Merge pull request #677 from RosettaCommons/rfalford12/change_default_normal2
Change membrane normal to be a unit vector by default
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Change the default membrane normal to keep unit length instead of normalizing to 15Å. This pull request accomplishes two main goals:
= Decouple the concept of the membrane normal, which represents orientation of the bilayer and the thickness of the bilayer. This is important for upcoming developments in the membrane representation
= Remove hardcoding of the membrane thickness throughout the code
An option is added to file_data.cc for outputting data for MEM where the normal is scaled to the thickness for visualization purposes only. To use this option, pass the flag -mp:output:normalize_to_thk. This change is now tracked by the mp_loadtime integration test.
This pull request preceeds another pull request that will completely remove core/conformation/membrane/types.hh to discoruage hard-coding and increase reliance on the MembraneInfo object.
Anticipated Test Changes:
Fingerprint Tests: No score changes, just prints the updated normal coords.
Unit Tests: Commits in this pull request update unit tests to check for a normal of unit length.
Integration Tests: Anticipated changes due to changed normal length. Coordinates change in mp_relax, mp_relax with ligand, mp_dock and mp_dock_setup. We have resolved this is due to an instability in the test server and not our code. mp_loadtime also changes due to the addition described above.
The following integration tests are expected to change: mp_loadtime, mp_relax, mp_relax_w_ligand, mp_dock, mp_dock_setup, mp_find_interface, mp_mutate_relax, mp_quick_relax, mp_score_jd2, mp_symdock, mp_symmetry_load, mp_transform
The documentation has also been updated to reflect this change here:
https://www.rosettacommons.org/docs/wiki/application_documentation/membrane_proteins/RosettaMP-KeyElements-MembraneRsd