commit 47669d9d2e9f659f4889dc89ee6305575dd87c2e Merge: 89d9069 696f5ca Date: Sun Nov 13 19:01:10 2016 -0800 Merge pull request #1621 from RosettaCommons/vmullig/fix_icc16 Fix additional issues to allow compilation with icc 16.0.2. This doesn't fix everything, yet, but gets us closer to being able to compile with icc. No test changes expected. commit 89d906968664951d6f34afdcb9a11b2da946a285 Merge: 671408a 798d14c Date: Sun Nov 13 12:18:49 2016 -0800 Merge pull request #1790 from RosettaCommons/rhiju/myosinRNPmodeling2 Rhiju/myosinRNPmodeling2 only rna/stepwise tests change, and they are expected. commit 671408aea0df11f5d29f1c4a23e7cae09add6ec3 Merge: ae02d6e 31592c9 Date: Sun Nov 13 02:40:23 2016 -0800 Merge pull request #1763 from RosettaCommons/rhiju/myosinRNPmodeling Modeling RNA-controllable myosin motor Confirmed that integration test changes are aesthetic. commit ae02d6ec16ffab626f75302cca735d2f048caef0 Merge: e978788 8485393 Date: Fri Nov 11 17:43:39 2016 -0800 Merge pull request #1782 from RosettaCommons/sboyken/fix_combining_networks fixing bug with combining multiple networks in HBNetStapleInterface and commenting line 1824 in HBNet.cc (right after break) that was causing cppcheck failure; cppcheck test now passes commit e9787889336be44db35f03e1f346610bbe1863a3 Merge: ec64f3a 5c226ac Date: Fri Nov 11 15:20:42 2016 -0700 Merge pull request #1787 from RosettaCommons/sergey/binder Refactoring default-return-policies. Separating configs options for static and member functions so different policies could be specified. This should take care of numeric.random.rg() bug. commit ec64f3a8f95a5816159310b8402b34323e2749cd Merge: 22f9835 0558d27 Date: Fri Nov 11 13:38:31 2016 -0800 Merge pull request #1773 from RosettaCommons/weitzner/expand_pyrosetta_toolbox Expand PyRosetta toolbox commit 22f983597f1fced56708d43efbe93aaa26049712 Merge: 9930c96 058b1e6 Date: Fri Nov 11 12:52:19 2016 -0800 Merge pull request #1788 from RosettaCommons/everyday847/fix_thermal_sampler_integration_test Fix the thermal_sampler integration test commit 9930c969f358257ac7f4942bfcc9b52aa3ec3986 Merge: a65c886 359c6b7 Date: Fri Nov 11 09:13:22 2016 -0600 Merge pull request #1770 from RosettaCommons/roccomoretti/residue_load_debug Add additional debugging information to help figure out why your protein isn't loading. (i.e. when Rosetta can't find the appropriate ResidueType.) Integration test changes expected in those integration tests with debug-level output. commit a65c886a06746e8fb0b542e3e09a7fa91b4e9774 Merge: 0625d71 8a3cf8d Date: Thu Nov 10 21:14:18 2016 -0700 Merge pull request #1785 from RosettaCommons/sergey/binder Updating PyRosetta. Fixing typo in build.py (thanks to @jadolfbr for finding this!) Adding extra check into setup script so it refuse to run if used from other than ‘setup’ dir. commit 0625d71eff37ee1326ec0bf15c4fa7bc104be645 Merge: bf3526f 7ac5d43 Date: Thu Nov 10 19:50:05 2016 -0800 Merge pull request #1783 from RosettaCommons/basantab/motif_stuff_small_fix Small fix on motif_hash_stuff.cc commit bf3526f01b7b07a145d6f76f8fe269996eb47323 Merge: 8f28abe 939bc56 Date: Thu Nov 10 14:07:02 2016 -0500 Merge pull request #1769 from RosettaCommons/jkleman/lipid-acc Jkleman/lipid acc updates to lipid accessibility calculation commit 8f28abe28c371338ecb946ff8ccda44eab36c97b Merge: fdcbb83 646123d Date: Thu Nov 10 01:10:21 2016 -0800 Merge pull request #1780 from RosettaCommons/vmullig/support_nmethyl_merge4 Incremental merge #3 for supporting N-methylation Full list of changes is in pull request #1508 . commit fdcbb83b9efb1c3bb0f0475e30d479a878a3a41e Merge: 6238c7e cd25075 Date: Wed Nov 9 13:31:33 2016 -0800 Merge pull request #1774 from RosettaCommons/dimaio/hyb_fix_boundserror Fix out of bounds error in hybridize commit 6238c7e203310702dbbc867881983c29175abf06 Merge: 85b7168 3422af0 Date: Tue Nov 8 19:25:49 2016 -0800 Merge pull request #1779 from RosettaCommons/rhiju/linear_chainbreak_shrink_cutoff reducing distance cutoff for computing linear_chainbreak deriv from 0… + Tests that change are ones that use linear_chainbreak. + In most cases, minimizer now reaches lower energy and spouts fewer 'Inaccurate G' warnings (though there are still some). commit 85b7168cddb3169cefc325835b02ac9502b78c01 Merge: 441415b 75d184f Date: Tue Nov 8 13:01:49 2016 -0800 Merge pull request #1777 from RosettaCommons/rhiju/chainbreak_energy_generalize Rhiju/chainbreak energy generalize Only test changes are aesthetic (or previously broken cppcheck & thermal_sampler). commit 441415b91d37956b4d262974895c6f0b65896a14 Merge: 8739b57 87529ce Date: Mon Nov 7 08:21:12 2016 -0800 Merge pull request #1776 from RosettaCommons/rhiju/make_dna_via_patched_rna Handle DNA in FARFAR (rna_denovo) [Only failing checks are thermal_sampler & cppcheck, both broken previously.] commit 8739b57ef2cf651f8a215e04c4abdc955c9717d9 Merge: f9fc030 580c8b2 Date: Sun Nov 6 15:54:34 2016 -0800 Merge pull request #1775 from RosettaCommons/rhiju/declare_chemical_bond_at_loop_cutpoints declare chemical bond when CUTPOINT_UPPER and CUTPOINT_LOWER are assigned at a chainbreak Only tests that change are ones that failed before (cppcheck; thermal_sampler in debug_release), and bridge_chains gets a much lower energy due to absence of repulsion between the atoms bonded across the chainbreak. commit f9fc0305175b872c98189722b1c8e702648987a5 Merge: 5d54dd7 61b5894 Date: Thu Nov 3 19:42:56 2016 -0400 Merge pull request #1765 from RosettaCommons/BYachnin/Fix_Segfault_after_Execution Removed tracer output in destructor to fix segfault. Several integration tests lose the tracer output core.chemical.ResidueType: Residue dstor as expected, including integration.release-debug (cyclization, ddG_of_mutation, fiber_diffraction_fad, fold_and_dock) and integration (cyclization, ddG_of_mutation, fiber_diffraction, and fold_and_dock). mac.clang.integration.features_parallel failed due to different sqlite versions on the test servers. commit 5d54dd7ccc45bb3087eaf9a7344cab7bf153235a Merge: bda5dbf 4414fcf Date: Thu Nov 3 16:35:21 2016 -0700 Merge pull request #1768 from RosettaCommons/everyday847/stepwise_performance_two Minor stepwise performance improvements and loop conversions commit bda5dbf6ac9204dad94c2f40f6ff3c0cc7b1479e Merge: 1ccd4b4 3ace926 Date: Thu Nov 3 14:38:33 2016 -0700 Merge pull request #1760 from RosettaCommons/everyday847/issue_with_virtual_atoms RNA cutpoint torsion issue + some miscellany commit 1ccd4b449eb2791c697c4eb7e8b4e6a14386dd04 Merge: c28dabb 3877eb8 Date: Thu Nov 3 15:14:27 2016 -0600 Merge pull request #1766 from RosettaCommons/sergey/binder Updating PyRosetta documentation generation script so it now generate docs for pyrosetta.* sub-modules. Refactoring toolbox modules so they could be imported in Python-3. commit c28dabb55571830bfd54566ea72b7238651c8f7b Merge: cb14486 10a603f Date: Thu Nov 3 09:17:06 2016 -0700 Merge pull request #1767 from RosettaCommons/everyday847/base_pair_constraint Base pair constraint mechanism commit cb14486eaf0a6dd8ff7eb99df2a07dcfee9fc756 Merge: 6922a68 41879e9 Date: Thu Nov 3 09:07:08 2016 -0700 Merge pull request #1762 from RosettaCommons/rhiju/make_dna_via_patched_rna creating patch Deoxy_O2prime to convert RNA to DNA residues only broken tests (cppcheck, integration for erraser_minimize, thermal_sampler) were broken before and watkins is on it. commit 6922a68c56c0a3c5f64570c55097ba5d5439e22c Merge: 8273fa0 2648af7 Date: Wed Nov 2 10:42:41 2016 -0700 Merge pull request #1761 from RosettaCommons/rhiju/make_7DA_UNP_not_RAD making 7DA.params an UNP aa so that it does not get designed Looks OK -- only rna_design changes, as expected -- no longer allowing 7-deaza-A in standard fixed-backbone RNA design. A few tests were previously broken (cppcheck; and integration for erraser_minimize & thermal_sampler were broken before -- @everyday847 please checkout). commit 8273fa01111f43a52fac7eee8c5149397aef6486 Merge: aa7e97e 5ae333f Date: Tue Nov 1 18:05:58 2016 -0700 Merge pull request #1759 from RosettaCommons/vmullig/temporarily_revert_rama_table_from_tim Temporarily reverting Tim's change to the custom Rama tables, which broke some stuff. Sorry folks -- we meant to commit this to a branch, not to master yet. commit aa7e97ec73a3ffbaff0c8696c700329cf5ab371d Merge: 53424f8 2f1164b Date: Tue Nov 1 12:22:20 2016 -0700 Merge pull request #1757 from RosettaCommons/everyday847/fix_new_delete_mismatch Fix an issue with a new[] / delete (no []) mismatch commit 53424f8dd6aea08eb4bc183253fc5ba406700183 Merge: ef21445 c61afff Date: Tue Nov 1 14:00:41 2016 -0500 Merge pull request #1752 from RosettaCommons/roccomoretti/dun_binary_log Attempt to address some issues with Dunbrack binary generation. Per the rosetta-devel discussion, it seems we have issues with reproducability of Dunbrack binary file generation. These are some simple fixes to help with avoiding/debugging them. Specifically, adding a tracer output statement to the validate_database integration test to print the SHA1 of the Dunbrack binary, as well as code to delete the Dunbrack binaries on the Benchmark server prior to running the integration test. @lyskov commit ef214459174ffa52797f3801f197e514410a9b3f Date: Tue Nov 1 11:51:39 2016 -0700 Update Generic_L_Alpha_Nmethyl_AA_ramatable_QM.txt Modified the N_methyl amino acid rama table. commit bdcdeeeb031f36880e83050637e29ef988124821 Merge: a8d9220 1dcb146 Date: Tue Nov 1 10:02:39 2016 -0600 Merge pull request #1755 from RosettaCommons/benchmark Fixing symlinks in profit tests. Thanks to @roccomoretti for pointing this out! commit a8d9220ddf4141bcc1d6d2a2aadb531ffd8f5f3f Merge: 67882a6 8b6607f Date: Tue Nov 1 08:59:10 2016 -0700 Merge pull request #1756 from RosettaCommons/weitzner/docking_high_res_factory Adding DockingHighResFactory commit 67882a64f2df0632b19394a641e082947970b2aa Merge: 6dd8a99 6ffd7da Date: Tue Nov 1 09:44:48 2016 -0400 Merge pull request #1751 from RosettaCommons/aleaverfay/spell_genealogist_right I spelled genealogist wrong over and over again. sigh commit 6dd8a99166e71bed1c58b917cb01f648d0886cec Merge: 35839bb 076548c Date: Tue Nov 1 08:14:41 2016 -0400 Merge pull request #1750 from RosettaCommons/aleaverfay/sjq_with_more_read_access The SJQ now keeps track of the job index ranges for preliminary job nodes so that derived job queens can determine what jobs have been output and what jobs have not been output yet. She also provides read access to the DIETs that track which jobs have completed (at all), completed successfully, failed, and which have been output. commit 35839bbbd94a659ea86ac85d3ab0c3f7dcd2c4ac Merge: cc089f6 2a7150d Date: Mon Oct 31 20:38:27 2016 -0700 Merge pull request #1754 from RosettaCommons/jyesselm/thermal_sampler_legacy Restore 'legacy' thermal sampler, rename 'current' thermal sampler to alpha commit cc089f6aa44ccb94750dda87866f68e7174f9b4c Merge: ab868f1 e4c3518 Date: Mon Oct 31 20:30:11 2016 -0700 Merge pull request #1673 from RosettaCommons/everyday847/use_rna_residuetype_more Use RNA_ResidueType as much as possible commit ab868f11b2fb7cb5fa14943fa886e41a850cfae1 Merge: 916d26c 2f7141d Date: Mon Oct 31 19:21:58 2016 -0700 Merge pull request #1753 from RosettaCommons/xingjiepan/fix_multi_loop_bug Fix the bug that LoopBuilder failed to build multiple loops. commit 916d26cf537c2ae6bcf32075aa06c070315bf9b8 Merge: 0af587f 2d29ba6 Date: Mon Oct 31 14:19:39 2016 -0700 Merge pull request #1748 from RosettaCommons/jadolfbr/nbr_selector Fix NeighborhoodResidueSelector to properly not include subset in selection if passed the boolean. Thanks Yang Hsai for the find. commit 0af587fd74d9d730b43979306f22d445e484d765 Merge: c4b8093 83ac45d Date: Mon Oct 31 08:00:29 2016 -0400 Merge pull request #1747 from RosettaCommons/aleaverfay/jd3_job_geneologist Protocols in JD3 are responsible for keeping track of indices for jobs that they have created, and it is a tedious task. The class being created in this pull request, the JobGeneologist, will keep track of the parent(s) for each batch of jobs for each node in the JobDAG. It helps by assigning ranges of jobs to different nodes so that job-index-ranges do not overlap, and the JobQueen never makes the mistake of assigning the same index to two separate jobs. The JobGeneologist also is capable of deducing which ancestral jobs no longer have any living descendants. Imagine this scenario. There's a multi stage protocol where, at the final stage when you're outputting the top structures generated by the protocol, you want to be able to output the intermediate structures from early stages that led to the final structures. Say Job 10 from stage 1 is promising, and serves as the "parent" (i.e. its output is the input to another job) to jobs 100-200 in stage 2. Of those jobs, only job 199 was not discarded, the others failed to pass some threshold. Then Job 199 is parent to jobs 1000-1100 in round 3, and of these jobs none were fruitful - they are all discarded. If the job queen for this protocol is going to avoid having unneeded results piling up, then she needs an algorithm to figure out that jobs 10 and 199 can now be discarded. This algorithm is actually really tedious! It would be a shame to force it on every JD3-protocol writer. The JobGeneologist manages the data and the logic needed for this task.