bcutdescriptor.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-10-14 20:29:40 +0200 (Sun, 14 Oct 2007) $
 *  $Revision: 9054 $
 *
 *  Copyright (C) 2004-2007  Rajarshi Guha <[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.molecular;

import Jama.EigenvalueDecomposition;
import Jama.Matrix;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.charges.Polarizability;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

/**
 * Eigenvalue based descriptor noted for its utility in chemical diversity.
 * Described by Pearlman et al. {@cdk.cite PEA99}.
 * <p/>
 * <p>The descriptor is based on a weighted version of the Burden matrix {@cdk.cite BUR89, BUR97}
 * which takes into account both the connectivity as well as atomic
 * properties of a molecule. The weights are a variety of atom properties placed along the
 * diagonal of the Burden matrix. Currently three weighting schemes are employed
 * <ul>
 * <li>atomic weight
 * <li>partial charge (Gasteiger Marsilli)
 * <li>polarizability {@cdk.cite KJ81}
 * </ul>
 * <p>By default, the descriptor will return the highest and lowest eigenvalues for the three
 * classes of descriptor in a single ArrayList (in the order shown above). However it is also
 * possible to supply a parameter list indicating how many of the highest and lowest eigenvalues
 * (for each class of descriptor) are required.
 * <p/>
 * <p>The descriptor works with the hydrogen depleted molecule and thus the maximum number
 * of eigenvalues calculated for any class of BCUT descriptor is equal to the number
 * of heavy atoms present.
 * <p>This descriptor uses these parameters:
 * <table border="1">
 * <tr>
 * <td>Name</td>
 * <td>Default</td>
 * <td>Description</td>
 * </tr>
 * <tr>
 * <td>nhigh</td>
 * <td>1</td>
 * <td>The number of highest eigenvalue</td>
 * </tr>
 * <tr>
 * <td>nlow</td>
 * <td>1</td>
 * <td>The number of lowest eigenvalue</td>
 * </tr>
 * </table>
 * <p/>
 * Returns an array of values in the following order
 * <ol>
 * <p/>
 * <li>BCUTw-1l, BCUTw-2l ... - <i>nhigh</i> lowest atom weighted BCUTS
 * <li>BCUTw-1h, BCUTw-2h ... - <i>nlow</i> highest atom weighted BCUTS
 * <li>BCUTc-1l, BCUTc-2l ... - <i>nhigh</i> lowest partial charge weighted BCUTS
 * <li>BCUTc-1h, BCUTc-2h ... - <i>nlow</i> highest partial charge weighted BCUTS
 * <li>BCUTp-1l, BCUTp-2l ... - <i>nhigh</i> lowest polarizability weighted BCUTS
 * <li>BCUTp-1h, BCUTp-2h ... - <i>nlow</i> highest polarizability weighted BCUTS
 *
 * @author Rajarshi Guha
 * @cdk.created 2004-11-30
 * @cdk.builddepends Jama-1.0.1.jar
 * @cdk.depends Jama-1.0.1.jar
 * @cdk.module qsar
 * @cdk.set qsar-descriptors
 * @cdk.dictref qsar-descriptors:BCUT
 * @cdk.keyword BCUT
 * @cdk.keyword descriptor
 */
public class BCUTDescriptor implements IMolecularDescriptor {
    private LoggingTool logger;

    // the number of negative & positive eigenvalues
    // to return for each class of BCUT descriptor
    private int nhigh;
    private int nlow;
    private boolean checkAromaticity = true;

    public BCUTDescriptor() {
        logger = new LoggingTool(this);

        // set the default number of BCUT's
        this.nhigh = 1;
        this.nlow = 1;
    }

    public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
                "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#BCUT",
                this.getClass().getName(),
                "$Id: BCUTDescriptor.java 9054 2007-10-14 18:29:40Z egonw $",
                "The Chemistry Development Kit");
    }

    /**
     * Sets the parameters attribute of the BCUTDescriptor object.
     *
     * @param params The new parameter values. This descriptor takes 3 parameters: number of highest
     *               eigenvalues and number of lowest eigenvalues. If 0 is specified for either (the default)
     *               then all calculated eigenvalues are returned. The third parameter checkAromaticity is a boolean.
     *               If checkAromaticity is true, the method check the aromaticity, if false, means that the aromaticity has
     *               already been checked.
     * @throws CDKException if the parameters are of the wrong type
     * @see #getParameters
     */
    public void setParameters(Object[] params) throws CDKException {
        // we expect 3 parameters
        if (params.length != 3) {
            throw new CDKException("BCUTDescriptor requires 3 parameters");
        }
        if (!(params[0] instanceof Integer) || !(params[1] instanceof Integer)) {
            throw new CDKException("Parameters must be of type Integer");
        } else if (!(params[2] instanceof Boolean)) {
            throw new CDKException("The third parameter must be of type Boolean");
        }
        // ok, all should be fine

        this.nhigh = ((Integer) params[0]).intValue();
        this.nlow = ((Integer) params[1]).intValue();
        this.checkAromaticity = ((Boolean) params[2]).booleanValue();

        if (this.nhigh < 0 || this.nlow < 0) {
            throw new CDKException("Number of eigenvalues to return must be positive or 0");
        }
    }

    /**
     * Gets the parameters attribute of the BCUTDescriptor object.
     *
     * @return Three element array of Integer and one boolean representing number of highest and lowest eigenvalues and the checkAromaticity flag
     *         to return respectively
     * @see #setParameters
     */
    public Object[] getParameters() {
        Object params[] = new Object[3];
        params[0] = new Integer(this.nhigh);
        params[1] = new Integer(this.nlow);
        params[2] = Boolean.valueOf(this.checkAromaticity);
        return (params);
    }

    /**
     * Gets the parameterNames attribute of the BCUTDescriptor object.
     *
     * @return The parameterNames value
     */
    public String[] getParameterNames() {
        String[] params = new String[3];
        params[0] = "nhigh";
        params[1] = "nlow";
        params[2] = "checkAromaticity";
        return (params);
    }


    /**
     * Gets the parameterType attribute of the BCUTDescriptor object.
     *
     * @param name Description of the Parameter (can be either 'nhigh' or 'nlow' or checkAromaticity)
     * @return The parameterType value
     */
    public Object getParameterType(String name) {
        Object object = null;
        if (name.equals("nhigh")) object = new Integer(1);
        if (name.equals("nlow")) object = new Integer(1);
        if (name.equals("checkAromaticity")) object = new Integer(1);
        return (object);
    }