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"page": "AAFGC", "title": "Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAFGC" ] }, { "page": "AAGeom", "title": "Geometrical Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAGeom" ] }, { "page": "AAGETAWAY", "title": "GETAWAY Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAGETAWAY" ] }, { "page": "AAindex", "title": "AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids", "topics": [ "AAindex" ] }, { "page": "AAInfo", "title": "Information Indices Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAInfo" ] }, { "page": "AAMetaInfo", "title": "Meta Information for the 20 Amino Acids", "topics": [ "AAMetaInfo" ] }, { "page": "AAMOE2D", "title": "2D Descriptors for 20 Amino Acids calculated by MOE 2011.10", "topics": [ "AAMOE2D" ] }, { "page": "AAMOE3D", "title": "3D Descriptors for 20 Amino Acids calculated by MOE 2011.10", "topics": [ "AAMOE3D" ] }, { "page": "AAMolProp", "title": "Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAMolProp" ] }, { "page": "AAPAM120", "title": "PAM120 Matrix for 20 Amino Acids", "topics": [ "AAPAM120" ] }, { "page": "AAPAM250", "title": "PAM250 Matrix for 20 Amino Acids", "topics": [ "AAPAM250" ] }, { "page": "AAPAM30", "title": "PAM30 Matrix for 20 Amino Acids", "topics": [ "AAPAM30" ] }, { "page": "AAPAM40", "title": "PAM40 Matrix for 20 Amino Acids", "topics": [ "AAPAM40" ] }, { "page": "AAPAM70", "title": "PAM70 Matrix for 20 Amino Acids", "topics": [ "AAPAM70" ] }, { "page": "AARandic", "title": "Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AARandic" ] }, { "page": "AARDF", "title": "RDF Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AARDF" ] }, { "page": "AATopo", "title": "Topological Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AATopo" ] }, { "page": "AATopoChg", "title": "Topological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AATopoChg" ] }, { "page": "AAWalk", "title": "Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAWalk" ] }, { "page": "AAWHIM", "title": "WHIM Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAWHIM" ] }, { "page": "acc", "title": "Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length", "topics": [ "acc" ] }, { "page": "calcDrugFPSim", "title": "Calculate Drug Molecule Similarity Derived by Molecular Fingerprints", "topics": [ "calcDrugFPSim" ] }, { "page": "calcDrugMCSSim", "title": "Calculate Drug Molecule Similarity Derived by Maximum Common Substructure Search", "topics": [ "calcDrugMCSSim" ] }, { "page": "calcParProtGOSim", "title": "Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity", "topics": [ "calcParProtGOSim" ] }, { "page": "calcParProtSeqSim", "title": "Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment", "topics": [ "calcParProtSeqSim" ] }, { "page": "calcTwoProtGOSim", "title": "Protein Similarity Calculation based on Gene Ontology (GO) Similarity", "topics": [ "calcTwoProtGOSim" ] }, { "page": "calcTwoProtSeqSim", "title": "Protein Sequence Alignment for Two Protein Sequences", "topics": [ "calcTwoProtSeqSim" ] }, { "page": "checkProt", "title": "Check if the protein sequence's amino acid types are the 20 default types", "topics": [ "checkProt" ] }, { "page": "convMolFormat", "title": "Chemical File Formats Conversion", "topics": [ "convMolFormat" ] }, { "page": "extractDrugAIO", "title": "Calculate All Molecular Descriptors in Rcpi at Once", "topics": [ "extractDrugAIO" ] }, { "page": "extractDrugALOGP", "title": "Calculate Atom Additive logP and Molar Refractivity Values Descriptor", "topics": [ "extractDrugALOGP" ] }, { "page": "extractDrugAminoAcidCount", "title": "Calculate the Number of Amino Acids Descriptor", "topics": [ "extractDrugAminoAcidCount" ] }, { "page": "extractDrugApol", "title": "Calculate the Sum of the Atomic Polarizabilities Descriptor", "topics": [ "extractDrugApol" ] }, { "page": "extractDrugAromaticAtomsCount", "title": "Calculate the Number of Aromatic Atoms Descriptor", "topics": [ "extractDrugAromaticAtomsCount" ] }, { "page": "extractDrugAromaticBondsCount", "title": "Calculate the Number of Aromatic Bonds Descriptor", "topics": [ "extractDrugAromaticBondsCount" ] }, { "page": "extractDrugAtomCount", "title": "Calculate the Number of Atom Descriptor", "topics": [ "extractDrugAtomCount" ] }, { "page": "extractDrugAutocorrelationCharge", "title": "Calculate the Moreau-Broto Autocorrelation Descriptors using Partial Charges", "topics": [ "extractDrugAutocorrelationCharge" ] }, { "page": "extractDrugAutocorrelationMass", "title": "Calculate the Moreau-Broto Autocorrelation Descriptors using Atomic Weight", "topics": [ "extractDrugAutocorrelationMass" ] }, { "page": "extractDrugAutocorrelationPolarizability", "title": "Calculate the Moreau-Broto Autocorrelation Descriptors using Polarizability", "topics": [ "extractDrugAutocorrelationPolarizability" ] }, { "page": "extractDrugBCUT", "title": "BCUT - Eigenvalue Based Descriptor", "topics": [ "extractDrugBCUT" ] }, { "page": "extractDrugBondCount", "title": "Calculate the Descriptor Based on the Number of Bonds of a Certain Bond Order", "topics": [ "extractDrugBondCount" ] }, { "page": "extractDrugBPol", "title": "Calculate the Descriptor that Describes the Sum of the Absolute Value of the Difference between Atomic Polarizabilities of All Bonded Atoms in the Molecule", "topics": [ "extractDrugBPol" ] }, { "page": "extractDrugCarbonTypes", "title": "Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization", "topics": [ "extractDrugCarbonTypes" ] }, { "page": "extractDrugChiChain", "title": "Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7", "topics": [ "extractDrugChiChain" ] }, { "page": "extractDrugChiCluster", "title": "Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6", "topics": [ "extractDrugChiCluster" ] }, { "page": "extractDrugChiPath", "title": "Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7", "topics": [ "extractDrugChiPath" ] }, { "page": "extractDrugChiPathCluster", "title": "Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6", "topics": [ "extractDrugChiPathCluster" ] }, { "page": "extractDrugCPSA", "title": "A Variety of Descriptors Combining Surface Area and Partial Charge Information", "topics": [ "extractDrugCPSA" ] }, { "page": "extractDrugDescOB", "title": "Calculate Molecular Descriptors Provided by OpenBabel", "topics": [ "extractDrugDescOB" ] }, { "page": "extractDrugECI", "title": "Calculate the Eccentric Connectivity Index Descriptor", "topics": [ "extractDrugECI" ] }, { "page": "extractDrugEstate", "title": "Calculate the E-State Molecular Fingerprints (in Compact Format)", "topics": [ "extractDrugEstate" ] }, { "page": "extractDrugEstateComplete", "title": "Calculate the E-State Molecular Fingerprints (in Complete Format)", "topics": [ "extractDrugEstateComplete" ] }, { "page": "extractDrugExtended", "title": "Calculate the Extended Molecular Fingerprints (in Compact Format)", "topics": [ "extractDrugExtended" ] }, { "page": "extractDrugExtendedComplete", "title": "Calculate the Extended Molecular Fingerprints (in Complete Format)", "topics": [ "extractDrugExtendedComplete" ] }, { "page": "extractDrugFMF", "title": "Calculate the FMF Descriptor", "topics": [ "extractDrugFMF" ] }, { "page": "extractDrugFragmentComplexity", "title": "Calculate Complexity of a System", "topics": [ "extractDrugFragmentComplexity" ] }, { "page": "extractDrugGraph", "title": "Calculate the Graph Molecular Fingerprints (in Compact Format)", "topics": [ "extractDrugGraph" ] }, { "page": "extractDrugGraphComplete", "title": "Calculate the Graph Molecular Fingerprints (in Complete Format)", "topics": [ "extractDrugGraphComplete" ] }, { "page": "extractDrugGravitationalIndex", "title": "Descriptor Characterizing the Mass Distribution of the Molecule.", "topics": [ "extractDrugGravitationalIndex" ] }, { "page": "extractDrugHBondAcceptorCount", "title": "Number of Hydrogen Bond Acceptors", "topics": [ "extractDrugHBondAcceptorCount" ] }, { "page": "extractDrugHBondDonorCount", "title": "Number of Hydrogen Bond Donors", "topics": [ "extractDrugHBondDonorCount" ] }, { "page": "extractDrugHybridization", "title": "Calculate the Hybridization Molecular Fingerprints (in Compact Format)", "topics": [ "extractDrugHybridization" ] }, { "page": "extractDrugHybridizationComplete", "title": "Calculate the Hybridization Molecular Fingerprints (in Complete Format)", "topics": [ "extractDrugHybridizationComplete" ] }, { "page": "extractDrugHybridizationRatio", "title": "Descriptor that Characterizing Molecular Complexity in Terms of Carbon Hybridization States", "topics": [ "extractDrugHybridizationRatio" ] }, { "page": "extractDrugIPMolecularLearning", "title": "Calculate the Descriptor that Evaluates the Ionization Potential", "topics": [ "extractDrugIPMolecularLearning" ] }, { "page": "extractDrugKappaShapeIndices", "title": "Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices", "topics": [ "extractDrugKappaShapeIndices" ] }, { "page": "extractDrugKierHallSmarts", "title": "Descriptor that Counts the Number of Occurrences of the E-State Fragments", "topics": [ "extractDrugKierHallSmarts" ] }, { "page": "extractDrugKR", "title": "Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)", "topics": [ "extractDrugKR" ] }, { "page": "extractDrugKRComplete", "title": "Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)", "topics": [ "extractDrugKRComplete" ] }, { "page": "extractDrugLargestChain", "title": "Descriptor that Calculates the Number of Atoms in the Largest Chain", "topics": [ "extractDrugLargestChain" ] }, { "page": "extractDrugLargestPiSystem", "title": "Descriptor that Calculates the Number of Atoms in the Largest Pi Chain", "topics": [ "extractDrugLargestPiSystem" ] }, { "page": "extractDrugLengthOverBreadth", "title": "Calculate the Ratio of Length to Breadth Descriptor", "topics": [ "extractDrugLengthOverBreadth" ] }, { "page": "extractDrugLongestAliphaticChain", "title": "Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain", "topics": [ "extractDrugLongestAliphaticChain" ] }, { "page": "extractDrugMACCS", "title": "Calculate the MACCS Molecular Fingerprints (in Compact Format)", "topics": [ "extractDrugMACCS" ] }, { "page": "extractDrugMACCSComplete", "title": "Calculate the MACCS Molecular Fingerprints (in Complete Format)", "topics": [ "extractDrugMACCSComplete" ] }, { "page": "extractDrugMannholdLogP", "title": "Descriptor that Calculates the LogP Based on a Simple Equation Using the Number of Carbons and Hetero Atoms", "topics": [ "extractDrugMannholdLogP" ] }, { "page": "extractDrugMDE", "title": "Calculate Molecular Distance Edge (MDE) Descriptors for C, N and O", "topics": [ "extractDrugMDE" ] }, { "page": "extractDrugMomentOfInertia", "title": "Descriptor that Calculates the Principal Moments of Inertia and Ratios of the Principal Moments", "topics": [ "extractDrugMomentOfInertia" ] }, { "page": "extractDrugOBFP2", "title": "Calculate the FP2 Molecular Fingerprints", "topics": [ "extractDrugOBFP2" ] }, { "page": "extractDrugOBFP3", "title": "Calculate the FP3 Molecular Fingerprints", "topics": [ "extractDrugOBFP3" ] }, { "page": "extractDrugOBFP4", "title": "Calculate the FP4 Molecular Fingerprints", "topics": [ "extractDrugOBFP4" ] }, { "page": "extractDrugOBMACCS", "title": "Calculate the MACCS Molecular Fingerprints", "topics": [ "extractDrugOBMACCS" ] }, { "page": "extractDrugPetitjeanNumber", "title": "Descriptor that Calculates the Petitjean Number of a Molecule", "topics": [ "extractDrugPetitjeanNumber" ] }, { "page": "extractDrugPetitjeanShapeIndex", "title": "Descriptor that Calculates the Petitjean Shape Indices", "topics": [ "extractDrugPetitjeanShapeIndex" ] }, { "page": "extractDrugPubChem", "title": "Calculate the PubChem Molecular Fingerprints (in Compact Format)", "topics": [ "extractDrugPubChem" ] }, { "page": "extractDrugPubChemComplete", "title": "Calculate the PubChem Molecular Fingerprints (in Complete Format)", "topics": [ "extractDrugPubChemComplete" ] }, { "page": "extractDrugRotatableBondsCount", "title": "Descriptor that Calculates the Number of Nonrotatable Bonds on A Molecule", "topics": [ "extractDrugRotatableBondsCount" ] }, { "page": "extractDrugRuleOfFive", "title": "Descriptor that Calculates the Number Failures of the Lipinski's Rule Of Five", "topics": [ "extractDrugRuleOfFive" ] }, { "page": "extractDrugShortestPath", "title": "Calculate the Shortest Path Molecular Fingerprints (in Compact Format)", "topics": [ "extractDrugShortestPath" ] }, { "page": "extractDrugShortestPathComplete", "title": "Calculate the Shortest Path Molecular Fingerprints (in Complete Format)", "topics": [ "extractDrugShortestPathComplete" ] }, { "page": "extractDrugStandard", "title": "Calculate the Standard Molecular Fingerprints (in Compact Format)", "topics": [ "extractDrugStandard" ] }, { "page": "extractDrugStandardComplete", "title": "Calculate the Standard Molecular Fingerprints (in Complete Format)", "topics": [ "extractDrugStandardComplete" ] }, { "page": "extractDrugTPSA", "title": "Descriptor of Topological Polar Surface Area Based on Fragment Contributions (TPSA)", "topics": [ "extractDrugTPSA" ] }, { "page": "extractDrugVABC", "title": "Descriptor that Calculates the Volume of A Molecule", "topics": [ "extractDrugVABC" ] }, { "page": "extractDrugVAdjMa", "title": "Descriptor that Calculates the Vertex Adjacency Information of A Molecule", "topics": [ "extractDrugVAdjMa" ] }, { "page": "extractDrugWeight", "title": "Descriptor that Calculates the Total Weight of Atoms", "topics": [ "extractDrugWeight" ] }, { "page": "extractDrugWeightedPath", "title": "Descriptor that Calculates the Weighted Path (Molecular ID)", "topics": [ "extractDrugWeightedPath" ] }, { "page": "extractDrugWHIM", "title": "Calculate Holistic Descriptors Described by Todeschini et al.", "topics": [ "extractDrugWHIM" ] }, { "page": "extractDrugWienerNumbers", "title": "Descriptor that Calculates Wiener Path Number and Wiener Polarity Number", "topics": [ "extractDrugWienerNumbers" ] }, { "page": "extractDrugXLogP", "title": "Descriptor that Calculates the Prediction of logP Based on the Atom-Type Method Called XLogP", "topics": [ "extractDrugXLogP" ] }, { "page": "extractDrugZagrebIndex", "title": "Descriptor that Calculates the Sum of the Squared Atom Degrees of All Heavy Atoms", "topics": [ "extractDrugZagrebIndex" ] }, { "page": "extractPCMBLOSUM", "title": "Generalized BLOSUM and PAM Matrix-Derived Descriptors", "topics": [ "extractPCMBLOSUM" ] }, { "page": "extractPCMDescScales", "title": "Scales-Based Descriptors with 20+ classes of Molecular Descriptors", "topics": [ "extractPCMDescScales" ] }, { "page": "extractPCMFAScales", "title": "Generalized Scales-Based Descriptors derived by Factor Analysis", "topics": [ "extractPCMFAScales" ] }, { "page": "extractPCMMDSScales", "title": "Generalized Scales-Based Descriptors derived by Multidimensional Scaling", "topics": [ "extractPCMMDSScales" ] }, { "page": "extractPCMPropScales", "title": "Generalized AA-Properties Based Scales Descriptors", "topics": [ "extractPCMPropScales" ] }, { "page": "extractPCMScales", "title": "Generalized Scales-Based Descriptors derived by Principal Components Analysis", "topics": [ "extractPCMScales" ] }, { "page": "extractProtAAC", "title": "Amino Acid Composition Descriptor", "topics": [ "extractProtAAC" ] }, { "page": "extractProtAPAAC", "title": "Amphiphilic Pseudo Amino Acid Composition Descriptor", "topics": [ "extractProtAPAAC" ] }, { "page": "extractProtCTDC", "title": "CTD Descriptors - Composition", "topics": [ "extractProtCTDC" ] }, { "page": "extractProtCTDD", "title": "CTD Descriptors - Distribution", "topics": [ "extractProtCTDD" ] }, { "page": "extractProtCTDT", "title": "CTD Descriptors - Transition", "topics": [ "extractProtCTDT" ] }, { "page": "extractProtCTriad", "title": "Conjoint Triad Descriptor", "topics": [ "extractProtCTriad" ] }, { "page": "extractProtDC", "title": "Dipeptide Composition Descriptor", "topics": [ "extractProtDC" ] }, { "page": "extractProtGeary", "title": "Geary Autocorrelation Descriptor", "topics": [ "extractProtGeary" ] }, { "page": "extractProtMoran", "title": "Moran Autocorrelation Descriptor", "topics": [ "extractProtMoran" ] }, { "page": "extractProtMoreauBroto", "title": "Normalized Moreau-Broto Autocorrelation Descriptor", "topics": [ "extractProtMoreauBroto" ] }, { "page": "extractProtPAAC", "title": "Pseudo Amino Acid Composition Descriptor", "topics": [ "extractProtPAAC" ] }, { "page": "extractProtPSSM", "title": "Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence", "topics": [ "extractProtPSSM" ] }, { "page": "extractProtPSSMAcc", "title": "Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance", "topics": [ "extractProtPSSMAcc" ] }, { "page": "extractProtPSSMFeature", "title": "Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)", "topics": [ "extractProtPSSMFeature" ] }, { "page": "extractProtQSO", "title": "Quasi-Sequence-Order (QSO) Descriptor", "topics": [ "extractProtQSO" ] }, { "page": "extractProtSOCN", "title": "Sequence-Order-Coupling Numbers", "topics": [ "extractProtSOCN" ] }, { "page": "extractProtTC", "title": "Tripeptide Composition Descriptor", "topics": [ "extractProtTC" ] }, { "page": "getCPI", "title": "Generating Compound-Protein Interaction Descriptors", "topics": [ "getCPI" ] }, { "page": "getDrug", "title": "Retrieve Drug Molecules in MOL and SMILES Format from Databases", "topics": [ "getDrug" ] }, { "page": "getFASTAFromKEGG", "title": "Retrieve Protein Sequence in FASTA Format from the KEGG Database", "topics": [ "getFASTAFromKEGG" ] }, { "page": "getFASTAFromUniProt", "title": "Retrieve Protein Sequence in FASTA Format from the UniProt Database", "topics": [ "getFASTAFromUniProt" ] }, { "page": "getMolFromCAS", "title": "Retrieve Drug Molecules in InChI Format from the CAS Database", "topics": [ "getMolFromCAS" ] }, { "page": "getMolFromChEMBL", "title": "Retrieve Drug Molecules in MOL Format from the ChEMBL Database", "topics": [ "getMolFromChEMBL" ] }, { "page": "getMolFromDrugBank", "title": "Retrieve Drug Molecules in MOL Format from the DrugBank Database", "topics": [ "getMolFromDrugBank" ] }, { "page": "getMolFromKEGG", "title": "Retrieve Drug Molecules in MOL Format from the KEGG Database", "topics": [ "getMolFromKEGG" ] }, { "page": "getMolFromPubChem", "title": "Retrieve Drug Molecules in MOL Format from the PubChem Database", "topics": [ "getMolFromPubChem" ] }, { "page": "getPDBFromRCSBPDB", "title": "Retrieve Protein Sequence in PDB Format from RCSB PDB", "topics": [ "getPDBFromRCSBPDB" ] }, { "page": "getPPI", "title": "Generating Protein-Protein Interaction Descriptors", "topics": [ "getPPI" ] }, { "page": "getProt", "title": "Retrieve Protein Sequence in various Formats from Databases", "topics": [ "getProt" ] }, { "page": "getSeqFromKEGG", "title": "Retrieve Protein Sequence from the KEGG Database", "topics": [ "getSeqFromKEGG" ] }, { "page": "getSeqFromRCSBPDB", "title": "Retrieve Protein Sequence from RCSB PDB", "topics": [ "getSeqFromRCSBPDB" ] }, { "page": "getSeqFromUniProt", "title": "Retrieve Protein Sequence from the UniProt Database", "topics": [ "getSeqFromUniProt" ] }, { "page": "getSmiFromChEMBL", "title": "Retrieve Drug Molecules in SMILES Format from the ChEMBL Database", "topics": [ "getSmiFromChEMBL" ] }, { "page": "getSmiFromDrugBank", "title": "Retrieve Drug Molecules in SMILES Format from the DrugBank Database", "topics": [ "getSmiFromDrugBank" ] }, { "page": "getSmiFromKEGG", "title": "Retrieve Drug Molecules in SMILES Format from the KEGG Database", "topics": [ "getSmiFromKEGG" ] }, { "page": "getSmiFromPubChem", "title": "Retrieve Drug Molecules in SMILES Format from the PubChem Database", "topics": [ "getSmiFromPubChem" ] }, { "page": "OptAA3d", "title": "OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)", "topics": [ "OptAA3d" ] }, { "page": "readFASTA", "title": "Read Protein Sequences in FASTA Format", "topics": [ "readFASTA" ] }, { "page": "readMolFromSDF", "title": "Read Molecules from SDF Files and Return Parsed Java Molecular Object", "topics": [ "readMolFromSDF" ] }, { "page": "readMolFromSmi", "title": "Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List", 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