Molecular Informatics Toolkit for Compound-Protein Interaction
in Drug Discovery
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Documentation for package ‘Rcpi’ version 1.44.0
Help Pages
-- A --
| AA2DACOR | 2D Autocorrelations Descriptors for 20 Amino Acids calculated by Dragon |
| AA3DMoRSE | 3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon |
| AAACF | Atom-Centred Fragments Descriptors for 20 Amino Acids calculated by Dragon |
| 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 by Dragon |
| AAConn | Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon |
| AAConst | Constitutional Descriptors for 20 Amino Acids calculated by Dragon |
| AACPSA | CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio |
| AADescAll | All 2D Descriptors for 20 Amino Acids calculated by Dragon |
| AAEdgeAdj | Edge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon |
| AAEigIdx | Eigenvalue-Based Indices Descriptors for 20 Amino Acids calculated by Dragon |
| AAFGC | Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon |
| AAGeom | Geometrical Descriptors for 20 Amino Acids calculated by Dragon |
| AAGETAWAY | GETAWAY Descriptors for 20 Amino Acids calculated by Dragon |
| AAindex | AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids |
| AAInfo | Information Indices Descriptors for 20 Amino Acids calculated by Dragon |
| 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 calculated by Dragon |
| 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 calculated by Dragon |
| AARDF | RDF Descriptors for 20 Amino Acids calculated by Dragon |
| AATopo | Topological Descriptors for 20 Amino Acids calculated by Dragon |
| AATopoChg | Topological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon |
| AAWalk | Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon |
| AAWHIM | WHIM Descriptors for 20 Amino Acids calculated by Dragon |
| acc | Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length |
-- C --
| calcDrugFPSim | Calculate Drug Molecule Similarity Derived by Molecular Fingerprints |
| calcDrugMCSSim | Calculate Drug Molecule Similarity Derived by Maximum Common Substructure Search |
| calcParProtGOSim | Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity |
| calcParProtSeqSim | Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment |
| calcTwoProtGOSim | Protein Similarity Calculation based on Gene Ontology (GO) Similarity |
| calcTwoProtSeqSim | Protein Sequence Alignment for Two Protein Sequences |
| checkProt | Check if the protein sequence's amino acid types are the 20 default types |
| convMolFormat | Chemical File Formats Conversion |
-- E --
| extractDrugAIO | Calculate All Molecular Descriptors in Rcpi at Once |
| extractDrugALOGP | Calculate Atom Additive logP and Molar Refractivity Values Descriptor |
| 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 Partial Charges |
| extractDrugAutocorrelationMass | Calculate the Moreau-Broto Autocorrelation Descriptors using Atomic Weight |
| extractDrugAutocorrelationPolarizability | Calculate the Moreau-Broto Autocorrelation Descriptors using Polarizability |
| extractDrugBCUT | BCUT - Eigenvalue Based Descriptor |
| extractDrugBondCount | Calculate the Descriptor Based on the Number of Bonds of a Certain Bond Order |
| extractDrugBPol | Calculate the Descriptor that Describes the Sum of the Absolute Value of the Difference between Atomic Polarizabilities of All Bonded Atoms in the Molecule |
| extractDrugCarbonTypes | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization |
| extractDrugChiChain | Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7 |
| extractDrugChiCluster | Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6 |
| 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 Orders 4, 5 and 6 |
| extractDrugCPSA | A Variety of Descriptors Combining Surface Area and Partial Charge Information |
| extractDrugDescOB | Calculate Molecular Descriptors Provided by OpenBabel |
| extractDrugECI | Calculate the Eccentric Connectivity Index Descriptor |
| extractDrugEstate | Calculate the E-State Molecular Fingerprints (in Compact Format) |
| extractDrugEstateComplete | Calculate the E-State Molecular Fingerprints (in Complete Format) |
| extractDrugExtended | Calculate the Extended Molecular Fingerprints (in Compact Format) |
| extractDrugExtendedComplete | Calculate the Extended Molecular Fingerprints (in Complete Format) |
| extractDrugFMF | Calculate the FMF Descriptor |
| extractDrugFragmentComplexity | Calculate Complexity of a System |
| extractDrugGraph | Calculate the Graph Molecular Fingerprints (in Compact Format) |
| extractDrugGraphComplete | Calculate the Graph Molecular Fingerprints (in Complete Format) |
| extractDrugGravitationalIndex | Descriptor Characterizing the Mass Distribution of the Molecule. |
| extractDrugHBondAcceptorCount | Number of Hydrogen Bond Acceptors |
| extractDrugHBondDonorCount | Number of Hydrogen Bond Donors |
| extractDrugHybridization | Calculate the Hybridization Molecular Fingerprints (in Compact Format) |
| extractDrugHybridizationComplete | Calculate the Hybridization Molecular Fingerprints (in Complete Format) |
| extractDrugHybridizationRatio | Descriptor that Characterizing Molecular Complexity in Terms of Carbon Hybridization States |
| extractDrugIPMolecularLearning | Calculate the Descriptor that Evaluates the Ionization Potential |
| extractDrugKappaShapeIndices | Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices |
| extractDrugKierHallSmarts | Descriptor that Counts the Number of Occurrences of the E-State Fragments |
| extractDrugKR | Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format) |
| extractDrugKRComplete | Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format) |
| extractDrugLargestChain | Descriptor that Calculates the Number of Atoms in the Largest Chain |
| extractDrugLargestPiSystem | Descriptor that Calculates the Number of Atoms in the Largest Pi Chain |
| extractDrugLengthOverBreadth | Calculate the Ratio of Length to Breadth Descriptor |
| extractDrugLongestAliphaticChain | Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain |
| extractDrugMACCS | Calculate the MACCS Molecular Fingerprints (in Compact Format) |
| extractDrugMACCSComplete | Calculate the MACCS Molecular Fingerprints (in Complete Format) |
| extractDrugMannholdLogP | Descriptor that Calculates the LogP Based on a Simple Equation Using the Number of Carbons and Hetero Atoms |
| extractDrugMDE | Calculate Molecular Distance Edge (MDE) Descriptors for C, N and O |
| extractDrugMomentOfInertia | Descriptor that Calculates the Principal Moments of Inertia and Ratios of the Principal Moments |
| 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 Format) |
| extractDrugPubChemComplete | Calculate the PubChem Molecular Fingerprints (in Complete Format) |
| extractDrugRotatableBondsCount | Descriptor that Calculates the Number of Nonrotatable Bonds on A Molecule |
| extractDrugRuleOfFive | Descriptor that Calculates the Number Failures of the Lipinski's Rule Of Five |
| extractDrugShortestPath | Calculate the Shortest Path Molecular Fingerprints (in Compact Format) |
| extractDrugShortestPathComplete | Calculate the Shortest Path Molecular Fingerprints (in Complete Format) |
| extractDrugStandard | Calculate the Standard Molecular Fingerprints (in Compact Format) |
| extractDrugStandardComplete | Calculate the Standard Molecular Fingerprints (in Complete Format) |
| extractDrugTPSA | Descriptor of Topological Polar Surface Area Based on Fragment Contributions (TPSA) |
| extractDrugVABC | Descriptor that Calculates the Volume of A Molecule |
| extractDrugVAdjMa | Descriptor that Calculates the Vertex Adjacency Information of A Molecule |
| 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 Polarity Number |
| extractDrugXLogP | Descriptor that Calculates the Prediction of logP Based on the Atom-Type Method Called XLogP |
| extractDrugZagrebIndex | Descriptor that Calculates the Sum of the Squared Atom Degrees of All Heavy Atoms |
| extractPCMBLOSUM | Generalized BLOSUM and PAM Matrix-Derived Descriptors |
| extractPCMDescScales | Scales-Based Descriptors with 20+ classes of Molecular Descriptors |
| extractPCMFAScales | Generalized Scales-Based Descriptors derived by Factor Analysis |
| extractPCMMDSScales | Generalized Scales-Based Descriptors derived by Multidimensional Scaling |
| extractPCMPropScales | Generalized AA-Properties Based Scales Descriptors |
| extractPCMScales | Generalized Scales-Based Descriptors derived by Principal Components Analysis |
| 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 protein sequence |
| extractProtPSSMAcc | Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance |
| extractProtPSSMFeature | Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) |
| extractProtQSO | Quasi-Sequence-Order (QSO) Descriptor |
| extractProtSOCN | Sequence-Order-Coupling Numbers |
| extractProtTC | Tripeptide Composition Descriptor |
-- G --
| getCPI | Generating Compound-Protein Interaction Descriptors |
| getDrug | Retrieve Drug Molecules in MOL and SMILES Format from Databases |
| getFASTAFromKEGG | Retrieve Protein Sequence in FASTA Format from the KEGG Database |
| getFASTAFromUniProt | Retrieve Protein Sequence in FASTA Format from the UniProt Database |
| getMolFromCAS | Retrieve Drug Molecules in InChI Format from the CAS Database |
| getMolFromChEMBL | Retrieve Drug Molecules in MOL Format from the ChEMBL Database |
| getMolFromDrugBank | Retrieve Drug Molecules in MOL Format from the DrugBank Database |
| getMolFromKEGG | Retrieve Drug Molecules in MOL Format from the KEGG Database |
| getMolFromPubChem | Retrieve Drug Molecules in MOL Format from the PubChem Database |
| 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 Database |
| getSmiFromDrugBank | Retrieve Drug Molecules in SMILES Format from the DrugBank Database |
| getSmiFromKEGG | Retrieve Drug Molecules in SMILES Format from the KEGG Database |
| getSmiFromPubChem | Retrieve Drug Molecules in SMILES Format from the PubChem Database |
-- O --
| OptAA3d | OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1) |
-- R --
| readFASTA | Read Protein Sequences in FASTA Format |
| readMolFromSDF | Read Molecules from SDF Files and Return Parsed Java Molecular Object |
| readMolFromSmi | Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List |
| readPDB | Read Protein Sequences in PDB Format |
-- S --
| searchDrug | Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search |
| segProt | Protein Sequence Segmentation |