From: Rajarshi G. <raj...@us...> - 2005-03-19 21:29:31
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1239/src/org/openscience/cdk/qsar Added Files: EccentricConnectivityIndexDescriptor.java Log Message: Added the code and associated test for the Eccentric Connectivity descriptor and updated the references --- NEW FILE: EccentricConnectivityIndexDescriptor.java --- /* * Copyright (C) 2004-2005 The Chemistry Development Kit (CDK) project * * Contact: cdk...@li... * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation; either version 2.1 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package org.openscience.cdk.qsar; import org.openscience.cdk.Bond; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.config.IsotopeFactory; import org.openscience.cdk.qsar.result.*; import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.graph.matrix.AdjacencyMatrix; import java.lang.Math; import java.util.Vector; /** * A topological descriptor combining distance and adjacency information. * This descriptor is described by Sharma et al. {@cdk.cite SHA97} and has been shown * to correlate well with a number of physical properties. The descriptor is also reported to * have good discriminatory ability. * <p> * The eccentric connectivity index for a hydrogen supressed molecular graph is given by the * expression * <center> * \xi^{c} = \sum_{i = 1}{n} E(i) V(i) * </center> * where E(i) is the eccentricity of the i<sup>th</sup> atom (path length from the * i<sup>th</sup> atom to the atom farthest from it) and V(i) is the vertex degree of the * i<sup>th</sup> atom. * * @author Rajarshi Guha * @cdk.created 2005-03-19 * @cdk.module qsar * @cdk.set qsar-descriptors */ public class EccentricConnectivityIndexDescriptor implements Descriptor { private LoggingTool logger; public EccentricConnectivityIndexDescriptor() { logger = new LoggingTool(this); } public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "http://qsar.sourceforge.net/dicts/qsar-descriptors:eccentricConnectivityIndex", this.getClass().getName(), "$Id: EccentricConnectivityIndexDescriptor.java,v 1.1 2005/03/19 21:29:21 rajarshi Exp $", "The Chemistry Development Kit"); }; /** * Sets the parameters attribute of the EccentricConnectivityIndexDescriptor object * *@param params The new parameters value *@exception CDKException Description of the Exception */ public void setParameters(Object[] params) throws CDKException { // no parameters for this descriptor } /** * Gets the parameters attribute of the EccentricConnectivityIndexDescriptor object * *@return The parameters value */ public Object[] getParameters() { // no parameters to return return(null); } /** * Gets the parameterNames attribute of the EccentricConnectivityIndexDescriptor object * *@return The parameterNames value */ public String[] getParameterNames() { // no param names to return return(null); } /** * Gets the parameterType attribute of the EccentricConnectivityIndexDescriptor object * *@param name Description of the Parameter *@return The parameterType value */ public Object getParameterType(String name) { return (null); } /** * Calculates the eccentric connectivity * *@param container Parameter is the atom container. *@return An IntegerResult value representing the eccentric connectivity index */ public DescriptorValue calculate(AtomContainer container) { AtomContainer local = AtomContainerManipulator.removeHydrogens(container); int natom = local.getAtomCount(); int[][] admat = AdjacencyMatrix.getMatrix(local); int[][] distmat = PathTools.computeFloydAPSP(admat); int eccenindex = 0; for (int i = 0; i < natom; i++) { int max = -1; for (int j = 0; j < natom; j++) { if (distmat[i][j] > max) max = distmat[i][j]; } int degree = local.getBondCount(i); eccenindex += max * degree; } IntegerResult retval = new IntegerResult(eccenindex); return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), retval); } } |