code: public static HELM2Notation convertIntoAnalogSequence(HELM2Notation helm2Notation)
  			throws FastaFormatException, AnalogSequenceException, ChemistryException, CTKException {
  		initMapAminoAcid();
  		initMapNucleotides();
  		initMapNucleotidesNaturalAnalog();
  		initMapTransformNucleotides();
  		/*
  		 * transform/convert only the peptides + rnas into the analog sequence
  		 */
  		List<PolymerNotation> polymers = helm2Notation.getListOfPolymers();
  		for (int i = 0; i < helm2Notation.getListOfPolymers().size(); i++) {
  			if (helm2Notation.getListOfPolymers().get(i).getPolymerID() instanceof RNAEntity) {
  				helm2Notation.getListOfPolymers().set(i, convertRNAIntoAnalogSequence(polymers.get(i)));
  			}
  			if (helm2Notation.getListOfPolymers().get(i).getPolymerID() instanceof PeptideEntity) {
  				helm2Notation.getListOfPolymers().set(i, convertPeptideIntoAnalogSequence(polymers.get(i)));
  			}
  		}
  
  		return helm2Notation;
  	}
docs: method to convert all Peptides and RNAs into the natural analogue
  sequence and generates HELM2Notation
  
  @param helm2Notation {@link HELM2Notation}
  @return analog helm2notation
  @throws FastaFormatException if it can not be converted to analog sequence
  @throws AnalogSequenceException
  if the natural analogue sequence can not be produced
  @throws ChemistryException if chemistry engine can not be initialized
  @throws CTKException general ChemToolKit exception passed to HELMToolKit