Package biotransformer.esaprediction
Class ESSpecificityPredictor
- java.lang.Object
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- biotransformer.esaprediction.ESSpecificityPredictor
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public class ESSpecificityPredictor extends java.lang.Object
Predicts whether a compound is a substrate of a given enzyme within a specific biosystem.- Author:
- Djoumbou Feunang, Yannick
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Constructor Summary
Constructors Constructor Description ESSpecificityPredictor(BioSystem bsys)
Creates a specific
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
isPotentialSubstrateByReactionPatternMatching(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz)
boolean
isValid_EC_2_8_2_2_substrate(org.openscience.cdk.interfaces.IAtomContainer substrate, boolean preprocess)
boolean
isValidCyp450Substrate(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz)
boolean
isValidCyp450Substrate(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz, java.util.ArrayList<ChemicalClassFinder.ChemicalClassName> chemClasses)
boolean
isValidSubstrate(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz)
boolean
isValidSubstrate(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz, java.util.ArrayList<ChemicalClassFinder.ChemicalClassName> chemClasses)
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Constructor Detail
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ESSpecificityPredictor
public ESSpecificityPredictor(BioSystem bsys)
Creates a specific- Parameters:
bsys
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Method Detail
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isValidCyp450Substrate
public boolean isValidCyp450Substrate(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz) throws java.lang.Exception
- Throws:
java.lang.Exception
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isValidCyp450Substrate
public boolean isValidCyp450Substrate(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz, java.util.ArrayList<ChemicalClassFinder.ChemicalClassName> chemClasses) throws java.lang.Exception
- Throws:
java.lang.Exception
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isValid_EC_2_8_2_2_substrate
public boolean isValid_EC_2_8_2_2_substrate(org.openscience.cdk.interfaces.IAtomContainer substrate, boolean preprocess) throws java.lang.Exception
- Throws:
java.lang.Exception
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isValidSubstrate
public boolean isValidSubstrate(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz) throws java.lang.Exception
- Throws:
java.lang.Exception
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isValidSubstrate
public boolean isValidSubstrate(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz, java.util.ArrayList<ChemicalClassFinder.ChemicalClassName> chemClasses) throws java.lang.Exception
- Throws:
java.lang.Exception
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isPotentialSubstrateByReactionPatternMatching
public boolean isPotentialSubstrateByReactionPatternMatching(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz) throws ambit2.smarts.query.SMARTSException, org.openscience.cdk.exception.CDKException, java.io.IOException
- Throws:
ambit2.smarts.query.SMARTSException
org.openscience.cdk.exception.CDKException
java.io.IOException
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