Class GeometricTetrahedralEncoderFactory

  • All Implemented Interfaces:

    public class GeometricTetrahedralEncoderFactory
    extends Object
    implements StereoEncoderFactory
    A stereo encoder factory for tetrahedral centres. This factory generates StereoEncoders for centres with specified by 2D and 3D coordinates. The required preconditions are the central atom must have 3/4 neighboring atoms, Sp3 hybridization and no query bonds (e.g. wiggly). If there is at least one up/down bond and all required atoms have coordinates a new 2D encoder is created. If the there are no stereo bonds (up/down) and all required atoms have 3D coordinates then a new 3D encoder is created.
    John May
    Source code:
    Belongs to CDK module:
    • Constructor Detail

      • GeometricTetrahedralEncoderFactory

        public GeometricTetrahedralEncoderFactory()
    • Method Detail

      • create

        public StereoEncoder create​(IAtomContainer container,
                                    int[][] graph)
        Create a stereo encoder for all potential 2D and 3D tetrahedral elements.
        Specified by:
        create in interface StereoEncoderFactory
        container - an atom container
        graph - adjacency list representation of the container
        a new encoder for tetrahedral elements