Package biotransformer.btransformers
Class Cyp450BTransformer
- java.lang.Object
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- biotransformer.btransformers.Biotransformer
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- biotransformer.btransformers.Cyp450BTransformer
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public class Cyp450BTransformer extends Biotransformer
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Field Summary
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Fields inherited from class biotransformer.btransformers.Biotransformer
bSystem, enzymesByreactionGroups, enzymesList, inchiGenFactory, mapper, reactionsByGroups, reactionsHash, smiGen
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Constructor Summary
Constructors Constructor Description Cyp450BTransformer(BioSystem.BioSystemName bioSName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.ArrayList<Biotransformation>
predictCyp450BiotransformationChain(org.openscience.cdk.interfaces.IAtomContainer substrate, boolean preprocess, boolean filter, int nrOfSteps, double threshold)
java.util.ArrayList<Biotransformation>
predictCyp450BiotransformationChain(org.openscience.cdk.interfaces.IAtomContainerSet substrates, boolean preprocess, boolean filter, int nrOfSteps, double threshold)
java.util.ArrayList<Biotransformation>
predictCyp450Biotransformations(java.lang.String sdfFileName, boolean preprocess, boolean filter, double threshold)
java.util.ArrayList<Biotransformation>
predictCyp450Biotransformations(org.openscience.cdk.interfaces.IAtomContainer substrate, boolean preprocess, boolean filter, double threshold)
java.util.ArrayList<Biotransformation>
predictCyp450Biotransformations(org.openscience.cdk.interfaces.IAtomContainerSet substrates, boolean preprocess, boolean filter, double threshold)
java.util.ArrayList<Biotransformation>
predictCyp450BiotransformationsForSpecificEnzymes(org.openscience.cdk.interfaces.IAtomContainer substrate, java.util.ArrayList<Enzyme.EnzymeName> enzymeNames, boolean preprocess, boolean filter, double threshold)
void
printStatistics()
void
simulateCyp450MetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFolder, boolean annotate)
void
simulateCyp450MetabolismAndSaveToSingleSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFileName, boolean annotate)
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Methods inherited from class biotransformer.btransformers.Biotransformer
applyPathwaySpecificBiotransformationChain, applyPathwaySpecificBiotransformations, applyPathwaySpecificBiotransformations, applyPathwaySpecificBiotransformationsChain, applyPathwaySpecificBiotransformationsChain, applyReactionAndReturnBiotransformations, applyReactionAndReturnBiotransformations, applyReactionAtOnceAndReturnBiotransformations, applyReactionAtOnceAndReturnBiotransformations, applyReactionAtOnceAndReturnBiotransformations, applyReactionAtOnceAndReturnBiotransformations, applyReactionChain, applyReactionChain, applyReactions, applyReactions, applyReactionsAndReturnBiotransformations, applyReactionsAndReturnBiotransformations, applyReactionsChainAndReturnBiotransformations, applyReactionsChainAndReturnBiotransformations, applyReactionsChainAndReturnBiotransformations, applyReactionsChainAndReturnBiotransformations, applyReactionsFromContainersAndReturnBiotransformations, extractProductsFromBiotransformations, extractProductsFromBiotransformationsWithTransformationData, extractProductsFromBiotransformationsWithTransformationData, extractProductsFromBiotransformationsWithTransformationData, extractProductsFromBiotransformationsWithTransformationData, generateAllMetabolitesFromAtomContainer, generateAllMetabolitesFromAtomContainer, generateAllMetabolitesFromAtomContainerViaTransformationAtAllLocations, getBioSystemName, getReactionsList, getSmiParser, isValidSubstrate, metabolizeWithEnzyme, metabolizeWithEnzyme, metabolizeWithEnzyme, metabolizeWithEnzyme, metabolizeWithEnzymes, metabolizeWithEnzymes, metabolizeWithEnzymesBreadthFirst, metabolizeWithEnzymesBreadthFirst, metabolizeWithEnzymesDephtFirst, saveBioTransformationProductsToCSV, saveBioTransformationProductsToCSV, saveBioTransformationProductsToCSV, saveBioTransformationProductsToCSV, saveBioTransformationProductsToSdf, saveBioTransformationProductsToSdf, saveBioTransformationProductsToSdf, saveBioTransformationProductsToSdf, saveBioTransformationProductsToSDF
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Constructor Detail
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Cyp450BTransformer
public Cyp450BTransformer(BioSystem.BioSystemName bioSName) throws org.codehaus.jackson.JsonParseException, org.codehaus.jackson.map.JsonMappingException, java.io.IOException, org.openscience.cdk.exception.CDKException
- Throws:
org.codehaus.jackson.JsonParseException
org.codehaus.jackson.map.JsonMappingException
java.io.IOException
org.openscience.cdk.exception.CDKException
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Method Detail
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predictCyp450Biotransformations
public java.util.ArrayList<Biotransformation> predictCyp450Biotransformations(org.openscience.cdk.interfaces.IAtomContainer substrate, boolean preprocess, boolean filter, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictCyp450BiotransformationsForSpecificEnzymes
public java.util.ArrayList<Biotransformation> predictCyp450BiotransformationsForSpecificEnzymes(org.openscience.cdk.interfaces.IAtomContainer substrate, java.util.ArrayList<Enzyme.EnzymeName> enzymeNames, boolean preprocess, boolean filter, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictCyp450Biotransformations
public java.util.ArrayList<Biotransformation> predictCyp450Biotransformations(org.openscience.cdk.interfaces.IAtomContainerSet substrates, boolean preprocess, boolean filter, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictCyp450Biotransformations
public java.util.ArrayList<Biotransformation> predictCyp450Biotransformations(java.lang.String sdfFileName, boolean preprocess, boolean filter, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictCyp450BiotransformationChain
public java.util.ArrayList<Biotransformation> predictCyp450BiotransformationChain(org.openscience.cdk.interfaces.IAtomContainer substrate, boolean preprocess, boolean filter, int nrOfSteps, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictCyp450BiotransformationChain
public java.util.ArrayList<Biotransformation> predictCyp450BiotransformationChain(org.openscience.cdk.interfaces.IAtomContainerSet substrates, boolean preprocess, boolean filter, int nrOfSteps, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateCyp450MetabolismAndSaveToSDF
public void simulateCyp450MetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFolder, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateCyp450MetabolismAndSaveToSingleSDF
public void simulateCyp450MetabolismAndSaveToSingleSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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printStatistics
public void printStatistics()
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