~ubuntu-branches/ubuntu/trusty/cdk/trusty-proposed

/*  $Revision: 7032 $ $Author: kaihartmann $ $Date: 2006-09-22 17:26:48 +0200 (Fri, 22 Sep 2006) $

 *  

 *  Copyright (C) 2006-2007  Egon Willighagen <ewilligh@uni-koeln.de>

 *

 *  Contact: cdk-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 java.util.Iterator;

 

import org.openscience.cdk.applications.jchempaint.JChemPaintModel;

import org.openscience.cdk.applications.jchempaint.dialogs.ValidateFrame;

import org.openscience.cdk.atomtype.IAtomTypeMatcher;

import org.openscience.cdk.atomtype.MM2AtomTypeMatcher;

import org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher;

import org.openscience.cdk.exception.CDKException;

import org.openscience.cdk.interfaces.IAtom;

import org.openscience.cdk.interfaces.IAtomContainer;

import org.openscience.cdk.interfaces.IChemModel;

import org.openscience.cdk.tools.manipulator.ChemModelManipulator;

 

/**

 * An action that triggers atom type perception by the CDK.

 * 

 * @cdk.module jchempaint

 * @author     E.L. Willighagen <ewilligh@uni-koeln.de>

 */

public class PerceiveAtomTypesAction extends JCPAction

{

 

    private static final long serialVersionUID = -3776589605934024224L;

    

    ValidateFrame frame = null;

 

        public void actionPerformed(ActionEvent event) {

                logger.debug("detected force field type list: ", type);

                IAtomTypeMatcher matcher = null;

                if ("mm2".equals(type)) {

                        matcher = new MM2AtomTypeMatcher();

                } else if ("mmff94".equals(type)) {

                        matcher = new MMFF94AtomTypeMatcher();

                }

                if (matcher == null) {

                        logger.warn("Not a known atom type list: " + type);

                        return;

                }

                

                JChemPaintModel jcpmodel = jcpPanel.getJChemPaintModel();

                IChemModel model = jcpmodel.getChemModel();

                

                Iterator containers = ChemModelManipulator.getAllAtomContainers(model).iterator();

                while (containers.hasNext()) {

                        IAtomContainer container = (IAtomContainer)containers.next();

                        Iterator atoms = container.atoms();

                        while (atoms.hasNext()) {

                                IAtom atom = (IAtom)atoms.next();

                                try {

                                        atom.setAtomTypeName(matcher.findMatchingAtomType(container, atom).getAtomTypeName());

                                } catch (CDKException e) {

                                        logger.error("Could not find atom type name for atom!", e);

                                        logger.debug(e);

                                }

                        }

                }

        }

 

}