## Uses of Class
biotransformer.transformation.Biotransformation

Packages that use Biotransformation
biotransformer.btransformers
biotransformer.transformation
biotransformer.utils

### Uses of Biotransformation in biotransformer.btransformers

Methods in biotransformer.btransformers that return types with arguments of type Biotransformation
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedConjuationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedConjuationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedConjugations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedDeconjuations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nrOfSteps)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedDeconjuationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedDeconjuationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedDeconjugations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedTransformations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedTransformations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedTransformationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`applyEcBasedTransformationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` EnvMicroBTransformer.`applyEnvMicrobialTransformations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)`
`java.util.ArrayList<Biotransformation>` EnvMicroBTransformer.`applyEnvMicrobialTransformations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` EnvMicroBTransformer.`applyEnvMicrobialTransformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` EnvMicroBTransformer.`applyEnvMicrobialTransformationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` EnvMicroBTransformer.`applyEnvMicrobialTransformationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialConjugations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialConjugations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialConjugationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialConjugationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialDeconjugations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialDeconjugations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialDeconjugationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialDeconjugationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialMetabolismHydrolysisAndRedoxChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialMetabolismHydrolysisAndRedoxChain​(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialMetabolismHydrolysisAndRedoxStep​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialMetabolismHydrolysisAndRedoxStep​(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialRedoxChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialRedoxReactions​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialRedoxReactions​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`applyGutMicrobialRedoxReactionsChain​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyPathwaySpecificBiotransformationChain​(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyPathwaySpecificBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)` Predicts the metabolism of a compound for a specific pathway, and returns metabolites with a minimal given score threshold.
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyPathwaySpecificBiotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)` Predicts the metabolism of a compound for a specific pathway, and returns metabolites with a minimal given score threshold.
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyPathwaySpecificBiotransformationsChain​(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyPathwaySpecificBiotransformationsChain​(org.openscience.cdk.interfaces.IAtomContainerSet targets, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`applyPhase2Transformations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`applyPhase2Transformations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`applyPhase2Transformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean precheck, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`applyPhase2TransformationsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`applyPhase2TransformationsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`applyPhase2TransformationsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`applyReactionAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionAtOnceAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionAtOnceAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionAtOnceAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionAtOnceAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionsAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionsAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` EnvMicroBTransformer.`applyReactionsAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`applyReactionsAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`applyReactionsFromContainersAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`metabolizeWithEnzyme​(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz, boolean preprocess, boolean filter, double threshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`metabolizeWithEnzyme​(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme enzyme, boolean preprocess, boolean filter, double threshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`metabolizeWithEnzyme​(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme enzyme, boolean preprocess, boolean filter, int nrOfSteps, double threshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`metabolizeWithEnzyme​(org.openscience.cdk.interfaces.IAtomContainerSet substrates, Enzyme enzyme, boolean preprocess, boolean filter, double threshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`metabolizeWithEnzymes​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`metabolizeWithEnzymes​(org.openscience.cdk.interfaces.IAtomContainerSet substrates, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, double threshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`metabolizeWithEnzymesBreadthFirst​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`metabolizeWithEnzymesBreadthFirst​(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Biotransformer.`metabolizeWithEnzymesDephtFirst​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` Cyp450BTransformer.`predictCyp450BiotransformationChain​(org.openscience.cdk.interfaces.IAtomContainer substrate, boolean preprocess, boolean filter, int nrOfSteps, double threshold)`
`java.util.ArrayList<Biotransformation>` Cyp450BTransformer.`predictCyp450BiotransformationChain​(org.openscience.cdk.interfaces.IAtomContainerSet substrates, boolean preprocess, boolean filter, int nrOfSteps, double threshold)`
`java.util.ArrayList<Biotransformation>` Cyp450BTransformer.`predictCyp450Biotransformations​(java.lang.String sdfFileName, boolean preprocess, boolean filter, double threshold)`
`java.util.ArrayList<Biotransformation>` Cyp450BTransformer.`predictCyp450Biotransformations​(org.openscience.cdk.interfaces.IAtomContainer substrate, boolean preprocess, boolean filter, double threshold)`
`java.util.ArrayList<Biotransformation>` Cyp450BTransformer.`predictCyp450Biotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet substrates, boolean preprocess, boolean filter, double threshold)`
`java.util.ArrayList<Biotransformation>` Cyp450BTransformer.`predictCyp450BiotransformationsForSpecificEnzymes​(org.openscience.cdk.interfaces.IAtomContainer substrate, java.util.ArrayList<Enzyme.EnzymeName> enzymeNames, boolean preprocess, boolean filter, double threshold)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`selectBiotransformationWithValidProducts​(java.util.ArrayList<Biotransformation> biotransformations)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`simulateECBasedMetabolismChain​(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`simulateECBasedMetabolismChain​(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`simulateECBasedMetabolismStep​(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`simulateECBasedMetabolismStep​(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`simulateECBasedPhaseIMetabolismChain​(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`simulateECBasedPhaseIMetabolismChain​(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`simulateECBasedPhaseIMetabolismStep​(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` ECBasedBTransformer.`simulateECBasedPhaseIMetabolismStep​(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` EnvMicroBTransformer.`simulateEnvMicrobialDegradation​(org.openscience.cdk.interfaces.IAtomContainerSet containers, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`simulateGutMicrobialMetabolism​(java.lang.String targetsFileNameInSDF, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`simulateGutMicrobialMetabolism​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int numberOfSteps)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`simulateGutMicrobialMetabolism​(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int numberOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`simulateGutMicrobialMetabolism​(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, int numberOfSteps)`
`java.util.ArrayList<Biotransformation>` HGutBTransformer.`simulateGutMicrobialMetabolism​(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, int numberOfSteps, java.lang.Double scoreThreshold)`

Method parameters in biotransformer.btransformers with type arguments of type Biotransformation
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`extractProductsFromBiotransformations​(java.util.ArrayList<Biotransformation> biotransformations)`
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`extractProductsFromBiotransformationsWithTransformationData​(java.util.ArrayList<Biotransformation> biotransformations)`
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`extractProductsFromBiotransformationsWithTransformationData​(java.util.ArrayList<Biotransformation> biotransformations, boolean annotate)`
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`extractProductsFromBiotransformationsWithTransformationData​(java.util.ArrayList<Biotransformation> biotransformations, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> customReactionHash)`
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`extractProductsFromBiotransformationsWithTransformationData​(java.util.ArrayList<Biotransformation> biotransformations, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> customReactionHash, boolean annotate)`
`void` Biotransformer.`saveBioTransformationProductsToCSV​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName)`
`void` Biotransformer.`saveBioTransformationProductsToCSV​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate)`
`void` Biotransformer.`saveBioTransformationProductsToCSV​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> customReactionHash)`
`void` Biotransformer.`saveBioTransformationProductsToCSV​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> customReactionHash, boolean annotate)`
`void` Biotransformer.`saveBioTransformationProductsToSdf​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName)`
`void` Biotransformer.`saveBioTransformationProductsToSdf​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate)`
`void` Biotransformer.`saveBioTransformationProductsToSdf​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> customReactionHash)`
`void` Biotransformer.`saveBioTransformationProductsToSdf​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> customReactionHash, boolean annotate)`
`void` Biotransformer.`saveBioTransformationProductsToSDF​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> customReactionHash, boolean annotate)`
`java.util.ArrayList<Biotransformation>` Phase2BTransformer.`selectBiotransformationWithValidProducts​(java.util.ArrayList<Biotransformation> biotransformations)`

### Uses of Biotransformation in biotransformer.transformation

Methods in biotransformer.transformation with parameters of type Biotransformation
`boolean` Biotransformation.`equals​(Biotransformation biotransformation)`

### Uses of Biotransformation in biotransformer.utils

Methods in biotransformer.utils that return types with arguments of type Biotransformation
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`applyGutMicrobialMetabolismHydrolysisAndRedoxChain​(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`applyPathwaySpecificBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer molecule, MetabolicPathway.MPathwayName pathway, boolean preprocess, boolean filter, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`applyPhaseIITransformationsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet products, int nrOfSteps, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`predictAllHumanBiotransformationChain​(org.openscience.cdk.interfaces.IAtomContainer substrate, int nrOfSteps, double threshold)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`predictAllHumanBiotransformationChain​(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, double threshold)`
`static java.util.ArrayList<Biotransformation>` Utilities.`selectUniqueBiotransformations​(java.util.ArrayList<Biotransformation> biotransformations)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`simulateAllHumanMetabolism​(org.openscience.cdk.interfaces.IAtomContainerSet containers, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`simulateECBasedPhaseIMetabolismChain​(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`simulateGutMicrobialMetabolism​(org.openscience.cdk.interfaces.IAtomContainer molecule, int nrOfSteps, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`simulateHumanSuperbioMetabolism​(org.openscience.cdk.interfaces.IAtomContainer target)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`simulateHumanSuperbioMetabolism​(org.openscience.cdk.interfaces.IAtomContainer target, java.lang.Double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`simulateOneStepAllHuman​(org.openscience.cdk.interfaces.IAtomContainer target)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`simulateOneStepAllHuman​(org.openscience.cdk.interfaces.IAtomContainer target, double scoreThreshold)`
`java.util.ArrayList<Biotransformation>` HumanSuperBioTransformer.`simulateOneStepAllHuman​(org.openscience.cdk.interfaces.IAtomContainerSet targets, double scoreThreshold)`

Methods in biotransformer.utils with parameters of type Biotransformation
`static boolean` Utilities.`containsBiotransformation​(java.util.ArrayList<Biotransformation> biotransformations, Biotransformation bt)`

Method parameters in biotransformer.utils with type arguments of type Biotransformation
`static boolean` Utilities.`containsBiotransformation​(java.util.ArrayList<Biotransformation> biotransformations, Biotransformation bt)`
`org.openscience.cdk.interfaces.IAtomContainerSet` HumanSuperBioTransformer.`extractAtomContainer​(java.util.ArrayList<Biotransformation> biotransformations)`
`org.openscience.cdk.interfaces.IAtomContainerSet` HumanSuperBioTransformer.`extractAtomContainerWithTransformationData​(java.util.ArrayList<Biotransformation> biotransformations, boolean annotate)`
`void` HumanSuperBioTransformer.`saveBioTransformationProductsToCSV​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate)`
`void` HumanSuperBioTransformer.`saveBioTransformationProductsToSdf​(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate)`
`static java.util.ArrayList<Biotransformation>` Utilities.`selectUniqueBiotransformations​(java.util.ArrayList<Biotransformation> biotransformations)`