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

Added support for having multiple intrahelical connections from a single "location" in a segment; allows two ssDNA strands to emerge from the ends of a dsDNA segment

Code now always places a ssDNA bead when an ssDNA segment is between two dsDNA segments.

Code now more robustly places a bead and intrahelical junctions

Updated algorithm that fits splines into beads to extend farther into intrahelically connected segments, and to use linear interpolation for quaternions, resulting in better all-atom models

Updated bead model potentials to work with antiparallel DNA; also made terminal_crossovers bond shorter at 1.2 nm (vs 1.85)

Added type_ argument to SingleStrandedSegment.add_crossover() for compatibility with DoubleStrandedSegment