commit c5f1815d372dbb5b8d106b9c76012b3f87f9f83b Merge: d4d14d6 8b1be26 Date: Tue Nov 27 13:23:30 2018 -0500 Merge pull request #3641 from RosettaCommons/vmullig/fix_simple_cycpep_predict_issues Fix a couple of problems with simple_cycpep_predict This pull request fixes a trivial issue with output logging with simple_cycpep_predict. It also seeks to track down and correct a problem seen on the NYU cluster with a double free or corruption error, but I haven't yet been able to reproduce that. This seems only to affect the multi-threaded behaviour, and has only been observed with an icc build. Edit: I'm just going to merge these cosmetic changes now, and will open a new PR if and when I track down the double free or corruption error. commit d4d14d64f3ca60c7ca6214197b831ee3154bd53e Merge: f939698 12a1954 Date: Mon Nov 26 16:16:03 2018 -0600 Merge pull request #3100 from RosettaCommons/roccomoretti/sym_scorefunction Make all ScoreFunctions symmetric-aware score functions. Change the implementation of the ScoreFunction class such that the distinction between a SymmetricScoreFunction and a plain ScoreFunction disappears. This means there's no longer a need to match the symmetric status of a scorefunction to that of a pose. As such, this PR also removes a number of places where such symmetric checking is handled. For compatibility with existing PyRosetta scripts, etc. the SymmetricScoreFunction class still exists, it's just a practically-no-difference wrapper around the regular ScoreFunction. Additionally, the `symmetry="1"` in XML will still be permitted for compatibility sake, albeit with a message that it's no longer needed. (There may be later changes to the internals of ScoreFunction, but that shouldn't change general usage.) POTENTIAL BREAKAGE NOTE: `is_symmetric(ScoreFunction)` and `make_score_function_consistent_with_symmetric_state_of_pose()` from src/core/pose/symmetry/util.hh no longer exist because they're not needed/their old behavior no longer makes sense logically under the new scheme. You can safely remove them from code/PyRosetta scripts -- all ScoreFunctions are consistent with the symmetric state of any pose, and can act like they're symmetric or asymmetric, as need. commit f93969809bdd488cf991dba44449d6a4c029f986 Merge: 7eaa6bb 060aaaf Date: Sun Nov 25 11:32:38 2018 -0800 Merge pull request #3636 from RosettaCommons/aloshbau/debug_CMFKIC aloshbau/debug_cmfkic commit 7eaa6bb42dbe93ff77be1c59ddfd4d7bb65ea2ca Merge: 9d49b2a 496ab99 Date: Sun Nov 25 09:17:35 2018 -0500 Merge pull request #3643 from RosettaCommons/lqtza/antibody_cc_exclude_by_pdbid Add filter for PDB ID to antibody grafting commit 9d49b2acd42189ae1de95b41fdea7a72b1bbadd5 Merge: c7d4681 a586b2d Date: Fri Nov 23 11:45:47 2018 -0500 Merge pull request #3645 from RosettaCommons/revert-3644-revert-3638-everyday847/disulfide_optimization_mover Revert "Revert "A disulfide optimization mover"" commit c7d46816ff18a88f5686e33c2689cef104abeb20 Merge: 4dc4b49 f6c55e7 Date: Wed Nov 21 16:29:03 2018 -0600 Merge pull request #3644 from RosettaCommons/revert-3638-everyday847/disulfide_optimization_mover Revert "A disulfide optimization mover" commit 4dc4b49a9e8ce1c667b7bef62dbadfc04342eaa9 Merge: 396982b fbd8a71 Date: Wed Nov 21 14:12:42 2018 -0800 Merge pull request #3640 from RosettaCommons/xingjiepan/fix_loop_modeler_bug_for_multiple_structures Fix the bug that makes LoopModeler crash when nstruct > 1 commit 396982bfbcb388bc936d8bafade801e312ecbbcc Merge: 6ad03a8 681a727 Date: Wed Nov 21 10:45:07 2018 -0500 Merge pull request #3638 from RosettaCommons/everyday847/disulfide_optimization_mover A disulfide optimization mover commit 6ad03a865d02c0945a9e434e73f4ecdd8e23f949 Merge: 6168999 758a1ac Date: Tue Nov 20 09:10:39 2018 -0500 Merge pull request #3569 from RosettaCommons/everyday847/fix_kinematic_closure_maybe Update RNA_KinematicCloser.cc commit 6168999668e8afa24a7e613a39d065aad057a33d Merge: f78f10d 6fa44bf Date: Mon Nov 19 10:55:35 2018 -0500 Merge pull request #3635 from RosettaCommons/everyday847/fix_mincst_bug Make minimize_with_cst process -s correctly commit f78f10d770c07bda909db2727455a45bc624de33 Merge: 5e12843 409cc2d Date: Fri Nov 16 17:52:09 2018 -0500 Merge pull request #3631 from CyrusBiotechnology/smlewis/CM_ntrials Fix an uninitialized variable in CoupledMovesProtocol commit 5e128431b51a87355a9a407c3d9f9984d8bbbf0f Merge: 1aba7c5 4987097 Date: Fri Nov 16 10:50:54 2018 -0500 Merge pull request #3598 from RosettaCommons/jtseffer/SID_rescore Jtseffer/sid rescore commit 1aba7c5a396423d07790d4146f6fd08cc4459114 Merge: adac37a a8b4b4e Date: Thu Nov 15 22:33:54 2018 -0500 Merge pull request #3625 from RosettaCommons/everyday847/polyaramids Add polyaramid params commit adac37a8be861634e4bfa7d8afccc1cfea2742fb Merge: febbd46 1843a97 Date: Wed Nov 14 09:35:40 2018 -0800 Merge pull request #3626 from RosettaCommons/fordas/pyrosetta_bootstrap_dev_env Add bootstrap pyrosetta dev env from prebuilt binaries. commit febbd46e06885642681a1f7bec064489211f8fad Merge: a9d4337 ff49c77 Date: Mon Nov 12 17:33:15 2018 -0500 Merge pull request #3612 from RosettaCommons/BYachnin/mhc-epitope-new mhc_epitope scoreterm, a flexible, packer-compatible deimmunization scoreterm This is the second attempt, after addressing a release mode unit test failure in PR #3390 . This PR introduces a new scoreterm, mhc_epitope, which can be used to identify and remove T-cell epitopes from proteins. It is packer compatible, using the "design guidance scoreterm" machinery introduced by @vmullig and @asford . Thanks to @vmullig for writing the original code that we copied, and for the thorough review! The code was developed by myself and @cbaileykellogg . The simplest mode involves turning on the scoreterm to work with the "ProPred" prediction matrices to remove epitopes (MHCEpitopePredictorMatrix). The threshold for what is considered to be an epitope (i.e. how aggressively to de-immunize) can be tuned using either raw scores or relative scores. Alternatively, the user can pre-compute epitope scores for a pre-defined set of sequences using more sophisticated prediction tools (e.g. NetMHC and IEDB). These should be stored in a SQL database to be accessed in the MHCEpitopePredictorExternal class. We will be providing some scripts in the tools repo to help users generate these SQL databases, and corresponding PSSMs to limit design space with task ops. This can also be implemented as a constraint mover, allowing specific regions to be targeted using residue selectors. These can use different predictor classes (e.g. use a general MHCEpitopePredictorMatrix in the scorefunction and a MHCEpitopePredictorExternal in specific regions with residue selectors) and other settings (thresholds, etc.). The scoreterm should behave well with symmetric proteins, ligands, non-canonical amino acids, and multi-chain systems. INTEGRATION TEST CHANGES: `mhc_epitope` fails because it is new 53 tests fail because of cosmetic addition of `EnergyMethodOptions::show: mhc_epitope_setup_files:` to output pdb files (we have added this as a new EnergyMethodOption): backbonegridsampler_multiresidue, bundlegridsampler, bundlegridsampler_copy_pitch, bundlegridsampler_design, bundlegridsampler_design_nstruct_mode, bundlegridsampler_epsilon, bundlegridsampler_z0_offset, bundlegridsampler_z1_offset, coupled_moves, ligand_dock_ensemble, mp_find_interface, mp_mutate_relax, mp_mutate_repack, oligourea_predict, pepspec, perturb_helical_bundle, remodel, remodel_disulfides, remodel_helical_repeat, scaffold_matcher, simple_cycpep_predict, simple_cycpep_predict_angle, simple_cycpep_predict_anglelength, simple_cycpep_predict_cartesian, simple_cycpep_predict_cispro, simple_cycpep_predict_cterm_isopeptide_lariat, simple_cycpep_predict_cterm_isopeptide_lariat_tailless, simple_cycpep_predict_design, simple_cycpep_predict_nterm_isopeptide_lariat, simple_cycpep_predict_nterm_isopeptide_lariat_tailless, simple_cycpep_predict_octahedral_metal, simple_cycpep_predict_settings, simple_cycpep_predict_sidechain_isopeptide, simple_cycpep_predict_sidechain_isopeptide_reverse, simple_cycpep_predict_square_planar_metal, simple_cycpep_predict_square_pyramidal_metal, simple_cycpep_predict_symm_gly, simple_cycpep_predict_symmetric_sampling, simple_cycpep_predict_tbmb, simple_cycpep_predict_terminal_disulfide, simple_cycpep_predict_terminal_disulfide_internal_permutations, simple_cycpep_predict_terminal_disulfide_tails, simple_cycpep_predict_tetrahedral_metal, simple_cycpep_predict_tetrahedral_metal_asp, simple_cycpep_predict_tma, simple_cycpep_predict_trigonal_planar_metal, simple_cycpep_predict_trigonal_pyramidal_metal, simple_grafting_movers, supercharge, sweep_respair_energies, test_energy_method_options, zinc_heterodimer, zinc_homodimer_design 3 tests fail because of cosmetic addition of `INSERT INTO "score_types" VALUES(1,376,'mhc_epitope');` (and re-ordering of other score_types) in output dump files (we have added this as a new score_type): database_jd2_compact_io, database_jd2_io, features hotspot_hashing is broken in master commit a9d433740da96f57b090feb46fc169e718aff5c8 Merge: 40d50eb 4d046f1 Date: Mon Nov 12 12:17:01 2018 -0700 Merge pull request #3622 from RosettaCommons/sergey/ui Changing RosettaCloud address to use HTTPS commit 40d50eb3a9b81b8eb466f917e5569d9ba7710fa6 Date: Mon Nov 12 10:37:42 2018 -0500 beautifying commit e47b5e08a9e6e37d5232c1bbcd816f77c010d7da Merge: 69a4a9f 5aa2f82 Date: Sun Nov 11 08:09:00 2018 -0800 Merge pull request #3583 from RosettaCommons/everyday847/updates_for_beta_aa_trna Updates for beta AA tRNA conjugation commit 69a4a9f13738160ffe1d80d05b273f41048a6d8c Merge: d31aab6 26e01b0 Date: Tue Nov 6 19:28:23 2018 -0800 Merge pull request #3424 from RosettaCommons/aloshbau/CoupledMoves Aloshbau/coupledmoves commit d31aab6b2d2bbb2646afab2313c3ef9d9c90872f Merge: 14e6b5a 1a20b9b Date: Tue Nov 6 16:06:09 2018 -0800 Merge pull request #3611 from RosettaCommons/fordas/packed_pose_score_update Add `update_scores` interface to packed pose. commit 14e6b5a23164e152c2e7dc1f7f7c684bdc3b19d5 Merge: f0ff0df 986cc45 Date: Tue Nov 6 15:07:24 2018 -0800 Merge pull request #3607 from RosettaCommons/fordas/pose_metric_deserialization Fix pose metric container deserialization. commit f0ff0df320ca82ee1d7e8ed7dc561fdf803d3dbb Date: Mon Nov 5 21:36:43 2018 -0500 beautifying commit 122b6ecdac32cc17cf54f8448031fb377310fb75 Merge: 0ebe527 2fc55ab Date: Mon Nov 5 18:02:19 2018 -0500 Merge pull request #3616 from RosettaCommons/BYachnin/release_unittest_build_fix Fix release mode unit test build with newer gcc compilers In newer gcc versions (6.3, for example), the unit test suite will not build because of a compiler warning that is treated as an error ('num' may be used uninitialized in this function). This small fix sets the value of res before running the code previously in isFloatNumber(), which fixes the error. There are no test failures other than unstable tests in master. commit 0ebe5274422f7b622cc522cd94ee9e3128993d9f Merge: 111952e 7eaa808 Date: Mon Nov 5 14:02:46 2018 -0800 Merge pull request #3610 from RosettaCommons/everyday847/repeated_fragment_moves Repeated fragment moves for an eventual, say, FARFAR3 commit 111952e63e0ba0d329938190cca888c5cc8fb8bd Merge: c1fd08d 390d5c9 Date: Mon Nov 5 15:18:20 2018 -0500 Merge pull request #3614 from RosettaCommons/vmullig/add_iron_rusty_settings Add site settings for the Flatiron Institute's Rusty/Iron cluster I won't bother to run tests for this, since no code changes and no problems can really arise from adding this file. This also corrects "UCSF to UCSD" in the Gordon site.settings file's comments. commit c1fd08d889c97965c65968702811bce710c1a5db Merge: c6f738a 1c29e3d Date: Mon Nov 5 11:14:28 2018 -0800 Merge pull request #3553 from CyrusBiotechnology/bfrenz/cartesian-ddg-legacyfix Fix to the legacy call in the cartesian ddg app. Bugfix on disulfides commit c6f738a7f2509b0898a662e32b74a9b5f5e4a5fe Merge: 3af644a 9ef998e Date: Mon Nov 5 09:59:00 2018 -0800 Merge pull request #3615 from RosettaCommons/fordas/xyzstripehash_mismatched_delete Fix mismatched new[]/delete in xyzStripeHash. commit 3af644ae4e87d9b37903d48bdf58270367eda8a2 Merge: 3a2fbbe 8c595bf Date: Sat Nov 3 13:04:59 2018 -0700 Merge pull request #3609 from RosettaCommons/everyday847/stochastic_erraser2 Adding stochastic elements to ERRASER2