org.openscience.cdk.similarity

Class DistanceMoment

java.lang.Object

org.openscience.cdk.similarity.DistanceMoment

public class DistanceMoment
extends Object

Fast similarity measure for 3D structures. This class implements a fast descriptor based 3D similarity measure described by Ballester et al ([Bellester, P.J. and Richards, W.G. , Ultrafast shape recognition to search compound databases for similar molecular shapes, Journal of Computational Chemistry, 2007, 28:1711-1723]). The approach calculates the distances of each atom to four specific points: the centroid of the molecule, the atom that is closest to the centroid, the atom that is farthest from the centroid and the atom that is farthest from the previous atom. Thus we get 4 sets of distance distributions. The final descriptor set is generated by evaluating the first three moments of each distance distribution. The similarity between two molecules is then evaluated using the inverse of a normalized Manhattan type metric. This class allows you to evaluate the 3D similarity between two specified molecules as well as generate the 12 descriptors used to characterize the 3D structure which can then be used for a variety of purposes such as storing in a database. Note: The methods of this class do not perform hydrogen removal. If you want to do the calculations excluding hydrogens, you'll need to do it yourself. Also, if the molecule has disconnected components, you should consider one (usually the largest), otherwise all components are considered in the calculation.

Author:

Rajarshi Guha

Source code:

master

Belongs to CDK module:

fingerprint

Keywords:

similarity, 3D, manhattan

Created on:

2007-03-11

Constructor Summary

Constructors

Constructor and Description
DistanceMoment()

Method Summary

Methods

Modifier and Type	Method and Description
static float	calculate(IAtomContainer query, IAtomContainer target) Evaluate the 3D similarity between two molecules.
static float[]	generateMoments(IAtomContainer atomContainer) Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.

Methods inherited from class java.lang.Object

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

Constructor Detail

DistanceMoment

public DistanceMoment()

Method Detail

generateMoments

public static float[] generateMoments(IAtomContainer atomContainer)
                               throws CDKException

Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.

Parameters:

atomContainer - The molecule to consider, should have 3D coordinates

Returns:

A 12 element array containing the descriptors.

Throws:

CDKException - if there are no 3D coordinates

calculate

public static float calculate(IAtomContainer query,
              IAtomContainer target)
                       throws CDKException

Evaluate the 3D similarity between two molecules. The method does not remove hydrogens. If this is required, remove them from the molecules before passing them here.

Parameters:

query - The query molecule

target - The target molecule

Returns:

The similarity between the two molecules (ranging from 0 to 1)

Throws:

CDKException - if either molecule does not have 3D coordinates