Ensure no duplicate bonds in ENM, logging violations; thanks to Elija Feigl for bringing duplicate bonds to our attention

Updated ENM to avoid situation where network is applied to single-stranded DNA at end of double-stranded helix

Fixed model_from_lists for 3'-to-5' structures; fixed issue with single-nucleotide 'crossovers'; added debug flag for tracing strands

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

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