/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project
*
* 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.Molecule;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.BooleanResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* This class evaluates if a proton is joined to a conjugated system.
*
* <p>This descriptor uses these parameters:
* <table>
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td>checkAromaticity</td>
* <td>false</td>
* <td>True is the aromaticity has to be checked</td>
* </tr>
* </table>
*
* @author mfe4
* @cdk.created 2004-11-03
* @cdk.module qsaratomic
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:isProtonInConjugatedPiSystem
*/
@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptorTest")
public class IsProtonInConjugatedPiSystemDescriptor implements IAtomicDescriptor {
private static final String[] names = {"protonInConjSystem"};
private boolean checkAromaticity = false;
private IAtomContainer acold=null;
private IAtomContainerSet acSet=null;
/**
* Constructor for the IsProtonInConjugatedPiSystemDescriptor object
*/
public IsProtonInConjugatedPiSystemDescriptor() { }
/**
* Gets the specification attribute of the
* IsProtonInConjugatedPiSystemDescriptor object
*
*@return The specification value
*/
@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#isProtonInConjugatedPiSystem",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor
* object
*
*@param params Parameters are an integer (heavy atom position) and a boolean (true if is needed a checkAromaticity)
*@exception CDKException Description of the Exception
*/
@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length > 1) {
throw new CDKException("IsProtonInConjugatedPiSystemDescriptor only expects one parameters");
}
if (!(params[0] instanceof Boolean)) {
throw new CDKException("The parameter must be of type Boolean");
}
checkAromaticity = (Boolean) params[0];
}
/**
* Gets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor
* 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] = checkAromaticity;
return params;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* The method is a proton descriptor that evaluates if a proton is joined to a conjugated system.
*
*@param atom The IAtom for which the DescriptorValue is requested
*@param atomContainer AtomContainer
*@return true if the proton is bonded to a conjugated system
*/
@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer) {
IAtomContainer clonedAtomContainer;
try {
clonedAtomContainer = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new BooleanResult(false),
names, e);
}
IAtom clonedAtom = clonedAtomContainer.getAtom(atomContainer.getAtomNumber(atom));
boolean isProtonInPiSystem = false;
Molecule mol = new Molecule(clonedAtomContainer);
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
} catch (CDKException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new BooleanResult(false),
names, e);
}
}
if(atom.getSymbol().equals("H")) {
if(acold!=clonedAtomContainer){
acold=clonedAtomContainer;
acSet = ConjugatedPiSystemsDetector.detect(mol);
}
java.util.Iterator<IAtomContainer> detected = acSet.atomContainers().iterator();
java.util.List neighboors = mol.getConnectedAtomsList(clonedAtom);
for (Object neighboor : neighboors) {
while (detected.hasNext()) {
IAtomContainer detectedAC = (IAtomContainer) detected.next();
if ((detectedAC != null) && (detectedAC.contains((IAtom) neighboor))) {
isProtonInPiSystem = true;
break;
}
}
}
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new BooleanResult(isProtonInPiSystem),
names);
}
/**
* Gets the parameterNames attribute of the
* IsProtonInConjugatedPiSystemDescriptor object
*
*@return The parameterNames value
*/
@TestMethod(value="testGetParameterNames")
public String[] getParameterNames() {
String[] params = new String[1];
params[0] = "checkAromaticity";
return params;
}
/**
* Gets the parameterType attribute of the
* IsProtonInConjugatedPiSystemDescriptor object
*
*@param name Description of the Parameter
*@return The parameterType value
*/
@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name) {
return true;
}
}