Class Phase2BTransformer


  • public class Phase2BTransformer
    extends Biotransformer
    Author:
    Yannick Djoumbou Feunang
    • Constructor Detail

      • Phase2BTransformer

        public Phase2BTransformer​(BioSystem.BioSystemName bioSName)
                           throws java.io.IOException,
                                  org.json.simple.parser.ParseException,
                                  org.openscience.cdk.exception.CDKException
        Throws:
        java.io.IOException
        org.json.simple.parser.ParseException
        org.openscience.cdk.exception.CDKException
    • Method Detail

      • applyPhase2Transformations

        public java.util.ArrayList<Biotransformation> applyPhase2Transformations​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                 boolean precheck,
                                                                                 boolean preprocess,
                                                                                 boolean filter)
                                                                          throws java.lang.Exception
        Parameters:
        target -
        preprocess -
        filter -
        Returns:
        an arraylist of biotransformations, which are instances of the Phase II metabolic reactions applied to the target, with the set minimum threshold of 0.0
        Throws:
        java.lang.Exception
      • applyPhase2Transformations

        public java.util.ArrayList<Biotransformation> applyPhase2Transformations​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                 boolean precheck,
                                                                                 boolean preprocess,
                                                                                 boolean filter,
                                                                                 double scoreThreshold)
                                                                          throws java.lang.Exception
        Parameters:
        target -
        preprocess -
        filter -
        scoreThreshold -
        Returns:
        an arraylist of biotransformations, which are instances of the Phase II metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • applyPhase2Transformations

        public java.util.ArrayList<Biotransformation> applyPhase2Transformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets,
                                                                                 boolean precheck,
                                                                                 boolean preprocess,
                                                                                 boolean filter,
                                                                                 double scoreThreshold)
                                                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • applyPhase2TransformationsChainAndReturnBiotransformations

        public java.util.ArrayList<Biotransformation> applyPhase2TransformationsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                                                 boolean precheck,
                                                                                                                 boolean preprocess,
                                                                                                                 boolean filter,
                                                                                                                 int nr_of_steps)
                                                                                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • applyPhase2TransformationsChainAndReturnBiotransformations

        public java.util.ArrayList<Biotransformation> applyPhase2TransformationsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                                                 boolean precheck,
                                                                                                                 boolean preprocess,
                                                                                                                 boolean filter,
                                                                                                                 int nr_of_steps,
                                                                                                                 java.lang.Double scoreThreshold)
                                                                                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • applyPhase2TransformationsChainAndReturnBiotransformations

        public java.util.ArrayList<Biotransformation> applyPhase2TransformationsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet targets,
                                                                                                                 boolean precheck,
                                                                                                                 boolean preprocess,
                                                                                                                 boolean filter,
                                                                                                                 int nr_of_steps,
                                                                                                                 java.lang.Double scoreThreshold)
                                                                                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • 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
        Overrides:
        applyReactionsAndReturnBiotransformations in class Biotransformer
        Throws:
        java.lang.Exception
      • applyReactionChainFromSDF

        public void applyReactionChainFromSDF​(java.lang.String inputFileName,
                                              boolean precheck,
                                              boolean preprocess,
                                              boolean filter,
                                              int nr_of_steps,
                                              java.lang.Double scoreThreshold)
                                       throws java.lang.Exception
        Throws:
        java.lang.Exception
      • applyReactionChainFromSdfToSingleSdf

        public void applyReactionChainFromSdfToSingleSdf​(java.lang.String inputFileName,
                                                         boolean precheck,
                                                         boolean preprocess,
                                                         boolean filter,
                                                         int nr_of_steps,
                                                         java.lang.Double scoreThreshold,
                                                         java.lang.String outputFileName,
                                                         boolean annotate)
                                                  throws java.lang.Exception
        Throws:
        java.lang.Exception
      • isPotentialHumanPhase2SubstrateByReactionPatternMatching

        public boolean isPotentialHumanPhase2SubstrateByReactionPatternMatching​(org.openscience.cdk.interfaces.IAtomContainer substrate)
                                                                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • isPotentialNonHumanPhase2SubstrateByReactionPatternMatching

        public boolean isPotentialNonHumanPhase2SubstrateByReactionPatternMatching​(org.openscience.cdk.interfaces.IAtomContainer substrate)
                                                                            throws java.lang.Exception
        Throws:
        java.lang.Exception
      • isPotentialPhase2SubstrateByReactionPatternMatching

        public boolean isPotentialPhase2SubstrateByReactionPatternMatching​(org.openscience.cdk.interfaces.IAtomContainer substrate)
                                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • reduceSet

        public org.openscience.cdk.interfaces.IAtomContainerSet reduceSet​(org.openscience.cdk.interfaces.IAtomContainerSet molecules)
                                                                   throws org.openscience.cdk.exception.CDKException,
                                                                          java.lang.Exception
        Throws:
        org.openscience.cdk.exception.CDKException
        java.lang.Exception
      • selectBiotransformationWithValidProducts

        public java.util.ArrayList<Biotransformation> selectBiotransformationWithValidProducts​(java.util.ArrayList<Biotransformation> biotransformations)
                                                                                        throws ambit2.smarts.query.SMARTSException,
                                                                                               org.openscience.cdk.exception.CDKException,
                                                                                               java.lang.CloneNotSupportedException
        Throws:
        ambit2.smarts.query.SMARTSException
        org.openscience.cdk.exception.CDKException
        java.lang.CloneNotSupportedException
      • printStatistics

        public void printStatistics()