Merge pull request #5186 from RosettaCommons/MentenAI/AxisCsts
This constraints the distance between an atom and the closest point to that atom on an axis. The axis is defined by two points, each of which are the midpoint of several AtomIDs. This should work with virtual atoms.
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Merge pull request #5168 from RosettaCommons/TENeary/sequence_symmetric_annealer_gcc_fix
Changed benchmark signature, updated methods and test to fix gcc unit test errors
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Merge pull request #5131 from RosettaCommons/jadolfbr/minmover
This is a basic PR to set the default MinMover mintype to what is currently the default across Rosetta.
Yes, there is more that could be done - including adding defaults to MinOptions to read from the options system, but I'm currently quite bogged down.
@teetsf found this issue while using the MinMover in code and not getting it to minimize as well as well as we had hoped and tracked it to the default mintype being used in MinMover.
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Merge pull request #5132 from RosettaCommons/roccomoretti/rs_single_quote
Enable RosettaScript parsing to allow single quotes on options
According to @mwfranklin on Slack, the XML validator is perfectly fine with `<ScoreFunction name='sf' weights='scorefxn.wts'/>`, but the Rosetta-specific Tag parser chokes on it, with a particularly obtuse error message.
Supporting single quotes is relatively straightforward.
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Merge pull request #4855 from RosettaCommons/vmullig/gcn_test
Add a test confirming that we can work with graph convolutional neural networks within Rosetta.
This tests the RosettaTensorflowManager with a graph convolutional neural network (GCN). I'll need GCNs shortly for peptides, and others have been applying these to proteins.
This PR also fixes a couple of off-by-one errors in the Tensorflow manager code.
- [x] ~~Pull request #4606 should be merged before this one.~~ --> ~~PR #4606 has been merged into this one, and both will be merged together.~~ --> At @JackMaguire's request, we'll reopen PR #4606 and merge it before this one to keep changes suitably incremental.
- [x] Conflicts with #4606 should be resolved before merging this, and `RosettaTensorflowSessionContainer::run_multi_input_session()` should be removed in favour of Jack's `RosettaTensorflowSessionContainer::run_multiheaded_session()`.
- [x] Add the test observers, description, etc.
- [x] Add a script to make the GCN (initialized with random weights).
- [x] Add the GCN to the Rosetta database. (Note: this is a few hundred kilobytes.)
- [x] Add expected output to the test directory.
- [x] Add a pilot app that loads the GCN, provides it with known inputs, and tests whether we get the expected output.
- [x] Exit with error status if the output does not match expected, within tolerance.
- [x] Fix bugs locally.
- [x] Check that this runs on the test server. It does!
- [x] Error if run in non-Tensorflow builds.
- [x] Beauty.
- [x] Fix `app_exception_handling` test in non-tensorflow build.
This PR also:
- [x] Updates the `tools` submodule to point at the latest master of that repo.
- [x] Removes an unused `RosettaTensorflowManager::set_session()` function. This function was unsafe, since it encourages creation of `RosettaTensorflowSessionContainers` (and Tensorflow sessions) by code external to the `RosettaTensorflowManager`. This prevents it from being a resource manager, and risks having things that it doesn't know about which compete for GPU access. (In any case, it probably wouldn't have been possible to use this, since the `RosettaTensorflowSessionContainer` class has a private constructor, and can only be constructed by the `RosettaTensorflowManager`.)
- [x] ~~Adds a `RosettaTensorflowSessionContainer::run_multi_input_session()` class method, for Tensorflow models that take multiple input tensors (possibly of different sizes or dimension). This is needed for graph convolutional neural networks, which are typically represented by two to three input tensors (the adjacency matrix, the node data tensor, and the edge data tensor).~~
- [x] TODO: switch to @JackMaguire's `run_multiheaded_session()` from pull request #4606. I've accidentally reinvented the wheel here, so I'll take my implementation out and use his.
- [x] Fixes an off-by-one error in some tensor accessors.
- [x] Updates the header-only Tensorflow C-API files from Tensorflow 1.14 (which can't read Tensorflow 2 models) to Tensorflow 1.15 (the most recent version of the C-API, which _can_ read Tensorflow 2 models). Note that I copied the new licence for 1.15 to replace the 1.14 licence, so there are some cosmetic changes to the licence file. (Tensorflow is Apache-licenced, and I previously checked with UW Comotion to ensure that we can include these headers.)
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Merge pull request #4525 from RosettaCommons/jkleman/SciBen_sfxns2
Jkleman/sci ben sfxns2:
scorefunction comparison for a handful of scientific benchmarks: docking, design, loop modeling, relax;
located in /Rosetta/main/tests/scientific/sfxn_comparison_tests/;
will NOT be scheduled like the regular scientific tests as these take a while to run;
will be scheduled about every 6 months;
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Merge pull request #5183 from RosettaCommons/vmullig/cite_symmdesign_paper
Update citations for symmetric design paper (was under review, now published).
This updates a citation listing in the database to include journal, volume, issue, page numbers, and DOI now that it's published. This is a minor change.
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Merge pull request #5182 from RosettaCommons/vmullig/update_rosettascripts_repo
Add NDM-1 design scripts to the RosettaScripts scripts repo, and update the submodule.
This adds the scripts used in **Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, Strynadka NCJ, and Baker D. (2020): Computationally-designed peptide macrocycle inhibitors of New Delhi metallo-beta-lactamase 1** to the RosettaScripts scripts repo, and updates the main repo to point at the current version of the scripts submodule.
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