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ElectronImpactNBEReaction.java

/*
 *  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2006-03-29 10:27:08 +0200 (Wed, 29 Mar 2006) $
 *  $Revision: 5855 $
 *
 *  Copyright (C) 2006-2007  Miguel Rojas <miguel.rojas@uni-koeln.de>
 *
 *  Contact: cdk-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.
 *
 *  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.reaction.type;


import java.util.List;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.SingleElectron;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.IMapping;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionSpecification;
import org.openscience.cdk.tools.LoggingTool;

/**
 * <p>IReactionProcess which make an alectron impact for for Non-Bondind Electron Lost. 
 * This reaction type is a representation of the processes which occure in the mass spectrometer.</p>
 * 
 *<pre>
 *  IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
 *  setOfReactants.addMolecule(new Molecule());
 *  IReactionProcess type = new ElectronImpactNBEReaction();
 *  Object[] params = {Boolean.FALSE};
    type.setParameters(params);
 *  IReactionSet setOfReactions = type.initiate(setOfReactants, null);
 *  </pre>
 * 
 * <p>We have the possibility to localize the reactive center. Good method if you
 * want to localize the reaction in a fixed point</p>
 * <pre>atoms[0].setFlag(CDKConstants.REACTIVE_CENTER,true);</pre>
 * <p>Moreover you must put the parameter Boolean.TRUE</p>
 * <p>If the reactive center is not localized then the reaction process will
 * try to find automatically the posible reactive center.</p>
 * 
 * 
 * @author         Miguel Rojas
 * 
 * @cdk.created    2006-04-01
 * @cdk.module     reaction
 * @cdk.set        reaction-types
 * @cdk.dictref    reaction-types:electronImpact
 * 
 **/
00074 public class ElectronImpactNBEReaction implements IReactionProcess{
      private LoggingTool logger;
      private boolean hasActiveCenter;

      /**
       * Constructor of the ElectronImpactNBEReaction object
       *
       */
00082       public ElectronImpactNBEReaction(){
            logger = new LoggingTool(this);
      }
      /**
       *  Gets the specification attribute of the ElectronImpactNBEReaction object
       *
       *@return    The specification value
       */
00090       public ReactionSpecification getSpecification() {
            return new ReactionSpecification(
                        "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#ElectronImpactNBEReaction",
                        this.getClass().getName(),
                        "$Id: ElectronImpactNBEReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
                        "The Chemistry Development Kit");
      }
      
      /**
       *  Sets the parameters attribute of the ElectronImpactNBEReaction object
       *
       *@param  params            The parameter is if the molecule has already fixed the center active or not. It 
       *                                        should be set before to inize the reaction with a setFlag:  CDKConstants.REACTIVE_CENTER
       *@exception  CDKException  Description of the Exception
       */
00105       public void setParameters(Object[] params) throws CDKException {
            if (params.length > 1) {
                  throw new CDKException("ElectronImpactNBEReaction only expects one parameter");
            }
            if (!(params[0] instanceof Boolean)) {
                  throw new CDKException("The parameter must be of type boolean");
            }
            hasActiveCenter = ((Boolean) params[0]).booleanValue();
      }


      /**
       *  Gets the parameters attribute of the ElectronImpactNBEReaction object
       *
       *@return    The parameters value
       */
00121       public Object[] getParameters() {
            Object[] params = new Object[1];
            params[0] = new Boolean (hasActiveCenter);
            return params;
      }
      
      /**
       *  Initiate process.
       *  It is needed to call the addExplicitHydrogensToSatisfyValency
       *  from the class tools.HydrogenAdder.
       *
       *@param  reactants         reactants of the reaction.
       *@param  agents            agents of the reaction (Must be in this case null).
       *
       *@exception  CDKException  Description of the Exception
       */
00137       public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{

            logger.debug("initiate reaction: ElectronImpactNBEReaction");
            
            if (reactants.getMoleculeCount() != 1) {
                  throw new CDKException("ElectronImpactNBEReaction only expects one reactant");
            }
            if (agents != null) {
                  throw new CDKException("ElectronImpactNBEReaction don't expects agents");
            }
            
            IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newReactionSet();
            
            /* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
            if(!hasActiveCenter){
                  setActiveCenters(reactants.getMolecule(0));
            }
            
            IMolecule reactant0 = reactants.getMolecule(0);
            IAtom atomi = null;
            for(int i = 0 ; i < reactant0.getAtomCount() ; i++){
                  atomi = reactant0.getAtom(i);
                  if(atomi.getFlag(CDKConstants.REACTIVE_CENTER)){
                        
                        IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
                        reaction.addReactant(reactants.getMolecule(0));
                        IMolecule reactant = reaction.getReactants().getMolecule(0);
                        
                        int posA = reactant.getAtomNumber(atomi);
                        
                        IMolecule reactantCloned;
                        try {
                              reactantCloned = (IMolecule) reactants.getMolecule(0).clone();
                        } catch (CloneNotSupportedException e) {
                              throw new CDKException("Could not clone IMolecule!", e);
                        }
                        
                        List lps = reactantCloned.getConnectedLonePairsList(reactantCloned.getAtom(posA));
                        reactantCloned.removeLonePair((ILonePair)lps.get(lps.size() - 1));

                        reactantCloned.addSingleElectron(new SingleElectron(reactantCloned.getAtom(posA)));
                        reactantCloned.getAtom(posA).setFormalCharge(1);

                        /* mapping */
                        IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(atomi, reactantCloned.getAtom(posA));
                    reaction.addMapping(mapping);
                        
                        reaction.addProduct(reactantCloned);


                        setOfReactions.addReaction(reaction);
                  }
            }
            return setOfReactions;  
            
            
      }
      /**
       * set the active center for this molecule. The active center will be heteroatoms which contain lone pair electrons.
       * 
       * @param reactant The molecule to set the activity
       * @throws CDKException 
       */
00200       private void setActiveCenters(IMolecule reactant) throws CDKException {
            for(int i = 0 ; i < reactant.getAtomCount() ; i++){
                  if(reactant.getConnectedLonePairsCount(reactant.getAtom(i)) > 0){
                        reactant.getAtom(i).setFlag(CDKConstants.REACTIVE_CENTER,true);
                  }
            }
      }
      /**
       *  Gets the parameterNames attribute of the ElectronImpactNBEReaction object
       *
       *@return    The parameterNames value
       */
00212       public String[] getParameterNames() {
            String[] params = new String[1];
            params[0] = "hasActiveCenter";
            return params;
      }


      /**
       *  Gets the parameterType attribute of the ElectronImpactNBEReaction object
       *
       *@param  name  Description of the Parameter
       *@return       The parameterType value
       */
00225       public Object getParameterType(String name) {
            return new Boolean(false);
      }
}

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