Merge pull request #5541 from RosettaCommons/vmullig/fix_unused_using_decls
Removing unused "using" declarations that clang-tidy was complaining about.
This should fix the clang-tidy tests.
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Merge pull request #5534 from RosettaCommons/vmullig/simple_cycpep_disulf_bug
Fixing little bug in simple_cycpep_predict application with terminal disulfides.
Previously, we were forcing the last disulfide residue to be the last residue. This is unnecessary.
The error was actually in native import, which I had neglected to test in the existing integration test. I've added another test that checks that this works.
One integration test is added by this PR, resulting in an expected red light on the integration tests.
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Merge pull request #5489 from RosettaCommons/vmullig/safer_binary_decoding
Revise utility::decode6bit() to avoid memory overruns
The function `utility::decode6bit()` accepts a pointer to a memory location and a string, decodes the string (converting every 4 characters into 3 bytes of arbitrary binary data), and populates a contiguous block of memory starting from the address stored in the pointer. There is no check that the memory that is overwritten is able to receive the data in question, and it's quite possible to run over the boundaries of a vector (especially if the vector length doesn't line up nicely with the 4 bytes of string per 3 bytes of data storage scheme). This PR alters the function signature so that it accepts a third input, the container size (in bytes), and refrains from writing beyond the container. While I don't think this fixes any existing bug (though it might -- it's hard to be 100% certain that there weren't cases in which container overruns were occurring), this does help to prevent mistakes in new code that calls this function. (I ran across this in the `vmullig/qpacker_benchmark` branch, pull request #4011, where I _was_ writing beyond the bounds of my vector and corrupting memory.)
DONE:
- [x] Teun's suggestions:
- [x] Update `/// @brief` for `encode6bit()`.
- [x] Add unit test.
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Merge pull request #5463 from RosettaCommons/roccomoretti/fix_test_residue_summary_metric
Fix test_residue_summary_metric for individual running.
The SimpleMetricTests:test_residue_summary_metric was relying on other test functions in the class for setting up the pose.
While this happened to work for Suite running, if you ran just the single test, then it failed.
Adjust it to properly set up the pose, independent of the other tests in the class.
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Merge pull request #5499 from RosettaCommons/roccomoretti-patch-1
Include Fixes for SplineFunc.cc
SplineFunc.cc has issues during compilation on some computers. (std::abs() issues) Adding a system header seems to fix it.
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dock pdb into density app (#5053)
This is one of the apps I've made as part of my thesis project.
it's purpose is to dock a pdb file, or ensemble of pdb files, into density and report back the ones that best fit the density
currently i've called it dgdp for density guided domain placement, but that's sort of a strange name. maybe I'll just take over frank's pilot apps name (dock_pdb_into_density)
It unfortunately overlaps with the DockIntoDensityMover a lot, but its differences are:
it can be parallelized much more
(which is necessary when docking large poses into density, otherwise one pdb can take 1+ days).
there are important differences in the ways clustering is performed
things are clustered not at the "point level" but rather over all points
different mapresolutions are used during different stages to obtain more accurate density scoring.
there is native checking implemented for multiple natives (ie multiple copies of the same chain in the complex)
it also comes with a python script that manages the job distribution on a Slurm cluster (although I will add an option to run it locally)
add documentation
test script
add some integration tests
review the code and see what crazy things I was doing 4 years ago
can confirm it's crazy
change fragment docker name to dockfragmentmover
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CartesianSampler option documentation/cleanup (#5394)
Have used this for a long time but realized many of my assumptions were wrong due to the lack of option docs.
Hopefully I can help future people, or future me by fixing them.
dump_pdb/dump_pdb_tag -- this just dumps a pdb at the beginning of the mover before anything happens. I don't think this is necessary.
removed an unused movemap that is instantiated for no reason
add some clarification to some options (aka remove some XRW_TODO)
update some new to make_shared
also updates the CartesianSampler to not apply frames across pose chains ( I think this is correct -- Cartesian sampler should be able to fix a chainbreak, (ie if C and N are too far away) but in that case rosetta will think the chains are the same)
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Merge pull request #5502 from RosettaCommons/jkleman/sciben_2021july_fixes
some small updates to scientific tests: renaming mp_f19_energy_landscape to mp_f19_tilt_angle, updating command.py and removing dock_glycan because it's now a legacy test
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