/* *  $RCSfile$ *  $Author: egonw $ *  $Date: 2007-10-25 11:54:10 +0200 (Thu, 25 Oct 2007) $ *  $Revision: 9202 $ * *  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.AtomContainerSet;import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;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.qsar.DescriptorSpecification;import org.openscience.cdk.qsar.DescriptorValue;import org.openscience.cdk.qsar.IAtomicDescriptor;import org.openscience.cdk.qsar.result.BooleanResult;/** *  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  qsar * @cdk.set     qsar-descriptors * @cdk.dictref qsar-descriptors:isProtonInConjugatedPiSystem */public class IsProtonInConjugatedPiSystemDescriptor  implements IAtomicDescriptor {    private boolean checkAromaticity = false;    private IAtomContainer acold=null;    private AtomContainerSet acSet=null;    /**     *  Constructor for the IsProtonInConjugatedPiSystemDescriptor object     */    public IsProtonInConjugatedPiSystemDescriptor() { }    /**     *  Gets the specification attribute of the     *  IsProtonInConjugatedPiSystemDescriptor object     *     *@return    The specification value     */    public DescriptorSpecification getSpecification() {        return new DescriptorSpecification(            "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#isProtonInConjugatedPiSystem",            this.getClass().getName(),            "$Id: IsProtonInConjugatedPiSystemDescriptor.java 9202 2007-10-25 09:54:10Z egonw $",            "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     */    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]).booleanValue();    }    /**     *  Gets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor     *  object     *     *@return    The parameters value     */    public Object[] getParameters() {        // return the parameters as used for the descriptor calculation        Object[] params = new Object[1];        params[0] = new Boolean(checkAromaticity);        return params;    }    /**     *  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     *@exception  CDKException  Possible Exceptions     */    public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer) throws CDKException {        IAtomContainer clonedAtomContainer;        try {            clonedAtomContainer = (IAtomContainer) atomContainer.clone();        } catch (CloneNotSupportedException e) {            throw new CDKException("Error during clone");        }        IAtom clonedAtom = clonedAtomContainer.getAtom(atomContainer.getAtomNumber(atom));                boolean isProtonInPiSystem = false;        Molecule mol = new Molecule(clonedAtomContainer);        if (checkAromaticity) {            HueckelAromaticityDetector.detectAromaticity(mol);        }        IAtom target = atom;        if(target.getSymbol().equals("H")) {        	if(acold!=clonedAtomContainer){        		acold=clonedAtomContainer;        		acSet = ConjugatedPiSystemsDetector.detect(mol);        	}        	java.util.Iterator detected = acSet.atomContainers();        	java.util.List neighboors = mol.getConnectedAtomsList(clonedAtom);        	for (int i = 0; i < neighboors.size(); i++) {        		while(detected.hasNext()) {        			IAtomContainer detectedAC = (IAtomContainer)detected.next();        			if ((detectedAC!= null) && (detectedAC.contains((IAtom)neighboors.get(i)))) {        				isProtonInPiSystem=true;        				break;        			}        		}        	}        }        return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new BooleanResult(isProtonInPiSystem));    }    /**     *  Gets the parameterNames attribute of the     *  IsProtonInConjugatedPiSystemDescriptor object     *     *@return    The parameterNames value     */    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     */    public Object getParameterType(String name) {        return new Boolean(true);    }}