Uses of Class
biotransformer.biomolecule.Enzyme
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Packages that use Enzyme Package Description biotransformer.biosystems biotransformer.btransformers -
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Uses of Enzyme in biotransformer.biosystems
Methods in biotransformer.biosystems that return types with arguments of type Enzyme Modifier and Type Method Description 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 Constructor Description BioSystem(BioSystem.BioSystemName bsName, java.util.ArrayList<Enzyme> enzymes)
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Uses of Enzyme in biotransformer.btransformers
Fields in biotransformer.btransformers with type parameters of type Enzyme Modifier and Type Field Description 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 Modifier and Type Method Description 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 Modifier and Type Method Description 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)
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