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## S

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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