMFeature
Profile-based protein representation derived by PSSM...
extractProtQSO
Quasi-Sequence-Order (QSO) Descriptor
extractProtSOCN
Sequence-Order-Coupling Numbers
extractProtTC
Tripeptide Composition Descriptor
getCPI
Generating Compound-Protein Interaction Descriptors
getDrug
Retrieve Drug Molecules in MOL and SMILES Format from...
getFASTAFromKEGG
Retrieve Protein Sequence in FASTA Format from the KEGG...
getFASTAFromUniProt
Retrieve Protein Sequence in FASTA Format from the UniProt...
getMolFromCAS
Retrieve Drug Molecules in InChI Format from the CAS Database
getMolFromChEMBL
Retrieve Drug Molecules in MOL Format from the ChEMBL...
getMolFromDrugBank
Retrieve Drug Molecules in MOL Format from the DrugBank...
getMolFromKEGG
Retrieve Drug Molecules in MOL Format from the KEGG Database
getMolFromPubChem
Retrieve Drug Molecules in MOL Format from the PubChem...
getPDBFromRCSBPDB
Retrieve Protein Sequence in PDB Format from RCSB PDB
getPPI
Generating Protein-Protein Interaction Descriptors
getProt
Retrieve Protein Sequence in various Formats from Databases
getSeqFromKEGG
Retrieve Protein Sequence from the KEGG Database
getSeqFromRCSBPDB
Retrieve Protein Sequence from RCSB PDB
getSeqFromUniProt
Retrieve Protein Sequence from the UniProt Database
getSmiFromChEMBL
Retrieve Drug Molecules in SMILES Format from the ChEMBL...
getSmiFromDrugBank
Retrieve Drug Molecules in SMILES Format from the DrugBank...
getSmiFromKEGG
Retrieve Drug Molecules in SMILES Format from the KEGG...
getSmiFromPubChem
Retrieve Drug Molecules in SMILES Format from the PubChem...
OptAA3d
OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10...
Rcpi-package
Toolkit for Compound-Protein Interaction in Drug Discovery
readFASTA
Read Protein Sequences in FASTA Format
readMolFromSDF
Read Molecules from SDF Files and Return Parsed Java...
readMolFromSmi
Read Molecules from SMILES Files and Return Parsed Java...
readPDB
Read Protein Sequences in PDB Format
searchDrug
Parallelized Drug Molecule Similarity Search by Molecular...
segProt
Protein Sequence Segmentation

Files in this package

Rcpi/DESCRIPTION
Rcpi/NAMESPACE
Rcpi/NEWS
Rcpi/NEWS.md
Rcpi/R
Rcpi/R/001-Rcpi-package.R
Rcpi/R/101-getDrugPubChem.R
Rcpi/R/102-getDrugChEMBL.R
Rcpi/R/103-getDrugCAS.R
Rcpi/R/104-getDrugKEGG.R
Rcpi/R/105-getDrugDrugBank.R
Rcpi/R/106-getDrug.R
Rcpi/R/201-getProtUniProt.R
Rcpi/R/202-getProtKEGG.R
Rcpi/R/203-getProtRCSBPDB.R
Rcpi/R/204-getProt.R
Rcpi/R/300-extractDrugAIO.R
Rcpi/R/301-extractDrugALOGP.R
Rcpi/R/302-extractDrugApol.R
Rcpi/R/304-extractDrugAminoAcidCount.R
Rcpi/R/305-extractDrugAromaticAtomsCount.R
Rcpi/R/306-extractDrugAromaticBondsCount.R
Rcpi/R/307-extractDrugAtomCount.R
Rcpi/R/308-extractDrugAutocorrelationCharge.R
Rcpi/R/309-extractDrugAutocorrelationMass.R
Rcpi/R/310-extractDrugAutocorrelationPolarizability.R
Rcpi/R/311-extractDrugBCUT.R
Rcpi/R/312-extractDrugBPol.R
Rcpi/R/314-extractDrugBondCount.R
Rcpi/R/315-extractDrugCPSA.R
Rcpi/R/316-extractDrugCarbonTypes.R
Rcpi/R/317-extractDrugChiChain.R
Rcpi/R/318-extractDrugChiCluster.R
Rcpi/R/319-extractDrugChiPathCluster.R
Rcpi/R/320-extractDrugChiPath.R
Rcpi/R/321-extractDrugECI.R
Rcpi/R/322-extractDrugFMF.R
Rcpi/R/323-extractDrugFragmentComplexity.R
Rcpi/R/324-extractDrugGravitationalIndex.R
Rcpi/R/325-extractDrugHBondAcceptorCount.R
Rcpi/R/326-extractDrugHBondDonorCount.R
Rcpi/R/327-extractDrugHybridizationRatio.R
Rcpi/R/328-extractDrugIPMolecularLearning.R
Rcpi/R/329-extractDrugKappaShapeIndices.R
Rcpi/R/330-extractDrugKierHallSmarts.R
Rcpi/R/331-extractDrugLargestChain.R
Rcpi/R/332-extractDrugLargestPiSystem.R
Rcpi/R/333-extractDrugLengthOverBreadth.R
Rcpi/R/334-extractDrugLongestAliphaticChain.R
Rcpi/R/335-extractDrugMDE.R
Rcpi/R/336-extractDrugMannholdLogP.R
Rcpi/R/337-extractDrugMomentOfInertia.R
Rcpi/R/338-extractDrugPetitjeanNumber.R
Rcpi/R/339-extractDrugPetitjeanShapeIndex.R
Rcpi/R/340-extractDrugRotatableBondsCount.R
Rcpi/R/341-extractDrugRuleOfFive.R
Rcpi/R/342-extractDrugTPSA.R
Rcpi/R/343-extractDrugVABC.R
Rcpi/R/344-extractDrugVAdjMa.R
Rcpi/R/345-extractDrugWHIM.R
Rcpi/R/346-extractDrugWeight.R
Rcpi/R/347-extractDrugWeightedPath.R
Rcpi/R/348-extractDrugWienerNumbers.R
Rcpi/R/349-extractDrugXLogP.R
Rcpi/R/350-extractDrugZagrebIndex.R
Rcpi/R/371-extractDrugStandard.R
Rcpi/R/372-extractDrugExtended.R
Rcpi/R/373-extractDrugGraph.R
Rcpi/R/374-extractDrugHybridization.R
Rcpi/R/375-extractDrugMACCS.R
Rcpi/R/376-extractDrugEstate.R
Rcpi/R/377-extractDrugPubChem.R
Rcpi/R/378-extractDrugKR.R
Rcpi/R/379-extractDrugShortestPath.R
Rcpi/R/380-extractDrugOBFP2.R
Rcpi/R/381-extractDrugOBFP3.R
Rcpi/R/382-extractDrugOBFP4.R
Rcpi/R/383-extractDrugOBMACCS.R
Rcpi/R/384-extractDrugDescOB.R
Rcpi/R/401-extractProtAAC.R
Rcpi/R/402-extractProtDC.R
Rcpi/R/403-extractProtTC.R
Rcpi/R/404-extractProtMoreauBroto.R
Rcpi/R/405-extractProtMoran.R
Rcpi/R/406-extractProtGeary.R
Rcpi/R/407-extractProtCTDC.R
Rcpi/R/408-extractProtCTDT.R
Rcpi/R/409-extractProtCTDD.R
Rcpi/R/410-extractProtCTriad.R
Rcpi/R/411-extractProtSOCN.R
Rcpi/R/412-extractProtQSO.R
Rcpi/R/413-extractProtPAAC.R
Rcpi/R/414-extractProtAPAAC.R
Rcpi/R/415-extractPCMScales.R
Rcpi/R/416-extractPCMDescScales.R
Rcpi/R/417-extractPCMPropScales.R
Rcpi/R/418-extractPCMFAScales.R
Rcpi/R/419-extractPCMMDSScales.R
Rcpi/R/420-extractPCMBLOSUM.R
Rcpi/R/421-extractProtPSSM.R
Rcpi/R/422-extractProtPSSMFeature.R
Rcpi/R/423-extractProtPSSMAcc.R
Rcpi/R/501-readFASTA.R
Rcpi/R/502-readPDB.R
Rcpi/R/503-readMolFromSDF.R
Rcpi/R/504-readMolFromSmi.R
Rcpi/R/505-convMolFormat.R
Rcpi/R/506-checkProt.R
Rcpi/R/507-segProt.R
Rcpi/R/508-acc.R
Rcpi/R/601-getCPI.R
Rcpi/R/602-getPPI.R
Rcpi/R/701-calcDrugFPSim.R
Rcpi/R/702-calcDrugMCSSim.R
Rcpi/R/703-calcProtGOSim.R
Rcpi/R/704-calcProtSeqSim.R
Rcpi/R/705-searchDrug.R
Rcpi/R/Rcpi-datalist.R
Rcpi/README.md
Rcpi/Rcpi.Rproj
Rcpi/_pkgdown.yml
Rcpi/build
Rcpi/build/vignette.rds
Rcpi/data
Rcpi/data/AA2DACOR.rda
Rcpi/data/AA3DMoRSE.rda
Rcpi/data/AAACF.rda
Rcpi/data/AABLOSUM100.rda
Rcpi/data/AABLOSUM45.rda
Rcpi/data/AABLOSUM50.rda
Rcpi/data/AABLOSUM62.rda
Rcpi/data/AABLOSUM80.rda
Rcpi/data/AABurden.rda
Rcpi/data/AACPSA.rda
Rcpi/data/AAConn.rda
Rcpi/data/AAConst.rda
Rcpi/data/AADescAll.rda
Rcpi/data/AAEdgeAdj.rda
Rcpi/data/AAEigIdx.rda
Rcpi/data/AAFGC.rda
Rcpi/data/AAGETAWAY.rda
Rcpi/data/AAGeom.rda
Rcpi/data/AAInfo.rda
Rcpi/data/AAMOE2D.rda
Rcpi/data/AAMOE3D.rda
Rcpi/data/AAMetaInfo.rda
Rcpi/data/AAMolProp.rda
Rcpi/data/AAPAM120.rda
Rcpi/data/AAPAM250.rda
Rcpi/data/AAPAM30.rda
Rcpi/data/AAPAM40.rda
Rcpi/data/AAPAM70.rda
Rcpi/data/AARDF.rda
Rcpi/data/AARandic.rda
Rcpi/data/AATopo.rda
Rcpi/data/AATopoChg.rda
Rcpi/data/AAWHIM.rda
Rcpi/data/AAWalk.rda
Rcpi/data/AAindex.rda
Rcpi/inst
Rcpi/inst/CITATION
Rcpi/inst/compseq
Rcpi/inst/compseq/DB00530.sdf
Rcpi/inst/compseq/DB00859.sdf
Rcpi/inst/compseq/DB00860.sdf
Rcpi/inst/compseq/tyrphostin.sdf
Rcpi/inst/doc
Rcpi/inst/doc/Rcpi-quickref.R
Rcpi/inst/doc/Rcpi-quickref.Rnw
Rcpi/inst/doc/Rcpi-quickref.pdf
Rcpi/inst/doc/Rcpi.R
Rcpi/inst/doc/Rcpi.Rnw
Rcpi/inst/doc/Rcpi.pdf
Rcpi/inst/protseq
Rcpi/inst/protseq/4HHB.pdb
Rcpi/inst/protseq/P00750.fasta
Rcpi/inst/protseq/P08218.fasta
Rcpi/inst/protseq/P10323.fasta
Rcpi/inst/protseq/P20160.fasta
Rcpi/inst/protseq/Plasminogen.fasta
Rcpi/inst/protseq/Q9NZP8.fasta
Rcpi/inst/sysdata
Rcpi/inst/sysdata/AAidx.csv
Rcpi/inst/sysdata/CTDict.rda
Rcpi/inst/sysdata/CTIndex.rda
Rcpi/inst/sysdata/Grantham.csv
Rcpi/inst/sysdata/OptAA3d.sdf
Rcpi/inst/sysdata/Schneider-Wrede.csv
Rcpi/inst/sysdata/TCDict.rda
Rcpi/inst/unitTests
Rcpi/inst/unitTests/test_acc.R
Rcpi/inst/unitTests/test_checkProt.R
Rcpi/inst/unitTests/test_extractDrugALOGP.R
Rcpi/inst/unitTests/test_extractPCMBLOSUM.R
Rcpi/inst/unitTests/test_extractProtAAC.R
Rcpi/inst/unitTests/test_getCPI.R
Rcpi/inst/unitTests/test_getPPI.R
Rcpi/inst/vignettedata
Rcpi/inst/vignettedata/FDAMDD.csv
Rcpi/inst/vignettedata/FDAMDD.smi
Rcpi/inst/vignettedata/GPCR.csv
Rcpi/inst/vignettedata/RI.csv
Rcpi/inst/vignettedata/RI.smi
Rcpi/inst/vignettedata/extracell.fasta
Rcpi/inst/vignettedata/mitochondrion.fasta
Rcpi/man
Rcpi/man/AA2DACOR.Rd
Rcpi/man/AA3DMoRSE.Rd
Rcpi/man/AAACF.Rd
Rcpi/man/AABLOSUM100.Rd
Rcpi/man/AABLOSUM45.Rd
Rcpi/man/AABLOSUM50.Rd
Rcpi/man/AABLOSUM62.Rd
Rcpi/man/AABLOSUM80.Rd
Rcpi/man/AABurden.Rd
Rcpi/man/AACPSA.Rd
Rcpi/man/AAConn.Rd
Rcpi/man/AAConst.Rd
Rcpi/man/AADescAll.Rd
Rcpi/man/AAEdgeAdj.Rd
Rcpi/man/AAEigIdx.Rd
Rcpi/man/AAFGC.Rd
Rcpi/man/AAGETAWAY.Rd
Rcpi/man/AAGeom.Rd
Rcpi/man/AAInfo.Rd
Rcpi/man/AAMOE2D.Rd
Rcpi/man/AAMOE3D.Rd
Rcpi/man/AAMetaInfo.Rd
Rcpi/man/AAMolProp.Rd
Rcpi/man/AAPAM120.Rd
Rcpi/man/AAPAM250.Rd
Rcpi/man/AAPAM30.Rd
Rcpi/man/AAPAM40.Rd
Rcpi/man/AAPAM70.Rd
Rcpi/man/AARDF.Rd
Rcpi/man/AARandic.Rd
Rcpi/man/AATopo.Rd
Rcpi/man/AATopoChg.Rd
Rcpi/man/AAWHIM.Rd
Rcpi/man/AAWalk.Rd
Rcpi/man/AAindex.Rd
Rcpi/man/OptAA3d.Rd
Rcpi/man/Rcpi-package.Rd
Rcpi/man/acc.Rd
Rcpi/man/calcDrugFPSim.Rd
Rcpi/man/calcDrugMCSSim.Rd
Rcpi/man/calcParProtGOSim.Rd
Rcpi/man/calcParProtSeqSim.Rd
Rcpi/man/calcTwoProtGOSim.Rd
Rcpi/man/calcTwoProtSeqSim.Rd
Rcpi/man/checkProt.Rd
Rcpi/man/convMolFormat.Rd
Rcpi/man/extractDrugAIO.Rd
Rcpi/man/extractDrugALOGP.Rd
Rcpi/man/extractDrugAminoAcidCount.Rd
Rcpi/man/extractDrugApol.Rd
Rcpi/man/extractDrugAromaticAtomsCount.Rd
Rcpi/man/extractDrugAromaticBondsCount.Rd
Rcpi/man/extractDrugAtomCount.Rd
Rcpi/man/extractDrugAutocorrelationCharge.Rd
Rcpi/man/extractDrugAutocorrelationMass.Rd
Rcpi/man/extractDrugAutocorrelationPolarizability.Rd
Rcpi/man/extractDrugBCUT.Rd
Rcpi/man/extractDrugBPol.Rd
Rcpi/man/extractDrugBondCount.Rd
Rcpi/man/extractDrugCPSA.Rd
Rcpi/man/extractDrugCarbonTypes.Rd
Rcpi/man/extractDrugChiChain.Rd
Rcpi/man/extractDrugChiCluster.Rd
Rcpi/man/extractDrugChiPath.Rd
Rcpi/man/extractDrugChiPathCluster.Rd
Rcpi/man/extractDrugDescOB.Rd
Rcpi/man/extractDrugECI.Rd
Rcpi/man/extractDrugEstate.Rd
Rcpi/man/extractDrugEstateComplete.Rd
Rcpi/man/extractDrugExtended.Rd
Rcpi/man/extractDrugExtendedComplete.Rd
Rcpi/man/extractDrugFMF.Rd
Rcpi/man/extractDrugFragmentComplexity.Rd
Rcpi/man/extractDrugGraph.Rd
Rcpi/man/extractDrugGraphComplete.Rd
Rcpi/man/extractDrugGravitationalIndex.Rd
Rcpi/man/extractDrugHBondAcceptorCount.Rd
Rcpi/man/extractDrugHBondDonorCount.Rd
Rcpi/man/extractDrugHybridization.Rd
Rcpi/man/extractDrugHybridizationComplete.Rd
Rcpi/man/extractDrugHybridizationRatio.Rd
Rcpi/man/extractDrugIPMolecularLearning.Rd
Rcpi/man/extractDrugKR.Rd
Rcpi/man/extractDrugKRComplete.Rd
Rcpi/man/extractDrugKappaShapeIndices.Rd
Rcpi/man/extractDrugKierHallSmarts.Rd
Rcpi/man/extractDrugLargestChain.Rd
Rcpi/man/extractDrugLargestPiSystem.Rd
Rcpi/man/extractDrugLengthOverBreadth.Rd
Rcpi/man/extractDrugLongestAliphaticChain.Rd
Rcpi/man/extractDrugMACCS.Rd
Rcpi/man/extractDrugMACCSComplete.Rd
Rcpi/man/extractDrugMDE.Rd
Rcpi/man/extractDrugMannholdLogP.Rd
Rcpi/man/extractDrugMomentOfInertia.Rd
Rcpi/man/extractDrugOBFP2.Rd
Rcpi/man/extractDrugOBFP3.Rd
Rcpi/man/extractDrugOBFP4.Rd
Rcpi/man/extractDrugOBMACCS.Rd
Rcpi/man/extractDrugPetitjeanNumber.Rd
Rcpi/man/extractDrugPetitjeanShapeIndex.Rd
Rcpi/man/extractDrugPubChem.Rd
Rcpi/man/extractDrugPubChemComplete.Rd
Rcpi/man/extractDrugRotatableBondsCount.Rd
Rcpi/man/extractDrugRuleOfFive.Rd
Rcpi/man/extractDrugShortestPath.Rd
Rcpi/man/extractDrugShortestPathComplete.Rd
Rcpi/man/extractDrugStandard.Rd
Rcpi/man/extractDrugStandardComplete.Rd
Rcpi/man/extractDrugTPSA.Rd
Rcpi/man/extractDrugVABC.Rd
Rcpi/man/extractDrugVAdjMa.Rd
Rcpi/man/extractDrugWHIM.Rd
Rcpi/man/extractDrugWeight.Rd
Rcpi/man/extractDrugWeightedPath.Rd
Rcpi/man/extractDrugWienerNumbers.Rd
Rcpi/man/extractDrugXLogP.Rd
Rcpi/man/extractDrugZagrebIndex.Rd
Rcpi/man/extractPCMBLOSUM.Rd
Rcpi/man/extractPCMDescScales.Rd
Rcpi/man/extractPCMFAScales.Rd
Rcpi/man/extractPCMMDSScales.Rd
Rcpi/man/extractPCMPropScales.Rd
Rcpi/man/extractPCMScales.Rd
Rcpi/man/extractProtAAC.Rd
Rcpi/man/extractProtAPAAC.Rd
Rcpi/man/extractProtCTDC.Rd
Rcpi/man/extractProtCTDD.Rd
Rcpi/man/extractProtCTDT.Rd
Rcpi/man/extractProtCTriad.Rd
Rcpi/man/extractProtDC.Rd
Rcpi/man/extractProtGeary.Rd
Rcpi/man/extractProtMoran.Rd
Rcpi/man/extractProtMoreauBroto.Rd
Rcpi/man/extractProtPAAC.Rd
Rcpi/man/extractProtPSSM.Rd
Rcpi/man/extractProtPSSMAcc.Rd
Rcpi/man/extractProtPSSMFeature.Rd
Rcpi/man/extractProtQSO.Rd
Rcpi/man/extractProtSOCN.Rd
Rcpi/man/extractProtTC.Rd
Rcpi/man/getCPI.Rd
Rcpi/man/getDrug.Rd
Rcpi/man/getFASTAFromKEGG.Rd
Rcpi/man/getFASTAFromUniProt.Rd
Rcpi/man/getMolFromCAS.Rd
Rcpi/man/getMolFromChEMBL.Rd
Rcpi/man/getMolFromDrugBank.Rd
Rcpi/man/getMolFromKEGG.Rd
Rcpi/man/getMolFromPubChem.Rd
Rcpi/man/getPDBFromRCSBPDB.Rd
Rcpi/man/getPPI.Rd
Rcpi/man/getProt.Rd
Rcpi/man/getSeqFromKEGG.Rd
Rcpi/man/getSeqFromRCSBPDB.Rd
Rcpi/man/getSeqFromUniProt.Rd
Rcpi/man/getSmiFromChEMBL.Rd
Rcpi/man/getSmiFromDrugBank.Rd
Rcpi/man/getSmiFromKEGG.Rd
Rcpi/man/getSmiFromPubChem.Rd
Rcpi/man/readFASTA.Rd
Rcpi/man/readMolFromSDF.Rd
Rcpi/man/readMolFromSmi.Rd
Rcpi/man/readPDB.Rd
Rcpi/man/searchDrug.Rd
Rcpi/man/segProt.Rd
Rcpi/tests
Rcpi/tests/runTests.R
Rcpi/vignettes
Rcpi/vignettes/Rcpi-quickref.Rnw
Rcpi/vignettes/Rcpi.Rnw
Rcpi/vignettes/Rcpi.bib
Rcpi/vignettes/fig
Rcpi/vignettes/fig/ex1-1.pdf
Rcpi/vignettes/fig/ex2-1.pdf
Rcpi/vignettes/fig/ex2-2.pdf
Rcpi/vignettes/fig/ex3-1.pdf
Rcpi/vignettes/fig/ex4-1.pdf
Rcpi/vignettes/fig/ex5-1.pdf
Rcpi/vignettes/fig/ex6-1.pdf
Rcpi/vignettes/fig/ex6-2.pdf
Rcpi/vignettes/fig/logo-panel-text.pdf