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
AACPSA                  CPSA Descriptors for 20 Amino Acids calculated
                        by Discovery Studio
AAConn                  Connectivity Indices Descriptors for 20 Amino
                        Acids calculated by Dragon
AAConst                 Constitutional Descriptors for 20 Amino Acids
                        calculated by Dragon
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
AAGETAWAY               GETAWAY Descriptors for 20 Amino Acids
                        calculated by Dragon
AAGeom                  Geometrical Descriptors for 20 Amino Acids
                        calculated by Dragon
AAInfo                  Information Indices 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
AAMetaInfo              Meta Information for the 20 Amino Acids
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
AARDF                   RDF Descriptors for 20 Amino Acids calculated
                        by Dragon
AARandic                Randic Molecular Profiles 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
AAWHIM                  WHIM Descriptors for 20 Amino Acids calculated
                        by Dragon
AAWalk                  Walk and Path Counts Descriptors for 20 Amino
                        Acids calculated by Dragon
AAindex                 AAindex Data of 544 Physicochemical and
                        Biological Properties for 20 Amino Acids
OptAA3d                 OptAA3d.sdf - 20 Amino Acids Optimized with MOE
                        2011.10 (Semiempirical AM1)
acc                     Auto Cross Covariance (ACC) for Generating
                        Scales-Based Descriptors of the Same Length
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
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
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
extractDrugBondCount    Calculate the Descriptor Based on the Number of
                        Bonds of a Certain Bond Order
extractDrugCPSA         A Variety of Descriptors Combining Surface Area
                        and Partial Charge Information
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
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
extractDrugKR           Calculate the KR (Klekota and Roth) Molecular
                        Fingerprints (in Compact Format)
extractDrugKRComplete   Calculate the KR (Klekota and Roth) Molecular
                        Fingerprints (in Complete Format)
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
extractDrugMACCS        Calculate the MACCS Molecular Fingerprints (in
                        Compact Format)
extractDrugMACCSComplete
                        Calculate the MACCS Molecular Fingerprints (in
                        Complete Format)
extractDrugMDE          Calculate Molecular Distance Edge (MDE)
                        Descriptors for C, N and O
extractDrugMannholdLogP
                        Descriptor that Calculates the LogP Based on a
                        Simple Equation Using the Number of Carbons and
                        Hetero Atoms
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
extractDrugWHIM         Calculate Holistic Descriptors Described by
                        Todeschini et al.
extractDrugWeight       Descriptor that Calculates the Total Weight of
                        Atoms
extractDrugWeightedPath
                        Descriptor that Calculates the Weighted Path
                        (Molecular ID)
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
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
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
searchDrug              Parallelized Drug Molecule Similarity Search by
                        Molecular Fingerprints Similarity or Maximum
                        Common Substructure Search
segProt                 Protein Sequence Segmentation
