chemaxon.marvin.alignment

Class MinMaxDistance

java.lang.Object

chemaxon.marvin.alignment.MinMaxDistance

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
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

Fields

Modifier and Type	Field and Description
static double	WEIGHT

Constructor Summary

Constructors

Constructor and Description
MinMaxDistance()

Method Summary

Modifier and Type	Method and Description
double	calcMaxDist()
double	calcMinDist() Calculates the minimum distance between two atoms in the molecule.
double	getMaxGradLimit()
java.util.Collection<AlignmentMolecule>	getMolecules()
chemaxon.marvin.alignment.NodeColor	getNodeColor()
AlignmentProperties.NodeType	getNodeType()
int	getStepLimit()
int	getTimeLimit()
boolean	isLicensed()
void	resetMap()
void	setAromatize(boolean arg0) Deprecated.
void	setAtom1(int atom1)
void	setAtom2(int atom2)
void	setDehidrogenize(boolean arg0) Deprecated.
void	setFlexibleRingRotatableBondCount(int arg0)
void	setFlexibleRingSize(int arg0)
void	setLicenseEnvironment(java.lang.String arg0)
void	setMinDistTryCount(int minDistTryCount)
void	setMolecule(Molecule m)
void	setNodeType(AlignmentProperties.NodeType arg0)
void	setProgressMonitor(MProgressMonitor arg0)
void	setProperty(AlignmentProperties arg0)
void	setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType arg0)
void	setStepLimit(int arg0)
void	setTimeLimit(int arg0)

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:

AlignmentException

calcMaxDist

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

Throws:

chemaxon.marvin.alignment.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
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)

getMolecules

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

isLicensed

public boolean isLicensed()

Specified by:

isLicensed in interface chemaxon.license.Licensable

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.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)