code: public static String getSMILESForAll(HELM2Notation helm2notation)
  			throws BuilderMoleculeException, CTKException, ChemistryException {
  		/* Build Molecues */
  		LOG.debug("Build single molecule(s)");
  		List<AbstractMolecule> molecules = BuilderMolecule.buildMoleculefromPolymers(helm2notation.getListOfPolymers(),
  				HELM2NotationUtils.getAllEdgeConnections(helm2notation.getListOfConnections()));
  		/* get for every molecule the smiles */
  		LOG.debug("Built single molecule(s)");
  		StringBuffer sb = new StringBuffer();
  		for (AbstractMolecule molecule : molecules) {
  			molecule = BuilderMolecule.mergeRgroups(molecule);
  			sb.append(Chemistry.getInstance().getManipulator().convertMolecule(molecule,
  					AbstractChemistryManipulator.StType.SMILES) + ".");
  		}
  		sb.setLength(sb.length() - 1);
  		LOG.debug("SMILES-All :" + sb.toString());
  		return sb.toString();
  	}
docs: method to generate smiles for the whole HELMNotation
  
  @param helm2notation
  input HELMNotation
  @return smiles for the whole HELMNotation
  @throws BuilderMoleculeException
  if the molecule can't be built
  @throws CTKException
  general ChemToolKit exception passed to HELMToolKit
  @throws ChemistryException
  if the Chemistry Engine can not be initialized