## Uses of Class
biotransformer.transformation.MetabolicReaction

Packages that use MetabolicReaction
biotransformer.biomolecule: This class implements the class of metabolic enzymes.
biotransformer.biosystems
biotransformer.btransformers
biotransformer.transformation
biotransformer.utils

### Uses of MetabolicReaction in biotransformer.biomolecule

Methods in biotransformer.biomolecule that return types with arguments of type MetabolicReaction
`java.util.ArrayList<MetabolicReaction>` Enzyme.`getReactionSet()`

Methods in biotransformer.biomolecule with parameters of type MetabolicReaction
`void` Enzyme.`addReaction​(MetabolicReaction reaction)`

Constructor parameters in biotransformer.biomolecule with type arguments of type MetabolicReaction
`Enzyme​(java.lang.String enzName, java.util.ArrayList<MetabolicReaction> reactionSet)`
`Enzyme​(java.lang.String enzName, java.util.ArrayList<MetabolicReaction> reactionSet, ambit2.smarts.SMIRKSManager smrkMan)`
`Enzyme​(java.lang.String enzName, java.util.ArrayList<MetabolicReaction> reactionSet, java.util.ArrayList<java.lang.String> cellLocations)`

### Uses of MetabolicReaction in biotransformer.biosystems

Methods in biotransformer.biosystems that return types with arguments of type MetabolicReaction
`java.util.LinkedHashMap<java.lang.String,​MetabolicReaction>` BioSystem.`getReactionsHash()`

### Uses of MetabolicReaction in biotransformer.btransformers

Fields in biotransformer.btransformers with type parameters of type MetabolicReaction
`java.util.LinkedHashMap<java.lang.String,​java.util.ArrayList<MetabolicReaction>>` Biotransformer.`reactionsByGroups`
`java.util.LinkedHashMap<java.lang.String,​MetabolicReaction>` Biotransformer.`reactionsHash`

Methods in biotransformer.btransformers that return types with arguments of type MetabolicReaction
`java.util.LinkedHashMap<java.lang.String,​java.util.ArrayList<MetabolicReaction>>` Biotransformer.`getReactionsList()`
`java.util.LinkedHashMap<java.lang.String,​java.util.ArrayList<MetabolicReaction>>` HGutBTransformer.`getReactionsList()` returns a linked hash map with the reactions associated with the human gut, in addition to standardization reactions.

Methods in biotransformer.btransformers with parameters of type MetabolicReaction
`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)`
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`generateAllMetabolitesFromAtomContainer​(org.openscience.cdk.interfaces.IAtomContainer molecule, MetabolicReaction mReaction, boolean preprocess)`

Method parameters in biotransformer.btransformers with type arguments of type MetabolicReaction
`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)`
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`applyReactionChain​(org.openscience.cdk.interfaces.IAtomContainer target, ambit2.smarts.SMIRKSManager smrkMan, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps)`
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`applyReactionChain​(org.openscience.cdk.interfaces.IAtomContainer target, ambit2.smarts.SMIRKSManager smrkMan, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)`
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`applyReactions​(org.openscience.cdk.interfaces.IAtomContainer target, ambit2.smarts.SMIRKSManager smrkMan, java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> reactions, boolean preprocess, boolean filter)`
`org.openscience.cdk.interfaces.IAtomContainerSet` Biotransformer.`applyReactions​(org.openscience.cdk.interfaces.IAtomContainer target, java.util.LinkedHashMap<java.lang.String,​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)`
`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, 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, 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)`

### Uses of MetabolicReaction in biotransformer.transformation

Fields in biotransformer.transformation with type parameters of type MetabolicReaction
`static java.util.ArrayList<MetabolicReaction>` MReactionSets.`standardizationReactions`

Methods in biotransformer.transformation that return types with arguments of type MetabolicReaction
`java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactions​(java.util.ArrayList<MetabolicReaction> reactions)`
`static java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactions​(java.util.ArrayList<MetabolicReaction> reactions, java.util.LinkedHashMap<MRPatterns.ReactionName,​MRPatterns.ReactionName[]> btph)`
`java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactions​(java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction> reactions)`
`static java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactions​(java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction> reactions, java.util.LinkedHashMap<MRPatterns.ReactionName,​MRPatterns.ReactionName[]> btph)`
`java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactionsLSM​(java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> reactions)`

Method parameters in biotransformer.transformation with type arguments of type MetabolicReaction
`java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactions​(java.util.ArrayList<MetabolicReaction> reactions)`
`static java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactions​(java.util.ArrayList<MetabolicReaction> reactions, java.util.LinkedHashMap<MRPatterns.ReactionName,​MRPatterns.ReactionName[]> btph)`
`java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactions​(java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction> reactions)`
`static java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactions​(java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction> reactions, java.util.LinkedHashMap<MRPatterns.ReactionName,​MRPatterns.ReactionName[]> btph)`
`java.util.LinkedHashMap<MRPatterns.ReactionName,​MetabolicReaction>` MReactionsFilter.`filterReactionsLSM​(java.util.LinkedHashMap<java.lang.String,​MetabolicReaction> reactions)`

### Uses of MetabolicReaction in biotransformer.utils

Methods in biotransformer.utils with parameters of type MetabolicReaction
`static boolean` ChemStructureExplorer.`compoundMatchesReactionConstraints​(MetabolicReaction reaction, org.openscience.cdk.interfaces.IAtomContainer molecule)` Given a molecule A and a MetabolicReaction M, find whether A matches all the structural constraints imposed by M