Merge pull request #2919 from RosettaCommons/aleaverfay/fix_features_integration_test
fix currently-failing features integration test
Putting the output name for the job into the Pose. Perhaps this is the appropriate way to deliver the job name to a Mover instead of through parse_my_tag. There seems to be a good amount of code already for grabbing the JOBDIST_OUTPUT_TAG scattered through the code base.
In my aleaverfay/revive_resource_manager branch, I had started down a path that would transmit currently-running-job information to Movers via parse_my_tag by putting strings into the DataMap. This would require, however, re-parsing a Mover for each job, and that has its own disadvantages. Putting the data into the Pose, however, seems like a fine way to get this done. I'm thinking this stopgap fix will migrate downward into the StandardJobQueen's pose_for_job() method.
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Merge pull request #2914 from RosettaCommons/vmullig/fix_betanov16_warning
Correct warnings in the rotamer library parser for canonical talaris and beta_nov16 libraries.
The warnings issued by the parser are currently inaccurate. Updating them for the beta_nov16 and talaris libraries.
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Merge pull request #2918 from RosettaCommons/jaumebonet/quickfix
fixed RmsdFromResidueSelectorFilter naming and behaviour in homodimer_fnd_ref2015_memb in integration test
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Merge pull request #2888 from RosettaCommons/jaumebonet/nubinitio
FoldFromLoops2.0 protocol
Vikram K. Mulligan 7 years Note: this commit broke the core:NMerSVMEnergyTests:test_eval_energy unit test in the gcc compliation (but not for other compilers). The unit.addsan test is also finding issues with this unit test, now.[list]
Vikram K. Mulligan 7 years Edit: I just saw Stephen Lewis' e-mail to the devel list. This issue is known to Indigo and Stephen, and is likely not caused by this particular commit. They are working to address it.[list]
Vikram K. Mulligan 7 years *Steven Lewis. Apologies, Steven -- there's a Canadian politician named Stephen Lewis.
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Merge pull request #2908 from RosettaCommons/roccomoretti/fix_movemapfactory_jump
Fix MoveMapFactory XSD
There was a mismatch between parse_my_tag and provide_xml_schema regarding jump/jumps, as well as misleading information about defaults.
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Merge pull request #2899 from CyrusBiotechnology/for_commons/indigo/nmer_refactor
From @indigogo at Cyrus.
* new unit test for core/scoring/methods/NMerSVMEnergy, the scoring method used for tcell epitope prediction. unit test just compares epitope predictions for rosetta's idealized trpcage pose
* refactoring of all 3 tcell epitope scoring terms (NMerSVMEnergy,NMerPSSMEnergy,NMerRefEnergy). no functional changes, just added full constructors like I should have done in the first place, also some new functions to extract model energies before everything is summed/averaged into total residue energy
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Merge pull request #2855 from RosettaCommons/vmullig/fix_adams_rotamer_order_issue
Fix issue with rotamer libraries that put rotamers in a wonky order.
The rotamer code assumes that rotamers are listed in rotlib files in order from lowest chi to highest (with chis defined on `[0,360)`). Unfortunately, not all NCAA rotamer libraries do this, which creates big problems with interpretation of the libraries. This pull request aims to eliminate this requirement for the rotamer order. Kudos to @atom-moyer for identifying the cause of the problem.
<b>EDIT:</b> This ended up requiring implementation of a new Voronoi-inspired method for determining the nearest rotamer well centre for noncanonicals. I _think_ that ```fa_dun``` scoring now works correctly for all noncanonicals.
Pull request #2887 should be merged before this one --> DONE.
Tasks:
- [x] Add unit test for equivalence of scoring of DAB with rotamers in the original order or in the corrected order.
- [x] Confirm that this _fails_ prior to making any code changes.
- [x] I'm going to rewrite rotamer library parsing, since that function's a mess.
- [x] Add a rotamer library parsing class.
- [x] Reproduce existing functionality, but in separate read, analysis, and configuration steps.
- [x] Use an instance of this class for parsing.
- [x] Fix unit tests broken by this refactoring.
- [x] Add a correction step between initial read and subsequent configuration of the rotamer library object in memory:
- [x] Check the rotwell assignments that were in the rotamer library file, and ask whether they are acceptable.
- [x] If not, figure out a remapping that makes them acceptable.
- [x] Apply the remapping globally (so if bin 1, chi 2, rotwell 3 used to correspond to bin 2, chi2, rotwell 3, and now rotwell 3 is rotwell 2, it remains true that bin 1, chi 2, rotwell 2 corresponds to bin 2, chi 2, rotwell 2).
- [x] Throw an error if no consistent remapping is possible (_i.e._ the numbering in the rotamer library wasn't just jumbled, but was actually inconsistent).
- [x] Revisit this and fix the sort logic.
- [x] Confirm unit test now _passes_.
- [x] Confirm that I haven't broken anything else.
- All other noncanonicals (TRP:N_methylation, peptoid 601, _etc._) seem to load properly.
- [x] The Dun02 rotamer libraries now fail to load, due to inconsistent rotamer well ordering. --> fixed by hard-coding an exception for the canonical Dun02 libraries.
- [x] Check the integration test changes. Are the NCAA rotamers as good or better?
- [x] Beauty.
- [x] Add an override that allows skipping the high-stringency check. It's probably too conservative in some cases.
- [x] Fix N-methyl tryptophan problem.
- [x] Fix beta-amino acid problem.
- [x] Add test for peptoids.
- [x] Add test for oligoureas.
- [x] Add a D-oligourea test.
- [x] Fix issue with D-residues.
@atom-moyer @twcraven @dougrenfrew @everyday847
Rocco Moretti 7 years Are the error/warning messages on the validate_database integration test overzealous? You have warning for beta/talaris which are probably not warranted. (I'd also argue the "canonical rotamer file for the old Dunbrack2002 libraries" warning should be suppressed if the person is explicitly asking for -restore_pre_talaris_2013_behavior
Vikram K. Mulligan 7 years I'd be inclined to keep the warning with the "-restore_pre_talaris_2013_behavior" flag, since it's good to know what all is affected when using a non-recommended flag. I had missed the warnings that occur with beta_nov16, though -- I hadn't realized that that scorefunction uses Dun02-formatted rotamer libraries. I'll open a pull request to remove the warning in that case.
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Merge pull request #2907 from RosettaCommons/everyday847/xcode_triage
Xcode project triage
I even tried removing werror just for this build type and the uses of pthread.h in cppdb (not cifparse, whoops) were still causing problems. (It complains that an annotation that pthread.h uses, Nullable, is a clang language extension.) So this is not a particularly resolvable error, I think? Or maybe we need to package our own pthread.h with that specifier removed...
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Merge pull request #2901 from RosettaCommons/vmullig/override_pseudobonds
Adding option to skip detection of pseudobonds.
Needed for certain peptide workflows. Note that this does not alter any default behaviour of Rosetta: pseudobond auto-detection is still on by default. It just lets us turn it off in the very unusual cases in which we have strange input files, for which the automatic pseudobond detection creates problems. (It's an "expert setting" in that sense, intended to be used only by those who know what they're doing in very rare cases.)
Tasks:
- [x] Add the option.
- [x] Have it do something.
- [x] Documentation.
- [x] Beauty.
@csykang
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