Merge pull request #3726 from RosettaCommons/georgkuenze/fix_nmr_code_quality_issues
Fixing some uninitialized and unread variable errors in RosettaNMR code which were not detected in my previous commit to master.
Merge pull request #3658 from RosettaCommons/JackMaguire/MCHBNetSymmFix
Shane Caldwell recently showed me a case where MC HBNet was unable to handle a symmetric pose because of the existence of an additional pure-virtual chain. With this PR, MC HBNet now has bounds-checking to make sure that it does not interact with chains that are not considered subunits.
Thanks to Scott for the review.
Merge pull request #3641 from RosettaCommons/vmullig/fix_simple_cycpep_predict_issues
Fix a couple of problems with simple_cycpep_predict
This pull request fixes a trivial issue with output logging with simple_cycpep_predict. It also seeks to track down and correct a problem seen on the NYU cluster with a double free or corruption error, but I haven't yet been able to reproduce that. This seems only to affect the multi-threaded behaviour, and has only been observed with an icc build.
Edit: I'm just going to merge these cosmetic changes now, and will open a new PR if and when I track down the double free or corruption error.
Revert PR 3390 "mhc_epitope scoreterm, a flexible, packer-compatible deimmunization scoreterm"
Revert "mhc_epitope scoreterm, a flexible, packer-compatible deimmunization scoreterm"
One of the release mode unit tests is failing, so we're revert the PR until we can figure out why that is and what to do about it.
Merge pull request #3564 from RosettaCommons/vmullig/fix_signed_char_issue
Fixing an issue with assignment of -1 to a char
According to the C++ standard, the `char` type can be signed or unsigned -- it's up to the implementation. We have a spot in the Rosetta code where -1 is assigned to a `char`, and although that's fine for compilation on most systems, it breaks the Blue Gene/Q build. (It also likely breaks Android builds -- they also tend to default to `char == unsigned char`.) The simple fix is to declare this `char` to be `signed` explicitly.
In general, if you assign numeric values to a `char` or do math other than just incrementing or decrementing, it's a good idea to make it explicit whether you're working with a signed or unsigned `char`.
Merge pull request #3543 from RosettaCommons/sergey/f2
Updating nlohmann/json library to 3.3.0. This should enable JSON support in GCC v4.8+ and fix PyRosetta GCC build
Merge pull request #3529 from RosettaCommons/bcov/FixApprox2
Fixed bug in approximate_buried_unsat_energy where packing with 0 rotamers caused a freeze
Merge pull request #3520 from RosettaCommons/orlypolo/change_default_dslf_energy_threshold
Change DisulfideInsertion test to allow a more linient threshold for …
Merge pull request #3500 from RosettaCommons/vmullig/fix_selection_warning
Removing a spurious warning when the last residue in a pose is selected.
Currently, when the last residue of a pose is selected by index, there's a spurious warning printed to the tracer about the selection being outside the range of residues in the pose. This is due to a ">=" comparison that should have been a ">" comparison. This fixes that.
Merge pull request #3485 from RosettaCommons/jadolfbr/minor_updates
IAM bugfix and add job_tag option to ProtocolSettingsMetric
This PR has a few minor fixes and changes:
- Fixes IAM for a test case that @aleaverfay had. It also adds this test case as an integration test.
- Fixes scoretype setting in `PerResidueEnergyMetric` and adds the option to `TotalEnergyMetric` (which may now need to be renamed) @teetsf Both are now tested in integration tests.
- Adds a better description of custom_type option and updates RMSDMetric docs. @roccomoretti
- Adds an option, `job_tag` that basically passes a string to the score file. This is really useful for rosetta_scripts_JD3 to tag the job name in the scorefile to make it easier to concat and analyze.
Adding a residue selector that applies to native poses
I'm adding a residue selector that wraps around another residue selector and applies it to the native pose instead of the given pose.
You can read more about it here: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/ResidueSelectors/ResidueSelectors#other_nativeselector
Thanks to @jadolfbr for the review and @roccomoretti for tips/comments