Package biotransformer.utils
Class MetaboliteFinder
- java.lang.Object
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- biotransformer.utils.MetaboliteFinder
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public class MetaboliteFinder extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
MetaboliteFinder.FinderOption
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Field Summary
Fields Modifier and Type Field Description EnvMicroBTransformer
ebt
HumanSuperBioTransformer
hsbt
org.openscience.cdk.inchi.InChIGeneratorFactory
inchiGenFactory
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Constructor Summary
Constructors Constructor Description MetaboliteFinder()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
compoundsHasToleratedMass(org.openscience.cdk.interfaces.IAtomContainer atc, java.util.ArrayList<java.lang.Double> masses, double tolerance)
org.openscience.cdk.interfaces.IAtomContainerSet
findAllEnvMicroMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, MetaboliteFinder.FinderOption opt)
void
findAllEnvMicroMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)
void
findAllEnvMicroMetabolitesToCSV(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)
org.openscience.cdk.interfaces.IAtomContainerSet
findAllHumanMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, MetaboliteFinder.FinderOption opt)
void
findAllHumanMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)
void
findAllHumanMetabolitesToCSV(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)
org.openscience.cdk.interfaces.IAtomContainer
findPathway(org.openscience.cdk.interfaces.IAtomContainer startingCompound, org.openscience.cdk.interfaces.IAtomContainer leafCompound, java.util.LinkedHashMap<java.lang.String,org.openscience.cdk.interfaces.IAtomContainerSet> compoundToParents, java.util.LinkedHashMap<java.lang.String,org.openscience.cdk.interfaces.IAtomContainer> inchikeyToContainers, boolean annotate)
org.openscience.cdk.interfaces.IAtomContainerSet
findSuperbioMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, boolean annotate, MetaboliteFinder.FinderOption opt)
void
findSuperbioMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)
void
findSuperbioMetabolitesToCSV(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)
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Field Detail
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hsbt
public HumanSuperBioTransformer hsbt
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ebt
public EnvMicroBTransformer ebt
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inchiGenFactory
public org.openscience.cdk.inchi.InChIGeneratorFactory inchiGenFactory
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Method Detail
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findAllHumanMetabolites
public void findAllHumanMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt) throws java.lang.Exception
- Throws:
java.lang.Exception
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findAllHumanMetabolitesToCSV
public void findAllHumanMetabolitesToCSV(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt) throws java.lang.Exception
- Throws:
java.lang.Exception
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findAllHumanMetabolites
public org.openscience.cdk.interfaces.IAtomContainerSet findAllHumanMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, MetaboliteFinder.FinderOption opt) throws java.lang.Exception
- Throws:
java.lang.Exception
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findSuperbioMetabolites
public void findSuperbioMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt) throws java.lang.Exception
- Throws:
java.lang.Exception
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findSuperbioMetabolitesToCSV
public void findSuperbioMetabolitesToCSV(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt) throws java.lang.Exception
- Throws:
java.lang.Exception
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findSuperbioMetabolites
public org.openscience.cdk.interfaces.IAtomContainerSet findSuperbioMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, boolean annotate, MetaboliteFinder.FinderOption opt) throws java.lang.Exception
- Throws:
java.lang.Exception
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findAllEnvMicroMetabolites
public void findAllEnvMicroMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt) throws java.lang.Exception
- Throws:
java.lang.Exception
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findAllEnvMicroMetabolitesToCSV
public void findAllEnvMicroMetabolitesToCSV(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt) throws java.lang.Exception
- Throws:
java.lang.Exception
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findAllEnvMicroMetabolites
public org.openscience.cdk.interfaces.IAtomContainerSet findAllEnvMicroMetabolites(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, MetaboliteFinder.FinderOption opt) throws java.lang.Exception
- Throws:
java.lang.Exception
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findPathway
public org.openscience.cdk.interfaces.IAtomContainer findPathway(org.openscience.cdk.interfaces.IAtomContainer startingCompound, org.openscience.cdk.interfaces.IAtomContainer leafCompound, java.util.LinkedHashMap<java.lang.String,org.openscience.cdk.interfaces.IAtomContainerSet> compoundToParents, java.util.LinkedHashMap<java.lang.String,org.openscience.cdk.interfaces.IAtomContainer> inchikeyToContainers, boolean annotate) throws java.lang.CloneNotSupportedException, org.openscience.cdk.exception.CDKException
- Throws:
java.lang.CloneNotSupportedException
org.openscience.cdk.exception.CDKException
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compoundsHasToleratedMass
public boolean compoundsHasToleratedMass(org.openscience.cdk.interfaces.IAtomContainer atc, java.util.ArrayList<java.lang.Double> masses, double tolerance)
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