# Toolkit for Compound-Protein Interaction in Drug Discovery

## Documentation for package ‘Rcpi’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C E G O R S

Rcpi-package | Toolkit for Compound-Protein Interaction in Drug Discovery

## -- 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 | Calculates All the Molecular Descriptors in the Rcpi Package at Once
extractDrugALOGP | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extractDrugAminoAcidCount | Calculates the Number of Amino Acids Descriptor
extractDrugApol | Calculates the Sum of the Atomic Polarizabilities Descriptor
extractDrugAromaticAtomsCount | Calculates the Number of Aromatic Atoms Descriptor
extractDrugAromaticBondsCount | Calculates the Number of Aromatic Bonds Descriptor
extractDrugAtomCount | Calculates the Number of Atom Descriptor
extractDrugAutocorrelationCharge | Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges
extractDrugAutocorrelationMass | Calculates the Moreau-Broto Autocorrelation Descriptors using Atomic Weight
extractDrugAutocorrelationPolarizability | Calculates the Moreau-Broto Autocorrelation Descriptors using Polarizability
extractDrugBCUT | BCUT - Eigenvalue Based Descriptor
extractDrugBondCount | Calculates the Descriptor Based on the Number of Bonds of a Certain Bond Order
extractDrugBPol | Calculates 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 | Calculates 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 | Calculates 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 | Descriptor that Calculates the Number of Hydrogen Bond Acceptors
extractDrugHBondDonorCount | Descriptor that Calculates the 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 | Calculates 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 | Calculates 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 --

Rcpi | 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 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