/* $Revision: 10995 $ $Author: miguelrojasch $ $Date: 2008-05-14 16:38:21 +0200 (Wed, 14 May 2008) $
*
* Copyright (C) 2006-2007 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 General Public License as published by
* the Free Software Foundation; either version 2 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.qsar.descriptors.molecular;
import java.util.ArrayList;
import java.util.Iterator;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor;
import org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.qsar.result.DoubleResultType;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.tools.IonizationPotentialTool;
import org.openscience.cdk.tools.LonePairElectronChecker;
/**
* This class returns the ionization potential of a molecule. Up to now is
* only possible for atomContainers which contain; see IPAtomicDescriptor and
* IPBondDescriptor.
*
* The descriptor assumes that explicit hydrogens have been added to the molecule
*
* <p>This descriptor uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td>addlp</td>
* <td>true</td>
* <td>If true lone pairs are added to the molecule</td>
* </tr>
* </table>
*
* @author Miguel Rojas
* @cdk.created 2006-05-26
* @cdk.module qsarionpot
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:ionizationPotential
* @cdk.keyword ionization potential
*
* @see IPAtomicHOSEDescriptor
* @see IPBondLearningDescriptor
*/
@TestClass(value="org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptorTest")
public class IPMolecularLearningDescriptor implements IMolecularDescriptor {
private boolean addlp = true;
private static final String[] names = {"MolIP"};
/**
* Constructor for the IPMolecularLearningDescriptor object
*/
public IPMolecularLearningDescriptor() { }
/**
* Gets the specification attribute of the IPMolecularLearningDescriptor object
*
*@return The specification value
*/
@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#ip",
this.getClass().getName(),
"$Id: IPMolecularLearningDescriptor.java 10995 2008-05-14 14:38:21Z miguelrojasch $",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the IPMolecularLearningDescriptor object
*
*@param params The new parameters value
*@exception CDKException Description of the Exception
*/
@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length != 1) throw new CDKException("One parameter expected");
if (!(params[0] instanceof Boolean)) throw new CDKException("Boolean parameter expected");
addlp = (Boolean) params[0];
}
/**
* Gets the parameters attribute of the IPMolecularLearningDescriptor object
*
* @return The parameters value
*/
@TestMethod(value="testGetParameters")
public Object[] getParameters() {
return new Object[]{addlp};
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* It calculates the first ionization energy of a molecule.
*
*@param atomContainer AtomContainer
*@return The first ionization energy
*/
@TestMethod(value = "testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer atomContainer) {
IAtomContainer local;
if (addlp) {
try {
local = (IAtomContainer) atomContainer.clone();
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
lpcheck.saturate(local);
} catch (CloneNotSupportedException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(Double.NaN), getDescriptorNames(), e);
} catch (CDKException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(Double.NaN), getDescriptorNames(), e);
}
} else local = atomContainer;
DoubleResult value;
try {
value = new DoubleResult(((DoubleArrayResult) calculatePlus(local).getValue()).get(0));
} catch (CDKException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(Double.NaN), getDescriptorNames(), e);
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
value, getDescriptorNames());
}
/**
* It calculates the 1,2,.. ionization energies of a molecule.
*
*@param container AtomContainer
*@return The 1, 2, .. ionization energies
*@exception CDKException Possible Exceptions
*/
@TestMethod(value="testIPDescriptor_2,testIPDescriptor_3")
public DescriptorValue calculatePlus(IAtomContainer container) throws CDKException {
ArrayList<Double> dar = new ArrayList<Double>();
for(Iterator<IAtom> itA = container.atoms().iterator(); itA.hasNext();){
IAtom atom = itA.next();
double value = IonizationPotentialTool.predictIP(container,atom);
if(value != 0)
dar.add(value);
}
for(Iterator<IBond> itB = container.bonds().iterator(); itB.hasNext();){
IBond bond = itB.next();
if(bond.getOrder() == IBond.Order.DOUBLE
& bond.getAtom(0).getSymbol().equals("C")
& bond.getAtom(1).getSymbol().equals("C")){
double value = IonizationPotentialTool.predictIP(container,bond);
if(value != 0)
dar.add(value);
}
}
DoubleArrayResult results = arrangingEnergy(dar);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), results,
getDescriptorNames(), null);
}
/**
* put in increasing order the ArrayList
*
* @param array The ArrayList to order
* @return The DoubleArrayResult ordered
*/
private DoubleArrayResult arrangingEnergy(ArrayList<Double> array){
DoubleArrayResult results = new DoubleArrayResult();
int count = array.size();
for(int i = 0; i < count; i++){
double min = array.get(0);
int pos = 0;
for(int j = 0; j < array.size(); j++){
double value = array.get(j);
if( value < min){
min = value;
pos = j;
}
}
array.remove(pos);
results.add(min);
}
return results;
}
/**
* 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 DoubleResultType();
}
/**
* Gets the parameterNames attribute of the IPMolecularLearningDescriptor object
*
*@return The parameterNames value
*/
@TestMethod(value="testGetParameterNames")
public String[] getParameterNames() {
return new String[] {"addlp"};
}
/**
* Gets the parameterType attribute of the IPMolecularLearningDescriptor object
*
*@param name Description of the Parameter
*@return The parameterType value
*/
@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name) {
return addlp;
}
}