Class Cyp450BTransformer

    • Constructor Detail

      • Cyp450BTransformer

        public Cyp450BTransformer​(BioSystem.BioSystemName bioSName)
                           throws org.codehaus.jackson.JsonParseException,
                                  org.codehaus.jackson.map.JsonMappingException,
                                  java.io.IOException,
                                  org.openscience.cdk.exception.CDKException
        Throws:
        org.codehaus.jackson.JsonParseException
        org.codehaus.jackson.map.JsonMappingException
        java.io.IOException
        org.openscience.cdk.exception.CDKException
    • Method Detail

      • predictCyp450Biotransformations

        public java.util.ArrayList<Biotransformation> predictCyp450Biotransformations​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                                                                      boolean preprocess,
                                                                                      boolean filter,
                                                                                      double threshold)
                                                                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictCyp450BiotransformationsForSpecificEnzymes

        public java.util.ArrayList<Biotransformation> predictCyp450BiotransformationsForSpecificEnzymes​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                                                                                        java.util.ArrayList<Enzyme.EnzymeName> enzymeNames,
                                                                                                        boolean preprocess,
                                                                                                        boolean filter,
                                                                                                        double threshold)
                                                                                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictCyp450Biotransformations

        public java.util.ArrayList<Biotransformation> predictCyp450Biotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet substrates,
                                                                                      boolean preprocess,
                                                                                      boolean filter,
                                                                                      double threshold)
                                                                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictCyp450Biotransformations

        public java.util.ArrayList<Biotransformation> predictCyp450Biotransformations​(java.lang.String sdfFileName,
                                                                                      boolean preprocess,
                                                                                      boolean filter,
                                                                                      double threshold)
                                                                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictCyp450BiotransformationChain

        public java.util.ArrayList<Biotransformation> predictCyp450BiotransformationChain​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                                                                          boolean preprocess,
                                                                                          boolean filter,
                                                                                          int nrOfSteps,
                                                                                          double threshold)
                                                                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictCyp450BiotransformationChain

        public java.util.ArrayList<Biotransformation> predictCyp450BiotransformationChain​(org.openscience.cdk.interfaces.IAtomContainerSet substrates,
                                                                                          boolean preprocess,
                                                                                          boolean filter,
                                                                                          int nrOfSteps,
                                                                                          double threshold)
                                                                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateCyp450MetabolismAndSaveToSDF

        public void simulateCyp450MetabolismAndSaveToSDF​(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
      • simulateCyp450MetabolismAndSaveToSingleSDF

        public void simulateCyp450MetabolismAndSaveToSingleSDF​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                               int nrOfSteps,
                                                               java.lang.Double scoreThreshold,
                                                               java.lang.String outputFileName,
                                                               boolean annotate)
                                                        throws java.lang.Exception
        Throws:
        java.lang.Exception
      • printStatistics

        public void printStatistics()