atomdegreedescriptor.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.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.IntegerResult;

/**
 * This class returns the number of not-Hs substituents of an atom, also defined as "atom degree".
 *
 * <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 2004-11-13
 * @cdk.module  qsar
 * @cdk.set     qsar-descriptors
 * @cdk.dictref qsar-descriptors:atomDegree
 */
public class AtomDegreeDescriptor implements IAtomicDescriptor {

    public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
                "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#atomDegree",
                this.getClass().getName(),
                "$Id: AtomDegreeDescriptor.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 AtomDegreeDescriptor object.
     *
     *@return    The parameters value
     *@see #setParameters
     */
    public Object[] getParameters() {
        return null;
    }


    /**
     * This method calculates the number of not-H substituents of an atom.
     *
     * @param  atom              The IAtom for which the DescriptorValue is requested
     * @param  container         The {@link IAtomContainer} for which this descriptor is to be calculated for
     * @return   The number of bonds on the shortest path between two atoms
     * @throws  CDKException  NOT CLEAR
     */
    public DescriptorValue calculate(IAtom atom, IAtomContainer container) throws CDKException {
        int atomDegree = 0;
        java.util.List neighboors = container.getConnectedAtomsList(atom);
        for (int i =0; i< neighboors.size();i++) {
            if(!((IAtom)neighboors.get(i)).getSymbol().equals("H")) atomDegree+=1;
        }
        return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(atomDegree));
    }


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


    /**
     * Gets the parameterType attribute of the AtomDegreeDescriptor 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;
    }
}