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AddHydrogenAction.java

/* $Revision: 8292 $ $Author: egonw $ $Date: 2007-05-01 21:15:34 +0200 (Tue, 01 May 2007) $
 *
 *  Copyright (C) 2003-2007  The JChemPaint project
 *
 *  Contact: jchempaint-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.
 *  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.HashMap;
import java.util.Iterator;

import javax.swing.undo.UndoableEdit;
import javax.vecmath.Point2d;

import org.openscience.cdk.Atom;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.applications.jchempaint.JChemPaintModel;
import org.openscience.cdk.applications.undoredo.AddHydrogenEdit;
import org.openscience.cdk.controller.Controller2DModel;
import org.openscience.cdk.geometry.GeometryTools;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.layout.HydrogenPlacer;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
import org.openscience.cdk.tools.manipulator.ReactionSetManipulator;


/**
 * An action triggering the addition of hydrogens to 
 * selected structures
 *
 * @cdk.module jchempaint
 * @author     steinbeck
 */
00058 public class AddHydrogenAction extends JCPAction
{

      private static final long serialVersionUID = 7696756423842199080L;
      private HydrogenAdder hydrogenAdder = null;
    private IAtomContainer changedAtomsAndBonds = null;
    private HashMap hydrogenAtomMap = null;

00066       public void actionPerformed(ActionEvent event)
      {
        this.hydrogenAtomMap = null;
        this.changedAtomsAndBonds = null;
            logger.debug("Trying to add hydrogen in mode: ", type);
            if (hydrogenAdder == null)
            {
                  hydrogenAdder = new HydrogenAdder("org.openscience.cdk.tools.ValencyChecker");
            }

            if (jcpPanel.getJChemPaintModel() != null)
            {
                  // now add hydrogens
                  JChemPaintModel jcpmodel = jcpPanel.getJChemPaintModel();
                  org.openscience.cdk.interfaces.IChemModel model = jcpmodel.getChemModel();
            
                  IChemObject object = getSource(event);
                  if (object != null)
                  {
                        if (object instanceof Atom)
                        {
                              logger.debug("Adding hydrogens to this specific atom");
                              Atom atom = (Atom) object;
                    addHydrogenToOneAtom(ChemModelManipulator.getRelevantAtomContainer(model, atom), atom);
                        } else if (object instanceof ChemModel) {
                    logger.debug("Adding hydrogens to all atoms");
                              addHydrogenToAllAtoms(model);
                        } else {
                              logger.error("Can only add hydrogens to Atom's");
                        }
                  } else
                  {
                logger.debug("Adding hydrogens to all atoms");
                        addHydrogenToAllAtoms(model);
                  }
            UndoableEdit edit = null;
            if (type.equals("explicit")) {
                edit = new  AddHydrogenEdit(model, changedAtomsAndBonds);
            }
            else if ( type.equals("implicit")) {
                edit = new  AddHydrogenEdit(model, hydrogenAtomMap);
            }
            else if (type.equals("allimplicit")) {
               edit = new  AddHydrogenEdit(model, hydrogenAtomMap);
            }
            jcpPanel.getUndoSupport().postEdit(edit);
                  jcpmodel.fireChange();
                  Controller2DModel controllerModel = jcpPanel.getJChemPaintModel().getControllerModel();
                  if (type.equals("implicit"))
                  {
                        if(!controllerModel.getAutoUpdateImplicitHydrogens()){
                              controllerModel.setAutoUpdateImplicitHydrogens(true);
                        }else{
                      controllerModel.setAutoUpdateImplicitHydrogens(false);
                        }
                  }
            }
      }


      /**
       *  Adds a feature to the HydrogenToAllAtoms attribute of the AddHydrogenAction
       *  object
       *
       *@param  model  The feature to be added to the HydrogenToAllAtoms attribute
       */
00132       private void addHydrogenToAllAtoms(org.openscience.cdk.interfaces.IChemModel model)
      {
            IMoleculeSet som = model.getMoleculeSet();
            org.openscience.cdk.interfaces.IReactionSet sor = model.getReactionSet();
            if (som != null)
            {
                  addHydrogenToAllMolecules(som);
            } else if (sor != null)
            {
                  logger.debug("#reactions ", sor.getReactionCount());
                  som = ReactionSetManipulator.getAllMolecules(sor);
                  logger.debug("Found molecules: ", som.getMoleculeCount());
                  addHydrogenToAllMolecules(som);
            }
      }


      /**
       *  Adds a feature to the HydrogenToAllMolecules attribute of the
       *  AddHydrogenAction object
       *
       *@param  som  The feature to be added to the HydrogenToAllMolecules attribute
       */
00155       private void addHydrogenToAllMolecules(IMoleculeSet som)
      {
            JChemPaintModel jcpmodel = jcpPanel.getJChemPaintModel();
            Controller2DModel controllerModel = jcpmodel.getControllerModel();
        try
            {
            java.util.Iterator mols = som.molecules();
                  while (mols.hasNext())
                  {
                        IMolecule molecule = (IMolecule)mols.next();
                        if (molecule != null)
                        {
                              if (type.equals("implicit"))
                              {
                                    if(!controllerModel.getAutoUpdateImplicitHydrogens()){
                                          hydrogenAtomMap = hydrogenAdder.addImplicitHydrogensToSatisfyValency(molecule);
                                    }else{
                                          for (int j = 0; j < molecule.getAtomCount(); j++)
                                          {
                                                logger.debug("Checking atom: ", j);
                                                molecule.getAtom(j).setHydrogenCount(0);
                                          }
                              }
                              } else if (type.equals("explicit"))
                              {
                                    double bondLength = GeometryTools.getBondLengthAverage(molecule, jcpmodel.getRendererModel().getRenderingCoordinates());
                                    if (Double.isNaN(bondLength))
                                    {
                                          logger.warn("Could not determine average bond length from structure!");
                                          bondLength = controllerModel.getBondPointerLength();
                                    }
                        changedAtomsAndBonds = hydrogenAdder.addExplicitHydrogensToSatisfyValency(molecule);
                        HydrogenPlacer hPlacer = new HydrogenPlacer();
                                    hPlacer.placeHydrogens2D(molecule, bondLength, jcpmodel.getRendererModel().getRenderingCoordinates());

                                    Iterator containers =  ChemModelManipulator.getAllAtomContainers(jcpmodel.getChemModel()).iterator();
                                    while (containers.hasNext()) {
                                          IAtomContainer atomCon = (IAtomContainer)containers.next(); 
                                          for (int k = 0; k < atomCon.getAtomCount(); k++)
                                          {
                                                IAtom currentAtom = atomCon.getAtom(k);
                                                if(jcpmodel.getRendererModel().getRenderingCoordinate(currentAtom)!=null){
                                                      currentAtom.setPoint2d(new Point2d((Point2d)jcpmodel.getRendererModel().getRenderingCoordinate(currentAtom)));
                                                }
                                          }
                                    }
                                    
                                    //((PopupController2D)jcpPanel.getDrawingPanel().getMouseListeners()[0]).updateMoleculeCoordinates();
                              } else if (type.equals("allimplicit"))
                              {
                                          // remove explicit hydrogen if necessary
                                          //org.openscience.cdk.interfaces.IAtom[] atoms = molecule.getAtoms();
                                          for (int j = 0; j < molecule.getAtomCount(); j++)
                                          {
                                                org.openscience.cdk.interfaces.IAtom atom = molecule.getAtom(j);
                                                logger.debug("Checking atom: ", j);
                                                if (atom.getSymbol().equals("H"))
                                                {
                                                      logger.debug("Atom is a hydrogen");
                                                      molecule.removeAtomAndConnectedElectronContainers(atom);
                                                      if(j-1!=molecule.getAtomCount())
                                                            j--;
                                                }
                                          }
                                          // add implicit hydrogen
                              hydrogenAtomMap = hydrogenAdder.addImplicitHydrogensToSatisfyValency(molecule);
                              }
                        } else
                        {
                              logger.error("Molecule is null! Cannot add hydrogens!");
                        }
                  }
            } catch (Exception exc)
            {
                  exc.printStackTrace();
                  logger.error("Error while adding hydrogen: ", exc.getMessage());
                  logger.debug(exc);
            }
      }


      /**
       *  Adds a feature to the HydrogenToOneAtom attribute of the AddHydrogenAction
       *  object
       *
       *@param  container  The feature to be added to the HydrogenToOneAtom attribute
       *@param  atom       The feature to be added to the HydrogenToOneAtom attribute
       */
00243       private void addHydrogenToOneAtom(IAtomContainer container, Atom atom)
      {
            JChemPaintModel jcpmodel = jcpPanel.getJChemPaintModel();
            Controller2DModel controllerModel = jcpmodel.getControllerModel();
            try
            {
                  if (type.equals("implicit"))
                  {
               int[] hydrogens = hydrogenAdder.addImplicitHydrogensToSatisfyValency(container, atom);
               hydrogenAtomMap.put(atom, hydrogens);
//                changedAtomsAndBonds = hydrogenAdder.addImplicitHydrogensToSatisfyValency(container, atom);
                  } else if (type.equals("explicit"))
                  {
                        double bondLength = GeometryTools.getBondLengthAverage(container, jcpmodel.getRendererModel().getRenderingCoordinates());
                        if (Double.isNaN(bondLength))
                        {
                              logger.warn("Could not determine average bond length from structure!");
                              bondLength = controllerModel.getBondPointerLength();
                        }
//                hydrogenAdder.addExplicitHydrogensToSatisfyValency(container, atom, container);
                changedAtomsAndBonds = hydrogenAdder.addExplicitHydrogensToSatisfyValency(container, atom, container);
                        HydrogenPlacer hPlacer = new HydrogenPlacer();
                        hPlacer.placeHydrogens2D(container, atom, bondLength);
                  }
            } catch (Exception exc)
            {
                  logger.error("Error while adding hydrogen: ", exc.getMessage());
                  logger.debug(exc);
            }
      }
}


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