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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
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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