Interface IDoubleBondStereochemistry

  • All Superinterfaces:
    Cloneable, ICDKObject, IStereoElement<IBond,​IBond>
    All Known Implementing Classes:

    public interface IDoubleBondStereochemistry
    extends IStereoElement<IBond,​IBond>
    Stereochemistry specification for double bond stereochemistry. The data model defines the double atoms and two ligands attached to those two atoms, linearly connected with the double bond in the middle. The IBonds that define the stereo element are defined as an array where the bonds are sorted according to the linear connectivity. Thus, the first and third bonds are the two bonds attached on either side of the double bond, and the second bond is the double bond. The stereo annotation then indicates if the ligand atoms are in the cis position (IDoubleBondStereochemistry.Conformation.TOGETHER) or in the trans position (IDoubleBondStereochemistry.Conformation.OPPOSITE), matching the orientation of the methyls in but-2-ene respectively as Z and E.
    Source code:
    Belongs to CDK module:
    • Method Detail

      • getBonds

        IBond[] getBonds()
        Returns an array of ligand bonds around the double bond.
        an array of two IBonds.
      • getStereoBond

        IBond getStereoBond()
        IBond that is the stereo center.
        the double IBond.
      • map

        IDoubleBondStereochemistry map​(Map<IAtom,​IAtom> atoms,
                                       Map<IBond,​IBond> bonds)
        Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping. This allows the stereo element to be transferred between a cloned or aligned (i.e. isomorphic) chemical graph. If no mapping is found for a given atom or bond it is left intact. However the provided atom and bonds maps must not be null.
        Specified by:
        map in interface IStereoElement<IBond,​IBond>
        atoms - used to convert the original atoms to their mapped counterparts
        bonds - used to convert the original bonds to their mapped counterparts
        a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.