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## P

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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