Fixed corner case bug where crossovers at end of ssDNA were not neccesarily recognized as intrahelical connections

now if the bead on the central helix is the same at each crossover, an angle potential is applied instead of skipping the crossover

Slightly reorganized simulation protocol; added options to mrdna script and simulate.py for using twist in the coarsest step

First, ssDNA segments are now broken at crossovers
Second, ssDNA segments aren't allowed to stack intrahelically