code: public static List<Nucleotide> getNucleotideList(PolymerNotation polymer)
  			throws RNAUtilsException, HELM2HandledException, ChemistryException {
  		checkRNA(polymer);
  		List<Nucleotide> nucleotides = new ArrayList<Nucleotide>();
  		/* check for HELM2Elements */
  		List<MonomerNotation> monomerNotations = polymer.getPolymerElements().getListOfElements();
  		for (int i = 0; i < monomerNotations.size(); i++) {
  			MonomerNotation monomerNotation = monomerNotations.get(i);
  			if ((!(monomerNotation instanceof MonomerNotationUnitRNA))
  					|| Integer.parseInt(monomerNotation.getCount()) != 1) {
  				LOG.info("MonomerNotation contains HELM2 Elements " + monomerNotation);
  				throw new HELM2HandledException("HELM2 Elements are involved");
  			}
  			try {
  				boolean last = false;
  				if (i == monomerNotations.size() - 1) {
  					last = true;
  				}
  				nucleotides.add(NucleotideParser.convertToNucleotide(monomerNotation.getUnit(), last));
  			} catch (MonomerException | NucleotideLoadingException | NotationException
  					| org.helm.notation2.exception.NotationException e) {
  				e.printStackTrace();
  				throw new RNAUtilsException("Nucleotide can not be read " + e.getMessage());
  			}
  		}
  		return nucleotides;
  	}
docs: method to get all nucleotides for one polymer
  
  @param polymer
  PolymerNotation
  @return List of nucleotides of the polmyer
  @throws RNAUtilsException
  if the polymer is not rna or dna or the nucleotide can not be
  read
  @throws HELM2HandledException
  if the polymer contains HELM2 features
  @throws ChemistryException if chemistry engine can not be initialized