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CleavageBondMultiReaction.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 org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionSpecification;
import org.openscience.cdk.tools.LoggingTool;

import java.util.Iterator;

/**
 * <p>IReactionProcess which a bond that is being broken to generate single electron
 * for each atom. This reaction is a extension of CleavageBondReaction. The difference
 * consists that this reaction makes a multifragmentation. It doesn't obtain the fragments
 * which are obtained before. The reason is that for big molecules we obtain a errorOfMemory.
 * 
 * 
 * <pre>A-B => [A*] + [B*]</pre>
 * <pre>
 *  IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
 *  setOfReactants.addMolecule(new Molecule());
 *  IReactionProcess type = new CleavageBondMultiReaction();
 *  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    2006-11-17
 * @cdk.module     reaction
 * @cdk.set        reaction-types
 * 
 **/
00074 public class CleavageBondMultiReaction implements IReactionProcess{
      private LoggingTool logger;
      private boolean hasActiveCenter;
      private IMoleculeSet moleculeSetTOTAL;
      private static final int BONDTOFLAG = 8;
      /**
       * Constructor of the CleavageBondMultiReaction object
       *
       */
00083       public CleavageBondMultiReaction(){
            moleculeSetTOTAL = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
      
            logger = new LoggingTool(this);
      }
      /**
       *  Gets the specification attribute of the CleavageBondMultiReaction object
       *
       *@return    The specification value
       */
00093       public ReactionSpecification getSpecification() {
            return new ReactionSpecification(
                        "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#CleavageBondMultiReaction",
                        this.getClass().getName(),
                        "$Id: CleavageBondMultiReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
                        "The Chemistry Development Kit");
      }
      
      /**
       *  Sets the parameters attribute of the CleavageBondMultiReaction 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
       */
00108       public void setParameters(Object[] params) throws CDKException {
            if (params.length > 1) {
                  throw new CDKException("CleavageBondMultiReaction 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 CleavageBondMultiReaction object
       *
       *@return    The parameters value
       */
00124       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
       */
00140       public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{
            logger.debug("initiate reaction: CleavageBondMultiReaction");
            
            
            if (reactants.getMoleculeCount() != 1) {
                  throw new CDKException("CleavageBondMultiReaction only expects one reactant");
            }
            if (agents != null) {
                  throw new CDKException("CleavageBondMultiReaction don't expects agents");
            }
            
            IReactionSet setOfReactions = reactants.getBuilder().newReactionSet();
            
            IMolecule reactant = reactants.getMolecule(0);
            if(existAC(moleculeSetTOTAL,reactant))
                  return setOfReactions;
            else
                  moleculeSetTOTAL.addMolecule(reactant);
            
            /* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
            if(!hasActiveCenter){
                  setActiveCenters(reactant);
            }

        Iterator bonds = reactants.getMolecule(0).bonds();
        while (bonds.hasNext()) {
            IBond aBond = (IBond) bonds.next();

                  if(aBond.getFlag(CDKConstants.REACTIVE_CENTER))
                        if(aBond.getAtom(0).getFormalCharge() == 0 && aBond.getAtom(1).getFormalCharge() == 0){
                        
                        int atom1 = reactants.getMolecule(0).getAtomNumber(aBond.getAtom(0));
                        int atom2 = reactants.getMolecule(0).getAtomNumber(aBond.getAtom(1));
                        cleanFlagBOND(reactants.getMolecule(0));
                        aBond.setFlag(BONDTOFLAG, true);
                        
                        IReaction reaction = reactants.getBuilder().newReaction();
                        reaction.addReactant(reactants.getMolecule(0));
                        
                        IMolecule reactantCloned;
                        try {
                              reactantCloned = (IMolecule) reactant.clone();
                        } catch (CloneNotSupportedException e) {
                              throw new CDKException("Could not clone IMolecule!", e);
                        }
                        
                        reactantCloned.addSingleElectron(reactant.getBuilder().newSingleElectron(reactantCloned.getAtom(atom1)));
                        reactantCloned.addSingleElectron(reactant.getBuilder().newSingleElectron(reactantCloned.getAtom(atom2)));
                        
                        double order = 0;
                        IBond bondClon = null;
                        for(int l = 0 ; l<reactantCloned.getBondCount();l++){
                              if(reactantCloned.getBond(l).getFlag(BONDTOFLAG)){
                                    IBond bondFlag = reactantCloned.getBond(l);
                                    order = bondFlag.getOrder();
                                    if(order == 1){
                                          reactantCloned.removeBond(bondFlag.getAtom(0), bondFlag.getAtom(1));
                                    }
                                    else{
                                          reactantCloned.getBond(l).setOrder(order-1);
                                          bondClon = reactantCloned.getBond(l);
                                    }
                                    break;
                              }
                        }

                        IMoleculeSet moleculeSet;
                        if(order == 1)/*break molecule*/{
                              moleculeSet = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
                              int exx = 0;
                              for(int z = 0 ; z < moleculeSet.getAtomContainerCount(); z++){
                                    IMolecule ac = moleculeSet.getMolecule(z);
                                    
                                    if(!existAC(moleculeSetTOTAL,ac)){
                                          exx++;
                                          reaction.addProduct(ac);
                                    }
                              }
                              if(exx == 0)
                                    return setOfReactions;
                        }
                        else{
                              if(existAC(moleculeSetTOTAL,reactantCloned))
                                    return setOfReactions;
                              else{
                                    reaction.addProduct(reactantCloned);
                              }
                        }
                              
                        
                        /*adding only that contains product*/
                        if(reaction.getProductCount() != 0)
                              setOfReactions.addReaction(reaction);
                        

                        aBond.setFlag(BONDTOFLAG, false);
                        
                        /* fragmentation again with the obtained fragments*/
                        if(reaction.getProductCount() != 0)
                        for(Iterator iter = reaction.getProducts().molecules(); iter.hasNext();){
                              IMolecule molF = (IMolecule) iter.next();
                              if(existAC(moleculeSetTOTAL,molF))
                                    continue;
                              IMoleculeSet moleculeSetF = molF.getBuilder().newMoleculeSet();
                              moleculeSetF.addMolecule(molF);
                              IReactionSet setOfReactionsF = initiate(moleculeSetF, null);
                              if(setOfReactionsF != null)
                              if(setOfReactionsF.getReactionCount() != 0)
                                    for(Iterator iterR = setOfReactionsF.reactions(); iterR.hasNext();){
                                          setOfReactions.addReaction((IReaction) iterR.next());
                                    }
                        }
                        
                  }
                        
            }
            
            return setOfReactions;  
      }
      /**
       * set the active center for this molecule. 
       * The active center will be those which correspond with A-B. If
       * the bond is simple, it will be breaked forming two fragments 
       * <pre>
       * A: Atom
       * #/=/-: bond
       * B: Atom
       *  </pre>
       * 
       * @param reactant The molecule to set the activity
       * @throws CDKException 
       */
00272     private void setActiveCenters(IMolecule reactant) throws CDKException {
        Iterator bonds = reactant.bonds();
        while (bonds.hasNext()) {
            IBond bond = (IBond) bonds.next();
            if (bond.getAtom(0).getFormalCharge() == 0 && bond.getAtom(1).getFormalCharge() == 0)
                bond.setFlag(CDKConstants.REACTIVE_CENTER, true);
        }
    }
      /**
       *  Gets the parameterNames attribute of the CleavageBondMultiReaction object
       *
       *@return    The parameterNames value
       */
00285       public String[] getParameterNames() {
            String[] params = new String[1];
            params[0] = "hasActiveCenter";
            return params;
      }


      /**
       *  Gets the parameterType attribute of the CleavageBondMultiReaction object
       *
       *@param  name  Description of the Parameter
       *@return       The parameterType value
       */
00298       public Object getParameterType(String name) {
            return new Boolean(false);
      }
      
      /**
     * clean the flags CDKConstants.REACTIVE_CENTER from the molecule
     * 
       * @param mol
       */
00307       public void cleanFlagBOND(IAtomContainer ac){
            for(int j = 0 ; j < ac.getBondCount(); j++)
                  ac.getBond(j).setFlag(BONDTOFLAG, false);
      }

      /**
       * controll if the new product was already found before
       * @param acSet 
       * @param fragment
       * @return True, if it contains
       */
00318       private boolean existAC(IAtomContainerSet acSet, IMolecule fragment) {
            QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(fragment);
            for(int i = 0; i < acSet.getAtomContainerCount(); i++){
                  IAtomContainer ac = acSet.getAtomContainer(i);
                  try {
                        if(UniversalIsomorphismTester.isIsomorph(ac, qAC))
                              return true;
                  } catch (CDKException e) {
                        e.printStackTrace();
                  }
            }
            return false;
      }
}

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