Class ScaffoldHelper


  • public class ScaffoldHelper
    extends java.lang.Object
    • Constructor Detail

      • ScaffoldHelper

        public ScaffoldHelper()
    • Method Detail

      • createMurckoScaffold

        public static void createMurckoScaffold​(StereoMolecule mol,
                                                boolean skeletonOnly)
        Modifies mol in-place to represent the Murcko scaffold from the original mol. If skeletonOnly is true, then all bond types are reduced to non-stereo-single bonds and all atoms are converted to carbon atoms.
        Parameters:
        mol - may be an empty molecule if there are no ring systems
        skeletonOnly - reduce to simple skeleton
      • getMurckoScaffold

        public static StereoMolecule getMurckoScaffold​(StereoMolecule mol,
                                                       boolean skeletonOnly)
        Creates Murcko scaffold as new StereoMolecule from mol without touching mol. If skeletonOnly is true, then all bond types are reduced to non-stereo-single bonds and all atoms are converted to carbon atoms.
        Parameters:
        mol -
        skeletonOnly - reduce to simple skeleton
        Returns:
        Murcko scaffold or null, if mol does not contain any rings
      • findMurckoScaffold

        public static boolean[] findMurckoScaffold​(StereoMolecule mol)
        This method flags all atoms that are a member of the Murcko fragment of mol. The Murcko fragment is detected in three steps: - flag all ring atoms - recursively flag all atoms that are on a direct path connecting any two flagged atoms - recursively flag all atoms that are connected to any flagged atom via double bond Hydrogen atoms are neglected.
        Parameters:
        mol -
        Returns:
        null if mol doesn't contain any rings
      • createMostCentralRingSystem

        public static void createMostCentralRingSystem​(StereoMolecule mol)
        Modifies mol in-place to represent the most central ring system of the original mol.
        Parameters:
        mol - may be an empty molecule if there are no ring systems
      • getMostCentralRingSystem

        public static StereoMolecule getMostCentralRingSystem​(StereoMolecule mol)
        Creates most central ring system as new StereoMolecule from mol without touching mol.
        Parameters:
        mol -
        Returns:
        most central ring system or null if there is none
      • findMostCentralRingSystem

        public static boolean[] findMostCentralRingSystem​(StereoMolecule mol)
        This method flags all atoms that are a member of that ring system in mol, which is most central within this molecule graph.
        Parameters:
        mol -
        Returns:
        null if mol does not contain any rings