/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project
*
* 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.molecular;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.PathTools;
import org.openscience.cdk.graph.matrix.ConnectionMatrix;
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.DoubleArrayResultType;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* This descriptor calculates the Wiener numbers. This includes the Wiener Path number
* and the Wiener Polarity Number.
* <BR>
* Further information is given in
* Wiener path number: half the sum of all the distance matrix entries; Wiener
* polarity number: half the sum of all the distance matrix entries with a
* value of 3. For more information see Todeschini R, Consonni V, Handbook of Molecular
* Descriptors, In: Mannhold R, Kubinyi H, Timmermann H (Eds.), Methods and Principles in
* Medicinal Chemistry, Vol. 11, Wiley-VCH 2000, Weinheim, New York.
* <p>
* This descriptor uses no parameters.
* <p>
* This descriptor works properly with AtomContainers whose atoms contain <b>implicit hydrogens</b>
* or <b>explicit hydrogens</b>.
*
* Returns the following values
* <ol>
* <li>WPATH - weiner path number
* <li>WPOL - weiner polarity number
* </ol>
*
* <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 December 7, 2004
* @cdk.created 2004-11-03
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:wienerNumbers
* @cdk.keyword Wiener number
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptorTest")
public class WienerNumbersDescriptor implements IMolecularDescriptor {
private static final String[] names = {"WPATH", "WPOL"};
double[][] matr = null;
DoubleArrayResult wienerNumbers = null;
ConnectionMatrix connectionMatrix = new ConnectionMatrix();
AtomContainerManipulator atm = new AtomContainerManipulator();
/**
* Constructor for the WienerNumbersDescriptor object.
*/
public WienerNumbersDescriptor() {
}
/**
* Returns a <code>Map</code> which specifies which descriptor
* is implemented by this class.
*
* These fields are used in the map:
* <ul>
* <li>Specification-Reference: refers to an entry in a unique dictionary
* <li>Implementation-Title: anything
* <li>Implementation-Identifier: a unique identifier for this version of
* this class
* <li>Implementation-Vendor: CDK, JOELib, or anything else
* </ul>
*
* @return An object containing the descriptor specification
*/
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#wienerNumbers",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the WienerNumbersDescriptor object.
*
* This descriptor does not take any parameters
*
*@param params The new parameters value
*@exception CDKException This method will not throw any exceptions
*@see #getParameters
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
// no parameters for this descriptor
}
/**
* Gets the parameters attribute of the WienerNumbersDescriptor object.
*
* This descriptor does not return any parameters
*
*@return The parameters value
*@see #setParameters
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
return (null);
// no parameters to return
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* Calculate the Wiener numbers.
*
*@param atomContainer The {@link IAtomContainer} for which this descriptor is to be calculated
*@return wiener numbers as array of 2 doubles
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer atomContainer) {
wienerNumbers = new DoubleArrayResult(2);
double wienerPathNumber = 0; //wienerPath
double wienerPolarityNumber = 0; //wienerPol
matr = ConnectionMatrix.getMatrix(AtomContainerManipulator.removeHydrogens(atomContainer));
int[][] distances = PathTools.computeFloydAPSP(matr);
int partial;
for (int i = 0; i < distances.length; i++) {
for (int j = 0; j < distances.length; j++) {
partial = distances[i][j];
wienerPathNumber += partial;
if (partial == 3) {
wienerPolarityNumber += 1;
}
}
}
wienerPathNumber = wienerPathNumber / 2;
wienerPolarityNumber = wienerPolarityNumber / 2;
wienerNumbers.add(wienerPathNumber);
wienerNumbers.add(wienerPolarityNumber);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
wienerNumbers, getDescriptorNames());
}
/**
* Returns the specific type of the DescriptorResult object.
* <p/>
* The return value from this method really indicates what type of result will
* be obtained from the {@link org.openscience.cdk.qsar.DescriptorValue} object. Note that the same result
* can be achieved by interrogating the {@link org.openscience.cdk.qsar.DescriptorValue} object; this method
* allows you to do the same thing, without actually calculating the descriptor.
*
* @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating
* the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object
*/
@TestMethod("testGetDescriptorResultType")
public IDescriptorResult getDescriptorResultType() {
return new DoubleArrayResultType(2);
}
/**
* Gets the parameterNames attribute of the WienerNumbersDescriptor object.
*
* This descriptor does not return any parameters
*
*@return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
// no param names to return
return (null);
}
/**
* Gets the parameterType attribute of the WienerNumbersDescriptor object.
*
*@param name Description of the Parameter
*@return An Object of class equal to that of the parameter being requested
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return (null);
}
}