code: private static void initMapAminoAcid() throws FastaFormatException, ChemistryException {
  		try {
  			aminoacids = MonomerFactory.getInstance().getMonomerDB().get("PEPTIDE");
  		} catch (IOException e) {
  			e.printStackTrace();
  			LOG.error("AminoAcids can not be initialized");
  			throw new FastaFormatException(e.getMessage());
  		}
  	}
docs: method to initialize map of existing amino acids in the database
  
  @throws FastaFormatException
  AminoAcids can not be initialized
  @throws ChemistryException
  if chemistry engine can not be initialized
  @throws CTKException
  general ChemToolKit exception passed to HELMToolKit