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
crossSetSim             Parallel Protein Sequence Similarity
                        Calculation Between Two Sets Based on Sequence
                        Alignment (In-Memory Version)
crossSetSimDisk         Parallel Protein Sequence Similarity
                        Calculation Between Two Sets Based on Sequence
                        Alignment (Disk-Based Version)
extractAAC              Amino Acid Composition Descriptor
extractAPAAC            Amphiphilic Pseudo Amino Acid Composition
                        (APseAAC) Descriptor
extractBLOSUM           BLOSUM and PAM Matrix-Derived Descriptors
extractCTDC             CTD Descriptors - Composition
extractCTDCClass        CTD Descriptors - Composition (with customized
                        amino acid classification support)
extractCTDD             CTD Descriptors - Distribution
extractCTDDClass        CTD Descriptors - Distribution (with customized
                        amino acid classification support)
extractCTDT             CTD Descriptors - Transition
extractCTDTClass        CTD Descriptors - Transition (with customized
                        amino acid classification support)
extractCTriad           Conjoint Triad Descriptor
extractCTriadClass      Conjoint Triad Descriptor (with customized
                        amino acid classification support)
extractDC               Dipeptide Composition Descriptor
extractDescScales       Scales-Based Descriptors with 20+ classes of
                        Molecular Descriptors
extractFAScales         Scales-Based Descriptors derived by Factor
                        Analysis
extractGeary            Geary Autocorrelation Descriptor
extractMDSScales        Scales-Based Descriptors derived by
                        Multidimensional Scaling
extractMoran            Moran Autocorrelation Descriptor
extractMoreauBroto      Normalized Moreau-Broto Autocorrelation
                        Descriptor
extractPAAC             Pseudo Amino Acid Composition (PseAAC)
                        Descriptor
extractPSSM             Compute PSSM (Position-Specific Scoring Matrix)
                        for given protein sequence
extractPSSMAcc          Profile-based protein representation derived by
                        PSSM (Position-Specific Scoring Matrix) and
                        auto cross covariance
extractPSSMFeature      Profile-based protein representation derived by
                        PSSM (Position-Specific Scoring Matrix)
extractProtFP           Amino Acid Properties Based Scales Descriptors
                        (Protein Fingerprint)
extractProtFPGap        Amino Acid Properties Based Scales Descriptors
                        (Protein Fingerprint) with Gap Support
extractQSO              Quasi-Sequence-Order (QSO) Descriptor
extractSOCN             Sequence-Order-Coupling Numbers
extractScales           Scales-Based Descriptors derived by Principal
                        Components Analysis
extractScalesGap        Scales-Based Descriptors derived by Principal
                        Components Analysis (with Gap Support)
extractTC               Tripeptide Composition Descriptor
getUniProt              Retrieve Protein Sequences from UniProt by
                        Protein ID
parGOSim                Protein Similarity Calculation based on Gene
                        Ontology (GO) Similarity
parSeqSim               Parallel Protein Sequence Similarity
                        Calculation Based on Sequence Alignment
                        (In-Memory Version)
parSeqSimDisk           Parallel Protein Sequence Similarity
                        Calculation Based on Sequence Alignment
                        (Disk-Based Version)
protcheck               Protein sequence amino acid type sanity check
protseg                 Protein Sequence Segmentation/Partition
readFASTA               Read Protein Sequences in FASTA Format
readPDB                 Read Protein Sequences in PDB Format
removeGaps              Remove or replace gaps from protein sequences.
twoGOSim                Protein Similarity Calculation based on Gene
                        Ontology (GO) Similarity
twoSeqSim               Protein Sequence Alignment for Two Protein
                        Sequences
