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📄 valencecarbonconnectivityorderzerodescriptor.java

📁 化学图形处理软件
💻 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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