AtomValenceDescriptor.java

/*  $Revision$ $Author$ $Date$
 *
 *  Copyright (C) 2004-2007  Matteo Floris <mfe4@users.sf.net>
 *                     2008  Egon Willighagen <egonw@users.sf.net>
 *
 *  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.atomic;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.AtomValenceTool;
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 valence of an atom.
 * This descriptor does not have any parameters.
 *
 * @author      mfe4
 * @cdk.created 2004-11-13
 * @cdk.module  qsaratomic
 * @cdk.githash
 * @cdk.set     qsar-descriptors
 * @cdk.dictref qsar-descriptors:atomValence
 * 
 * @see         org.openscience.cdk.qsar.AtomValenceTool
 */
@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptorTest")
public class AtomValenceDescriptor implements IAtomicDescriptor {

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

    /**
     * Gets the specification attribute of the AtomValenceDescriptor object
     *
     * @return The specification value
     */
    @TestMethod(value="testGetSpecification")
    public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
                "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#atomValence",
                this.getClass().getName(),
                "$Id$",
                "The Chemistry Development Kit");
    }

    /**
     * This descriptor does have any parameter.
     */
    @TestMethod(value="testSetParameters_arrayObject")
    public void setParameters(Object[] params) throws CDKException {
    }


    /**
     *  Gets the parameters attribute of the VdWRadiusDescriptor object.
     *
     *@return    The parameters value
     * @see #setParameters
     */
    @TestMethod(value="testGetParameters")
    public Object[] getParameters() {
        return null;
    }

    @TestMethod(value="testNamesConsistency")
    public String[] getDescriptorNames() {
        return new String[]{"val"};
    }

    /**
     * This method calculates the valence of an atom.
     *
     * @param atom          The IAtom for which the DescriptorValue is requested
     * @param container      Parameter is the atom container.
     * @return The valence of an atom     
     */

    @TestMethod(value="testCalculate_IAtomContainer")
    public DescriptorValue calculate(IAtom atom, IAtomContainer container) {
        int atomValence = AtomValenceTool.getValence(atom);
        return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
        	new IntegerResult(atomValence), getDescriptorNames());
    }


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

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