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CarbonylEliminationReaction.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.Iterator;
import java.util.List;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.LonePair;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
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 participate mass spectrum process.  
 * This reaction could be represented as RC-C#[O+] => R[C] + |C#[O+]</p>
 * <p>Make sure that the molecule has the corresponend lone pair electrons
 * for each atom. You can use the method: <pre> LonePairElectronChecker </pre>
 * 
 * <pre>
 *  IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
 *  setOfReactants.addMolecule(new Molecule());
 *  IReactionProcess type = new CarbonylEliminationReaction();
 *  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    2006-10-16
 * @cdk.module     reaction
 * @cdk.set        reaction-types
 * 
 **/
00077 public class CarbonylEliminationReaction implements IReactionProcess{
      private LoggingTool logger;
      private boolean hasActiveCenter;
      private static final int BONDTOFLAG1 = 8;
      private static final int BONDTOFLAG2 = 9;
      
      /**
       * Constructor of the CarbonylEliminationReaction object
       *
       */
00087       public CarbonylEliminationReaction(){
            logger = new LoggingTool(this);
      }
      /**
       *  Gets the specification attribute of the CarbonylEliminationReaction object
       *
       *@return    The specification value
       */
00095       public ReactionSpecification getSpecification() {
            return new ReactionSpecification(
                        "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#CarbonylEliminationReaction",
                        this.getClass().getName(),
                        "$Id: RadicalSiteInitiationReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
                        "The Chemistry Development Kit");
      }
      
      /**
       *  Sets the parameters attribute of the CarbonylEliminationReaction 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
       */
00110       public void setParameters(Object[] params) throws CDKException {
            if (params.length > 1) {
                  throw new CDKException("CarbonylEliminationReaction only expects one parameter");
            }
            if (!(params[0] instanceof Boolean)) {
                  throw new CDKException("The parameter 1 must be of type boolean");
            }
            hasActiveCenter = ((Boolean) params[0]).booleanValue();
      }


      /**
       *  Gets the parameters attribute of the CarbonylEliminationReaction object
       *
       *@return    The parameters value
       */
00126       public Object[] getParameters() {
            Object[] params = new Object[1];
            params[0] = new Boolean (hasActiveCenter);
            return params;
      }
      
      /**
       *  Initiate process.
       *
       *@param  reactants         reactants of the reaction.
       *@param  agents            agents of the reaction (Must be in this case null).
       *
       *@exception  CDKException  Description of the Exception
       */
00140       public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{
            logger.debug("initiate reaction: CarbonylEliminationReaction");
            
            if (reactants.getMoleculeCount() != 1) {
                  throw new CDKException("CarbonylEliminationReaction only expects one reactant");
            }
            if (agents != null) {
                  throw new CDKException("CarbonylEliminationReaction don't expects agents");
            }
            
            IReactionSet setOfReactions = reactants.getBuilder().newReactionSet();
            IMolecule reactant = reactants.getMolecule(0);

            /* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
            if(!hasActiveCenter){
                  setActiveCenters(reactant);
            }
            
            for(int i = 0 ; i < reactant.getBondCount() ; i++) {
                  IBond bond = reactant.getBond(i);
                  if(bond.getOrder() == 3 ){
                        IAtom atom1 = null;
                        IAtom atom2 = null;
                        if(bond.getAtom(0).getSymbol().equals("C") && bond.getAtom(1).getSymbol().equals("O") && 
                                    bond.getAtom(0).getFormalCharge() == 0 && bond.getAtom(1).getFormalCharge() == 1) {
                              atom1 = bond.getAtom(1); /*Oxygen*/
                              atom2 = bond.getAtom(0);
                        }else if(bond.getAtom(1).getSymbol().equals("C") && bond.getAtom(0).getSymbol().equals("O") && 
                                                bond.getAtom(1).getFormalCharge() == 0 && bond.getAtom(0).getFormalCharge() == 1){
                              atom1 = bond.getAtom(0);/*Oxygen*/
                              atom2 = bond.getAtom(1);
                        }
                        if(atom1 != null && atom2 != null)
                        if(atom1.getFlag(CDKConstants.REACTIVE_CENTER) && atom2.getFlag(CDKConstants.REACTIVE_CENTER)){
                              List atomConL = reactant.getConnectedAtomsList(atom2);
                               Iterator iterator = atomConL.iterator();
                               IAtom atom3 = null;
                               while(iterator.hasNext()){
                                     IAtom a = (IAtom) iterator.next();
                                     if(a != atom1)
                                           atom3 = a;
                               }
                               if(atom3 != null){
                                     IBond bondCon = reactant.getBond(atom2, atom3);
                              
                                          IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
                                          reaction.addReactant(reactant);

                                          cleanFlagBOND(reactants.getMolecule(0));
                                          /* positions atoms and bonds */
                                          int atom1P = reactant.getAtomNumber(atom1);
                                          bond.setFlag(BONDTOFLAG1, true);
                                          int atom2P = reactant.getAtomNumber(atom2);
                                          bondCon.setFlag(BONDTOFLAG2, true);
                                          int atom3P = reactant.getAtomNumber(atom3);

                                          /* action */
                                          IMolecule acCloned;
                                          try {
                                                acCloned = (IMolecule) reactant.clone();
                                          } catch (CloneNotSupportedException e) {
                                                throw new CDKException("Could not clone IMolecule!", e);
                                          }
                                          
                                          int charge = acCloned.getAtom(atom3P).getFormalCharge();
                                          acCloned.getAtom(atom3P).setFormalCharge(charge+1);
                                          
                                          acCloned.addLonePair(new LonePair(acCloned.getAtom(atom2P)));
                                          acCloned.getAtom(atom2P).setFormalCharge(-1);
                                          
                                          IBond bondClon = null;
                                          for(int l = 0 ; l<acCloned.getBondCount();l++){
                                                if(acCloned.getBond(l).getFlag(BONDTOFLAG1)){
                                                      IBond bb = acCloned.getBond(l);
                                                      bondClon = bb;
                                                }else if(acCloned.getBond(l).getFlag(BONDTOFLAG2)){
                                                      IBond bb = acCloned.getBond(l);
                                                      acCloned.removeBond(bb.getAtom(0), bb.getAtom(1));
                                                }
                                          }
                                          
                                          /* mapping */
                                          IMapping mapping = atom1.getBuilder().newMapping(atom1, acCloned.getAtom(atom1P));
                                      reaction.addMapping(mapping);
                                      mapping = atom1.getBuilder().newMapping(atom2, acCloned.getAtom(atom2P));
                                      reaction.addMapping(mapping);
                                      mapping = atom1.getBuilder().newMapping(atom3, acCloned.getAtom(atom3P));
                                      reaction.addMapping(mapping);
                                      mapping = atom1.getBuilder().newMapping(bond, bondClon);
                                      reaction.addMapping(mapping);
                                      
                                          IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(acCloned);
                                          for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++){
                                                reaction.addProduct(moleculeSet.getMolecule(z));
                                          }
                                          
                                          setOfReactions.addReaction(reaction);

                                          bond.setFlag(BONDTOFLAG1, false);
                                          bondCon.setFlag(BONDTOFLAG2, false);
                                    }
                              }
                        }
                  }
            return setOfReactions;
            
      }
      /**
       * set the active center for this molecule. 
       * The active center will be those which correspond with RC-C#[O+]. 
       * <pre>
       * C: Atom
       * -: single bond
       * C: Atom
       * #: triple bond
       * O: Atom with formal charge = 1
       *  </pre>
       * 
       * @param reactant The molecule to set the activity
       * @throws CDKException 
       */
00261       private void setActiveCenters(IMolecule reactant) throws CDKException {
            for(int i = 0 ; i < reactant.getBondCount() ; i++) {
                  IBond bond = reactant.getBond(i);
                  if(bond.getOrder() == 3 ){
                        IAtom atom1 = null;
                        IAtom atom2 = null;
                        if(bond.getAtom(0).getSymbol().equals("C") && bond.getAtom(1).getSymbol().equals("O") && 
                                    bond.getAtom(0).getFormalCharge() == 0 && bond.getAtom(1).getFormalCharge() == 1) {
                              atom1 = bond.getAtom(1); /*Oxygen*/
                              atom2 = bond.getAtom(0);
                        }else if(bond.getAtom(1).getSymbol().equals("C") && bond.getAtom(0).getSymbol().equals("O") && 
                                                bond.getAtom(1).getFormalCharge() == 0 && bond.getAtom(0).getFormalCharge() == 1){
                              atom1 = bond.getAtom(0);/*Oxygen*/
                              atom2 = bond.getAtom(1);
                        }
                        if(atom1 != null && atom2 != null){
                               List atomConL = reactant.getConnectedAtomsList(atom2);
                               Iterator iterator = atomConL.iterator();
                               IAtom atom3 = null;
                               while(iterator.hasNext()){
                                     IAtom a = (IAtom) iterator.next();
                                     if(a != atom1)
                                           atom3 = a;
                               }
                               if(atom3 != null){
                                     IBond bondCon = reactant.getBond(atom2, atom3);
                                     atom1.setFlag(CDKConstants.REACTIVE_CENTER,true);
                                     bond.setFlag(CDKConstants.REACTIVE_CENTER,true); 
                                     atom2.setFlag(CDKConstants.REACTIVE_CENTER,true);
                                     bondCon.setFlag(CDKConstants.REACTIVE_CENTER,true); 
                                     atom3.setFlag(CDKConstants.REACTIVE_CENTER,true);
                               }
                        }
                  }
            }
      }
      /**
       *  Gets the parameterNames attribute of the CarbonylEliminationReaction object
       *
       *@return    The parameterNames value
       */
00302       public String[] getParameterNames() {
            String[] params = new String[1];
            params[0] = "hasActiveCenter";
            return params;
      }


      /**
       *  Gets the parameterType attribute of the CarbonylEliminationReaction object
       *
       *@param  name  Description of the Parameter
       *@return       The parameterType value
       */
00315       public Object getParameterType(String name) {
            return new Boolean(false);
      }
      /**
     * clean the flags CDKConstants.REACTIVE_CENTER from the molecule
     * 
       * @param mol
       */
00323       public void cleanFlagBOND(IAtomContainer ac){
            for(int j = 0 ; j < ac.getBondCount(); j++){
                  ac.getBond(j).setFlag(BONDTOFLAG1, false);
                  ac.getBond(j).setFlag(BONDTOFLAG2, false);
            }
      }
}

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