Class ECBasedBTransformer


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

      • ECBasedBTransformer

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

      • applyEcBasedDeconjuations

        public java.util.ArrayList<Biotransformation> applyEcBasedDeconjuations​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                boolean preprocess,
                                                                                boolean filter,
                                                                                int nrOfSteps)
                                                                         throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        nrOfSteps - - number of steps
        Returns:
        an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with a threshold of 0.0
        Throws:
        java.lang.Exception
      • applyEcBasedDeconjugations

        public java.util.ArrayList<Biotransformation> applyEcBasedDeconjugations​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                 boolean preprocess,
                                                                                 boolean filter,
                                                                                 int nr_of_steps,
                                                                                 double scoreThreshold)
                                                                          throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        scoreThreshold - - minimum score threshold for selected metbaolic reactions
        Returns:
        an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • applyEcBasedDeconjuationsChain

        public java.util.ArrayList<Biotransformation> applyEcBasedDeconjuationsChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                     boolean preprocess,
                                                                                     boolean filter,
                                                                                     int nr_of_steps)
                                                                              throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        nr_of_steps - - number of steps
        Returns:
        an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the minimum threshold of 0.0
        Throws:
        java.lang.Exception - - Throw an exception
      • applyEcBasedDeconjuationsChain

        public java.util.ArrayList<Biotransformation> applyEcBasedDeconjuationsChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                     boolean preprocess,
                                                                                     boolean filter,
                                                                                     int nr_of_steps,
                                                                                     double scoreThreshold)
                                                                              throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        nr_of_steps - - number of steps
        Returns:
        an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • applyEcBasedTransformations

        public java.util.ArrayList<Biotransformation> applyEcBasedTransformations​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                  boolean preprocess,
                                                                                  boolean filter)
                                                                           throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        Returns:
        an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with a threshold of 0.0
        Throws:
        java.lang.Exception - - throw any exception
      • applyEcBasedTransformations

        public java.util.ArrayList<Biotransformation> applyEcBasedTransformations​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                  boolean preprocess,
                                                                                  boolean filter,
                                                                                  double scoreThreshold)
                                                                           throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        scoreThreshold - - minimum threshold for reaction scores
        Returns:
        an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • applyEcBasedTransformationsChain

        public java.util.ArrayList<Biotransformation> applyEcBasedTransformationsChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                       boolean preprocess,
                                                                                       boolean filter,
                                                                                       int nr_of_steps)
                                                                                throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        nr_of_steps - - number of steps
        Returns:
        an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the minimum threshold of 0.0
        Throws:
        java.lang.Exception - - throw any exception
      • applyEcBasedTransformationsChain

        public java.util.ArrayList<Biotransformation> applyEcBasedTransformationsChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                       boolean preprocess,
                                                                                       boolean filter,
                                                                                       int nr_of_steps,
                                                                                       double scoreThreshold)
                                                                                throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        nr_of_steps - - number of steps
        Returns:
        an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception - - throw any exception
      • applyEcBasedConjugations

        public java.util.ArrayList<Biotransformation> applyEcBasedConjugations​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                               boolean preprocess,
                                                                               boolean filter,
                                                                               double scoreThreshold)
                                                                        throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        nr_of_steps - - number of steps
        scoreThreshold - - minimum threshold for reaction scores
        Returns:
        an arraylist of biotransformations, which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • applyEcBasedConjuationsChain

        public java.util.ArrayList<Biotransformation> applyEcBasedConjuationsChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                   boolean preprocess,
                                                                                   boolean filter,
                                                                                   int nr_of_steps)
                                                                            throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        nr_of_steps - - number of steps
        Returns:
        an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the minimum threshold of 0.0
        Throws:
        java.lang.Exception
      • applyEcBasedConjuationsChain

        public java.util.ArrayList<Biotransformation> applyEcBasedConjuationsChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                   boolean preprocess,
                                                                                   boolean filter,
                                                                                   int nr_of_steps,
                                                                                   double scoreThreshold)
                                                                            throws java.lang.Exception
        Parameters:
        target - - The molecule to transform
        preprocess - - specify whether to perform molecule preprocessing
        filter - - apply reaction filtering
        nr_of_steps - - number of steps
        Returns:
        an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the EC-based metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • simulateECBasedPhaseIMetabolismStep

        public java.util.ArrayList<Biotransformation> simulateECBasedPhaseIMetabolismStep​(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                                                          boolean preprocess,
                                                                                          boolean filter,
                                                                                          java.lang.Double scoreThreshold)
      • simulateECBasedPhaseIMetabolismStep

        public java.util.ArrayList<Biotransformation> simulateECBasedPhaseIMetabolismStep​(org.openscience.cdk.interfaces.IAtomContainerSet molecules,
                                                                                          boolean preprocess,
                                                                                          boolean filter,
                                                                                          java.lang.Double scoreThreshold)
                                                                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateECBasedPhaseIMetabolismChain

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

        public java.util.ArrayList<Biotransformation> simulateECBasedPhaseIMetabolismChain​(org.openscience.cdk.interfaces.IAtomContainerSet molecules,
                                                                                           boolean preprocess,
                                                                                           boolean filter,
                                                                                           int nrOfSteps,
                                                                                           java.lang.Double scoreThreshold)
                                                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateECBasedMetabolismStep

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

        public java.util.ArrayList<Biotransformation> simulateECBasedMetabolismStep​(org.openscience.cdk.interfaces.IAtomContainerSet molecules,
                                                                                    boolean preprocess,
                                                                                    boolean filter,
                                                                                    java.lang.Double scoreThreshold)
                                                                             throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateECBasedMetabolismChain

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

        public java.util.ArrayList<Biotransformation> simulateECBasedMetabolismChain​(org.openscience.cdk.interfaces.IAtomContainerSet molecules,
                                                                                     boolean preprocess,
                                                                                     boolean filter,
                                                                                     int nrOfSteps,
                                                                                     java.lang.Double scoreThreshold)
                                                                              throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateECBasedMetabolismAndSaveToSDF

        public void simulateECBasedMetabolismAndSaveToSDF​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                          int nrOfSteps,
                                                          java.lang.Double scoreThreshold,
                                                          java.lang.String outputFolder,
                                                          boolean annotate)
                                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateECBasedMetabolismAndSaveToSDF

        public void simulateECBasedMetabolismAndSaveToSDF​(java.lang.String sdfFileName,
                                                          int nrOfSteps,
                                                          java.lang.Double scoreThreshold,
                                                          java.lang.String outputFolder,
                                                          boolean annotate)
                                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • isDeconjugationCandidate

        public boolean isDeconjugationCandidate​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                         throws ambit2.smarts.query.SMARTSException,
                                                org.openscience.cdk.exception.CDKException,
                                                java.io.IOException
        Throws:
        ambit2.smarts.query.SMARTSException
        org.openscience.cdk.exception.CDKException
        java.io.IOException
      • isConjugationCandidate

        public boolean isConjugationCandidate​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                       throws ambit2.smarts.query.SMARTSException,
                                              org.openscience.cdk.exception.CDKException,
                                              java.io.IOException
        Throws:
        ambit2.smarts.query.SMARTSException
        org.openscience.cdk.exception.CDKException
        java.io.IOException
      • printStatistics

        public void printStatistics()