code: public static List<Monomer> getListOfHandledMonomersOnlyBase(List<MonomerNotation> monomerNotations)
        throws HELM2HandledException, NotationException, ChemistryException{
      LOG.debug("Get all bases of the rna");
      List<Monomer> items = new ArrayList<Monomer>();
  
      for (MonomerNotation monomerNotation : monomerNotations) {
        /* group element */
        if (monomerNotation instanceof MonomerNotationGroup) {
          throw new HELM2HandledException("Functions can't be called for HELM2 objects");
        } else {
          try {
            int count = Integer.parseInt(monomerNotation.getCount());
            if (count != 1) {
              throw new HELM2HandledException("Functions can't be called for HELM2 objects");
            }
  
            // for (int j = 0; j < count; j++) {
            items.addAll(Validation.getAllMonomersOnlyBase(monomerNotation));
            // }
          } catch (NumberFormatException |  MonomerException | IOException | CTKException e) {
            e.printStackTrace();
            throw new HELM2HandledException("Functions can't be called for HELM2 objects");
          }
  
        }
      }
      return items;
    }
docs: method to get all HELM1 valid MonomerNotations Only on these monomers
  required HELM1 functions are performed
  
  @param monomerNotations List of MonomerNotation
  @return List of Monomer
  @throws HELM2HandledException if HELM2 features are there
  @throws NotationException if notation is not valid
  @throws ChemistryException if the Chemistry Engine can not be initialized