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