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- GALACTOSYL_1_ALKYL_2_ACYL_SULFATION - biotransformer.transformation.MRPatterns.ReactionName
- GALACTOSYLCERAMIDE_3P_SULFATION - biotransformer.transformation.MRPatterns.ReactionName
- GALACTOSYLCERAMIDE_GALACTO_HYDROLISIS - biotransformer.transformation.MRPatterns.ReactionName
- GALLOYL_ESTER_HYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- GANGLIOSIDE_GD3_ACETYLGALACTOSAMINE_TRANSFER - biotransformer.transformation.MRPatterns.ReactionName
- GANGLIOSIDE_GM3_ACETYLGALACTOSAMINE_TRANSFER - biotransformer.transformation.MRPatterns.ReactionName
- generalStatistics - Static variable in class biotransformer.utils.Statistics
- generateAllFeatures(ArrayList<String>, ArrayList<ArrayList<String>>, String) - Method in class biotransformer.utils.FeatureGenerator
-
This function is used to generate all the features for the molecules contained in the input file
- generateAllMetabolitesFromAtomContainer(IAtomContainer, SMIRKSReaction, boolean) - Method in class biotransformer.btransformers.Biotransformer
- generateAllMetabolitesFromAtomContainer(IAtomContainer, MetabolicReaction, boolean) - Method in class biotransformer.btransformers.Biotransformer
- generateAllMetabolitesFromAtomContainerViaTransformationAtAllLocations(IAtomContainer, SMIRKSReaction, boolean) - Method in class biotransformer.btransformers.Biotransformer
- generateAtomicFeatures(IAtomContainer) - Method in class biotransformer.utils.FeatureGenerator
-
This function is used to generate the atomic features for a single molecule
- generateAtomicFeatures(IAtomContainerSet) - Method in class biotransformer.utils.FeatureGenerator
-
This function is used to generate the atomic features for the molecules contained in the input file.
- generateAtomType(IAtomContainer) - Method in class biotransformer.utils.FeatureGenerator
-
This function is used to generate the atomic type for a single molecule.
- generateBioTransformerDB() - Method in class biotransformer.utils.ErdbTask
- generateBTRailsCountFingerprint(IAtomContainer) - Static method in class biotransformer.fingerprint.ChemStructureFingerprinter
- generateClassyfireAtomFingeprint(IAtomContainer, LinkedHashMap<String, String>) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
- generateClassyfireCountFingerprintAsDouble(IAtomContainer, LinkedHashMap<String, String>) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
- generateClassyfireFingerprint(IAtomContainer) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
-
This function generates a unique fingerprint for a molecule.
- generateClassyfireFingerprintAsDouble(IAtomContainer, LinkedHashMap<String, String>) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
-
This function generates a unique fingerprint for a molecule.
- generateClassyfireRinFingerprintAsDouble(IAtomContainer) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
- generateCommandLine(Options, String[]) - Static method in class executable.BiotransformerExecutable
- generateCsv(HashMap<String, Double>, String) - Static method in class biotransformer.utils.ChemStructureSimilarity
- generateCustomBoMFingeprint(IAtomContainer, LinkedHashMap<String, String>, IChemObjectBuilder) - Method in class biotransformer.utils.ChemSearcher
- generateDEREP_NPFingerprint(String) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
- generateDEREP_NPFingerprint(IAtomContainer, boolean) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
- generateExtendedMolecularFeatures(IAtomContainer) - Method in class biotransformer.utils.FeatureGenerator
-
This function generates molecular features for a single molecule
- generateIsomericSmiles(IAtomContainer) - Static method in class biotransformer.utils.ChemStructureExplorer
- generateMolecularFeatures(IAtomContainer) - Method in class biotransformer.utils.FeatureGenerator
-
This function generates molecular features for a single molecule
- generateMolecularFeatures(IAtomContainerSet, String) - Method in class biotransformer.utils.FeatureGenerator
-
This function is used to generate the molecular features for the molecules contained in the input file.
- generatePath(IAtomContainer, int) - Method in class biotransformer.utils.FeatureGenerator
-
This function is used to generate the environmental features for a single molecule.
- generateReactantsSetFromTSV() - Method in class biotransformer.utils.ErdbTask
- generateStatistics() - Method in class biotransformer.utils.Statistics
- getBioSystemName() - Method in class biotransformer.btransformers.Biotransformer
- getBioSystemName() - Method in class biotransformer.transformation.Biotransformation
- getBitValues() - Method in class biotransformer.fingerprint.SFingerprint
- getBitValuesDouble() - Method in class biotransformer.fingerprint.SFingerprint
- getBTRMID() - Method in class biotransformer.transformation.MetabolicReaction
- getCDKAtomContainerSet() - Static method in class biotransformer.utils.Utilities
- getComonName() - Method in class biotransformer.transformation.MetabolicReaction
- getCustomAtomFingerprintPatterns() - Static method in class biotransformer.utils.ChemSearcher
- getCustomBoMFingerprintPatterns() - Static method in class biotransformer.utils.ChemSearcher
- getDEREP_NPFingerprintPatterns() - Static method in class biotransformer.fingerprint.ChemStructureFingerprinter
- getEnzymeHash() - Method in class biotransformer.biosystems.BioSystem
- getEnzymeNames() - Method in class biotransformer.transformation.Biotransformation
- getEnzymesList() - Method in class biotransformer.biosystems.BioSystem
- geterateSerialAtomfingerprintToArraylist(File, LinkedHashMap<String, String>) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
- getfeatureMap() - Method in class biotransformer.fingerprint.SFingerprint
- getFingerprintPatterns() - Static method in class biotransformer.fingerprint.ChemStructureFingerprinter
- getInChIGenFactory() - Method in class biotransformer.utils.HumanSuperBioTransformer
- getInstance() - Static method in class biotransformer.utils.CompoundDictionary
- getMajorIsotopeMass(IAtomContainer) - Static method in class biotransformer.utils.ChemStructureExplorer
- getMatchingAtoms(IAtomContainer, SMARTSQueryTool) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
- getMetPathwaysHash() - Method in class biotransformer.biosystems.BioSystem
- getMiniFingerprintPatterns() - Static method in class biotransformer.fingerprint.ChemStructureFingerprinter
- getMolecularFormula(IAtomContainer) - Static method in class biotransformer.utils.ChemStructureExplorer
- getName() - Method in class biotransformer.biomolecule.Enzyme
- getNegativeReactantsSMARTS() - Method in class biotransformer.transformation.MetabolicReaction
- getOnBits() - Method in class biotransformer.fingerprint.SFingerprint
- getOnFeatures(LinkedHashMap<String, String>) - Method in class biotransformer.fingerprint.SFingerprint
- getPhaseIIfingerpint() - Static method in class biotransformer.fingerprint.ChemStructureFingerprinter
- getPrimaryUniprotId() - Method in class biotransformer.biomolecule.Enzyme
- getProducts() - Method in class biotransformer.transformation.Biotransformation
- getReactantSMARTS() - Method in class biotransformer.transformation.MetabolicReaction
- getReactionEquation() - Method in class biotransformer.transformation.MetabolicReaction
- getReactionName() - Method in class biotransformer.transformation.MetabolicReaction
- getReactionSet() - Method in class biotransformer.biomolecule.Enzyme
- getReactionsHash() - Method in class biotransformer.biosystems.BioSystem
- getReactionsList() - Method in class biotransformer.btransformers.Biotransformer
- getReactionsList() - Method in class biotransformer.btransformers.HGutBTransformer
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returns a linked hash map with the reactions associated with the human gut, in addition to standardization reactions.
- getReactionSMIRKS() - Method in class biotransformer.transformation.MetabolicReaction
- getReactionsNames() - Method in class biotransformer.biomolecule.Enzyme
- getReactionsORatios() - Method in class biotransformer.biosystems.BioSystem
- getReactionType() - Method in class biotransformer.transformation.Biotransformation
- getRINAtomFingerprintPatterns() - Static method in class biotransformer.fingerprint.ChemStructureFingerprinter
- getRINFingerprintPatterns() - Static method in class biotransformer.fingerprint.ChemStructureFingerprinter
- getScore() - Method in class biotransformer.transformation.Biotransformation
- getSmarts() - Static method in class biotransformer.utils.ChemStructureSimilarity
- getSmiParser() - Method in class biotransformer.btransformers.Biotransformer
- getSmirksManager() - Method in class biotransformer.biosystems.BioSystem
- getSmirksReaction() - Method in class biotransformer.transformation.MetabolicReaction
- getSubstrates() - Method in class biotransformer.transformation.Biotransformation
- getSynonymsObjectViaInChIKey(String) - Static method in class biotransformer.utils.ChemdbRest
- getTestFingerprintPatterns() - Static method in class biotransformer.fingerprint.ChemStructureFingerprinter
- getUniprotIds() - Method in class biotransformer.biomolecule.Enzyme
- GLUCOSYLCERAMIDE_BETA_1_4_GALACTOSYL_TRANSFER - biotransformer.transformation.MRPatterns.ReactionName
- GLUCOSYLCERAMIDE_GLUCO_HYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- GLUCURONIDATION_OF_ALICYCLIC_SECONDARY_AMINE - biotransformer.transformation.MRPatterns.ReactionName
- GLUCURONIDATION_OF_ALIPHATIC_TERTIARY_AMINE - biotransformer.transformation.MRPatterns.ReactionName
- GLUCURONIDATION_OF_AMINE_OXIDE - biotransformer.transformation.MRPatterns.ReactionName
- GLUCURONIDATION_OF_PRIM_SEC_ALIPH_AND_BENZYLIC_ALCOHOLS - biotransformer.transformation.MRPatterns.ReactionName
- GLUCURONIDATION_OF_PRIMARY_AROMATIC_AMINE - biotransformer.transformation.MRPatterns.ReactionName
- GLUCURONIDATION_OF_SEC_DIARYL_OR_ALKYLARYLAMINE - biotransformer.transformation.MRPatterns.ReactionName
- GLUTAMATION_OF_ALIPHATIC_ACID - biotransformer.transformation.MRPatterns.ReactionName
- GLUTAMATION_OF_BENZYLIC_ACID - biotransformer.transformation.MRPatterns.ReactionName
- GLUTATHIONE_CONJUGATE - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- GLYCEROL_3_PHOSPHATE_INOSITOL - biotransformer.biomolecule.StructuralChemicalCategory.SCCategoryName
- GLYCEROL_3_PHOSPHATE_INOSITOL - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- GLYCEROLIPID - biotransformer.biomolecule.StructuralChemicalCategory.SCCategoryName
- GLYCEROLIPID - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- GLYCEROLIPID_METABOLISM - biotransformer.transformation.MetabolicPathway.MPathwayName
- GLYCERONE_PHOSPHATE_O_ACYLATION - biotransformer.transformation.MRPatterns.ReactionName
- GLYCEROPHOSPHODIESTER_HYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- GLYCEROPHOSPHOLIPID - biotransformer.biomolecule.StructuralChemicalCategory.SCCategoryName
- GLYCEROPHOSPHOLIPID - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- GLYCEROPHOSPHOLIPID_METABOLISM - biotransformer.transformation.MetabolicPathway.MPathwayName
- GLYCINATED_C23_BILE_ACID_DECONJUGATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- GLYCINATED_C24_BILE_ACID_DECONJUGATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- GLYCINATED_COMPOUND - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- GLYCINATION_OF_ALIPHATIC_ACID - biotransformer.transformation.MRPatterns.ReactionName
- GLYCINATION_OF_ARYL_ACID - biotransformer.transformation.MRPatterns.ReactionName
- GLYCOSIDE_HYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- GLYCOSYLATED_COMPOUND - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- GLYCOSYLCERAMIDE_GLYCOSYL_HYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- GLYCOSYLPHOSPHATIDYLINOSITOL_HYDROLYSIS_TO_PHOSPHATIDATE - biotransformer.transformation.MRPatterns.ReactionName
- GM2_GANGLIOSIDE_GALACTOSYL_TRANSFER - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_4_HYDROXYAZAPHOSPHORINE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ACYL_CHLORIDE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ALKYLARYL_PHOSPHATE_OR_PHOSPHOROTHIOATE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ALPHA_BETA_UNSATURATED_CARBONYL_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ALPHA_BETA_UNSATURATED_CARBONYL_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ARENE_EPOXIDE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ARYL_HALIDE_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ARYL_HALIDE_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ARYL_HALIDE_PATTERN3 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_CARBOXIMIDIC_ACID - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_EPOXIDE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_EWG_SUBSTITUTED_BENZENE_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_EWG_SUBSTITUTED_BENZENE_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_HALO_S_TRIAZINE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ISOCYANATE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ISOTHIOCYANATE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_NITRILE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ORGANODISULFIDE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ORGANOHALIDE_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_ORGANOHALIDE_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_QUINONE_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_QUINONE_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_SULFATE - biotransformer.transformation.MRPatterns.ReactionName
- GSH_CONJUGATION_OF_SULFHYDRYL - biotransformer.transformation.MRPatterns.ReactionName
- GUTMICRO - biotransformer.biosystems.BioSystem.BioSystemName
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