Merge pull request #5326 from RosettaCommons/jkleman/SciBen_small_fixes
Jkleman/sci ben small fixes: mostly cosmetic changes to PDFing, readme's, citations, etc. Cutoff's for FlexPepDock changed according to the paper (as per Ora). Ligand docking: removing betaNov16 and talaris for ligand docking regular runs and using PDB files instead of zipped ones to increase compression according to Sergey.
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Merge pull request #5346 from RosettaCommons/vmullig/more_verbose_tensorflow_error
Make a Tensorflow error message more verbose to aid debugging
Once in a while, I'm seeing a failure in the Tensorflow tests (_e.g._ https://b3.graylab.jhu.edu/sub-test/224304352), in a piece of code that combines a vector of N-tensors into an (N+1)-tensor. This _might_ be due to float-float comparisons (and I hope that's all it is), but I would have thought that `memcpy` would guarantee that float-float comparisons would be valid. For this reason, I'm going to make the error messages more verbose so that we can see for ourselves what's going wrong when this test fails on the test server.
@JackMaguire
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Merge pull request #5340 from RosettaCommons/vmullig/fix_trRosetta_valgrind_test
Trying to fix failing Valgrind trRosetta tests.
I think I have a little mistake in the test scripts. This does indeed fix the Valgrind test.
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Merge pull request #5333 from RosettaCommons/vmullig/fix_trRosetta_integration_test
Fix the trRosetta_test_predict_ubiquitin integration test in non-Tensorflow builds.
The non-Tensorflow version of the trRosetta_test_predict_ubiquitin integration test just checks that the trRosetta application exits with a suitable error message if Rosetta wasn't built with Tensorflow support. (The error message explains how to build Rosetta properly). To avoid spurious integration test changes, the test script uses `sed` to remove some lines that would change with each run. Unfortunately, on Macs `sed` doesn't work properly (one needs to install `gsed` for ordinary functionality), so the lines stay in and the test spurious fails every time it runs. This PR tries to fix that.
Other little things:
- This PR fixes a spelling mistake in the error message ("octothorp", not "octothorpe").
- This PR updates the documentation submodule to point to the latest master of the documentation repository.
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Merge pull request #5119 from RosettaCommons/vmullig/trRosetta_into_Rosetta
Put trRosetta into Rosetta to allow protocol development on top, and to provide access to Foldit
*Note: since incremental merges 1-3 are now merged (pull requests #5308, #5309, and #5314), this PR only adds the trRosetta application and puts an option in for the AbinitioRelax application to use trRosetta. Most of the files changed are unit test files (though they're in the integration test suite since we lack a dedicated unit test suite for the Tensorflow build.)*
This is something that we talked about a while back; apologies for only getting to it now. This PR aims to:
- [x] Add trRosetta to the Rosetta database. (Note: since the model is 91 MB, this has been added as a submodule that gets pulled automatically only if the `extras=tensorflow` or `extras=tensorflow_gpu` options are used). The trRosetta licence is the MIT licence, which is compatible with the Rosetta licence, and I've talked to Sergey, Ivan, and Jianyi to get their blessing for this.
- [x] Add hooks to the protocols layer for passing in the trRosetta inputs (sequences) and receiving back outputs (distance and angle constraints) as objects compatible with downstream Rosetta manipulation, tied in to the `RosettaTensorflowManager`.
- [x] Add a standard way of adding the constraints to a pose (a constraints generator).
- [x] CitationManager functions for constraints generator.
- [x] Add distance constraints.
- [x] Add phi constraints.
- [x] Add theta constraints.
- [x] Add omega constraints.
- [x] Options for adding each of these independently.
- [x] Options for controlling the probability cutoffs for distance, omega, phi, and theta constraints.
- [x] Documentation for options making it clear that "phi", "omega", etc. don't have their usual meanings, here.
- [x] Convert the Python minimization protocol to a Rosetta mover.
- [x] `parse_my_tag()` function.
- [x] `provide_xml_schema()` function.
- [x] `provide_citation_info()` function.
- [x] `apply()` function.
- [x] Fullatom refinement steps.
- [x] Compute RMSD to native.
- [x] Options for controlling the probability cutoffs for distance, omega, phi, and theta constraints.
- [x] Add settings for scorefunctions for the various stages:
- [x] Initialize from options system.
- [x] Initialize from XML.
- ~~Handle gapped FASTAs:~~ --> Put off to future PR, where I'll add residue selector support.
- ~~Check that the FASTA width _with_ gaps matches the MSA width.~~
- ~~Map constraints from MSA numbering to _ungapped_ FASTA numbering. (Need to set up a map for this.)~~
- [x] Add option of using trRosetta constraints in classic _ab initio_.
- [x] In fullatom phase as well.
- [x] Citations.
- [x] Documentation.
- [x] Add an app for running the trRosetta minimization protocol.
- [x] Suitable error if not compiled with `extras=tensorflow` or `extras=tensorflow_gpu`, with instructions for compilation. (Put code for writing the instructions in `basic::tensorflow_manager`.)
- [x] Fix compilation when `extras=tensorflow` is not used.
- [x] Check `tensorflow_gpu` performance. --> A quick test on my laptop shows about a fourfold speedup on the laptop GPU compared to the CPU.
- [x] Unit tests (pass/fail tests in `integration.tensorflow` suite).
- [x] Constraints generator.
- [x] Distance constraints.
- [x] Check error in distance constraints. It still seems higher than it should be. --> Little mistake fixed.
- [x] Phi constraints.
- [x] Theta constraints.
- [x] Omega constraints.
- [x] Integration tests:
- [x] RosettaScripts.
- [x] trRosettaProtocol mover.
- [x] Check why this does not output RMSD values. --> Fixed in pull request #5301.
- [x] Constraints generator.
- [x] trRosetta app.
- [x] With Ramachandran initialization.
- [x] With initialization by bins.
- [x] Classic ab initio app.
- [x] Make `hb_cen_soft` into an option that can be set from code/RosettaScripts.
- [x] Documentation --> RosettaCommons/documentation#44 adds documentation for the C++ trRosetta.
- [x] Beauty.
As a guide, here's what will ultimately be in master. The stuff in basic is already there. PR #5308 adds the stuff in protocols.2. PR #5309 adds the trRosettaConstraintGenerator. Once those are merged, the trRosettaProtocolMover, the trRosetta app, and the changes to AbinitioRelax are what remain.
Before merging this:
- [x] Revert change to `.vscode/c_cpp_properties.json`.
- [x] Pull request #4606 must be merged.
- [x] Pull request #4855 must be merged.
- [x] Pull request #5224 must be merged.
- [x] Pull request #5225 must be merged.
- [x] Pull request #5301 must be merged.
- [x] Pull request #5236 must be merged.
- [x] Pull request #5308 must be merged. This is an incremental merge that cherry-picks the `trRosettaProtocolBase` and `trRosettaProtocol_v1` classes from this one, along with their associated tests.
- [x] Pull request #5309 must be merged. This is an incremental merge that cherry-picks the `trRosettaConstriantGenerator` class from this one, along with its associated tests.
- [x] Pull request #5314 must be merged. This is an incremental merge that cherry-picks the `trRosettaProtocolMover` from this PR, along with its tests.
Note:
- Pull request #5235 is an efficiency tweak that will benefit the stuff implemented in this PR, but it does not have to be merged before this PR.
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Merge pull request #5271 from RosettaCommons/jkleman/SciBen_mpddg_sfxn_comp
* added sfxn comparison tests for membrane ddG
* updates sfxn comparison tests for docking
* fixed nstruct for fragment picking for more efficient running
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Merge pull request #5239 from RosettaCommons/bud-graziano/RosettaSurf
Merge ShapeSimilarity and ElectrostaticSimilarity metrics as part of the RosettaSurf protocol
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Merge pull request #5314 from RosettaCommons/vmullig/trRosetta_into_Rosetta_incremental_merge_3
Incremental merge #3 to get trRosetta into Rosetta
This is the third in a series of incremental merges to put trRosetta into Rosetta, to allow protocol development on top. This PR adds the trRosettaProtocolMover, a RosettaScripts and PyRosetta-scriptable mover that takes an MSA as input and produces a predicted structure pose as output (using the trRosettaConstraintGenerator and trRosettaProtocol, already merged into master, under the hood). The image below serves as a guide: everything below the trRosettaProtocolMover is already in master, this PR adds the trRosettaProtocolMover, and everything above it remains to be merged.
Although this PR changes 48 files, most of those are unit test files that were added. Note that for Tensorflow modules, the unit tests are implemented as part of our integration test suite (though they are pass-fail tests), since we have no unit test suite for the Tensorflow build.
This PR is intended to be merged before PR #5119.
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