Merge pull request #3923 from RosettaCommons/JackMaguire/FinallyFixAddsan
Fixing Multistage Rosetta Scripts' failed addsan test. Thanks to @roccomoretti for the review!
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3839 from RosettaCommons/lqtza/scs_blast_updates_for_auto_db
Enable use of new antibody database (lives in additional_protocol_data).
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3938 from RosettaCommons/vmullig/no_thread_local
Replace an instance of thread_local with THREAD_LOCAL.
The thread_local keyword is not supported by all compilers. We use a custom THREAD_LOCAL macro which is defined as thread_local in those compilation environments that support the keyword, and as nothing in those that do not.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3934 from RosettaCommons/tjbrunette/mac_clang_junc_filter_fix
fixes issue with mac clang test that wasn't tested by the standard tests
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3932 from RosettaCommons/tjbrunette/revert_junc_filter_revert_v2
Tjbrunette/revert junc filter re-reverts code that was previously committed a week ago. I fixed the RNA_design app that was commented out. I should have caught this during the first commit.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3874 from RosettaCommons/JWLabonte/kinases/GSK3B
Kinases: adding 1st example of a phosphorylating EnzymaticMover
This merge adds a new EnzymaticMover to Rosetta to simulate phosphorylation of Poses.
Theses changes also take better advantage of inheritance to simplify code further and set-up the EnzymaticMover framework to use the command-line options system and RosettaScripts.
Full documentation of EnzymaticMovers is now posted here:
https://www.rosettacommons.org/docs/wiki/rosetta_basics/structural_concepts/EnzymaticMover
All unit tests pass. glycosylation integration test changes are expected.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3914 from RosettaCommons/jadolfbr/rs_output_fix
Enable a change to only have the ParsedProtocol mover of RosettaScripts rescore the pose at the end of a protocol only if the output tag instead of obliterating the energies entirely by default.
After much discussion, the pose is only rescored if you tell it to.
Vikram K. Mulligan 5 years I love this commit message. I take it to mean, "The pose is only rescored if you have a long discussion with it, in which you tell it to rescore itself." :P
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.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3925 from RosettaCommons/BYachnin/fix_buns_reporter_handling
The documentation and code comments for the BuriedUnsatisfiedHBonds filter loudly state that if no reporter behaviours are selected, `report_all_heavy_atom_unsats` will be set to true by default. If we actually run it this way, though, it returns 911. I've changed the default behaviour in parse_my_tag, and also in the compute function, as a fallback for PyRosetta/C++, to act as though `report_all_heavy_atom_unsats` is set to true.
The ppi_v3_suiteA tests will fail. These tests were using the BUnS filter using the default settings, and getting the "911" result for the error case of now reporters being set to true. This is now corrected, with a reasonable value being output as the BUnS result. Other test failures appear to be timeouts or unstable.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #3924 from RosettaCommons/tjbrunette/junc_filter
fix issue with rna_design uncommented. This code makes hbnet compatible with silent files. Thus the integration test change for hbnet. Also, this includes bug fixes for loop closure, and structProfile.
notify author
notify list [rosetta-logs@googlegroups.com]