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HyperconjugationReaction.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.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
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.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;

/**
 * <p>HyperconjugationReaction is the stabilising interaction that results 
 * from the interaction of the electrons in a s-bond (for our case only C-H)
 * with an adjacent empty (or partially filled) p-orbital.</p>
 * <p>Based on the valence bond model of bonding, hyperconjugation can be described as 
 * "double bond - no bond resonance"</p>
 * <p>This reaction could be represented like</p>
 * <pre>[C+]-C => C=C + [H+] </pre>
 * 
 * <pre>
 *  IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
 *  setOfReactants.addMolecule(new Molecule());
 *  IReactionProcess type = new HyperconjugationReaction();
 *  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    2006-07-04
 * @cdk.module     reaction
 * @cdk.set        reaction-types
 * 
 **/
00080 public class HyperconjugationReaction implements IReactionProcess{
      private LoggingTool logger;
      private boolean hasActiveCenter;

      /**
       * Constructor of the HyperconjugationReaction object
       *
       */
00088       public HyperconjugationReaction(){
            logger = new LoggingTool(this);
      }
      /**
       *  Gets the specification attribute of the HyperconjugationReaction object
       *
       *@return    The specification value
       */
00096       public ReactionSpecification getSpecification() {
            return new ReactionSpecification(
                        "http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict#HyperconjugationReaction",
                        this.getClass().getName(),
                        "$Id: HyperconjugationReaction.java,v 1.6 2006/04/01 08:26:47 mrc Exp $",
                        "The Chemistry Development Kit");
      }
      
      /**
       *  Sets the parameters attribute of the HyperconjugationReaction 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
       */
00111       public void setParameters(Object[] params) throws CDKException {
            if (params.length > 1) {
                  throw new CDKException("HyperconjugationReaction 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 HyperconjugationReaction object
       *
       *@return    The parameters value
       */
00127       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
       */
00143       public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException{

            logger.debug("initiate reaction: HyperconjugationReaction");
            
            if (reactants.getMoleculeCount() != 1) {
                  throw new CDKException("HyperconjugationReaction only expects one reactant");
            }
            if (agents != null) {
                  throw new CDKException("HyperconjugationReaction 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);
            }
            IAtomContainerSet acSet = reactant.getBuilder().newAtomContainerSet();
            
            //IAtom[] atoms = reactant.getAtoms();
            IAtom atomi = null;
            IAtom atomj = null;
            IAtom atomk = null;
            for(int i = 0 ; i < reactant.getAtomCount() ; i++) {
                  atomi = reactant.getAtom(i);
                  if(atomi.getFlag(CDKConstants.REACTIVE_CENTER)&& atomi.getFormalCharge() == 1&& !(atomi.getSymbol().equals("H"))){
                        java.util.List atoms1 = reactant.getConnectedAtomsList(atomi);
                        for(int j = 0; j < atoms1.size(); j++) {
                              atomj = (IAtom)atoms1.get(j);
                              if(atomj.getFlag(CDKConstants.REACTIVE_CENTER)&& !(atomj.getSymbol().equals("H"))){
                                    IBond bond = reactant.getBond(atomi, atomj);
                                    if(bond.getOrder() == 1) {
                                          if(bond.getFlag(CDKConstants.REACTIVE_CENTER)){
                                                java.util.List atoms2 = reactant.getConnectedAtomsList(atomj);
                                                for(int k = 0; k < atoms2.size() ; k++) {
                                                      atomk = (IAtom)atoms2.get(k);
                                                      if(atomk.getSymbol().equals("H")){

                                                            int atom1 = reactants.getMolecule(0).getAtomNumber(atomi);
                                                            int atom2 = reactants.getMolecule(0).getAtomNumber(atomj);
                                                            int atomH = reactants.getMolecule(0).getAtomNumber(atomk);
                                                            int bond1 =  reactants.getMolecule(0).getBondNumber(bond);

                                                            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);
                                                            }

                                                            double order = reactantCloned.getBond(bond1).getOrder();
                                                            reactantCloned.getBond(bond1).setOrder(order + 1);

                                                            int charge = reactantCloned.getAtom(atom1).getFormalCharge();
                                                            reactantCloned.getAtom(atom1).setFormalCharge(charge-1);

                                                            reactantCloned.removeAtomAndConnectedElectronContainers(reactantCloned.getAtom(atomH));


                                                            /* mapping */
                                                            IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(bond, reactantCloned.getBond(bond1));
                                                            reaction.addMapping(mapping);
                                                            mapping = DefaultChemObjectBuilder.getInstance().newMapping(atomi, reactantCloned.getAtom(atom1));
                                                            reaction.addMapping(mapping);
                                                            mapping = DefaultChemObjectBuilder.getInstance().newMapping(atomj, reactantCloned.getAtom(atom2));
                                                            reaction.addMapping(mapping);

                                                            if(existAC(acSet,reactantCloned))
                                                                  continue;
                                                            acSet.addAtomContainer(reactantCloned);

                                                            reaction.addProduct(reactantCloned);

                                                            IAtom hydrogen = reactants.getBuilder().newAtom("H");
                                                            hydrogen.setFormalCharge(1);
                                                            IMolecule proton = reactants.getBuilder().newMolecule();
                                                            proton.addAtom(hydrogen);
                                                            reaction.addProduct(proton);

                                                            setOfReactions.addReaction(reaction);
                                                      }
                                                }
                                          }
                                    }
                              }
                        }
                  }
            }

            
            return setOfReactions;  
            
            
      }
      /**
       * set the active center for this molecule. 
       * The active center will be those which correspond with [A+]-B([H]). 
       * <pre>
       * A: Atom with charge
       * -: Singlebond
       * B: Atom
       *  </pre>
       * 
       * @param reactant The molecule to set the activity
       * @throws CDKException 
       */
00253       private void setActiveCenters(IMolecule reactant) throws CDKException {
            //IAtom[] atoms = reactant.getAtoms();
            IAtom atomi = null;
            IAtom atomj = null;
            IAtom atomk = null;
            for(int i = 0 ; i < reactant.getAtomCount() ; i++) {
                  atomi = reactant.getAtom(i);
                  if(!atomi.getSymbol().equals("H")&& atomi.getFormalCharge() == 1){
                        java.util.List atoms1 = reactant.getConnectedAtomsList(atomi);
                        for(int j = 0; j < atoms1.size(); j++) {
                              atomj = (IAtom)atoms1.get(j);
                              if(!atomj.getSymbol().equals("H") && atomj.getFormalCharge() == 0){
                                    IBond bond = reactant.getBond(atomi, atomj);
                                    if(bond.getOrder() == 1){
                                          java.util.List atoms2 = reactant.getConnectedAtomsList(atomj);
                                          for(int k = 0; k < atoms2.size() ; k++){
                                                atomk = (IAtom)atoms2.get(k);
                                                if(atomk.getSymbol().equals("H")){
                                                      atomi.setFlag(CDKConstants.REACTIVE_CENTER,true);
                                                      atomj.setFlag(CDKConstants.REACTIVE_CENTER,true);
                                                      bond.setFlag(CDKConstants.REACTIVE_CENTER,true);
                                                }
                                          }
                                    }

                              }
                        }
                  }
            }
      }
      /**
       * controll if the new product was already found before
       * @param acSet 
       * @param fragment
       * @return True, if it contains
       */
00289       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;
      }
      /**
       *  Gets the parameterNames attribute of the HyperconjugationReaction object
       *
       *@return    The parameterNames value
       */
00307       public String[] getParameterNames() {
            String[] params = new String[1];
            params[0] = "hasActiveCenter";
            return params;
      }


      /**
       *  Gets the parameterType attribute of the HyperconjugationReaction object
       *
       *@param  name  Description of the Parameter
       *@return       The parameterType value
       */
00320       public Object getParameterType(String name) {
            return new Boolean(false);
      }
}

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