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

Functions

AA2DACOR Man page
AA3DMoRSE Man page
AAACF Man page
AABLOSUM100 Man page
AABLOSUM45 Man page
AABLOSUM50 Man page
AABLOSUM62 Man page
AABLOSUM80 Man page
AABurden Man page
AAConn Man page
AAConst Man page
AACPSA Man page
AADescAll Man page
AAEdgeAdj Man page
AAEigIdx Man page
AAFGC Man page
AAGeom Man page
AAGETAWAY Man page
AAindex Man page
AAInfo Man page
AAMetaInfo Man page
AAMOE2D Man page
AAMOE3D Man page
AAMolProp Man page
AAPAM120 Man page
AAPAM250 Man page
AAPAM30 Man page
AAPAM40 Man page
AAPAM70 Man page
AARandic Man page
AARDF Man page
AATopo Man page
AATopoChg Man page
AAWalk Man page
AAWHIM Man page
acc Man page
calcDrugFPSim Man page
calcDrugMCSSim Man page
calcParProtGOSim Man page
calcParProtSeqSim Man page
calcTwoProtGOSim Man page
calcTwoProtSeqSim Man page
checkProt Man page
convMolFormat Man page
extractDrugAIO Man page
extractDrugALOGP Man page
extractDrugAminoAcidCount Man page
extractDrugApol Man page
extractDrugAromaticAtomsCount Man page
extractDrugAromaticBondsCount Man page
extractDrugAtomCount Man page
extractDrugAutocorrelationCharge Man page
extractDrugAutocorrelationMass Man page
extractDrugAutocorrelationPolarizability Man page
extractDrugBCUT Man page
extractDrugBondCount Man page
extractDrugBPol Man page
extractDrugCarbonTypes Man page
extractDrugChiChain Man page
extractDrugChiCluster Man page
extractDrugChiPath Man page
extractDrugChiPathCluster Man page
extractDrugCPSA Man page
extractDrugDescOB Man page
extractDrugECI Man page
extractDrugEstate Man page
extractDrugEstateComplete Man page
extractDrugExtended Man page
extractDrugExtendedComplete Man page
extractDrugFMF Man page
extractDrugFragmentComplexity Man page
extractDrugGraph Man page
extractDrugGraphComplete Man page
extractDrugGravitationalIndex Man page
extractDrugHBondAcceptorCount Man page
extractDrugHBondDonorCount Man page
extractDrugHybridization Man page
extractDrugHybridizationComplete Man page
extractDrugHybridizationRatio Man page
extractDrugIPMolecularLearning Man page
extractDrugKappaShapeIndices Man page
extractDrugKierHallSmarts Man page
extractDrugKR Man page
extractDrugKRComplete Man page
extractDrugLargestChain Man page
extractDrugLargestPiSystem Man page
extractDrugLengthOverBreadth Man page
extractDrugLongestAliphaticChain Man page
extractDrugMACCS Man page
extractDrugMACCSComplete Man page
extractDrugMannholdLogP Man page
extractDrugMDE Man page
extractDrugMomentOfInertia Man page
extractDrugOBFP2 Man page
extractDrugOBFP3 Man page
extractDrugOBFP4 Man page
extractDrugOBMACCS Man page
extractDrugPetitjeanNumber Man page
extractDrugPetitjeanShapeIndex Man page
extractDrugPubChem Man page
extractDrugPubChemComplete Man page
extractDrugRotatableBondsCount Man page
extractDrugRuleOfFive Man page
extractDrugShortestPath Man page
extractDrugShortestPathComplete Man page
extractDrugStandard Man page
extractDrugStandardComplete Man page
extractDrugTPSA Man page
extractDrugVABC Man page
extractDrugVAdjMa Man page
extractDrugWeight Man page
extractDrugWeightedPath Man page
extractDrugWHIM Man page
extractDrugWienerNumbers Man page
extractDrugXLogP Man page
extractDrugZagrebIndex Man page
extractPCMBLOSUM Man page
extractPCMDescScales Man page
extractPCMFAScales Man page
extractPCMMDSScales Man page
extractPCMPropScales Man page
extractPCMScales Man page
extractProtAAC Man page
extractProtAPAAC Man page
extractProtCTDC Man page
extractProtCTDD Man page
extractProtCTDT Man page
extractProtCTriad Man page
extractProtDC Man page
extractProtGeary Man page
extractProtMoran Man page
extractProtMoreauBroto Man page
extractProtPAAC Man page
extractProtPSSM Man page
extractProtPSSMAcc Man page
extractProtPSSMFeature Man page
extractProtQSO Man page
extractProtSOCN Man page
extractProtTC Man page
getCPI Man page
getDrug Man page
getFASTAFromKEGG Man page
getFASTAFromUniProt Man page
getMolFromCAS Man page
getMolFromChEMBL Man page
getMolFromDrugBank Man page
getMolFromKEGG Man page
getMolFromPubChem Man page
getPDBFromRCSBPDB Man page
getPPI Man page
getProt Man page
getSeqFromKEGG Man page
getSeqFromRCSBPDB Man page
getSeqFromUniProt Man page
getSmiFromChEMBL Man page
getSmiFromDrugBank Man page
getSmiFromKEGG Man page
getSmiFromPubChem Man page
OptAA3d Man page
Rcpi Man page
Rcpi-package Man page
readFASTA Man page
readMolFromSDF Man page
readMolFromSmi Man page
readPDB Man page
searchDrug Man page
segProt Man page

Files

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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