Rewrites the sequence based on the exchanging bonds
get_sequence_bonds.RdIn this convention, the residue in upper case indicates a presence of peptide bond proceeding it that is able to undergo the exchange. The first residue is by default in lower case as it is not proceeded by exchangable hydrogen from peptide bond. Second residue, based on the calculated value of hamuro retention between pair of first and second residue, is either in lower or upper case, depending on the threshold. The rest of residues are in upper case, with exception of proline, that due to its structure, is blocking the hydrogen from proceeding bond from exchange. Function from prepHaDeX.