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- P_HYDROXIANILINE_OXIDATION - biotransformer.transformation.MRPatterns.ReactionName
- P_HYDROXYLATION_OF_ANILIDES - biotransformer.transformation.MRPatterns.ReactionName
- P_HYDROXYLATION_OF_MONOSUBSTITUTED_BENZENE - biotransformer.transformation.MRPatterns.ReactionName
- P_HYDROXYLATION_OF_PHENOLS - biotransformer.transformation.MRPatterns.ReactionName
- P_METHYL_HYDROXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- parseSdf(String) - Static method in class biotransformer.utils.FileUtilities
- parseSdfAndAddTitles(String, InChIGeneratorFactory) - Static method in class biotransformer.utils.FileUtilities
- partitionSetForPhaseIIMetabolism(IAtomContainerSet) - Method in class biotransformer.utils.HumanSuperBioTransformer
- PEPTIDE_ALPHA_N_ACETYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PEPTIDOAMIDOGLYCOLATE_PEPTIDYLAMIDE_LIGATION - biotransformer.transformation.MRPatterns.ReactionName
- PEPTIDYLAMIDOGLYCOLATE_PEPTIDYLAMIDE_LIGATION - biotransformer.transformation.MRPatterns.ReactionName
- Phase2BTransformer - Class in biotransformer.btransformers
- Phase2BTransformer(BioSystem.BioSystemName) - Constructor for class biotransformer.btransformers.Phase2BTransformer
- PHENOL_O_DEGLYCOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHENOL_O_GLUCURONIDATION - biotransformer.transformation.MRPatterns.ReactionName
- PHENOL_O_SULFONATION - biotransformer.transformation.MRPatterns.ReactionName
- PHENOLIC_ACID_DECARBOXYLASE - biotransformer.biomolecule.Enzyme.EnzymeName
- PHENOLIC_ACID_DECARBOXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHENOLIC_P_DEHYDROXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHENOLIC_STEROID_SULFONATION - biotransformer.transformation.MRPatterns.ReactionName
- PHENYLACETATE_ESTER_HYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- PHENYLVALEROLACTONE_FORMATION - biotransformer.transformation.MRPatterns.ReactionName
- PHENYLVALEROLACTONE_TO_PHENYLVALERIC_ACID - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATE_MONOESTER_DEPHOSPHORYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDATE_2_ACYLHYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYL_N_DIMETHYLETHANOLAMINE_N_METHYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYL_N_MONOMETHYLETHANOLAMINE_N_METHYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLCHOLINE_1_ACYLHYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLCHOLINE_2_ACYLHYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLCHOLINE_CEREBROSTEROL_O_ACYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLCHOLINE_CHOLESTEROL_O_ACYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLCHOLINE_PHOSPHATIDOHYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLCHOLINE_SITOSTEROL_O_ACYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLCHOLINE_STEROL_O_ACYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLETHANOLAMINE_2_ACYLHYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLETHANOLAMINE_N_METHYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLGLYCEROPHOSPHATE_DEPHOSPHORYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLINOSITOL_3_PHOSPHATE_DEPHOSPHORYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLINOSITOL_34_BISPHOSPHATE_DEPHOSPHORYLATION_4 - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLINOSITOL_345_TRISPHOSPHATE_DEPHOSPHORYLATION_3 - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLINOSITOL_345_TRISPHOSPHATE_DEPHOSPHORYLATION_5 - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLINOSITOL_35_BISPHOSPHATE_DEPHOSPHORYLATION_3 - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLINOSITOL_45_BISPHOSPHATE_CLEAVAGE - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLINOSITOL_45_BISPHOSPHATE_DEPHOSPHORYLATION_4 - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLINOSITOL_45_BISPHOSPHATE_DEPHOSPHORYLATION_5 - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLINOSITOL_N_ACETYLGLUCOSAMINYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLSERINE_DECARBOXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLSERINE_SYNTHESIS_FROM_PHOSPHATIDYLCHOLINE - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHATIDYLSERINE_SYNTHESIS_FROM_PHOSPHATIDYLETHANOLAMINE - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHINE_OXIDATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHOCHOLINE_TRANSFER_TO_12_DIACYLGLYCEROL - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHONIC_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHONIUM_YLIDE_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHORIC_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- PHOSPHORIC_STANDARDIZATION_2 - biotransformer.transformation.MRPatterns.ReactionName
- PLASMALOGEN_SYNTHESIS_REVERSE - biotransformer.transformation.MRPatterns.ReactionName
- PLASMENYLCHOLINE_2_ACYLHYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- PLASMENYLETHANOLAMINE_2_ACYLHYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- predictAllHumanBiotransformationChain(IAtomContainer, int, double) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictAllHumanBiotransformationChain(IAtomContainerSet, int, double) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictAllHumanBiotransformationChainAndSaveToCSV(IAtomContainer, int, double, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictAllHumanBiotransformationChainAndSaveToCSV(IAtomContainerSet, int, double, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictAllHumanBiotransformationChainAndSaveToSDF(IAtomContainer, int, double, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictAllHumanBiotransformationChainAndSaveToSDF(IAtomContainerSet, int, double, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictCyp450BiotransformationChain(IAtomContainer, boolean, boolean, int, double) - Method in class biotransformer.btransformers.Cyp450BTransformer
- predictCyp450BiotransformationChain(IAtomContainerSet, boolean, boolean, int, double) - Method in class biotransformer.btransformers.Cyp450BTransformer
- predictCyp450Biotransformations(String, boolean, boolean, double) - Method in class biotransformer.btransformers.Cyp450BTransformer
- predictCyp450Biotransformations(IAtomContainer, boolean, boolean, double) - Method in class biotransformer.btransformers.Cyp450BTransformer
- predictCyp450Biotransformations(IAtomContainerSet, boolean, boolean, double) - Method in class biotransformer.btransformers.Cyp450BTransformer
- predictCyp450BiotransformationsForSpecificEnzymes(IAtomContainer, ArrayList<Enzyme.EnzymeName>, boolean, boolean, double) - Method in class biotransformer.btransformers.Cyp450BTransformer
- predictMetabolismAllHumanFromSDFAndSavetoSDF(String, String, double, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictMetabolismAllHumanFromSDFAndSavetoSDF(String, String, int, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictMetabolismAllHumanFromSDFAndSavetoSDF(String, String, int, double, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictMetabolismAllHumanFromSDFAndSavetoSingleSDF(String, String, int, double, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- predictMetabolismAllHumanFromSDFtoSDF(String, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- preprocessContainer(IAtomContainer) - Static method in class biotransformer.utils.ChemStructureManipulator
-
This function applies some preprocessing operations, such as setting the flag of atoms from aromatic rings to "ISAROMATIC", and kelulizing molecules.
- PRIMARY_AMINE_HYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- PRIMARY_AMINE_HYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- PRIMARY_AMINE_N_SULFONATION - biotransformer.transformation.MRPatterns.ReactionName
- PRIMARY_ARYLAMIDE_N_HYDROXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- PRIMARY_BILE_ACID - biotransformer.biomolecule.StructuralChemicalCategory.SCCategoryName
- PRIMARY_BILE_ACID_BIOSYNTHESIS - biotransformer.transformation.MetabolicPathway.MPathwayName
- print(ArrayList<String>) - Static method in class biotransformer.utils.Utilities
- printStatistics() - Method in class biotransformer.btransformers.Cyp450BTransformer
- printStatistics() - Method in class biotransformer.btransformers.ECBasedBTransformer
- printStatistics() - Method in class biotransformer.btransformers.EnvMicroBTransformer
- printStatistics() - Method in class biotransformer.btransformers.HGutBTransformer
- printStatistics() - Method in class biotransformer.btransformers.Phase2BTransformer
- pubChemCompoundURL - Static variable in class biotransformer.utils.ChemdbRest
- PYRIDINE_GLUCURONIDATION - biotransformer.transformation.MRPatterns.ReactionName
- PYRIDINE_N_OXIDATION - biotransformer.transformation.MRPatterns.ReactionName
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