Improved scripts for building cadnano structures; seems it will be neccesary to make contour go from nt[0]-0.5 to nt[-1]+0.5

Changed how crossover dihedrals are written when local_twist is False; fixed routines that walk through helices

Streamlined walking through strands for atomic model; added on_fwd_strand attribute to Location class

Fixed some small bugs; updated intrahelical iteration to use linked-list scheme; updated bead generation