Package org.openscience.cdk.geometry.cip

Class CIPTool

  • public class CIPTool
extends Object
    Tool to help determine the R,S and stereochemistry definitions of a subset of the CIP rules [Cahn, R.S. et. al.. Angew. Chem. Int. Ed.. 1966. 5]. The used set up sub rules are specified in the CIPLigandRule class.

    Basic use starts from a ITetrahedralChirality and therefore assumes atoms with four neighbours: 

     IAtom[] ligandAtoms =
   mol.getConnectedAtomsList(centralAtom).toArray(new IAtom[4]);
 ITetrahedralChirality tetraStereo = new TetrahedralChirality(
   centralAtom, ligandAtoms, Stereo.ANTI_CLOCKWISE
 );
 CIP_CHIRALITY cipChirality = CIPTool.getCIPChirality(mol, tetraStereo);
    The IBond.Stereo value can be reconstructed from 3D coordinates with the StereoTool.
    Source code:
    main
    Belongs to CDK module:
    cip

    • Field Detail

      • HYDROGEN

        public static final int HYDROGEN
        IAtom index to indicate an implicit hydrogen, not present in the chemical graph.
        See Also:
        Constant Field Values

    • Constructor Detail

      • CIPTool

        public CIPTool()

    • Method Detail

      • getCIPChirality

        public static CIPTool.CIP_CHIRALITY getCIPChirality​(org.openscience.cdk.geometry.cip.LigancyFourChirality stereoCenter)
        Returns the R or S chirality according to the CIP rules, based on the given chirality information.
        Parameters:
        stereoCenter - Chiral center for which the CIP chirality is to be determined as LigancyFourChirality object.
        Returns:
        A CIPTool.CIP_CHIRALITY value.

      • label

        public static void label​(IAtomContainer container)
        Convenience method for labelling all stereo elements. The CIPTool.CIP_CHIRALITY is determined for each element and stored as as String on the CDKConstants.CIP_DESCRIPTOR property key. Atoms/bonds that are not stereocenters have no label assigned and the property will be null.
        Parameters:
        container - structure to label

      • checkIfAllLigandsAreDifferent

        public static boolean checkIfAllLigandsAreDifferent​(ILigand[] ligands)
        Checks if each next ILigand is different from the previous one according to the CIPLigandRule. It assumes that the input is sorted based on that rule.
        Parameters:
        ligands - array of ILigand to check
        Returns:
        true, if all ligands are different

      • order

        public static ILigand[] order​(ILigand[] ligands)
        Reorders the ILigand objects in the array according to the CIP rules.
        Parameters:
        ligands - Array of ILigands to be reordered.
        Returns:
        Reordered array of ILigands.

      • defineLigancyFourChirality

        public static org.openscience.cdk.geometry.cip.LigancyFourChirality defineLigancyFourChirality​(IAtomContainer container,
                                                                                               int chiralAtom,
                                                                                               int ligand1,
                                                                                               int ligand2,
                                                                                               int ligand3,
                                                                                               int ligand4,
                                                                                               ITetrahedralChirality.Stereo stereo)
        Creates a ligancy for chirality around a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer. For the four ligand atoms, HYDROGEN can be passed as index, which will indicate the presence of an implicit hydrogen, not explicitly present in the chemical graph of the given container.
        Parameters:
        container - IAtomContainer for which the returned ILigands are defined
        chiralAtom - int pointing to the IAtom index of the chiral atom
        ligand1 - int pointing to the IAtom index of the first ILigand
        ligand2 - int pointing to the IAtom index of the second ILigand
        ligand3 - int pointing to the IAtom index of the third ILigand
        ligand4 - int pointing to the IAtom index of the fourth ILigand
        stereo - ITetrahedralChirality.Stereo for the chirality
        Returns:
        the created LigancyFourChirality

      • defineLigand

        public static ILigand defineLigand​(IAtomContainer container,
                                   VisitedAtoms visitedAtoms,
                                   int chiralAtom,
                                   int ligandAtom)
        Creates a ligand attached to a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer. For ligand atom, HYDROGEN can be passed as index, which will indicate the presence of an implicit hydrogen, not explicitly present in the chemical graph of the given container.
        Parameters:
        container - IAtomContainer for which the returned ILigands are defined
        visitedAtoms - a list of atoms already visited in the analysis
        chiralAtom - an integer pointing to the IAtom index of the chiral atom
        ligandAtom - an integer pointing to the IAtom index of the ILigand
        Returns:
        the created ILigand

      • getLigandLigands

        public static ILigand[] getLigandLigands​(ILigand ligand)
        Returns a CIP-expanded array of side chains of a ligand. If the ligand atom is only connected to the chiral atom, the method will return an empty list. The expansion involves the CIP rules, so that a double bonded oxygen will be represented twice in the list.
        Parameters:
        ligand - the ILigand for which to return the ILigands
        Returns:
        a ILigand array with the side chains of the ligand atom