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F
- FATTY_ACID - biotransformer.biomolecule.StructuralChemicalCategory.SCCategoryName
- FATTY_ACID - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- FATTY_ACID_DEGRADATION - biotransformer.transformation.MetabolicPathway.MPathwayName
- FATTY_ACID_ELONGATION - biotransformer.transformation.MetabolicPathway.MPathwayName
- FeatureGenerator - Class in biotransformer.utils
- FeatureGenerator() - Constructor for class biotransformer.utils.FeatureGenerator
- FileUtilities - Class in biotransformer.utils
- FileUtilities() - Constructor for class biotransformer.utils.FileUtilities
- filter() - Method in class biotransformer.utils.ErdbTask
- filterEnzymesAndReactions() - Method in class biotransformer.transformation.MetabolicPathway
- filterReactions(ArrayList<MetabolicReaction>) - Method in class biotransformer.transformation.MReactionsFilter
- filterReactions(ArrayList<MetabolicReaction>, LinkedHashMap<MRPatterns.ReactionName, MRPatterns.ReactionName[]>) - Static method in class biotransformer.transformation.MReactionsFilter
- filterReactions(LinkedHashMap<MRPatterns.ReactionName, MetabolicReaction>) - Method in class biotransformer.transformation.MReactionsFilter
- filterReactions(LinkedHashMap<MRPatterns.ReactionName, MetabolicReaction>, LinkedHashMap<MRPatterns.ReactionName, MRPatterns.ReactionName[]>) - Static method in class biotransformer.transformation.MReactionsFilter
- filterReactionsLSM(LinkedHashMap<String, MetabolicReaction>) - Method in class biotransformer.transformation.MReactionsFilter
- findAllAncestors(String, LinkedHashMap<String, ArrayList<String>>) - Method in class biotransformer.utils.BioTransformerDBBuilder
- findAllEnvMicroMetabolites(IAtomContainer, ArrayList<String>, double, int, boolean, MetaboliteFinder.FinderOption) - Method in class biotransformer.utils.MetaboliteFinder
- findAllEnvMicroMetabolites(IAtomContainer, ArrayList<String>, double, int, boolean, String, MetaboliteFinder.FinderOption) - Method in class biotransformer.utils.MetaboliteFinder
- findAllEnvMicroMetabolitesToCSV(IAtomContainer, ArrayList<String>, double, int, boolean, String, MetaboliteFinder.FinderOption) - Method in class biotransformer.utils.MetaboliteFinder
- findAllHumanMetabolites(IAtomContainer, ArrayList<String>, double, int, boolean, MetaboliteFinder.FinderOption) - Method in class biotransformer.utils.MetaboliteFinder
- findAllHumanMetabolites(IAtomContainer, ArrayList<String>, double, int, boolean, String, MetaboliteFinder.FinderOption) - Method in class biotransformer.utils.MetaboliteFinder
- findAllHumanMetabolitesToCSV(IAtomContainer, ArrayList<String>, double, int, boolean, String, MetaboliteFinder.FinderOption) - Method in class biotransformer.utils.MetaboliteFinder
- findAllMatchingStructures(String, IAtomContainer) - Method in class biotransformer.utils.ChemStructureExplorer
-
Given a molecule M and a SMARTS expression S, return all the substructures of M that match the expression S
- findAllOccurences(String, IAtomContainer) - Static method in class biotransformer.utils.ChemStructureExplorer
-
Given a molecule A and a SMARTS expression S, list all occurrences of S in A.
- findChemicalClass(IAtomContainer) - Static method in class biotransformer.utils.ChemicalClassFinder
- findPathway(IAtomContainer, IAtomContainer, LinkedHashMap<String, IAtomContainerSet>, LinkedHashMap<String, IAtomContainer>, boolean) - Method in class biotransformer.utils.MetaboliteFinder
- findSuperbioMetabolites(IAtomContainer, ArrayList<String>, double, boolean, MetaboliteFinder.FinderOption) - Method in class biotransformer.utils.MetaboliteFinder
- findSuperbioMetabolites(IAtomContainer, ArrayList<String>, double, boolean, String, MetaboliteFinder.FinderOption) - Method in class biotransformer.utils.MetaboliteFinder
- findSuperbioMetabolitesToCSV(IAtomContainer, ArrayList<String>, double, boolean, String, MetaboliteFinder.FinderOption) - Method in class biotransformer.utils.MetaboliteFinder
- FLAVAN_3_OL_C_RING_FISSION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- FLAVAN_3_OL_C_RING_FISSION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- FLAVANON_3_OL_C_RING_FISSION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVANONE_C_RING_FISSION - biotransformer.transformation.MRPatterns.ReactionName
-
Blaut, M.
- FLAVONE_3P_O_METHYLATION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOID_C_GLYCOSIDASE - biotransformer.biomolecule.Enzyme.EnzymeName
- FLAVONOID_C_RING_REDUCTION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3_O_DEGLUCOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3_O_GLUCOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3O_BETA_GLUCOSIDE_O_MANNOSYL_TRANSFER - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3O_BETA_GLUCOSIDE_O_MANNOSYL_TRANSFER_REVERSE - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3O_GLUCOSIDE_GLUCOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3O_GLUCOSIDE_L_DERHAMNOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3O_GLUCOSIDE_L_RHAMNOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3O_GLUCOSYL_12_GLUCOSIDE_DEGLUCOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3O_GLUCOSYL_12_GLUCOSYL_12_GLUCOSYL_DEGLUCOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVONOL_3O_GLUCOSYL_12_GLUCOSYL_GLUCOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- FLAVYLIUM_HYDRATION - biotransformer.transformation.MRPatterns.ReactionName
- FMO1 - biotransformer.biomolecule.Enzyme.EnzymeName
- FMO2 - biotransformer.biomolecule.Enzyme.EnzymeName
- FMO3 - biotransformer.biomolecule.Enzyme.EnzymeName
- FORMATION_OF_IMINIUM_IN_PYRROLIDINE_RING - biotransformer.transformation.MRPatterns.ReactionName
- FORMATION_OF_IMMINIUM_ION_FROM_DI_N_SUBSTITUTED_PIPERAZINE - biotransformer.transformation.MRPatterns.ReactionName
- FORMATION_OF_IMMINIUM_ION_FROM_N_SUBSTITUTED_PIPERIDINE - biotransformer.transformation.MRPatterns.ReactionName
- FORMATION_OF_PYRIDINIUM_FROM_4_SUBSTITUTED_PIPERIDINE - biotransformer.transformation.MRPatterns.ReactionName
- FORMULA - biotransformer.utils.MetaboliteFinder.FinderOption
- FURAN_23_EPOXIDATION - biotransformer.transformation.MRPatterns.ReactionName
- FURAN_23_EPOXIDATION_2 - biotransformer.transformation.MRPatterns.ReactionName
- FURAN_EPOXIDATION - biotransformer.transformation.MRPatterns.ReactionName
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