Package biotransformer.btransformers
Class Biotransformer
- java.lang.Object
-
- biotransformer.btransformers.Biotransformer
-
- Direct Known Subclasses:
Cyp450BTransformer
,Deglycolyzer
,ECBasedBTransformer
,EnvMicroBTransformer
,HGutBTransformer
,Phase2BTransformer
public class Biotransformer extends java.lang.Object
- Author:
- Djoumbou Feunang, Yannick
-
-
Field Summary
Fields Modifier and Type Field Description BioSystem
bSystem
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<Enzyme>>
enzymesByreactionGroups
java.util.ArrayList<Enzyme>
enzymesList
org.openscience.cdk.inchi.InChIGeneratorFactory
inchiGenFactory
org.codehaus.jackson.map.ObjectMapper
mapper
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<MetabolicReaction>>
reactionsByGroups
java.util.LinkedHashMap<java.lang.String,MetabolicReaction>
reactionsHash
org.openscience.cdk.smiles.SmilesGenerator
smiGen
-
Constructor Summary
Constructors Constructor Description Biotransformer(BioSystem.BioSystemName bioSName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.ArrayList<Biotransformation>
applyPathwaySpecificBiotransformationChain(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyPathwaySpecificBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
Predicts the metabolism of a compound for a specific pathway, and returns metabolites with a minimal given score threshold.java.util.ArrayList<Biotransformation>
applyPathwaySpecificBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
Predicts the metabolism of a compound for a specific pathway, and returns metabolites with a minimal given score threshold.java.util.ArrayList<Biotransformation>
applyPathwaySpecificBiotransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyPathwaySpecificBiotransformationsChain(org.openscience.cdk.interfaces.IAtomContainerSet targets, MetabolicPathway.MPathwayName pathwayName, 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.util.ArrayList<Biotransformation>
applyReactionAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
org.openscience.cdk.interfaces.IAtomContainerSet
applyReactionChain(org.openscience.cdk.interfaces.IAtomContainer target, ambit2.smarts.SMIRKSManager smrkMan, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps)
org.openscience.cdk.interfaces.IAtomContainerSet
applyReactionChain(org.openscience.cdk.interfaces.IAtomContainer target, ambit2.smarts.SMIRKSManager smrkMan, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
org.openscience.cdk.interfaces.IAtomContainerSet
applyReactions(org.openscience.cdk.interfaces.IAtomContainer target, ambit2.smarts.SMIRKSManager smrkMan, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions, boolean preprocess, boolean filter)
org.openscience.cdk.interfaces.IAtomContainerSet
applyReactions(org.openscience.cdk.interfaces.IAtomContainer target, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionsAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter)
java.util.ArrayList<Biotransformation>
applyReactionsAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
applyReactionsFromContainersAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
org.openscience.cdk.interfaces.IAtomContainerSet
extractProductsFromBiotransformations(java.util.ArrayList<Biotransformation> biotransformations)
org.openscience.cdk.interfaces.IAtomContainerSet
extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations)
org.openscience.cdk.interfaces.IAtomContainerSet
extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, boolean annotate)
org.openscience.cdk.interfaces.IAtomContainerSet
extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash)
org.openscience.cdk.interfaces.IAtomContainerSet
extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate)
org.openscience.cdk.interfaces.IAtomContainerSet
generateAllMetabolitesFromAtomContainer(org.openscience.cdk.interfaces.IAtomContainer molecule, ambit2.smarts.SMIRKSReaction reaction, boolean preprocess)
org.openscience.cdk.interfaces.IAtomContainerSet
generateAllMetabolitesFromAtomContainer(org.openscience.cdk.interfaces.IAtomContainer molecule, MetabolicReaction mReaction, boolean preprocess)
org.openscience.cdk.interfaces.IAtomContainerSet
generateAllMetabolitesFromAtomContainerViaTransformationAtAllLocations(org.openscience.cdk.interfaces.IAtomContainer molecule, ambit2.smarts.SMIRKSReaction reaction, boolean preprocess)
BioSystem.BioSystemName
getBioSystemName()
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<MetabolicReaction>>
getReactionsList()
org.openscience.cdk.smiles.SmilesParser
getSmiParser()
boolean
isValidSubstrate(org.openscience.cdk.interfaces.IAtomContainer target, Enzyme.EnzymeName enzymeName)
java.util.ArrayList<Biotransformation>
metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz, boolean preprocess, boolean filter, double threshold)
java.util.ArrayList<Biotransformation>
metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme enzyme, boolean preprocess, boolean filter, double threshold)
java.util.ArrayList<Biotransformation>
metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme enzyme, boolean preprocess, boolean filter, int nrOfSteps, double threshold)
java.util.ArrayList<Biotransformation>
metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainerSet substrates, Enzyme enzyme, boolean preprocess, boolean filter, double threshold)
java.util.ArrayList<Biotransformation>
metabolizeWithEnzymes(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
metabolizeWithEnzymes(org.openscience.cdk.interfaces.IAtomContainerSet substrates, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, double threshold)
java.util.ArrayList<Biotransformation>
metabolizeWithEnzymesBreadthFirst(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
metabolizeWithEnzymesBreadthFirst(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
metabolizeWithEnzymesDephtFirst(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold)
void
saveBioTransformationProductsToCSV(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName)
void
saveBioTransformationProductsToCSV(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate)
void
saveBioTransformationProductsToCSV(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash)
void
saveBioTransformationProductsToCSV(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate)
void
saveBioTransformationProductsToSdf(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName)
void
saveBioTransformationProductsToSdf(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, boolean annotate)
void
saveBioTransformationProductsToSdf(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash)
void
saveBioTransformationProductsToSdf(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate)
void
saveBioTransformationProductsToSDF(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate)
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Field Detail
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bSystem
public BioSystem bSystem
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smiGen
public org.openscience.cdk.smiles.SmilesGenerator smiGen
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inchiGenFactory
public org.openscience.cdk.inchi.InChIGeneratorFactory inchiGenFactory
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reactionsByGroups
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<MetabolicReaction>> reactionsByGroups
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enzymesByreactionGroups
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<Enzyme>> enzymesByreactionGroups
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enzymesList
public java.util.ArrayList<Enzyme> enzymesList
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reactionsHash
public java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactionsHash
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mapper
public org.codehaus.jackson.map.ObjectMapper mapper
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Constructor Detail
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Biotransformer
public Biotransformer(BioSystem.BioSystemName bioSName) throws org.codehaus.jackson.JsonParseException, org.codehaus.jackson.map.JsonMappingException, java.io.IOException, org.openscience.cdk.exception.CDKException
- Throws:
org.codehaus.jackson.JsonParseException
org.codehaus.jackson.map.JsonMappingException
java.io.IOException
org.openscience.cdk.exception.CDKException
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Method Detail
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getBioSystemName
public BioSystem.BioSystemName getBioSystemName()
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getReactionsList
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<MetabolicReaction>> getReactionsList()
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generateAllMetabolitesFromAtomContainer
public org.openscience.cdk.interfaces.IAtomContainerSet generateAllMetabolitesFromAtomContainer(org.openscience.cdk.interfaces.IAtomContainer molecule, MetabolicReaction mReaction, boolean preprocess) throws java.lang.Exception
- Parameters:
molecule
- : A molecule of interestmReaction
- : A MetabolicReactionpreprocess
- : A boolean that specifies whether to apply preprocessing or not- Returns:
- : A set of metabolites or products generated by applying the reaction to the molecule of interest
- Throws:
java.lang.Exception
- : Throws an Exception
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generateAllMetabolitesFromAtomContainer
public org.openscience.cdk.interfaces.IAtomContainerSet generateAllMetabolitesFromAtomContainer(org.openscience.cdk.interfaces.IAtomContainer molecule, ambit2.smarts.SMIRKSReaction reaction, boolean preprocess) throws java.lang.Exception
- Parameters:
molecule
- : A molecule of interestreaction
- : A SMIRKSReactionpreprocess
- : A boolean that specifies whether to apply preprocessing or not- Returns:
- : A set of metabolites or products generated by applying the reaction to the molecule of interest
- Throws:
java.lang.Exception
- : Throws an Exception
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generateAllMetabolitesFromAtomContainerViaTransformationAtAllLocations
public org.openscience.cdk.interfaces.IAtomContainerSet generateAllMetabolitesFromAtomContainerViaTransformationAtAllLocations(org.openscience.cdk.interfaces.IAtomContainer molecule, ambit2.smarts.SMIRKSReaction reaction, boolean preprocess) 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) 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
- 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) 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
- Throws:
java.lang.Exception
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applyReactionsFromContainersAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionsFromContainersAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionsChainAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionsChainAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionsChainAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionsChainAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactions
public org.openscience.cdk.interfaces.IAtomContainerSet applyReactions(org.openscience.cdk.interfaces.IAtomContainer target, ambit2.smarts.SMIRKSManager smrkMan, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions, boolean preprocess, boolean filter) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactions
public org.openscience.cdk.interfaces.IAtomContainerSet applyReactions(org.openscience.cdk.interfaces.IAtomContainer target, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionChain
public org.openscience.cdk.interfaces.IAtomContainerSet applyReactionChain(org.openscience.cdk.interfaces.IAtomContainer target, ambit2.smarts.SMIRKSManager smrkMan, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionChain
public org.openscience.cdk.interfaces.IAtomContainerSet applyReactionChain(org.openscience.cdk.interfaces.IAtomContainer target, ambit2.smarts.SMIRKSManager smrkMan, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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metabolizeWithEnzyme
public java.util.ArrayList<Biotransformation> metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme.EnzymeName enz, boolean preprocess, boolean filter, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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metabolizeWithEnzyme
public java.util.ArrayList<Biotransformation> metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme enzyme, boolean preprocess, boolean filter, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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metabolizeWithEnzyme
public java.util.ArrayList<Biotransformation> metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainer substrate, Enzyme enzyme, boolean preprocess, boolean filter, int nrOfSteps, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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metabolizeWithEnzyme
public java.util.ArrayList<Biotransformation> metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainerSet substrates, Enzyme enzyme, boolean preprocess, boolean filter, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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isValidSubstrate
public boolean isValidSubstrate(org.openscience.cdk.interfaces.IAtomContainer target, Enzyme.EnzymeName enzymeName) throws java.lang.Exception
- Throws:
java.lang.Exception
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metabolizeWithEnzymes
public java.util.ArrayList<Biotransformation> metabolizeWithEnzymes(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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metabolizeWithEnzymes
public java.util.ArrayList<Biotransformation> metabolizeWithEnzymes(org.openscience.cdk.interfaces.IAtomContainerSet substrates, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, double threshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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metabolizeWithEnzymesDephtFirst
public java.util.ArrayList<Biotransformation> metabolizeWithEnzymesDephtFirst(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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metabolizeWithEnzymesBreadthFirst
public java.util.ArrayList<Biotransformation> metabolizeWithEnzymesBreadthFirst(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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metabolizeWithEnzymesBreadthFirst
public java.util.ArrayList<Biotransformation> metabolizeWithEnzymesBreadthFirst(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<Enzyme> enzymes, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionAtOnceAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionAtOnceAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionAtOnceAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyReactionAtOnceAndReturnBiotransformations
public java.util.ArrayList<Biotransformation> applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nrOfSteps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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getSmiParser
public org.openscience.cdk.smiles.SmilesParser getSmiParser()
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extractProductsFromBiotransformations
public org.openscience.cdk.interfaces.IAtomContainerSet extractProductsFromBiotransformations(java.util.ArrayList<Biotransformation> biotransformations) throws java.lang.Exception
- Throws:
java.lang.Exception
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extractProductsFromBiotransformationsWithTransformationData
public org.openscience.cdk.interfaces.IAtomContainerSet extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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extractProductsFromBiotransformationsWithTransformationData
public org.openscience.cdk.interfaces.IAtomContainerSet extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash) throws java.lang.Exception
- Throws:
java.lang.Exception
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extractProductsFromBiotransformationsWithTransformationData
public org.openscience.cdk.interfaces.IAtomContainerSet extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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extractProductsFromBiotransformationsWithTransformationData
public org.openscience.cdk.interfaces.IAtomContainerSet extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations) 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) 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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saveBioTransformationProductsToSdf
public void saveBioTransformationProductsToSdf(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash) 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, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyPathwaySpecificBiotransformationChain
public java.util.ArrayList<Biotransformation> applyPathwaySpecificBiotransformationChain(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, int nr_of_steps) 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) 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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saveBioTransformationProductsToCSV
public void saveBioTransformationProductsToCSV(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash) 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, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, 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, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyPathwaySpecificBiotransformations
public java.util.ArrayList<Biotransformation> applyPathwaySpecificBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
Predicts the metabolism of a compound for a specific pathway, and returns metabolites with a minimal given score threshold.- Parameters:
target
- - An AtomContainer that represent a chemical compoundpathwayName
- - the name of a MetabolicPathway object. It must belong to the MPathwayName enum.preprocess
- - specifies whether the compounds must be pre-processed.filter
- - specifies whether the reactions should be filtered, according to priority rules.scoreThreshold
- - the minimal score that a metabolite must have to be returned.- Returns:
- an ArrayList of biotransformations
- Throws:
java.lang.Exception
- : Throws an Exception
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applyPathwaySpecificBiotransformations
public java.util.ArrayList<Biotransformation> applyPathwaySpecificBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, java.lang.Double scoreThreshold) throws java.lang.Exception
Predicts the metabolism of a compound for a specific pathway, and returns metabolites with a minimal given score threshold.- Parameters:
targets
- - A set of chemical compoundspathwayName
- - the name of a MetabolicPathway object. It must belong to the MPathwayName enum.preprocess
- - specifies whether the compounds must be pre-processed.filter
- - specifies whether the reactions should be filtered, according to priority rules.scoreThreshold
- - the minimal score that a metabolite must have to be returned.- Returns:
- an ArrayList of biotransformations
- Throws:
java.lang.Exception
- : Throws an Exception
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applyPathwaySpecificBiotransformationsChain
public java.util.ArrayList<Biotransformation> applyPathwaySpecificBiotransformationsChain(org.openscience.cdk.interfaces.IAtomContainerSet targets, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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applyPathwaySpecificBiotransformationsChain
public java.util.ArrayList<Biotransformation> applyPathwaySpecificBiotransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicPathway.MPathwayName pathwayName, boolean preprocess, boolean filter, int nr_of_steps, java.lang.Double scoreThreshold) throws java.lang.Exception
- Throws:
java.lang.Exception
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