Package chemaxon.marvin.alignment

Class MinMaxDistance

java.lang.Object
chemaxon.marvin.alignment.MinMaxDistance
All Implemented Interfaces:
chemaxon.license.Licensable
@PublicApi public class MinMaxDistance extends Object
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()

    • setProperty

      public void setProperty(AlignmentProperties arg0)

    • getMaxGradLimit

      public double getMaxGradLimit()

    • getNodeType

      public AlignmentProperties.NodeType getNodeType()

    • getNodeColor

      public chemaxon.marvin.alignment.NodeColor getNodeColor()

    • setAromatize

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setAromatize(boolean arg0)
      Deprecated, for removal: This API element is subject to removal in a future version.

    • setDehidrogenize

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setDehidrogenize(boolean arg0)
      Deprecated, for removal: This API element is subject to removal in a future version.

    • setFlexibleRingSize

      public void setFlexibleRingSize(int arg0)

    • setFlexibleRingRotatableBondCount

      public void setFlexibleRingRotatableBondCount(int arg0)

    • getMolecules

      public Collection<AlignmentMolecule> getMolecules()

    • isLicensed

      public boolean isLicensed()
      Specified by:
      isLicensed in interface chemaxon.license.Licensable

    • setLicenseEnvironment

      public void setLicenseEnvironment(String arg0)
      Specified by:
      setLicenseEnvironment in interface chemaxon.license.Licensable

    • getStepLimit

      public int getStepLimit()

    • setStepLimit

      public void setStepLimit(int arg0)

    • getTimeLimit

      public int getTimeLimit()

    • setNodeType

      public void setNodeType(AlignmentProperties.NodeType arg0)

    • setTimeLimit

      public void setTimeLimit(int arg0)

    • setProgressMonitor

      public void setProgressMonitor(MProgressMonitor arg0)

    • setProximity

      public void setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType arg0)