org.openscience.cdk.qsar.descriptors.molecular
Class ChiIndexUtils

java.lang.Object
  org.openscience.cdk.qsar.descriptors.molecular.ChiIndexUtils

public class ChiIndexUtils
extends Object

Utility methods for chi index calculations.

These methods are common to all the types of chi index calculations and can be used to evaluate path, path-cluster, cluster and chain chi indices.

Author:

Rajarshi Guha

Belongs to CDK module:

qsarmolecular

Source code:

HEAD

Constructor Summary

ChiIndexUtils()

Method Summary

static double	evalSimpleIndex(IAtomContainer atomContainer, List<List<Integer>> fragLists) Evaluates the simple chi index for a set of fragments.
static double	evalValenceIndex(IAtomContainer atomContainer, List fragList) Evaluates the valence corrected chi index for a set of fragments.
static List<List<Integer>>	getFragments(IAtomContainer atomContainer, QueryAtomContainer[] queries) Gets the fragments from a target AtomContainer matching a set of query fragments.

Methods inherited from class java.lang.Object

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

Constructor Detail

ChiIndexUtils

public ChiIndexUtils()

Method Detail

getFragments

public static List<List<Integer>> getFragments(IAtomContainer atomContainer,
                                               QueryAtomContainer[] queries)

Gets the fragments from a target AtomContainer matching a set of query fragments.

This method returns a list of lists. Each list contains the atoms of the target AtomContainer that arise in the mapping of bonds in the target molecule to the bonds in the query fragment. The query fragments should be constructed using the createAnyAtomAnyBondContainer method of the QueryAtomContainerCreator CDK class, since we are only interested in connectivity and not actual atom or bond type information.

Parameters:

atomContainer - The target AtomContainer

queries - An array of query fragments

Returns:

A list of lists, each list being the atoms that match the query fragments

evalSimpleIndex

public static double evalSimpleIndex(IAtomContainer atomContainer,
                                     List<List<Integer>> fragLists)

Evaluates the simple chi index for a set of fragments.

Parameters:

atomContainer - The target AtomContainer

fragLists - A list of fragments

Returns:

The simple chi index

evalValenceIndex

public static double evalValenceIndex(IAtomContainer atomContainer,
                                      List fragList)
                               throws CDKException

Evaluates the valence corrected chi index for a set of fragments.

This method takes into account the S and P atom types described in Kier & Hall (1986), page 20 for which empirical delta V values are used.

Parameters:

atomContainer - The target AtomContainer

fragList - A list of fragments

Returns:

The valence corrected chi index

Throws:

CDKException - if the IsotopeFactory cannot be created