chemaxon.util

Class MolAligner

java.lang.Object

chemaxon.util.MolAligner

@PublicAPI
public class MolAligner
extends java.lang.Object

Tool for aligning a target molecule to a pattern molecule. Can be used for 2D and 3D alignment as well.

Author:

Vencel Bors, Feb. 14, 2011

Constructor Summary

Constructors

Constructor and Description
MolAligner() Creates a new MolAligner object.
MolAligner(Molecule patternMolecule, Molecule targetMolecule) Creates a new MolAligner object while setting the pattern and target molecules

Method Summary

Modifier and Type	Method and Description
void	align() Execute best alignment based on hit map provided earlier
void	align(int[] hit) Calculates and performs the best alignment possible specified by the hit map array.
void	calculate(int[] hit) Calculate best alignment based on the hit map
double	getError() Get the error for the best alignment
void	setPatternMolecule(Molecule mol) Sets pattern molecule and calculates its dimension
void	setTargetMolecule(Molecule mol) Sets target molecule and calculates its dimension

Methods inherited from class java.lang.Object

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

Constructor Detail

MolAligner

public MolAligner()

Creates a new MolAligner object.

MolAligner

public MolAligner(Molecule patternMolecule,
                  Molecule targetMolecule)

Creates a new MolAligner object while setting the pattern and target molecules

Parameters:

patternMolecule - the pattern molecule

targetMolecule -

Method Detail

setPatternMolecule

public void setPatternMolecule(Molecule mol)

Sets pattern molecule and calculates its dimension

Parameters:

mol - pattern molecule

setTargetMolecule

public void setTargetMolecule(Molecule mol)

Sets target molecule and calculates its dimension

Parameters:

mol - molecule to align

getError

public double getError()

Get the error for the best alignment

Returns:

the root mean square deviation of the mapping atoms

calculate

public void calculate(int[] hit)

Calculate best alignment based on the hit map

Parameters:

hit - hit map array, use -1 for no matching atom index

align

public void align()

Execute best alignment based on hit map provided earlier

See Also:

calculate(int[]), align(int[])

align

public void align(int[] hit)

Calculates and performs the best alignment possible specified by the hit map array.

Parameters:

hit - hit map array, use -1 for no matching atom index

See Also:

calculate(int[]), align()