It has become clear that when one creates hash codes to compare two ProForma strings, collapsing everything to formulas will not work. This PR addresses that by:
changing the proteoform hash to use modifications (not always formulas)
handling formulas with duplicate elements
updating ptmlist.txt (for future work of conversion)
It has become clear that when one creates hash codes to compare two ProForma strings, collapsing everything to formulas will not work. This PR addresses that by: