chemaxon.util
Class MolAligner

java.lang.Object
  chemaxon.util.MolAligner

public final class MolAligner
extends java.lang.Object

Tool for aligning molecules

Author:

Szilard Dorant

Nested Class Summary

class

MolAligner.AlignmentResult

Field Summary

double[][]

fragCenter Rotation center - a double[] for each fragment

Constructor Summary

MolAligner()
Creates a new instance of MolAligner

Method Summary

double	align(Molecule mol, int[] indexes) Alignes (rotates) a specified molecule to the pattern molecule in 2D according to the specified atom pairs.
MolAligner.AlignmentResult	calculate(int[] indexes)
static void	main(java.lang.String[] args) For testing purposes.
void	rotate(MolAligner.AlignmentResult alignment) Rotates the target structure according to the specified alignment. 2D target will be set to 3D if query was 3D.
void	setPatternMolecule(Molecule mol) Sets the molecule that will be used as a pattern for alignment.
void	setTargetMolecule(Molecule mol) Sets the molecule to rotate.

Methods inherited from class java.lang.Object

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

Field Detail

fragCenter

public double[][] fragCenter

Rotation center - a double[] for each fragment

Constructor Detail

MolAligner

public MolAligner()

Creates a new instance of MolAligner

Method Detail

setPatternMolecule

public void setPatternMolecule(Molecule mol)

Sets the molecule that will be used as a pattern for alignment. WARNING: S-groups will be expanded.

setTargetMolecule

public void setTargetMolecule(Molecule mol)

Sets the molecule to rotate. S-groups will be temporarily expanded for alignment, but later restored after alignment;

Parameters:

mol - the molecle to rotate

align

public double align(Molecule mol,
                    int[] indexes)
             throws java.lang.IllegalArgumentException

Alignes (rotates) a specified molecule to the pattern molecule in 2D according to the specified atom pairs. S-groups will be temporarily expanded for alignment, but later restored.

Parameters:

mol - the molecule to be aligned

indexes - the atom indexes of the pattern in the order of the atoms of the molecule to be aligned. Negative values are ignored. The size of this array should be at least the number of atoms in the pattern molecule (in case of RgMolecules, the non R-group atoms of the root). If the size of the array is grater, the excess elements are ignored.

Returns:

the error of the alignment, can be used to try to align multiple hits and choose the best solution.

Throws:

java.lang.IllegalArgumentException

rotate

public void rotate(MolAligner.AlignmentResult alignment)

Rotates the target structure according to the specified alignment. 2D target will be set to 3D if query was 3D. S-groups will be restored to their original state.

Parameters:

alignment - the alignment result to use

calculate

public MolAligner.AlignmentResult calculate(int[] indexes)

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

For testing purposes.

Throws:

java.lang.Exception