Package biotransformer.btransformers
Class EnvMicroBTransformer
- java.lang.Object
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- biotransformer.btransformers.Biotransformer
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- biotransformer.btransformers.EnvMicroBTransformer
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public class EnvMicroBTransformer 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 EnvMicroBTransformer()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.ArrayList<Biotransformation>
applyEnvMicrobialTransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter)
java.util.ArrayList<Biotransformation>
applyEnvMicrobialTransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyEnvMicrobialTransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyEnvMicrobialTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyEnvMicrobialTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target, boolean preprocess, boolean filter, int nr_of_steps, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionsAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
void
printStatistics()
java.util.ArrayList<Biotransformation>
simulateEnvMicrobialDegradation(org.openscience.cdk.interfaces.IAtomContainerSet containers, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
void
simulateEnvMicrobialDegradationAndSaveToCSV(org.openscience.cdk.interfaces.IAtomContainer container, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFileName, boolean annotate)
void
simulateEnvMicrobialDegradationAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainer container, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFileName, boolean annotate)
void
simulateEnvMicrobialDegradationAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, boolean preprocess, boolean filter, 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, 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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Method Detail
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applyEnvMicrobialTransformations
public java.util.ArrayList<Biotransformation> applyEnvMicrobialTransformations(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 environmental microbial reactions applied to the target, with a threshold of 0.0
- Throws:
java.lang.Exception
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applyEnvMicrobialTransformations
public java.util.ArrayList<Biotransformation> applyEnvMicrobialTransformations(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 environmental microbial metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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applyEnvMicrobialTransformations
public java.util.ArrayList<Biotransformation> applyEnvMicrobialTransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean preprocess, boolean filter, double scoreThreshold) throws java.lang.Exception
- Parameters:
targets
-preprocess
-filter
-scoreThreshold
-- Returns:
- an arraylist of biotransformations, which are instances of the environmental microbial metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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applyEnvMicrobialTransformationsChain
public java.util.ArrayList<Biotransformation> applyEnvMicrobialTransformationsChain(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 environmental microbial metabolic reactions applied to the target, with the minimum threshold of 0.0
- Throws:
java.lang.Exception
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applyEnvMicrobialTransformationsChain
public java.util.ArrayList<Biotransformation> applyEnvMicrobialTransformationsChain(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 environmental microbial metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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simulateEnvMicrobialDegradationAndSaveToSDF
public void simulateEnvMicrobialDegradationAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainer container, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateEnvMicrobialDegradationAndSaveToCSV
public void simulateEnvMicrobialDegradationAndSaveToCSV(org.openscience.cdk.interfaces.IAtomContainer container, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateEnvMicrobialDegradation
public java.util.ArrayList<Biotransformation> simulateEnvMicrobialDegradation(org.openscience.cdk.interfaces.IAtomContainerSet containers, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateEnvMicrobialDegradationAndSaveToSDF
public void simulateEnvMicrobialDegradationAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold, java.lang.String outputFolder, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionsAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionsAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Overrides:
applyReactionsAndReturnBiotransformations
in classBiotransformer
- Throws:
java.lang.Exception
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printStatistics
public void printStatistics()
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