Class TorsionDescriptorHelper


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

      • TorsionDescriptorHelper

        public TorsionDescriptorHelper​(StereoMolecule mol)
      • TorsionDescriptorHelper

        public TorsionDescriptorHelper​(StereoMolecule mol,
                                       int[] rotatableBond)
    • Method Detail

      • getTorsionDescriptor

        public TorsionDescriptor getTorsionDescriptor()
        Creates a TorsionDescriptor from the coordinates of the molecule passed to the constructor using the default method to detect rotatable bonds. The torsion descriptor is not canonical, unless the passed molecule is canonical. Rotatable bonds need to carry at least one external non-hydrogen neighbor on each side.
      • getTorsionDescriptor

        public TorsionDescriptor getTorsionDescriptor​(Conformer conformer)
        Creates a TorsionDescriptor from the coordinates of the passed conformer assuming that its underlying molecule is the same that waas passed to this TorsionDescriptorHelper's constructor. This TorsionDescriptorHelper uses the default method to detect rotatable bonds. The torsion descriptor is not canonical, unless the passed molecule is canonical. Rotatable bonds need to carry at least one external non-hydrogen neighbor on each side.
      • findRotatableBonds

        public static int[] findRotatableBonds​(StereoMolecule mol)
        Calculates an array of all rotatable bonds that can be used multiple times as parameter to calculateDescriptor(). If the molecule contains marked atoms, these are not considered part of the molecule, when detecting rotatable bonds. Any non-aromatic, non-3-ring single bond with at least one non-H, non-marked neighbor to either side is considered a rotatable bond, if none of the bond atoms is marked. An exception are linear chains of sp-hybridized atoms, of which not more than one bond is considered rotatable.