commit ebee9f505da801d17837b6e348f870db27cc9d74 Date: Fri Jul 21 21:38:58 2017 -0700 Beautifying master. commit 79f0e054ed29a125e8bf7df775ac62dddaf10b3a Merge: 8a21c04 1e7c3dd Date: Fri Jul 21 09:58:41 2017 +0200 Merge pull request #2404 from RosettaCommons/bazzoli/add_interface_energy_app Adds public app analysis/interface_energy. commit 8a21c04b5d6929364354cbc81a2bbc1af4fc577b Merge: 44e1f4d 0e75542 Date: Wed Jul 19 19:26:57 2017 -0700 Merge pull request #2390 from RosettaCommons/everyday847/full_model_jq Make jd3 versions of common RNA applications commit 44e1f4d47ba4dc0d4b4bde6af7b2226d6e0c4e49 Merge: ab5b5bd 18aa7ef Date: Tue Jul 18 18:42:49 2017 -0700 Merge pull request #2400 from RosettaCommons/bfrenz/maintain_sugar_names Bfrenz/maintain sugar names commit ab5b5bd1f62c7367e625bec7b24f5fe11117ded4 Merge: fe37478 b223866 Date: Tue Jul 18 18:06:41 2017 -0500 Merge pull request #2395 from RosettaCommons/roccomoretti/jd2ectomy Laying the groundwork for a jd2-ectomy A number of people have made use of the JD2 system when writing their Movers, etc. -- that is, they're not implementing something that has a direct dependence on JD2, but use various convenience functions in JD2 which allows you get various job-running data (e.g. output name) This has worked for the past decade or so, but now that JD3 is staring us in the face, it would be good to move such code off of a strict JD2-dependency. This PR goes through and, as much as reasonably possible, attempts to remove the direct dependence on JD2 Jobs, JobDistributors, JobOutputters, etc. from everywhere that's not intimately tied to the JD2 system. The form this takes in the current PR is that a number of utility functions have been added to src/protocols/jd2/util.hh, so instead of doing something like protocols::jd2::JobDistributor::get_instance()->current_job()->input_tag() you can do protocols::jd2::current_input_tag(). While the implementation of protocols::jd2::current_input_tag() still has the same reliance on the JD2 system, it serves as a single point which can be generalized when we come up with a JD2-independent system for passing around the input tag. (It should also be easier to mode it to a different namespace.) commit fe37478bd1ee69d96966c2ea0644748e59ca600b Merge: 06c0359 0d849ff Date: Mon Jul 17 15:47:37 2017 -0500 Merge pull request #2396 from RosettaCommons/roccomoretti/fix_talaris_warning Fix issue where 'pre_talaris_2013_standard' was being classified as a talaris scorefunction. commit 06c03594340447733b8415647ca05a0ff2619f6e Merge: fa91853 ecf1efa Date: Mon Jul 17 11:51:48 2017 -0700 Merge pull request #2383 from RosettaCommons/bfrenz/auto_glycan_with_links_records Bfrenz/auto glycan with links records commit fa91853df5aabfa228b1ba02e1d0e2ab94ae2fb8 Merge: e424716 1781c81 Date: Fri Jul 14 23:13:10 2017 -0700 Merge pull request #2397 from RosettaCommons/vmullig/fix_link_issue Fixing a minor issue with using simple_cycpep_predict with native PDB files containing LINK records Requested by @gbhardwaj . When provided with a native structure with a LINK record specifying cyclic geometry, simple_cycpep_predict would attempt to set up cyclic geometry anew, first stripping off terminal types. When the terminal types were absent, it would crash. This fixes that. commit e4247166b964f2eaa51d0b121623210c3703a25e Merge: 59a652f bef2fd9 Date: Fri Jul 14 11:25:12 2017 -0700 Merge pull request #2073 from RosettaCommons/bfrenz/FixDensScaling This code fixes the issue where the order in which you called protocols effected the density scoring values do the the initialize fast scoring first time function using the pose to setup the density scoring. Hopefully the effect is minor but density weights may need to change as a result. Especially if your protocol operated using a centroid model as input to rosetta. commit 59a652f08f663811ae603354624566a214e775e2 Merge: 80f93bd 8d78c68 Date: Fri Jul 14 08:27:19 2017 -0400 Merge pull request #2384 from RosettaCommons/aleaverfay/jd3_multiple_results_per_job JD3: Jobs produce multiple of JobSummary/JobResult pairs Imagine that a job produces 1000 poses because it's efficient for it to produce many at once. What then? Should it put all 1000 poses into a single JobResult? When the JobQueen selects Pose 884 to advance to the next round of the protocol, will all 1000 Poses be sent as a single serialized JobResult to the remote node, so it can extract all 1000, and then take the single Pose it cares about? That seems like a bad idea! JD3's initial design didn't plan for this. The new system I'm working on here instead has a Job produce a list of outputs allowing the JobDistributor to serialize and store them all separately. Then when result 884 needs to get sent to the remote node as input to the next job, only a single Pose has to be transferred. Also, the other 999 poses can be deallocated. Job's ```run()``` method now returns a ```CompletedJobResult``` as before, but this previous typedef is now a struct containing a vector1 of JobSummary/JobResult pairs in addition to a JobStatus. If a job produces more than one Pose, each Pose could (should) be put into separate PoseJobResult and entered into a separate entry in the CompletedJobOutput array. The JobQueen's interface now changes: * ```note_job_completed(...)``` now informs the JQ of the number of job results produced * ```completed_job_summary( ... )``` now includes the index of the JobSummary (1..nresults for that job) * ```completed_job_result( ... )``` similarly includes the index of the JobResult * ```jobs_that_should_be_output``` now returns a list of Size/Size pairs * ```job_results_that_should_be_discarded``` also returns a list of Size/Size pairs The PoseOutputters now handle extra outputs the same way that JD2 handles multiple Pose outputs for a single job -- i.e. the names given to the extra poses written as .pdbs or silent structures append an extra _0001, _0002 after the job_id; e.g. job 4311 run on PDB 1l2y.pdb which produces < 9999 output Poses would write to 1l2y_4311_0001.pdb, 1l2y_4311_0002.pdb, etc. There's really no reason for the integration test changes I'm seeing on the server, and I'm suspicious that it's just a hiccup related to Frank's merge of PR #2371 which fixed several bugs in symmetric minimization. commit 80f93bd0a1c30f6b8bf909077746f0e53defb77f Merge: 46dab53 184ea9d Date: Thu Jul 13 12:26:41 2017 -0700 Merge pull request #2393 from RosettaCommons/everyday847/stepwise_integration_test_pre_fix Pre-emptive alteration to 'stepwise' silent file tags (just in integration tests) The 14 integration test changes to stepwise integration tests are EXPECTED; they reflect a nomenclature change so it will be easier to detect REAL changes later. commit 46dab53953a8e5c886dfaa41995aa122f4418f92 Merge: 9ae4e0d 021d47a Date: Thu Jul 13 10:27:13 2017 -0700 Merge pull request #2388 from RosettaCommons/tjbrunette/near_native_fast_fix fix to closure_type flag in NearNativeLoopCloser commit 9ae4e0d3fa705e124e1d9a95fa0f1114d9aa3b3c Merge: c6d0f56 3b27f23 Date: Thu Jul 13 09:02:05 2017 -0700 Merge pull request #2391 from RosettaCommons/everyday847/my_app A fragment assembly UI app commit c6d0f5696c3ef819c890b389610d84e6e1c9ead2 Merge: 2e801d8 eb28cb9 Date: Wed Jul 12 12:00:31 2017 -0500 Merge pull request #2387 from RosettaCommons/jadolfbr/code_template_namespaces Fix Code Template Namespacing This addresses #2386 - Add full pathing or typedefs to function variables to make the templates independent of final namespace as they should be. commit 2e801d80f3974c79e2782836afcbdeeb8bb1febb Merge: e78c594 e56392f Date: Mon Jul 10 10:13:20 2017 -0700 Merge pull request #2371 from RosettaCommons/aleaverfay/cart_min_deriv_unit_tests This checkin fixes two bugs with Cartesian minimization of symmetric poses. One was related to the recent change of symmetric atom tree minimizer to better support lattice symmetries. This change modified the edge weights on minimization graph, however CartesianMin still needed the old weights. This checkin changes the logic so the weights are modified as needed in SymAtomTree minimize, while keeping the minimization graph as it was before this change. This checkin also fixes a longstanding bug in symmetric CartesianMinimization when only part of the structure only was allowed to move. In these cases, the domain map was built assuming an asymmetric pose, leading to not all energy edges getting calculated during cartesian minimization. This has been fixed (and @aleaverfay has added an integration test ensuring this works). Thanks Andrew for finding these issues. Integration changes expected in all tests that minimize with symmetry. commit e78c594d33dc5d237b6dbfdf29b2e11d0a91403c Merge: 4c640b3 78ed43d Date: Sun Jul 9 14:00:34 2017 -0600 Merge pull request #2385 from RosettaCommons/sergey/ui Updating UI project commit 4c640b3c8c3f8f0499dbcebdb4c3af2ff0c7f277 Merge: 946605b 991e610 Date: Sat Jul 8 20:37:20 2017 -0400 Merge pull request #2349 from RosettaCommons/JWLabonte/lipids/database This merge will add a few more lipid building blocks to the database for (an attempt at) explicit modeling of lipids. An integration test has also been added that demonstrates loading in an explicit lipid monolayer of 99 2-oleoyl-1-palmitoylphosphatidylcholine units, scoring, and minimizing. Please note that this integration test demonstrates a framework; it in no way implies any sort of scientific validity to the output structures. There is currently no reliable protocol for explicitly modeling lipid membranes in Rosetta. All unit tests pass. Several integration tests show new tracer output. commit 946605bf6d7697b50c22aebef88c2e6859e447d9 Merge: 653c91a 7fb54ee Date: Thu Jul 6 19:36:36 2017 -0400 Merge pull request #2382 from RosettaCommons/JWLabonte/sugars/database Carbohydrates: Another Xylose All tests pass. Expected integration change reporting +1 ResidueType. commit 653c91abf625d300c3b4741d4dc96cd9e7731217 Merge: 6976f92 82c4fec Date: Wed Jul 5 22:22:14 2017 -0700 Merge pull request #2379 from RosettaCommons/everyday847/GAI_mods Some modifications to be able to model guanidinium ions during stepwise commit 6976f9214ba08b86240f61b75d7931d8c369f456 Merge: 915493d 12303c8 Date: Wed Jul 5 15:10:45 2017 -0700 Merge pull request #2380 from RosettaCommons/everyday847/helix_dumper Dump helices created through RNA_DeNovoSetup commit 915493dc9687b61c9ac27e3a6ab80d1ac18f62e0 Merge: 0ce57b4 4510c95 Date: Wed Jul 5 12:39:02 2017 -0700 Merging everyday847/itest_fix (so that my previous PR's itest will run better) and beautifying master. commit 0ce57b45c47f8f4de4a74aa718848ca7f293526a Merge: 7574ee9 5a22d6d Date: Wed Jul 5 13:12:52 2017 -0600 Merge pull request #2345 from RosettaCommons/fordas/pyrosetta_setuptools_bootstrap Update pyrosetta distro to bootstrap minimum setuptools. commit 7574ee949dc8f6aa8dfcdea9258058fba83dc347 Merge: 9df6b18 a2f572a Date: Wed Jul 5 11:17:07 2017 -0700 Merge pull request #2381 from RosettaCommons/bfrenz/RosettaES_scripts_fix fixed flags in runES.sh commit 9df6b1896e697b50bad09daa0a36eb71a1f1e882 Merge: 655f177 2f7f1e0 Date: Wed Jul 5 10:47:26 2017 -0700 Merge pull request #2378 from RosettaCommons/everyday847/5prime_cap Model mRNA in rna_denovo commit 655f17710a5c33d1cd512710e52ab669ff4ec294 Merge: 2d053fa 58a743b Date: Wed Jul 5 08:22:04 2017 -0700 Merge pull request #2376 from RosettaCommons/rhiju/fix_ref2015_for_stepwise Hot fix for ref2015 in stepwise RNA/protein commit 2d053fa81df68d203dc133e9b88575bc45f28c50 Merge: 1ed4df4 809ee63 Date: Mon Jul 3 12:57:17 2017 -0500 Merge pull request #1872 from RosettaCommons/jadolfbr/dump_pdb_residue Jadolfbr/dump pdb residue Enables the dump_pdb_residue function of pdb_writer to work in PyRosetta. Forgot this PR was still open. https://www.rosettacommons.org/node/9826 commit 1ed4df4743945a0fc41141cd8e91625b0cbcfbd4 Merge: d13ada4 50a73a4 Date: Mon Jul 3 12:53:58 2017 -0500 Merge pull request #2370 from RosettaCommons/jadolfbr/fix_glycan_data Update Glycan Conformer data This updates the glycan conformer data using higher-level filtering using the glycosciences pdbcare 'bit' values. This edges more on the cautious side in order to filter torsions that may or may not be correct. commit d13ada4d1c7ac0e4ec116f336e997a16c79593af Merge: ec07326 c0aa186 Date: Sun Jul 2 13:12:08 2017 -0600 Merge pull request #2369 from RosettaCommons/sergey/binder Updating LLVM Git repositories paths and point them to GitHub commit ec0732620c91601c264bde15a75928d17d02364f Merge: e21a430 0f52ece Date: Sat Jul 1 09:32:19 2017 -0700 Merge pull request #2366 from RosettaCommons/possu@u.washington.edu/repeat_update bug fixes. cosmetic changes to remodel related integration tests. commit e21a430f963c7556cc3c6b1dda89da1ed2be3c83 Merge: 7482423 50c5bc5 Date: Fri Jun 30 23:43:05 2017 -0700 Merge pull request #2373 from RosettaCommons/vmullig/fix_genkic_sugars Fix the genkic_sugars integration test in debug mode Some debug_assert is tripping up the test. I need to figure out what's wrong and fix it. Update: the logic for detecting noncanonical connections assumed that the only time that a polymer residue would lack a lower connection would be if it were a lower terminus type. This assumption is not true for all glycans. The simple fix is to check for a lower connection instead of checking for the lower terminus type. commit 7482423d9e64d4b3589f4a8950ac81ed93c5a707 Merge: f1b7bfe 19d5ab9 Date: Fri Jun 30 17:22:36 2017 -0500 Merge pull request #2368 from RosettaCommons/jadolfbr/glycan_info Minor updates to glycan_info pilot app to output a bit more information per-glycan.