code: public static HELM2Notation readPeptide(String notation)
  			throws FastaFormatException, NotationException, ChemistryException {
  		HELM2Notation helm2notation = new HELM2Notation();
  		PolymerNotation polymer = new PolymerNotation("PEPTIDE1");
  		helm2notation.addPolymer(new PolymerNotation(polymer.getPolymerID(),
  				FastaFormat.generateElementsOfPeptide(notation, polymer.getPolymerID())));
  		return helm2notation;
  	}
docs: method to read a peptide sequence and generate a HELM2Notation object of
  it
  
  @param notation peptide sequence
  @return HELM2Notation object
  @throws FastaFormatException
  if the peptide sequence is not in the right format
  @throws NotationException
  if the notation object can not be built
  @throws ChemistryException if chemistry engine can not be initialized