code: private static PolymerNotation convertPeptideIntoAnalogSequence(PolymerNotation polymer)
  			throws AnalogSequenceException {
  
  		for (int i = 0; i < polymer.getPolymerElements().getListOfElements().size(); i++) {
  			/* Change current MonomerNotation */
  			polymer.getPolymerElements().getListOfElements().set(i,
  					generateMonomerNotationPeptide(polymer.getPolymerElements().getListOfElements().get(i)));
  		}
  
  		return polymer;
  	}
docs: method to convert the sequence of a PolymerNotation into the natural
  analogue sequence
  
  @param polymer
  PolymerNotation
  @return PolymerNotation with the natural analogue sequence
  @throws AnalogSequenceException
  if the natural analog sequence can not be produced