chemaxon.marvin.alignment
Class MinMaxDistance

java.lang.Object
  chemaxon.marvin.alignment.MinMaxDistance

All Implemented Interfaces:

chemaxon.license.Licensable

public class MinMaxDistance
extends java.lang.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

Author:

Adrian Kalaszi

Field Summary

static double

WEIGHT

Constructor Summary

MinMaxDistance()

Method Summary

double	calcMaxDist()
double	calcMinDist() Calculates the minimum distance between two atoms in the molecule.
java.util.Collection<AlignmentMolecule>	getMolecules()
chemaxon.marvin.alignment.NodeColor	getNodeColor()
AlignmentProperties.NodeType	getNodeType()
int	getStepLimit()
int	getTimeLimit()
boolean	isLicensed() Returns information about the licensing of the product.
void	resetMap()
void	setAromatize(boolean aromatize)
void	setAtom1(int atom1)
void	setAtom2(int atom2)
void	setDehidrogenize(boolean hy)
void	setFlexibleRingRotatableBondCount(int b)
void	setFlexibleRingSize(int s)
void	setLicenseEnvironment(java.lang.String env) Every license can have a modifier environment that's typically an integration environment.
void	setMinDistTryCount(int minDistTryCount)
void	setMolecule(Molecule m)
void	setNodeType(AlignmentProperties.NodeType t)
void	setProgressMonitor(chemaxon.common.util.MProgressMonitor progressMonitor)
void	setProperty(AlignmentProperties props)
void	setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType pot)
void	setStepLimit(int stepLimit)
void	setTimeLimit(int timeLimit) Sets the maximum time used for the alignment.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

WEIGHT

public static final double WEIGHT

See Also:

Constant Field Values

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()

setProperty

public void setProperty(AlignmentProperties props)

getNodeType

public AlignmentProperties.NodeType getNodeType()

getNodeColor

public chemaxon.marvin.alignment.NodeColor getNodeColor()

setAromatize

public void setAromatize(boolean aromatize)

setDehidrogenize

public void setDehidrogenize(boolean hy)

setFlexibleRingSize

public void setFlexibleRingSize(int s)

setFlexibleRingRotatableBondCount

public void setFlexibleRingRotatableBondCount(int b)

getMolecules

public java.util.Collection<AlignmentMolecule> getMolecules()

isLicensed

public boolean isLicensed()

Description copied from interface: chemaxon.license.Licensable

Returns information about the licensing of the product. Example implementation: return LicenseHandler.isLicensed( LicenseHandler.MY_IDENTIFIER, licenseEnvironment );

Specified by:

isLicensed in interface chemaxon.license.Licensable

Returns:

true if the product is correctly licensed

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Description copied from interface: chemaxon.license.Licensable

Every license can have a modifier environment that's typically an integration environment. All being Licensable should be prepared to store and show a set environment to the LicenseHandler. Example implementation:

 private String licenseEnvironment = "";
 public void setLicenseEnvironment(String env) {
     licenseEnvironment = env;
 }
 

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

Parameters:

env - environment String to be stored and passed to the LicenseHandler in the isLicensed method

getStepLimit

public int getStepLimit()

setStepLimit

public void setStepLimit(int stepLimit)

getTimeLimit

public int getTimeLimit()

setNodeType

public void setNodeType(AlignmentProperties.NodeType t)

setTimeLimit

public void setTimeLimit(int timeLimit)

Sets the maximum time used for the alignment. If reached returns the partly aligned structures.

Parameters:

timeLimit - time limit in millisecond. if -1 then disabled.

setProgressMonitor

public void setProgressMonitor(chemaxon.common.util.MProgressMonitor progressMonitor)

setProximity

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