Merge pull request #5417 from RosettaCommons/vmullig/fix_unused_value_werror
Fix unused value error flagged by clang-analysis test. This is a minor, one-line fix.
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Merge pull request #5415 from RosettaCommons/BYachnin/mhc_epitope_citation_info
Update MHCEpitopeEnergy Citation Info
This PR add the citation information for the recently published MHCEpitopeEnergy paper. In addition to adding the citation to the database and registering the EnergyMethod and Constraint Mover with the CitationManager, this also adds functionality to the MHCEpitopeEnergySetup class to automatically register MHCEpitopePredictors with the CitationManager when they are used, provided that they include citation information. I have essentially tried to replicate how this is handled for Movers, etc.
Integration test failures due to added citations and changes to the database are the expected cosmetic changes.
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Merge pull request #5400 from RosettaCommons/vmullig/add_constraint_output
Add means of dumping trRosetta constraints and other constraints to CST files.
Thanks to @danpf for the review.
This pull request adds a simple metric for recording all the constraints in a pose or selection in a format matching that used by (non-enzdes) constraints files. It also adds a flag to the trRosetta app so that trRosetta constraints can be written to disk if one so desires.
- [x] Pull request #5411 must be merged before this one.
TODO:
- [x] Add a `ConstraintsMetric` simple metric, which writes out all the constraints in a pose or selection.
- [x] Write `ConstraintsMetric::calculate()`.
- [x] Write `ConstraintsMetric::parse_my_tag()`.
- [x] Write `ConstraintsMetric::provide_xml_schema()`.
- [x] Write `ConstraintsMetric::provide_citation_info()`.
- [x] Support for residue selectors.
- [x] Unit test.
- [x] Integration test.
- [x] Add a way to read in spline functions in a single line.
- [x] Document this.
- [x] Add documentation for ub_function and lb_function.
- [x] Add a way to write out spline functions in a single line.
- [x] Unit test comparing read-in constraints to written-out constraints.
- [x] AtomPair / Harmonic.
- [x] AtomPair / Spline.
- [x] Angle / CircularHarmonic.
- [x] Angle / Spline.
- [x] Dihedral / CircularHarmonic.
- [x] Dihedral / Spline.
- [x] Add a flag to the trRosetta app to dump out trRosetta constraints to a file.
- [x] Add a flag to the trRosetta app to skip structure prediction phase.
- [x] Integration test for above two flags with trRosetta app.
- [x] Beauty.
- [x] Documentation: provided in RosettaCommons/documentation#45.
Note: this simple metric can probably replace the `CstInfoMover`, which predates our simple metrics framework. We might want to deprecate that mover (with a suitable deprecation message pointing users to this simple metric) once this is in.
@jkleman
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Merge pull request #5399 from RosettaCommons/roccomoretti/integration_test_python2
Don't crash integration.py if Python2 not found.
In integration.py, don't hard-fail if Python2 is not available.
Obviously, any integration test which requires Python2 won't work, but at least any other tests being run won't be affected.
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Merge pull request #5412 from RosettaCommons/alamo/FixDerivativesDEEREnergy
Fixing a bug that causes DEEREnergy.cc to crash during derivative calculations
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Merge pull request #5411 from RosettaCommons/vmullig/add_constraint_metric_incremental_merge_1
Incremental merge 1 for the ConstraintsMetric
To get this working with trRosetta, I need to add a way to read in and write out spline functions in a single line. I'll continue to do that in pull request #5400, but for now the basic functionality of the `ConstraintsMetric` should work. So that can be merged here.
This PR:
- Adds the ConstraintsMover, which summarizes the constraints in a pose or sub-region, in CST file format.
- Adds a unit test.
Before merging I'll:
- [x] Add documentation --> DONE.
- [x] Fix serialization.
- [x] Add integration test.
@jkleman
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Merge pull request #5173 from RosettaCommons/sarahbiehn/depc_ms
Score term depc_ms to reward residues based on diethylpyrocarbonate covalent labeling MS data
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Enable setting specific dihedral constraint angles in DihedralConstraintGenerator (#5402)
This adds code that should make it simple to set the dihedralconstraint angle when using the DihedralConstraintGenerator.
Simple stuff, few variables, getters/setters.
Currently if dihedral reference and dihedral angle is set, it defaults to dihedral reference and warns the user
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Merge pull request #5407 from RosettaCommons/JackMaguire/FilterValueMetric
This PR adds FilterValueMetric to the SimpleMetric init files and inserts it into an existing integration test. We also fixed a bug when parsing the filter xml tag.
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