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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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