Uses of Class
biotransformer.transformation.MetabolicReaction
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Packages that use MetabolicReaction Package Description biotransformer.biomolecule This class implements the class of metabolic enzymes.biotransformer.biosystems biotransformer.btransformers biotransformer.transformation biotransformer.utils -
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Uses of MetabolicReaction in biotransformer.biomolecule
Methods in biotransformer.biomolecule that return types with arguments of type MetabolicReaction Modifier and Type Method Description java.util.ArrayList<MetabolicReaction>
Enzyme. getReactionSet()
Methods in biotransformer.biomolecule with parameters of type MetabolicReaction Modifier and Type Method Description void
Enzyme. addReaction(MetabolicReaction reaction)
Constructor parameters in biotransformer.biomolecule with type arguments of type MetabolicReaction Constructor Description Enzyme(java.lang.String enzName, java.util.ArrayList<MetabolicReaction> reactionSet)
Enzyme(java.lang.String enzName, java.util.ArrayList<MetabolicReaction> reactionSet, ambit2.smarts.SMIRKSManager smrkMan)
Enzyme(java.lang.String enzName, java.util.ArrayList<MetabolicReaction> reactionSet, java.util.ArrayList<java.lang.String> cellLocations)
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Uses of MetabolicReaction in biotransformer.biosystems
Methods in biotransformer.biosystems that return types with arguments of type MetabolicReaction Modifier and Type Method Description java.util.LinkedHashMap<java.lang.String,MetabolicReaction>
BioSystem. getReactionsHash()
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Uses of MetabolicReaction in biotransformer.btransformers
Fields in biotransformer.btransformers with type parameters of type MetabolicReaction Modifier and Type Field Description java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<MetabolicReaction>>
Biotransformer. reactionsByGroups
java.util.LinkedHashMap<java.lang.String,MetabolicReaction>
Biotransformer. reactionsHash
Methods in biotransformer.btransformers that return types with arguments of type MetabolicReaction Modifier and Type Method Description java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<MetabolicReaction>>
Biotransformer. getReactionsList()
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<MetabolicReaction>>
HGutBTransformer. getReactionsList()
returns a linked hash map with the reactions associated with the human gut, in addition to standardization reactions.Methods in biotransformer.btransformers with parameters of type MetabolicReaction Modifier and Type Method Description java.util.ArrayList<Biotransformation>
Biotransformer. applyReactionAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess)
java.util.ArrayList<Biotransformation>
Biotransformer. applyReactionAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
Phase2BTransformer. applyReactionAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
Biotransformer. applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, MetabolicReaction reaction, boolean preprocess, java.lang.Double scoreThreshold)
org.openscience.cdk.interfaces.IAtomContainerSet
Biotransformer. generateAllMetabolitesFromAtomContainer(org.openscience.cdk.interfaces.IAtomContainer molecule, MetabolicReaction mReaction, boolean preprocess)
Method parameters in biotransformer.btransformers with type arguments of type MetabolicReaction Modifier and Type Method Description java.util.ArrayList<Biotransformation>
Biotransformer. 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>
Biotransformer. applyReactionAtOnceAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
Biotransformer. 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
Biotransformer. 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
Biotransformer. 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
Biotransformer. 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
Biotransformer. 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>
Biotransformer. applyReactionsAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter)
java.util.ArrayList<Biotransformation>
Biotransformer. applyReactionsAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
EnvMicroBTransformer. applyReactionsAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
Phase2BTransformer. applyReactionsAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, java.lang.Double scoreThreshold)
java.util.ArrayList<Biotransformation>
Biotransformer. applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
Biotransformer. 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>
Biotransformer. applyReactionsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets, java.util.ArrayList<MetabolicReaction> reactions, boolean preprocess, boolean filter, int nr_of_steps)
java.util.ArrayList<Biotransformation>
Biotransformer. 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>
Biotransformer. 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
Biotransformer. extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash)
org.openscience.cdk.interfaces.IAtomContainerSet
Biotransformer. extractProductsFromBiotransformationsWithTransformationData(java.util.ArrayList<Biotransformation> biotransformations, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate)
void
Biotransformer. saveBioTransformationProductsToCSV(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash)
void
Biotransformer. saveBioTransformationProductsToCSV(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate)
void
Biotransformer. saveBioTransformationProductsToSdf(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash)
void
Biotransformer. saveBioTransformationProductsToSdf(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate)
void
Biotransformer. saveBioTransformationProductsToSDF(java.util.ArrayList<Biotransformation> biotransformations, java.lang.String outputFileName, java.util.LinkedHashMap<java.lang.String,MetabolicReaction> customReactionHash, boolean annotate)
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Uses of MetabolicReaction in biotransformer.transformation
Fields in biotransformer.transformation with type parameters of type MetabolicReaction Modifier and Type Field Description static java.util.ArrayList<MetabolicReaction>
MReactionSets. standardizationReactions
Methods in biotransformer.transformation that return types with arguments of type MetabolicReaction Modifier and Type Method Description java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactions(java.util.ArrayList<MetabolicReaction> reactions)
static java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactions(java.util.ArrayList<MetabolicReaction> reactions, java.util.LinkedHashMap<MRPatterns.ReactionName,MRPatterns.ReactionName[]> btph)
java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactions(java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction> reactions)
static java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactions(java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction> reactions, java.util.LinkedHashMap<MRPatterns.ReactionName,MRPatterns.ReactionName[]> btph)
java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactionsLSM(java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions)
Method parameters in biotransformer.transformation with type arguments of type MetabolicReaction Modifier and Type Method Description java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactions(java.util.ArrayList<MetabolicReaction> reactions)
static java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactions(java.util.ArrayList<MetabolicReaction> reactions, java.util.LinkedHashMap<MRPatterns.ReactionName,MRPatterns.ReactionName[]> btph)
java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactions(java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction> reactions)
static java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactions(java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction> reactions, java.util.LinkedHashMap<MRPatterns.ReactionName,MRPatterns.ReactionName[]> btph)
java.util.LinkedHashMap<MRPatterns.ReactionName,MetabolicReaction>
MReactionsFilter. filterReactionsLSM(java.util.LinkedHashMap<java.lang.String,MetabolicReaction> reactions)
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Uses of MetabolicReaction in biotransformer.utils
Methods in biotransformer.utils with parameters of type MetabolicReaction Modifier and Type Method Description static boolean
ChemStructureExplorer. compoundMatchesReactionConstraints(MetabolicReaction reaction, org.openscience.cdk.interfaces.IAtomContainer molecule)
Given a molecule A and a MetabolicReaction M, find whether A matches all the structural constraints imposed by M
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