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
Autocorrelation         Calculates the Moreau-Broto Autocorrelation
                        Descriptors using Partial Charges
BMgetDNAGenBank         Get DNA/RNA Sequences from Genbank by GI ID
BioMedR-package         Toolkit for Compound-Protein Interaction in
                        Drug Discovery
Constitutional          Calculates the Number of Amino Acids Descriptor
NNeighbors              Nearest Neighbors
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
apfp                    Frequent Atom Pairs
atomprop                Standard atomic weights
bcl                     2D descriptors of bcl2
calcDrugFPSim           Calculate Drug Molecule Similarity Derived by
                        Molecular Fingerprints
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
checkDNA                Check if the DNA sequence are in the 4 default
                        types
checkProt               Check if the protein sequence's amino acid
                        types are the 20 default types
clusterCMP              cluster compounds using a descriptor database
clusterJP               Jarvis-Patrick Clustering
clusterMDS              visualize clustering result using
                        multi-dimensional scaling
clusterStat             generate statistics on sizes of clusters
connectivity            Calculate the Kier and Hall Chi Chain Indices
                        of Orders 3, 4, 5, 6 and 7
convAPtoFP              Fingerprints from descriptor vectors
convSDFtoAP             Atom pair library
extrDNADAC              The Dinucleotide-based Auto Covariance
                        Descriptor
extrDNADACC             The Dinucleotide-based Auto-cross Covariance
                        Descriptor
extrDNADCC              The Dinucleotide-based Cross Covariance
                        Descriptor
extrDNAIncDiv           The Increment Of Diversity Descriptors
extrDNAPseDNC           The Pseudo Dinucleotide Composition Descriptor
extrDNAPseKNC           The Pseudo K-tupler Composition Descriptor
extrDNATAC              The Trinucleotide-based Auto Covariance
                        Descriptor
extrDNATACC             The Trinucleotide-based Auto-cross Covariance
                        Descriptor
extrDNATCC              The Trinucleotide-based Cross Covariance
                        Descriptor
extrDNAkmer             The Basic Kmer Descriptor
extrDrugAIO             Calculates All the Molecular Descriptors in the
                        BioMedR Package at Once
extrDrugAP              Calculate the Atom Pair Fingerprints
extrDrugBCUT            BCUT - Eigenvalue Based Descriptor
extrDrugCPSA            A Variety of Descriptors Combining Surface Area
                        and Partial Charge Information
extrDrugEstate          Calculate the E-State Molecular Fingerprints
                        (in Compact Format)
extrDrugEstateComplete
                        Calculate the E-State Molecular Fingerprints
                        (in Complete Format)
extrDrugExtended        Calculate the Extended Molecular Fingerprints
                        (in Compact Format)
extrDrugExtendedComplete
                        Calculate the Extended Molecular Fingerprints
                        (in Complete Format)
extrDrugGraph           Calculate the Graph Molecular Fingerprints (in
                        Compact Format)
extrDrugGraphComplete   Calculate the Graph Molecular Fingerprints (in
                        Complete Format)
extrDrugHybridization   Calculate the Hybridization Molecular
                        Fingerprints (in Compact Format)
extrDrugHybridizationComplete
                        Calculate the Hybridization Molecular
                        Fingerprints (in Complete Format)
extrDrugHybridizationRatio
                        Descriptor that Characterizing Molecular
                        Complexity in Terms of Carbon Hybridization
                        States
extrDrugIPMolecularLearning
                        Calculates the Descriptor that Evaluates the
                        Ionization Potential
extrDrugKR              Calculate the KR (Klekota and Roth) Molecular
                        Fingerprints (in Compact Format)
extrDrugKRComplete      Calculate the KR (Klekota and Roth) Molecular
                        Fingerprints (in Complete Format)
extrDrugKappaShapeIndices
                        Descriptor that Calculates Kier and Hall Kappa
                        Molecular Shape Indices
extrDrugKierHallSmarts
                        Descriptor that Counts the Number of
                        Occurrences of the E-State Fragments
extrDrugMACCS           Calculate the MACCS Molecular Fingerprints (in
                        Compact Format)
extrDrugMACCSComplete   Calculate the MACCS Molecular Fingerprints (in
                        Complete Format)
extrDrugMannholdLogP    Descriptor that Calculates the LogP Based on a
                        Simple Equation Using the Number of Carbons and
                        Hetero Atoms
extrDrugPubChem         Calculate the PubChem Molecular Fingerprints
                        (in Compact Format)
extrDrugPubChemComplete
                        Calculate the PubChem Molecular Fingerprints
                        (in Complete Format)
extrDrugShortestPath    Calculate the Shortest Path Molecular
                        Fingerprints (in Compact Format)
extrDrugShortestPathComplete
                        Calculate the Shortest Path Molecular
                        Fingerprints (in Complete Format)
extrDrugStandard        Calculate the Standard Molecular Fingerprints
                        (in Compact Format)
extrDrugStandardComplete
                        Calculate the Standard Molecular Fingerprints
                        (in Complete Format)
extrDrugWHIM            Calculate Holistic Descriptors Described by
                        Todeschini et al.
extrPCMBLOSUM           Generalized BLOSUM and PAM Matrix-Derived
                        Descriptors
extrPCMDescScales       Scales-Based Descriptors with 20+ classes of
                        Molecular Descriptors
extrPCMFAScales         Generalized Scales-Based Descriptors derived by
                        Factor Analysis
extrPCMMDSScales        Generalized Scales-Based Descriptors derived by
                        Multidimensional Scaling
extrPCMPropScales       Generalized AA-Properties Based Scales
                        Descriptors
extrPCMScaleGap         Scales-Based Descriptors derived by Principal
                        Components Analysis (with Gap Support)
extrPCMScales           Generalized Scales-Based Descriptors derived by
                        Principal Components Analysis
extrProtAAC             Amino Acid Composition Descriptor
extrProtAPAAC           Amphiphilic Pseudo Amino Acid Composition
                        Descriptor
extrProtCTDC            CTD Descriptors - Composition
extrProtCTDCClass       CTD Descriptors - Composition (with Customized
                        Amino Acid Classification Support)
extrProtCTDD            CTD Descriptors - Distribution
extrProtCTDDClass       CTD Descriptors - Distribution (with Customized
                        Amino Acid Classification Support)
extrProtCTDT            CTD Descriptors - Transition
extrProtCTDTClass       CTD Descriptors - Transition (with Customized
                        Amino Acid Classification Support)
extrProtCTriad          Conjoint Triad Descriptor
extrProtCTriadClass     Conjoint Triad Descriptor (with Customized
                        Amino Acid Classification Support)
extrProtDC              Dipeptide Composition Descriptor
extrProtFPGap           Amino Acid Properties Based Scales Descriptors
                        (Protein Fingerprint) with Gap Support
extrProtGeary           Geary Autocorrelation Descriptor
extrProtMoran           Moran Autocorrelation Descriptor
extrProtMoreauBroto     Normalized Moreau-Broto Autocorrelation
                        Descriptor
extrProtPAAC            Pseudo Amino Acid Composition Descriptor
extrProtPSSM            Compute PSSM (Position-Specific Scoring Matrix)
                        for given protein sequence
extrProtPSSMAcc         Profile-based protein representation derived by
                        PSSM (Position-Specific Scoring Matrix) and
                        auto cross covariance
extrProtPSSMFeature     Profile-based protein representation derived by
                        PSSM (Position-Specific Scoring Matrix)
extrProtQSO             Quasi-Sequence-Order (QSO) Descriptor
extrProtSOCN            Sequence-Order-Coupling Numbers
extrProtTC              Tripeptide Composition Descriptor
geometric               Descriptor Characterizing the Mass Distribution
                        of the Molecule.
getCPI                  Generating Interaction Descriptors
getDrug                 Retrieve Drug Molecules in MOL and SMILES
                        Format from Databases
getProt                 Retrieve Protein Sequence in various Formats
                        from Databases
make_kmer_index         Calculate The Basic Kmer Feature Vector
parGOSim                Protein/DNA Sequence Similarity Calculation
                        based on Gene Ontology (GO) Similarity
parSeqSim               Parallellized Protein/DVA Sequence Similarity
                        Calculation based on Sequence Alignment
plotStructure           Plots compound structure(s) for molecules
                        stored in SDF and SDFset containers
pls.cv                  The Cross-Validation of Classification and
                        Regression models using Partial Least Squares
property                Calculates Atom Additive logP and Molar
                        Refractivity Values Descriptor
readFASTA               Read Protein/DNA 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
revchars                The Reverse chars
rf.cv                   The Cross-Validation of Classification and
                        Regression models using Random Forest
rf.fs                   Random Forest Cross-Valdidation for feature
                        selection
sdfbcl                  SD file in 'SDFset' object
searchDrug              Parallelized Drug Molecule Similarity Search by
                        Molecular Fingerprints Similarity or Maximum
                        Common Substructure Search
segProt                 Protein Sequence Segmentation
topology                Topological Descriptor Characterizing the
                        Carbon Connectivity in Terms of Hybridization
twoGOSim                Protein/DNA Similarity Calculation based on
                        Gene Ontology (GO) Similarity
twoSeqSim               Protein/DNA Sequence Alignment for Two Protein
                        Sequences
