Class ESSpecificityPredictor


  • public class ESSpecificityPredictor
    extends java.lang.Object
    Predicts whether a compound is a substrate of a given enzyme within a specific biosystem.
    Author:
    Djoumbou Feunang, Yannick
    • Constructor Detail

      • ESSpecificityPredictor

        public ESSpecificityPredictor​(BioSystem bsys)
        Creates a specific
        Parameters:
        bsys -
    • Method Detail

      • isValidCyp450Substrate

        public boolean isValidCyp450Substrate​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                              Enzyme.EnzymeName enz)
                                       throws java.lang.Exception
        Throws:
        java.lang.Exception
      • isValidCyp450Substrate

        public boolean isValidCyp450Substrate​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                              Enzyme.EnzymeName enz,
                                              java.util.ArrayList<ChemicalClassFinder.ChemicalClassName> chemClasses)
                                       throws java.lang.Exception
        Throws:
        java.lang.Exception
      • isValid_EC_2_8_2_2_substrate

        public boolean isValid_EC_2_8_2_2_substrate​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                                    boolean preprocess)
                                             throws java.lang.Exception
        Throws:
        java.lang.Exception
      • isValidSubstrate

        public boolean isValidSubstrate​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                        Enzyme.EnzymeName enz)
                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • isPotentialSubstrateByReactionPatternMatching

        public boolean isPotentialSubstrateByReactionPatternMatching​(org.openscience.cdk.interfaces.IAtomContainer substrate,
                                                                     Enzyme.EnzymeName enz)
                                                              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