code: protected static PolymerListElements generateElementsOfPeptide(String sequence, HELMEntity entity)
  			throws FastaFormatException, ChemistryException {
  		initMapAminoAcid();
  		sequence = cleanup(sequence);
  		try {
  			PolymerListElements elements = new PolymerListElements(entity);
  			List<String> aaList = AminoAcidParser.getAminoAcidList(sequence);
  			for (String aa : aaList) {
  				if (aa.length() > 1) {
  					aa = "[" + aa + "]";
  				}
  
  				elements.addMonomerNotation(aa);
  			}
  			return elements;
  		} catch (org.helm.notation2.parser.exceptionparser.NotationException | IOException | MonomerException
  				| org.helm.notation2.exception.NotationException e) {
  			e.printStackTrace();
  			LOG.error("PolymerListElements can not be initialized");
  			throw new FastaFormatException("PolymerListElements can not be initialized " + e.getMessage());
  		}
  
  	}
docs: method to fill a peptide polymer with its elements (MonomerNotationUnits)
  
  @param sequence
  peptide sequence
  @param entity
  HELMEntity
  @return PolymerListElements
  @throws FastaFormatException
  if the input sequence is not correct
  @throws ChemistryException
  if chemistry engine can not be initialized