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- C23_BILE_ACID - biotransformer.biomolecule.StructuralChemicalCategory.SCCategoryName
- C23_BILE_ACID - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- C23_BILE_ACID_7ALPHA_DEHYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- C23_BILE_ACID_COA_ESTERIFICATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- C23_BILE_ACID_COA_GLYCINATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- C23_BILE_ACID_COA_TAURINATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- C24_BILE_ACID - biotransformer.biomolecule.StructuralChemicalCategory.SCCategoryName
- C24_BILE_ACID - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- C24_BILE_ACID_7ALPHA_DEHYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- C24_BILE_ACID_C24_COOH_GLUCURONIDATION - biotransformer.transformation.MRPatterns.ReactionName
- C24_BILE_ACID_COA_ESTERIFICATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- C24_BILE_ACID_COA_GLYCINATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- C24_BILE_ACID_COA_TAURINATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- C24_BILE_ACID_ETHYLATION - biotransformer.transformation.MRPatterns.ReactionName
- calculateTanimoto(IAtomContainer, IAtomContainer, LinkedHashMap<String, String>) - Static method in class biotransformer.utils.ChemStructureSimilarity
- calculateTanimotoWithCustomSmarts(IAtomContainer, IAtomContainer, String[]) - Static method in class biotransformer.utils.ChemStructureSimilarity
- calculateTanimotoWithCustomSmartsAndCounts(IAtomContainer, IAtomContainer, String[]) - Static method in class biotransformer.utils.ChemStructureSimilarity
- calculateTanimotoWithMACCS(IAtomContainer, IAtomContainer) - Static method in class biotransformer.utils.ChemStructureSimilarity
- CARBAMATE_N_GLUCURONIDATION - biotransformer.transformation.MRPatterns.ReactionName
- CARBAMATE_SULFONATION - biotransformer.transformation.MRPatterns.ReactionName
- CARBAMIDIC_ACID_TO_UREA_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- CARBAMIDOTHIOIC_ACID_TO_THIOUREA_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- CARBONYL_REDUCTION - biotransformer.transformation.MRPatterns.ReactionName
- CARBOXAMIDE_STANDARDIZATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- CARBOXAMIDE_STANDARDIZATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- CARBOXYLIC_ACID_ANION_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- CARDIOLIPIN_DEACYLATION - biotransformer.transformation.MRPatterns.ReactionName
- CARDIOLIPIN_SYNTHESIS - biotransformer.transformation.MRPatterns.ReactionName
- CATECHOL_DEHYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- CATECHOL_DEHYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- CATECHOL_O_METHYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- CATECHOL_O_METHYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- CATECHOL_O_METHYLATION_PATTERN3 - biotransformer.transformation.MRPatterns.ReactionName
- CERAMIDE_GLUCOSYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- CERAMIDE_GLUCOSYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- CERAMIDE_GLUCOSYLATION_PATTERN3 - biotransformer.transformation.MRPatterns.ReactionName
- CERAMIDE_PHOSPHORYLATION - biotransformer.transformation.MRPatterns.ReactionName
- CEREBROSIDE_3_SULFATE_SULFOHYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- CHALCONE_DIHYDROGENATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- CHALCONE_DIHYDROGENATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- checkConnectivity(IAtomContainer) - Static method in class biotransformer.utils.ChemStructureExplorer
-
This functions looks at a molecule and returns each of its components (moieties) as separate molecules.
- ChemdbRest - Class in biotransformer.utils
- ChemdbRest() - Constructor for class biotransformer.utils.ChemdbRest
- chemicalClassDefinitions - Static variable in class biotransformer.utils.ChemicalClassFinder
- ChemicalClassFinder - Class in biotransformer.utils
- ChemicalClassFinder() - Constructor for class biotransformer.utils.ChemicalClassFinder
- ChemicalClassFinder.ChemicalClassName - Enum in biotransformer.utils
- ChemSearcher - Class in biotransformer.utils
- ChemSearcher() - Constructor for class biotransformer.utils.ChemSearcher
- ChemStructureExplorer - Class in biotransformer.utils
- ChemStructureExplorer() - Constructor for class biotransformer.utils.ChemStructureExplorer
- ChemStructureFingerprinter - Class in biotransformer.fingerprint
- ChemStructureFingerprinter() - Constructor for class biotransformer.fingerprint.ChemStructureFingerprinter
- ChemStructureManipulator - Class in biotransformer.utils
- ChemStructureManipulator() - Constructor for class biotransformer.utils.ChemStructureManipulator
- ChemStructureSimilarity - Class in biotransformer.utils
- ChemStructureSimilarity() - Constructor for class biotransformer.utils.ChemStructureSimilarity
- CHOLINE_LYSIS_TO_TRIMETHYLAMINE - biotransformer.transformation.MRPatterns.ReactionName
- CLEAVAGE_OF_THIOCARBAMATE - biotransformer.transformation.MRPatterns.ReactionName
- CMP_N_ACYLNEURAMINATE_HYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- COENZYME_A_DERIVATIVE - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- COENZYME_A_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- commonName - Variable in class biotransformer.transformation.MetabolicReaction
- CompoundDictionary - Class in biotransformer.utils
- compoundMatchesClassSmartsDefinitions(IAtomContainer, ChemicalClassFinder.ChemicalClassName) - Static method in class biotransformer.utils.ChemicalClassFinder
- compoundMatchesReactionConstraints(MetabolicReaction, IAtomContainer) - Static method in class biotransformer.utils.ChemStructureExplorer
-
Given a molecule A and a MetabolicReaction M, find whether A matches all the structural constraints imposed by M
- compoundsHasToleratedMass(IAtomContainer, ArrayList<Double>, double) - Method in class biotransformer.utils.MetaboliteFinder
- computePhysicoChemicalProperties(IAtomContainer) - Static method in class biotransformer.utils.ChemStructureExplorer
- containsBiotransformation(ArrayList<Biotransformation>, Biotransformation) - Static method in class biotransformer.utils.Utilities
- containsCarbon(IAtomContainer) - Static method in class biotransformer.utils.ChemStructureExplorer
- CORTICOSTEROID_21_DEHYDROXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- countUniqueCompounds(String) - Static method in class biotransformer.utils.FileUtilities
- createAtomContainerFromSmiles(String, boolean) - Static method in class biotransformer.utils.ChemStructureExplorer
- createAtomContainerFromSmilesWithProperties(String, boolean) - Static method in class biotransformer.utils.ChemStructureExplorer
- createEmptyAtomContainerSet() - Static method in class biotransformer.utils.Utilities
- CURCUMINOID - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- current - Static variable in class biotransformer.version.Version
- CYCLOGUANIDE_FORMATION - biotransformer.transformation.MRPatterns.ReactionName
- CYP_NADH_TERTIARY_AMINE_C_HYDROXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- CYP1A1 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP1A2 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP1B1 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2A13 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2A6 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2B1 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2B6 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2C18 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2C19 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2C8 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2C9 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2D4 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2D6 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2E1 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP2F1 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP3A4 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP3A5 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP3A7 - biotransformer.biomolecule.Enzyme.EnzymeName
- Cyp450BTransformer - Class in biotransformer.btransformers
- Cyp450BTransformer(BioSystem.BioSystemName) - Constructor for class biotransformer.btransformers.Cyp450BTransformer
- CYP4A11 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYP4B1 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYPB5_CYPBR5 - biotransformer.biomolecule.Enzyme.EnzymeName
- CYTIDINE_TRANSFER_TO_N_ACYLNEURAMINATE - biotransformer.transformation.MRPatterns.ReactionName
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