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ConvertToRadicalAction.java

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-01-04 18:26:00 +0100 (Thu, 04 Jan 2007) $
 * $Revision: 7634 $
 *
 * Copyright (C) 2003-2007  The JChemPaint project
 *
 * Contact: jchempaint-devel@lists.sf.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.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * 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.applications.jchempaint.action;

import java.awt.event.ActionEvent;

import javax.swing.JOptionPane;
import javax.swing.undo.UndoableEdit;

import org.openscience.cdk.Atom;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.ElectronContainer;
import org.openscience.cdk.SingleElectron;
import org.openscience.cdk.applications.jchempaint.JChemPaintModel;
import org.openscience.cdk.applications.undoredo.ConvertToRadicalEdit;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;

/**
 * @cdk.module jchempaint
 */
00049 public class ConvertToRadicalAction extends JCPAction {

      private static final long serialVersionUID = 1898335761308427006L;
      
00053       public void actionPerformed(ActionEvent event) {
        logger.debug("Converting to radical: ", type);
        IChemObject object = getSource(event);
        JChemPaintModel jcpmodel = jcpPanel.getJChemPaintModel();
        org.openscience.cdk.interfaces.IChemModel model = jcpmodel.getChemModel();
        if (object != null) {
            if (object instanceof Atom) {
                Atom atom = (Atom)object;
                
                IAtomContainer relevantContainer = ChemModelManipulator.getRelevantAtomContainer(model, atom);
                double number = controlLonePair(relevantContainer, atom);
                
                if(number > 0.0)
                {
                  SingleElectron singleElectron = new SingleElectron(atom);
                    relevantContainer.addSingleElectron(singleElectron);
                    UndoableEdit  edit = new ConvertToRadicalEdit(relevantContainer, 
                              singleElectron);
                    jcpPanel.getUndoSupport().postEdit(edit);
                    logger.info("Added single electron to atom");
                    logger.debug("new AC: ", relevantContainer);
                    
                }
                else JOptionPane.showMessageDialog(jcpPanel,"A radical cannot be added to this atom." +
                  " Re-try with less hydrogens.");

            
            } else {
                logger.error("Object not an Atom! Cannot convert into a radical!");
            }
        } else {
            logger.warn("Cannot convert a null object!");
        }
        jcpmodel.fireChange();
    }
    private double controlLonePair(IAtomContainer container, Atom atom)
    {
      double nLonePair = 0.0;
      AtomTypeFactory atomATF = null;
            try
            {
                  atomATF = AtomTypeFactory.getInstance(
                "org/openscience/cdk/config/data/valency2_atomtypes.xml",
                atom.getBuilder()
            );
            
                  if(atomATF != null)
                  {

                        IAtomType atomType = atomATF.getAtomType(atom.getSymbol());
                  double bondOrderSum = container.getBondOrderSum(atom);
                        int charge = atom.getFormalCharge();
                        int hcount = atom.getHydrogenCount();
                        int valency = atomType.getValency();
                        nLonePair = (valency - (hcount + bondOrderSum) - charge) / 2;
                  }
            } catch (Exception ex1)
            {
                  logger.error(ex1.getMessage());
                  logger.debug(ex1);
            }
            return nLonePair;
            
            
    }
}

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