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Revisions №60803

branch: master 「№60803」
Commited by: Brahm Yachnin
GitHub commit link: 「27feef9d29c2ac42」 「№3937」
Difference from previous tested commit:  code diff
Commit date: 2019-06-26 10:39:24
linux.clang linux.gcc linux.srlz mac.clang
linux.PyRosetta.unit linux.gcc.python37.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration performance profile release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release util.apps

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!