📄 valencecarbonconnectivityorderzerodescriptor.java
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/* $RCSfile$ * $Author: rajarshi $ * $Date: 2007-02-01 20:46:29 +0100 (Thu, 01 Feb 2007) $ * $Revision: 7844 $ * * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project * * Contact: cdk-devel@lists.sourceforge.net * * 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., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */package org.openscience.cdk.qsar.descriptors.molecular;import org.openscience.cdk.config.IsotopeFactory;import org.openscience.cdk.exception.CDKException;import org.openscience.cdk.interfaces.IAtom;import org.openscience.cdk.interfaces.IAtomContainer;import org.openscience.cdk.interfaces.IElement;import org.openscience.cdk.qsar.DescriptorSpecification;import org.openscience.cdk.qsar.DescriptorValue;import org.openscience.cdk.qsar.IMolecularDescriptor;import org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor;import org.openscience.cdk.qsar.result.DoubleResult;import org.openscience.cdk.qsar.result.IDescriptorResult;import org.openscience.cdk.tools.LoggingTool;import java.util.Map;/** * Atomic valence connectivity index (order 0). See * <a href="http://www.edusoft-lc.com/molconn/manuals/400/chaptwo.html">http://www.edusoft-lc.com/molconn/manuals/400/chaptwo.html</a> and * <a href="http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH">http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH</a>. * * <p>Returned value is: * <ul> * <li>chi0vC is the Carbon valence connectivity index (order 0); * </ul> * where the valence is the number of s and p valence electrons of atom. * * <p>This descriptor uses these parameters: * <table border="1"> * <tr> * <td>Name</td> * <td>Default</td> * <td>Description</td> * </tr> * <tr> * <td></td> * <td></td> * <td>no parameters</td> * </tr> * </table> * * @author mfe4 * @cdk.created 2004-11-03 * @cdk.module qsar * @cdk.set qsar-descriptors * @cdk.dictref qsar-descriptors:chi0vC */public class ValenceCarbonConnectivityOrderZeroDescriptor implements IMolecularDescriptor { private LoggingTool logger; private static Map valences; private AtomValenceDescriptor avd = null; /** * Constructor for the ValenceCarbonConnectivityOrderZeroDescriptor object */ public ValenceCarbonConnectivityOrderZeroDescriptor() { logger = new LoggingTool(this); if (valences == null) { avd = new AtomValenceDescriptor(); valences = avd.valencesTable; } } /** * Gets the specification attribute of the * ValenceCarbonConnectivityOrderZeroDescriptor object * *@return The specification value */ public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#chi0vC", this.getClass().getName(), "$Id: ValenceCarbonConnectivityOrderZeroDescriptor.java 7844 2007-02-01 19:46:29Z rajarshi $", "The Chemistry Development Kit"); } /** * Sets the parameters attribute of the * ValenceCarbonConnectivityOrderZeroDescriptor 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 * ValenceCarbonConnectivityOrderZeroDescriptor object * *@return The parameters value */ public Object[] getParameters() { // no parameters to return return (null); } /** * calculates the Carbon valence connectivity index (order 0) descriptor for an atom container * *@param atomContainer AtomContainer *@return Carbon valence connectivity index (order 0) *@exception CDKException Possible Exceptions */ public DescriptorValue calculate(IAtomContainer atomContainer) throws CDKException { int valence = 0; int atomicNumber = 0; int hcount = 0; int atomValue = 0; double chi0vC = 0; java.util.List neighatoms = null; IAtom atom = null; IElement element = null; IsotopeFactory elfac = null; String symbol = null; for (int i = 0; i < atomContainer.getAtomCount(); i++) { atom = atomContainer.getAtom(i); symbol = atom.getSymbol(); if(!symbol.equals("H")) { try { elfac = IsotopeFactory.getInstance(atomContainer.getBuilder()); } catch (Exception exc) { logger.debug(exc); throw new CDKException("Problem instantiating IsotopeFactory: " + exc.toString(), exc); } try { element = elfac.getElement(symbol); } catch (Exception exc) { logger.debug(exc); throw new CDKException("Problem getting isotope " + symbol + " from ElementFactory: " + exc.toString(), exc); } atomicNumber = element.getAtomicNumber(); valence = ((Integer)valences.get(symbol)).intValue(); hcount = 0; atomValue = 0; neighatoms = atomContainer.getConnectedAtomsList(atom); for (int a = 0; a < neighatoms.size(); a++) { if (((IAtom)neighatoms.get(a)).getSymbol().equals("H")) { hcount += 1; } } hcount += atomContainer.getAtom(i).getHydrogenCount(); atomValue = (valence - hcount) / (atomicNumber - valence - 1); if (atomValue > 0) { if(symbol.equals("C")) { chi0vC += (1/(Math.sqrt(atomValue))); // chi0vC } } } } return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(chi0vC), new String[]{"chi0vC"}); } /** * Returns the specific type of the DescriptorResult object. * <p/> * The return value from this method really indicates what type of result will * be obtained from the {@link org.openscience.cdk.qsar.DescriptorValue} object. Note that the same result * can be achieved by interrogating the {@link org.openscience.cdk.qsar.DescriptorValue} object; this method * allows you to do the same thing, without actually calculating the descriptor. * * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating * the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object */ public IDescriptorResult getDescriptorResultType() { return new DoubleResult(0.0); } /** * Gets the parameterNames attribute of the * ValenceCarbonConnectivityOrderZeroDescriptor object * *@return The parameterNames value */ public String[] getParameterNames() { // no param names to return return (null); } /** * Gets the parameterType attribute of the * ValenceCarbonConnectivityOrderZeroDescriptor object * *@param name Description of the Parameter *@return The parameterType value */ public Object getParameterType(String name) { return (null); }}
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