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.

Added support for reading in orientation; added enrgmd script for output enrgmd files without running simulations

Automatically write atomic ENM in multiresolution_simulation; fixed error in ENM causing failure for square lattice