Merge pull request #3863 from RosettaCommons/roccomoretti/hush_unit_tests
Turn down noise in muted unit tests
Some of the unit tests are printing too much info to stdout when muted (ideally should be none). Adjust the tests such that they don't print anything when muted.
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Merge pull request #3849 from RosettaCommons/JackMaguire/UpdateOverrides
Renaming shadowed variables.
Part 1 of 3-ish PRs to allow Rosetta to compile with the -Wshadow flag.
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Merge pull request #3844 from RosettaCommons/JWLabonte/PDB_IO
PDB IO: Smarter Title Section generation
This merge will deal with two requests that I have received following PR #2468.
- An option, `-write_pdb_title_section_records`, is provided, which may be set to false by those who wish to skip any title section at all in their `.pdb` files.
- A framework is set up to have Rosetta write `REMARK 3` records instead of `REMARK 220` records, if the `Pose` contains crystal density. (This will not work fully until PR #3627 is merged.)
It also corrects the output of parametric data, forcing it to use `REMARK 250` records for output.
All integration test changes involve the change in Crick parameter output, as expected. All other tests pass that weren't already seriously broken. (Someone(s), please fix!)
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Merge pull request #3854 from RosettaCommons/JackMaguire/UnorderedSets
Sergey gave us advice at Winter RosettaCON to decrease the max_load_factor of our unordered_sets and unordered_maps from the default value of 1 to 0.7-ish to make lookups faster. We don't have many unordered containers in Rosetta but I found a handful that could benefit from this change.
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Merge pull request #3833 from RosettaCommons/sergey/binder
PyRosetta update
- [x] updating logic of `--external-link` option so it only allow linking to libraries compiled with PyRosetta build options, this should prevent `off-by-22` runtime error
- [x] Updating teaching module imports.
- [x] Updating Binder.
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Merge pull request #1802 from RosettaCommons/JWLabonte/sugars/glycomutagenesis
Shotgun Glycomutagenesis
This merge will introduce an application for shotgun glycomutagenesis, using the `GlycosyltransferaseMover`.
It depends on PRs #1786 and #1537.
The code is hacky, in my opinion, but that's why it's a pilot app, not a public app. I also need some of the underlying `EnzymeMover` code in master so I can complete and expand it for other PTMs for my student's research.
This merge also fixes a bug in which `-no_pro_close_ring_closure` was turned on by default when `-include_sugars` was on. (I think we do want `-no_pro_close_ring_closure` on ultimately, but only once we ensure that the other ring close method is being used as well.)
Because of the bug fix, all tests using the `-include_sugars` flag will have minor scoring differences. The unit test timeouts are a known major issue unrelated to this PR.
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Merge pull request #3797 from RosettaCommons/jadolfbr/sm_in_pyrosetta
This Address #3777 - getting SimpleMetrics to work seamlessly in PyRosetta
This PR makes `pose.scores` work by accessing the `ScoreMap` 'class' directly instead of individual extra scores functions. Unit tests for this functionality are added to the PyRosetta unit testing framework, as well as additional tests for SimpleMetrics in C++ testing framework. The `ScoreMap` itself is now unit tested to work with SMs and an additional clear function has been added to the `SimpleMetricData` class.
This PR also deprecates the old-style PyRosetta score file, which was ALWAYS bad and too different from C++ Rosetta scorefile output to be of much use in general protocols. If one tries to use the old-style format, we exit with a helpful message.
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Merge pull request #3848 from RosettaCommons/yingyue0414-patch-1
This merge corrects the beta-D-Altropyranose conformation in `source/test/core/chemical/carbohydrates/stereochem_test.key` and adds `to2-beta-D-Altp.params` to test the change.
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