## Uses of Class
biotransformer.biomolecule.Enzyme

Packages that use Enzyme
biotransformer.biosystems
biotransformer.btransformers

### Uses of Enzyme in biotransformer.biosystems

Methods in biotransformer.biosystems that return types with arguments of type Enzyme
`java.util.LinkedHashMap<Enzyme.EnzymeName,​Enzyme>` BioSystem.`getEnzymeHash()`
`java.util.ArrayList<Enzyme>` BioSystem.`getEnzymesList()`
`java.util.LinkedHashMap<MetabolicPathway.MPathwayName,​java.util.ArrayList<Enzyme>>` BioSystem.`getMetPathwaysHash()`

Constructor parameters in biotransformer.biosystems with type arguments of type Enzyme
`BioSystem​(BioSystem.BioSystemName bsName, java.util.ArrayList<Enzyme> enzymes)`

### Uses of Enzyme in biotransformer.btransformers

Fields in biotransformer.btransformers with type parameters of type Enzyme
`java.util.LinkedHashMap<java.lang.String,​java.util.ArrayList<Enzyme>>` Biotransformer.`enzymesByreactionGroups`
`java.util.ArrayList<Enzyme>` Biotransformer.`enzymesList`

Methods in biotransformer.btransformers with parameters of type Enzyme
`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)`

Method parameters in biotransformer.btransformers with type arguments of type Enzyme
`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)`