Package chemaxon.alignment

Class MinMaxDistance

java.lang.Object
chemaxon.alignment.AlignmentBase
chemaxon.alignment.MinMaxDistance
All Implemented Interfaces:
Licensable
@PublicApi public final class MinMaxDistance extends AlignmentBase
Calculates the minimum or maximum intermolecular Cartesian distance between atoms by rotating flexible bonds. Molecule mol = MolImporter.importMol("CCCCCCCCC"); mol.clean(3,""); MinMaxDistance mm = new MinMaxDistance() mm.setMolecule(mol); mm.setAtom1(0); mm.setAtom2(5); double max = mm.calcMaxDist(); double min = mm.calcMinDist();
Since:
Marvin 5.3

  • Field Details

  • Constructor Details

    • MinMaxDistance

      public MinMaxDistance()

  • Method Details

    • setMolecule

      public void setMolecule(Molecule m) throws AlignmentException
      Throws:
      AlignmentException

    • setAtom1

      public void setAtom1(int atom1)

    • setAtom2

      public void setAtom2(int atom2)

    • setMinDistTryCount

      public void setMinDistTryCount(int minDistTryCount)
      Parameters:
      minDistTryCount - number of extra trials. Before every extra trial, the conformation modified using random dihedrals

    • calcMinDist

      public double calcMinDist() throws AlignmentException
      Calculates the minimum distance between two atoms in the molecule. The molecule is treated flexible, the closest possible distance is the sum of the van der Waals radii of atoms.
      Returns:
      the minimum distance in Angstrom
      Throws:
      AlignmentException

    • calcMaxDist

      public double calcMaxDist() throws AlignmentException
      Throws:
      AlignmentException

    • resetMap

      public void resetMap()