Class MarkushStructure

  • All Implemented Interfaces:
    java.io.Serializable

    public class MarkushStructure
    extends java.lang.Object
    implements java.io.Serializable
    See Also:
    Serialized Form
    • Constructor Detail

      • MarkushStructure

        public MarkushStructure()
      • MarkushStructure

        public MarkushStructure​(StereoMolecule[] fragment,
                                int coreCount)
    • Method Detail

      • getCoreStructure

        public StereoMolecule getCoreStructure​(int no)
      • getCoreCount

        public int getCoreCount()
      • getRGroupCount

        public int getRGroupCount()
      • addRGroup

        public void addRGroup​(StereoMolecule substituents)
        This adds a substituent list representing one R-group as multiple fragments within one StereoMolecule. Every fragment is supposed to contain one atom with atomicNo=0 that is considered the attachment point. Fragments may contain atoms representing other R-groups (R1-R16). The first call of this method adds R1, the second R2, etc.
        Parameters:
        substituents - multiple fragments representing R-group substituents
      • validate

        public java.lang.String validate()
                                  throws java.lang.Exception
        Check the validity of a defined Markush structure. This method must be called before the enumeration.
        Returns:
        a warning if defined R-groups are unreferenced
        Throws:
        java.lang.Exception - if an error prevents proper enumeration
      • getNextEnumeration

        public StereoMolecule getNextEnumeration()
        After calling validate() this method may be called until null is returned to construct one by one a new representation of the Markush structure.