Interface ITetrahedralChirality

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

    public interface ITetrahedralChirality
    extends IStereoElement<IAtom,​IAtom>
    Stereochemistry specification for quadrivalent atoms. The data model defines the central, chiral IAtom, and its four ligand IAtoms, directly bonded to the chiral atom via an IBond. The ordering of the four ligands is important, and defines together with the ITetrahedralChirality.Stereo to spatial geometry around the chiral atom. The first ligand points towards to observer, and the three other ligands point away from the observer; the ITetrahedralChirality.Stereo then defines the order of the second, third, and fourth ligand to be clockwise or anti-clockwise. If the tetrahedral centre has an implicit hydrogen or lone pair then the chiral atom is also stored as one of the ligands. This serves as a placeholder to indicate where the implicit hydrogen or lone pair would be.
    Source code:
    Belongs to CDK module:
    • Method Detail

      • getLigands

        IAtom[] getLigands()
        Returns an array of ligand atoms around the chiral atom. If the chiral centre has an implicit hydrogen or lone pair one of the ligands will be the chiral atom (getChiralAtom()).
        an array of four IAtoms.
      • getChiralAtom

        IAtom getChiralAtom()
        Atom that is the chirality center.
        the chiral IAtom.
      • setStereo

        void setStereo​(ITetrahedralChirality.Stereo stereo)
        Set the stereochemistry of this tetrahedral centre.
        stereo - the new stereo assignment
      • map

        ITetrahedralChirality 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<IAtom,​IAtom>
        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.