/* $Revision$ $Author$ $Date$
*
* 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.CDKConstants;
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.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* This descriptor returns 1 if the protons is directly bonded to an aromatic system,
* it returns 2 if the distance between aromatic system and proton is 2 bonds,
* and it return 0 for other positions. It is needed to use addExplicitHydrogensToSatisfyValency method.
*
* <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:isProtonInAromaticSystem
*/
@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptorTest")
public class IsProtonInAromaticSystemDescriptor implements IAtomicDescriptor {
private static final String[] names = {"protonInArmaticSystem"};
private boolean checkAromaticity = false;
/**
* Constructor for the IsProtonInAromaticSystemDescriptor object
*/
public IsProtonInAromaticSystemDescriptor() { }
/**
* Gets the specification attribute of the IsProtonInAromaticSystemDescriptor
* object
*
*@return The specification value
*/
@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#isProtonInAromaticSystem",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor
* object
*
*@param params The new parameters value
*@exception CDKException Possible Exceptions
*/
@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length > 1) {
throw new CDKException("IsProtonInAromaticSystemDescriptor only expects two parameters");
}
if (!(params[0] instanceof Boolean)) {
throw new CDKException("The second parameter must be of type Boolean");
}
checkAromaticity = (Boolean) params[0];
}
/**
* Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor
* 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 evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds.
* 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 true if the proton is bonded to an aromatic atom.
*/
@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 IntegerResult((int) Double.NaN),
names, e);
}
IAtom clonedAtom = clonedAtomContainer.getAtom(atomContainer.getAtomNumber(atom));
int isProtonInAromaticSystem = 0;
IMolecule mol = atom.getBuilder().newMolecule(clonedAtomContainer);
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
} catch (CDKException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult((int) Double.NaN),
names, e);
}
}
java.util.List neighboor = mol.getConnectedAtomsList(clonedAtom);
IAtom neighbour0 = (IAtom)neighboor.get(0);
if(atom.getSymbol().equals("H")) {
//logger.debug("aromatic proton");
if(neighbour0.getFlag(CDKConstants.ISAROMATIC)) {
isProtonInAromaticSystem = 1;
}
else {
java.util.List betaAtoms = clonedAtomContainer.getConnectedAtomsList(neighbour0);
for (Object betaAtom : betaAtoms) {
if (((IAtom) betaAtom).getFlag(CDKConstants.ISAROMATIC)) {
isProtonInAromaticSystem = 2;
} else {
isProtonInAromaticSystem = 0;
}
}
}
}
else {
isProtonInAromaticSystem = 0;
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult(isProtonInAromaticSystem),
names);
}
/**
* Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor
* 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 IsProtonInAromaticSystemDescriptor
* object
*
*@param name Description of the Parameter
*@return The parameterType value
*/
@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name) {
return true;
}
}