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

Fixed bug introduced in commit 47b578f2 where ArbdModel.__init__ arguments were incorrectly provided by SegmentModel.__init__