Added fill_sequence parameter to SegmentModel.set_sequence and to the mrdna and enrgmd scripts, with default value 'T', since that is most common for origami. Thanks to Elija Feigl for recommending the change.

Slightly reorganized simulation protocol; added options to mrdna script and simulate.py for using twist in the coarsest step

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