Class HumanSuperBioTransformer


  • public class HumanSuperBioTransformer
    extends java.lang.Object
    • Field Detail

      • smiParser

        public org.openscience.cdk.smiles.SmilesParser smiParser
      • smiGen

        public org.openscience.cdk.smiles.SmilesGenerator smiGen
    • Constructor Detail

      • HumanSuperBioTransformer

        public HumanSuperBioTransformer()
                                 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

      • getInChIGenFactory

        public org.openscience.cdk.inchi.InChIGeneratorFactory getInChIGenFactory()
      • simulateHumanSuperbioMetabolism

        public java.util.ArrayList<Biotransformation> simulateHumanSuperbioMetabolism​(org.openscience.cdk.interfaces.IAtomContainer target)
                                                                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateHumanSuperbioMetabolism

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

        public void simulateHumanSuperbioMetabolismAndSaveToSDF​(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                                java.lang.String outputFileName,
                                                                boolean annotate)
                                                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateHumanSuperbioMetabolismFromSDF

        public void simulateHumanSuperbioMetabolismFromSDF​(java.lang.String inputFileName,
                                                           boolean annotate)
                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateHumanSuperbioMetabolismFromSDF

        public void simulateHumanSuperbioMetabolismFromSDF​(java.lang.String inputFileName,
                                                           java.lang.String outputFolder,
                                                           boolean annotate)
                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateHumanSuperbioMetabolismAndSaveToSDF

        public void simulateHumanSuperbioMetabolismAndSaveToSDF​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                                java.lang.String outputFolder,
                                                                boolean annotate)
                                                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateHumanSuperbioMetabolismAndSaveToCSV

        public void simulateHumanSuperbioMetabolismAndSaveToCSV​(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                                java.lang.String outputFileName,
                                                                boolean annotate)
                                                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateAllHumanMetabolism

        public java.util.ArrayList<Biotransformation> simulateAllHumanMetabolism​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                                                 double scoreThreshold)
                                                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateAllHumanMetabolismAndSavetoCSV

        public void simulateAllHumanMetabolismAndSavetoCSV​(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                           java.lang.String outputFileName,
                                                           double scoreThreshold,
                                                           boolean annotate)
                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateAllHumanMetabolismAndSavetoSDF

        public void simulateAllHumanMetabolismAndSavetoSDF​(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                           java.lang.String outputFileName,
                                                           double scoreThreshold,
                                                           boolean annotate)
                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictAllHumanBiotransformationChainAndSaveToCSV

        public void predictAllHumanBiotransformationChainAndSaveToCSV​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                                                      int nrOfSteps,
                                                                      double threshold,
                                                                      java.lang.String outputFileName,
                                                                      boolean annotate)
      • predictAllHumanBiotransformationChainAndSaveToCSV

        public void predictAllHumanBiotransformationChainAndSaveToCSV​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                                      int nrOfSteps,
                                                                      double threshold,
                                                                      java.lang.String outputFileName,
                                                                      boolean annotate)
      • predictAllHumanBiotransformationChainAndSaveToSDF

        public void predictAllHumanBiotransformationChainAndSaveToSDF​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                                      int nrOfSteps,
                                                                      double threshold,
                                                                      java.lang.String outputFileName,
                                                                      boolean annotate)
      • simulateAllHumanMetabolismAndSavetoSDF

        public void simulateAllHumanMetabolismAndSavetoSDF​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                           java.lang.String outputFileName,
                                                           double scoreThreshold,
                                                           boolean annotate)
                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • partitionSetForPhaseIIMetabolism

        public java.util.LinkedHashMap<java.lang.String,​org.openscience.cdk.interfaces.IAtomContainerSet> partitionSetForPhaseIIMetabolism​(org.openscience.cdk.interfaces.IAtomContainerSet products)
                                                                                                                                          throws org.openscience.cdk.exception.CDKException,
                                                                                                                                                 java.lang.Exception
        Throws:
        org.openscience.cdk.exception.CDKException
        java.lang.Exception
      • simulateHumanSuperbioMetabolismFromSDFtoSingleSDF

        public void simulateHumanSuperbioMetabolismFromSDFtoSingleSDF​(java.lang.String inputFileName,
                                                                      java.lang.String outputFileName,
                                                                      boolean annotate)
                                                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateHumanSuperbioMetabolismFromSDFtoSingleCSV

        public void simulateHumanSuperbioMetabolismFromSDFtoSingleCSV​(java.lang.String inputFileName,
                                                                      java.lang.String outputFileName,
                                                                      boolean annotate)
                                                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateOneStepAllHuman

        public java.util.ArrayList<Biotransformation> simulateOneStepAllHuman​(org.openscience.cdk.interfaces.IAtomContainer target)
                                                                       throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateOneStepAllHuman

        public java.util.ArrayList<Biotransformation> simulateOneStepAllHuman​(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                              double scoreThreshold)
                                                                       throws java.lang.Exception
        Throws:
        java.lang.Exception
      • applyPathwaySpecificBiotransformations

        public java.util.ArrayList<Biotransformation> applyPathwaySpecificBiotransformations​(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                                                             MetabolicPathway.MPathwayName pathway,
                                                                                             boolean preprocess,
                                                                                             boolean filter,
                                                                                             double scoreThreshold)
                                                                                      throws java.lang.Exception
        Throws:
        java.lang.Exception
      • simulateGutMicrobialMetabolism

        public java.util.ArrayList<Biotransformation> simulateGutMicrobialMetabolism​(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                                                     int nrOfSteps,
                                                                                     double scoreThreshold)
                                                                              throws java.lang.Exception
        Throws:
        java.lang.Exception
      • applyPhaseIITransformationsChainAndReturnBiotransformations

        public java.util.ArrayList<Biotransformation> applyPhaseIITransformationsChainAndReturnBiotransformations​(org.openscience.cdk.interfaces.IAtomContainerSet products,
                                                                                                                  int nrOfSteps,
                                                                                                                  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
      • simulateOneStepAllHuman

        public java.util.ArrayList<Biotransformation> simulateOneStepAllHuman​(org.openscience.cdk.interfaces.IAtomContainerSet targets,
                                                                              double scoreThreshold)
                                                                       throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictAllHumanBiotransformationChain

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

        public java.util.ArrayList<Biotransformation> predictAllHumanBiotransformationChain​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                                                            int nrOfSteps,
                                                                                            double threshold)
                                                                                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictMetabolismAllHumanFromSDFtoSDF

        public void predictMetabolismAllHumanFromSDFtoSDF​(java.lang.String inputFileName,
                                                          java.lang.String outputFileName,
                                                          boolean annotate)
                                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictAllHumanBiotransformationChainAndSaveToSDF

        public void predictAllHumanBiotransformationChainAndSaveToSDF​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                                                      int nrOfSteps,
                                                                      double threshold,
                                                                      java.lang.String outputFileName,
                                                                      boolean annotate)
                                                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictMetabolismAllHumanFromSDFAndSavetoSDF

        public void predictMetabolismAllHumanFromSDFAndSavetoSDF​(java.lang.String inputFileName,
                                                                 java.lang.String outputFileName,
                                                                 int nrOfSteps,
                                                                 boolean annotate)
                                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictMetabolismAllHumanFromSDFAndSavetoSDF

        public void predictMetabolismAllHumanFromSDFAndSavetoSDF​(java.lang.String inputFileName,
                                                                 java.lang.String outputF,
                                                                 double screThreshold,
                                                                 boolean annotate)
                                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictMetabolismAllHumanFromSDFAndSavetoSDF

        public void predictMetabolismAllHumanFromSDFAndSavetoSDF​(java.lang.String inputFileName,
                                                                 java.lang.String outputFolder,
                                                                 int nrOfSteps,
                                                                 double scoreThreshold,
                                                                 boolean annotate)
                                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • predictMetabolismAllHumanFromSDFAndSavetoSingleSDF

        public void predictMetabolismAllHumanFromSDFAndSavetoSingleSDF​(java.lang.String inputFileName,
                                                                       java.lang.String outputFileName,
                                                                       int nrOfSteps,
                                                                       double scoreThreshold,
                                                                       boolean annotate)
                                                                throws java.lang.Exception
        Throws:
        java.lang.Exception
      • standardizeMoleculeWithCopy

        public org.openscience.cdk.interfaces.IAtomContainer standardizeMoleculeWithCopy​(org.openscience.cdk.interfaces.IAtomContainer target)
                                                                                  throws java.lang.Exception
        Throws:
        java.lang.Exception
      • applyGutMicrobialMetabolismHydrolysisAndRedoxChain

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

        public org.openscience.cdk.interfaces.IAtomContainerSet extractAtomContainer​(java.util.ArrayList<Biotransformation> biotransformations)
                                                                              throws java.lang.Exception
        Throws:
        java.lang.Exception
      • extractAtomContainerWithTransformationData

        public org.openscience.cdk.interfaces.IAtomContainerSet extractAtomContainerWithTransformationData​(java.util.ArrayList<Biotransformation> biotransformations,
                                                                                                           boolean annotate)
                                                                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • saveBioTransformationProductsToSdf

        public void saveBioTransformationProductsToSdf​(java.util.ArrayList<Biotransformation> biotransformations,
                                                       java.lang.String outputFileName,
                                                       boolean annotate)
                                                throws java.lang.Exception
        Throws:
        java.lang.Exception
      • saveBioTransformationProductsToCSV

        public void saveBioTransformationProductsToCSV​(java.util.ArrayList<Biotransformation> biotransformations,
                                                       java.lang.String outputFileName,
                                                       boolean annotate)
                                                throws java.lang.Exception
        Throws:
        java.lang.Exception