descriptors/atomic/PiElectronegativityDescriptor.java

/* Copyright (C) 2004-2007  Miguel Rojas <miguel.rojas@uni-koeln.de>
 *
 *  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.charges.Electronegativity;
import org.openscience.cdk.charges.PiElectronegativity;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.AbstractAtomicDescriptor;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.tools.LonePairElectronChecker;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

/**
 *  Pi electronegativity is given by X = a + bq + c(q*q)
 *
  *
 * <table border="1"><caption>Parameters for this descriptor:</caption>
 *   <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 2006-05-17
 * @cdk.module  qsaratomic
 * @cdk.githash
 * @cdk.dictref qsar-descriptors:piElectronegativity
 *
 * @see Electronegativity
 */
public class PiElectronegativityDescriptor extends AbstractAtomicDescriptor implements IAtomicDescriptor {

    /**Number of maximum iterations*/
    private int                   maxIterations   = -1;
    /**Number of maximum resonance structures*/
    private int                   maxResonStruc   = -1;
    /** make a lone pair electron checker. Default true*/
    private boolean               lpeChecker      = true;

    private static final String[] NAMES = {"elecPiA"};
    private PiElectronegativity   electronegativity;

    /**
     *  Constructor for the PiElectronegativityDescriptor object
     */
    public PiElectronegativityDescriptor() {
        electronegativity = new PiElectronegativity();
    }

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

    /**
     *  Sets the parameters attribute of the PiElectronegativityDescriptor
     *  object
     *
     *@param  params            The number of maximum iterations. 1= maxIterations. 2= maxResonStruc.
     *@exception  CDKException  Description of the Exception
     */
    @Override
    public void setParameters(Object[] params) throws CDKException {
        if (params.length > 3) throw new CDKException("PartialPiChargeDescriptor only expects three parameter");

        if (!(params[0] instanceof Integer)) throw new CDKException("The parameter must be of type Integer");
        maxIterations = (Integer) params[0];

        if (params.length > 1 && params[1] != null) {
            if (!(params[1] instanceof Boolean)) throw new CDKException("The parameter must be of type Boolean");
            lpeChecker = (Boolean) params[1];
        }

        if (params.length > 2 && params[2] != null) {
            if (!(params[2] instanceof Integer)) throw new CDKException("The parameter must be of type Integer");
            maxResonStruc = (Integer) params[2];
        }
    }

    /**
     *  Gets the parameters attribute of the PiElectronegativityDescriptor
     *  object
     *
     *@return    The parameters value
     */
    @Override
    public Object[] getParameters() {
        // return the parameters as used for the descriptor calculation
        Object[] params = new Object[3];
        params[0] = maxIterations;
        params[1] = lpeChecker;
        params[2] = maxResonStruc;
        return params;
    }

    @Override
    public String[] getDescriptorNames() {
        return NAMES;
    }

    /**
     *  The method calculates the pi electronegativity of a given atom
     *  It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
     *
     *@param  atom              The IAtom for which the DescriptorValue is requested
     *@param  atomContainer                AtomContainer
     *@return                   return the pi electronegativity
     */
    @Override
    public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer) {
        IAtomContainer clone;
        IAtom localAtom;
        try {
            clone = (IAtomContainer) atomContainer.clone();
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(clone);
            if (lpeChecker) {
                LonePairElectronChecker lpcheck = new LonePairElectronChecker();
                lpcheck.saturate(atomContainer);
            }
            localAtom = clone.getAtom(atomContainer.indexOf(atom));
        } catch (CloneNotSupportedException e) {
            return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(
                    Double.NaN), NAMES, null);
        } catch (CDKException e) {
            return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(
                    Double.NaN), NAMES, null);
        }

        if (maxIterations != -1 && maxIterations != 0) electronegativity.setMaxIterations(maxIterations);
        if (maxResonStruc != -1 && maxResonStruc != 0) electronegativity.setMaxResonStruc(maxResonStruc);

        double result = electronegativity.calculatePiElectronegativity(clone, localAtom);

        return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(result),
                                   NAMES);
    }

    /**
     *  Gets the parameterNames attribute of the SigmaElectronegativityDescriptor
     *  object
     *
     *@return    The parameterNames value
     */
    @Override
    public String[] getParameterNames() {
        String[] params = new String[3];
        params[0] = "maxIterations";
        params[1] = "lpeChecker";
        params[2] = "maxResonStruc";
        return params;
    }

    /**
     *  Gets the parameterType attribute of the SigmaElectronegativityDescriptor
     *  object
     *
     *@param  name  Description of the Parameter
     *@return       The parameterType value
     */
    @Override
    public Object getParameterType(String name) {
        if ("maxIterations".equals(name)) return Integer.MAX_VALUE;
        if ("lpeChecker".equals(name)) return Boolean.TRUE;
        if ("maxResonStruc".equals(name)) return Integer.MAX_VALUE;
        return null;
    }
}