code: protected static PolymerListElements generateElementsforRNA(String sequence, HELMEntity entity)
  			throws FastaFormatException, NotationException, ChemistryException, NucleotideLoadingException {
  		initMapNucleotides();
  		initMapNucleotidesNaturalAnalog();
  		PolymerListElements elements = new PolymerListElements(entity);
  		sequence = cleanup(sequence);
  		sequence = prepareSequence(sequence);
  		List<Nucleotide> normalNucleotideList = getNormalList(sequence);
  		for (Nucleotide nucleotide : normalNucleotideList) {
  			elements.addMonomerNotation(nucleotide.getNotation());
  		}
  		/* remove the phosphat of the last group */
  		String id = elements.getCurrentMonomerNotation().getUnit();
  		try {
  			elements.changeMonomerNotation(new MonomerNotationUnitRNA(id.substring(0, id.length() - 1), "RNA"));
  		} catch (org.helm.notation2.parser.exceptionparser.NotationException e) {
  			e.printStackTrace();
  			throw new FastaFormatException("PolymerListElements can not be initialized " + e.getMessage());
  		}
  
  		return elements;
  	}
docs: method to fill a rna polymer with its elements (MonomerNotationUnits)
  
  @param sequence
  rna sequence
  @param entity
  HELMEntity
  @return PolymerListElements
  @throws FastaFormatException
  if the input sequence is not correct
  @throws NotationException
  if notation is not valid
  @throws ChemistryException if chemistry engine can not be initialized
  @throws NucleotideLoadingException if nucleotides can not be loaded