Merge pull request #399 from RosettaCommons/jkleman/jkleman/mp_updates
MP updates:
* rewrote and extensively tested SpanningTopology constructor from PDB
* it is vastly improved and recognizes spans better
* I tested on 34 previously broken cases, except a handful they work now
* small problems that still occur are due to Dssp recognizing loops instead of
secondary structure elements
* a difference now is that spans that might not completely span the membrane
might be recognized as "TMspans"
* also, loop residues (except up to 3 residue loops bridging spans) are
now excluded from the spans (and there seem to be quite a couple in the
structures that I looked at)
* this impacts the spanfile_from_pdb app!!!
* added unit tests for this constructor
* added unit test for average_antiparallel_embeddings in MembraneGeometryUtil