Merge pull request #4047 from RosettaCommons/rfalford12/membrane-efxn-sci-benchmark2
Membrane energy function scientific benchmarks part #1: Energy landscape and sequence recovery
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This pull request will add two scientific benchmark tests for membrane energy functions. They can be used to compare implicit membrane models, and have been most recently used to demonstrate sizeable scientific improvements by franklin2019.
* **mp_f19_efxn_landscape** Test the water-to-bilayer partitioning energy behavior of the energy function
* **mp_f19_sequence_recovery**: Sequence recovery benchmark
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Merge pull request #3937 from RosettaCommons/BYachnin/iedb_database_files
This PR adds a "default" de-immunization database to the Rosetta database which allows users to penalize sequences that are IEDB, experimentally-validated epitopes. We are including a copy of the database, and also a script that will refresh it, and an "info" file to provide date and user information from when the database was last updated by an individual user. There are also unit tests that check the database "integrity" for when users refresh it and commit the update.
We use this command string:
mhc_data_db.py --allele_set hlaII --assay_mhc_ligand_binding all --assay_mhc_ligand_elution all --cores all --db iedb_data.db --overwrite
This PR also includes some minor improvements to the MHCEpitope classes, including looking harder for database files and providing appropriate warnings for large file sizes. Documentation of permission to include Propred and IEDB resources with Rosetta are also included.
All tests pass, except recurring script failures in integration tests.
Thanks to @lyskov for the review!
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Merge pull request #4048 from RosettaCommons/mlnance/carbohydrates/default_bb_true_movemap_RingPlaneFlipMover
Make RingPlaneFlipMover's default MoveMap allow bb movement
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Merge pull request #4036 from RosettaCommons/roccomoretti/integration_python3
Switch the test server to run integration.py with Python3.
Use Python3 on the test server (the same one running the benchmark.py script), such that Sergey only has to manage dependencies for one(ish) Python version.
While at this point we should be able to run integration.py with either Python2 or Python3, not all of the sub-scripts being run in the command files of the integration tests themselves can do so. To address this, add python2 and python3 substitution variables in the integration test scripts (to go along with the existing python one), for those tests which need a specific version. -- Please continue to use `%(python)s` if it the 2/3 choice doesn't matter - this will be whatever python with which the integration.py script was launched. The interpreter for python2 or python3 may be autodiscovered based on your path, and might not be the one you really want to use.
This also updates the integration command files for those scripts which need to use Python2.
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Merge pull request #4045 from RosettaCommons/vmullig/fix_extra_semi_colon
Remove extra semi-colon to fix build tests that are currently failing in master.
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