commit c48be2695c4ba637c6fa19ee5d289fd9a8aa99ef Merge: b4291ec 3cf06be Date: Sun Feb 21 11:50:06 2021 -0500 Merge pull request #5209 from RosettaCommons/jkleman/SciBen_small_updates adjusting cutoffs for sfxn comparison tests commit b4291eceef636604217b6f93f95aeb0a83a86a68 Merge: d739e36 a481df2 Date: Sat Feb 20 12:03:38 2021 -0500 Merge pull request #4208 from RosettaCommons/jadolfbr/glycan_mpi_bm Add glycan modeling scientific benchmark - thanks Jared!!! commit d739e36cafca09102a44b83c8e88e847e46bd04e Merge: 2f07551 209f8fc Date: Fri Feb 19 13:51:50 2021 -0600 Merge pull request #5251 from RosettaCommons/roccomoretti/cleanup_code_templates Clean up code templates. There were some issues with the formatting of code templates (stray whitespace, missing quotes). commit 2f07551448f5467ed3f25b6dddb4775d62815ade Merge: cbb5a35 17e26e5 Date: Fri Feb 19 09:44:35 2021 -0800 Merge pull request #4921 from RosettaCommons/guangfeng/galigdock_genparams Fix single bond conjugation commit cbb5a358827b446e0b94c075835291bba0ff3dd6 Merge: 17f6b54 117a512 Date: Fri Feb 19 16:47:53 2021 +0000 Merge pull request #5248 from RosettaCommons/TENeary/ssa_test_hotfix Increased timeout for SequenceSymmetricAnnealerTests commit 17f6b5496ee436a4a0909b22412e3a4412b866f6 Merge: edd2dcd bb4120b Date: Wed Feb 17 15:50:55 2021 -0700 Merge pull request #5244 from RosettaCommons/benchmark updating Benchmark scripts commit edd2dcd21e3bfbf1eb00085360bb17d6015bbbe5 Merge: 342d773 3a15eda Date: Tue Feb 16 11:40:43 2021 -0600 Merge pull request #5227 from RosettaCommons/jadolfbr/update_notebook_header Point notebook version to current, which includes bugfixes in RS integration notebook. commit 342d7732fd9e57ce6f4dd1d070ee06a2594f68e7 Merge: 22c26d3 dcf47ae Date: Tue Feb 16 11:57:02 2021 -0500 Merge pull request #5243 from RosettaCommons/JackMaguire/citations Adding three wonderful and awe-inspiring citations to the citation manager commit 22c26d3c7a6e8beed4201c4162b4c5d15d0b360c Merge: 7cd8f86 474fe9e Date: Sun Feb 14 15:14:38 2021 -0600 Merge pull request #5237 from RosettaCommons/roccomoretti/fix_boost_warnings Fix Boost Deprecation Warnings We're currently encountering a number of deprecation warnings from Boost. Infuriatingly, that's not because of anything we're doing in Rosetta, but instead it's due to Boost's own usage of Boost headers. Since we initially updated to Boost 1.74 and ran into these issues, fixes for them have been posted to the upstream repos. This PR selectively updates the Boost submodules at issue to a version which has the fixes. (It's not a general update of Boost.) commit 7cd8f867496c2dd9147795fa146d36e4f5e1eb9e Merge: be1c2e2 3b74d4f Date: Sat Feb 13 19:22:48 2021 -0600 Merge pull request #5217 from RosettaCommons/alamo/deer_rewrites_feb2021 Bug fixes for some files in core/scoring/epr_deer commit be1c2e2a8dab3e44995ea998eeb29d12ee2ebe4c Merge: 438e69d 2b6ca4b Date: Sat Feb 13 09:36:58 2021 -0500 Merge pull request #5238 from RosettaCommons/ssrb19/docking_scientific_test_corrections Clarified comments on docking scientific benchmark commit 438e69da6996b5014465071bbd66fe602a9831f0 Merge: 671af91 587cb1d Date: Fri Feb 12 00:14:47 2021 -0500 Merge pull request #5232 from RosettaCommons/revert-5230-everyday847/new_rna_metrics Temporarily revert "New RNA metrics" (which broke the build) - Thanks Vikram!!! commit 671af91fa906ece3f9b5dee467525c0ce91ed105 Merge: 200eef5 6ff93a2 Date: Thu Feb 11 15:19:14 2021 -0800 Merge pull request #5230 from RosettaCommons/everyday847/new_rna_metrics New RNA metrics commit 200eef5c7cad55462fbcb0b80c60e279ea1da3ed Merge: 3e306fa 9502cc8 Date: Tue Feb 9 17:15:40 2021 -0700 Merge pull request #5210 from RosettaCommons/sergey/binder Fixing PyRosetta debug build. Enabling FaWaterToBilayerEnergy in PyRosetta Conda builds. commit 3e306fa982689bf33fd855a4ba57c8ac24d29747 Merge: c07233a 94de01e Date: Mon Feb 8 13:22:21 2021 -0500 Merge pull request #5216 from RosettaCommons/mlnance-patch-carb_weights Update tracer output re default carb-specific sf weights commit c07233a180569088c9e84814a632605cdfbcbed6 Merge: 8dbef34 a54c9e2 Date: Sun Feb 7 20:21:49 2021 -0500 Merge pull request #5218 from RosettaCommons/vmullig/fix_glcyo_valgrind_issue Fix an uninitialized variable issue in glycopeptide docking flagged by Valgrind The options system read is done only if the user has specified the option, so a default value is needed for `interface_distance_` in the `GlycopeptideDockingFlags` class; otherwise this is uninitialized if the user doesn't provide a value with a commandline flag. I'm providing a default that matches the default in both the options system and in the `RestrictToInterface` task operation (which this variable is used to configure). Admittedly, better still would be having the default set in only one place. commit 8dbef3435adb61a31c3adc7754416e66ab4ce9d9 Merge: 8221a4e 9be5315 Date: Sat Feb 6 12:48:48 2021 -0500 Merge pull request #4222 from RosettaCommons/jfell13/RosettaCM RosettaCM scientific test: merging this to have it in master. Jason Fell needs to look at the cutoffs again. Seems like there are still discrepancies between the paper (Song 2013 Structure) and the data here, I am not sure where it's coming from. commit 8221a4ee6471bfd5b6e3bd8ab43400b78bcf078c Merge: a3d7eb0 44ea572 Date: Fri Feb 5 09:05:54 2021 +0200 Merge pull request #5214 from RosettaCommons/python2_3_syntax updating a small change in tools into main commit a3d7eb023bf89809be34d2c12605eb480f56862f Merge: 2edc982 38b82c8 Date: Tue Feb 2 17:43:41 2021 -0500 Merge pull request #3493 from RosettaCommons/ysrinivasan/glycosylation Ysrinivasan/glycosylation commit 2edc982fb388b0230747e8468fdd5f288be1f380 Date: Tue Feb 2 01:13:44 2021 -0500 beautifying commit 2e6b58e942e8d5b106111043daef5e114cae1a43 Merge: e99c1fb 11e1eef Date: Mon Feb 1 07:53:55 2021 -0500 Merge pull request #5208 from RosettaCommons/JackMaguire/PyRotamerEliminator Fixing failing PyRosetta build commit e99c1fb62a39bd52a34923330d9028f121fbb878 Merge: 8c7b03f 7ea7db2 Date: Sun Jan 31 14:23:05 2021 +0200 Merge pull request #5211 from RosettaCommons/DZ_python2_to_3_syntax Adding a few changes of python syntax in tools to the main repo commit 8c7b03f82f880cbdec2845162e3b4925f91f6434 Merge: 5c8f7d5 eebbcaf Date: Sat Jan 30 02:14:22 2021 -0500 Merge pull request #5202 from RosettaCommons/vmullig/citation_script Add a python script to automatically update the citations list in the database given a new PubMed ID This adds a script to the `code_templates` directory called `add_citation_by_pubmed_id.py`. As the name suggests, it adds a new citation to `database/citations/rosetta_citations.txt` from an input PubMed ID. Example usage: ``` >~/rosetta_devcopy/Rosetta/main/source$ ./code_templates/add_citation_by_pubmed_id.py --pmid 31239046 Successfully imported pubmed-lookup package. Successfully found article titled "Using Rosetta for RNA homology modeling.". Adding PubMed ID 31239046 (DOI 10.1016/bs.mie.2019.05.026). to citations file. Wrote sorted citations list to "../database/citations/rosetta_citations.txt". Please be sure to commit your changes with "git add ../database/citations/rosetta_citations.txt && git commit". ``` After running this, `git diff` gives you the following: ``` diff --git a/database/citations/rosetta_citations.txt b/database/citations/rosetta_citations.txt index f8a24ebe767..855c5019c6f 100644 --- a/database/citations/rosetta_citations.txt +++ b/database/citations/rosetta_citations.txt @@ -504,6 +504,33 @@ [END_DOI] [END_CITATION] +[BEGIN_CITATION] + [BEGIN_PRIMARY_AUTHORS] + "" "Watkins" "AM" + [END_PRIMARY_AUTHORS] + [BEGIN_COAUTHORS] + "" "Rangan" "R" + [END_COAUTHORS] + [BEGIN_SENIOR_AUTHORS] + "" "Das" "R" + [END_SENIOR_AUTHORS] + [BEGIN_YEAR] + 2019 + [END_YEAR] + [BEGIN_TITLE] + Using Rosetta for RNA homology modeling. + [END_TITLE] + [BEGIN_JOURNAL] + Methods Enzymol + [END_JOURNAL] + [BEGIN_VOLUME_ISSUE_PAGES] + 623:177-207 + [END_VOLUME_ISSUE_PAGES] + [BEGIN_DOI] + 10.1016/bs.mie.2019.05.026 + [END_DOI] +[END_CITATION] + [BEGIN_CITATION] [BEGIN_PRIMARY_AUTHORS] "Vikram Khipple" "Mulligan" "VK" @@ -539,3 +566,4 @@ 10.1002/pro.3974 [END_DOI] [END_CITATION] ``` It's not quite perfect since it doesn't fill in the first names, but it's close enough. commit 5c8f7d5d10ac03ba32be1d653cbb59135bec71ff Merge: 1df8899 7440dad Date: Thu Jan 28 20:58:58 2021 -0500 Merge pull request #5195 from RosettaCommons/JackMaguire/PyRotamerEliminator Adding PyRosetta interface for creating a new RotamerSetsOperation commit 1df889908f6b5bdceccbdd1095c399242bd78cdc Merge: a50baef 526ebce Date: Wed Jan 27 20:50:14 2021 -0500 Merge pull request #5200 from RosettaCommons/JackMaguire/defunct_dfunc Giving the LinearPenaltyFunction a derivative Thanks for the review, Vikram! commit a50baef153a74a04529168be8dd27d4982ec1e88 Merge: ced40d8 8c33656 Date: Tue Jan 26 17:56:45 2021 -0800 Merge pull request #5204 from RosettaCommons/yhsia/taskawaresymminmover_tracer_debug changed TaskAwareSymMinMover MoveMap TR to TR.Debug commit ced40d88759e4301be084a9d32a4ad8691f42afa Merge: 8c59622 3c90dee Date: Tue Jan 26 17:38:25 2021 +0000 Merge pull request #5201 from RosettaCommons/TENeary/docs_update_sequence_symmetric_annealer Updated docs repo to point to most recent master. commit 8c59622444c3adf4afca6e8e23db4930078ec81b Merge: 4eb8441 58953cd Date: Mon Jan 25 10:03:11 2021 -0500 Merge pull request #5186 from RosettaCommons/MentenAI/AxisCsts This constraints the distance between an atom and the closest point to that atom on an axis. The axis is defined by two points, each of which are the midpoint of several AtomIDs. This should work with virtual atoms. commit 4eb84417e47d96eb2a2219a1cdff9d2186a0f74b Date: Fri Jan 22 12:20:47 2021 -0800 Fix Windows build (#5196) commit dad6bc802d0b463d84d2f00be25afc29b84c8f92 Merge: f604bd1 c6f90ba Date: Fri Jan 22 13:54:47 2021 -0600 Merge pull request #5188 from RosettaCommons/alamo/deer_rewrites_jan2021 Refactored and cleaned up core/scoring/epr_deer (Take 2) commit f604bd157be03abae465b127e0140329129cda6c Merge: 189d3a7 9c4e5d9 Date: Fri Jan 22 19:07:02 2021 +0000 Merge pull request #5168 from RosettaCommons/TENeary/sequence_symmetric_annealer_gcc_fix Changed benchmark signature, updated methods and test to fix gcc unit test errors commit 189d3a74e3920bed0ec590840a844581ae3e9c91 Merge: ef9434c 7661a54 Date: Fri Jan 22 10:58:59 2021 -0600 Merge pull request #5131 from RosettaCommons/jadolfbr/minmover This is a basic PR to set the default MinMover mintype to what is currently the default across Rosetta. Yes, there is more that could be done - including adding defaults to MinOptions to read from the options system, but I'm currently quite bogged down. @teetsf found this issue while using the MinMover in code and not getting it to minimize as well as well as we had hoped and tracked it to the default mintype being used in MinMover. commit ef9434c3fc16da3cea5900a708376d82ff20ea21 Merge: c63087d 6ca69f2 Date: Fri Jan 22 09:10:42 2021 -0600 Merge pull request #5132 from RosettaCommons/roccomoretti/rs_single_quote Enable RosettaScript parsing to allow single quotes on options According to @mwfranklin on Slack, the XML validator is perfectly fine with ``, but the Rosetta-specific Tag parser chokes on it, with a particularly obtuse error message. Supporting single quotes is relatively straightforward. commit c63087d4de69d6ffc65a448c1bb1678b2f052c8e Merge: 8a234d1 5a8f2e3 Date: Fri Jan 22 09:55:28 2021 -0500 Merge pull request #4855 from RosettaCommons/vmullig/gcn_test Add a test confirming that we can work with graph convolutional neural networks within Rosetta. This tests the RosettaTensorflowManager with a graph convolutional neural network (GCN). I'll need GCNs shortly for peptides, and others have been applying these to proteins. This PR also fixes a couple of off-by-one errors in the Tensorflow manager code. - [x] ~~Pull request #4606 should be merged before this one.~~ --> ~~PR #4606 has been merged into this one, and both will be merged together.~~ --> At @JackMaguire's request, we'll reopen PR #4606 and merge it before this one to keep changes suitably incremental. - [x] Conflicts with #4606 should be resolved before merging this, and `RosettaTensorflowSessionContainer::run_multi_input_session()` should be removed in favour of Jack's `RosettaTensorflowSessionContainer::run_multiheaded_session()`. - [x] Add the test observers, description, etc. - [x] Add a script to make the GCN (initialized with random weights). - [x] Add the GCN to the Rosetta database. (Note: this is a few hundred kilobytes.) - [x] Add expected output to the test directory. - [x] Add a pilot app that loads the GCN, provides it with known inputs, and tests whether we get the expected output. - [x] Exit with error status if the output does not match expected, within tolerance. - [x] Fix bugs locally. - [x] Check that this runs on the test server. It does! - [x] Error if run in non-Tensorflow builds. - [x] Beauty. - [x] Fix `app_exception_handling` test in non-tensorflow build. This PR also: - [x] Updates the `tools` submodule to point at the latest master of that repo. - [x] Removes an unused `RosettaTensorflowManager::set_session()` function. This function was unsafe, since it encourages creation of `RosettaTensorflowSessionContainers` (and Tensorflow sessions) by code external to the `RosettaTensorflowManager`. This prevents it from being a resource manager, and risks having things that it doesn't know about which compete for GPU access. (In any case, it probably wouldn't have been possible to use this, since the `RosettaTensorflowSessionContainer` class has a private constructor, and can only be constructed by the `RosettaTensorflowManager`.) - [x] ~~Adds a `RosettaTensorflowSessionContainer::run_multi_input_session()` class method, for Tensorflow models that take multiple input tensors (possibly of different sizes or dimension). This is needed for graph convolutional neural networks, which are typically represented by two to three input tensors (the adjacency matrix, the node data tensor, and the edge data tensor).~~ - [x] TODO: switch to @JackMaguire's `run_multiheaded_session()` from pull request #4606. I've accidentally reinvented the wheel here, so I'll take my implementation out and use his. - [x] Fixes an off-by-one error in some tensor accessors. - [x] Updates the header-only Tensorflow C-API files from Tensorflow 1.14 (which can't read Tensorflow 2 models) to Tensorflow 1.15 (the most recent version of the C-API, which _can_ read Tensorflow 2 models). Note that I copied the new licence for 1.15 to replace the 1.14 licence, so there are some cosmetic changes to the licence file. (Tensorflow is Apache-licenced, and I previously checked with UW Comotion to ensure that we can include these headers.) commit 8a234d1e41142ce7bd58f06351f25b54fd1986d3 Merge: f28e5ff 785bdfd Date: Thu Jan 21 17:02:18 2021 -0700 Merge pull request #5194 from RosettaCommons/arlosi/winbuild adding `windows` Benchmark script commit f28e5ffc6381f546e8edec1a7336f23b460f6627 Merge: 61635ee 9142c2c Date: Wed Jan 20 17:06:30 2021 -0700 Merge pull request #5193 from RosettaCommons/benchmark Updating unit tests run.py script, adding `--verbose` command line option commit 61635ee2d06c0e4fbf5f64f8183f34928d47543c Merge: 779257c 70efbf3 Date: Thu Jan 14 18:57:54 2021 -0500 Merge pull request #4525 from RosettaCommons/jkleman/SciBen_sfxns2 Jkleman/sci ben sfxns2: scorefunction comparison for a handful of scientific benchmarks: docking, design, loop modeling, relax; located in /Rosetta/main/tests/scientific/sfxn_comparison_tests/; will NOT be scheduled like the regular scientific tests as these take a while to run; will be scheduled about every 6 months; commit 779257cbfaf84282bde2650f54068b1ae69bbcc4 Merge: 653e6ac 9c47824 Date: Thu Jan 14 03:54:44 2021 -0500 Merge pull request #5183 from RosettaCommons/vmullig/cite_symmdesign_paper Update citations for symmetric design paper (was under review, now published). This updates a citation listing in the database to include journal, volume, issue, page numbers, and DOI now that it's published. This is a minor change. commit 653e6ac42c0f0e154bb265620ddc7e6266d82fbf Merge: b6fe148 2dade26 Date: Wed Jan 13 22:19:32 2021 -0500 Merge pull request #5182 from RosettaCommons/vmullig/update_rosettascripts_repo Add NDM-1 design scripts to the RosettaScripts scripts repo, and update the submodule. This adds the scripts used in **Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, Strynadka NCJ, and Baker D. (2020): Computationally-designed peptide macrocycle inhibitors of New Delhi metallo-beta-lactamase 1** to the RosettaScripts scripts repo, and updates the main repo to point at the current version of the scripts submodule. commit b6fe14891f20d7c65df865cd23824c1ba69da7c8 Merge: 6f0b235 0a79498 Date: Wed Jan 13 20:24:10 2021 -0500 Merge pull request #5136 from aleaverfay/fix_switch_chain_order_pdb_info_bug Add nullptr check for pdb_info to SwitchChainOrderMover SwitchChainOrderMover needs to check that the input pose's PDBInfo object is not null before trying to copy data out of it. Thanks @rpark01 commit 6f0b235be63a2bde515f63a0521c210958dcdbc1 Merge: d2d537f 25f35e9 Date: Wed Jan 13 09:55:00 2021 -0600 Merge pull request #4987 from RosettaCommons/jadolfbr/custom_type_as_name This PR is orthogonal to @roccomoretti 's awesome additions in PR #4986. It adds two options to control the final naming of the metrics when used with RunSimpleMetrics. -simple_metrics:use_name_as_custom_type This option simply uses the tag name as the custom_type. If custom_type is given, it will override this option. -simple_metrics:use_name_as_metric This option uses the tag name as the core name. It ignores custom_type. Prefix/Suffix from RunSM is still added. commit d2d537f6e495ef27f1b9623ed1d370ac20f5babb Merge: 28db469 cb075ac Date: Mon Jan 11 09:23:28 2021 -0500 Merge pull request #5164 from RosettaCommons/AmeyaHarmalkar/backrub_movemap Allows Backrub to define pivot residues based on movemap and movemap_factory (#5163) commit 28db46952b3ccc4dd137188de1c2c51d1fd3adf2 Merge: ac7752d 2d25345 Date: Mon Jan 11 08:54:22 2021 -0500 Merge pull request #4660 from RosettaCommons/JackMaguire/PreallocateThreads Adding thread preallocation functionality to the ThreadManager commit ac7752d164edb0123f027d8fb805df5a9142ef9a Merge: 418492d f3f389c Date: Mon Jan 11 08:31:44 2021 -0500 Merge pull request #5048 from RosettaCommons/MentenAI/SmartDesign_p1 Adding observer interface for the packer commit 418492db5e216b884a12d5f855ee49f7a57563b7 Merge: d980821 f4cdc14 Date: Mon Jan 11 03:32:05 2021 -0500 Merge pull request #5176 from RosettaCommons/vmullig/fix_hyp_cutpoints Fix a typo in the cutpoint patch affecting HYP and DHYP residue types. Virtual atom OVU1 was at some point mistranscribed as "OVR1", and this got copied a few times. This is a minor fix. commit d980821a24c3b1542ed7852d98d11ba369c43dfd Merge: 958fb90 e996964 Date: Fri Jan 8 07:33:12 2021 -0500 Merge pull request #5169 from RosettaCommons/MentenAI/IG2Disk Decreasing memory usage of the InteractionGraphSummaryMetric by writing directly to disk commit 958fb90765c7ce7956b3db57399c6cd3119d6cd6 Merge: 7b1a888 e805e8c Date: Thu Jan 7 13:50:12 2021 -0500 Merge pull request #5050 from RosettaCommons/jkleman/SciBen_ligands scientific benchmarks ligands: fixing ligand_scoring_ranking benchmark with Shannon's help - thanks Shannon! commit 7b1a8888dce1e21c697fea3718f692979e85aca3 Merge: 7e929be 8c5882b Date: Thu Jan 7 12:21:03 2021 -0500 Merge pull request #5056 from RosettaCommons/jkleman/SciBen_mhc Mostly cosmetic changes to the following scientific tests: * MHC_epitope * mp_dock * make_fragments * fragment_picking commit 7e929be75c296a759c9507dbae49e20cf5f51dae Merge: 11a8eec 16e7159 Date: Wed Jan 6 10:46:00 2021 -0600 Merge pull request #5155 from RosettaCommons/ninabozhanova/cro_reader ChromophoreDataReader class and unit tests for the class. The class reads information about correspondence between FP chromophore's and standard Rosetta residue's atom names from a provided text file. commit 11a8eec5580272904124a41070495d9491db07cc Merge: d3f6bcd ffb3ea3 Date: Mon Jan 4 21:30:21 2021 -0500 Merge pull request #4606 from RosettaCommons/JackMaguire/tensorflow_manager_pr3 Third incremental merge of the TensorFlowManager commit d3f6bcdbbd6cec7039a5732e11fdf5ffe5ccc9a5 Merge: 1ae38b9 c07ec20 Date: Mon Jan 4 17:11:10 2021 -0500 Merge pull request #5157 from RosettaCommons/vmullig/improve_d_aa_import Improve import of D- and L-amino acids that cannot be distringuished by 3-letter code D-amino acids that are mirror images of canonical L-amino acids have unique three-letter codes in Rosetta, and certain noncanonicals have also been given distinct three-letter codes. With only three letters to play with, though, it's not possible to ensure that omitting the third letter and prepending "D" would generate a unique three-letter code. (Even with the canonical amino acids, this would create name conflicts: "DAS" would be the code for both D-Asp and D-Asn, if we hadn't manually specified that the latter would be "DAN".) For this reason, Rosetta doesn't even try to assign unique three-letter codes when it auto-generates D-amino acid versions of canonical L-amino acids; it just keeps the same three-letter code for both. This creates problems on read-in. This pull request ensures that if a structure is read in containing an alpha-, beta-, or gamma-amino acid for which the L- and D-amino acid three-letter codes are the same, the chirality is auto-determined by calling Andy's detect_ld_chirality_from_polymer_residue() function. @everyday847 @dougrenfrew @JackMaguire commit 1ae38b9c580a824e6c8872ed6da68a4a6a311a70 Merge: 5cf92ed 080de5d Date: Mon Dec 28 16:57:29 2020 -0700 Merge pull request #5166 from RosettaCommons/sergey/rosie updating ROSIE scripts commit 5cf92ed272722577eefe3583f7883d761a93806e Merge: e37c919 6e50f43 Date: Tue Dec 22 00:54:15 2020 -0500 Merge pull request #5156 from RosettaCommons/vmullig/fix_gcc_10_compilation Fix gcc 10 build. The gcc 10 compiler complains about a few minor things that the gcc 9 compiler is happy with. This PR aims to fix those. commit e37c9194bf7387d31ef04807aced716bbb7323af Merge: 209fec9 6fd37da Date: Mon Dec 21 15:33:18 2020 +0000 Merge pull request #5066 from RosettaCommons/TENeary/sequence_symmetry_update SequenceSymmetricAnnealer update to allow use of any generic ResidueSelectors commit 209fec98116cc1f8763110d5d381c283efb22e16 Date: Sat Dec 19 21:11:24 2020 -0800 update pyrosetta_scripts submodule (#5154) commit 5dee8ba67c4d3cc4d6a22d14a30801167cf1510c Merge: 072ce4b 7336831 Date: Fri Dec 18 14:24:45 2020 -0800 Merge pull request #5151 from RosettaCommons/weitzner/fix-hdf5-cmake-build Fix HDF5 cmake build commit 072ce4bc24aa689bbc6b75800d9ba1af6b8fa6e7 Merge: 9fc8c1a aee5901 Date: Fri Dec 18 14:11:23 2020 -0800 Merge pull request #5148 from RosettaCommons/everyday847/recces_updates RECCES updates and bugfixes commit 9fc8c1aad302d7ede6374a81669fc3764a940c7a Merge: c37fbbc 4e84ebe Date: Fri Dec 18 11:50:10 2020 -0700 Merge pull request #5149 from RosettaCommons/benchmark fixing scientific.cofactor_binding_sites test commit c37fbbcaf2d41c98f10479240f4d461701719b8e Merge: 896736e 0ef726b Date: Thu Dec 17 12:14:13 2020 -0600 Merge pull request #5093 from RosettaCommons/ninabozhanova/chromophore Adding ReadResidueCoordinatesFromPDB class, which reads and saves xyz coordinates for the specified residue(s) from a PDB file, and a unit test for it. commit 896736e33ce1615124f6da60794dba432d876a57 Merge: 8ad9c9f c889c29 Date: Wed Dec 16 15:00:15 2020 -0500 Merge pull request #4917 from RosettaCommons/bcov/dont_reinit_mover Option to not reload XML for every structure commit 8ad9c9f1a9359f05c5c863b9e3c9ccfd2b30bc9a Merge: 5a82c7c 92ed084 Date: Tue Dec 15 17:54:38 2020 -0500 Merge pull request #5139 from RosettaCommons/vmullig/BuriedUnsatHbonds2_to_protocols Move BuriedUnsatHbonds2 filter from devel to protocols This was requested by a user. @aleaverfay reports that this can be moved to protocols. Tasks: - [x] Move files. - [x] Update namespaces. - [x] Update `.src.settings` files. - [x] Check compilation. - [x] Check unit test compilation. - [x] Check that there exists a unit or integration test. --> Yes, several integration tests. - [x] Check that XSD functions exist. - [x] Add a description to the XSD function. - [x] Check that parse_my_tag function exists. - [x] Documentation. - [x] Beauty. Integration test changes are all cosmetic and expected. commit 5a82c7c9b91219aa82625e19a363f55d6426f91e Merge: 1295438 67ea6e7 Date: Sun Dec 13 14:11:30 2020 -0700 Merge pull request #5126 from RosettaCommons/benchmark Benchmark scripts update: adding SLURM driver