Package chemaxon.marvin.alignment

Class PairwiseAlignment

java.lang.Object

chemaxon.marvin.alignment.PairwiseAlignment

All Implemented Interfaces:

PairwiseComparison

@PublicApi
public class PairwiseAlignment
extends Object
implements PairwiseComparison

Align pairs of molecules (query and the target) using the shape Alignment

Constructor Summary

Constructors

Constructor	Description
PairwiseAlignment()
PairwiseAlignment(AlignmentProperties ap)

Method Summary

Modifier and Type	Method	Description
void	addNodeColorWeight(int t1, int t2, double w)
Molecule	getAlignedMoleculesAsFragments()	After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.
Molecule	getAlignedQuery()
Molecule	getAlignedTarget()
double	getShapeTanimoto()
void	removeAllMolecules()
void	setCount(int count)
void	setFlexibleRingSize(int s)
void	setLicenseEnvironment(String env)
void	setMinimumCommonSize(int mcs)	Deprecated, for removal: This API element is subject to removal in a future version.
void	setMode(AlignmentAccuracyMode mode)
void	setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)
void	setProgressMonitor(MProgressMonitor mp)
void	setQuery(AlignmentMolecule m)
void	setQuery(Molecule m)
void	setQueryRigidForced(boolean forced)	Set this molecule to be rigid in the input conformation even if it contains rotatable bonds
void	setTargetRigidForced(boolean targetRigid)	Set this molecule to be rigid in the input conformation even if it contains rotatable bonds
double	similarity(AlignmentMolecule am)
double	similarity(Molecule m)	Calculates the 3D similarity between the previously set query and the target.

Methods inherited from class java.lang.Object

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

Constructor Details

PairwiseAlignment

public PairwiseAlignment(AlignmentProperties ap)

PairwiseAlignment

public PairwiseAlignment()

Method Details

addNodeColorWeight

public void addNodeColorWeight(int t1,
 int t2,
 double w)

Specified by:

addNodeColorWeight in interface PairwiseComparison

removeAllMolecules

public void removeAllMolecules()

Specified by:

removeAllMolecules in interface PairwiseComparison

setQuery

public void setQuery(Molecule m)
              throws AlignmentException

Specified by:

setQuery in interface PairwiseComparison

Throws:

AlignmentException

setQuery

public void setQuery(AlignmentMolecule m)
              throws AlignmentException

Specified by:

setQuery in interface PairwiseComparison

Throws:

AlignmentException

setMode

public void setMode(AlignmentAccuracyMode mode)

similarity

public double similarity(Molecule m)
                  throws AlignmentException

Description copied from interface: PairwiseComparison

Calculates the 3D similarity between the previously set query and the target.

Specified by:

similarity in interface PairwiseComparison

Parameters:

m - target to calculate similarity

Returns:

the similarity value.

Throws:

AlignmentException

similarity

public double similarity(AlignmentMolecule am)
                  throws AlignmentException

Specified by:

similarity in interface PairwiseComparison

Throws:

AlignmentException

setCount

public void setCount(int count)

Specified by:

setCount in interface PairwiseComparison

getAlignedMoleculesAsFragments

public Molecule getAlignedMoleculesAsFragments()

Description copied from interface: PairwiseComparison

After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.

Specified by:

getAlignedMoleculesAsFragments in interface PairwiseComparison

Returns:

the aligned molecules.

getShapeTanimoto

public double getShapeTanimoto()
                        throws AlignmentException

Specified by:

getShapeTanimoto in interface PairwiseComparison

Throws:

AlignmentException

setProgressBar

public void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)

Specified by:

setProgressBar in interface PairwiseComparison

setProgressMonitor

public void setProgressMonitor(MProgressMonitor mp)

getAlignedTarget

public Molecule getAlignedTarget()

Specified by:

getAlignedTarget in interface PairwiseComparison

Returns:

the target molecule in the final orientation and conformation.

getAlignedQuery

public Molecule getAlignedQuery()

Specified by:

getAlignedQuery in interface PairwiseComparison

setQueryRigidForced

public void setQueryRigidForced(boolean forced)

Description copied from interface: PairwiseComparison

Set this molecule to be rigid in the input conformation even if it contains rotatable bonds

Specified by:

setQueryRigidForced in interface PairwiseComparison

Parameters:

forced - if true than rigid.

setTargetRigidForced

public void setTargetRigidForced(boolean targetRigid)

Description copied from interface: PairwiseComparison

Set this molecule to be rigid in the input conformation even if it contains rotatable bonds

Specified by:

setTargetRigidForced in interface PairwiseComparison

Parameters:

targetRigid - if true than rigid.

setMinimumCommonSize

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public void setMinimumCommonSize(int mcs)

Deprecated, for removal: This API element is subject to removal in a future version.

setFlexibleRingSize

public void setFlexibleRingSize(int s)

setLicenseEnvironment

public void setLicenseEnvironment(String env)

Specified by:

setLicenseEnvironment in interface PairwiseComparison