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.

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

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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.

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

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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. 

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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.

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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.

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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. 

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

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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.

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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.

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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.

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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.

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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.)

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

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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).

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