Merge pull request #5962 from RosettaCommons/vmullig/fix_unit_test_breakage_from_packer_change
Fix unit test breakage, and restore skipping of final temperature jump in packing
This reverts pull request #5960 to restore pull request #5920, and fixes the unit test failure in the process.
TODO:
- [x] Fix failure in `AntibodySeqDesign:test_normal_tf_generation` unit test. --> A UTracer can simply be updated. The difference is likely a trajectory difference.
Merge pull request #5916 from RosettaCommons/vmullig/fix_new_macos_errors
Fix issues flagged by latest clang on MacOS
The new version of clang on MacOS flags a bunch of issues in the code. Fixing these so that I can finish pull request #5915.
Merge pull request #5880 from RosettaCommons/revert-5869-davidesala/CCM_release
Revert "documentation improved"
Reverts #5869
This broke most unit and integration tests, since the XSD no longer generates properly. @davidesala, after this reversion is merged, please create a PR to revert this reversion (you can do that through the Github web interface), pull that branch, fix the problem in the branch, and run full tests before re-merging.
Merge pull request #5693 from RosettaCommons/roccomoretti/update_submodules
Update various submodules
The assorted submodules have accumulated additional commits in their master branches versus their state in the main repo. Update the various submodules to their most recent master branch status.
(Submodules for build & PyRosetta build weren't touched -- it's assumed that they're at the state they're supposed to be.)
Merge pull request #5769 from RosettaCommons/vmullig/generalize_virtual_residue
Generalize the virtual residue patch.
Currently, the protein virtual residue patch is special-cased for each amino acid type, and doesn't support terminal types. This is silly. We have a `VIRTUALIZE_ALL` `PatchOperation` (which is used for RNA); we might as well use it for everything.
Tasks:
- [x] Switch patch to use `VIRTUALIZE_ALL`.
- [x] Rename patch from `VirtualProteinResidue` to `VirtualResidue`.
- [x] Ensure the `VIRTUALIZE_ALL` `PatchOperation` also zeros the net formal charge.
- [x] Unit test to confirm that this lets us virtualize all residues in a pose.