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- S_2_HYDROXYACYL_GLUTATHIONE_HYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- S_3_HYDROXYACYL_COA_DEHYDROGENATION - biotransformer.transformation.MRPatterns.ReactionName
-
EC-Based Reactions
- S_DEALKYLATION - biotransformer.transformation.MRPatterns.ReactionName
- S_DEALKYLATION_OF_ALKYLTHIOETHERS - biotransformer.transformation.MRPatterns.ReactionName
- S_DEMETHYLATION_OF_SULFUR_ADJACENT_TO_AROMATIC_RING - biotransformer.transformation.MRPatterns.ReactionName
- S_HYDROXYLATION_OF_ALKYLTHIOETHERS - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_ALIPHATIC_SULFHYDRYL_TO_SULFENIC_ACID - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_ALKYLARYLTHIOETHER_TO_SULFOXIDE - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_ARYL_OR_VINYL_SULFHYDRYL_TO_SULFENIC_ACID - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_DIALKYLTHIOETHER_TO_SULFOXIDE - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_DIARYLTHIOETHER_TO_SULFOXIDE - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_DITHIOCARBAMATE - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_ORGANOSULFUROUS_COMPOUNDS - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_SULFOXIDE_TO_SULFONE - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_THIOAMIDE - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_THIOCARBAMATE - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_THIOCARBAMIDE_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_THIOCARBAMIDE_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_THIOCARBAMIDE_PATTERN3 - biotransformer.transformation.MRPatterns.ReactionName
- S_OXIDATION_OF_THIOCARBAMIDE_PATTERN4 - biotransformer.transformation.MRPatterns.ReactionName
- SACCHARIDE - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- SATURATED_FATTY_ACID - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- saveAtomContainerSetToCSV(IAtomContainerSet, String) - Static method in class biotransformer.utils.FileUtilities
- saveAtomContainerSetToSDF(IAtomContainerSet, String) - Static method in class biotransformer.utils.FileUtilities
- saveAtomContainersToString(IAtomContainerSet) - Static method in class biotransformer.utils.FileUtilities
- saveAtomContainerToString(IAtomContainer) - Static method in class biotransformer.utils.FileUtilities
- saveBioTransformationProductsToCSV(ArrayList<Biotransformation>, String) - Method in class biotransformer.btransformers.Biotransformer
- saveBioTransformationProductsToCSV(ArrayList<Biotransformation>, String, boolean) - Method in class biotransformer.btransformers.Biotransformer
- saveBioTransformationProductsToCSV(ArrayList<Biotransformation>, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- saveBioTransformationProductsToCSV(ArrayList<Biotransformation>, String, LinkedHashMap<String, MetabolicReaction>) - Method in class biotransformer.btransformers.Biotransformer
- saveBioTransformationProductsToCSV(ArrayList<Biotransformation>, String, LinkedHashMap<String, MetabolicReaction>, boolean) - Method in class biotransformer.btransformers.Biotransformer
- saveBioTransformationProductsToSdf(ArrayList<Biotransformation>, String) - Method in class biotransformer.btransformers.Biotransformer
- saveBioTransformationProductsToSdf(ArrayList<Biotransformation>, String, boolean) - Method in class biotransformer.btransformers.Biotransformer
- saveBioTransformationProductsToSdf(ArrayList<Biotransformation>, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- saveBioTransformationProductsToSdf(ArrayList<Biotransformation>, String, LinkedHashMap<String, MetabolicReaction>) - Method in class biotransformer.btransformers.Biotransformer
- saveBioTransformationProductsToSdf(ArrayList<Biotransformation>, String, LinkedHashMap<String, MetabolicReaction>, boolean) - Method in class biotransformer.btransformers.Biotransformer
- saveBioTransformationProductsToSDF(ArrayList<Biotransformation>, String, LinkedHashMap<String, MetabolicReaction>, boolean) - Method in class biotransformer.btransformers.Biotransformer
- saveSerialAtomFingerprinterToCSV(File, LinkedHashMap<String, String>) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
- SECONDARY_AMINE_HYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- SECONDARY_AMINE_HYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- SECONDARY_AMINE_HYDROXYLATION_PATTERN3 - biotransformer.transformation.MRPatterns.ReactionName
- SECONDARY_AMINE_N_SULFONATION - biotransformer.transformation.MRPatterns.ReactionName
- SECONDARY_ARYLAMIDE_N_HYDROXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- SECONDARY_BILE_ACID - biotransformer.biomolecule.StructuralChemicalCategory.SCCategoryName
- SECONDARY_BILE_ACID_BIOSYNTHESIS - biotransformer.transformation.MetabolicPathway.MPathwayName
- SECONDARY_N_DEALKYLATION - biotransformer.transformation.MRPatterns.ReactionName
- selectBiotransformationWithValidProducts(ArrayList<Biotransformation>) - Method in class biotransformer.btransformers.Phase2BTransformer
- selectUniqueBiotransformations(ArrayList<Biotransformation>) - Static method in class biotransformer.utils.Utilities
- SELENITE_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- serial_fingerprinter_sdf(File) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
- serialAtomfingerprinterToSdf(File, LinkedHashMap<String, String>) - Method in class biotransformer.fingerprint.ChemStructureFingerprinter
-
This function creates a tsv file with the atom fingerprints
- SERINE_TRANSFER_TO_CDP_DIACYLGLYCEROL - biotransformer.transformation.MRPatterns.ReactionName
- setEnzymeNames(ArrayList<Enzyme.EnzymeName>) - Method in class biotransformer.transformation.Biotransformation
- setOfNetgativeReactantSMARTS - Static variable in class biotransformer.transformation.MRPatterns
- setOfReactantSMARTS - Static variable in class biotransformer.transformation.MRPatterns
- setOfSMIRKS - Static variable in class biotransformer.transformation.MRPatterns
- setprimaryUniprotId(String) - Method in class biotransformer.biomolecule.Enzyme
- setPriorityHash() - Method in class biotransformer.transformation.MReactionsFilter
- setReactionEquation(String) - Method in class biotransformer.transformation.MetabolicReaction
- setUniprotIds(ArrayList<String>) - Method in class biotransformer.biomolecule.Enzyme
- SFingerprint - Class in biotransformer.fingerprint
- SFingerprint(ArrayList<Double>, LinkedHashMap<String, String>) - Constructor for class biotransformer.fingerprint.SFingerprint
- SHORT_CHAIN_ACYL_COA_DEHYDROGENATION - biotransformer.transformation.MRPatterns.ReactionName
- SILICATE_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- simulateAllHumanMetabolism(IAtomContainerSet, double) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateAllHumanMetabolismAndSavetoCSV(IAtomContainer, String, double, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateAllHumanMetabolismAndSavetoSDF(IAtomContainer, String, double, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateAllHumanMetabolismAndSavetoSDF(IAtomContainerSet, String, double, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateCyp450MetabolismAndSaveToSDF(IAtomContainerSet, int, Double, String, boolean) - Method in class biotransformer.btransformers.Cyp450BTransformer
- simulateCyp450MetabolismAndSaveToSingleSDF(IAtomContainerSet, int, Double, String, boolean) - Method in class biotransformer.btransformers.Cyp450BTransformer
- simulateECBasedMetabolismAndSaveToSDF(String, int, Double, String, boolean) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateECBasedMetabolismAndSaveToSDF(IAtomContainerSet, int, Double, String, boolean) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateECBasedMetabolismChain(IAtomContainer, boolean, boolean, int, Double) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateECBasedMetabolismChain(IAtomContainerSet, boolean, boolean, int, Double) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateECBasedMetabolismStep(IAtomContainer, boolean, boolean, Double) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateECBasedMetabolismStep(IAtomContainerSet, boolean, boolean, Double) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateECBasedPhaseIMetabolismChain(IAtomContainer, boolean, boolean, int, Double) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateECBasedPhaseIMetabolismChain(IAtomContainerSet, boolean, boolean, int, Double) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateECBasedPhaseIMetabolismChain(IAtomContainerSet, boolean, boolean, int, Double) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateECBasedPhaseIMetabolismStep(IAtomContainer, boolean, boolean, Double) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateECBasedPhaseIMetabolismStep(IAtomContainerSet, boolean, boolean, Double) - Method in class biotransformer.btransformers.ECBasedBTransformer
- simulateEnvMicrobialDegradation(IAtomContainerSet, boolean, boolean, int, Double) - Method in class biotransformer.btransformers.EnvMicroBTransformer
- simulateEnvMicrobialDegradationAndSaveToCSV(IAtomContainer, boolean, boolean, int, Double, String, boolean) - Method in class biotransformer.btransformers.EnvMicroBTransformer
- simulateEnvMicrobialDegradationAndSaveToSDF(IAtomContainer, boolean, boolean, int, Double, String, boolean) - Method in class biotransformer.btransformers.EnvMicroBTransformer
- simulateEnvMicrobialDegradationAndSaveToSDF(IAtomContainerSet, boolean, boolean, int, Double, String, boolean) - Method in class biotransformer.btransformers.EnvMicroBTransformer
- simulateGutMicrobialMetabolism(String, boolean, boolean, int, Double) - Method in class biotransformer.btransformers.HGutBTransformer
- simulateGutMicrobialMetabolism(IAtomContainer, boolean, boolean, int) - Method in class biotransformer.btransformers.HGutBTransformer
- simulateGutMicrobialMetabolism(IAtomContainer, boolean, boolean, int, Double) - Method in class biotransformer.btransformers.HGutBTransformer
- simulateGutMicrobialMetabolism(IAtomContainer, int, double) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateGutMicrobialMetabolism(IAtomContainerSet, boolean, boolean, int) - Method in class biotransformer.btransformers.HGutBTransformer
- simulateGutMicrobialMetabolism(IAtomContainerSet, boolean, boolean, int, Double) - Method in class biotransformer.btransformers.HGutBTransformer
- simulateGutMicrobialMetabolismAndSave(String, boolean, boolean, int, Double, String) - Method in class biotransformer.btransformers.HGutBTransformer
- simulateGutMicrobialMetabolismAndSave(String, boolean, boolean, int, Double, String, boolean) - Method in class biotransformer.btransformers.HGutBTransformer
- simulateGutMicrobialMetabolismAndSaveToSDF(IAtomContainerSet, int, Double, String) - Method in class biotransformer.btransformers.HGutBTransformer
- simulateGutMicrobialMetabolismAndSaveToSDF(IAtomContainerSet, int, Double, String, boolean) - Method in class biotransformer.btransformers.HGutBTransformer
- simulateHumanSuperbioMetabolism(IAtomContainer) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateHumanSuperbioMetabolism(IAtomContainer, Double) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateHumanSuperbioMetabolismAndSaveToCSV(IAtomContainer, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateHumanSuperbioMetabolismAndSaveToSDF(IAtomContainer, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateHumanSuperbioMetabolismAndSaveToSDF(IAtomContainerSet, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateHumanSuperbioMetabolismFromSDF(String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateHumanSuperbioMetabolismFromSDF(String, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateHumanSuperbioMetabolismFromSDFtoSingleCSV(String, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateHumanSuperbioMetabolismFromSDFtoSingleSDF(String, String, boolean) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateOneStepAllHuman(IAtomContainer) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateOneStepAllHuman(IAtomContainer, double) - Method in class biotransformer.utils.HumanSuperBioTransformer
- simulateOneStepAllHuman(IAtomContainerSet, double) - Method in class biotransformer.utils.HumanSuperBioTransformer
- smiGen - Variable in class biotransformer.btransformers.Biotransformer
- smiGen - Static variable in class biotransformer.utils.ChemStructureExplorer
- smiGen - Variable in class biotransformer.utils.HumanSuperBioTransformer
- smiParser - Variable in class biotransformer.utils.HumanSuperBioTransformer
- SN_GLYCEROL_3_PHOSPHATE_TRANSFER_TO_CDP_DIACYLGLYCEROL - biotransformer.transformation.MRPatterns.ReactionName
- SPHINGANINE_C4_HYDROXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- SPHINGOLIPID - biotransformer.biomolecule.StructuralChemicalCategory.SCCategoryName
- SPHINGOLIPID - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- SPHINGOLIPID_10_DESATURATION - biotransformer.transformation.MRPatterns.ReactionName
- SPHINGOLIPID_4_DESATURATION - biotransformer.transformation.MRPatterns.ReactionName
- SPHINGOLIPID_8E_DESATURATION - biotransformer.transformation.MRPatterns.ReactionName
- SPHINGOLIPID_8Z_DESATURATION - biotransformer.transformation.MRPatterns.ReactionName
- SPHINGOLIPID_C9_METHYLATION - biotransformer.transformation.MRPatterns.ReactionName
- SPHINGOLIPID_METABOLISM - biotransformer.transformation.MetabolicPathway.MPathwayName
- SPHINGOMYELIN_PHOSPHOCHLINE_CLEAVAGE - biotransformer.transformation.MRPatterns.ReactionName
- SPHINGOSINE_N_ACYLATION_REVERSE - biotransformer.transformation.MRPatterns.ReactionName
- standardizationReactions - Static variable in class biotransformer.transformation.MReactionSets
- standardizeMoleculeWithCopy(IAtomContainer) - Static method in class biotransformer.utils.ChemStructureManipulator
- standardizeMoleculeWithCopy(IAtomContainer) - Method in class biotransformer.utils.HumanSuperBioTransformer
- standardizeMoleculeWithCopy(IAtomContainer, boolean) - Static method in class biotransformer.utils.ChemStructureManipulator
- Statistics - Class in biotransformer.utils
- Statistics() - Constructor for class biotransformer.utils.Statistics
- STEROID_3_SULFATE_HYDROLYSIS_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- STEROID_3_SULFATE_HYDROLYSIS_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROID_3_SULFONATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROID_DELTA_ISOMERIZATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_11_BETA_HYDROXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_12_OH_SULFATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_12_OH_SULFATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_14_ALPHA_DEMETHYLATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_16_HYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_16_HYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_17_ALPHA_HYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_17_ALPHA_HYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_2_HYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_2_HYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_21_HYDROXYLATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_3_OH_SULFATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_3BETA_DEGLUCOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_3BETA_GLUCOSYLATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_4_HYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_4_HYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_6_HYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_6_HYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_7_HYDROXYLATION_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_7_HYDROXYLATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_7_HYDROXYLATION_PATTERN3 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_7_OH_SULFATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_7_OH_SULFATION_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_C_17_ACYL_CLEAVAGE_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_C_17_ACYL_CLEAVAGE_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_C_17_ACYL_CLEAVAGE_PATTERN3 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_C_17_ACYL_CLEAVAGE_PATTERN4 - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_O_ACYLATION - biotransformer.transformation.MRPatterns.ReactionName
- STEROL_O_ACYLATION_REVERSE - biotransformer.transformation.MRPatterns.ReactionName
- STERYL_ESTER_ACYLHYDROLYSIS - biotransformer.transformation.MRPatterns.ReactionName
- STILBENOID - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- str - Static variable in class biotransformer.utils.FeatureGenerator
-
definition for all the adopted SYBYL atom types
- STRUCTURAL_REARRANGEMENT_OF_ANTHOCYANIDIN_1 - biotransformer.transformation.MRPatterns.ReactionName
- STRUCTURAL_REARRANGEMENT_OF_ANTHOCYANIDIN_2 - biotransformer.transformation.MRPatterns.ReactionName
- STRUCTURAL_REARRANGEMENT_OF_ANTHOCYANIDIN_3 - biotransformer.transformation.MRPatterns.ReactionName
- STRUCTURAL_REARRANGEMENT_OF_ANTHOCYANIDIN_4 - biotransformer.transformation.MRPatterns.ReactionName
- StructuralChemicalCategory - Class in biotransformer.biomolecule
- StructuralChemicalCategory() - Constructor for class biotransformer.biomolecule.StructuralChemicalCategory
- StructuralChemicalCategory.SCCategoryName - Enum in biotransformer.biomolecule
- SULFATE_ESTER - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- SULFATED_COMPOUND - biotransformer.utils.ChemicalClassFinder.ChemicalClassName
- SULFATION_OF_PHENOLIC_STEROID - biotransformer.transformation.MRPatterns.ReactionName
- SULFATION_OF_PRIMARY_ALCOHOL - biotransformer.transformation.MRPatterns.ReactionName
- SULFATION_OF_SECONDARY_ALCOHOL - biotransformer.transformation.MRPatterns.ReactionName
- SULFINE_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- SULFITE_REDUCTION - biotransformer.transformation.MRPatterns.ReactionName
- SULFONAMIDE_N_GLUCURONIDATION - biotransformer.transformation.MRPatterns.ReactionName
- SULFONATION_OF_ALIPHATIC_ALCOHOL - biotransformer.transformation.MRPatterns.ReactionName
- SULFONATION_OF_HYDROXYLAMINE - biotransformer.transformation.MRPatterns.ReactionName
- SULFONE_REDUCTION_TO_SULFOXIDE - biotransformer.transformation.MRPatterns.ReactionName
- SULFONE_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- SULFONIC_ACID_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- SULFONIUM_YLIDE_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- SULFOTRANSFERASE - biotransformer.biomolecule.Enzyme.EnzymeName
- SULFOXIDE_REDUCTION_TO_THIOETHER_PATTERN1 - biotransformer.transformation.MRPatterns.ReactionName
- SULFOXIDE_REDUCTION_TO_THIOETHER_PATTERN2 - biotransformer.transformation.MRPatterns.ReactionName
- SULFOXIDE_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
- SULFOXONIUM_YLIDE_STANDARDIZATION - biotransformer.transformation.MRPatterns.ReactionName
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