Merge pull request #3508 from RosettaCommons/roccomoretti/update_scibench_data
Update benchmarking data submodule.
Update to most recent (submodule) master.
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Merge pull request #3511 from RosettaCommons/roccomoretti/clang7_updates
Clang 7 fix.
A new warning in Clang 7 pointed to a potential bug in DihedralDistanceMetric.
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Merge PR #3492 (aleaverfay/jd3_fix_mpi_hang_in_distributed_output2)
Fixing a race condition in the way JD0 sent spin-down signals to remote nodes at the very end of a trajectory. Previously, JD0 would tell any node to spin down after that node had completed outputting the last result it needed to (i.e. and there were no more results to output), including the archive nodes. However, if an archive node spins down, then it can't serve up the results that the worker/output nodes might be requesting. If a worker/output node requested a job of the archive after it had spun down, it would simply hang waiting for a reply.
This is a particularly poor moment in a job for results to get lost: they've already been generated, all the computational cost of creating them has been paid!
The solution is to delay spinning down the archive nodes until after all of the worker/output nodes have reported that they have completed their work. Super simple.
There is a new unit test that a) works in the new code, and b) fails in the old code. In particular, the unit test ensures that the spin-down signal to the archive is sent after the spin-down signal to the worker/outputter. To verify that the unit test fails in the old code yourself, you can cherry pick 674b9a66e on top of dc1c89dea8. (In order to run the JD3WorkPoolJobDistributor unit tests, you need to use the debug + serialization build).
I should definitely have looked into this more closely months ago when @thieker brought it to my attention!
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Merge pull request #3475 from RosettaCommons/orlypolo/change_default_dslf_energy_threshold
change default value for max_dslf_energy in DisulfideInsertionMover
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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.
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Merge pull request #3496 from RosettaCommons/sergey/binder
Updating Binder submodule. This should fix PyRosetta build issues when build with Apple Clang v10 and when building with GCC on Ubuntu.
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Merge pull request #3486 from RosettaCommons/bcov/RotamerSetsOperation2
Adding RotamerSetsObjects framework and the first one: PruneBuriedUnsatsOperation
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Merge pull request #3489 from RosettaCommons/roccomoretti/enzdes_benchmark
Convert enzyme design benchmark to new scientific benchmarks server setup.
It's not exactly the same as the old enzdes_benchmark, as I've converted it to use rosetta_scripts (versus the pilot app it was using), updating it to use ref2015, as well a supplementing things with new recovery metrics.
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Merge pull request #3477 from RosettaCommons/vmullig/simpler_polylinear_interpolation
Actually correct "as-angles" polylinear interpolation
For peptoids and N-methyl amino acids, we need the polylinear interpolation used to interpolate well centres to work near the -180/180 wraparound point. Andy and I scratched our heads for a long time about little numerical problems that we were seeing in the derivatives with his approach from pull request #2851. In the end, we decided that, since the goal was to avoid weird behaviour at the wraparound point for interpolated angle values, we could achieve that just as easily by much simpler means. The basic approach here is:
- Determine if the values being interpolated are generally closer to 0 or to the 180/-180 discontinuity.
- If the former, interpolate as values.
- If the latter, shift into the [0,360) range, interpolate as values, then shift back to (-180,180].
~~This might break down if unusually extreme values are being interpolated, but then, interpolation isn't well suited to really extreme cases.~~
**UPDATE:** This _was_ breaking in cases relevant to peptoids, so I went back and implemented an _actually_ correct N-dimensional polylinear interpolation scheme. The new approach uses a recursive function that carries out a series of evaluations for successively lower dimensions. The 1-dimensional interpolator avoids the 0/360 or -180/180 angle discontinuities by using the shortest interpolation between two values, as described above; since higher-dimensional interpolators call the 1D interpolator, they also handle the discontinuity properly.
Tasks:
- [x] Implement the interpolation
- [x] Check whether it solves the remaining problems in the peptoid branch (#2513).
- Not all of them. But that's okay -- it's a start.
- [x] Check that this works with the lysine Dunbrack test cherry-picked from closed pull request #2851.
- [x] Shorten this test.
- [x] Check additional unit tests pulled from that branch.
- [x] Check what this does to canonical scoring. I may have to special-case the N=2 case.
- I think we're okay. The generalization covers the N=2 case correctly.
- [x] Beauty.
- [x] Documentation.
So there are a bunch of integration test trajectory changes from this branch, but no changes to scoring and no unit test failures. This tends to happen when one refactors Dunbrack or other core scoring code. Andy and I have both looked at the integration tests, and we're both pretty convinced that the failures fall into one of two categories:
- Very tiny numerical differences that accumulate, since we're doing some math in a different way.
- Changes to exotic noncanonicals that we actually expect (since we're interpolating Dunbrack libraries that rely on more than two mainchain torsions properly, now).
**SO EXPECT A BUNCH OF INTEGRATION TEST CHANGES, IF YOUR TEST DOES PACKING OR MINIMIZATION AND USES FA_DUN.**
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Merge pull request #3429 from RosettaCommons/JackMaguire/BlosumTO
This PR does two things:
- Adds a XML tag interface for Jared's ConservativeDesignOperation
- Includes rosetta_scripts integration test for ConservativeDesignOperation
- Creates a SimpleMetric that measures Sequence similarity
- Includes two small unit tests
- Added this metric to the simple_metrics integration test
Thanks to Jared for the review and Sergey for the binder fixes
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