Package chemaxon.marvin.alignment

Class MMPAlignmentResult

java.lang.Object

chemaxon.marvin.alignment.MMPAlignmentResult

All Implemented Interfaces:

chemaxon.marvin.alignment.AlignmentResult

@PublicAPI
public class MMPAlignmentResult
extends Object
implements chemaxon.marvin.alignment.AlignmentResult

Results of the MMPAlignment process.

Method Summary

Modifier and Type	Method	Description
Molecule	getMolecule1Aligned()
Molecule	getMolecule2Aligned()
double	getRmsd()
double	getShapeScore()
double	getShapeTanimoto()
Molecule	toMolecule()	Creates a single two-fragment molecule from the reference and aligned molecule.

Methods inherited from class java.lang.Object

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

Method Details

getMolecule1Aligned

public Molecule getMolecule1Aligned()

Specified by:

getMolecule1Aligned in interface chemaxon.marvin.alignment.AlignmentResult

Returns:

the first (reference) molecule of the alignment with the new coordinates. If this molecule is set as rigid in AlignmentProperties.FlexibilityMode then the original coordinates are returned.

getMolecule2Aligned

public Molecule getMolecule2Aligned()

Specified by:

getMolecule2Aligned in interface chemaxon.marvin.alignment.AlignmentResult

Returns:

the molecule "toAlign" with the modified coordinates.

getShapeScore

public double getShapeScore()

Returns:

The shape overlay - atom type score, which is maximized during the alignment.

getShapeTanimoto

public double getShapeTanimoto()

getRmsd

public double getRmsd()

Returns:

coordinate RMSD of the MCS for the reference-toAlign atoms.

toMolecule

public Molecule toMolecule()

Creates a single two-fragment molecule from the reference and aligned molecule.

Specified by:

toMolecule in interface chemaxon.marvin.alignment.AlignmentResult

Returns:

a two-fragment molecule from the reference and aligned molecule the MCS rmsd, and Shape Tanimoto values are added as properties.