/* *  $RCSfile$ *  $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.CDKConstants;import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;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.interfaces.IRingSet;import org.openscience.cdk.nonotify.NNMolecule;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.ringsearch.AllRingsFinder;/** *  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  qsar * @cdk.set     qsar-descriptors * @cdk.dictref qsar-descriptors:isProtonInAromaticSystem */public class IsProtonInAromaticSystemDescriptor implements IAtomicDescriptor {	private boolean checkAromaticity = false;	/**	 *  Constructor for the IsProtonInAromaticSystemDescriptor object	 */	public IsProtonInAromaticSystemDescriptor() { }	/**	 *  Gets the specification attribute of the IsProtonInAromaticSystemDescriptor	 *  object	 *	 *@return    The specification value	 */	public DescriptorSpecification getSpecification() {        return new DescriptorSpecification(            "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#isProtonInAromaticSystem",		    this.getClass().getName(),		    "$Id: IsProtonInAromaticSystemDescriptor.java 9202 2007-10-25 09:54:10Z egonw $",            "The Chemistry Development Kit");	}	/**	 *  Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor	 *  object	 *	 *@param  params            The new parameters value	 *@exception  CDKException  Possible Exceptions	 */	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]).booleanValue();	}	/**	 *  Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor	 *  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 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.	 *@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));        int isProtonInAromaticSystem = 0;		IMolecule mol = new NNMolecule(clonedAtomContainer);		if (checkAromaticity) {			IRingSet rs = (new AllRingsFinder()).findAllRings(mol);			HueckelAromaticityDetector.detectAromaticity(mol, rs, true);		}		java.util.List neighboor = mol.getConnectedAtomsList(clonedAtom);		IAtom target = atom;		IAtom neighbour0 = (IAtom)neighboor.get(0);		if(target.getSymbol().equals("H")) {			//logger.debug("aromatic proton");			if(neighbour0.getFlag(CDKConstants.ISAROMATIC)) {				isProtonInAromaticSystem = 1;			}			else {				java.util.List betaAtoms = clonedAtomContainer.getConnectedAtomsList(neighbour0);				for (int i = 0; i < betaAtoms.size(); i++) {					if(((IAtom)betaAtoms.get(i)).getFlag(CDKConstants.ISAROMATIC)) {						isProtonInAromaticSystem = 2;						break;					}				}			}		}		else {			isProtonInAromaticSystem = 0;		}		return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(isProtonInAromaticSystem));		}	/**	 *  Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor	 *  object	 *	 *@return    The parameterNames value	 */	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	 */	public Object getParameterType(String name) {		return new Boolean(true);	}}