Merge pull request #4308 from RosettaCommons/roccomoretti/reorganize_rosettascript_handling Reorganize RosettaScriptsParser tag handling. RosettaScriptsParser::generate_mover_for_protocol() was a bit of a muddle. Break out the detailed handling into sub-functions. Also, iterate through the subtags once, in order, rather than in multiple stages. * This may cause issues for some existing RosettaScripts, which (incorrectly) rely on having sections like RESIDUE_SELECTORS or SCOREFUNCTIONS _after_ the mover/filter section which use them. These should be rare, and can be fixed by reordering the tags. (Remembering you can repeat sections.)

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Merge pull request #4311 from RosettaCommons/vmullig/make_orient_function_const Identified a function that can and should be const. This was a small mistake corrected in a much longer pull request which might not make its way into master for a while. I want to make sure that this change goes in now, since any changes to this function that would prevent it from being const would mess up what I'm doing in that branch.

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Merge pull request #4313 from RosettaCommons/vmullig/relax_peptoid_check Allow the simple_cycpep_predict -user_set_alpha_dihedrals flag to work for peptoids, too.

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Merge pull request #4304 from RosettaCommons/jadolfbr/fix_insert_conf_by_jump This is a simple change that clears the `GlycanTreeSet` and observers at the beginning of the `insert_conformation_by_jump` function, and then sets it up at the end. This is due to the way this function deals with observers - instead of adding a residue, and then calling residue append, it adds ALL residues to the pose and THEN calls residue append for all the residues at the end.

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Merge pull request #4306 from RosettaCommons/sergey/b3 Updating benchmark.py script so it could work with B3 back-end daemon

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Merge pull request #4264 from RosettaCommons/bcov/ApproxNat1AndDunbrack ApproximateBuriedUnsat upgrades and -dunbrack_prob_semi flags

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Merge pull request #4291 from RosettaCommons/vmullig/bind_fragmentstore_vartypes_to_python Bind FragmentStore variables to allow access to Python. This incorporates changes from Brian Weitzner and Bobby Langan, and suggestions from Sergey Lyskov.

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Merge pull request #4301 from RosettaCommons/vmullig/clean_up_new_in_header Removing instances of make_shared in header; moving to cc file.

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Merge pull request #4300 from RosettaCommons/roccomoretti/pyrosetta_nocrash Turn off crash reporter for PyRosetta The crash reporter system isn't really well suited for PyRosetta. I thought I had turned it off, but it turns out the PyRosetta build is getting its settings from somewhere else these days.

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Merge pull request #4307 from RosettaCommons/JackMaguire/missingsemicolon Fixing bug reported here: https://www.rosettacommons.org/node/10662

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Merge pull request #4305 from RosettaCommons/vmullig/explicit_genkic_error Making a GenKIC error more explicit.

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Merge pull request #4134 from RosettaCommons/bcov/MaxHBondEnergy2 Change MAX_HB_ENERGY to an option and add to BUNSFilter

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Merge pull request #4302 from RosettaCommons/vmullig/remove_XRW_TEMP_lines_from_codebase Removing the irritating XRW TEMP lines that are cluttering up the codebase.

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Merge pull request #4299 from RosettaCommons/vmullig/better_jd2_termination_message I don't know what "Got some signal... It is: 15" means, and neither should a user. I'm trying to clarify some of the error messages that JD2 produces on abnormal termination.

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Merge pull request #4298 from RosettaCommons/vmullig/fix_gcc_9_build Fixing compilation on gcc 9.1.0 by initializing some uninitialized vectors and matrices.

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Merge pull request #4061 from RosettaCommons/jkrys/fragments_picking_test Jkrys/fragments picking test - Justyna's fragment picking test

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