protontotalpartialchargedescriptor.java

化学图形处理软件

/*
 *  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-02-07 23:20:44 +0100 (Wed, 07 Feb 2007) $
 *  $Revision: 7895 $
 *
 *  Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
 *
 *  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.Molecule;
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.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;

/**
 *  The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE)
 * <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:protonPartialCharge
 */
public class ProtonTotalPartialChargeDescriptor implements IAtomicDescriptor {

    private GasteigerMarsiliPartialCharges peoe = null;


    /**
     *  Constructor for the ProtonTotalPartialChargeDescriptor object
     */
    public ProtonTotalPartialChargeDescriptor() { }


    /**
     *  Gets the specification attribute of the ProtonTotalPartialChargeDescriptor
     *  object
     *
     *@return    The specification value
     */
    public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
            "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#protonPartialCharge",
            this.getClass().getName(),
            "$Id: ProtonTotalPartialChargeDescriptor.java 7895 2007-02-07 22:20:44Z egonw $",
            "The Chemistry Development Kit");
    }


    /**
     * This descriptor does not have any parameter to be set.
     */
    public void setParameters(Object[] params) throws CDKException {
    	// no parameters
    }


    /**
     *  Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor
     *  object
     *
     *@return    The parameters value
     *@see #setParameters
     */
    public Object[] getParameters() {
        return null;
    }


    /**
     *  The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili
     *  It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
     *
     *@param  atom              The IAtom for which the DescriptorValue is requested
     *@param  ac                AtomContainer
     *@return                   an array of doubles with partial charges of [heavy, proton_1 ... proton_n]
     *@exception  CDKException  Possible Exceptions
     */
    public DescriptorValue calculate(IAtom atom, IAtomContainer ac) throws CDKException {
        Molecule mol = new Molecule(ac);
        try {
        	
            peoe = new GasteigerMarsiliPartialCharges();
            peoe.setMaxGasteigerIters(6);
        //	HydrogenAdder hAdder = new HydrogenAdder();
        //	hAdder.addExplicitHydrogensToSatisfyValency(mol);
            peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true);
        } catch (Exception ex1) {
            throw new CDKException("Problems with assignGasteigerMarsiliPartialCharges due to " + ex1.toString(), ex1);
        }
        IAtom target = atom;
        java.util.List neighboors = mol.getConnectedAtomsList(target);
        DoubleArrayResult protonPartialCharge = new DoubleArrayResult(neighboors.size() + 1);
        protonPartialCharge.add( target.getCharge() );
        for (int i = 0; i < neighboors.size(); i++) {
        	IAtom neighbour = (IAtom)neighboors.get(i);
            if (neighbour.getSymbol().equals("H")) {
                protonPartialCharge.add( neighbour.getCharge() );
            }
        }
        return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), protonPartialCharge);
    }


    /**
     *  Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor
     *  object
     *
     * @return    The parameterNames value
     */
    public String[] getParameterNames() {
        return new String[0];
    }


    /**
     *  Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor
     *  object
     *
     * @param  name  Description of the Parameter
     * @return       An Object of class equal to that of the parameter being requested
     */
    public Object getParameterType(String name) {
        return null;
    }
}