Merge pull request #3913 from RosettaCommons/jadolfbr/glycan_no_inner
This merge holds a few changes and bug fixes for glycan modeling, antibody work, and simple metrics. Nothing too major.
1) Remove `AntibodyDesignProtocol`; make AntibodyDesignMover's parser interface more feature-complete with the command line. This simplifies the antibody design code into a single main mover, instead of two of them. Features from the protocol that were useful are added to the mover. Support for `get_additional_output` functionality is added. Removed some unused options.
2) Remove inner bb sampling from glycan modeling. This resulted in better energies, but reduced control of sampling time. Removing it.
3) Adding author tags to my parsable classes as we are moving towards full XSD documentation of most classes.
4) Make the `TotalEnergyMetric` work for different size reference poses as was originally intended.
5) Make a few carbohydrate tools into public apps as they are tested and now have public-facing documentation.
6) Simplify/Clean up Mover interface. No code changes, only the presentation and organization of Mover.hh as it was a mess. I can now read it. We really should remove the JD1 stuff from the base-class at some point. Perhaps through integrated DataMap functionality in the Mover base class?
7) Add better documentation for reference_pose XSD, instructing the user that this is created via a `SavePoseMover`.
8) Fix `RestrictToCDRsAndNeighbors` task op for camelid antibodies. Add unit tests for this and other antibody task ops for camelid antibodies.