Package chemaxon.marvin.alignment

Class 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

    • Constructor Detail

      • MinMaxDistance

        public MinMaxDistance()

    • Method Detail

      • setMolecule

        public void setMolecule​(Molecule m)
                 throws chemaxon.marvin.alignment.AlignmentException
        Throws:
        chemaxon.marvin.alignment.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 chemaxon.marvin.alignment.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:
        chemaxon.marvin.alignment.AlignmentException

      • calcMaxDist

        public double calcMaxDist()
                   throws chemaxon.marvin.alignment.AlignmentException
        Throws:
        chemaxon.marvin.alignment.AlignmentException

      • resetMap

        public void resetMap()

      • getMaxGradLimit

        public double getMaxGradLimit()

      • getNodeColor

        public chemaxon.marvin.alignment.NodeColor getNodeColor()

      • setAromatize

        @Deprecated
public void setAromatize​(boolean arg0)
        Deprecated.

      • setDehidrogenize

        @Deprecated
public void setDehidrogenize​(boolean arg0)
        Deprecated.

      • setFlexibleRingSize

        public void setFlexibleRingSize​(int arg0)

      • setFlexibleRingRotatableBondCount

        public void setFlexibleRingRotatableBondCount​(int arg0)

      • 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()

      • setTimeLimit

        public void setTimeLimit​(int arg0)

      • setProgressMonitor

        public void setProgressMonitor​(MProgressMonitor arg0)

      • setProximity

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