structureresonancegenerator.java

化学图形处理软件

						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
	 */
	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
	 */
	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
	 */
	private IAtomContainer setID(IAtomContainer atomContainer){
		for(int i = 0 ; i < atomContainer.getAtomCount(); i++){
			atomContainer.getAtom(i).setID(""+atomContainer.getAtomNumber(atomContainer.getAtom(i)));
		}
		return atomContainer;
	}

}