Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

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

AuthorNan Xiao [aut, cre], Dongsheng Cao [aut], Qingsong Xu [aut]
Date of publicationNone
MaintainerNan Xiao <me@nanx.me>
LicenseArtistic-2.0
Version1.10.6
http://nanx.me/Rcpi/
https://github.com/road2stat/Rcpi

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: Calculate All Molecular Descriptors in Rcpi at Once

extractDrugALOGP: Calculate Atom Additive logP and Molar Refractivity Values...

extractDrugAminoAcidCount: Calculate the Number of Amino Acids Descriptor

extractDrugApol: Calculate the Sum of the Atomic Polarizabilities Descriptor

extractDrugAromaticAtomsCount: Calculate the Number of Aromatic Atoms Descriptor

extractDrugAromaticBondsCount: Calculate the Number of Aromatic Bonds Descriptor

extractDrugAtomCount: Calculate the Number of Atom Descriptor

extractDrugAutocorrelationCharge: Calculate the Moreau-Broto Autocorrelation Descriptors using...

extractDrugAutocorrelationMass: Calculate the Moreau-Broto Autocorrelation Descriptors using...

extractDrugAutocorrelationPolarizability: Calculate the Moreau-Broto Autocorrelation Descriptors using...

extractDrugBCUT: BCUT - Eigenvalue Based Descriptor

extractDrugBondCount: Calculate the Descriptor Based on the Number of Bonds of a...

extractDrugBPol: Calculate 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: Calculate 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: Calculate 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: Number of Hydrogen Bond Acceptors

extractDrugHBondDonorCount: 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: Calculate 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: Calculate 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

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