/* $Revision$ $Author$ $Date$
*
* 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.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.qsar.AbstractAtomicDescriptor;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.result.DoubleResult;
/**
* The calculation of sigma partial charges in sigma-bonded systems of an heavy atom
* was made by Marsilli-Gasteiger. It is implemented with the Partial Equalization
* of Orbital Electronegativity (PEOE).
*
* <p>This descriptor uses these parameters:
* <table border="1">
* <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 2006-04-15
* @cdk.module qsaratomic
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:partialSigmaCharge
* @see GasteigerMarsiliPartialCharges
*/
@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptorTest")
public class PartialSigmaChargeDescriptor extends AbstractAtomicDescriptor {
private static final String[] names = {"partialSigmaCharge"};
private GasteigerMarsiliPartialCharges peoe = null;
/**Number of maximum iterations*/
private int maxIterations;
/**
* Constructor for the PartialSigmaChargeDescriptor object
*/
public PartialSigmaChargeDescriptor() {
peoe = new GasteigerMarsiliPartialCharges();
}
/**
* Gets the specification attribute of the PartialSigmaChargeDescriptor
* object
*
*@return The specification value
*/
@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#partialSigmaCharge",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the PartialSigmaChargeDescriptor
* object
*
*@param params Number of maximum iterations
*@exception CDKException Description of the Exception
*/
@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length > 1) {
throw new CDKException("PartialSigmaChargeDescriptor only expects one parameter");
}
if (!(params[0] instanceof Integer)) {
throw new CDKException("The parameter 1 must be of type Integer");
}
maxIterations = (Integer) params[0];
}
/**
* Gets the parameters attribute of the PartialSigmaChargeDescriptor object
*
*@return The parameters value
*/
@TestMethod(value="testGetParameters")
public Object[] getParameters() {
// return the parameters as used for the descriptor calculation
Object[] params = new Object[1];
params[0] = maxIterations;
return params;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili
* It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
* For this method will be only possible if the heavy atom has single bond.
*
*@param atom The IAtom for which the DescriptorValue is requested
*@param ac AtomContainer
*@return Value of the alpha partial charge
*/
@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom, IAtomContainer ac) {
// FIXME: for now I'll cache the original charges, and restore them at the end of this method
Double originalCharge = atom.getCharge();
if (!isCachedAtomContainer(ac)) {
IMolecule mol = atom.getBuilder().newMolecule(ac);
if (maxIterations != 0) peoe.setMaxGasteigerIters(maxIterations);
try {
peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true);
for (int i = 0; i < ac.getAtomCount(); i++) {
// assume same order, so mol.getAtom(i) == ac.getAtom(i)
cacheDescriptorValue(ac.getAtom(i), ac, new DoubleResult(mol.getAtom(i).getCharge()));
}
} catch (Exception e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(Double.NaN),
names, e);
}
}
atom.setCharge(originalCharge);
return getCachedDescriptorValue(atom) != null
? new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
getCachedDescriptorValue(atom),
names)
: null;
}
/**
* Gets the parameterNames attribute of the PartialSigmaChargeDescriptor
* object
*
*@return The parameterNames value
*/
@TestMethod(value="testGetParameterNames")
public String[] getParameterNames() {
String[] params = new String[1];
params[0] = "maxIterations";
return params;
}
/**
* Gets the parameterType attribute of the PartialSigmaChargeDescriptor
* object
*
*@param name Description of the Parameter
*@return The parameterType value
*/
@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name) {
if ("maxIterations".equals(name)) return Integer.MAX_VALUE;
return null;
}
}