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## C

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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