in calcScoresForMSMS the loop which goes through the masses surrounds the loop which goes through the sequence. if we put the sequence loop on the outside this will confer some advantages:

translateNucleotideSequence won’t have to be called over and over.
the code which produces a probable MSMS spectrum for a given sequence could be called just once.

I need to make one large-enough matrix to hold all calculated internal weights of a sequence so that the system is not spending so much time on malloc and free().

On home machine with longshort.pkl the storage matrix code performed at 2:13