chemaxon.marvin.alignment

Class PairwiseSimilarity3D

java.lang.Object

chemaxon.marvin.alignment.PairwiseSimilarity3D

All Implemented Interfaces:

PairwiseComparison

public final class PairwiseSimilarity3D
extends Object
implements PairwiseComparison

Align pairs of molecules (query and the target) using the atom/atom matcher Similarity3D

Author:

Adrian Kalaszi

Constructor Summary

Constructors

Constructor and Description
PairwiseSimilarity3D()
PairwiseSimilarity3D(boolean fastmode)

Method Summary

Methods

Modifier and Type	Method and 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	setLicenseEnvironment(String env)
void	setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface bar)
void	setQuery(AlignmentMolecule query)
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 target)
double	similarity(Molecule target) 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 Detail

PairwiseSimilarity3D

public PairwiseSimilarity3D(boolean fastmode)

PairwiseSimilarity3D

public PairwiseSimilarity3D()

Method Detail

removeAllMolecules

public void removeAllMolecules()

Specified by:

removeAllMolecules in interface PairwiseComparison

setQuery

public void setQuery(Molecule m)
              throws chemaxon.marvin.alignment.AlignmentException

Specified by:

setQuery in interface PairwiseComparison

Throws:

chemaxon.marvin.alignment.AlignmentException

setQuery

public void setQuery(AlignmentMolecule query)
              throws chemaxon.marvin.alignment.AlignmentException

Specified by:

setQuery in interface PairwiseComparison

Throws:

chemaxon.marvin.alignment.AlignmentException

setProgressBar

public void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface bar)

Specified by:

setProgressBar in interface PairwiseComparison

similarity

public double similarity(Molecule target)
                  throws chemaxon.marvin.alignment.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:

target - target to calculate similarity

Returns:

the similarity value.

Throws:

AlignmentException

similarity

public double similarity(AlignmentMolecule target)
                  throws chemaxon.marvin.alignment.AlignmentException

Specified by:

similarity in interface PairwiseComparison

Throws:

chemaxon.marvin.alignment.AlignmentException

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.

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.

addNodeColorWeight

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

Specified by:

addNodeColorWeight in interface PairwiseComparison

getShapeTanimoto

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

Specified by:

getShapeTanimoto in interface PairwiseComparison

Throws:

chemaxon.marvin.alignment.AlignmentException

setLicenseEnvironment

public void setLicenseEnvironment(String env)

Specified by:

setLicenseEnvironment in interface PairwiseComparison

setCount

public void setCount(int count)

Specified by:

setCount in interface PairwiseComparison