/*
* Copyright (C) 2004-2007 Rajarshi Guha <rajarshi@users.sourceforge.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.molecular;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.geometry.GeometryTools;
import org.openscience.cdk.graph.PathTools;
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;
import javax.vecmath.Point3d;
/**
* Evaluates the Petitjean shape indices,
* <p/>
* These original Petitjean number was described by Petitjean ({@cdk.cite PET92})
* and considered the molecular graph. This class also implements the geometric analog
* of the topological shape index described by Bath et al ({@cdk.cite BAT95}).
* <p/>
* The descriptor returns a <code>DoubleArrayResult</code> which contains
* <ol>
* <li>topoShape - topological shape index
* <li>geomShape - geometric shape index
* </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 Rajarshi Guha
* @cdk.created 2006-01-14
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:petitjeanShapeIndex
* @cdk.keyword Petit-Jean, shape index
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptorTest")
public class PetitjeanShapeIndexDescriptor implements IMolecularDescriptor {
private static final String[] names = {"topoShape", "geomShape"};
public PetitjeanShapeIndexDescriptor() {
}
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#petitjeanShapeIndex",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
*
* @param params The new parameters value
* @throws org.openscience.cdk.exception.CDKException
* Description of the Exception
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
// no parameters for this descriptor
}
/**
* Gets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
*
* @return The parameters value
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
// no parameters to return
return (null);
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* Gets the parameterNames attribute of the PetitjeanShapeIndexDescriptor object.
*
* @return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
// no param names to return
return (null);
}
/**
* Gets the parameterType attribute of the PetitjeanShapeIndexDescriptor object.
*
* @param name Description of the Parameter
* @return The parameterType value
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return (null);
}
/**
* Calculates the two Petitjean shape indices.
*
* @param container Parameter is the atom container.
* @return A DoubleArrayResult value representing the Petitjean shape indices
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
IAtomContainer local = AtomContainerManipulator.removeHydrogens(container);
int tradius = PathTools.getMolecularGraphRadius(local);
int tdiameter = PathTools.getMolecularGraphDiameter(local);
DoubleArrayResult retval = new DoubleArrayResult();
retval.add((double) (tdiameter - tradius) / (double) tradius);
// get the 3D distance matrix
if (GeometryTools.has3DCoordinates(container)) {
int natom = container.getAtomCount();
double[][] distanceMatrix = new double[natom][natom];
for (int i = 0; i < natom; i++) {
for (int j = 0; j < natom; j++) {
if (i == j) {
distanceMatrix[i][j] = 0.0;
continue;
}
Point3d a = container.getAtom(i).getPoint3d();
Point3d b = container.getAtom(j).getPoint3d();
distanceMatrix[i][j] = Math.sqrt((a.x - b.x) * (a.x - b.x) +
(a.y - b.y) * (a.y - b.y) +
(a.z - b.z) * (a.z - b.z));
}
}
double gradius = 999999;
double gdiameter = -999999;
double[] geta = new double[natom];
for (int i = 0; i < natom; i++) {
double max = -99999;
for (int j = 0; j < natom; j++) {
if (distanceMatrix[i][j] > max) max = distanceMatrix[i][j];
}
geta[i] = max;
}
for (int i = 0; i < natom; i++) {
if (geta[i] < gradius) gradius = geta[i];
if (geta[i] > gdiameter) gdiameter = geta[i];
}
retval.add((gdiameter - gradius) / gradius);
} else {
retval.add(Double.NaN);
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), retval,
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);
}
}