Beautifying master. It hasn't been beautified in some time. Please be sure to use Andrew's new beautify_changed_files_in_branch.py script to beautify your branch before merging into master from this point onward. (It's a very fast script -- it just takes a few seconds.)

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Merge pull request #2074 from RosettaCommons/vmullig/fix_christine_nmethylation_issue Make the UnsatSelector compatible with symmetry Christine Kang reported an issue in trying to N-methylate peptides with symmetry. It turns out that the problem isn't with the N-methylation code, but with the UnsatSelector, which was being used to select positions in which the amide proton isn't involved in a hydrogen bond. This pull request aims to make the UnsatSelector compatible with symmetry. While I'm at it, I'm adding serialization support for the UnsatSelector, too. Tasks: - [x] Make the UnsatSelector symmetry-compatible. - [x] Make the UnsatSelector serializable. - [x] Beauty. While I'm at it: - [x] Modify FastRelax so that the scorefunction is made symmetric or asymmetric to match the pose. It's silly to ask the user to keep declaring separate symmetric or asymmetric scorefunctions -- it's just one more barrier to learning Rosetta. - [x] Do the same with FastDesign.

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Merge pull request #2078 from RosettaCommons/vmullig/refactor_xsd_functions_a_wee_bit Expose useful XSD-parsing functions in utility, and add a few more I'm cherry-picking some Rosetta changes from my GUI branch. Note that none of this makes Rosetta aware of the GUI in any way -- these are just utility functions that make it easier for the GUI to get information from the RosettaScripts XSD about the interfaces for movers, filters, etc. It makes sense for them to live in Rosetta since many different pieces of UI and non-UI code may want to use them.

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Merge pull request #2085 from RosettaCommons/roccomoretti/cmake_nan_inf Update CMake for NaN/Inf issues. Pull Request #1737 fixed the scons build system for proper Inf/NaN handling, but the CMake subsystem was overlooked. This pull request fixes the issue, by adding the proper exclusion flags to the CMake build systems.

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Shushing an integration test that's producing spurious differences. It need not output the core.init tracer.

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Merge pull request #2081 from RosettaCommons/rhiju/better_loop_close Rhiju/better loop close Tests that change are expected -- restoring `thermal_sampler` and changes in FARFAR/rna_denovo.

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Merge pull request #2064 from RosettaCommons/hahnbeom/beta_nov16_bugfix beta_nov16, fixing minor bugs & adding support to FastDesign scheduling

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Merge pull request #2072 from RosettaCommons/roccomoretti/rs_include_fix Attempt to fix behavior of read_in_and_recursively_replace_includes() Brian Weitzner observed that RosettaScripts was **SLOW** with very large XMLs. He identified read_in_and_recursively_replace_includes() as the holdup. The previous version was using a rather sub-optimal algorithm, with a bunch of wasted effort. This PR changes the algorithm used to a more efficient one. Instead of exponential-ish behavior with XML file size, we now have linear-ish behavior.

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Merge pull request #2080 from RosettaCommons/roccomoretti/ReturnSidechainMover_fix Update ReturnSidechainMover to be less sensitive An external user was having issues with ReturnSidechainMover and patched residue types (like phosphorylated tyrosine) due to centroid/full atom residue type name mismatches. Don't error out if the sequence doesn't match -- Output a warning message instead. (This also prints better diagnostics, to help track down the issue.)

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Merge pull request #2079 from RosettaCommons/roccomoretti/with_message Adjust output printing for utility_exit() Just utility_exit()-ing without a message is very user unfriendly. Fix a few instances of that, and also bump tracer priority for other locations.

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Merge pull request #2070 from RosettaCommons/revert-2069-revert-2029-roccomoretti/ubsan_fixes Revert "Revert "Fix integration.ubsan"" Re-instate the ubsan fixes of PR #2029 that were reverted by PR #2069 due to build issues.

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Merge pull request #2061 from RosettaCommons/rhiju/on_the_fly_cubic_interpolation On-the-fly cubic interpolation All tests pass (except ones that were broken, and a new one to test cubic-interpolated 6D loop_close).

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Argh. Sorry; problems are endless.

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Whoops -- broke PyRosetta unit tests with an undefined function that I should have removed completely. Apologies!

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Merge pull request #2076 from RosettaCommons/everyday847/fix_unit_tests Fixed unit test -- sorry!

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Fix two integration test issues. 1) The integration test ignore_list wasn't set up with MPI in mind - this fixes that oversight (MPI adds additional characters between the tracer name and the output) 2) Fix the currently broken header_using_check integration test, and add a README.txt to help future people know what's going on with the test.

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