Changed how particles are named so that it no longer reflects the number of nucleotides represented, but is more robust to clashes

Added routines for inserting and removing DNA; made it so atomic simulation doesn't resize model dimensions

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

Add public versions of _generate_atomic_model and _generate_bead_model; moved generation of strands in __init__ to precede generation of beads comands,

Previous commit fixed an issue for from_pdb reader, which used "sscrossover" connections, but broke models from the vHelix reader which used "intrahelical" connections. Now we convert "sscrossover" connections at the ends of segments into "intrahelical" connections.