whimdescriptor.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-10-14 20:35:55 +0200 (Sun, 14 Oct 2007) $
 *  $Revision: 9057 $
 *
 *  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.Molecule;
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.LoggingTool;

import javax.vecmath.Point3d;
import java.util.Hashtable;


/**
 * Holistic descriptors described by Todeschini et al {@cdk.cite TOD98}.
 * The descriptors are based on a number of atom weightings. There are 6 different
 * possible weightings:
 * <ol>
 * <li>unit weights
 * <li>atomic masses
 * <li>van der Waals volumes
 * <li>Mulliken atomic electronegativites
 * <li>atomic polarizabilities
 * <li>E-state values described by Kier &amp; Hall
 * </ol>
 * Currently weighting schemes 1,2,3,4 &amp; 5 are implemented. The weight values
 * are taken from {@cdk.cite TOD98} and as a result 19 elements are considered.
 * <p/>
 * <p>For each weighting scheme we can obtain
 * <ul>
 * <li>11 directional WHIM descriptors (&lambda;<sub>1 .. 3</sub>, &nu;<sub>1 .. 2</sub>, &gamma;<sub>1 .. 3</sub>,  &eta;<sub>1 .. 3</sub>)
 * <li>6 non-directional WHIM descriptors (T, A, V, K, G, D)
 * </ul>
 * <p/>
 * <p>Though {@cdk.cite TOD98} mentions that for planar molecules only 8 directional WHIM
 * descriptors are required the current code will return all 11.
 * <p/>
 * The descriptor returns 17 values for a given weighting scheme, named as follows:
 * <ol>
 * <li>Wlambda1
 * <li>Wlambda2
 * <li>wlambda3
 * <li>Wnu1
 * <li>Wnu2
 * <li>Wgamma1
 * <li>Wgamma2
 * <li>Wgamma3
 * <li>Weta1
 * <li>Weta2
 * <li>Weta3
 * <li>WT
 * <li>WA
 * <li>WV
 * <li>WK
 * <li>WG
 * <li>WD
 * </ol>
 * Each name will have a suffix of the form <i>.X</i> where <i>X</i> indicates
 * the weighting scheme used. Possible values of <i>X</i> are
 * <ul>
 * <li>unity
 * <li>mass
 * <li>volume
 * <li>eneg
 * <li>polar
 * </ul>
 * <p/>
 * <p/>
 * <p>This descriptor uses these parameters:
 * <table border="1">
 * <tr>
 * <td>Name</td>
 * <td>Default</td>
 * <td>Description</td>
 * </tr>
 * <tr>
 * <td>type</td>
 * <td>unity</td>
 * <td>Type of weighting as described above</td>
 * </tr>
 * </table>
 *
 * @author Rajarshi Guha
 * @cdk.created 2004-12-1
 * @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:WHIM
 * @cdk.keyword WHIM
 * @cdk.keyword descriptor
 */
public class WHIMDescriptor implements IMolecularDescriptor {

    LoggingTool logger;
    String type = "";
    Hashtable hashatwt, hashvdw, hasheneg, hashpol;

    public WHIMDescriptor() {
        logger = new LoggingTool(this);
        this.type = "unity"; // default weighting scheme

        // set up the values from TOD98

        this.hashatwt = new Hashtable();
        this.hashvdw = new Hashtable();
        this.hasheneg = new Hashtable();
        this.hashpol = new Hashtable();

        this.hashatwt.put("H", new Double(0.084));
        this.hashatwt.put("B", new Double(0.900));
        this.hashatwt.put("C", new Double(1.000));
        this.hashatwt.put("N", new Double(1.166));
        this.hashatwt.put("O", new Double(1.332));
        this.hashatwt.put("F", new Double(1.582));
        this.hashatwt.put("Al", new Double(2.246));
        this.hashatwt.put("Si", new Double(2.339));
        this.hashatwt.put("P", new Double(2.579));
        this.hashatwt.put("S", new Double(2.670));
        this.hashatwt.put("Cl", new Double(2.952));
        this.hashatwt.put("Fe", new Double(4.650));
        this.hashatwt.put("Co", new Double(4.907));
        this.hashatwt.put("Ni", new Double(4.887));
        this.hashatwt.put("Cu", new Double(5.291));
        this.hashatwt.put("Zn", new Double(5.445));
        this.hashatwt.put("Br", new Double(6.653));
        this.hashatwt.put("Sn", new Double(9.884));
        this.hashatwt.put("I", new Double(10.566));

        this.hashvdw.put("H", new Double(0.299));
        this.hashvdw.put("B", new Double(0.796));
        this.hashvdw.put("C", new Double(1.000));
        this.hashvdw.put("N", new Double(0.695));
        this.hashvdw.put("O", new Double(0.512));
        this.hashvdw.put("F", new Double(0.410));
        this.hashvdw.put("Al", new Double(1.626));
        this.hashvdw.put("Si", new Double(1.424));
        this.hashvdw.put("P", new Double(1.181));
        this.hashvdw.put("S", new Double(1.088));
        this.hashvdw.put("Cl", new Double(1.035));
        this.hashvdw.put("Fe", new Double(1.829));
        this.hashvdw.put("Co", new Double(1.561));
        this.hashvdw.put("Ni", new Double(0.764));
        this.hashvdw.put("Cu", new Double(0.512));
        this.hashvdw.put("Zn", new Double(1.708));
        this.hashvdw.put("Br", new Double(1.384));
        this.hashvdw.put("Sn", new Double(2.042));
        this.hashvdw.put("I", new Double(1.728));

        this.hasheneg.put("H", new Double(0.944));
        this.hasheneg.put("B", new Double(0.828));
        this.hasheneg.put("C", new Double(1.000));
        this.hasheneg.put("N", new Double(1.163));
        this.hasheneg.put("O", new Double(1.331));
        this.hasheneg.put("F", new Double(1.457));
        this.hasheneg.put("Al", new Double(0.624));
        this.hasheneg.put("Si", new Double(0.779));
        this.hasheneg.put("P", new Double(0.916));
        this.hasheneg.put("S", new Double(1.077));
        this.hasheneg.put("Cl", new Double(1.265));
        this.hasheneg.put("Fe", new Double(0.728));
        this.hasheneg.put("Co", new Double(0.728));
        this.hasheneg.put("Ni", new Double(0.728));
        this.hasheneg.put("Cu", new Double(0.740));
        this.hasheneg.put("Zn", new Double(0.810));
        this.hasheneg.put("Br", new Double(1.172));
        this.hasheneg.put("Sn", new Double(0.837));
        this.hasheneg.put("I", new Double(1.012));

        this.hashpol.put("H", new Double(0.379));
        this.hashpol.put("B", new Double(1.722));
        this.hashpol.put("C", new Double(1.000));
        this.hashpol.put("N", new Double(0.625));
        this.hashpol.put("O", new Double(0.456));
        this.hashpol.put("F", new Double(0.316));
        this.hashpol.put("Al", new Double(3.864));
        this.hashpol.put("Si", new Double(3.057));
        this.hashpol.put("P", new Double(2.063));
        this.hashpol.put("S", new Double(1.648));
        this.hashpol.put("Cl", new Double(1.239));
        this.hashpol.put("Fe", new Double(4.773));
        this.hashpol.put("Co", new Double(4.261));
        this.hashpol.put("Ni", new Double(3.864));
        this.hashpol.put("Cu", new Double(3.466));
        this.hashpol.put("Zn", new Double(4.034));
        this.hashpol.put("Br", new Double(1.733));
        this.hashpol.put("Sn", new Double(4.375));
        this.hashpol.put("I", new Double(3.040));
    }

    public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
                "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#WHIM",
                this.getClass().getName(),
                "$Id: WHIMDescriptor.java 9057 2007-10-14 18:35:55Z egonw $",
                "The Chemistry Development Kit");
    }

    ;

    /**
     * Sets the parameters attribute of the WHIMDescriptor object.
     *
     * @param params The new parameter values. The Object array should have a single element
     *               which should be a String. The possible values of this String are: unity,
     *               mass, volume, eneg, polar
     * @throws CDKException if the parameters are of the wrong type
     * @see #getParameters
     */
    public void setParameters(Object[] params) throws CDKException {
        if (params.length != 1) {
            throw new CDKException("WHIMDescriptor requires 1 parameter");
        }
        if (!(params[0] instanceof String)) {
            throw new CDKException("Parameters must be of type String");
        }
        this.type = (String) params[0];
        if (!this.type.equals("unity") &&
                !this.type.equals("mass") &&
                !this.type.equals("volume") &&
                !this.type.equals("eneg") &&
                !this.type.equals("polar"))
            throw new CDKException("Weighting scheme must be one of those specified in the API");
    }

    /**
     * Gets the parameters attribute of the WHIMDescriptor object.
     *
     * @return Two element array of Integer representing number of highest and lowest eigenvalues
     *         to return respectively
     * @see #setParameters
     */
    public Object[] getParameters() {
        Object[] o = new Object[1];
        o[0] = this.type;
        return (o);
    }

    /**
     * Gets the parameterNames attribute of the WHIMDescriptor object.