code: private void setMonomerFactoryToDefault(String helm) throws MonomerLoadingException, ChemistryException {
  		if (helm.contains("<Xhelm>")) {
  			LOG.info("Refresh local Monomer Store in case of Xhelm");
  			MonomerFactory.refreshMonomerCache();
  		}
  	}
docs: method to set the MonomerFactory to the default one, this is only done in
  case of xHELM input
  
  @param helm
  input HELM
  @throws MonomerLoadingException
  if the MonomerFactory can not be loaded
  @throws ChemistryException
  if chemistry engine can not be initialized