code: public static final void replaceSMILESWithTemporaryIds(HELM2Notation helm2notation) throws NotationException,
  			HELM2HandledException, ChemistryException, CTKException, MonomerLoadingException, JDOMException {
  		for (int i = 0; i < helm2notation.getListOfPolymers().size(); i++) {
  			/* First save intern smiles to the MonomerFactory */
  			MethodsMonomerUtils.getListOfHandledMonomers(helm2notation.getListOfPolymers().get(i).getListMonomers());
  
  			for (int j = 0; j < helm2notation.getListOfPolymers().get(i).getPolymerElements().getListOfElements()
  					.size(); j++) {
  				MonomerNotation monomerNotation = replaceSMILESWithTemporaryIdsMonomerNotation(
  						helm2notation.getListOfPolymers().get(i).getPolymerElements().getListOfElements().get(j));
  				if (monomerNotation != null) {
  					helm2notation.getListOfPolymers().get(i).getPolymerElements().getListOfElements().set(j,
  							monomerNotation);
  				}
  			}
  		}
  
  	}
docs: This function replaces smiles in complex notation with temporary ids
  
  @param helm2notation
  given helm2 notation
  @throws NotationException
  if notation is not valid
  @throws ChemistryException
  if chemistry engine can not be initialized
  @throws HELM2HandledException
  if it contains HELM2 specific features, so that it can not be
  casted to HELM1 Format
  @throws CTKException
  general ChemToolKit exception passed to HELMToolKit
  @throws MonomerLoadingException
  if monomers can not be loaded
  @throws JDOMException
  if smiles can not be replace with the temporary ids