/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.Electronegativity;
import org.openscience.cdk.charges.PiElectronegativity;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.tools.LonePairElectronChecker;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* Pi electronegativity is given by X = a + bq + c(q*q)
*
*
* <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 2006-05-17
* @cdk.module qsaratomic
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:piElectronegativity
*
* @see Electronegativity
*/
@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptorTest")
public class PiElectronegativityDescriptor implements IAtomicDescriptor {
/**Number of maximum iterations*/
private int maxIterations = -1;
/**Number of maximum resonance structures*/
private int maxResonStruc = -1;
/** make a lone pair electron checker. Default true*/
private boolean lpeChecker = true;
private static final String[] descriptorNames = {"elecPiA"};
private PiElectronegativity electronegativity;
/**
* Constructor for the PiElectronegativityDescriptor object
*/
public PiElectronegativityDescriptor() {
electronegativity = new PiElectronegativity();
}
/**
* Gets the specification attribute of the PiElectronegativityDescriptor
* object
*
*@return The specification value
*/
@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#piElectronegativity",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the PiElectronegativityDescriptor
* object
*
*@param params The number of maximum iterations. 1= maxIterations. 2= maxResonStruc.
*@exception CDKException Description of the Exception
*/
@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length > 3)
throw new CDKException("PartialPiChargeDescriptor only expects three parameter");
if (!(params[0] instanceof Integer) )
throw new CDKException("The parameter must be of type Integer");
maxIterations = (Integer) params[0];
if(params.length > 1 && params[1] != null){
if (!(params[1] instanceof Boolean) )
throw new CDKException("The parameter must be of type Boolean");
lpeChecker = (Boolean) params[1];
}
if(params.length > 2 && params[2] != null){
if (!(params[2] instanceof Integer) )
throw new CDKException("The parameter must be of type Integer");
maxResonStruc = (Integer) params[2];
}
}
/**
* Gets the parameters attribute of the PiElectronegativityDescriptor
* object
*
*@return The parameters value
*/
@TestMethod(value="testGetParameters")
public Object[] getParameters() {
// return the parameters as used for the descriptor calculation
Object[] params = new Object[3];
params[0] = maxIterations;
params[1] = lpeChecker;
params[2] = maxResonStruc;
return params;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return descriptorNames;
}
/**
* The method calculates the pi electronegativity of a given atom
* It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
*
*@param atom The IAtom for which the DescriptorValue is requested
*@param atomContainer AtomContainer
*@return return the pi electronegativity
*/
@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer) {
IAtomContainer clone;
IAtom localAtom;
try {
clone = (IAtomContainer) atomContainer.clone();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(clone);
if (lpeChecker) {
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
lpcheck.saturate(atomContainer);
}
localAtom = clone.getAtom(atomContainer.getAtomNumber(atom));
} catch (CloneNotSupportedException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(Double.NaN), descriptorNames, null);
} catch (CDKException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(Double.NaN), descriptorNames, null);
}
if (maxIterations != -1 && maxIterations != 0) electronegativity.setMaxIterations(maxIterations);
if (maxResonStruc != -1 && maxResonStruc != 0) electronegativity.setMaxResonStruc(maxResonStruc);
double result = electronegativity.calculatePiElectronegativity(clone, localAtom);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(result), descriptorNames);
}
/**
* Gets the parameterNames attribute of the SigmaElectronegativityDescriptor
* object
*
*@return The parameterNames value
*/
@TestMethod(value="testGetParameterNames")
public String[] getParameterNames() {
String[] params = new String[3];
params[0] = "maxIterations";
params[1] = "lpeChecker";
params[2] = "maxResonStruc";
return params;
}
/**
* Gets the parameterType attribute of the SigmaElectronegativityDescriptor
* 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;
if ("lpeChecker".equals(name)) return Boolean.TRUE;
if ("maxResonStruc".equals(name)) return Integer.MAX_VALUE;
return null;
}
}