If a GU is placed in a junction, the energy between it and the next basepair in the string shall be in a certain range. (if that is hook end of the neck or multiloop end of a neck or near any type of loop. 1-1 included – but bulges excluded)
I would like a strategy that in case a GU-pair show up in a junction says:
Give 0 if energy is -2.1 and -2.5 or between that GU-pair and the next basepair
Give 0 if energy is -1.4
Give -1 for other energy values than the above mentioned.