Package org.openscience.cdk.similarity
Class DistanceMoment
java.lang.Object
org.openscience.cdk.similarity.DistanceMoment
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.
. Journal of Computational Chemistry. 2007. 28]). 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:
 main
 Belongs to CDK module:
 fingerprint
 Keywords:
 similarity, 3D, manhattan
 Created on:
 20070311

Constructor Summary

Method Summary
Modifier and TypeMethodDescriptionstatic 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.

Constructor Details

DistanceMoment
public DistanceMoment()


Method Details

generateMoments
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
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 moleculetarget
 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
