Class EnvMicroBTransformer

    • Constructor Detail

      • EnvMicroBTransformer

        public EnvMicroBTransformer()
                             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
    • Method Detail

      • applyEnvMicrobialTransformations

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

        public java.util.ArrayList<Biotransformation> applyEnvMicrobialTransformations​(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 environmental microbial metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • applyEnvMicrobialTransformations

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

        public java.util.ArrayList<Biotransformation> applyEnvMicrobialTransformationsChain​(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 environmental microbial metabolic reactions applied to the target, with the minimum threshold of 0.0
        Throws:
        java.lang.Exception
      • applyEnvMicrobialTransformationsChain

        public java.util.ArrayList<Biotransformation> applyEnvMicrobialTransformationsChain​(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 environmental microbial metabolic reactions applied to the target, with the set minimum threshold
        Throws:
        java.lang.Exception
      • simulateEnvMicrobialDegradationAndSaveToSDF

        public void simulateEnvMicrobialDegradationAndSaveToSDF​(org.openscience.cdk.interfaces.IAtomContainer container,
                                                                boolean preprocess,
                                                                boolean filter,
                                                                int nrOfSteps,
                                                                java.lang.Double scoreThreshold,
                                                                java.lang.String outputFileName,
                                                                boolean annotate)
                                                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateEnvMicrobialDegradationAndSaveToCSV

        public void simulateEnvMicrobialDegradationAndSaveToCSV​(org.openscience.cdk.interfaces.IAtomContainer container,
                                                                boolean preprocess,
                                                                boolean filter,
                                                                int nrOfSteps,
                                                                java.lang.Double scoreThreshold,
                                                                java.lang.String outputFileName,
                                                                boolean annotate)
                                                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateEnvMicrobialDegradation

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

        public void simulateEnvMicrobialDegradationAndSaveToSDF​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                                boolean preprocess,
                                                                boolean filter,
                                                                int nrOfSteps,
                                                                java.lang.Double scoreThreshold,
                                                                java.lang.String outputFolder,
                                                                boolean annotate)
                                                         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
      • printStatistics

        public void printStatistics()