commit 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6
Merge: e863e58 b669b4f
Date:   Mon Apr 19 19:41:37 2021 -0600

    Merge pull request #5358 from RosettaCommons/klimaj/molfile_to_params
    
    Broaden the allowed root atoms in molfile_to_params.py

commit e863e58ce2b5bf1f83473dd5854e8440aabb11cc
Merge: 1a2dbae 86a9eed
Date:   Sat Apr 17 10:12:03 2021 -0700

    Merge pull request #5355 from RosettaCommons/guangfeng/galiganddock_update2
    
    Bugfixes and updates in GALigandDock and GenericBondedPotential

commit 1a2dbaedf3f0984a3585e9bcf34a616d5af80dde
Merge: b8329db 9f99329
Date:   Fri Apr 16 11:12:56 2021 -0500

    Merge pull request #5353 from RosettaCommons/roccomoretti/ignore_big_files
    
    Add .gitignore entries for some potentially big files
    
    From my quick run of my large file detection script (RosettaCommons/tools#99), I identified a number of filetypes that can be quite large which were likely added to the repo accidentally. Add these files to the .gitignore such that future people will be less likely to accidentally commit them.

commit b8329db0115bfb5b66f98ce3b33224ecc672d042
Merge: e0c2f36 69dfcf8
Date:   Thu Apr 15 13:47:21 2021 -0400

    Merge pull request #5354 from RosettaCommons/jkleman/SciBen_more_small_fixes
    
    Jkleman/sci ben more small fixes:
    various small fixes to scientific benchmarks

commit e0c2f36c08419d20759d74978fdea29166abbfbe
Merge: 74752e1 852f9bb
Date:   Tue Apr 13 13:42:06 2021 -0400

    Merge pull request #5279 from RosettaCommons/AmeyaHarmalkar/flexible_dock_sci_tests
    
    Adds flexible docking Scientific Tests

commit 74752e1d0d95c9f4d6cde2fae00e712c22b3d5f4
Merge: a81f6bd 60d5148
Date:   Tue Apr 13 11:37:47 2021 -0400

    Merge pull request #5326 from RosettaCommons/jkleman/SciBen_small_fixes
    
    Jkleman/sci ben small fixes: mostly cosmetic changes to PDFing, readme's, citations, etc. Cutoff's for FlexPepDock changed according to the paper (as per Ora). Ligand docking: removing betaNov16 and talaris for ligand docking regular runs and using PDB files instead of zipped ones to increase compression according to Sergey.

commit a81f6bd5d65d434fe237ca332eaa239883018ac9
Merge: d9a3bd2 cc09521
Date:   Sun Apr 11 03:33:53 2021 -0400

    Merge pull request #5346 from RosettaCommons/vmullig/more_verbose_tensorflow_error
    
    Make a Tensorflow error message more verbose to aid debugging
    
    Once in a while, I'm seeing a failure in the Tensorflow tests (_e.g._ https://b3.graylab.jhu.edu/sub-test/224304352), in a piece of code that combines a vector of N-tensors into an (N+1)-tensor.  This _might_ be due to float-float comparisons (and I hope that's all it is), but I would have thought that `memcpy` would guarantee that float-float comparisons would be valid.  For this reason, I'm going to make the error messages more verbose so that we can see for ourselves what's going wrong when this test fails on the test server.
    
    @JackMaguire

commit d9a3bd213c46a251cee43ec975f038b61f5b88bb
Merge: 6872805 1d285cc
Date:   Fri Apr 9 11:40:46 2021 -0600

    Merge pull request #5343 from RosettaCommons/benchmark
    
    Updating benchmark.py to allow usage of the same Python interpreter when running tests

commit 68728050491ac89a7566607bf770822ce0dee21b
Merge: 59497d6 d586440
Date:   Thu Apr 8 04:37:37 2021 -0400

    Merge pull request #5340 from RosettaCommons/vmullig/fix_trRosetta_valgrind_test
    
    Trying to fix failing Valgrind trRosetta tests.
    
    I think I have a little mistake in the test scripts.  This does indeed fix the Valgrind test.

commit 59497d678347f6dacb1c7d46bbc96fc41380d1c4
Merge: 27ac80f 6f79469
Date:   Wed Apr 7 17:45:07 2021 -0400

    Merge pull request #5333 from RosettaCommons/vmullig/fix_trRosetta_integration_test
    
    Fix the trRosetta_test_predict_ubiquitin integration test in non-Tensorflow builds.
    
    The non-Tensorflow version of the trRosetta_test_predict_ubiquitin integration test just checks that the trRosetta application exits with a suitable error message if Rosetta wasn't built with Tensorflow support.  (The error message explains how to build Rosetta properly).  To avoid spurious integration test changes, the test script uses `sed` to remove some lines that would change with each run.  Unfortunately, on Macs `sed` doesn't work properly (one needs to install `gsed` for ordinary functionality), so the lines stay in and the test spurious fails every time it runs.  This PR tries to fix that.
    
    Other little things:
    - This PR fixes a spelling mistake in the error message ("octothorp", not "octothorpe").
    - This PR updates the documentation submodule to point to the latest master of the documentation repository.

commit 27ac80f34c3ced07833df4679868c2d80ed646fd
Merge: b0f375c 7875ba9
Date:   Wed Apr 7 15:08:30 2021 -0600

    Merge pull request #5336 from RosettaCommons/benchmark
    
    updating release scripts

commit b0f375c4dc0c8a7f8cc8e2ac6fa3b71fcdcc2402
Merge: c8fc770 4f927f79
Date:   Fri Apr 2 16:15:01 2021 -0600

    Merge pull request #5331 from RosettaCommons/benchmark
    
    fixing antibody-grafting scientific test

commit c8fc770a7ca5656d8bfbbd5374248de9d53e7220
Merge: 7d1d5c1 31ddd62
Date:   Wed Mar 31 19:11:27 2021 -0400

    Merge pull request #5119 from RosettaCommons/vmullig/trRosetta_into_Rosetta
    
    Put trRosetta into Rosetta to allow protocol development on top, and to provide access to Foldit
    
    *Note: since incremental merges 1-3 are now merged (pull requests #5308, #5309, and #5314), this PR only adds the trRosetta application and puts an option in for the AbinitioRelax application to use trRosetta.  Most of the files changed are unit test files (though they're in the integration test suite since we lack a dedicated unit test suite for the Tensorflow build.)*
    
    This is something that we talked about a while back; apologies for only getting to it now.  This PR aims to:
    
    - [x] Add trRosetta to the Rosetta database.  (Note: since the model is 91 MB, this has been added as a submodule that gets pulled automatically only if the `extras=tensorflow` or `extras=tensorflow_gpu` options are used).  The trRosetta licence is the MIT licence, which is compatible with the Rosetta licence, and I've talked to Sergey, Ivan, and Jianyi to get their blessing for this.
    - [x] Add hooks to the protocols layer for passing in the trRosetta inputs (sequences) and receiving back outputs (distance and angle constraints) as objects compatible with downstream Rosetta manipulation, tied in to the `RosettaTensorflowManager`.
    - [x] Add a standard way of adding the constraints to a pose (a constraints generator).
         - [x] CitationManager functions for constraints generator.
         - [x] Add distance constraints.
         - [x] Add phi constraints.
         - [x] Add theta constraints.
         - [x] Add omega constraints.
         - [x] Options for adding each of these independently.
         - [x] Options for controlling the probability cutoffs for distance, omega, phi, and theta constraints.
         - [x] Documentation for options making it clear that "phi", "omega", etc. don't have their usual meanings, here.
    - [x] Convert the Python minimization protocol to a Rosetta mover.
         - [x] `parse_my_tag()` function.
         - [x] `provide_xml_schema()` function.
         - [x] `provide_citation_info()` function.
         - [x] `apply()` function.
              - [x] Fullatom refinement steps.
              - [x] Compute RMSD to native.
         - [x] Options for controlling the probability cutoffs for distance, omega, phi, and theta constraints.
         - [x]  Add settings for scorefunctions for the various stages:
              - [x] Initialize from options system.
              - [x] Initialize from XML.
         - ~~Handle gapped FASTAs:~~ --> Put off to future PR, where I'll add residue selector support.
              - ~~Check that the FASTA width _with_ gaps matches the MSA width.~~
              - ~~Map constraints from MSA numbering to _ungapped_ FASTA numbering.  (Need to set up a map for this.)~~
    - [x] Add option of using trRosetta constraints in classic _ab initio_.
         - [x] In fullatom phase as well.
         - [x] Citations.
         - [x] Documentation.
    - [x] Add an app for running the trRosetta minimization protocol.
         - [x] Suitable error if not compiled with `extras=tensorflow` or `extras=tensorflow_gpu`, with instructions for compilation.  (Put code for writing the instructions in `basic::tensorflow_manager`.)
    - [x] Fix compilation when `extras=tensorflow` is not used.
    - [x] Check `tensorflow_gpu` performance. --> A quick test on my laptop shows about a fourfold speedup on the laptop GPU compared to the CPU.
    - [x] Unit tests (pass/fail tests in `integration.tensorflow` suite).
         - [x] Constraints generator.
              - [x] Distance constraints.
                   - [x] Check error in distance constraints.  It still seems higher than it should be. --> Little mistake fixed.
              - [x] Phi constraints.
              - [x] Theta constraints.
              - [x] Omega constraints.
    - [x] Integration tests:
         - [x] RosettaScripts.
              - [x] trRosettaProtocol mover.
                   - [x] Check why this does not output RMSD values. --> Fixed in pull request #5301.
              - [x] Constraints generator.
         - [x] trRosetta app.
              - [x] With Ramachandran initialization.
              - [x] With initialization by bins.
         - [x] Classic ab initio app.
    - [x] Make `hb_cen_soft` into an option that can be set from code/RosettaScripts.
    - [x] Documentation --> RosettaCommons/documentation#44 adds documentation for the C++ trRosetta.
    - [x] Beauty.
    
    As a guide, here's what will ultimately be in master.  The stuff in basic is already there.  PR #5308 adds the stuff in protocols.2.  PR #5309 adds the trRosettaConstraintGenerator.  Once those are merged, the trRosettaProtocolMover, the trRosetta app, and the changes to AbinitioRelax are what remain.
    
    ![image](https://user-images.githubusercontent.com/4205776/112569688-08256000-8dbb-11eb-8cfc-2eb28fe9d3dc.png)
    
    Before merging this:
    - [x] Revert change to `.vscode/c_cpp_properties.json`.
    - [x] Pull request #4606 must be merged.
    - [x] Pull request #4855 must be merged.
    - [x] Pull request #5224 must be merged.
    - [x] Pull request #5225 must be merged.
    - [x] Pull request #5301 must be merged.
    - [x] Pull request #5236 must be merged.
    - [x] Pull request #5308 must be merged.  This is an incremental merge that cherry-picks the `trRosettaProtocolBase` and `trRosettaProtocol_v1` classes from this one, along with their associated tests.
    - [x] Pull request #5309 must be merged.  This is an incremental merge that cherry-picks the `trRosettaConstriantGenerator` class from this one, along with its associated tests.
    - [x] Pull request #5314 must be merged.  This is an incremental merge that cherry-picks the `trRosettaProtocolMover` from this PR, along with its tests.
    
    Note:
    - Pull request #5235 is an efficiency tweak that will benefit the stuff implemented in this PR, but it does not have to be merged before this PR.
    
    ![image](https://user-images.githubusercontent.com/4205776/101086651-2e5e9000-357f-11eb-880f-0f780f8f70b3.png)

commit 7d1d5c103e0ce113887abd129e409d49cc178f3a
Merge: 87c04a2 439c554
Date:   Wed Mar 31 11:25:48 2021 -0700

    Merge pull request #5325 from RosettaCommons/guangfeng/fix_unused_variable
    
    Quick fix of complaints from code quality check
    
    > lgtm!
    
    Thanks!

commit 87c04a2129ebf398809224a4b349559d7d7d2269
Merge: 6dd9ffa c06a79d
Date:   Tue Mar 30 15:46:32 2021 -0400

    Merge pull request #5302 from RosettaCommons/rahelf/iam_disulfide_detect
    
    Detection of disulfides during RAbD

commit 6dd9ffa2fdaaf5cc5e222b8f13ae74467d7fee87
Merge: ce326d2 b4011fd
Date:   Tue Mar 30 12:09:16 2021 -0500

    Merge pull request #5316 from RosettaCommons/tjonesster/m1CompileSupport
    
    Added support for compiling on macos running on the new M1 chip

commit ce326d22714489c6c21c9c68df7b6ac1738032c1
Merge: cb2d2cf 87a793c
Date:   Tue Mar 30 09:39:46 2021 -0700

    Merge pull request #4830 from RosettaCommons/dimaio/galigand_dock_multires_ligand
    
    Dimaio/galigand dock multires ligand

commit cb2d2cf9fe67136b95f9d91b3fe91d26b6e8f572
Merge: a9d8142 737094e
Date:   Tue Mar 30 12:35:42 2021 -0400

    Merge pull request #5318 from RosettaCommons/mlnance/fixed_glycan_foldtree_setup
    
    Fix foldtree setup for conjugated and branched glycans

commit a9d81423eda08644432dd6fc94ac3a88313631f2
Merge: c526077 820d3ed
Date:   Tue Mar 30 12:33:51 2021 -0400

    Merge pull request #5271 from RosettaCommons/jkleman/SciBen_mpddg_sfxn_comp
    
    * added sfxn comparison tests for membrane ddG
    * updates sfxn comparison tests for docking
    * fixed nstruct for fragment picking for more efficient running

commit c52607701b457f2bb537b11f9a6f46f3ed2f7d07
Merge: 7112320 f680618
Date:   Tue Mar 30 10:53:43 2021 +0200

    Merge pull request #5239 from RosettaCommons/bud-graziano/RosettaSurf
    
    Merge ShapeSimilarity and ElectrostaticSimilarity metrics as part of the RosettaSurf protocol

commit 711232075deb5fc323919f4fe972bff2017a6cc3
Merge: 551c481 5122a68
Date:   Mon Mar 29 23:55:17 2021 -0400

    Merge pull request #5314 from RosettaCommons/vmullig/trRosetta_into_Rosetta_incremental_merge_3
    
    Incremental merge #3 to get trRosetta into Rosetta
    
    This is the third in a series of incremental merges to put trRosetta into Rosetta, to allow protocol development on top.  This PR adds the trRosettaProtocolMover, a RosettaScripts and PyRosetta-scriptable mover that takes an MSA as input and produces a predicted structure pose as output (using the trRosettaConstraintGenerator and trRosettaProtocol, already merged into master, under the hood).  The image below serves as a guide: everything below the trRosettaProtocolMover is already in master, this PR adds the trRosettaProtocolMover, and everything above it remains to be merged.
    
    Although this PR changes 48 files, most of those are unit test files that were added.  Note that for Tensorflow modules, the unit tests are implemented as part of our integration test suite (though they are pass-fail tests), since we have no unit test suite for the Tensorflow build.
    
    This PR is intended to be merged before PR #5119.
    
    ![image](https://user-images.githubusercontent.com/4205776/112569688-08256000-8dbb-11eb-8cfc-2eb28fe9d3dc.png)

commit 551c4818621a531b62a5d38a88b6f775740bd22b
Merge: 3c7c8ca 1934c1b
Date:   Mon Mar 29 19:32:46 2021 -0500

    Merge pull request #5303 from RosettaCommons/roccomoretti/membrane_in_pose
    
    Move old-style membrane info printing from tracer to Pose.
    
     Turn the noisy membrane output to debug level, and stick the info in the pose instead. The most recent set of info gets overwritten in the pose. In-Tracer output can be recovered with the option `-out:levels core.scoring.MembranePotential:debug`.
    
    To enable this in an easy-to-use fashion, Pose comments are now written to output PDBs when they're present. (They were already included in silent files.) Pose-comment read-in is still controlled by an option.

commit 3c7c8ca0dddd4de6983e72f146bcca37ca2816b5
Merge: 9cfcb2b 6b6a862
Date:   Mon Mar 29 17:35:28 2021 -0600

    Merge pull request #5319 from RosettaCommons/sergey/f
    
    fixing issues with Python-3 PyMOL scripts

commit 9cfcb2b83f948a4469e815640c0d983ad84c6454
Merge: 58921fe 6a383e4
Date:   Mon Mar 29 12:31:04 2021 -0500

    Merge pull request #5310 from RosettaCommons/roccomoretti/speedup_glycopeptidedocking
    
    Speed up glycopeptide docking integration tests.
    
    The glycopeptide docking tests have been timing out on the test server with a magenta failure for some time now. These can be sped up (for the integration test, at least) by reducing the number of cycles being used in the refinement. Add options to permit this, and use them in the integration tests.

commit 58921fe0a40fe2028a7057f91d1a48f78df7274d
Date:   Sun Mar 28 18:06:29 2021 -0400

    RosettaAI: Setting rosetta_scripts_scripts submodule to latest origin/master version.

commit 1c80030ac3dddd13e6d446b7ac5fda92cb370779
Merge: ed6a556 8e61a5b
Date:   Sun Mar 28 00:51:40 2021 -0400

    Merge pull request #5309 from RosettaCommons/vmullig/trRosetta_into_Rosetta_incremental_merge_2
    
    Incremental merge 2 for putting trRosetta into Rosetta
    
    This merge adds the trRosettaConstraintGenerator and all its associated test files.  It must be merged prior to pull request #5119.
    
    - [x] Pull request #5308 must be merged before this one.
    - [x] Need to fix a few test failures.
    - [x] Andy caught a bug: a3m files that contain a comment line that starts with an octothorp cause NaN errors.  (And HHBlits produces a3m files with an initial comment line starting with an octothorp.)
    
    As a guide, once PR #5308 is merged, the stuff in this diagram that's in protocols.2 or basic will be in master already.  This PR adds the trRosettaConstraintGenerator.  The trRosettaProtocolMover, the trRosetta application, and the modifications to the AbinitioRelax application will be in a subsequent PR.
    
    ![image](https://user-images.githubusercontent.com/4205776/112569688-08256000-8dbb-11eb-8cfc-2eb28fe9d3dc.png)

commit ed6a5560506cfd327d4a6a3e2c9b0c9f6f4a6535
Merge: 14730b1 405ea8e
Date:   Fri Mar 26 16:09:25 2021 -0500

    Merge pull request #5307 from RosettaCommons/roccomoretti/fix_advanced_docking
    
    Python3 updates in tools dir. This should hopefully fix the advanced_protein-protein_docking test on the test server.

commit 14730b1d0b988c5b3f2dba064e1cf9c160dea809
Merge: 699ec9c 0527d46
Date:   Fri Mar 26 16:08:44 2021 -0500

    Merge pull request #5306 from RosettaCommons/roccomoretti/fix_clang_tidy_RNA
    
    Fix issue with Clang Tidy in RNA_CoarseDistEnergy in master. Virtual is redundant with override.

commit 699ec9c33a981997a850931385a8ac6e7bd5811f
Merge: e7954d6 061eceb
Date:   Fri Mar 26 04:08:27 2021 -0400

    Merge pull request #5308 from RosettaCommons/Rosetta/trRosetta_into_Rosetta_incremental_merge_1
    
    Incremental merge 1 for trRosetta integration into Rosetta
    
    This PR attempts to pull the basic trRosetta calculator functionality (the `trRosettaProtocolBase` and `trRosettaProtocol_v1` classes) into their own pull request, along with all the test files for this base functionality, while leaving the mover and constraint generator (and all of their tests) for a later pull request.  It is intended to be merged before pull requests #5119 and #5309.
    
    As a guide, the infrastructure in basic in this image is already in master.  This PR adds the stuff in protocols.2.  Subsequent PRs will add the stuff that's higher up.
    
    ![image](https://user-images.githubusercontent.com/4205776/112569688-08256000-8dbb-11eb-8cfc-2eb28fe9d3dc.png)

commit e7954d66c7692e9c55c7388929425b9c1fa80c71
Merge: 6fe6731 e2ba1ec
Date:   Thu Mar 25 12:54:04 2021 -0700

    Merge pull request #5240 from RosettaCommons/tlinsky/update_denovo_design
    
    Update de novo fold architect code

commit 6fe67310248c335ba51421b50c1f7828815b00f9
Merge: 976bc18 69f9bbd
Date:   Wed Mar 24 21:59:47 2021 -0400

    Merge pull request #5225 from RosettaCommons/vmullig/citations_in_rosettascripts_info
    
    Ensure that the RosettaScripts -info flag writes out citation information as well.
    
    This was requested by someone a while back.
    
    TODO:
    - [x] Add functions to get citations for all relevant modules.
    - [x] Conversion function in `CitationManager` that takes a `CitationCollectionList` and writes human-readable citations to a `std::ostream`.
    - [x] Beauty.
    - [x] Check integration tests.
    - [x] Pull request #5224 must be merged before this one.

commit 976bc1819fa86e425c9d8f9712a5f09a7412de19
Merge: 84c2110 3a344ea
Date:   Wed Mar 24 17:51:52 2021 -0400

    Merge pull request #5301 from RosettaCommons/vmullig/init_native_in_rosettascripts
    
    Ensuring that movers have access to the native pose in RosettaScripts
    
    Currently, the ParsedProtocol's native pointer is never set, so `Mover::get_native_pose()` returns `nullptr`.  This corrects that.  At least one integration test changes (I now see GDT and RMSD being calculated in the Enzrevert_xml test, which is good).
    
    This PR also switches a few uses of `new` to `make_shared`.  This may account for some random trajectory changes seen in the integration tests.
    
    This PR should be merged before #5119, which adds trRosetta into Rosetta.

commit 84c211018eb4bbb50a9c02a554e9172e6ebb025d
Merge: 2be8bdd 8d8df8f
Date:   Wed Mar 24 17:11:19 2021 -0400

    Merge pull request #5224 from RosettaCommons/vmullig/citations_for_constraint_generators
    
    Add support for CitationManager citations to the ConstraintGenerators
    
    `ConstraintGenerators` are also RosettaScripts-scriptable.  This PR ensures that their published references or unpublished author information are written out when they are used.
    
    This PR is a prerequisite for PR #5119, which puts trRosetta into Rosetta.
    
    Tasks:
    - [x] Add `provide_citation_info()` virtual function to `ConstraintGenerator` base class.
    - [x] Ensure that RosettaScripts/JD2 read this and register citations with the `CitationManager`.
    - [x] Add unpublished author info to the unpulblished constraint generators.
    - [x] Add `ConstraintGenerator` support to the RosettaScripts `-info` flag.
    - [x] Add a `ConstraintGenerator` example to the RosettaScripts `-info` integration test.
    - [x] Figure out why the output is currently empty and fix. --> ConstraintGenerator xsds were being assigned a funny name.  Corrected now.
    - [x] Beauty.
    - [x] Check tests.

commit 2be8bddcb7b92347a32408deb451aa1072ffac97
Merge: db2473f 0f90afc
Date:   Wed Mar 24 17:09:15 2021 -0400

    Merge pull request #5300 from RosettaCommons/revert-5293-vmullig/shush_membrane_potential
    
    Revert "Switching some noisy tracer output in the MembranePotential to debug output."
    
    @jkleman informs me that currently, this is the only way to get membrane information out. In the future, we should ensure that this is written out with the pose instead of to the tracer, but for now, we'll revert this.
    
    The discussion on the PR:
    
    Rocco: @jkleman What's the use case here? What are you using the results thus printed for, and how often do you need it? If it's not a frequent use case, simply adding -out:levels core.scoring.MembranePotential:debug to your command line when you need it should result in things printing like they did. If it is a frequent use case, then we probably should seriously consider better ways of getting the info, other than voluminous tracer printing.
    
    Me: I think it is a frequent use case. I agree: relying on tracer output for essential information is a bad idea. Best would be writing to the pose (on PDB output) and storing in binary silent files, but I don't have time to implement that at the moment, so temporarily I wanted to restore the old status quo.
    
    Julia: @roccomoretti yes, it's a frequent use case. For anyone using the old RosettaMembrane code, the tracer output is the only way to get the membrane information, i.e. how the protein is embedded into the membrane. Best case would be to put it into the pose directly but fixing this hasn't been the highest priority on my TODO list. This does not affect the new RosettaMP framework.
    
    So we'll come up with a better solution at some point, but for now we'll just make do with noisy tracers.

commit db2473f1d6d5e9d091a28cbf69dd36ce52a9cbb8
Merge: f15a3ac 45076e4
Date:   Tue Mar 23 08:22:08 2021 -0500

    Merge pull request #5286 from RosettaCommons/roccomoretti/DEER_abs
    
    Fix potential rounding in DEEROverlapMethod
    
    Clang 10 indicates issues with the abs() being used, as it's the C library (integer) abs() function, rather than the overloaded C++ library one. ("using integer absolute value function 'abs' when argument is of floating point type"). Prepending std:: should fix this.
    
    (If integer truncation is desired, then we should be more explicit about it.)

commit f15a3acf0ce8e1e89a8fcaa699e79f1091fc2199
Merge: 8f53ba1 a9393f9
Date:   Tue Mar 23 00:25:02 2021 -0700

    Merge pull request #4083 from RosettaCommons/everyday847/tinyfold_rosetta
    
    Expand coarse_rna for toyfold model

commit 8f53ba16bf3c5f070d9240cd0d908a39a3e100ff
Merge: e9f4797 af92ca2
Date:   Tue Mar 23 03:05:44 2021 -0400

    Merge pull request #5236 from RosettaCommons/vmullig/hb_cen_soft_options
    
    Allow the hb_cen_soft option to be set from code without relying on the global options system. This is a prerequisite for getting trRosetta into Rosetta (e.g. for use by Foldit).

commit e9f47978df05d6d2de96236c2d949ecf9436018a
Merge: 907f30c 6d3833e
Date:   Fri Mar 19 09:06:15 2021 -0500

    Merge pull request #5294 from RosettaCommons/jadolfbr/update_notebook_head
    
    Update notebook submodule to current HEAD that reflects rabd code changes

commit 907f30c089b3883ce9dd52327145e56656345182
Merge: 532be15 2aeacd8
Date:   Thu Mar 18 18:57:43 2021 -0400

    Merge pull request #5293 from RosettaCommons/vmullig/shush_membrane_potential
    
    Switching some noisy tracer output in the MembranePotential to debug output.  This was likely hurting performance.

commit 532be1556a07041232a2ded530fa281aa86c7185
Merge: 02ff523 8b85dc4
Date:   Wed Mar 17 19:26:06 2021 -0600

    Merge pull request #5288 from RosettaCommons/sergey/binder
    
    adding PyMOL-Rosetta-relay-client.python2.py script and minor bug fixes

commit 02ff5238ae8d9de047217ca5bc6e82f190a1a3d7
Merge: ff1342d 077247c
Date:   Wed Mar 17 10:24:25 2021 -0500

    Merge pull request #5284 from RosettaCommons/roccomoretti/single_random_assert
    
    Fix ParsedProtocol with single_random
    
    An assert in ParsedProtocol triggers if you use the single_random protocol. The assert was erroneously testing if the number of steps was equal to the number of submovers, which isn't the case for single_random, as it only picks out a single submover.

commit ff1342dd9a7fa5ae545ad5635ae94ce5f0df7c2f
Date:   Tue Mar 16 14:28:06 2021 -0400

    beautifying

commit c7b20279d543ff37adce9d485d9ee3e15739d143
Merge: 5ea06dd 25f58c7
Date:   Sun Mar 14 20:00:57 2021 -0700

    Merge pull request #5275 from RosettaCommons/yhsia/sym_issues
    
    Add asu_only option in DsspMover and LayerSelector to only do calculations on the asymmetric unit to speed up cases with large symmetries.

commit 5ea06dde281daaf879657754254d6329e23e8f27
Merge: ef3ef84 c54ffc0
Date:   Sun Mar 14 17:49:50 2021 -0400

    Merge pull request #5228 from RosettaCommons/vmullig/correct_canonical_spelling
    
    Correct spelling of "canonical" in Rosetta source code.  Noncannonicals can't be used to repel pirate attacks. Noncanonicals are what we usually mean.

commit ef3ef84b7cbee20cc5a106b2155e4a4a1c129e27
Merge: 820d571 8b4c556
Date:   Thu Mar 11 22:51:08 2021 -0500

    Merge pull request #5274 from RosettaCommons/everyday847/ncbb_stuff
    
    Update some OOP modeling utilities; add sequence to scorefiles

commit 820d57129386de22d129c00e41846b86445d3a2d
Merge: e794d44 7251c64
Date:   Tue Mar 9 11:21:25 2021 -0700

    Merge pull request #5278 from RosettaCommons/benchmark
    
    updating rsync address for pdb.org archive

commit e794d44210b60f05ced9ea915e66d1ade6195f97
Merge: 61a18df 56ecba6
Date:   Mon Mar 8 11:46:03 2021 -0700

    Merge pull request #5258 from RosettaCommons/sergey/binder
    
    adding PyMOL-Rosetta relay scripts

commit 61a18df7426addb92c02f6f1e222cb7aca4e6353
Merge: b60efc3 d32dddb
Date:   Mon Mar 8 09:46:28 2021 -0500

    Merge pull request #5241 from RosettaCommons/SudhanshuShanker/ssgm_only
    
    Disulfide support for glycomutagenesis protocol

commit b60efc3a64649f46edb7299de0c7d2e27fb564b4
Merge: d75c330 404441d
Date:   Fri Mar 5 11:30:05 2021 -0600

    Merge pull request #5273 from RosettaCommons/roccomoretti/inaccurate_g
    
    More accurate Inaccurate G! message.
    
    This "Error" message really isn't being treated as such. Internally we've been conditioned to ignore it, and recently there's been a number of external users expressing concerns.
    
    Turn it down to an Info-level message. It's still present for the developers to use to debug whatever issue it represents, but it hopefully will no longer frighten end users.

commit d75c33090ac69511957a3e3832e7f6f9ebc3024a
Merge: dd5dfba aaed2d4
Date:   Thu Mar 4 18:31:37 2021 -0800

    Merge pull request #5265 from RosettaCommons/drhicks1/peptide_cyclize
    
    Drhicks1/peptide cyclize

commit dd5dfba03145ff9b1505371a7ca60ceed1afd5c0
Merge: 289a181 374378e
Date:   Thu Mar 4 13:59:41 2021 -0500

    Merge pull request #5262
    
    Option to randomize the Jump residue of partner2 for docking FoldTree setup

commit 289a18160b1ac8e884cacbd1ece60b4db2254472
Merge: d0b5bd6 860c297
Date:   Thu Mar 4 09:58:52 2021 -0600

    Merge pull request #5270 from RosettaCommons/roccomoretti/shell_gcc
    
    Remove unneeded shell_gcc line from build system.
    
    This was unused and potentially problematic, if the system didn't have gcc present.

commit d0b5bd6d7c6319a6ec189dd6f2b86de0308bba47
Merge: 30a8373 0ecb04a
Date:   Wed Mar 3 08:03:01 2021 -0500

    Merge pull request #5260 from RosettaCommons/AmeyaHarmalkar/docking_scientific_tests
    
    Updating docking metrics and plots for docking scientific benchmark, using the CAPRI metrics. Now the readme also explains in detail how this is achieved.
    
    THANKS AMEYA!!!

commit 30a8373c8bd79ffe70576d2ef0df731c92e5f338
Merge: 6dfb23e 9742450
Date:   Sat Feb 27 13:36:23 2021 -0500

    Merge pull request #5254 from RosettaCommons/jkleman/SciBen_more_fixes
    
    Jkleman/sci ben more fixes: fixed RosettaCM test by adjusting cutoffs, fixed glycan structure prediction

commit 6dfb23ee688c4025ea2e692f20d68104ba9f112d
Merge: 977d187 d2e4e9f
Date:   Fri Feb 26 23:25:26 2021 -0800

    Merge pull request #5264 from RosettaCommons/everyday847/fix_alignment
    
    Fix option type disaster

commit 977d187ba6436b5dd06b73fa48d091194c778d28
Merge: 3e5b589 97584bd
Date:   Sat Feb 27 02:20:56 2021 -0500

    Merge pull request #5263 from RosettaCommons/vmullig/clangfix_deer
    
    Fix a small issue in the DEER code that clang-tidy complained about
    
    This should fix the clang-tidy test.
    
    Tasks:
    - [x] Make type of inner product explicit.

commit 3e5b58908c70d5bd4570fa54e3618897d09ead88
Date:   Fri Feb 26 02:41:39 2021 -0500

    beautifying

commit d49492bc8f06679f1f0bb96c774e5561e78ecd93
Merge: 884a289 13f221b
Date:   Wed Feb 24 17:05:29 2021 -0800

    Merge pull request #5257 from RosettaCommons/drhicks1/shape_comp
    
    Drhicks1/shape comp

commit 884a289b9b43cc7672f270d17b4bbfed25c84b06
Merge: c988cee 929b55a7
Date:   Wed Feb 24 18:57:18 2021 -0500

    Merge PR #5246: Carbohydrate-oriented changes needed before integrating GlycanDock protocol into master
    
    Assuming the changes seen in swm_dna_bridge aren't due to this PR as it has been showing changes in previous merges

commit c988cee989e45992fcb4db62afe20a5dcea9bec8
Merge: 5ab5b8b 0282050
Date:   Tue Feb 23 12:56:18 2021 -0600

    Merge pull request #4818 from RosettaCommons/jadolfbr/rabd_updates
    
    Thanks to @rahelf and @skelow for identifying these bugs and their aid in fixing them!
    
    Bug Fixes
    =======
    - `INCLUDE_ONLY` was not being read, and this was used in the documentation - and should be main CDRSet option.
    - Fixed issue where the final cluster reported could be different than what the cluster actually was through `identify_cdr_clusters` app
    - Removed the constructor that takes an ab_info object. ab_info is now always correctly initialized from pose.
    - This also fixes light_chain not being correctly set from xml/pyrosetta.
    
    Optimizations
    ==========
    - High Res dock cycles have been greatly reduced to speed up integrated docking and allow more robust protocols. Options are now present to control the first and second cycles of the DockMCM (high-res) protocol in cmd-line,RS, and in code.

commit 5ab5b8b4763fbd16f7bd7e736256387ab93f25ba
Merge: bc36ab4 a02ff1a
Date:   Tue Feb 23 12:41:34 2021 -0600

    Merge pull request #4901 from RosettaCommons/jadolfbr/nbr_res_selector
    
    Add a per-residue SimpleMetric, SideChainNeighborCountMetric, to count sidechain neighbors in the same way that LayerDesign works.
    Refactor LayerSelector to enable the use of the same core code to do the calculations.

commit bc36ab47069f898d814eb79199a1ba9059e45a72
Merge: c48be26 5f7ecb1
Date:   Mon Feb 22 15:12:27 2021 -0800

    Merge pull request #5234 from RosettaCommons/everyday847/new_rna_metrics
    
    Repair defect that broke build on RNA metrics