StructureResonanceGenerator.java

/* $RCSfile$
 * $Author: miguelrojasch $
 * $Date: 2006-05-11 14:25:07 +0200 (Do, 11 Mai 2006) $
 * $Revision: 6221 $
 *
 *  Copyright (C) 2004-2007  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.tools;


import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IMoleculeSet;
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.type.DisplacementChargeFromAcceptorReaction;
import org.openscience.cdk.reaction.type.DisplacementChargeFromDonorReaction;
import org.openscience.cdk.reaction.type.HyperconjugationReaction;
import org.openscience.cdk.reaction.type.RearrangementAnion1Reaction;
import org.openscience.cdk.reaction.type.RearrangementAnion2Reaction;
import org.openscience.cdk.reaction.type.RearrangementAnion3Reaction;
import org.openscience.cdk.reaction.type.RearrangementCation1Reaction;
import org.openscience.cdk.reaction.type.RearrangementCation2Reaction;
import org.openscience.cdk.reaction.type.RearrangementCation3Reaction;
import org.openscience.cdk.reaction.type.RearrangementRadical1Reaction;
import org.openscience.cdk.reaction.type.RearrangementRadical2Reaction;
import org.openscience.cdk.reaction.type.RearrangementRadical3Reaction;

/**
 * <p>This class try to generate resonance structure for a determinate molecule.</p>
 * <p>Make sure that the molecule has the corresponend lone pair electrons
 * for each atom. You can use the method: <pre> LonePairElectronChecker </pre>
 * <p>It is needed to call the addExplicitHydrogensToSatisfyValency
 *  from the class tools.HydrogenAdder.</p>
 * <p>It is based on rearrengements of electrons and charge</p>
 * <p>The method is based on call by reactions which occur in a resonance.</p>
 * 
 * <pre>
 * StructureResonanceGenerator srG = new StructureReseonanceGenerator(true,true,true,true,false);
 * MoleculeSet setOf = gf.getResonances(new Molecule());
 * </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 as 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  2006-5-05
 * @cdk.module   reaction
 * 
 * @see DisplacementChargeFromAcceptorReaction
 * @see DisplacementChargeFromDonorReaction
 * @see RearrangementAnion1Reaction
 * @see RearrangementAnion2Reaction
 * @see RearrangementAnion3Reaction
 * @see RearrangementCation1Reaction
 * @see RearrangementCation2Reaction
 * @see RearrangementCation3Reaction
 * @see RearrangementRadical1Reaction
 * @see RearrangementRadical2Reaction
 * @see RearrangementRadical3Reaction
 * @see HyperconjugationReaction
 * 
 **/
00089 public class StructureResonanceGenerator {
      
      private boolean cationR = true;
      private boolean anionR = true;
      private boolean radicalR = true;
      private boolean bondR = true;
      private boolean hasActiveCenter = false;
      private boolean hyperconjugationR = false;
      /**-1 means that there is not restrictions how many structures will be obtained*/
00098       private int maxStructuresToObtain = -1;
      
      private LoggingTool logger = new LoggingTool(StructureResonanceGenerator.class);
      
      /**
       * Constructor of StructureResonanceGenerator object
       *
       * Default search: (Radical,Cation,Anion,Bond,hyperconjugation, no limit resonance structures)
       */
00107       public StructureResonanceGenerator(){
            this(true,true,true,true,false,false, -1);
      }
      /**
       * Constructor of StructureResonanceGenerator object
       *
       * @param cationR           True, search of Cation.
       * @param anionR            True, search of Anion.
       * @param radicalR          True, search of Radical.
       * @param bondR             True, search of Bond.
       * @param hyperconjugationR True, search of hyperconjugation.
       * @param hasActiveCenter   True, search of active Center.
       */
00120       public StructureResonanceGenerator(
                  boolean cationR,
                  boolean anionR,
                  boolean radicalR,
                  boolean bondR,
                  boolean hyperconjugationR,
                  boolean hasActiveCenter,
                  int maxStructuresToObtain){
            this.cationR = cationR;
            this.anionR = anionR;
            this.radicalR = radicalR;
            this.bondR = bondR;
            this.hyperconjugationR = hyperconjugationR;
            this.hasActiveCenter = hasActiveCenter;
            this.maxStructuresToObtain = maxStructuresToObtain;
            
      }
      /**
       * <p>Get the resonance structures from an atomContainer. </p>
       * <p>This generator of resonances is limited only strutcures whose have the same order sum of bonds or higher.
       * 
       * @param atomContainer The atomContainer to analize
       * @return The different resonance structures
       */
00144       public IAtomContainerSet getStructures(IAtomContainer atomContainer) {
            IAtomContainerSet setOfAC = atomContainer.getBuilder().newAtomContainerSet();
            
            IAtomContainerSet set = getAllStructures(atomContainer); 
            /*analize sum of bonds */
            double bondSum = 0;
            for(int i = 0; i < atomContainer.getBondCount(); i++)
                  bondSum = bondSum + atomContainer.getBond(i).getOrder();
            for(int i = 0; i < set.getAtomContainerCount(); i++){
                  double bondSumI = 0;
                  for(int j = 0; j < set.getAtomContainer(i).getBondCount(); j++)
                        bondSumI += set.getAtomContainer(i).getBond(j).getOrder();
                  if(bondSumI >= bondSum)
                        setOfAC.addAtomContainer(set.getAtomContainer(i));
            }
            return setOfAC;
      }
      /**
       * <p>Get all resonance structures from an atomContainer. </p>
       * 
       * @param atomContainer The atomContainer to analize
       * @return The different resonance structures
       */
00167       public IAtomContainerSet getAllStructures(IAtomContainer atomContainer){
            
            IAtomContainerSet setOfAtomContainer = atomContainer.getBuilder().newAtomContainerSet();
            setOfAtomContainer.addAtomContainer(atomContainer);
            Object[] params = new Object[1];
            if(hasActiveCenter)
                  params[0] = Boolean.TRUE;
            else
                  params[0] = Boolean.FALSE;

            try {
                  for(int i = 0 ; i < setOfAtomContainer.getAtomContainerCount() ; i++){

                        IMoleculeSet setOfReactants = atomContainer.getBuilder().newMoleculeSet();
                        setOfReactants.addAtomContainer(setOfAtomContainer.getAtomContainer(i));
                        if(cationR){
                              /* RearrangementCation1Reaction */
                              IReactionProcess type  = new RearrangementCation1Reaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          IReactionSet setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("RearrangementCation1Reaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }

                              /* RearrangementCation2Reaction*/
                              type  = new RearrangementCation2Reaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          setOfReactions = type.initiate(setOfReactants, null);
                          
                              if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("RearrangementCation2Reaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                              /* RearrangementCation3Reaction*/
                              type  = new RearrangementCation3Reaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("RearrangementCation3Reaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                        }
                        if(anionR){
                              /* RearrangementAnion1Reaction*/
                              IReactionProcess type  = new RearrangementAnion1Reaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          IReactionSet setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("RearrangementAnion1Reaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                              /* RearrangementAnion2Reaction*/
                          type  = new RearrangementAnion2Reaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("RearrangementAnion2Reaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                              /* RearrangementAnion3Reaction*/
                              type  = new RearrangementAnion3Reaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("RearrangementAnion3Reaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                        }
                        if(radicalR){
                              /* RearrangementRadical1Reaction*/
                              IReactionProcess type  = new RearrangementRadical1Reaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          IReactionSet setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("RearrangementRadical1Reaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                              /* RearrangementRadical2Reaction*/
                              type  = new RearrangementRadical2Reaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("RearrangementRadical2Reaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                              /* RearrangementRadical3Reaction*/
                              type  = new RearrangementRadical3Reaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("RearrangementRadical3Reaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                        }
                        if(bondR){
                              /* DisplacementChargeFromAcceptorReaction*/
                              IReactionProcess type  = new DisplacementChargeFromAcceptorReaction();
                          type.setParameters(params);

                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          IReactionSet setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("DisplacementChargeFromAcceptorReaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                          /* DisplacementChargeFromDonorReaction*/
                              type  = new DisplacementChargeFromDonorReaction();
                          type.setParameters(params);
                              
                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                    for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                          IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                        logger.debug("DisplacementChargeFromDonorReaction");
                                          if(!existAC(setOfAtomContainer,set))
                                                setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                    }
                        }
                        if(hyperconjugationR){
                              /* HyperconjugationReaction*/
                              IReactionProcess type  = new HyperconjugationReaction();
                          type.setParameters(params);

                          removeFlags(setOfAtomContainer.getAtomContainer(i));
                          IReactionSet setOfReactions = type.initiate(setOfReactants, null);
                          
                          if(setOfReactions.getReactionCount() != 0)
                                    for(int k = 0 ; k < setOfReactions.getReactionCount() ; k++)
                                          for(int j = 0 ; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount() ; j++){
                                                IAtomContainer set = setOfReactions.getReaction(k).getProducts().getAtomContainer(j);
//                                              logger.debug("HyperconjugationReaction");
                                                if(!existAC(setOfAtomContainer,set))
                                                      setOfAtomContainer.addAtomContainer(setOfReactions.getReaction(k).getProducts().getAtomContainer(j));
                                          }
                      }

                        /* this makes a limition of the search */
                        if(maxStructuresToObtain != -1)
                              if(setOfAtomContainer.getAtomContainerCount() > maxStructuresToObtain)
                                    break;
                        
                        if(i == 0 && setOfAtomContainer.getAtomContainerCount() > 9)
                              return setOfAtomContainer;
                  }
            } catch (CDKException e) {
                  logger.error("Error while getting all resonance structures: ");
                  logger.error(e.getMessage());
                  logger.debug(e);
            }
            return setOfAtomContainer;
      }
      /**
       * Search if the setOfAtomContainer contains the atomContainer 
       * 
       * @param set            ISetOfAtomContainer object where to search
       * @param atomContainer  IAtomContainer to search
       * @return                     True, if the atomContainer is contained
       */
00396       private boolean existAC(IAtomContainerSet set, IAtomContainer atomContainer) {
//          logger.debug("smiles: "+(new SmilesGenerator(set.getBuilder())).createSMILES((IMolecule) atomContainer));
            atomContainer = setID(atomContainer);
            for(int i = 0 ; i < set.getAtomContainerCount(); i++){
                  IAtomContainer ac = setID(set.getAtomContainer(i));
                  QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(ac);
//                QueryAtomContainer qAC = QueryAtomContainerCreator.createAnyAtomContainer(atomContainer,false);
                  try {
                        if(UniversalIsomorphismTester.isIsomorph(atomContainer,qAC)){
//                            logger.debug("exist");
                              return true;
                        }
                  } catch (CDKException e1) {
                        System.err.println(e1);
                        logger.error(e1.getMessage());
                        logger.debug(e1);
                  }
            }
            return false;
      }
      /**
       * remove the possible flags about CDKConstants.REACTIVE_CENTER
       * 
       * @param atomContainer
       * @return
       */
00422       private IAtomContainer removeFlags(IAtomContainer atomContainer){
            for(int i = 0 ; i < atomContainer.getAtomCount(); i++)
                  atomContainer.getAtom(i).setFlag(CDKConstants.REACTIVE_CENTER,false);

            for(int i = 0 ; i < atomContainer.getBondCount(); i++)
                  atomContainer.getBond(i).setFlag(CDKConstants.REACTIVE_CENTER,false);
            return atomContainer;
      }
      /**
       * Set the ID as position
       * 
       * @param atomContainer
       * @return
       */
00436       private IAtomContainer setID(IAtomContainer atomContainer){
            for(int i = 0 ; i < atomContainer.getAtomCount(); i++){
                  atomContainer.getAtom(i).setID(""+atomContainer.getAtomNumber(atomContainer.getAtom(i)));
            }
            return atomContainer;
      }

}