Merge pull request #5458 from RosettaCommons/vmullig/BB8_rama Adding Ramachandran lines to BB8 params file. We weren't quite sure what we should do for the Ramachandran map for phenyl-serine. Options were: - Phenylalanine's Ramachandran map. - Threonine's Ramachandran map. - Generate a Ramahandarn map _de novo_ using: - MM force fields. - QM calculations. Of the _de novo_ options, MM is unlikely to be accurate enough, and QM would be very expensive with the side-chain degrees of freedom (and may not be as accurate as just stealing a statistical potential from a canonical -- even generating an accurate mainchain potential for alanine by QM is hard). Choosing between Phe and Thr, Thr seemed like the better bet since the beta-branching is likely to affect the mainchain conformational preferences more than the aromatic group will.

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Merge pull request #5457 from RosettaCommons/vmullig/fix_clang_tidy_HomogeneousTransform Fixing an error flagged by clang-tidy that really could lead to a bug. A function that the symmetry code is invoking uses abs (which takes integers) instead of std::abs (which can operate on floats). Thanks for the reviews, Jack and Rocco!

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Merge pull request #5439 from RosettaCommons/revert-5438-revert-5434-jflat06/map_sym_res_pairs-fix Revert "Revert "Fix map_symmetric_res_pairs to work properly with non-cyclic symmetries," which broke the build."

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beautifying

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Merge pull request #5396 from RosettaCommons/roccomoretti/cleanup_fwd Clean up forward headers. Part of the "try to speed up compilation" series: Go through the forward headers, and clean up unneeded includes. (Under the philosophy that the forward headers should be as minimal as possible to define the existence of types.) A number of individual deletions, but main ones: * There were some "all" headers that really weren't being used, and probably shouldn't be used (include the individual subheaders instead) - those were deleted * There's no appreciable difference between owning_ptr.fwd.hh and owning_ptr.hh (and corresponding access_ptr files) - delete the fwd.hh versions and just use the regular hh ones. * Replace vector1.hh with vector1.fwd.hh in forward headers, where practical. On my machine there's about a half second of compile time difference between the two. * Fix up some locations where APs were being defined as shared_ptr instead of weak_ptr. Large numbers of #include additions to fix up compilation. Additionally, I added an option to the Windows compile on the test server to increase the number of errors it reports when it fails. (Instead of just the first.) I figure this will help when people don't have a local Windows build they can run, and have to fix the errors based on the server results.

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Merge pull request #5449 from RosettaCommons/vmullig/fix_BB8 A minor fix to the backbone atoms of the phenylserine params file (BB8). BB8 needed a little repair. The mainchain coordinates were slightly off, and the H and O atoms did not depend on the lower and upper connections, respectively. 

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Merge pull request #5289 from RosettaCommons/SudhanshuShanker/ssgm_only Sudhanshu shanker/ssgm only Adds a new scoring column for aglycosylated variants for the glycomutagenesis app.

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Merge pull request #5444 from RosettaCommons/roccomoretti/python39 Fix build system for Python 3.9 Python 3.9 has some checks for cases where the standard interpreter works with is, but where the language specification doesn't permit it. Our cxxtestgen.py is falling afoul of those checks, which causes a large amount of spurious warnings.

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Merge pull request #5442 from RosettaCommons/gandrianov/comment_bonds Add --comment_bonds flag

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Merge pull request #5441 from RosettaCommons/JWLabonte/sugars/branching Carbohydrates: Adding missing 5-branch This merge simply adds a missing patch file necessary for exocyclic branching from aldofuranoses.

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Merge pull request #5440 from RosettaCommons/woodsh17/metable_code_quality Memb_Etable fixing code quality failed test

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Merge pull request #5438 from RosettaCommons/revert-5434-jflat06/map_sym_res_pairs-fix Revert "Fix map_symmetric_res_pairs to work properly with non-cyclic symmetries," which broke the build.

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Merge pull request #5434 from RosettaCommons/jflat06/map_sym_res_pairs-fix Fix map_symmetric_res_pairs to work properly with non-cyclic symmetries.

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Merge pull request #5435 from RosettaCommons/weitzner/fix-buns-filter Don't read options with no default value without checking if they are set first!

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Merge pull request #5432 from RosettaCommons/vmullig/update_citationmanager_error_message Update an error message if the citation database is out of date with the code

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Merge pull request #5295 from RosettaCommons/sergey/binder PyRosetta update

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