The code that reads the spanfile (rosetta_source/src/core/scoring/MembraneTopology.cc:initialize) is chock-full of the construction "tmhelix" and similar - in other words, I think it is only looking for transmembrane helices. I'm not even sure that this code allows things other than helix (the papers I've seen don't suggest that it does, nor does the documentation).
The code that reads the spanfile (rosetta_source/src/core/scoring/MembraneTopology.cc:initialize) is chock-full of the construction "tmhelix" and similar - in other words, I think it is only looking for transmembrane helices. I'm not even sure that this code allows things other than helix (the papers I've seen don't suggest that it does, nor does the documentation).