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CreateSmilesAction.java

/*
 *  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-05-01 21:15:34 +0200 (Tue, 01 May 2007) $
 *  $Revision: 8292 $
 *
 *  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 java.util.Iterator;

import javax.swing.JFrame;

import org.openscience.cdk.ChemModel;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.applications.jchempaint.dialogs.TextViewDialog;
import org.openscience.cdk.geometry.GeometryTools;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.layout.HydrogenPlacer;
import org.openscience.cdk.smiles.SmilesGenerator;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;


/**
 * Creates a SMILES from the current model
 *
 * @cdk.module jchempaint
 * @author     steinbeck
 */
00053 public class CreateSmilesAction extends JCPAction
{

      private static final long serialVersionUID = -4886982931009753342L;
      
      TextViewDialog dialog = null;
      JFrame frame = null;

00061       public void actionPerformed(ActionEvent e)
      {
            logger.debug("Trying to create smile: ", type);
            /*
             *  if (jcpPanel.getFrame() != null)
             *  {
             *  try
             *  {
             *  Frame frame = (Frame)jcpPanel.getFrame();
             *  }
             *  catch(Exception exc)
             *  {
             *  logger.debug("Could not cast JCP frame to Frame");
             *  }
             *  }
             */
            if (dialog == null)
            {
                  dialog = new TextViewDialog(frame, "SMILES", null, false, 40, 2);
            }
            String smiles = "";
            String chiralsmiles ="";
            try
            {
                  ChemModel model = (ChemModel) jcpPanel.getJChemPaintModel().getChemModel();
            SmilesGenerator generator = new SmilesGenerator();
            Iterator containers = ChemModelManipulator.getAllAtomContainers(model).iterator();
            while (containers.hasNext()) {
                  IAtomContainer container = (IAtomContainer)containers.next();
                  Molecule molecule = new Molecule(container);
                  Molecule moleculewithh=(Molecule)molecule.clone();
                  new HydrogenAdder().addExplicitHydrogensToSatisfyValency(moleculewithh);
                  double bondLength = GeometryTools.getBondLengthAverage(container,jcpPanel.getJChemPaintModel().getRendererModel().getRenderingCoordinates());
                  new HydrogenPlacer().placeHydrogens2D(moleculewithh, bondLength);
                  smiles += generator.createSMILES(molecule);
                  boolean[] bool=new boolean[moleculewithh.getBondCount()];
                  SmilesGenerator sg = new SmilesGenerator();
                  for(int i=0;i<bool.length;i++){
                        if (sg.isValidDoubleBondConfiguration(moleculewithh, moleculewithh.getBond(i)))
                              bool[i]=true;
                  }
                  chiralsmiles += generator.createChiralSMILES(moleculewithh,bool);
                  if (containers.hasNext()) {
                        chiralsmiles += ".";
                        smiles += ".";
                  }
            }
                  dialog.setMessage("Generated SMILES:", "SMILES: "+smiles+System.getProperty("line.separator")+"chiral SMILES: "+chiralsmiles);
            } catch (Exception exception)
            {
                  String message = "Error while creating SMILES: " + exception.getMessage();
                  logger.error(message);
                  logger.debug(exception);
                  dialog.setMessage("Error", message);
            }
            dialog.show();
      }
}


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