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## G

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
  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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