Class BicycloStereoDescriptor

java.lang.Object
chemaxon.struc.BicycloStereoDescriptor

@PublicApi public class BicycloStereoDescriptor extends Object
This class is the atom index based representation which can be assigned to 'endo', 'exo', 'syn', 'anti' ligands of bicyclo[x.y.z]alkanes in case of 0 dimension molecules. The descriptor is a record of the elements as follows - ring connection atom of the ligand - orientation of the ligand (towards lowest bridge, etc.) - atom array of the first bridge - atom array of the second bridge

Bridges are identified by the highest contained atom index, higher bridge is the one with the highest atom index, lower is the other one.

Since:
Marvin 5.5
  • Field Details

    • TOWARDS_HIGHER_BRIDGE

      public static final int TOWARDS_HIGHER_BRIDGE
      The ligand is towards the bridge with the higher index.
      See Also:
    • TOWARDS_LOWER_BRIDGE

      public static final int TOWARDS_LOWER_BRIDGE
      The ligand is towards the bridge with the lower index.
      See Also:
    • TOWARDS_EITHER_BRIDGE

      public static final int TOWARDS_EITHER_BRIDGE
      Direction of the ligand is not defined, it can be oriented towards both of the bridges (e.g. it is connected to the ring system by a wiggly bond).
      See Also:
  • Constructor Details

    • BicycloStereoDescriptor

      public BicycloStereoDescriptor(MolAtom connectionAtom, int stereoValue, MolAtom[] bridge1, MolAtom[] bridge2)
      Creates a new stereo descriptor for bicyclo stereo.
      Parameters:
      connectionAtom - the ring atom connected to the ligand
      stereoValue - the stereo value
      bridge1 - the atoms of the first bridge
      bridge2 - the atoms of the other bridge
  • Method Details

    • getConnectionAtom

      public MolAtom getConnectionAtom()
      Returns the ring atom connected to the ligand.
      Returns:
      the connection atom.
    • getConnectionAtomIndex

      public int getConnectionAtomIndex()
      Returns the ring atom index connected to the ligand.
      Returns:
      the connection atom index.
    • getStereoValue

      public int getStereoValue()
      Return the bicyclo stereo value.
      Returns:
      the bicyclo stereo value.
      See Also:
    • getHighBridgeAtoms

      public MolAtom[] getHighBridgeAtoms()
      Return the atoms of the bridge with the higher index.
      Returns:
      the atoms of the bridge with the higher index.
    • getLowBridgeAtoms

      public MolAtom[] getLowBridgeAtoms()
      Return the atoms of the bridge with the lower index.
      Returns:
      the atoms of the bridge with the lower index.
    • getHighBridgeAtomIndexes

      public int[] getHighBridgeAtomIndexes()
      Return the atom indexes of the atoms of the bridge with the higher index.
      Returns:
      the atoms of the bridge with the higher index.
    • getLowBridgeAtomIndexes

      public int[] getLowBridgeAtomIndexes()
      Return the atom indexes of the atoms of the bridge with the lower index.
      Returns:
      the atoms of the bridge with the lower index.
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • compareTo

      public boolean compareTo(BicycloStereoDescriptor bicycloStereoDescriptor)
      Compares two bicyclostereo descriptors.
      Parameters:
      bicycloStereoDescriptor - the descriptor to be compared
      Returns:
      true if the argument descriptors is equal to this descriptor, false otherwise