partialsigmachargedescriptor.java

化学图形处理软件

/*
 *  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2006-03-29 10:27:08 +0200 (Wed, 29 Mar 2006) $
 *  $Revision: 5855 $
 *
 *  Copyright (C) 2004-2007  Miguel Rojas <[e-mail]>
 *
 *  Contact: [e-mail]
 *
 *  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.atomic;

import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.nonotify.NNMolecule;
import org.openscience.cdk.qsar.AbstractAtomicDescriptor;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.result.DoubleResult;

/**
 *  The calculation of sigma partial charges in sigma-bonded systems of an heavy atom
 *  was made by Marsilli-Gasteiger. It is implemented with the Partial Equalization
 *  of Orbital Electronegativity (PEOE).
 *  
 * <p>This descriptor uses these parameters:
 * <table border="1">
 *   <tr>
 *     <td>Name</td>
 *     <td>Default</td>
 *     <td>Description</td>
 *   </tr>
 *   <tr>
 *     <td>maxIterations</td>
 *     <td>0</td>
 *     <td>Number of maximum iterations</td>
 *   </tr>
 * </table>
 *
 *
 * @author      Miguel Rojas
 * @cdk.created 2006-04-15
 * @cdk.module  qsar
 * @cdk.set     qsar-descriptors
 * @cdk.dictref qsar-descriptors:partialSigmaCharge
 * @see GasteigerMarsiliPartialCharges
 */
public class PartialSigmaChargeDescriptor extends AbstractAtomicDescriptor {

    private GasteigerMarsiliPartialCharges peoe = null;
    /**Number of maximum iterations*/
	private int maxIterations;

    /**
     *  Constructor for the PartialSigmaChargeDescriptor object
     */
    public PartialSigmaChargeDescriptor() { 
        peoe = new GasteigerMarsiliPartialCharges();
    }


    /**
     *  Gets the specification attribute of the PartialSigmaChargeDescriptor
     *  object
     *
     *@return    The specification value
     */
    public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
            "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#partialSigmaCharge",
            this.getClass().getName(),
            "$Id: PartialSigmaChargeDescriptor.java 5855 2006-03-29 10:27:08 +0200 (Wed, 29 Mar 2006) egonw $",
            "The Chemistry Development Kit");
    }


    /**
     *  Sets the parameters attribute of the PartialSigmaChargeDescriptor
     *  object
     *
     *@param  params            Number of maximum iterations
     *@exception  CDKException  Description of the Exception
     */
    public void setParameters(Object[] params) throws CDKException {
        if (params.length > 1) {
            throw new CDKException("PartialSigmaChargeDescriptor only expects one parameter");
        }
        if (!(params[0] instanceof Integer)) {
            throw new CDKException("The parameter 2 must be of type Integer");
        }
        maxIterations = ((Integer) params[0]).intValue();
    }


    /**
     *  Gets the parameters attribute of the PartialSigmaChargeDescriptor object
     *
     *@return    The parameters value
     */
    public Object[] getParameters() {
        // return the parameters as used for the descriptor calculation
        Object[] params = new Object[1];
        params[0] = new Integer(maxIterations);
        return params;
    }


    /**
     *  The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili
     *  It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
     *  For this method will be only possible if the heavy atom has single bond.
     *
     *@param  atom              The IAtom for which the DescriptorValue is requested
     *@param  ac                AtomContainer
     *@return                   Value of the alpha partial charge
     *@exception  CDKException  Possible Exceptions
     */
    public DescriptorValue calculate(IAtom atom, IAtomContainer ac) throws CDKException {
    	if (!isCachedAtomContainer(ac)) {
    		IMolecule mol = new NNMolecule(ac);
        	if(maxIterations != 0) peoe.setMaxGasteigerIters(maxIterations);
	        try {
				peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true);
	        
				for (int i=0; i<ac.getAtomCount(); i++) {
					// assume same order, so mol.getAtom(i) == ac.getAtom(i)
					cacheDescriptorValue(ac.getAtom(i), ac, new DoubleResult(mol.getAtom(i).getCharge()));
				}
			} catch (Exception e) {
				throw new CDKException("An error occured while calculating Gasteiger partial charges: " + e.getMessage(), e);
			}
        }
        
        return getCachedDescriptorValue(atom) != null 
            ? new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), getCachedDescriptorValue(atom)) 
            : null;
    }


    /**
     *  Gets the parameterNames attribute of the PartialSigmaChargeDescriptor
     *  object
     *
     *@return    The parameterNames value
     */
    public String[] getParameterNames() {
        String[] params = new String[1];
        params[0] = "maxIterations";
        return params;
    }


    /**
     *  Gets the parameterType attribute of the PartialSigmaChargeDescriptor
     *  object
     *
     *@param  name  Description of the Parameter
     *@return       The parameterType value
     */
    public Object getParameterType(String name) {
    	Integer[] object = {new Integer(0)};
        return object;
    }
}