Package biotransformer.btransformers
Class HGutBTransformer
- java.lang.Object
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- biotransformer.btransformers.Biotransformer
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- biotransformer.btransformers.HGutBTransformer
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public class HGutBTransformer 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 HGutBTransformer()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.ArrayList<Biotransformation>
applyGutMicrobialConjugations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)
java.util.ArrayList<Biotransformation>
applyGutMicrobialConjugations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialConjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyGutMicrobialConjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialDeconjugations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)
java.util.ArrayList<Biotransformation>
applyGutMicrobialDeconjugations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialDeconjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyGutMicrobialDeconjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialMetabolismHydrolysisAndRedoxChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialMetabolismHydrolysisAndRedoxChain(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialMetabolismHydrolysisAndRedoxStep(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialMetabolismHydrolysisAndRedoxStep(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialRedoxChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialRedoxReactions(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)
java.util.ArrayList<Biotransformation>
applyGutMicrobialRedoxReactions(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyGutMicrobialRedoxReactionsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<MetabolicReaction>>
getReactionsList()
returns a linked hash map with the reactions associated with the human gut, in addition to standardization reactions.boolean
isConjugationCandidate(org.openscience.cdk.interfaces.IAtomContainer molecule)
boolean
isDeconjugationCandidate(org.openscience.cdk.interfaces.IAtomContainer molecule)
void
printStatistics()
java.util.ArrayList<Biotransformation>
simulateGutMicrobialMetabolism(java.lang.String targetsFileNameInSDF, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int numberOfSteps)
java.util.ArrayList<Biotransformation>
simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int numberOfSteps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, int numberOfSteps)
java.util.ArrayList<Biotransformation>
simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, int numberOfSteps, java.lang.Double scoreThreshold)
void
simulateGutMicrobialMetabolismAndSave(java.lang.String targetsFileNameInSDF, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold, java.lang.String metabolitesFileNameInSDF)
void
simulateGutMicrobialMetabolismAndSave(java.lang.String targetsFileNameInSDF, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold, java.lang.String metabolitesFileNameInSDF, boolean annotate)
void
simulateGutMicrobialMetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFolder)
void
simulateGutMicrobialMetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFolder, 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, getSmiParser, isValidSubstrate, metabolizeWithEnzyme, metabolizeWithEnzyme, metabolizeWithEnzyme, metabolizeWithEnzyme, metabolizeWithEnzymes, metabolizeWithEnzymes, metabolizeWithEnzymesBreadthFirst, metabolizeWithEnzymesBreadthFirst, metabolizeWithEnzymesDephtFirst, saveBioTransformationProductsToCSV, saveBioTransformationProductsToCSV, saveBioTransformationProductsToCSV, saveBioTransformationProductsToCSV, saveBioTransformationProductsToSdf, saveBioTransformationProductsToSdf, saveBioTransformationProductsToSdf, saveBioTransformationProductsToSdf, saveBioTransformationProductsToSDF
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Method Detail
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getReactionsList
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<MetabolicReaction>> getReactionsList()
returns a linked hash map with the reactions associated with the human gut, in addition to standardization reactions.- Overrides:
getReactionsList
in classBiotransformer
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applyGutMicrobialDeconjugations
public java.util.ArrayList<Biotransformation> applyGutMicrobialDeconjugations(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 human gut microbial reactions applied to the target, with a threshold of 0.0
- Throws:
java.lang.Exception
- - throw any exception
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applyGutMicrobialDeconjugations
public java.util.ArrayList<Biotransformation> applyGutMicrobialDeconjugations(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 filtering- Returns:
- an arraylist of biotransformations, which are instances of the human gut microbial reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
- - throw any exception
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applyGutMicrobialDeconjugationsChain
public java.util.ArrayList<Biotransformation> applyGutMicrobialDeconjugationsChain(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 human gut microbial metabolic reactions applied to the target, with the minimum threshold of 0.0
- Throws:
java.lang.Exception
- - throw any exception
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applyGutMicrobialDeconjugationsChain
public java.util.ArrayList<Biotransformation> applyGutMicrobialDeconjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.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
- - The minimum score for a reaction- Returns:
- an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the human gut microbial metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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applyGutMicrobialRedoxReactions
public java.util.ArrayList<Biotransformation> applyGutMicrobialRedoxReactions(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 human gut microbial reactions applied to the target, with a threshold of 0.0
- Throws:
java.lang.Exception
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applyGutMicrobialRedoxReactions
public java.util.ArrayList<Biotransformation> applyGutMicrobialRedoxReactions(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 human gut microbial reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
- - throw any exception
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applyGutMicrobialRedoxReactionsChain
public java.util.ArrayList<Biotransformation> applyGutMicrobialRedoxReactionsChain(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 human gut microbial metabolic reactions applied to the target, with the minimum threshold of 0.0
- Throws:
java.lang.Exception
- - throw any exception
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applyGutMicrobialRedoxChain
public java.util.ArrayList<Biotransformation> applyGutMicrobialRedoxChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.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 human gut microbial metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
- -throw any exception
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applyGutMicrobialConjugations
public java.util.ArrayList<Biotransformation> applyGutMicrobialConjugations(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 human gut microbial reactions applied to the target, with a threshold of 0.0
- Throws:
java.lang.Exception
- - throw any exception
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applyGutMicrobialConjugations
public java.util.ArrayList<Biotransformation> applyGutMicrobialConjugations(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 filtering- Returns:
- an arraylist of biotransformations, which are instances of the human gut microbial reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
- - throw any exception
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applyGutMicrobialConjugationsChain
public java.util.ArrayList<Biotransformation> applyGutMicrobialConjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps) throws java.lang.Exception
- Parameters:
target
-preprocess
-filter
-nr_of_steps
-- Returns:
- an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the human gut microbial metabolic reactions applied to the target, with the minimum threshold of 0.0
- Throws:
java.lang.Exception
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applyGutMicrobialConjugationsChain
public java.util.ArrayList<Biotransformation> applyGutMicrobialConjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Parameters:
target
-preprocess
-filter
-nr_of_steps
-- Returns:
- an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the human gut microbial metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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applyGutMicrobialMetabolismHydrolysisAndRedoxStep
public java.util.ArrayList<Biotransformation> applyGutMicrobialMetabolismHydrolysisAndRedoxStep(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyGutMicrobialMetabolismHydrolysisAndRedoxStep
public java.util.ArrayList<Biotransformation> applyGutMicrobialMetabolismHydrolysisAndRedoxStep(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyGutMicrobialMetabolismHydrolysisAndRedoxChain
public java.util.ArrayList<Biotransformation> applyGutMicrobialMetabolismHydrolysisAndRedoxChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyGutMicrobialMetabolismHydrolysisAndRedoxChain
public java.util.ArrayList<Biotransformation> applyGutMicrobialMetabolismHydrolysisAndRedoxChain(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateGutMicrobialMetabolism
public java.util.ArrayList<Biotransformation> simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int numberOfSteps) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateGutMicrobialMetabolism
public java.util.ArrayList<Biotransformation> simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int numberOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateGutMicrobialMetabolism
public java.util.ArrayList<Biotransformation> simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, int numberOfSteps) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateGutMicrobialMetabolism
public java.util.ArrayList<Biotransformation> simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, int numberOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateGutMicrobialMetabolism
public java.util.ArrayList<Biotransformation> simulateGutMicrobialMetabolism(java.lang.String targetsFileNameInSDF, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateGutMicrobialMetabolismAndSave
public void simulateGutMicrobialMetabolismAndSave(java.lang.String targetsFileNameInSDF, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold, java.lang.String metabolitesFileNameInSDF) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateGutMicrobialMetabolismAndSave
public void simulateGutMicrobialMetabolismAndSave(java.lang.String targetsFileNameInSDF, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold, java.lang.String metabolitesFileNameInSDF, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateGutMicrobialMetabolismAndSaveToSDF
public void simulateGutMicrobialMetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFolder) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateGutMicrobialMetabolismAndSaveToSDF
public void simulateGutMicrobialMetabolismAndSaveToSDF(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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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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