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RadicalSiteInitiationReaction.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.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.interfaces.ISingleElectron;
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. Homolitic dissocitation. 
 * This reaction could be represented as A-B-[c*] => [A*] + B=C.</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 RadicalSiteInitiationReaction();
 *  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    2006-05-05
 * @cdk.module     reaction
 * @cdk.set        reaction-types
 * 
 **/
00077 public class RadicalSiteInitiationReaction implements IReactionProcess{
      private LoggingTool logger;
      private boolean hasActiveCenter;
      private static final int BONDTOFLAG = 8;
      
      /**
       * Constructor of the RadicalSiteInitiationReaction object
       *
       */
00086       public RadicalSiteInitiationReaction(){
            logger = new LoggingTool(this);
      }
      /**
       *  Gets the specification attribute of the RadicalSiteInitiationReaction object
       *
       *@return    The specification value
       */
00094       public ReactionSpecification getSpecification() {
            return new ReactionSpecification(
                        "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#RearrangementRadical3Reaction",
                        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 RadicalSiteInitiationReaction 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
       */
00109       public void setParameters(Object[] params) throws CDKException {
            if (params.length > 1) {
                  throw new CDKException("RadicalSiteInitiationReaction 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 RadicalSiteInitiationReaction object
       *
       *@return    The parameters value
       */
00125       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
       */
00139       public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{
            logger.debug("initiate reaction: RadicalSiteInitiationReaction");
            
            if (reactants.getMoleculeCount() != 1) {
                  throw new CDKException("RadicalSiteInitiationReaction only expects one reactant");
            }
            if (agents != null) {
                  throw new CDKException("RadicalSiteInitiationReaction 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);
            }
            
            IMolecule reactant0 = reactants.getMolecule(0);
            IAtom atomi = null;
            IBond bondj;
            IBond bondk;
            for(int i = 0 ; i < reactant0.getAtomCount() ; i++){
                  atomi = reactant0.getAtom(i);
                  if(atomi.getFlag(CDKConstants.REACTIVE_CENTER)&& reactant.getConnectedSingleElectronsCount(atomi) == 1 ){
                        
                        java.util.List bonds = reactant.getConnectedBondsList(atomi);
                        
                        for(int j = 0 ; j < bonds.size() ; j++){
                              bondj = (IBond)bonds.get(j);
                              if(bondj.getFlag(CDKConstants.REACTIVE_CENTER)&& bondj.getOrder() < 3.0 ){
                                    IAtom atom = bondj.getConnectedAtom(reactant.getAtom(i));
                                    if(atom.getFormalCharge() != 0)
                                          continue;
                                    java.util.List bondsI = reactant.getConnectedBondsList(atom);
                                    for(int k = 0 ; k < bondsI.size() ; k++){
                                          bondk = (IBond)bondsI.get(k);
                                          if(bondk.getFlag(CDKConstants.REACTIVE_CENTER) && bondk.getOrder() ==  1.0 && !bondk.equals(bondj)){
                                                IAtom atomConn = bondk.getConnectedAtom(atom);
                                                if(atomConn.getFlag(CDKConstants.REACTIVE_CENTER) && atomConn.getFormalCharge() == 0
                                                            && !atomConn.equals(atomi) && !atomConn.getSymbol().equals("H")){
                                                      
                                                      IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
                                                      reaction.addReactant(reactant);

                                                      cleanFlagBOND(reactants.getMolecule(0));
                                                      /* positions atoms and bonds */
                                                      int atom0P = reactant.getAtomNumber(atomi);
                                                      bondj.setFlag(BONDTOFLAG, true);
                                                      int bond2P = reactant.getBondNumber(bondk);
                                                      int atom1P = reactant.getAtomNumber(atom);
                                                      int atom2P = reactant.getAtomNumber(atomConn);
                                                      /* action */
                                                      IMolecule acCloned;
                                                      try {
                                                            acCloned = (IMolecule) reactant.clone();
                                                      } catch (CloneNotSupportedException e) {
                                                            throw new CDKException("Could not clone IMolecule!", e);
                                                      }

                                                      acCloned.removeBond(bond2P);
                                                      
                                                      List selectron = acCloned.getConnectedSingleElectronsList(acCloned.getAtom(atom0P));
                                                      acCloned.removeSingleElectron((ISingleElectron)selectron.get(selectron.size() -1));
                                                      selectron = acCloned.getConnectedSingleElectronsList(acCloned.getAtom(atom0P));
                                                      
                                                      acCloned.addSingleElectron(new SingleElectron(acCloned.getAtom(atom2P)));     

                                                      
                                                      double order = 0;
                                                      IBond bondjClon = null;
                                                      for(int l = 0 ; l < acCloned.getBondCount();l++){
                                                            if(acCloned.getBond(l).getFlag(BONDTOFLAG)){
                                                                  order = acCloned.getBond(l).getOrder();
                                                                  acCloned.getBond(l).setOrder(order+1);
                                                                  bondjClon = acCloned.getBond(l);
                                                                  break;
                                                            }
                                                      }

                                                      
                                                      /* mapping */
                                                      IMapping mapping = atom.getBuilder().newMapping(atomi, acCloned.getAtom(atom0P));
                                                  reaction.addMapping(mapping);
                                                  mapping = atom.getBuilder().newMapping(atom, acCloned.getAtom(atom1P));
                                                  reaction.addMapping(mapping);
                                                  mapping = atom.getBuilder().newMapping(atomConn, acCloned.getAtom(atom2P));
                                                  reaction.addMapping(mapping);
                                                  mapping = atom.getBuilder().newMapping(bondj, bondjClon);
                                                  reaction.addMapping(mapping);
                                                  /*breaked bond*/
//                                                mapping = atom.getBuilder().newMapping(bondk, acCloned.getBond(bond2P));
//                                                reaction.addMapping(mapping);
                                                  
                                                      IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(acCloned);
                                                      for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++){
                                                            reaction.addProduct(moleculeSet.getMolecule(z));
                                                      }
                                                      
                                                      setOfReactions.addReaction(reaction);

                                                      bondj.setFlag(BONDTOFLAG, false);
                                                }
                                          }
                                    }
                              }
                        }
                  }
            }
            return setOfReactions;
            
      }
      /**
       * set the active center for this molecule. 
       * The active center will be those which correspond with A-B-[C*]. 
       * <pre>
       * A: Atom
       * -: bond
       * B: Atom
       * -: bond
       * C: Atom with single electron
       *  </pre>
       * 
       * @param reactant The molecule to set the activity
       * @throws CDKException 
       */
00265       private void setActiveCenters(IMolecule reactant) throws CDKException {
            IAtom atomi = null;
            IBond bondj = null;
            IBond bondk = null;
            for(int i = 0 ; i < reactant.getAtomCount() ; i++) {
                  atomi = reactant.getAtom(i);
                  if(reactant.getConnectedSingleElectronsCount(atomi) == 1 ){
                        java.util.List bonds = reactant.getConnectedBondsList(atomi);
                        for(int j = 0 ; j < bonds.size() ; j++){
                              bondj = (IBond)bonds.get(j);
                              if(bondj.getOrder() < 3.0){
                                    IAtom atom = bondj.getConnectedAtom(atomi);
                                    if(atom.getFormalCharge() != 0)
                                          continue;
                                    java.util.List bondsI = reactant.getConnectedBondsList(atom);
                                    for(int k = 0 ; k < bondsI.size() ; k++){
                                          bondk = (IBond)bondsI.get(k);
                                          if(bondk.getOrder() == 1 && !bondk.equals(bondj)){
                                          IAtom atomConn = bondk.getConnectedAtom(atom);
                                          if(atomConn.getFormalCharge() == 0 && !atomConn.getSymbol().equals("H")){
                                                atomi.setFlag(CDKConstants.REACTIVE_CENTER,true);
                                                atom.setFlag(CDKConstants.REACTIVE_CENTER,true);
                                                atomConn.setFlag(CDKConstants.REACTIVE_CENTER,true);
                                                bondj.setFlag(CDKConstants.REACTIVE_CENTER,true);
                                                bondk.setFlag(CDKConstants.REACTIVE_CENTER,true); 
                                          }
                                    }
                                    }
                              }
                        }
                  }
            }
      }
      /**
       *  Gets the parameterNames attribute of the RadicalSiteInitiationReaction object
       *
       *@return    The parameterNames value
       */
00303       public String[] getParameterNames() {
            String[] params = new String[1];
            params[0] = "hasActiveCenter";
            return params;
      }


      /**
       *  Gets the parameterType attribute of the RadicalSiteInitiationReaction object
       *
       *@param  name  Description of the Parameter
       *@return       The parameterType value
       */
00316       public Object getParameterType(String name) {
            return new Boolean(false);
      }
      /**
     * clean the flags BONDTOFLAG from the molecule
     * 
       * @param mol
       */
00324       public void cleanFlagBOND(IAtomContainer ac){
            for(int j = 0 ; j < ac.getBondCount(); j++)
                  ac.getBond(j).setFlag(BONDTOFLAG, false);
      }
}

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