/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.bond;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.charges.GasteigerPEPEPartialCharges;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.qsar.AbstractBondDescriptor;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.tools.LonePairElectronChecker;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* The calculation of bond total Partial charge is calculated
* determining the difference the Partial Total Charge on atoms
* A and B of a bond. Based in Gasteiger Charge.
* <p>This descriptor uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td>bondPosition</td>
* <td>0</td>
* <td>The position of the target bond</td>
* </tr>
* </table>
*
* @author Miguel Rojas
* @cdk.created 2006-05-18
* @cdk.module qsarbond
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:bondPartialTCharge
*
* @see org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
* @see org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
*/
@TestClass(value="org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptorTest")
public class BondPartialTChargeDescriptor extends AbstractBondDescriptor {
private GasteigerMarsiliPartialCharges peoe = null;
private GasteigerPEPEPartialCharges pepe = null;
/**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 = {"pCB"};
/**
* Constructor for the BondPartialTChargeDescriptor object
*/
public BondPartialTChargeDescriptor() {
peoe = new GasteigerMarsiliPartialCharges();
pepe = new GasteigerPEPEPartialCharges();
}
/**
* Gets the specification attribute of the BondPartialTChargeDescriptor
* object
*
*@return The specification value
*/
@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#bondPartialTCharge",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* This descriptor does have any parameter.
*/
@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 BondPartialTChargeDescriptor object.
*
*@return The parameters value
* @see #setParameters
*/
@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;
}
private DescriptorValue getDummyDescriptorValue(Exception e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(Double.NaN), descriptorNames, e);
}
/**
* The method calculates the bond total Partial charge of a given bond
* It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
*
*@param ac AtomContainer
*@return return the sigma electronegativity
*/
@TestMethod(value="testCalculate_IBond_IAtomContainer,testBondTElectronegativityDescriptor,testBondTElectronegativityDescriptor_Allyl_bromide")
public DescriptorValue calculate(IBond bond, IAtomContainer ac) {
// FIXME: for now I'll cache a few modified atomic properties, and restore them at the end of this method
Double originalCharge1 = bond.getAtom(0).getCharge();
String originalAtomtypeName1 = bond.getAtom(0).getAtomTypeName();
Integer originalNeighborCount1 = bond.getAtom(0).getFormalNeighbourCount();
IAtomType.Hybridization originalHybridization1 = bond.getAtom(0).getHybridization();
Integer originalValency1 = bond.getAtom(0).getValency();
Double originalCharge2 = bond.getAtom(1).getCharge();
String originalAtomtypeName2 = bond.getAtom(1).getAtomTypeName();
Integer originalNeighborCount2 = bond.getAtom(1).getFormalNeighbourCount();
IAtomType.Hybridization originalHybridization2 = bond.getAtom(1).getHybridization();
Integer originalValency2 = bond.getAtom(1).getValency();
if (!isCachedAtomContainer(ac)) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
if (lpeChecker) {
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
lpcheck.saturate(ac);
}
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
if(maxIterations != -1) peoe.setMaxGasteigerIters(maxIterations);
if(maxIterations != -1) pepe.setMaxGasteigerIters(maxIterations);
if(maxResonStruc != -1) pepe.setMaxResoStruc(maxResonStruc);
try {
peoe.assignGasteigerMarsiliSigmaPartialCharges(ac, true);
List<Double> peoeBond = new ArrayList<Double>();
for(Iterator<IBond> it = ac.bonds().iterator() ; it.hasNext(); ) {
IBond bondi = it.next();
double result = Math.abs(bondi.getAtom(0).getCharge()-bondi.getAtom(1).getCharge());
peoeBond.add(result);
}
for(Iterator<IAtom> it = ac.atoms().iterator(); it.hasNext();)
it.next().setCharge(0.0);
pepe.assignGasteigerPiPartialCharges(ac, true);
for(int i = 0 ; i < ac.getBondCount(); i++ ) {
IBond bondi = ac.getBond(i);
double result = Math.abs(bondi.getAtom(0).getCharge()-bondi.getAtom(1).getCharge());
cacheDescriptorValue(bondi, ac, new DoubleResult(peoeBond.get(i)+result));
}
} catch (Exception e) {
return getDummyDescriptorValue(e);
}
}
bond.getAtom(0).setCharge(originalCharge1);
bond.getAtom(0).setAtomTypeName(originalAtomtypeName1);
bond.getAtom(0).setHybridization(originalHybridization1);
bond.getAtom(0).setValency(originalValency1);
bond.getAtom(0).setFormalNeighbourCount(originalNeighborCount1);
bond.getAtom(1).setCharge(originalCharge2);
bond.getAtom(1).setAtomTypeName(originalAtomtypeName2);
bond.getAtom(1).setHybridization(originalHybridization2);
bond.getAtom(1).setValency(originalValency2);
bond.getAtom(1).setFormalNeighbourCount(originalNeighborCount2);
return getCachedDescriptorValue(bond) != null
? new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
getCachedDescriptorValue(bond), descriptorNames)
: null;
}
/**
* Gets the parameterNames attribute of the BondPartialTChargeDescriptor 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 BondPartialTChargeDescriptor object.
*
* @param name Description of the Parameter
* @return An Object of class equal to that of the parameter being requested
*/
@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;
}
}