java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedConjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedConjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedConjugations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedDeconjuations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nrOfSteps) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedDeconjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedDeconjuationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedDeconjugations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedTransformations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedTransformations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.applyEcBasedTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
EnvMicroBTransformer.applyEnvMicrobialTransformations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter) |
|
java.util.ArrayList<Biotransformation> |
EnvMicroBTransformer.applyEnvMicrobialTransformations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
EnvMicroBTransformer.applyEnvMicrobialTransformations(org.openscience.cdk.interfaces.IAtomContainerSet targets,
boolean preprocess,
boolean filter,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
EnvMicroBTransformer.applyEnvMicrobialTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps) |
|
java.util.ArrayList<Biotransformation> |
EnvMicroBTransformer.applyEnvMicrobialTransformationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialConjugations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialConjugations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialConjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialConjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialDeconjugations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialDeconjugations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialDeconjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialDeconjugationsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialMetabolismHydrolysisAndRedoxChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialMetabolismHydrolysisAndRedoxChain(org.openscience.cdk.interfaces.IAtomContainerSet targets,
boolean preprocess,
boolean filter,
int nr_of_steps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialMetabolismHydrolysisAndRedoxStep(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialMetabolismHydrolysisAndRedoxStep(org.openscience.cdk.interfaces.IAtomContainerSet targets,
boolean preprocess,
boolean filter,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialRedoxChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialRedoxReactions(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialRedoxReactions(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.applyGutMicrobialRedoxReactionsChain(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int nr_of_steps) |
|
java.util.ArrayList<Biotransformation> |
Biotransformer.applyPathwaySpecificBiotransformationChain(org.openscience.cdk.interfaces.IAtomContainer target,
MetabolicPathway.MPathwayName pathwayName,
boolean preprocess,
boolean filter,
int nr_of_steps) |
|
java.util.ArrayList<Biotransformation> |
Biotransformer.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> |
Biotransformer.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> |
Biotransformer.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> |
Biotransformer.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> |
Phase2BTransformer.applyPhase2Transformations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean precheck,
boolean preprocess,
boolean filter) |
|
java.util.ArrayList<Biotransformation> |
Phase2BTransformer.applyPhase2Transformations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean precheck,
boolean preprocess,
boolean filter,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
Phase2BTransformer.applyPhase2Transformations(org.openscience.cdk.interfaces.IAtomContainerSet targets,
boolean precheck,
boolean preprocess,
boolean filter,
double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
Phase2BTransformer.applyPhase2TransformationsChainAndReturnBiotransformations(org.openscience.cdk.interfaces.IAtomContainer target,
boolean precheck,
boolean preprocess,
boolean filter,
int nr_of_steps) |
|
java.util.ArrayList<Biotransformation> |
Phase2BTransformer.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> |
Phase2BTransformer.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> |
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) |
|
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) |
|
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) |
|
java.util.ArrayList<Biotransformation> |
Biotransformer.metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainer substrate,
Enzyme.EnzymeName enz,
boolean preprocess,
boolean filter,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Biotransformer.metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainer substrate,
Enzyme enzyme,
boolean preprocess,
boolean filter,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Biotransformer.metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainer substrate,
Enzyme enzyme,
boolean preprocess,
boolean filter,
int nrOfSteps,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Biotransformer.metabolizeWithEnzyme(org.openscience.cdk.interfaces.IAtomContainerSet substrates,
Enzyme enzyme,
boolean preprocess,
boolean filter,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Biotransformer.metabolizeWithEnzymes(org.openscience.cdk.interfaces.IAtomContainer target,
java.util.ArrayList<Enzyme> enzymes,
boolean preprocess,
boolean filter,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
Biotransformer.metabolizeWithEnzymes(org.openscience.cdk.interfaces.IAtomContainerSet substrates,
java.util.ArrayList<Enzyme> enzymes,
boolean preprocess,
boolean filter,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Biotransformer.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> |
Biotransformer.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> |
Biotransformer.metabolizeWithEnzymesDephtFirst(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> |
Cyp450BTransformer.predictCyp450BiotransformationChain(org.openscience.cdk.interfaces.IAtomContainer substrate,
boolean preprocess,
boolean filter,
int nrOfSteps,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Cyp450BTransformer.predictCyp450BiotransformationChain(org.openscience.cdk.interfaces.IAtomContainerSet substrates,
boolean preprocess,
boolean filter,
int nrOfSteps,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Cyp450BTransformer.predictCyp450Biotransformations(java.lang.String sdfFileName,
boolean preprocess,
boolean filter,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Cyp450BTransformer.predictCyp450Biotransformations(org.openscience.cdk.interfaces.IAtomContainer substrate,
boolean preprocess,
boolean filter,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Cyp450BTransformer.predictCyp450Biotransformations(org.openscience.cdk.interfaces.IAtomContainerSet substrates,
boolean preprocess,
boolean filter,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Cyp450BTransformer.predictCyp450BiotransformationsForSpecificEnzymes(org.openscience.cdk.interfaces.IAtomContainer substrate,
java.util.ArrayList<Enzyme.EnzymeName> enzymeNames,
boolean preprocess,
boolean filter,
double threshold) |
|
java.util.ArrayList<Biotransformation> |
Phase2BTransformer.selectBiotransformationWithValidProducts(java.util.ArrayList<Biotransformation> biotransformations) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.simulateECBasedMetabolismChain(org.openscience.cdk.interfaces.IAtomContainer molecule,
boolean preprocess,
boolean filter,
int nrOfSteps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.simulateECBasedMetabolismChain(org.openscience.cdk.interfaces.IAtomContainerSet molecules,
boolean preprocess,
boolean filter,
int nrOfSteps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.simulateECBasedMetabolismStep(org.openscience.cdk.interfaces.IAtomContainer molecule,
boolean preprocess,
boolean filter,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.simulateECBasedMetabolismStep(org.openscience.cdk.interfaces.IAtomContainerSet molecules,
boolean preprocess,
boolean filter,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.simulateECBasedPhaseIMetabolismChain(org.openscience.cdk.interfaces.IAtomContainer molecule,
boolean preprocess,
boolean filter,
int nrOfSteps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.simulateECBasedPhaseIMetabolismChain(org.openscience.cdk.interfaces.IAtomContainerSet molecules,
boolean preprocess,
boolean filter,
int nrOfSteps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.simulateECBasedPhaseIMetabolismStep(org.openscience.cdk.interfaces.IAtomContainer molecule,
boolean preprocess,
boolean filter,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
ECBasedBTransformer.simulateECBasedPhaseIMetabolismStep(org.openscience.cdk.interfaces.IAtomContainerSet molecules,
boolean preprocess,
boolean filter,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
EnvMicroBTransformer.simulateEnvMicrobialDegradation(org.openscience.cdk.interfaces.IAtomContainerSet containers,
boolean preprocess,
boolean filter,
int nrOfSteps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.simulateGutMicrobialMetabolism(java.lang.String targetsFileNameInSDF,
boolean preprocess,
boolean filter,
int nr_of_steps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int numberOfSteps) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainer target,
boolean preprocess,
boolean filter,
int numberOfSteps,
java.lang.Double scoreThreshold) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet targets,
boolean preprocess,
boolean filter,
int numberOfSteps) |
|
java.util.ArrayList<Biotransformation> |
HGutBTransformer.simulateGutMicrobialMetabolism(org.openscience.cdk.interfaces.IAtomContainerSet targets,
boolean preprocess,
boolean filter,
int numberOfSteps,
java.lang.Double scoreThreshold) |
|