Package biotransformer.btransformers
Class ECBasedBTransformer
- java.lang.Object
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- biotransformer.btransformers.Biotransformer
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- biotransformer.btransformers.ECBasedBTransformer
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public class ECBasedBTransformer extends Biotransformer
- Author:
- Djoumbou Feunang, Yannick
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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 ECBasedBTransformer(BioSystem.BioSystemName bioSName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.ArrayList<Biotransformation>
applyEcBasedConjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyEcBasedConjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyEcBasedConjugations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyEcBasedDeconjuations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nrOfSteps)
java.util.ArrayList<Biotransformation>
applyEcBasedDeconjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyEcBasedDeconjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyEcBasedDeconjugations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyEcBasedTransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)
java.util.ArrayList<Biotransformation>
applyEcBasedTransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyEcBasedTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyEcBasedTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)
boolean
isConjugationCandidate(org.openscience.cdk.interfaces.IAtomContainer molecule)
boolean
isDeconjugationCandidate(org.openscience.cdk.interfaces.IAtomContainer molecule)
void
printStatistics()
void
simulateECBasedMetabolismAndSaveToSDF(java.lang.String sdfFileName, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFolder, boolean annotate)
void
simulateECBasedMetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFolder, boolean annotate)
java.util.ArrayList<Biotransformation>
simulateECBasedMetabolismChain(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateECBasedMetabolismChain(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateECBasedMetabolismStep(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateECBasedMetabolismStep(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateECBasedPhaseIMetabolismChain(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateECBasedPhaseIMetabolismChain(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateECBasedPhaseIMetabolismStep(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateECBasedPhaseIMetabolismStep(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
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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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ECBasedBTransformer
public ECBasedBTransformer(BioSystem.BioSystemName bioSName) throws java.io.IOException, org.json.simple.parser.ParseException, org.openscience.cdk.exception.CDKException
- Throws:
org.json.simple.parser.ParseException
java.io.IOException
org.openscience.cdk.exception.CDKException
java.net.URISyntaxException
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Method Detail
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applyEcBasedDeconjuations
public java.util.ArrayList<Biotransformation> applyEcBasedDeconjuations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nrOfSteps) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringnrOfSteps
- - number of steps- Returns:
- an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with a threshold of 0.0
- Throws:
java.lang.Exception
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applyEcBasedDeconjugations
public java.util.ArrayList<Biotransformation> applyEcBasedDeconjugations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringscoreThreshold
- - minimum score threshold for selected metbaolic reactions- Returns:
- an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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applyEcBasedDeconjuationsChain
public java.util.ArrayList<Biotransformation> applyEcBasedDeconjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringnr_of_steps
- - number of steps- Returns:
- an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the minimum threshold of 0.0
- Throws:
java.lang.Exception
- - Throw an exception
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applyEcBasedDeconjuationsChain
public java.util.ArrayList<Biotransformation> applyEcBasedDeconjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringnr_of_steps
- - number of steps- Returns:
- an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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applyEcBasedTransformations
public java.util.ArrayList<Biotransformation> applyEcBasedTransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filtering- Returns:
- an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with a threshold of 0.0
- Throws:
java.lang.Exception
- - throw any exception
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applyEcBasedTransformations
public java.util.ArrayList<Biotransformation> applyEcBasedTransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringscoreThreshold
- - minimum threshold for reaction scores- Returns:
- an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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applyEcBasedTransformationsChain
public java.util.ArrayList<Biotransformation> applyEcBasedTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringnr_of_steps
- - number of steps- Returns:
- an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the minimum threshold of 0.0
- Throws:
java.lang.Exception
- - throw any exception
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applyEcBasedTransformationsChain
public java.util.ArrayList<Biotransformation> applyEcBasedTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringnr_of_steps
- - number of steps- Returns:
- an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
- - throw any exception
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applyEcBasedConjugations
public java.util.ArrayList<Biotransformation> applyEcBasedConjugations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringnr_of_steps
- - number of stepsscoreThreshold
- - minimum threshold for reaction scores- Returns:
- an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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applyEcBasedConjuationsChain
public java.util.ArrayList<Biotransformation> applyEcBasedConjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringnr_of_steps
- - number of steps- Returns:
- an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the minimum threshold of 0.0
- Throws:
java.lang.Exception
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applyEcBasedConjuationsChain
public java.util.ArrayList<Biotransformation> applyEcBasedConjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold) throws java.lang.Exception
- Parameters:
target
- - The molecule to transformpreprocess
- - specify whether to perform molecule preprocessingfilter
- - apply reaction filteringnr_of_steps
- - number of steps- Returns:
- an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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simulateECBasedPhaseIMetabolismStep
public java.util.ArrayList<Biotransformation> simulateECBasedPhaseIMetabolismStep(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
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simulateECBasedPhaseIMetabolismStep
public java.util.ArrayList<Biotransformation> simulateECBasedPhaseIMetabolismStep(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateECBasedPhaseIMetabolismChain
public java.util.ArrayList<Biotransformation> simulateECBasedPhaseIMetabolismChain(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateECBasedPhaseIMetabolismChain
public java.util.ArrayList<Biotransformation> simulateECBasedPhaseIMetabolismChain(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateECBasedMetabolismStep
public java.util.ArrayList<Biotransformation> simulateECBasedMetabolismStep(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateECBasedMetabolismStep
public java.util.ArrayList<Biotransformation> simulateECBasedMetabolismStep(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateECBasedMetabolismChain
public java.util.ArrayList<Biotransformation> simulateECBasedMetabolismChain(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateECBasedMetabolismChain
public java.util.ArrayList<Biotransformation> simulateECBasedMetabolismChain(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateECBasedMetabolismAndSaveToSDF
public void simulateECBasedMetabolismAndSaveToSDF(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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simulateECBasedMetabolismAndSaveToSDF
public void simulateECBasedMetabolismAndSaveToSDF(java.lang.String sdfFileName, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFolder, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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isDeconjugationCandidate
public boolean isDeconjugationCandidate(org.openscience.cdk.interfaces.IAtomContainer molecule) 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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isConjugationCandidate
public boolean isConjugationCandidate(org.openscience.cdk.interfaces.IAtomContainer molecule) 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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printStatistics
public void printStatistics()
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