Class MetaboliteFinder


  • public class MetaboliteFinder
    extends java.lang.Object
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean compoundsHasToleratedMass​(org.openscience.cdk.interfaces.IAtomContainer atc, java.util.ArrayList<java.lang.Double> masses, double tolerance)  
      org.openscience.cdk.interfaces.IAtomContainerSet findAllEnvMicroMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, MetaboliteFinder.FinderOption opt)  
      void findAllEnvMicroMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)  
      void findAllEnvMicroMetabolitesToCSV​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)  
      org.openscience.cdk.interfaces.IAtomContainerSet findAllHumanMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, MetaboliteFinder.FinderOption opt)  
      void findAllHumanMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)  
      void findAllHumanMetabolitesToCSV​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, int nrOfSteps, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)  
      org.openscience.cdk.interfaces.IAtomContainer findPathway​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, org.openscience.cdk.interfaces.IAtomContainer leafCompound, java.util.LinkedHashMap<java.lang.String,​org.openscience.cdk.interfaces.IAtomContainerSet> compoundToParents, java.util.LinkedHashMap<java.lang.String,​org.openscience.cdk.interfaces.IAtomContainer> inchikeyToContainers, boolean annotate)  
      org.openscience.cdk.interfaces.IAtomContainerSet findSuperbioMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, boolean annotate, MetaboliteFinder.FinderOption opt)  
      void findSuperbioMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)  
      void findSuperbioMetabolitesToCSV​(org.openscience.cdk.interfaces.IAtomContainer startingCompound, java.util.ArrayList<java.lang.String> mass_formulas, double massTolerance, boolean annotate, java.lang.String outputFileName, MetaboliteFinder.FinderOption opt)  
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • MetaboliteFinder

        public MetaboliteFinder()
                         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

      • findAllHumanMetabolites

        public void findAllHumanMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                            java.util.ArrayList<java.lang.String> mass_formulas,
                                            double massTolerance,
                                            int nrOfSteps,
                                            boolean annotate,
                                            java.lang.String outputFileName,
                                            MetaboliteFinder.FinderOption opt)
                                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • findAllHumanMetabolitesToCSV

        public void findAllHumanMetabolitesToCSV​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                                 java.util.ArrayList<java.lang.String> mass_formulas,
                                                 double massTolerance,
                                                 int nrOfSteps,
                                                 boolean annotate,
                                                 java.lang.String outputFileName,
                                                 MetaboliteFinder.FinderOption opt)
                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • findAllHumanMetabolites

        public org.openscience.cdk.interfaces.IAtomContainerSet findAllHumanMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                                                                        java.util.ArrayList<java.lang.String> mass_formulas,
                                                                                        double massTolerance,
                                                                                        int nrOfSteps,
                                                                                        boolean annotate,
                                                                                        MetaboliteFinder.FinderOption opt)
                                                                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • findSuperbioMetabolites

        public void findSuperbioMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                            java.util.ArrayList<java.lang.String> mass_formulas,
                                            double massTolerance,
                                            boolean annotate,
                                            java.lang.String outputFileName,
                                            MetaboliteFinder.FinderOption opt)
                                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • findSuperbioMetabolitesToCSV

        public void findSuperbioMetabolitesToCSV​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                                 java.util.ArrayList<java.lang.String> mass_formulas,
                                                 double massTolerance,
                                                 boolean annotate,
                                                 java.lang.String outputFileName,
                                                 MetaboliteFinder.FinderOption opt)
                                          throws java.lang.Exception
        Throws:
        java.lang.Exception
      • findSuperbioMetabolites

        public org.openscience.cdk.interfaces.IAtomContainerSet findSuperbioMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                                                                        java.util.ArrayList<java.lang.String> mass_formulas,
                                                                                        double massTolerance,
                                                                                        boolean annotate,
                                                                                        MetaboliteFinder.FinderOption opt)
                                                                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • findAllEnvMicroMetabolites

        public void findAllEnvMicroMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                               java.util.ArrayList<java.lang.String> mass_formulas,
                                               double massTolerance,
                                               int nrOfSteps,
                                               boolean annotate,
                                               java.lang.String outputFileName,
                                               MetaboliteFinder.FinderOption opt)
                                        throws java.lang.Exception
        Throws:
        java.lang.Exception
      • findAllEnvMicroMetabolitesToCSV

        public void findAllEnvMicroMetabolitesToCSV​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                                    java.util.ArrayList<java.lang.String> mass_formulas,
                                                    double massTolerance,
                                                    int nrOfSteps,
                                                    boolean annotate,
                                                    java.lang.String outputFileName,
                                                    MetaboliteFinder.FinderOption opt)
                                             throws java.lang.Exception
        Throws:
        java.lang.Exception
      • findAllEnvMicroMetabolites

        public org.openscience.cdk.interfaces.IAtomContainerSet findAllEnvMicroMetabolites​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                                                                           java.util.ArrayList<java.lang.String> mass_formulas,
                                                                                           double massTolerance,
                                                                                           int nrOfSteps,
                                                                                           boolean annotate,
                                                                                           MetaboliteFinder.FinderOption opt)
                                                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • findPathway

        public org.openscience.cdk.interfaces.IAtomContainer findPathway​(org.openscience.cdk.interfaces.IAtomContainer startingCompound,
                                                                         org.openscience.cdk.interfaces.IAtomContainer leafCompound,
                                                                         java.util.LinkedHashMap<java.lang.String,​org.openscience.cdk.interfaces.IAtomContainerSet> compoundToParents,
                                                                         java.util.LinkedHashMap<java.lang.String,​org.openscience.cdk.interfaces.IAtomContainer> inchikeyToContainers,
                                                                         boolean annotate)
                                                                  throws java.lang.CloneNotSupportedException,
                                                                         org.openscience.cdk.exception.CDKException
        Throws:
        java.lang.CloneNotSupportedException
        org.openscience.cdk.exception.CDKException
      • compoundsHasToleratedMass

        public boolean compoundsHasToleratedMass​(org.openscience.cdk.interfaces.IAtomContainer atc,
                                                 java.util.ArrayList<java.lang.Double> masses,
                                                 double tolerance)