commit 767c1ea25c572fbc078db45ad65dddb507240ad3 Merge: b0524c8 9e072b1 Date: Thu Aug 22 09:19:33 2019 -0400 Fix bug: InterfaceGroupByVector order dependency (#4142) The InterfaceGroupByVector selector was sensitive to the order in which residues were presented it, failing to detect interactions between residue i in group 1 and residue j in group 2 if j < i. Why? The UpperEdgeGraph stores only the edges to higher- indexed nodes and is used for neighbor detection because it is fast to add edges to this kind of graph. It's not the right choice, however, if you're trying to iterate across all neighbors of a particular set of residues. Because the InterfaceGroupByVector class used this graph, it would miss residues at the interface between two sets if the lower-indexed residues were listed second; e.g. if you have a pose w/ chains A and B (and A comes first) and you created an IGBV where you said the two groups were chain B and chain A (in that order), then the IGBV would find no residues at the interface. commit b0524c8c5b0fafa583aa52b781e752fcb8849251 Merge: fb62f21 c4c809b Date: Thu Aug 22 08:00:14 2019 -0400 Merge pull request #4117 from RosettaCommons/JackMaguire/TestLinkResidues2 Adding SequenceSymmetricAnnealer commit fb62f2109284d8f12da7c18ea9129b648a290e98 Merge: 6b543d5 2a6e18b Date: Thu Aug 22 01:00:43 2019 -0400 Merge pull request #4164 from RosettaCommons/vmullig/polar_sasa Adding options for measuring polar or hydrophobic SASA to SasaMetric. Tasks: - [x] Add option for polar SASA. - [x] Add option for hydrophobic SASA. - [x] Have these options do something. - [x] Unit test. - [x] Integration test. - [x] Documentation --> Will be auto-generated, since SasaMetric and PerResidueSasaMetric rely on auto-generated XSD documentation. - [x] Beauty. commit 6b543d55f349f22a33554bfafad6bd735f9a0f0d Merge: 11d91ba ec11a13 Date: Tue Aug 20 15:19:36 2019 -0600 Merge pull request #4158 from RosettaCommons/sergey/f3 fixing Rosetta build on Alpine Linux commit 11d91ba50abac88222366366b2619494f7b0374c Merge: e48c5ac a2dcd51 Date: Mon Aug 19 20:55:39 2019 -0700 Merge pull request #4163 from RosettaCommons/vmullig/fix_count_cycpep_sequences_issues Fix issues created by count_cycpep_sequences merge. This fixes: - The code_quality tests. - Ubuntu compilation. commit e48c5acf3d36adae84c574fe2f8137e615beec05 Merge: ab1c16c 9f9f4f0 Date: Mon Aug 19 14:20:28 2019 -0700 Merge pull request #4169 from RosettaCommons/vmullig/fix_simple_cycpep_predict_rand_init Fixing random number initialization in SimpleCycpepPredictApplication_MPI. commit ab1c16cfc6dc8561cdac36a618fdddfff14406d5 Merge: 9965188 45b56a9 Date: Mon Aug 19 11:12:00 2019 -0400 Merge pull request #4160 from RosettaCommons/JackMaguire/FixFastRelaxScriptTest Fixing the fast_relax_scripts test commit 9965188f0ac1fa6bbbde5c907635d76f30ba190b Merge: 768f9e3 9eab4b2 Date: Mon Aug 19 09:24:28 2019 -0500 Merge pull request #4156 from RosettaCommons/roccomoretti/tensorflow_test_noise Silence noise in tensorflow tests. Right now the tensorflow integration tests are red on the server because commit information is making it into the logs. Correct that. commit 768f9e3acc1da2cf190a22af1a960150de4c6faa Merge: 3563333 6d2a11a Date: Sat Aug 17 16:31:37 2019 -0700 Merge pull request #4147 from RosettaCommons/vmullig/count_cycpep_unique_sequences Add an app to count the unique cyclic peptide sequences given a symmetry type, using Burnside's lemma ...Also known as the lemma that is not Burnside's. Thanks to Todd Yeates for the math for this. This app: - [x] Computes the number of unique sequences using expressions derived by Todd using Burnside's lemma. - [x] Does this for SN-symmetric sequences, too. - [x] Debug N>2. - ~~Supports problems with achiral options.~~ -> Future pull request. - [x] Optionally counts the number of unique sequences by brute force (which only works for small numbers of unique sequences). - [x] Does this for SN-symmetric sequnces, too. - [x] Supports problems with achiral options (e.g. GLY, AIB). - [x] Optionally writes out all the unique sequences (provided they're a small enough number to write out). - [x] Promote this to a public app. - [x] Documentation. - [x] Beauty. - [x] Integration test. Documentation is here: https://www.rosettacommons.org/docs/latest/application_documentation/count-cycpep-sequences commit 3563333779a88f00b3523e637e5ceb01c13379ca Merge: 490d6d7 af91254 Date: Sat Aug 17 10:51:39 2019 -0700 Merge pull request #3810 from RosettaCommons/klimaj/add_viewer Add Jupyter notebook macromolecular visualization tools to pyrosetta.distributed commit 490d6d7834e127fbc06ee377f98ef66301f14b42 Merge: 3ce2887 99e14d2 Date: Fri Aug 16 14:19:22 2019 -0400 Merge pull request #4154 from RosettaCommons/JackMaguire/SmallHBNetRefactor Exposing HBNet option to PyRosetta I'm playing with HBNet in PyRosetta and found an option that did not have a getter/setter pair (My fault. I added the option a long time ago and only gave it an XML interface). This PR changes the default values of the option and adds a getter/setter. Thanks Steven for the review! commit 3ce28879356132ed7337a2418727be594c38b4fb Merge: 4209c09 f262a2b Date: Thu Aug 15 22:22:10 2019 -0400 Merge pull request #4152 from RosettaCommons/BYachnin/mhc_epitope_scientific_test_favournative_fix It turns out that the FavorNativeMover will re-weight all scorefunctions that have a non-zero res_type_constraint. As a consequence, the "base" ref2015 scores that were reported by this scientific test actually included the res_type_constraint contributions, even though it shouldn't have. This PR uses an alternative mover that doesn't touch the scorefunction weights. Because the this is roughly a constant value added to all scores and for testing purposes, only the percentile rank is used, this shouldn't affect the pass/fail status of the test. The correct values will now be shown in the scorefiles and results page. I also tweaked the cutoffs to improve test stability. Because this PR only touches the scientific test files, I will only run the mhc_epitope scientific test +/- debug mode. commit 4209c09b6a56ec9bfaa8eab6ef26ae878543b8c6 Merge: f876b9b 260c53d Date: Thu Aug 15 18:57:25 2019 -0600 Merge pull request #4157 from RosettaCommons/revert-4155-revert-4135-cdbahl/FragmentStore-python-bindings Revert "Revert "Adding FragmentStore python bindings"": - all changes from https://github.com/RosettaCommons/main/pull/4135 - fixing h5_fragment_store_provider.py when running with Python-2.7 - updating release.PyRosetta4 test so it always provide sub-test info - updating release.PyRosetta4.conda test so it always provide sub-test info commit f876b9ba4605d47d168a5cf1cc953db058c56c90 Merge: 6680a40 cf60126 Date: Thu Aug 15 15:16:20 2019 -0700 Merge pull request #4155 from RosettaCommons/revert-4135-cdbahl/FragmentStore-python-bindings Revert "Adding FragmentStore python bindings" (Doing a no-review admin revert.) commit 6680a402905d661f53c202ccf80b1089ba77baf4 Merge: 686681e 8aef846 Date: Thu Aug 15 11:51:33 2019 -0400 Merge pull request #4139 from RosettaCommons/BYachnin/antibody_cst_mover_fixes Make antibody constraint mover rosetta_scripts "compliant" The ParatopeSiteConstraintMover and ParatopeEpitopeSiteConstraintMover had a couple of issues preventing their use in rosetta_scripts: -They did not have a clone() function, causing rscripts to error out if they were used. -There was a mismatch between parse_my_tag and provide_xml_schema for the option interface_distance or interface_dis. This is a quick fix for these two issues in both movers. commit 686681e0609a56137d4695b44bd83449d7f4d4e3 Merge: 475059b 367abf3 Date: Wed Aug 14 14:24:53 2019 -0500 Merge pull request #4136 from RosettaCommons/nikoniko90/pocketcutpoints Nikoniko90/pocketcutpoints commit 475059b928b5258b69c06e72b6c362e6fce15b76 Merge: 4ba93ff 3b69978 Date: Wed Aug 14 15:06:58 2019 -0400 Merge pull request #4144 from CyrusBiotechnology/CYRUS-801-forcommons/nmer_speedup Bugfix NmerRefEnergy. David Pearlman found that a large protein (it's a crispr) took thousands of seconds to run through our epitope scan protocol. Now it takes about 30 seconds, nearly all of which is initializing the score terms' const data from disk (and pose construction). Profiling revealed string construction was the problem. Turns out to be an unneeded deep copy operation. Thanks @decarboxy @roccomoretti @everyday847 for advice on how to profile. Tag @indigogo @BYachnin for awareness. commit 4ba93ff6123d7a13fd4cf41950ab066649b42091 Merge: d51367e 8d48bd5 Date: Wed Aug 14 10:46:31 2019 -0700 Merge pull request #4149 from RosettaCommons/vmullig/fix_clang_build_after_gcc_9_fixes Fix clang/Mac build after Rocco's fixes for gcc/9. Rocco's fixes revealed a couple of unused private member variables in a class, which were previously being touched by an explicit copy constructor that has been removed, and which clang now complains about. (Note: this is not meant to be a criticism of Rocco's changes. They were needed, and they revealed a problem previously masked.) commit d51367ed5f293d4203e0fa5ab9b85b2f71054808 Merge: 99dd42e a7bd2ad Date: Wed Aug 14 11:59:36 2019 -0400 Merge pull request #4130 from RosettaCommons/everyday847/mpi_enabled_rna_score jd2-enable rna_score commit 99dd42e6190c739d1031b40cb6faa5c49da98a0c Merge: a344719 e5ef7d8 Date: Wed Aug 14 07:30:43 2019 -0700 Merge pull request #4140 from RosettaCommons/roccomoretti/disable_sewing_hasher_tests Disable continuous_sewing_hasher and discontinuous_sewing_hasher integeration tests. Per the decision at PreRosettaCon, disable these constantly-failing tests. We don't actually need to disable them wholesale, just the parts which take forever. We can still test the (quick) setup command portion. Anyone should feel free to reenable them later, if they can find a way of making them run faster. The reason for disabling instead of fixing is simply because there's not much interest in spending time with these legacy protocols. commit a344719efdaf62331a97b569a153371d8ee2f299 Merge: 6c2d2cb 0e37839 Date: Wed Aug 14 08:38:07 2019 -0500 Merge pull request #4118 from RosettaCommons/JackMaguire/cxx17functionattributes Compilers allow for various function attributes to help annotate code functionality. Most attributes are not useful for us in Rosetta, but a few can be useful for development purposes. For example, [[unused]] makes debug-mode compilation easier/cleaner in the early stages of development. Starting in c++17, compilers are told to ignore attributes that they do not recognize, which greatly increases portability. This PR adds a macro that allows you to write attributes that will only be applied if your version of c++ is c++17 or later, along with 4 whitelisted attributes: PURE, CONST, UNUSED, and NODISCARD commit 6c2d2cb3162bd8539024466213003f5bad199694 Merge: 52681d9 7e4320f Date: Tue Aug 13 22:48:03 2019 -0400 Merge pull request #4135 from RosettaCommons/cdbahl/FragmentStore-python-bindings Adding FragmentStore python bindings commit 52681d9013e2b13679d53dbb12013d5de9bfdde1 Merge: 2e1b6f9 415b68c Date: Tue Aug 13 16:13:19 2019 -0500 Merge pull request #3990 from RosettaCommons/JackMaguire/MonomerDesign2019 Updating FastRelax/FastDesign to make MonomerRelax2019/MonomerDesign2019 the new default relaxscripts commit 2e1b6f9e2fa4673432fbac7fe04dcc359ba3f561 Merge: aac5238 6214943 Date: Tue Aug 13 12:25:54 2019 -0700 Merge pull request #4074 from RosettaCommons/roccomoretti/crash_display_change Adjust the application signature for new crash reporter scheme. The crash reporter PR (#2978) introduces a slight change in how exceptions should be handled in executables. Instead of the application displaying the message itself, it should call the Exception::display() function, which will handle doing the appropriate display (and any applicable crash report generation). Most of this is just somewhat mechanical changes to the source/src/apps files. (I've also updated the code templates) But I also have changes to the JD2 & JD3 exception handling, such that errors which are caught by the JD machinery will also generate the appropriate logs. commit aac52386ebf13d9fed03d4635166089365627b44 Merge: 74e7600 2755ef1 Date: Tue Aug 13 07:54:05 2019 -0700 Merge pull request #4143 from RosettaCommons/roccomoretti/update_release_settings Add additional info for site.settings.release. There are a couple of common modifications end users often need. Provide stub templates for them in site.settings.release such that they're easier to describe. commit 74e760039c0de7cdb845f2d1647987926763f80a Merge: 346e9d0 b207cbd Date: Mon Aug 12 22:11:11 2019 -0600 Merge pull request #4138 from RosettaCommons/sergey/binder Updating Binder submodule commit 346e9d0427535c7e70489b9e9d306d7d4fc43f8d Merge: f8f5672 144e19f Date: Mon Aug 12 13:56:43 2019 -0700 Merge pull request #4096 from RosettaCommons/roccomoretti/ignore_rna_loop_data Ignore autogenerated loop files in the database. There are some cached files in database/scoring/loop_close/6D_potentials/rna/ which get autogenerated (e.g. by unit tests) Add them to a gitignore file, so they don't clutter up git status reports. commit f8f5672a9e3c6f83bee4e047c6895556c911083b Merge: 1e60c63 e152580 Date: Mon Aug 12 09:55:38 2019 -0700 Merge pull request #4124 from RosettaCommons/roccomoretti/gcc_9.1_fixes Fixes for GCC 9.1 compilation Most of the issues with compiling with GCC 9.1 are making sure that the copy constructor and the assignment operator (if both are used) are either both explicit or both implicit. Most changes are mechanical, but there are a few locations where there are copy and assignment discrepancies (or where there were but are no longer.) commit 1e60c63beb532fd475f0f704d68d462b8af2a977 Merge: b59e0c7 5e2996c Date: Fri Aug 9 15:19:57 2019 -0600 Merge pull request #4094 from RosettaCommons/sergey/binder adding PyRosetta.notebooks submodule, fixing PyRosetta thread build commit b59e0c7003cf3b107996c8d00ea9f199406c6d97 Date: Thu Aug 8 23:43:17 2019 -0400 beautifying commit e61833b2b6b8a77f8d168c486262faceaebbd392 Merge: 79a06db 933910c Date: Thu Aug 8 11:16:51 2019 -0700 Merge pull request #4131 from RosettaCommons/vmullig/remove_code_duplication Removing some code duplication. A function override in SymmetricRotamerSets does exactly what the base class function does. commit 79a06dbab09b0d76b25885e8eac45845e63be93b Merge: eca38ed b9fe998 Date: Wed Aug 7 20:59:13 2019 -0700 Merge pull request #4013 from RosettaCommons/JWLabonte/rings/aromatics Rings: Adding aromatic ring conformers to Rosetta This merge expands the `RingConformerSet` code to allow for alternate ring conformer sets for aromatic rings. This will lay a framework for future possible addition of other unsaturated ring systems to the database, such as dehydrosaccharides. It also will allow for the canonical aromatic amino acids to store their ring atoms without breaking all other related ring conformer code, and this is needed to enable C–H-to-π scoring in a general way. (See #2482.) Here is a summary of the major changes: - `ADD_RING` lines in `.params` files will now have an optional `AROMATIC` parameter. If not specified, the ring is assumed to be `ALIPHATIC`. For example: ```ADD_RING 1 AROMATIC CG CD1 NE1 CE2 CD2``` _vs._ ```ADD_RING 1 C1 C2 C3 C4 C5 O5``` - `ADD_RING` will now automatically add the `CYCLIC` property. - `ADD_RING` will now automatically assign default nu torsion angle definitions if they are not specified in the file and if there is only a single ring. This assignment happens at the first step of `ResidueType::finalize()`. - Aromatic rings have a single, planar `RingConformer`, so any calls to the `RingConformerSet` will always return the planar conformer. All unit tests pass. There are a LOT of integration test changes, ~90. The majority of these are trajectory changes from tweaks to the `AtomTree` as a result of new `CUT_BOND` records. Several other tests are simply output changes. Full details can be found in the PR discussion. commit eca38ed9811cf2b537c5db55594d1bbf92488832 Merge: b50f5e0 c6637f4 Date: Tue Aug 6 22:46:22 2019 -0700 Merge pull request #3976 from RosettaCommons/BobbyLangan/switch-grafting Adding GraftSwitchMover for LOCKR design commit b50f5e01ce7d671469fe272cb48f636ccdf0b15e Date: Tue Aug 6 17:51:39 2019 -0400 beautifying commit 1dc8f079b7a39918d69580913c6f0e730b5d1ec6 Merge: 25b607d 5c064fd Date: Mon Aug 5 16:39:43 2019 -0700 Merge pull request #4121 from RosettaCommons/danpf/mmtf use models in mmtf commit 25b607dba6acee9173435025b535990e5480172e Merge: 7d7f350 56b80d2 Date: Mon Aug 5 11:44:46 2019 -0600 Merge pull request #4129 from RosettaCommons/sergey/f Fixing PyRosetta documentation generation, thanks to @JackMaguire for review! commit 7d7f350b730377b0a2c0ae52b186e45bf7b1fb0b Merge: ad33235 ba0db14 Date: Mon Aug 5 10:12:32 2019 -0400 Merge pull request #4128 from RosettaCommons/ramyarangan/partition_checkpoint Fix checkpointing when using rna_partition in design commit ad332351b631fa87da6c89fa8ee417bcb62cfecc Merge: 381228d 79887d4 Date: Sun Aug 4 21:54:20 2019 +0200 Merge pull request #4019 from RosettaCommons/lqtza/make_antibody_h3_scientific_test Antibody H3 and SnugDock Scientific Tests commit 381228d167b650dcf489f48220ca952b0f1ddcff Merge: 530a4cb a2547af Date: Sat Aug 3 08:24:03 2019 -0400 Merge pull request #4122 from RosettaCommons/JackMaguire/update_rosetta_scripts_scripts Updating rosetta_scripts_scripts submodule commit 530a4cbe08e6dc5b7c0d50425bda790f49e61885 Merge: 757359f 221a477 Date: Fri Aug 2 12:36:43 2019 -0500 Merge pull request #4126 from RosettaCommons/roccomoretti/fix_clang_8.0 Fix warnings when compiling with Clang 8.0 We were summing a string literal with an integer, which probably wasn't what we wanted to do. commit 757359f41776ea85850e8b62e4b709cae63f18d6 Merge: 000b97c 239403b Date: Fri Aug 2 08:52:13 2019 -0700 Merge pull request #4103 from RosettaCommons/tigerous/sci-tests-loop-model-ccd-12res Tigerous/sci tests loop model ccd 12res commit 000b97c973d4487786f53c6515b76d632f6a3c22 Merge: 45bad70 48c0522 Date: Fri Aug 2 08:51:45 2019 -0700 Merge pull request #4102 from RosettaCommons/tigerous/sci-tests-loop-model-kic-12res Tigerous/sci tests loop model kic 12res commit 45bad7036de5cb48bf9e8f4144bf7b09106e2214 Merge: 5b1142a 0987ef5 Date: Fri Aug 2 08:51:05 2019 -0700 Merge pull request #4101 from RosettaCommons/tigerous/sci-tests-loop-model-kic-fragments-12res Tigerous/sci tests loop model kic fragments 12res commit 5b1142a6318407d2851a8cf3d0344ea79e0ba977 Merge: 818fbd5 9c90973 Date: Fri Aug 2 08:50:36 2019 -0700 Merge pull request #4100 from RosettaCommons/tigerous/sci-tests-loop-model-ngk-12res Tigerous/sci tests loop model ngk 12res commit 818fbd5ffc1d15d81ae3db2bf79023f5e3515284 Merge: 30fc508 5e78ff8 Date: Thu Aug 1 22:24:35 2019 -0400 Merge pull request #4127 from RosettaCommons/JackMaguire/code_templates Slight changes to code templates. Thanks to Jared and Vikram for the approvals! commit 30fc508eea38b90b841d09ae4d3c18a4bb401921 Merge: fbb3a09 45d9609 Date: Thu Aug 1 10:22:37 2019 -0500 Merge pull request #4110 from RosettaCommons/jadolfbr/mmtf_pose_output This PR adds an mmTFPoseOutputter and spec for JD3 output. It also adds directory creation during output (write_output) functions in the outputters. A bit of cleanup here and there. commit fbb3a090bb03fba6677478f034727c70913187bb Merge: 8673b00 eb7b739 Date: Wed Jul 31 15:24:06 2019 -0700 Merge pull request #4120 from RosettaCommons/dimaio/voxel_refine_bug Fix a bug that can occur in voxel refinement commit 8673b008b34ea52b047efcdde006c3cc0934121b Merge: c61f506 983e65c Date: Wed Jul 31 11:54:52 2019 -0400 Merge pull request #4059 from RosettaCommons/rfalford12/membrane-pyrosetta-sci-benchmark Membrane energy function scientific benchmarks part #3: ddG of mutation ===== This pull request will add the ddG of mutation scientific benchmark tests for membrane energy functions. This test is part of a suite of four tests that can be used to compare implicit membrane models, and have been most recently used to demonstrate sizeable scientific improvements by franklin2019. commit c61f50614797b0aec04292269f066e1b3a3ded3b Merge: a317120 65523c1 Date: Wed Jul 31 11:50:17 2019 -0400 Merge pull request #4114 from RosettaCommons/everyday847/simple_design_features SWM Design: support for all IUPAC characters (like 'n') commit a317120b629ca36e08c413ec405f96e9dd4922ce Merge: 2c6ea1d 9cdc615 Date: Tue Jul 30 14:38:51 2019 -0400 Merge pull request #4119 from RosettaCommons/JWLabonte/tracers AtomTree: Changing tracer volume on something that is not really an error This merge will silence an error message given when the AtomTree cannot find a DoF for a torsion angle, even though the atoms exist. This often occurs in the case of cyclic systems. The way the code is currently written, Conformation will simply calculate the angles on the fly in such a case, so there is no need to report an error; Rosetta can handle this case just fine. If it can't, such as if being asked to minimize that DoF, it will fail later anyhow with a clear error message. This merge will change about three dozen integration tests, which are currently outputting these errors while actually running to completion without any issue. All unit tests pass. I have checked all integration test changes, and they are as expected. commit 2c6ea1d261c503329476036f28f795b380fc43b5 Merge: 9a323bc fb5470d Date: Mon Jul 29 14:28:50 2019 -0700 Merge pull request #4106 from RosettaCommons/danpf/mmtf Add linkinformation + ssbond information to mmtfio