Function reference • Rcpi

Protein sequence retrivial

Functions for retrieving protein sequence data from online databases.

getProt(): Retrieve Protein Sequence in various Formats from Databases

getFASTAFromUniProt(): Retrieve Protein Sequence in FASTA Format from the UniProt Database

getFASTAFromKEGG(): Retrieve Protein Sequence in FASTA Format from the KEGG Database

getPDBFromRCSBPDB(): Retrieve Protein Sequence in PDB Format from RCSB PDB

getSeqFromUniProt(): Retrieve Protein Sequence from the UniProt Database

getSeqFromKEGG(): Retrieve Protein Sequence from the KEGG Database

getSeqFromRCSBPDB(): Retrieve Protein Sequence from RCSB PDB

Drug molecular data retrivial

Functions for retrieving drug molecular data from online databases.

getDrug(): Retrieve Drug Molecules in MOL and SMILES Format from Databases

getMolFromDrugBank(): Retrieve Drug Molecules in MOL Format from the DrugBank Database

getMolFromPubChem(): Retrieve Drug Molecules in MOL Format from the PubChem Database

getMolFromChEMBL(): Retrieve Drug Molecules in MOL Format from the ChEMBL Database

getMolFromKEGG(): Retrieve Drug Molecules in MOL Format from the KEGG Database

getMolFromCAS(): Retrieve Drug Molecules in InChI Format from the CAS Database

getSmiFromDrugBank(): Retrieve Drug Molecules in SMILES Format from the DrugBank Database

getSmiFromPubChem(): Retrieve Drug Molecules in SMILES Format from the PubChem Database

getSmiFromChEMBL(): Retrieve Drug Molecules in SMILES Format from the ChEMBL Database

getSmiFromKEGG(): Retrieve Drug Molecules in SMILES Format from the KEGG Database

Protein sequence descriptors

Functions and datasets for computing commonly used protein sequence derived descriptors.

extractProtAAC(): Amino Acid Composition Descriptor

extractProtDC(): Dipeptide Composition Descriptor

extractProtTC(): Tripeptide Composition Descriptor

extractProtMoreauBroto(): Normalized Moreau-Broto Autocorrelation Descriptor

extractProtMoran(): Moran Autocorrelation Descriptor

extractProtGeary(): Geary Autocorrelation Descriptor

extractProtCTDC(): CTD Descriptors - Composition

extractProtCTDT(): CTD Descriptors - Transition

extractProtCTDD(): CTD Descriptors - Distribution

extractProtCTriad(): Conjoint Triad Descriptor

extractProtSOCN(): Sequence-Order-Coupling Numbers

extractProtQSO(): Quasi-Sequence-Order (QSO) Descriptor

extractProtPAAC(): Pseudo Amino Acid Composition Descriptor

extractProtAPAAC(): Amphiphilic Pseudo Amino Acid Composition Descriptor

AAindex: AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids

Profile-based protein sequence descriptors

Functions for generating profile-based protein representations.

extractProtPSSM(): Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence

extractProtPSSMFeature(): Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)

extractProtPSSMAcc(): Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance

Scales-based descriptors for proteochemometrics modeling

Functions for generating scales-based descriptors for proteochemometrics (PCM) modeling.

extractPCMScales(): Generalized Scales-Based Descriptors derived by Principal Components Analysis

extractPCMPropScales(): Generalized AA-Properties Based Scales 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

extractPCMBLOSUM(): Generalized BLOSUM and PAM Matrix-Derived Descriptors

acc(): Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length

Molecular descriptor sets for generating scales-based descriptors

Molecular descriptor sets of the 20 amino acids for generating scales-based descriptors.

OptAA3d: OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)

AAMetaInfo: Meta Information for the 20 Amino Acids

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

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

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

AAInfo: Information Indices Descriptors for 20 Amino Acids calculated by Dragon

AAMolProp: Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon

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

AACPSA: CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio

AADescAll: All 2D Descriptors for 20 Amino Acids calculated by Dragon

AAMOE2D: 2D Descriptors for 20 Amino Acids calculated by MOE 2011.10

AAMOE3D: 3D Descriptors for 20 Amino Acids calculated by MOE 2011.10

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

AABLOSUM100: BLOSUM100 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

AAPAM120: PAM120 Matrix for 20 Amino Acids

AAPAM250: PAM250 Matrix for 20 Amino Acids

Molecular descriptors

Functions for computing commonly used molecular descriptors.

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

extractDrugFMF(): Calculate the FMF Descriptor

extractDrugFragmentComplexity(): Calculate Complexity of a System

extractDrugGravitationalIndex(): Descriptor Characterizing the Mass Distribution of the Molecule.

extractDrugHBondAcceptorCount(): Number of Hydrogen Bond Acceptors

extractDrugHBondDonorCount(): Number of Hydrogen Bond Donors

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

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

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

extractDrugPetitjeanNumber(): Descriptor that Calculates the Petitjean Number of a Molecule

extractDrugPetitjeanShapeIndex(): Descriptor that Calculates the Petitjean Shape Indices

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

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

Molecular fingerprints

Functions for computing commonly used molecular fingerprints.

extractDrugStandard(): Calculate the Standard Molecular Fingerprints (in Compact Format)

extractDrugStandardComplete(): Calculate the Standard Molecular Fingerprints (in Complete Format)

extractDrugExtended(): Calculate the Extended Molecular Fingerprints (in Compact Format)

extractDrugExtendedComplete(): Calculate the Extended Molecular Fingerprints (in Complete Format)

extractDrugGraph(): Calculate the Graph Molecular Fingerprints (in Compact Format)

extractDrugGraphComplete(): Calculate the Graph Molecular Fingerprints (in Complete Format)

extractDrugHybridization(): Calculate the Hybridization Molecular Fingerprints (in Compact Format)

extractDrugHybridizationComplete(): Calculate the Hybridization Molecular Fingerprints (in Complete Format)

extractDrugMACCS(): Calculate the MACCS Molecular Fingerprints (in Compact Format)

extractDrugMACCSComplete(): Calculate the MACCS Molecular Fingerprints (in Complete Format)

extractDrugEstate(): Calculate the E-State Molecular Fingerprints (in Compact Format)

extractDrugEstateComplete(): Calculate the E-State Molecular Fingerprints (in Complete Format)

extractDrugPubChem(): Calculate the PubChem Molecular Fingerprints (in Compact Format)

extractDrugPubChemComplete(): Calculate the PubChem Molecular Fingerprints (in Complete Format)

extractDrugKR(): Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)

extractDrugKRComplete(): Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)

extractDrugShortestPath(): Calculate the Shortest Path Molecular Fingerprints (in Compact Format)

extractDrugShortestPathComplete(): Calculate the Shortest Path Molecular Fingerprints (in Complete Format)

extractDrugOBFP2(): Calculate the FP2 Molecular Fingerprints

extractDrugOBFP3(): Calculate the FP3 Molecular Fingerprints

extractDrugOBFP4(): Calculate the FP4 Molecular Fingerprints

extractDrugOBMACCS(): Calculate the MACCS Molecular Fingerprints

PPI and CPI descriptors

Functions for computing protein-protein and compound-protein interation descriptors.

getPPI(): Generating Protein-Protein Interaction Descriptors

getCPI(): Generating Compound-Protein Interaction Descriptors

Similarity and similarity searching

Functions for computing sequence/molecular similarities and similarity searching.

calcDrugFPSim(): Calculate Drug Molecule Similarity Derived by Molecular Fingerprints

calcDrugMCSSim(): Calculate Drug Molecule Similarity Derived by Maximum Common Substructure Search

searchDrug(): Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search

calcTwoProtSeqSim(): Protein Sequence Alignment for Two Protein Sequences

calcParProtSeqSim(): Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment

calcTwoProtGOSim(): Protein Similarity Calculation based on Gene Ontology (GO) Similarity

calcParProtGOSim(): Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity

Protein sequence data processing

Functions for processing protein sequence data.

readFASTA(): Read Protein Sequences in FASTA Format

readPDB(): Read Protein Sequences in PDB Format

segProt(): Protein Sequence Segmentation

checkProt(): Check if the protein sequence's amino acid types are the 20 default types

Molecular data processing

Functions for processing molecular data.

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

convMolFormat(): Chemical File Formats Conversion

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