Fixed multiple issues; 3-prime ends of nucleotides now terminate correctly; strands not cleared unless atoms exist; strands regenerated with atomic model; cadnano models initialized with more correct azimuthal angle

Updated imports to be compatible with new package structure; updated paths to resources to use new get_resource_path() function

Moved run_simulate_protocols outside of cadnano_segments since more modular; increased density of coarsest DNA model

Improved cadnano segment protocol; using 1.03 instead of 1 for max beads, resulting in more 1-bp beads

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