Made cadnano reader set azimuthal angle more accurately; some problems could arise with cadnano2 files that are saved in cadnano2.5 due to incorrect assignment of eulerZ in cadnano2.5

Removed os.sync() lines prior to running arbd/oxDNA simulations because they can hang indefinitely; needs testing

Improved atomic pdb basepair assignment by making distance metric symmetric and by assigning basepairs in order of quality of fit

Reordered A/B in minimizeRmsd() to be consistent with supplied arguments; does not affect return values

a) some intrinsic flexibility associated with the first crossover
b) the spring for the twist of the helix
c) intrinsic flexibility associated with the second crossover

1) Proper accounting for a single bond representing a double crossover
2) Parallel-helix dihedral angle spring constant is now computed from three "springs" placed in series that represent:
   a) the flexibility of the bond on one side of the crossover
   b) the intrinsic flexibility of the crossover
   c) the flexibility of the bond on the other side of the crossover