Merge pull request #2496 from RosettaCommons/hahnbeom/casp12_tools Hahnbeom/casp12 tools

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Merge pull request #2483 from RosettaCommons/atom-moyer/pyrosetta-method2class_binding Added infrastructure for binding methods/attributes to classes in python.

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Merge pull request #2504 from RosettaCommons/sccontreras/sccontreras/updatesometracers noticed some tracers were outdated Expect integration test changes that use constraint TR output

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Beautifying master.

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Merge pull request #2503 from RosettaCommons/roccomoretti/more_verbose_movemap_show Add additional information to MoveMap::show() output

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Merge pull request #2474 from RosettaCommons/BYachnin/enzdes_covalent_metals_bugfix Set up covalent enzdes constraints to use -metal_connect patch.

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The beautifier test failure in master was driving me nuts. Beautifying FoldTree.cc.

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Merge pull request #2470 from RosettaCommons/conf_functions2 This PR moves GlycanTreeSet and most core torsion setter and getter functions to conformation. This now enables these functions to be called by conformation itself after the full torsion refactor that @JWLabonte is working on. This makes GlycanTreeSet a member of Conformation, enabling its use in a symmetric conformation as well. Further, it uses observer functions but is now not a PoseObserver, while still being an observer. Also Fixes a bug in GlycanTreeRelax where the later layer was not being properly modeled. Lastly, with the general move to Conformation, Labonte has refactored the align_virtual_atoms_to_carbohydrate_residue function to be run directly in Conformation during updates of torsions - keeping them up to date at all times.

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Updating configuration option for Python-2.7 on Ubuntu

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Merge pull request #2481 from RosettaCommons/sergey/f Refactoring benchmark scripts: adding get_path_to_python_executable and updating build_pyrosetta.

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Merge pull request #2497 from RosettaCommons/vmullig/thread_efficiency_incremental_merge_1 Incremental merge of thread efficiency tweaks Merging some of the changes from pull request #2479, since some of the other changes that are planned might take longer. This removes mutexes from core::chemical::ResidueProperties::get_variant_type_from_string() and core::chemical::ResidueProperties::get_property_from_string(), converting the relevant maps to const static data.

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Merge pull request #331 from RosettaCommons/vmullig/fifty_shades_of_rama Trying to get rid of the perverse behaviour in Rama if phi or psi is zero. Failing PyRosetta unit tests are in fact failing in master as well -- they're due to the new dunder code.

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Merge pull request #2487 from RosettaCommons/jklai/hydrate This PR adds in the default weights for score12 with the Hydrate/SPaDES protocol (other scoring function weights to come in the future). Also made a few fixes and optimizations that were identified by Andy Watkins. Thanks to him for identifying the issues and helping me with fixing them. The hydrate integration tests are expected to change. The other tests are not expected to change except for a few tests that had previously failed (clang code quality).

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Merge pull request #2472 from RosettaCommons/jadolfbr/symm_glycan_relax2 Major GlycanRelax Updates + BugFixes This PR adds/updates a few things: - Adds Symmetry Support to GlycanRelax/GlycanTreeRelax - Adds ResidueSelector Support to SimpleGlycosylateMover - Makes ALL glycan-based classes use ResidueSelectors instead of Movemaps. Users should not be using Movemaps ATM other than @JWLabonte. A Unit-Tested function is now in `core/pose/carbohydrates` that takes a ResidueSelector and returns a MoveMap. This will eventually be done through the MoveMap Factory if we will refactor stuff to use it. - Fixes bugs where the MoveMap was not properly being set for GlycanRelax as Movemaps + non-protein torsions are absolutely awful. - Fixes a bug where the ASN-linkage was not being properly sampled by the LinkageConformerMover - Enables more torsions to sample that were otherwise being turned off. - Adds option to minimize rings. - Adds pass-through GlycanRelax rounds option for GlycanTreeRelax - Add `--level` option to `run/test.py` - Make the Minimizer for GlycanRelax use the neighbor list now that I actually know what it is.

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Remove tracer output -- there was so much in one case that it timeout killed an itest, which is unacceptable

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Merge pull request #2492 from RosettaCommons/revert-2383-bfrenz/auto_glycan_with_links_records Revert "Bfrenz/auto glycan with links records" Reverts RosettaCommons/main#2383 This PR causes most of our straight-from-the-pdb benchmark structures to fail loading and breaks the logic of the option in the first place. @raemisch and I will work with @BrandonFrenz in order to get this into Rosetta in a way that does not break existing functionality or logic. In the interim, we will add a set of structures that need to load either as unit tests or an integration test now that we actually have them. Either way they would fail loading.

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