Man pages for Bioconductor-mirror/Rcpi
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

AA2DACOR2D Autocorrelations Descriptors for 20 Amino Acids calculated...
AA3DMoRSE3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon
AAACFAtom-Centred Fragments Descriptors for 20 Amino Acids...
AABLOSUM100BLOSUM100 Matrix for 20 Amino Acids
AABLOSUM45BLOSUM45 Matrix for 20 Amino Acids
AABLOSUM50BLOSUM50 Matrix for 20 Amino Acids
AABLOSUM62BLOSUM62 Matrix for 20 Amino Acids
AABLOSUM80BLOSUM80 Matrix for 20 Amino Acids
AABurdenBurden Eigenvalues Descriptors for 20 Amino Acids calculated...
AAConnConnectivity Indices Descriptors for 20 Amino Acids...
AAConstConstitutional Descriptors for 20 Amino Acids calculated by...
AACPSACPSA Descriptors for 20 Amino Acids calculated by Discovery...
AADescAllAll 2D Descriptors for 20 Amino Acids calculated by Dragon
AAEdgeAdjEdge Adjacency Indices Descriptors for 20 Amino Acids...
AAEigIdxEigenvalue-Based Indices Descriptors for 20 Amino Acids...
AAFGCFunctional Group Counts Descriptors for 20 Amino Acids...
AAGeomGeometrical Descriptors for 20 Amino Acids calculated by...
AAGETAWAYGETAWAY Descriptors for 20 Amino Acids calculated by Dragon
AAindexAAindex Data of 544 Physicochemical and Biological Properties...
AAInfoInformation Indices Descriptors for 20 Amino Acids calculated...
AAMetaInfoMeta Information for the 20 Amino Acids
AAMOE2D2D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMOE3D3D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMolPropMolecular Properties Descriptors for 20 Amino Acids...
AAPAM120PAM120 Matrix for 20 Amino Acids
AAPAM250PAM250 Matrix for 20 Amino Acids
AAPAM30PAM30 Matrix for 20 Amino Acids
AAPAM40PAM40 Matrix for 20 Amino Acids
AAPAM70PAM70 Matrix for 20 Amino Acids
AARandicRandic Molecular Profiles Descriptors for 20 Amino Acids...
AARDFRDF Descriptors for 20 Amino Acids calculated by Dragon
AATopoTopological Descriptors for 20 Amino Acids calculated by...
AATopoChgTopological Charge Indices Descriptors for 20 Amino Acids...
AAWalkWalk and Path Counts Descriptors for 20 Amino Acids...
AAWHIMWHIM Descriptors for 20 Amino Acids calculated by Dragon
accAuto Cross Covariance (ACC) for Generating Scales-Based...
calcDrugFPSimCalculate Drug Molecule Similarity Derived by Molecular...
calcDrugMCSSimCalculate Drug Molecule Similarity Derived by Maximum Common...
calcParProtGOSimProtein Sequence Similarity Calculation based on Gene...
calcParProtSeqSimParallellized Protein Sequence Similarity Calculation based...
calcTwoProtGOSimProtein Similarity Calculation based on Gene Ontology (GO)...
calcTwoProtSeqSimProtein Sequence Alignment for Two Protein Sequences
checkProtCheck if the protein sequence's amino acid types are the 20...
convMolFormatChemical File Formats Conversion
extractDrugAIOCalculate All Molecular Descriptors in Rcpi at Once
extractDrugALOGPCalculate Atom Additive logP and Molar Refractivity Values...
extractDrugAminoAcidCountCalculate the Number of Amino Acids Descriptor
extractDrugApolCalculate the Sum of the Atomic Polarizabilities Descriptor
extractDrugAromaticAtomsCountCalculate the Number of Aromatic Atoms Descriptor
extractDrugAromaticBondsCountCalculate the Number of Aromatic Bonds Descriptor
extractDrugAtomCountCalculate the Number of Atom Descriptor
extractDrugAutocorrelationChargeCalculate the Moreau-Broto Autocorrelation Descriptors using...
extractDrugAutocorrelationMassCalculate the Moreau-Broto Autocorrelation Descriptors using...
extractDrugAutocorrelationPolarizabilityCalculate the Moreau-Broto Autocorrelation Descriptors using...
extractDrugBCUTBCUT - Eigenvalue Based Descriptor
extractDrugBondCountCalculate the Descriptor Based on the Number of Bonds of a...
extractDrugBPolCalculate the Descriptor that Describes the Sum of the...
extractDrugCarbonTypesTopological Descriptor Characterizing the Carbon Connectivity...
extractDrugChiChainCalculate the Kier and Hall Chi Chain Indices of Orders 3, 4,...
extractDrugChiClusterEvaluates the Kier and Hall Chi cluster indices of orders 3,...
extractDrugChiPathCalculate the Kier and Hall Chi Path Indices of Orders 0 to 7
extractDrugChiPathClusterCalculate the Kier and Hall Chi Path Cluster Indices of...
extractDrugCPSAA Variety of Descriptors Combining Surface Area and Partial...
extractDrugDescOBCalculate Molecular Descriptors Provided by OpenBabel
extractDrugECICalculate the Eccentric Connectivity Index Descriptor
extractDrugEstateCalculate the E-State Molecular Fingerprints (in Compact...
extractDrugEstateCompleteCalculate the E-State Molecular Fingerprints (in Complete...
extractDrugExtendedCalculate the Extended Molecular Fingerprints (in Compact...
extractDrugExtendedCompleteCalculate the Extended Molecular Fingerprints (in Complete...
extractDrugFMFCalculate the FMF Descriptor
extractDrugFragmentComplexityCalculate Complexity of a System
extractDrugGraphCalculate the Graph Molecular Fingerprints (in Compact...
extractDrugGraphCompleteCalculate the Graph Molecular Fingerprints (in Complete...
extractDrugGravitationalIndexDescriptor Characterizing the Mass Distribution of the...
extractDrugHBondAcceptorCountNumber of Hydrogen Bond Acceptors
extractDrugHBondDonorCountNumber of Hydrogen Bond Donors
extractDrugHybridizationCalculate the Hybridization Molecular Fingerprints (in...
extractDrugHybridizationCompleteCalculate the Hybridization Molecular Fingerprints (in...
extractDrugHybridizationRatioDescriptor that Characterizing Molecular Complexity in Terms...
extractDrugIPMolecularLearningCalculate the Descriptor that Evaluates the Ionization...
extractDrugKappaShapeIndicesDescriptor that Calculates Kier and Hall Kappa Molecular...
extractDrugKierHallSmartsDescriptor that Counts the Number of Occurrences of the...
extractDrugKRCalculate the KR (Klekota and Roth) Molecular Fingerprints...
extractDrugKRCompleteCalculate the KR (Klekota and Roth) Molecular Fingerprints...
extractDrugLargestChainDescriptor that Calculates the Number of Atoms in the Largest...
extractDrugLargestPiSystemDescriptor that Calculates the Number of Atoms in the Largest...
extractDrugLengthOverBreadthCalculate the Ratio of Length to Breadth Descriptor
extractDrugLongestAliphaticChainDescriptor that Calculates the Number of Atoms in the Longest...
extractDrugMACCSCalculate the MACCS Molecular Fingerprints (in Compact...
extractDrugMACCSCompleteCalculate the MACCS Molecular Fingerprints (in Complete...
extractDrugMannholdLogPDescriptor that Calculates the LogP Based on a Simple...
extractDrugMDECalculate Molecular Distance Edge (MDE) Descriptors for C, N...
extractDrugMomentOfInertiaDescriptor that Calculates the Principal Moments of Inertia...
extractDrugOBFP2Calculate the FP2 Molecular Fingerprints
extractDrugOBFP3Calculate the FP3 Molecular Fingerprints
extractDrugOBFP4Calculate the FP4 Molecular Fingerprints
extractDrugOBMACCSCalculate the MACCS Molecular Fingerprints
extractDrugPetitjeanNumberDescriptor that Calculates the Petitjean Number of a Molecule
extractDrugPetitjeanShapeIndexDescriptor that Calculates the Petitjean Shape Indices
extractDrugPubChemCalculate the PubChem Molecular Fingerprints (in Compact...
extractDrugPubChemCompleteCalculate the PubChem Molecular Fingerprints (in Complete...
extractDrugRotatableBondsCountDescriptor that Calculates the Number of Nonrotatable Bonds...
extractDrugRuleOfFiveDescriptor that Calculates the Number Failures of the...
extractDrugShortestPathCalculate the Shortest Path Molecular Fingerprints (in...
extractDrugShortestPathCompleteCalculate the Shortest Path Molecular Fingerprints (in...
extractDrugStandardCalculate the Standard Molecular Fingerprints (in Compact...
extractDrugStandardCompleteCalculate the Standard Molecular Fingerprints (in Complete...
extractDrugTPSADescriptor of Topological Polar Surface Area Based on...
extractDrugVABCDescriptor that Calculates the Volume of A Molecule
extractDrugVAdjMaDescriptor that Calculates the Vertex Adjacency Information...
extractDrugWeightDescriptor that Calculates the Total Weight of Atoms
extractDrugWeightedPathDescriptor that Calculates the Weighted Path (Molecular ID)
extractDrugWHIMCalculate Holistic Descriptors Described by Todeschini et al.
extractDrugWienerNumbersDescriptor that Calculates Wiener Path Number and Wiener...
extractDrugXLogPDescriptor that Calculates the Prediction of logP Based on...
extractDrugZagrebIndexDescriptor that Calculates the Sum of the Squared Atom...
extractPCMBLOSUMGeneralized BLOSUM and PAM Matrix-Derived Descriptors
extractPCMDescScalesScales-Based Descriptors with 20+ classes of Molecular...
extractPCMFAScalesGeneralized Scales-Based Descriptors derived by Factor...
extractPCMMDSScalesGeneralized Scales-Based Descriptors derived by...
extractPCMPropScalesGeneralized AA-Properties Based Scales Descriptors
extractPCMScalesGeneralized Scales-Based Descriptors derived by Principal...
extractProtAACAmino Acid Composition Descriptor
extractProtAPAACAmphiphilic Pseudo Amino Acid Composition Descriptor
extractProtCTDCCTD Descriptors - Composition
extractProtCTDDCTD Descriptors - Distribution
extractProtCTDTCTD Descriptors - Transition
extractProtCTriadConjoint Triad Descriptor
extractProtDCDipeptide Composition Descriptor
extractProtGearyGeary Autocorrelation Descriptor
extractProtMoranMoran Autocorrelation Descriptor
extractProtMoreauBrotoNormalized Moreau-Broto Autocorrelation Descriptor
extractProtPAACPseudo Amino Acid Composition Descriptor
extractProtPSSMCompute PSSM (Position-Specific Scoring Matrix) for given...
extractProtPSSMAccProfile-based protein representation derived by PSSM...
extractProtPSSMFeatureProfile-based protein representation derived by PSSM...
extractProtQSOQuasi-Sequence-Order (QSO) Descriptor
extractProtSOCNSequence-Order-Coupling Numbers
extractProtTCTripeptide Composition Descriptor
getCPIGenerating Compound-Protein Interaction Descriptors
getDrugRetrieve Drug Molecules in MOL and SMILES Format from...
getFASTAFromKEGGRetrieve Protein Sequence in FASTA Format from the KEGG...
getFASTAFromUniProtRetrieve Protein Sequence in FASTA Format from the UniProt...
getMolFromCASRetrieve Drug Molecules in InChI Format from the CAS Database
getMolFromChEMBLRetrieve Drug Molecules in MOL Format from the ChEMBL...
getMolFromDrugBankRetrieve Drug Molecules in MOL Format from the DrugBank...
getMolFromKEGGRetrieve Drug Molecules in MOL Format from the KEGG Database
getMolFromPubChemRetrieve Drug Molecules in MOL Format from the PubChem...
getPDBFromRCSBPDBRetrieve Protein Sequence in PDB Format from RCSB PDB
getPPIGenerating Protein-Protein Interaction Descriptors
getProtRetrieve Protein Sequence in various Formats from Databases
getSeqFromKEGGRetrieve Protein Sequence from the KEGG Database
getSeqFromRCSBPDBRetrieve Protein Sequence from RCSB PDB
getSeqFromUniProtRetrieve Protein Sequence from the UniProt Database
getSmiFromChEMBLRetrieve Drug Molecules in SMILES Format from the ChEMBL...
getSmiFromDrugBankRetrieve Drug Molecules in SMILES Format from the DrugBank...
getSmiFromKEGGRetrieve Drug Molecules in SMILES Format from the KEGG...
getSmiFromPubChemRetrieve Drug Molecules in SMILES Format from the PubChem...
OptAA3dOptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10...
Rcpi-packageToolkit for Compound-Protein Interaction in Drug Discovery
readFASTARead Protein Sequences in FASTA Format
readMolFromSDFRead Molecules from SDF Files and Return Parsed Java...
readMolFromSmiRead Molecules from SMILES Files and Return Parsed Java...
readPDBRead Protein Sequences in PDB Format
searchDrugParallelized Drug Molecule Similarity Search by Molecular...
segProtProtein Sequence Segmentation
Bioconductor-mirror/Rcpi documentation built on June 23, 2017, 4:19 p.m.