Merge pull request #3262 from RosettaCommons/JWLabonte/sugars/sampling2 Carbohydrates: Adding TautomerizeAnomerMover This merge introduces a new sugar-specific `Mover` that will convert a random reducing-end saccharide residue into its anomer; that is, this `Mover` will swap an α-sugar into a β-sugar and _vice versa_. Reducing-end sugars tautomerize readily in aqueous solutions between the two isomeric forms, and it is generally not certain which form is preferred (if any) in sugar-binding proteins. All tests pass.

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Merge pull request #3883 from RosettaCommons/MelanieAprahamian/solvent_exposure_fix small update to per_residue_solvent_exposure and CovalentLabelingEnergy

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Merge pull request #3886 from RosettaCommons/vmullig/split_unit_tests_2 Split the test suite that is ACTUALLY timing out. I split the wrong one previously. Whoops.

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Merge pull request #3873 from RosettaCommons/roccomoretti/fix_san Fixes for *san, Valgrind, and ClangSA Grab bag of changes in an attempt to make the "best effort" tests green again.

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Merge pull request #3881 from RosettaCommons/benchmark Refactoring Conda release script so it uses our own hosting

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Merge pull request #3872 from CyrusBiotechnology/indigo/nmer_svm_loadfname_fix From @indigogo at Cyrus; merging on their behalf (write perms) NmerSVM fixing bug; needed to split on newline, not space in svm list Very simple bugfix; when reading a file that contains a list of paths to svm models files, we need to split the string containing the entire file on newline, not space, when parsing that string into a vector.

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Merge pull request #3879 from RosettaCommons/JackMaguire/CurrRotVec Updating ResidueArrayAnnealableEnergy::calculate_energy function signature to include the current rotamer assignments. Thanks to Vikram for the speedy review!

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Merge pull request #3882 from RosettaCommons/roccomoretti/fix_recon_design_mpi_2 More fixes for recon_design_mpi. The MPI logs need to get cleaned of their timing/version information.

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Merge pull request #3852 from RosettaCommons/jadolfbr/fix_sm_filters2 update SM filter warning message and int test

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Merge pull request #3864 from RosettaCommons/roccomoretti/multi_unit_run Fixes/additions to the unit test running script. * Parallelize the test discovery phase, to reduce lag before actually launching the test * Allow users to specify multiple unit tests to run on the command, a la integration.py * Convert the -1 option from a test specification option to a running mode option (the current ways of using run.py should transfer.) * Adjust the mute defaults such that we mute by default unless running a single test. * Adjust timeout such that it's turned off when running explicitly specified tests * Change things such that you use the same Python for scons path introspection as you're using to run the script.

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Merge pull request #3876 from RosettaCommons/vmullig/fix_peptoid_clustering Fix a bug with energy-based clustering and N-methylation The alignment atoms were not being chosen properly in N-methylated peptides. Note that this was early code for me, and is very badly written -- it's much more delicate than it needs to be. I don't have time to rewrite it from scratch, but I'm adding a check that will at least produce an exception if the problem recurs. Details: I have a vector of atoms to be used in the RMSD, and in N-methyl amino acids, you may or may not want to use the carbon on the nitrogen in the RMSD. I had one place in my code where it was assumed that you would, and another where it was assumed that you wouldn't. The effect was that a reference structure's vector of atom coordinates had 5*N entries, the structure to be aligned had a vector with 5*N entries in which only the first 4*N entries were being populated, and the two vectors didn't line up correctly. There are obviously much less fragile ways to write this that don't involve keeping track if which vector index corresponds to what, but like I said, this was early code for me and rewriting it entirely would take a lot of time.

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Merge pull request #3875 from RosettaCommons/basantab/fix_RandomMutationMover_segfault Add check to prevent segfault in RandomMutation mover

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Merge pull request #3554 from RosettaCommons/vmullig/fix_bunsat_filter Fix the BuriedUnsatHbondFilter when the user specifies that all hydrogen bonds should be counted. Currently, this behaviour is completely broken.

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Merge pull request #3870 from RosettaCommons/roccomoretti/silence_recon_mpi Fix recon_design_mpi. Add the appropriate flags such that it's no longer a permanent diff.

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Merge pull request #3867 from RosettaCommons/vmullig/fix_motifgraftmover Fixing uninitialized variable error that's bothering gcc 8.2 The recent changes to the MotifGraftMover left gcc 8.2 complaining about an unintialized variable. Technically, the value would never be used uninitialized, but it would have been hard for the compiler to know that (and anyways, it was fragile -- a small change to the code would result in the variable being used uninitialized). This initializes the relevant variable.

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Merge pull request #3845 from RosettaCommons/BYachnin/mhc_epitope-map-predictor Added a "PreLoaded" MHCEpitopePredictor, analogous to "External" but held entirely in memory MHCEpitopeEnergy currently allows for two Predictor classes that are used to obtain epitope scores from peptides: Matrix, which uses the Propred matrices to score peptides, and External, which uses an external SQL database (located on disk) to score peptides. This database is generated by the user based on the epitope prediction method and design space to be explored in a particular protein. This PR provides functionality analogous to "External," but loads the database entirely into memory prior to scoring. In cases where the database is sufficiently small (i.e. will not use too much RAM), this will be faster than External, particularly in cases where multiple processes are accessing the same database file during packing. In addition, the ability to read "CSV" files for this purpose is enabled. We also have introduced the database "unseen handler" (i.e. how to deal with peptides that are not in the database) "ignore," which will score unknown peptides with "0." This is suited for a database containing the IEDB experimentally-validated list of epitopes, which should introduce penalties for recognized peptides and no penalty for other peptides. Integration test failure in mhc_epitope is from cosmetic changes to the tracer output. mhc_epitope_nmer_preload is a new integration test, and so it fails. recon_design_mpi is unstable in master, and continuous_sewing_hasher and discontinuous_sewing_hasher fail in master.

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