Merge pull request #179 from RosettaCommons/roccomoretti/integration_fixes
Trying to convert magenta to green on the integration tests
A bunch of failures were from the elimination of pose.update_residue_neighbors() in RosettaScripts. I added that back on a sub-protocol level where appropriate. However, as Filters get const poses they don't necessarily get a chance to update the neighbors. So I put back in the call before the filters run. I also fixed the issue with update_residue_neighbors() on an empty pose (the reason it was removed) and added a unit test for that functionality.
**Integration tests still broken (see pull request for details):**
coupled_moves & hybridization - should be fixed in other branches.
antibody_graft - Anyone from the Gray lab (or elsewhere) know how this is supposed to work?
filter_termini_near_interface - Anyone from the Kuhlman lab (or elsewhere) know how this is supposed to work?
dock_with_hotspot_place_simultaneously & inverse_rotamer_remodel - These are working on my machine. I'm not sure why they're crashing on the test server, and only on the release mode build.