Package biotransformer.utils
Class HumanSuperBioTransformer
- java.lang.Object
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- biotransformer.utils.HumanSuperBioTransformer
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public class HumanSuperBioTransformer extends java.lang.Object
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Constructor Summary
Constructors Constructor Description HumanSuperBioTransformer()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.ArrayList<Biotransformation>
applyGutMicrobialMetabolismHydrolysisAndRedoxChain(org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyPathwaySpecificBiotransformations(org.openscience.cdk.interfaces.IAtomContainer molecule, MetabolicPathway.MPathwayName pathway, boolean preprocess, boolean filter, double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyPhaseIITransformationsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet products, int nrOfSteps, double scoreThreshold)
org.openscience.cdk.interfaces.IAtomContainerSet
extractAtomContainer(java.util.ArrayList<Biotransformation> biotransformations)
org.openscience.cdk.interfaces.IAtomContainerSet
extractAtomContainerWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, boolean annotate)
org.openscience.cdk.inchi.InChIGeneratorFactory
getInChIGenFactory()
java.util.LinkedHashMap<java.lang.String,org.openscience.cdk.interfaces.IAtomContainerSet>
partitionSetForPhaseIIMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet products)
java.util.ArrayList<Biotransformation>
predictAllHumanBiotransformationChain(org.openscience.cdk.interfaces.IAtomContainer substrate, int nrOfSteps, double threshold)
java.util.ArrayList<Biotransformation>
predictAllHumanBiotransformationChain(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, double threshold)
void
predictAllHumanBiotransformationChainAndSaveToCSV(org.openscience.cdk.interfaces.IAtomContainer substrate, int nrOfSteps, double threshold, java.lang.String outputFileName, boolean annotate)
void
predictAllHumanBiotransformationChainAndSaveToCSV(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, double threshold, java.lang.String outputFileName, boolean annotate)
void
predictAllHumanBiotransformationChainAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainer substrate, int nrOfSteps, double threshold, java.lang.String outputFileName, boolean annotate)
void
predictAllHumanBiotransformationChainAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, double threshold, java.lang.String outputFileName, boolean annotate)
void
predictMetabolismAllHumanFromSDFAndSavetoSDF(java.lang.String inputFileName, java.lang.String outputF, double screThreshold, boolean annotate)
void
predictMetabolismAllHumanFromSDFAndSavetoSDF(java.lang.String inputFileName, java.lang.String outputFileName, int nrOfSteps, boolean annotate)
void
predictMetabolismAllHumanFromSDFAndSavetoSDF(java.lang.String inputFileName, java.lang.String outputFolder, int nrOfSteps, double scoreThreshold, boolean annotate)
void
predictMetabolismAllHumanFromSDFAndSavetoSingleSDF(java.lang.String inputFileName, java.lang.String outputFileName, int nrOfSteps, double scoreThreshold, boolean annotate)
void
predictMetabolismAllHumanFromSDFtoSDF(java.lang.String inputFileName, java.lang.String outputFileName, boolean annotate)
void
saveBioTransformationProductsToCSV(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate)
void
saveBioTransformationProductsToSdf(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate)
java.util.ArrayList<Biotransformation>
simulateAllHumanMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet containers, double scoreThreshold)
void
simulateAllHumanMetabolismAndSavetoCSV(org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String outputFileName, double scoreThreshold, boolean annotate)
void
simulateAllHumanMetabolismAndSavetoSDF(org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String outputFileName, double scoreThreshold, boolean annotate)
void
simulateAllHumanMetabolismAndSavetoSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, java.lang.String outputFileName, double scoreThreshold, boolean annotate)
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>
simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainer molecule, int nrOfSteps, double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateHumanSuperbioMetabolism(org.openscience.cdk.interfaces.IAtomContainer target)
java.util.ArrayList<Biotransformation>
simulateHumanSuperbioMetabolism(org.openscience.cdk.interfaces.IAtomContainer target, java.lang.Double scoreThreshold)
void
simulateHumanSuperbioMetabolismAndSaveToCSV(org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String outputFileName, boolean annotate)
void
simulateHumanSuperbioMetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String outputFileName, boolean annotate)
void
simulateHumanSuperbioMetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, java.lang.String outputFolder, boolean annotate)
void
simulateHumanSuperbioMetabolismFromSDF(java.lang.String inputFileName, boolean annotate)
void
simulateHumanSuperbioMetabolismFromSDF(java.lang.String inputFileName, java.lang.String outputFolder, boolean annotate)
void
simulateHumanSuperbioMetabolismFromSDFtoSingleCSV(java.lang.String inputFileName, java.lang.String outputFileName, boolean annotate)
void
simulateHumanSuperbioMetabolismFromSDFtoSingleSDF(java.lang.String inputFileName, java.lang.String outputFileName, boolean annotate)
java.util.ArrayList<Biotransformation>
simulateOneStepAllHuman(org.openscience.cdk.interfaces.IAtomContainer target)
java.util.ArrayList<Biotransformation>
simulateOneStepAllHuman(org.openscience.cdk.interfaces.IAtomContainer target, double scoreThreshold)
java.util.ArrayList<Biotransformation>
simulateOneStepAllHuman(org.openscience.cdk.interfaces.IAtomContainerSet targets, double scoreThreshold)
org.openscience.cdk.interfaces.IAtomContainer
standardizeMoleculeWithCopy(org.openscience.cdk.interfaces.IAtomContainer target)
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Method Detail
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getInChIGenFactory
public org.openscience.cdk.inchi.InChIGeneratorFactory getInChIGenFactory()
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simulateHumanSuperbioMetabolism
public java.util.ArrayList<Biotransformation> simulateHumanSuperbioMetabolism(org.openscience.cdk.interfaces.IAtomContainer target) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateHumanSuperbioMetabolism
public java.util.ArrayList<Biotransformation> simulateHumanSuperbioMetabolism(org.openscience.cdk.interfaces.IAtomContainer target, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateHumanSuperbioMetabolismAndSaveToSDF
public void simulateHumanSuperbioMetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateHumanSuperbioMetabolismFromSDF
public void simulateHumanSuperbioMetabolismFromSDF(java.lang.String inputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateHumanSuperbioMetabolismFromSDF
public void simulateHumanSuperbioMetabolismFromSDF(java.lang.String inputFileName, java.lang.String outputFolder, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateHumanSuperbioMetabolismAndSaveToSDF
public void simulateHumanSuperbioMetabolismAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, java.lang.String outputFolder, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateHumanSuperbioMetabolismAndSaveToCSV
public void simulateHumanSuperbioMetabolismAndSaveToCSV(org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateAllHumanMetabolism
public java.util.ArrayList<Biotransformation> simulateAllHumanMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet containers, double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateAllHumanMetabolismAndSavetoCSV
public void simulateAllHumanMetabolismAndSavetoCSV(org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String outputFileName, double scoreThreshold, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateAllHumanMetabolismAndSavetoSDF
public void simulateAllHumanMetabolismAndSavetoSDF(org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String outputFileName, double scoreThreshold, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictAllHumanBiotransformationChainAndSaveToCSV
public void predictAllHumanBiotransformationChainAndSaveToCSV(org.openscience.cdk.interfaces.IAtomContainer substrate, int nrOfSteps, double threshold, java.lang.String outputFileName, boolean annotate)
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predictAllHumanBiotransformationChainAndSaveToCSV
public void predictAllHumanBiotransformationChainAndSaveToCSV(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, double threshold, java.lang.String outputFileName, boolean annotate)
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predictAllHumanBiotransformationChainAndSaveToSDF
public void predictAllHumanBiotransformationChainAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, double threshold, java.lang.String outputFileName, boolean annotate)
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simulateAllHumanMetabolismAndSavetoSDF
public void simulateAllHumanMetabolismAndSavetoSDF(org.openscience.cdk.interfaces.IAtomContainerSet containers, java.lang.String outputFileName, double scoreThreshold, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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partitionSetForPhaseIIMetabolism
public java.util.LinkedHashMap<java.lang.String,org.openscience.cdk.interfaces.IAtomContainerSet> partitionSetForPhaseIIMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet products) throws org.openscience.cdk.exception.CDKException, java.lang.Exception
- Throws:
org.openscience.cdk.exception.CDKException
java.lang.Exception
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simulateHumanSuperbioMetabolismFromSDFtoSingleSDF
public void simulateHumanSuperbioMetabolismFromSDFtoSingleSDF(java.lang.String inputFileName, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateHumanSuperbioMetabolismFromSDFtoSingleCSV
public void simulateHumanSuperbioMetabolismFromSDFtoSingleCSV(java.lang.String inputFileName, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateOneStepAllHuman
public java.util.ArrayList<Biotransformation> simulateOneStepAllHuman(org.openscience.cdk.interfaces.IAtomContainer target) throws java.lang.Exception
- Throws:
java.lang.Exception
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simulateOneStepAllHuman
public java.util.ArrayList<Biotransformation> simulateOneStepAllHuman(org.openscience.cdk.interfaces.IAtomContainer target, double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyPathwaySpecificBiotransformations
public java.util.ArrayList<Biotransformation> applyPathwaySpecificBiotransformations(org.openscience.cdk.interfaces.IAtomContainer molecule, MetabolicPathway.MPathwayName pathway, boolean preprocess, boolean filter, 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 molecule, int nrOfSteps, double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyPhaseIITransformationsChainAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyPhaseIITransformationsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet products, int nrOfSteps, 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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simulateOneStepAllHuman
public java.util.ArrayList<Biotransformation> simulateOneStepAllHuman(org.openscience.cdk.interfaces.IAtomContainerSet targets, double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictAllHumanBiotransformationChain
public java.util.ArrayList<Biotransformation> predictAllHumanBiotransformationChain(org.openscience.cdk.interfaces.IAtomContainer substrate, int nrOfSteps, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictAllHumanBiotransformationChain
public java.util.ArrayList<Biotransformation> predictAllHumanBiotransformationChain(org.openscience.cdk.interfaces.IAtomContainerSet containers, int nrOfSteps, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictMetabolismAllHumanFromSDFtoSDF
public void predictMetabolismAllHumanFromSDFtoSDF(java.lang.String inputFileName, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictAllHumanBiotransformationChainAndSaveToSDF
public void predictAllHumanBiotransformationChainAndSaveToSDF(org.openscience.cdk.interfaces.IAtomContainer substrate, int nrOfSteps, double threshold, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictMetabolismAllHumanFromSDFAndSavetoSDF
public void predictMetabolismAllHumanFromSDFAndSavetoSDF(java.lang.String inputFileName, java.lang.String outputFileName, int nrOfSteps, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictMetabolismAllHumanFromSDFAndSavetoSDF
public void predictMetabolismAllHumanFromSDFAndSavetoSDF(java.lang.String inputFileName, java.lang.String outputF, double screThreshold, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictMetabolismAllHumanFromSDFAndSavetoSDF
public void predictMetabolismAllHumanFromSDFAndSavetoSDF(java.lang.String inputFileName, java.lang.String outputFolder, int nrOfSteps, double scoreThreshold, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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predictMetabolismAllHumanFromSDFAndSavetoSingleSDF
public void predictMetabolismAllHumanFromSDFAndSavetoSingleSDF(java.lang.String inputFileName, java.lang.String outputFileName, int nrOfSteps, double scoreThreshold, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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standardizeMoleculeWithCopy
public org.openscience.cdk.interfaces.IAtomContainer standardizeMoleculeWithCopy(org.openscience.cdk.interfaces.IAtomContainer target) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyGutMicrobialMetabolismHydrolysisAndRedoxChain
public java.util.ArrayList<Biotransformation> applyGutMicrobialMetabolismHydrolysisAndRedoxChain(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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extractAtomContainer
public org.openscience.cdk.interfaces.IAtomContainerSet extractAtomContainer(java.util.ArrayList<Biotransformation> biotransformations) throws java.lang.Exception
- Throws:
java.lang.Exception
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extractAtomContainerWithTransformationData
public org.openscience.cdk.interfaces.IAtomContainerSet extractAtomContainerWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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saveBioTransformationProductsToSdf
public void saveBioTransformationProductsToSdf(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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saveBioTransformationProductsToCSV
public void saveBioTransformationProductsToCSV(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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