Package biotransformer.btransformers
Class Phase2BTransformer
- java.lang.Object
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- biotransformer.btransformers.Biotransformer
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- biotransformer.btransformers.Phase2BTransformer
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public class Phase2BTransformer extends Biotransformer
- Author:
- Yannick Djoumbou Feunang
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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 Phase2BTransformer(BioSystem.BioSystemName bioSName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.ArrayList<Biotransformation>
applyPhase2Transformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter)
java.util.ArrayList<Biotransformation>
applyPhase2Transformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyPhase2Transformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean precheck, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyPhase2TransformationsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyPhase2TransformationsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyPhase2TransformationsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold)
void
applyReactionChainFromSDF(java.lang.String inputFileName, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
void
applyReactionChainFromSdfToSingleSdf(java.lang.String inputFileName, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold, java.lang.String outputFileName, boolean annotate)
java.util.ArrayList<Biotransformation>
applyReactionsAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
boolean
isPotentialHumanPhase2SubstrateByReactionPatternMatching(org.openscience.cdk.interfaces.IAtomContainer substrate)
boolean
isPotentialNonHumanPhase2SubstrateByReactionPatternMatching(org.openscience.cdk.interfaces.IAtomContainer substrate)
boolean
isPotentialPhase2SubstrateByReactionPatternMatching(org.openscience.cdk.interfaces.IAtomContainer substrate)
void
printStatistics()
org.openscience.cdk.interfaces.IAtomContainerSet
reduceSet(org.openscience.cdk.interfaces.IAtomContainerSet molecules)
java.util.ArrayList<Biotransformation>
selectBiotransformationWithValidProducts(java.util.ArrayList<Biotransformation> biotransformations)
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Methods inherited from class biotransformer.btransformers.Biotransformer
applyPathwaySpecificBiotransformationChain, applyPathwaySpecificBiotransformations, applyPathwaySpecificBiotransformations, applyPathwaySpecificBiotransformationsChain, applyPathwaySpecificBiotransformationsChain, 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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Constructor Detail
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Phase2BTransformer
public Phase2BTransformer(BioSystem.BioSystemName bioSName) throws java.io.IOException, org.json.simple.parser.ParseException, org.openscience.cdk.exception.CDKException
- Throws:
java.io.IOException
org.json.simple.parser.ParseException
org.openscience.cdk.exception.CDKException
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Method Detail
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applyPhase2Transformations
public java.util.ArrayList<Biotransformation> applyPhase2Transformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter) throws java.lang.Exception
- Parameters:
target
-preprocess
-filter
-- Returns:
- an arraylist of biotransformations, which are instances of the Phase II metabolic reactions applied to the target, with the set minimum threshold of 0.0
- Throws:
java.lang.Exception
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applyPhase2Transformations
public java.util.ArrayList<Biotransformation> applyPhase2Transformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter, double scoreThreshold) throws java.lang.Exception
- Parameters:
target
-preprocess
-filter
-scoreThreshold
-- Returns:
- an arraylist of biotransformations, which are instances of the Phase II metabolic reactions applied to the target, with the set minimum threshold
- Throws:
java.lang.Exception
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applyPhase2Transformations
public java.util.ArrayList<Biotransformation> applyPhase2Transformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean precheck, boolean preprocess, boolean filter, double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyPhase2TransformationsChainAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyPhase2TransformationsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyPhase2TransformationsChainAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyPhase2TransformationsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyPhase2TransformationsChainAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyPhase2TransformationsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold) throws java.lang.Exception
- Overrides:
applyReactionAndReturnBiotransformations
in classBiotransformer
- 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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applyReactionChainFromSDF
public void applyReactionChainFromSDF(java.lang.String inputFileName, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionChainFromSdfToSingleSdf
public void applyReactionChainFromSdfToSingleSdf(java.lang.String inputFileName, boolean precheck, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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isPotentialHumanPhase2SubstrateByReactionPatternMatching
public boolean isPotentialHumanPhase2SubstrateByReactionPatternMatching(org.openscience.cdk.interfaces.IAtomContainer substrate) throws java.lang.Exception
- Throws:
java.lang.Exception
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isPotentialNonHumanPhase2SubstrateByReactionPatternMatching
public boolean isPotentialNonHumanPhase2SubstrateByReactionPatternMatching(org.openscience.cdk.interfaces.IAtomContainer substrate) throws java.lang.Exception
- Throws:
java.lang.Exception
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isPotentialPhase2SubstrateByReactionPatternMatching
public boolean isPotentialPhase2SubstrateByReactionPatternMatching(org.openscience.cdk.interfaces.IAtomContainer substrate) throws java.lang.Exception
- Throws:
java.lang.Exception
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reduceSet
public org.openscience.cdk.interfaces.IAtomContainerSet reduceSet(org.openscience.cdk.interfaces.IAtomContainerSet molecules) throws org.openscience.cdk.exception.CDKException, java.lang.Exception
- Throws:
org.openscience.cdk.exception.CDKException
java.lang.Exception
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selectBiotransformationWithValidProducts
public java.util.ArrayList<Biotransformation> selectBiotransformationWithValidProducts(java.util.ArrayList<Biotransformation> biotransformations) throws ambit2.smarts.query.SMARTSException, org.openscience.cdk.exception.CDKException, java.lang.CloneNotSupportedException
- Throws:
ambit2.smarts.query.SMARTSException
org.openscience.cdk.exception.CDKException
java.lang.CloneNotSupportedException
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printStatistics
public void printStatistics()
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