code: public static List<String> getAminoAcidList(String peptideSequence)
        throws MonomerException, NotationException, MonomerLoadingException, ChemistryException {
  
      if (null == peptideSequence) {
        throw new NotationException("Peptide Sequence must be specified");
      }
  
      String cleanSeq = cleanup(peptideSequence);
  
      Map<String, Monomer> peptideMap = MonomerFactory.getInstance().getMonomerDB().get(Monomer.PEPTIDE_POLYMER_TYPE);
      Set<String> keySet = peptideMap.keySet();
  
      // walk the sequence
      List<String> l = new ArrayList<String>();
      int pos = 0;
      while (pos < cleanSeq.length()) {
        boolean found = false;
        for (Iterator i = keySet.iterator(); i.hasNext();) {
          String symbol = (String) i.next();
  
          if (cleanSeq.startsWith(symbol, pos)) {
            found = true;
            l.add(symbol);
            pos = pos + symbol.length();
            break;
          }
        }
        if (!found) {
          throw new NotationException(
              "Sequence contains unknown amino acid starting at "
                  + cleanSeq.substring(pos));
        }
      }
  
      return l;
    }
docs: This method converts peptide sequence into a List of amino acid
  
  @param peptideSequence given peptide sequence
  @return list of amino acid
  @throws org.helm.notation2.exception.MonomerException if peptide contains unknown monomers
  @throws org.helm.notation2.exception.NotationException if peptide sequence is null
  @throws MonomerLoadingException monomer store could not be loaded
  @throws ChemistryException if chemistry could not be initialized