Merge pull request #4164 from RosettaCommons/vmullig/polar_sasa
Adding options for measuring polar or hydrophobic SASA to SasaMetric.
Tasks:
- [x] Add option for polar SASA.
- [x] Add option for hydrophobic SASA.
- [x] Have these options do something.
- [x] Unit test.
- [x] Integration test.
- [x] Documentation --> Will be auto-generated, since SasaMetric and PerResidueSasaMetric rely on auto-generated XSD documentation.
- [x] Beauty.
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Merge pull request #4163 from RosettaCommons/vmullig/fix_count_cycpep_sequences_issues
Fix issues created by count_cycpep_sequences merge.
This fixes:
- The code_quality tests.
- Ubuntu compilation.
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Merge pull request #4169 from RosettaCommons/vmullig/fix_simple_cycpep_predict_rand_init
Fixing random number initialization in SimpleCycpepPredictApplication_MPI.
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Merge pull request #4156 from RosettaCommons/roccomoretti/tensorflow_test_noise
Silence noise in tensorflow tests.
Right now the tensorflow integration tests are red on the server because commit information is making it into the logs. Correct that.
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Merge pull request #4147 from RosettaCommons/vmullig/count_cycpep_unique_sequences
Add an app to count the unique cyclic peptide sequences given a symmetry type, using Burnside's lemma
...Also known as the lemma that is not Burnside's. Thanks to Todd Yeates for the math for this. This app:
- [x] Computes the number of unique sequences using expressions derived by Todd using Burnside's lemma.
- [x] Does this for SN-symmetric sequences, too.
- [x] Debug N>2.
- ~~Supports problems with achiral options.~~ -> Future pull request.
- [x] Optionally counts the number of unique sequences by brute force (which only works for small numbers of unique sequences).
- [x] Does this for SN-symmetric sequnces, too.
- [x] Supports problems with achiral options (e.g. GLY, AIB).
- [x] Optionally writes out all the unique sequences (provided they're a small enough number to write out).
- [x] Promote this to a public app.
- [x] Documentation.
- [x] Beauty.
- [x] Integration test.
Documentation is here: https://www.rosettacommons.org/docs/latest/application_documentation/count-cycpep-sequences
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Merge pull request #4154 from RosettaCommons/JackMaguire/SmallHBNetRefactor
Exposing HBNet option to PyRosetta
I'm playing with HBNet in PyRosetta and found an option that did not have a getter/setter pair (My fault. I added the option a long time ago and only gave it an XML interface). This PR changes the default values of the option and adds a getter/setter.
Thanks Steven for the review!
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Merge pull request #4152 from RosettaCommons/BYachnin/mhc_epitope_scientific_test_favournative_fix
It turns out that the FavorNativeMover will re-weight all scorefunctions that have a non-zero res_type_constraint. As a consequence, the "base" ref2015 scores that were reported by this scientific test actually included the res_type_constraint contributions, even though it shouldn't have.
This PR uses an alternative mover that doesn't touch the scorefunction weights. Because the this is roughly a constant value added to all scores and for testing purposes, only the percentile rank is used, this shouldn't affect the pass/fail status of the test. The correct values will now be shown in the scorefiles and results page.
I also tweaked the cutoffs to improve test stability.
Because this PR only touches the scientific test files, I will only run the mhc_epitope scientific test +/- debug mode.
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Merge pull request #4157 from RosettaCommons/revert-4155-revert-4135-cdbahl/FragmentStore-python-bindings
Revert "Revert "Adding FragmentStore python bindings"":
- all changes from https://github.com/RosettaCommons/main/pull/4135
- fixing h5_fragment_store_provider.py when running with Python-2.7
- updating release.PyRosetta4 test so it always provide sub-test info
- updating release.PyRosetta4.conda test so it always provide sub-test info
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Merge pull request #4139 from RosettaCommons/BYachnin/antibody_cst_mover_fixes
Make antibody constraint mover rosetta_scripts "compliant"
The ParatopeSiteConstraintMover and ParatopeEpitopeSiteConstraintMover had a couple of issues preventing their use in rosetta_scripts:
-They did not have a clone() function, causing rscripts to error out if they were used.
-There was a mismatch between parse_my_tag and provide_xml_schema for the option interface_distance or interface_dis.
This is a quick fix for these two issues in both movers.
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Merge pull request #4144 from CyrusBiotechnology/CYRUS-801-forcommons/nmer_speedup
Bugfix NmerRefEnergy. David Pearlman found that a large protein (it's a crispr) took thousands of seconds to run through our epitope scan protocol. Now it takes about 30 seconds, nearly all of which is initializing the score terms' const data from disk (and pose construction). Profiling revealed string construction was the problem. Turns out to be an unneeded deep copy operation. Thanks @decarboxy @roccomoretti @everyday847 for advice on how to profile. Tag @indigogo @BYachnin for awareness.
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Merge pull request #4149 from RosettaCommons/vmullig/fix_clang_build_after_gcc_9_fixes
Fix clang/Mac build after Rocco's fixes for gcc/9.
Rocco's fixes revealed a couple of unused private member variables in a class, which were previously being touched by an explicit copy constructor that has been removed, and which clang now complains about. (Note: this is not meant to be a criticism of Rocco's changes. They were needed, and they revealed a problem previously masked.)
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