/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.molecular;
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.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.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import java.util.Iterator;
/**
* This Class contains a method that returns the number of aromatic atoms in an AtomContainer.
*
* <p>This descriptor uses these parameters:
* <table border="1">
* <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>
*
* Returns a single value with name <i>nAromBond</i>
*
* @author mfe4
* @cdk.created 2004-11-03
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:aromaticBondsCount
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptorTest")
public class AromaticBondsCountDescriptor implements IMolecularDescriptor {
private boolean checkAromaticity = false;
private static final String[] names = {"nAromBond"};
/**
* Constructor for the AromaticBondsCountDescriptor object.
*/
public AromaticBondsCountDescriptor() { }
/**
* Returns a <code>Map</code> which specifies which descriptor
* is implemented by this class.
*
* These fields are used in the map:
* <ul>
* <li>Specification-Reference: refers to an entry in a unique dictionary
* <li>Implementation-Title: anything
* <li>Implementation-Identifier: a unique identifier for this version of
* this class
* <li>Implementation-Vendor: CDK, JOELib, or anything else
* </ul>
*
* @return An object containing the descriptor specification
*/
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#aromaticBondsCount",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the AromaticBondsCountDescriptor object.
*
* This descriptor takes one parameter, which should be Boolean to indicate whether
* aromaticity has been checked (TRUE) or not (FALSE).
*
* @param params The new parameters value
* @exception CDKException if more than one parameter or a non-Boolean parameter is specified
*@see #getParameters
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length != 1) {
throw new CDKException("AromaticBondsCountDescriptor expects one parameter");
}
if (!(params[0] instanceof Boolean)) {
throw new CDKException("The first parameter must be of type Boolean");
}
// ok, all should be fine
checkAromaticity = (Boolean) params[0];
}
/**
* Gets the parameters attribute of the AromaticBondsCountDescriptor object.
*
*@return The parameters value
*@see #setParameters
*/
@TestMethod("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;
}
/**
* Calculate the count of aromatic atoms in the supplied {@link IAtomContainer}.
*
* The method take a boolean checkAromaticity: if the boolean is true, it means that
* aromaticity has to be checked.
*
*@param atomContainer The {@link IAtomContainer} for which this descriptor is to be calculated
*@return the number of aromatic atoms of this AtomContainer
*@see #setParameters
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer atomContainer) {
IAtomContainer ac;
try {
ac = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult((int) Double.NaN), getDescriptorNames(),
new CDKException("Error during clone"));
}
int aromaticBondsCount = 0;
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
} catch (CDKException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult((int) Double.NaN), getDescriptorNames(),
new CDKException("Error during atom type perception"));
}
try {
CDKHueckelAromaticityDetector.detectAromaticity(ac);
} catch (CDKException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult((int) Double.NaN), getDescriptorNames(),
new CDKException("Error during aromaticity detection: " + e.getMessage()));
}
}
Iterator bonds = ac.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = (IBond) bonds.next();
if (bond.getFlag(CDKConstants.ISAROMATIC)) {
aromaticBondsCount += 1;
}
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult(aromaticBondsCount), getDescriptorNames());
}
/**
* 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 IntegerResult(1);
}
/**
* Gets the parameterNames attribute of the AromaticBondsCountDescriptor object.
*
*@return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
String[] params = new String[1];
params[0] = "checkAromaticity";
return params;
}
/**
* Gets the parameterType attribute of the AromaticBondsCountDescriptor object.
*
*@param name Description of the Parameter
*@return An Object of class equal to that of the parameter being requested
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return true;
}
}