code: private HELM2Notation readNotation(String notation)
  			throws ParserException, JDOMException, IOException, MonomerException, ChemistryException {
  		/* xhelm notation */
  		if (notation.contains("<Xhelm>")) {
  			LOG.info("xhelm is used as input");
  			String xhelm = notation;
  			Element xHELMRootElement = getXHELMRootElement(xhelm);
  
  			notation = xHelmNotationParser.getHELMNotationString(xHELMRootElement);
  			MonomerStore store = xHelmNotationParser.getMonomerStore(xHELMRootElement);
  			updateMonomerStore(store);
  
  		}
  		return HELM2NotationUtils.readNotation(notation);
  	}
docs: method to read the HELM string, the HELM can be in version 1 or 2, or in
  Xhelm format
  
  @param notation
  HELM input
  @return ContainerHELM2
  @throws ParserException
  @throws IOException
  @throws JDOMException
  @throws MonomerException
  @throws ChemistryException