Package chemaxon.marvin.alignment
Class MinMaxDistance
- java.lang.Object
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- chemaxon.marvin.alignment.MinMaxDistance
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- 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
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Field Summary
Fields Modifier and Type Field Description static double
WEIGHT
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Constructor Summary
Constructors Constructor Description MinMaxDistance()
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description double
calcMaxDist()
double
calcMinDist()
Calculates the minimum distance between two atoms in the molecule.double
getMaxGradLimit()
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(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)
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Field Detail
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WEIGHT
public static final double WEIGHT
- See Also:
- Constant Field Values
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Method Detail
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setMolecule
public void setMolecule(Molecule m) throws chemaxon.marvin.alignment.AlignmentException
- Throws:
chemaxon.marvin.alignment.AlignmentException
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setAtom1
public void setAtom1(int atom1)
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setAtom2
public void setAtom2(int atom2)
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setMinDistTryCount
public void setMinDistTryCount(int minDistTryCount)
- Parameters:
minDistTryCount
- number of extra trials. Before every extra trial, the conformation modified using random dihedrals
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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
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calcMaxDist
public double calcMaxDist() throws chemaxon.marvin.alignment.AlignmentException
- Throws:
chemaxon.marvin.alignment.AlignmentException
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resetMap
public void resetMap()
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setProperty
public void setProperty(AlignmentProperties arg0)
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getMaxGradLimit
public double getMaxGradLimit()
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getNodeType
public AlignmentProperties.NodeType getNodeType()
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getNodeColor
public chemaxon.marvin.alignment.NodeColor getNodeColor()
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setAromatize
@Deprecated public void setAromatize(boolean arg0)
Deprecated.
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setDehidrogenize
@Deprecated public void setDehidrogenize(boolean arg0)
Deprecated.
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setFlexibleRingSize
public void setFlexibleRingSize(int arg0)
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setFlexibleRingRotatableBondCount
public void setFlexibleRingRotatableBondCount(int arg0)
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getMolecules
public Collection<AlignmentMolecule> getMolecules()
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isLicensed
public boolean isLicensed()
- Specified by:
isLicensed
in interfacechemaxon.license.Licensable
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setLicenseEnvironment
public void setLicenseEnvironment(String arg0)
- Specified by:
setLicenseEnvironment
in interfacechemaxon.license.Licensable
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getStepLimit
public int getStepLimit()
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setStepLimit
public void setStepLimit(int arg0)
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getTimeLimit
public int getTimeLimit()
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setNodeType
public void setNodeType(AlignmentProperties.NodeType arg0)
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setTimeLimit
public void setTimeLimit(int arg0)
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setProgressMonitor
public void setProgressMonitor(MProgressMonitor arg0)
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setProximity
public void setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType arg0)
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