Fixed two small bugs, one involving use of is for string comparison, the other involving an incorrect function call when a restraint is added to the system with only one argument

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

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