Package chemaxon.marvin.alignment

Interface PairwiseComparison

All Known Implementing Classes:

PairwiseAlignment, PairwiseSimilarity3D

@PublicAPI
public interface PairwiseComparison

This interface designed for comparing two molecules in 3D by various overlay methodologies. One of molecules is called the query and the other is the target. The comparison results in the best overlay: the orientation and the conformation. The shape Tanimoto and the overlay score may be retrieved. Example usage:

 PairwiseComparison pc = new PairwiseAlignment();
 pc.setQueryRigidForced(true);
 pc.setTargetRigidForced(false);
 pc.setCount(4);
 pc.setQuery(Molecule query);
 double score = pc.similarity(Molecule target);
 double tanimoto = pc.getShapeTanimoto();
 

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	setLicenseEnvironment(String env)
void	setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)
void	setQuery(AlignmentMolecule query)
void	setQuery(Molecule query)
void	setQueryRigidForced(boolean forced)	Set this molecule to be rigid in the input conformation even if it contains rotatable bonds
void	setTargetRigidForced(boolean forced)	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.

Method Detail

setQuery

void setQuery(Molecule query)
       throws chemaxon.marvin.alignment.AlignmentException

Throws:

chemaxon.marvin.alignment.AlignmentException

similarity

double similarity(Molecule target)
           throws chemaxon.marvin.alignment.AlignmentException

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

Parameters:

target - target to calculate similarity

Returns:

the similarity value.

Throws:

chemaxon.marvin.alignment.AlignmentException

setQuery

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

Throws:

chemaxon.marvin.alignment.AlignmentException

similarity

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

Throws:

chemaxon.marvin.alignment.AlignmentException

getAlignedMoleculesAsFragments

Molecule getAlignedMoleculesAsFragments()

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

Returns:

the aligned molecules.

getAlignedTarget

Molecule getAlignedTarget()

Returns:

the target molecule in the final orientation and conformation.

getAlignedQuery

Molecule getAlignedQuery()

removeAllMolecules

void removeAllMolecules()

setProgressBar

void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)

setQueryRigidForced

void setQueryRigidForced(boolean forced)

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

Parameters:

forced - if true than rigid.

setTargetRigidForced

void setTargetRigidForced(boolean forced)

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

Parameters:

forced - if true than rigid.

addNodeColorWeight

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

getShapeTanimoto

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

Throws:

chemaxon.marvin.alignment.AlignmentException

setLicenseEnvironment

void setLicenseEnvironment(String env)

setCount

void setCount(int count)