Merge pull request #4522 from RosettaCommons/benchmark - adding support for persistent Python virtual environments - disabling iPython history in notebook test - fixing issue with index.html generation so PyRosetta release links should work again - unifying Conda package requirements across unit tests and release.conda -fixing release tests on B3 back-ends - removing individual virtual env setup from integration tests - updating Python versions

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Merge pull request #4530 from RosettaCommons/dolevrahat/FPD_add_cst_in_min Add fullatom constriants in FlexPepDock in minimization mode

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• code_quality.clang_tidy 「2」

Merge pull request #4521 from RosettaCommons/yhsia/SSElementSelector_sym_fix SSElementSelector to run DSSP on only the ASU instead of full pose

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• code_quality.clang_tidy 「2」

Merge pull request #4551 from RosettaCommons/vmullig/fix_clang_tidy_citationmanager Fixing clang tidy test. I forgot to switch "virtual" to "override" in a recent merge. This also updates the code templates for general classes to use `override` instead of `virtual` for the destructor. (`ReferenceCount::~ReferenceCount()` is `virtual`.)

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Merge pull request #4550 from RosettaCommons/vmullig/no_cite_nodesign_packer_palette Minor adjustment to the NoDesignPackerPalette Tweak the citation registration for the NoDesignPackerPalette. Currently, this is being reported as an unpublished used module in any RosettaScripts script that uses FastRelax (which uses the NoDesignPackerPalette under the hood). This is not a sufficiently important use of the NoDesignPackerPalette to warrant pointing it out to the user. I'm moving the registration with the CitationManager to the parse_my_tag() function so that only explicitly-scripted NoDesignPackerPalettes trigger an unpublished module warning. (This should NOT be the general pattern followed for all unpublished modules).

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Merge pull request #4544 from RosettaCommons/vmullig/peptidestubmover_respect_ACE_and_NME Feature addition for the PeptideStubMover Currently, the `PeptideStubMover` can only append or prepend to naked termini or to the default terminal types. However, it would be convenient to be able to append to a C-methylamidated residue or to prepend on an N-acetylated residue, preserving the mainchain dihedral values when we do so (since these terminal modifications are meant to emulate an amide bond to a preceding or following residue). This pull request adds this ability. This PR also makes a minor change to the `FoldTree` and `Edge` classes (adding a new `Edge` constructor and a new `FoldTree::add_edge()` method for convenience, each of which takes slightly different parameters than the existing methods). I've ensured that these are covered in the `FoldTree` unit tests. Tasks: - [x] Add the feature. - [x] Unit-test it. - [x] Debug it. - [x] Beauty. - [x] Documentation.

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Merge pull request #4549 from RosettaCommons/vmullig/citation_manager_incremental_merge_1 Incremental merge #1 for the citation manager This is a first incremental merge for the citation manager. All of the functionality is there, now, and works for all JD2 apps and for RosettaScripts. Future incremental merges will make this work for JD3 and PyRosetta, and will add additional citations. This is part of the functionality implemented in pull request #3087.

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Merge pull request #4547 from RosettaCommons/dimaio/misc_updates A few unrelated but very minor updates: - fix stability issue in make_symmdef_file.pl (was iterating though an unordered list) - updates to a pilot app - small bugfix to crystal refinement (only affecting extras=python builds)

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beautifying

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Merge pull request #4548 from RosettaCommons/everyday847/rna_minimize_align_pdb Enable use of align_pdb in rna_minimize

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Merge pull request #4546 from RosettaCommons/danpf/hybrid_pmt_fixes Fix broken xcode build

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Merge pull request #4536 from RosettaCommons/teunhoevenaars/jacobi_loop_closure_1 Fixes after initial Jacobi loop closure merge and addition of Loop definition to RosettaScript

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Merge pull request #4534 from RosettaCommons/rpavlovicz/ddg_water_min_fix fix control of rigid body movement of waters during minimziation of d…

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Merge pull request #4511 from RosettaCommons/yingyue0414-patch-ketohexopyranosyl Add Ketohexopyranosyls to Database This pull request is expected to add all ketohexopyranosyl residues (as well as the common modified ones) to database. add stereochemistry data of ketohexopyranosyl residues and include all ketohexopyranosyl residues in stereochem_test Since the anomeric carbon (in this case C2) has a hydroxymethyl group (C1, O1), the alpha- and beta-ketohexopyranosyls are expected to be in different chair forms. In most cases: **alpha: 4C1 beta: 1C4** This means that the .params files of alpha/beta-ketohexopyranosyls cannot be converted and created through bulk generation script. The bond angles and torsions are assumed to be the same as the standard bond angles and torsions of aldohexopyranoses.

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Merge pull request #4490 from RosettaCommons/Add-params-of-Aldopentofuranosyls-to-Database Add Aldopentofuranosyls to Database Add to5-alpha/beta-D-Arabinofuranosyls based on the to5-L-Arabinofuranosyls already present in the database (bond angles and torsions angles conform to the two exisiting files). Those files are further taken as an example .params file for to2- and to3- arabinofuranosyls as well as other aldopentofuranosyl parameter files.

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Merge pull request #4538 from RosettaCommons/JWLabonte/PTMs/Ard1 PTMs: Fixing species name Ard1 was in the wrong folder. This merge will fix that.

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