Merge pull request #708 from RosettaCommons/jkleman/mp_updates2
Jkleman/mp updates2
= protocols/membrane/util:
added functions pose_tm_com, rsd_closest_to_pose_tm_com, create_membrane_foldtree_anchor_pose_tmcom
added unit tests for them
= MembranePositionFromTopologyMover:
cleaned up foldtree code and created new foldtree
likely to cause integration test changes in mpfastrelax and depending protocols
= OptimizeMembranePositionMover:
cleaned up foldtree code and created new foldtree
likely to cause integration test changes in depending protocols
transformed pose into membrane first instead of computing membrane from topology, this is much more correct because the center and normal search depends on it
= TransformIntoMembraneMover:
removed the option of optimizing the embedding within the mover, this is much cleaner and doesn't lead to circular calling of OptimizeMembraneMover and TransformIntoMembraneMover
= TranslationRotationMover:
added checks
= integration tests:
added normalize_to_thk flag to integration tests!
added integration test for mp_interface_statistics
added integration test for mp_transform_optimize
added integration test for visualizing embedding
Apps
= mp_transform:
debugged version where the membrane position is optimized in addition to just transforming it into the default membrane this is now not in JD2 any more because the protocol differs and I need to access MEM after optimizing the membrane this also depended on leaving optimization and transformation more or less independent
= helix_from_sequence:
removed option to optimize embedding, was incorrect and will be added back soon
integration test changes: mostly cosmetic, otherwise expected