Class HGutBTransformer

    • Constructor Detail

      • HGutBTransformer

        public HGutBTransformer()
                         throws java.io.IOException,
                                org.openscience.cdk.exception.CDKException
        Throws:
        java.io.IOException
        org.openscience.cdk.exception.CDKException
    • Method Detail

      • getReactionsList

        public java.util.LinkedHashMap<java.lang.String,​java.util.ArrayList<MetabolicReaction>> getReactionsList()
        returns a linked hash map with the reactions associated with the human gut, in addition to standardization reactions.
        Overrides:
        getReactionsList in class Biotransformer
      • applyGutMicrobialDeconjugations

        public java.util.ArrayList<Biotransformation> applyGutMicrobialDeconjugations​(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 human gut microbial reactions applied to the target, with a threshold of 0.0
        Throws:
        java.lang.Exception - - throw any exception
      • applyGutMicrobialDeconjugations

        public java.util.ArrayList<Biotransformation> applyGutMicrobialDeconjugations​(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
        Returns:
        an arraylist of biotransformations, which are instances of the human gut microbial reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception - - throw any exception
      • applyGutMicrobialDeconjugationsChain

        public java.util.ArrayList<Biotransformation> applyGutMicrobialDeconjugationsChain​(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 human gut microbial metabolic reactions applied to the target, with the minimum threshold of 0.0
        Throws:
        java.lang.Exception - - throw any exception
      • applyGutMicrobialDeconjugationsChain

        public java.util.ArrayList<Biotransformation> applyGutMicrobialDeconjugationsChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                           boolean preprocess,
                                                                                           boolean filter,
                                                                                           int nr_of_steps,
                                                                                           java.lang.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 - - The minimum score for a reaction
        Returns:
        an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the human gut microbial metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • applyGutMicrobialRedoxReactions

        public java.util.ArrayList<Biotransformation> applyGutMicrobialRedoxReactions​(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 human gut microbial reactions applied to the target, with a threshold of 0.0
        Throws:
        java.lang.Exception
      • applyGutMicrobialRedoxReactions

        public java.util.ArrayList<Biotransformation> applyGutMicrobialRedoxReactions​(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 human gut microbial reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception - - throw any exception
      • applyGutMicrobialRedoxReactionsChain

        public java.util.ArrayList<Biotransformation> applyGutMicrobialRedoxReactionsChain​(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 human gut microbial metabolic reactions applied to the target, with the minimum threshold of 0.0
        Throws:
        java.lang.Exception - - throw any exception
      • applyGutMicrobialRedoxChain

        public java.util.ArrayList<Biotransformation> applyGutMicrobialRedoxChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                  boolean preprocess,
                                                                                  boolean filter,
                                                                                  int nr_of_steps,
                                                                                  java.lang.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 human gut microbial metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception - -throw any exception
      • applyGutMicrobialConjugations

        public java.util.ArrayList<Biotransformation> applyGutMicrobialConjugations​(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 human gut microbial reactions applied to the target, with a threshold of 0.0
        Throws:
        java.lang.Exception - - throw any exception
      • applyGutMicrobialConjugations

        public java.util.ArrayList<Biotransformation> applyGutMicrobialConjugations​(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
        Returns:
        an arraylist of biotransformations, which are instances of the human gut microbial reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception - - throw any exception
      • applyGutMicrobialConjugationsChain

        public java.util.ArrayList<Biotransformation> applyGutMicrobialConjugationsChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                         boolean preprocess,
                                                                                         boolean filter,
                                                                                         int nr_of_steps)
                                                                                  throws java.lang.Exception
        Parameters:
        target -
        preprocess -
        filter -
        nr_of_steps -
        Returns:
        an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the human gut microbial metabolic reactions applied to the target, with the minimum threshold of 0.0
        Throws:
        java.lang.Exception
      • applyGutMicrobialConjugationsChain

        public java.util.ArrayList<Biotransformation> applyGutMicrobialConjugationsChain​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                         boolean preprocess,
                                                                                         boolean filter,
                                                                                         int nr_of_steps,
                                                                                         java.lang.Double scoreThreshold)
                                                                                  throws java.lang.Exception
        Parameters:
        target -
        preprocess -
        filter -
        nr_of_steps -
        Returns:
        an arraylist of biotransformations obtained after the specified number of steps (nr_of_steps), which are instances of the human gut microbial metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • applyGutMicrobialMetabolismHydrolysisAndRedoxStep

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

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

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

        public java.util.ArrayList<Biotransformation> applyGutMicrobialMetabolismHydrolysisAndRedoxChain​(org.openscience.cdk.interfaces.IAtomContainerSet targets,
                                                                                                         boolean preprocess,
                                                                                                         boolean filter,
                                                                                                         int nr_of_steps,
                                                                                                         java.lang.Double scoreThreshold)
                                                                                                  throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateGutMicrobialMetabolism

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

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

        public java.util.ArrayList<Biotransformation> simulateGutMicrobialMetabolism​(org.openscience.cdk.interfaces.IAtomContainerSet targets,
                                                                                     boolean preprocess,
                                                                                     boolean filter,
                                                                                     int numberOfSteps)
                                                                              throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateGutMicrobialMetabolism

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

        public java.util.ArrayList<Biotransformation> simulateGutMicrobialMetabolism​(java.lang.String targetsFileNameInSDF,
                                                                                     boolean preprocess,
                                                                                     boolean filter,
                                                                                     int nr_of_steps,
                                                                                     java.lang.Double scoreThreshold)
                                                                              throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateGutMicrobialMetabolismAndSave

        public void simulateGutMicrobialMetabolismAndSave​(java.lang.String targetsFileNameInSDF,
                                                          boolean preprocess,
                                                          boolean filter,
                                                          int nr_of_steps,
                                                          java.lang.Double scoreThreshold,
                                                          java.lang.String metabolitesFileNameInSDF)
                                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateGutMicrobialMetabolismAndSave

        public void simulateGutMicrobialMetabolismAndSave​(java.lang.String targetsFileNameInSDF,
                                                          boolean preprocess,
                                                          boolean filter,
                                                          int nr_of_steps,
                                                          java.lang.Double scoreThreshold,
                                                          java.lang.String metabolitesFileNameInSDF,
                                                          boolean annotate)
                                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateGutMicrobialMetabolismAndSaveToSDF

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

        public void simulateGutMicrobialMetabolismAndSaveToSDF​(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
      • 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()