Class ChemicalClassFinder


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

      • chemicalClassDefinitions

        public static java.util.LinkedHashMap<ChemicalClassFinder.ChemicalClassName,​java.util.LinkedHashMap<java.lang.String,​java.lang.String[]>> chemicalClassDefinitions
    • Constructor Detail

      • ChemicalClassFinder

        public ChemicalClassFinder()
    • Method Detail

      • compoundMatchesClassSmartsDefinitions

        public static boolean compoundMatchesClassSmartsDefinitions​(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                                    ChemicalClassFinder.ChemicalClassName className)
                                                             throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • findChemicalClass

        public static ChemicalClassFinder.ChemicalClassName findChemicalClass​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                                                       throws ambit2.smarts.query.SMARTSException,
                                                                              java.lang.CloneNotSupportedException,
                                                                              org.openscience.cdk.exception.CDKException
        Throws:
        ambit2.smarts.query.SMARTSException
        java.lang.CloneNotSupportedException
        org.openscience.cdk.exception.CDKException
      • AssignChemicalClasses

        public static java.util.ArrayList<ChemicalClassFinder.ChemicalClassName> AssignChemicalClasses​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                                                                                throws ambit2.smarts.query.SMARTSException,
                                                                                                       java.lang.CloneNotSupportedException,
                                                                                                       org.openscience.cdk.exception.CDKException
        Throws:
        ambit2.smarts.query.SMARTSException
        java.lang.CloneNotSupportedException
        org.openscience.cdk.exception.CDKException
      • isUnsubstitutedSatudatedFattyAcid

        public static boolean isUnsubstitutedSatudatedFattyAcid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
      • isFattyAcid

        public static boolean isFattyAcid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
      • isUnsaturatedFattyAcid

        public static boolean isUnsaturatedFattyAcid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
      • isSaturatedFattyAcid

        public static boolean isSaturatedFattyAcid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                            throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isAlphaHydroxyFattyAcid

        public static boolean isAlphaHydroxyFattyAcid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
      • isBetaHydroxyFattyAcid

        public static boolean isBetaHydroxyFattyAcid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
      • isOmegaHydroxyFattyAcid

        public static boolean isOmegaHydroxyFattyAcid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
      • isEtherLipid

        public static boolean isEtherLipid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                    throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isGlyceroLipid

        public static boolean isGlyceroLipid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                      throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isGlycerophosphoLipid

        public static boolean isGlycerophosphoLipid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                             throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isSphingoLipid

        public static boolean isSphingoLipid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                      throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isGlycerol_3_PhosphateInositol

        public static boolean isGlycerol_3_PhosphateInositol​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                                      throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isC23BileAcid

        public static boolean isC23BileAcid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                     throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isC24BileAcid

        public static boolean isC24BileAcid​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                     throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isSulfateEster

        public static boolean isSulfateEster​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                      throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isTetrapyrrole

        public static boolean isTetrapyrrole​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                      throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isOligoOrPolysaccharide

        public static boolean isOligoOrPolysaccharide​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                               throws ambit2.smarts.query.SMARTSException,
                                                      org.openscience.cdk.exception.CDKException
        Throws:
        ambit2.smarts.query.SMARTSException
        org.openscience.cdk.exception.CDKException
      • isGlycosylatedCompound

        public static boolean isGlycosylatedCompound​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                              throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isSulfatedCompound

        public static boolean isSulfatedCompound​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                          throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isGlutathioneConjugate

        public static boolean isGlutathioneConjugate​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                              throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isAcylCoAConjugate

        public static boolean isAcylCoAConjugate​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                          throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • isGlycinatedCompound

        public static boolean isGlycinatedCompound​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                            throws ambit2.smarts.query.SMARTSException
        Throws:
        ambit2.smarts.query.SMARTSException
      • main

        public static void main​(java.lang.String[] args)
                         throws ambit2.smarts.query.SMARTSException,
                                java.lang.CloneNotSupportedException,
                                org.openscience.cdk.exception.CDKException
        Throws:
        ambit2.smarts.query.SMARTSException
        java.lang.CloneNotSupportedException
        org.openscience.cdk.exception.CDKException