Package chemaxon.marvin.alignment
Class MinMaxDistance
java.lang.Object
chemaxon.marvin.alignment.MinMaxDistance
- All Implemented Interfaces:
chemaxon.license.Licensable
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
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptiondouble
double
Calculates the minimum distance between two atoms in the molecule.double
chemaxon.marvin.alignment.NodeColor
int
int
boolean
void
resetMap()
void
setAromatize
(boolean arg0) Deprecated, for removal: This API element is subject to removal in a future version.void
setAtom1
(int atom1) void
setAtom2
(int atom2) void
setDehidrogenize
(boolean arg0) Deprecated, for removal: This API element is subject to removal in a future version.void
setFlexibleRingRotatableBondCount
(int arg0) void
setFlexibleRingSize
(int arg0) void
setLicenseEnvironment
(String arg0) void
setMinDistTryCount
(int minDistTryCount) void
void
void
void
void
setProximity
(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType arg0) void
setStepLimit
(int arg0) void
setTimeLimit
(int arg0)
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Field Details
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WEIGHT
public static final double WEIGHT- See Also:
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Constructor Details
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MinMaxDistance
public MinMaxDistance()
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Method Details
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setMolecule
- Throws:
chemaxon.marvin.alignment.AlignmentException
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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
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calcMinDist
public double calcMinDist() throws chemaxon.marvin.alignment.AlignmentExceptionCalculates 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() -
setProperty
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getMaxGradLimit
public double getMaxGradLimit() -
getNodeType
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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
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isLicensed
public boolean isLicensed()- Specified by:
isLicensed
in interfacechemaxon.license.Licensable
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setLicenseEnvironment
- Specified by:
setLicenseEnvironment
in interfacechemaxon.license.Licensable
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getStepLimit
public int getStepLimit() -
setStepLimit
public void setStepLimit(int arg0) -
getTimeLimit
public int getTimeLimit() -
setNodeType
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setTimeLimit
public void setTimeLimit(int arg0) -
setProgressMonitor
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setProximity
public void setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType arg0)
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