Logo Search packages:      
Sourcecode: cdk version File versions  Download package

BreakingBondReaction.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.LonePair;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.ReactionSpecification;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.ValencyChecker;

import java.io.IOException;
import java.util.Iterator;

/**
 * <p>IReactionProcess which a bond that is being broken to generate charges. 
 * As there are two directions for breaking a bond in a polar manner, 
 * each bond is investigated twice:</p>
 * <pre>A-B => [A+] + |[B-]</pre>
 * <pre>A-B => |[A-] + [B+]</pre>
 * <pre> It will not be created structures no possible, for example; C=O => [C-][O+].
 * <pre>
 *  IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
 *  setOfReactants.addMolecule(new Molecule());
 *  IReactionProcess type = new BreakingBondReaction();
 *  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    2006-06-09
 * @cdk.module     reaction
 * @cdk.set        reaction-types
 * 
 **/
00073 public class BreakingBondReaction implements IReactionProcess{
      private LoggingTool logger;
      private boolean hasActiveCenter;
      private ValencyChecker valChecker;
      private static final int BONDTOFLAG = 8;
      /**
       * Constructor of the BreakingBondReaction object
       *
       */
00082       public BreakingBondReaction(){
            logger = new LoggingTool(this);
            try{
                  valChecker = new ValencyChecker();
            }catch(IOException e){
                  e.printStackTrace();
            }catch(ClassNotFoundException e){
                  e.printStackTrace();
            }
      }
      /**
       *  Gets the specification attribute of the BreakingBondReaction object
       *
       *@return    The specification value
       */
00097       public ReactionSpecification getSpecification() {
            return new ReactionSpecification(
                        "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#BreakingBondReaction",
                        this.getClass().getName(),
                        "$Id: BreakingBondReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
                        "The Chemistry Development Kit");
      }
      
      /**
       *  Sets the parameters attribute of the BreakingBondReaction 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
       */
00112       public void setParameters(Object[] params) throws CDKException {
            if (params.length > 1) {
                  throw new CDKException("BreakingBondReaction 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 BreakingBondReaction object
       *
       *@return    The parameters value
       */
00128       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
       */
00144       public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{

            logger.debug("initiate reaction: BreakingBondReaction");
            
            if (reactants.getMoleculeCount() != 1) {
                  throw new CDKException("BreakingBondReaction only expects one reactant");
            }
            if (agents != null) {
                  throw new CDKException("BreakingBondReaction don't expects agents");
            }
            
            IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newReactionSet();
            IMolecule reactant = reactants.getMolecule(0);
            
            /* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
            if(!hasActiveCenter){
                  setActiveCenters(reactant);
            }
            
//          IBond[] bonds = reactants.getMolecule(0).getBonds();
        Iterator bonds = reactants.getMolecule(0).bonds();
        while (bonds.hasNext()) {
            IBond bond = (IBond) bonds.next();

                  if(bond.getFlag(CDKConstants.REACTIVE_CENTER))
                        if(bond.getAtom(0).getFormalCharge() == 0 && bond.getAtom(1).getFormalCharge() == 0){
                        
                        int atom1 = reactants.getMolecule(0).getAtomNumber(bond.getAtom(0));
                        int atom2 = reactants.getMolecule(0).getAtomNumber(bond.getAtom(1));
                        cleanFlagBOND(reactants.getMolecule(0));
                        bond.setFlag(BONDTOFLAG, true);
                        /**/
                        for (int j = 0; j < 2; j++){
                              IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
                              reaction.addReactant(reactants.getMolecule(0));
                              
                              IMolecule reactantCloned;
                              try {
                                    reactantCloned = (IMolecule) reactant.clone();
                              } catch (CloneNotSupportedException e) {
                                    throw new CDKException("Could not clone IMolecule!", e);
                              }
                              
                              IBond aBond = null;
                              double order = 0;
                              for(int l = 0 ; l<reactantCloned.getBondCount();l++){
                                    if(reactantCloned.getBond(l).getFlag(BONDTOFLAG)){
                                          order = reactantCloned.getBond(l).getOrder();
                                          reactantCloned.getBond(l).setOrder(order-1);
                                          aBond = reactantCloned.getBond(l);
                                          break;
                                    }
                              }

                              int charge = 0;
                              if (j == 0){
                                    charge = reactantCloned.getAtom(atom1).getFormalCharge();
                                    reactantCloned.getAtom(atom1).setFormalCharge(charge+1);
                                    if(!reactantCloned.getAtom(atom2).getSymbol().equals("H"))
                                          if(!valChecker.isSaturated(reactantCloned.getAtom(atom1), reactantCloned))
                                                continue;
                                    
                                    charge = reactantCloned.getAtom(atom2).getFormalCharge();
                                    reactantCloned.getAtom(atom2).setFormalCharge(charge-1);
                                    reactantCloned.addLonePair(new LonePair(reactantCloned.getAtom(atom2)));
                                    /* an acceptor atom cannot be charged positive*/
                                    if(!reactantCloned.getAtom(atom2).getSymbol().equals("H"))
                                          if(!valChecker.isSaturated(reactantCloned.getAtom(atom1),reactantCloned))
                                                continue;
                                    if(order == 1)/*break molecule*/
                                          reactantCloned.removeBond(reactantCloned.getAtom(atom1), reactantCloned.getAtom(atom2));
                                    
                              } else{
                                    charge = reactantCloned.getAtom(atom2).getFormalCharge();
                                    reactantCloned.getAtom(atom2).setFormalCharge(charge+1);
                                    
                                    if(!reactantCloned.getAtom(atom2).getSymbol().equals("H"))
                                          if(!valChecker.isSaturated(reactantCloned.getAtom(atom2), reactantCloned))
                                                continue;
                                    
                                    charge = reactantCloned.getAtom(atom1).getFormalCharge();
                                    reactantCloned.getAtom(atom1).setFormalCharge(-1);
                                    reactantCloned.addLonePair(new LonePair(reactantCloned.getAtom(atom1)));
                                    /* an acceptor atom cannot be charged positive*/
                                    if(!reactantCloned.getAtom(atom2).getSymbol().equals("H"))
                                          if(!valChecker.isSaturated(reactantCloned.getAtom(atom2),reactantCloned))
                                                continue;
                                    if(order == 1)/*break molecule*/
                                          reactantCloned.removeBond(reactantCloned.getAtom(atom1), reactantCloned.getAtom(atom2));
                              }
                              
                              /* mapping */
                              IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(reactants.getMolecule(0).getAtom(atom1), reactantCloned.getAtom(atom1));
                          reaction.addMapping(mapping);
                          mapping = DefaultChemObjectBuilder.getInstance().newMapping(reactants.getMolecule(0).getAtom(atom2), reactantCloned.getAtom(atom2));
                          reaction.addMapping(mapping);
                          if(order != 1){
                                    mapping = DefaultChemObjectBuilder.getInstance().newMapping(bond, aBond);
                                    reaction.addMapping(mapping);
                              }
                          if(order > 1)
                                    reaction.addProduct(reactantCloned);
                          else{
                                IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
                                    for(int z = 0; z < moleculeSet.getAtomContainerCount() ; z++){
                                          reaction.addProduct(moleculeSet.getMolecule(z));
                                    }
                          }
                              /*adding only that contains product*/
                              if(reaction.getProductCount() != 0)
                                    setOfReactions.addReaction(reaction);
                        }
                        bond.setFlag(BONDTOFLAG, false);
                        
                  }
                        
            }
            
            return setOfReactions;  
      }
//    /**
//     * controll if the new product was already found before
//     * @param acSet 
//     * @param fragment
//     * @return True, if it contains
//     */
//    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;
//    }
      /**
       * 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 
       */
00296     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) {
                IAtom atom1 = bond.getAtom(0);
                IAtom atom2 = bond.getAtom(1);
                atom1.setFlag(CDKConstants.REACTIVE_CENTER, true);
                atom2.setFlag(CDKConstants.REACTIVE_CENTER, true);
                bond.setFlag(CDKConstants.REACTIVE_CENTER, true);
            }
        }
    }
      /**
       *  Gets the parameterNames attribute of the BreakingBondReaction object
       *
       *@return    The parameterNames value
       */
00314       public String[] getParameterNames() {
            String[] params = new String[1];
            params[0] = "hasActiveCenter";
            return params;
      }


      /**
       *  Gets the parameterType attribute of the BreakingBondReaction object
       *
       *@param  name  Description of the Parameter
       *@return       The parameterType value
       */
00327       public Object getParameterType(String name) {
            return new Boolean(false);
      }
      
      /**
     * clean the flags CDKConstants.REACTIVE_CENTER from the molecule
     * 
       * @param ac
       */
00336       public void cleanFlagBOND(IAtomContainer ac){
            for(int j = 0 ; j < ac.getBondCount(); j++)
                  ac.getBond(j).setFlag(BONDTOFLAG, false);
      }/**
     * clean the flags CDKConstants.REACTIVE_CENTER from the molecule
     * 
       * @param molecule
       */
00344       public void cleanFlagReactiveCenter(IMolecule molecule){
            for(int j = 0 ; j < molecule.getAtomCount(); j++)
                  molecule.getAtom(j).setFlag(CDKConstants.REACTIVE_CENTER, false);
            for(int j = 0 ; j < molecule.getBondCount(); j++)
                  molecule.getBond(j).setFlag(CDKConstants.REACTIVE_CENTER, false);
      }
}

Generated by  Doxygen 1.6.0   Back to index