isprotoninconjugatedpisystemdescriptor.java

化学图形处理软件

/*
 *  $RCSfile$
 *  $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: [e-mail]
 *
 *  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);
    }
}