Merge pull request #1851 from RosettaCommons/vmullig/fix_TBMB_error Fixes a small error in the ThreefoldLinkerMover. The chirality of linker cysteines was being inverted. ThreefoldLinkerMover and simple_cycpep_predict integration test changes expected.

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Merge pull request #1848 from RosettaCommons/jadolfbr/calibur Jadolfbr/calibur This PR finally makes calibur clustering a tested, documented, public application - Clean up output to allow easy recognition of output cluster info and easy parsing/pymol loading - Add integration test for each way to use calibur. Test it all! Woot! - Write documentation (https://www.rosettacommons.org/docs/wiki/application_documentation/analysis/calibur-clustering) This just finishes things up. Thanks @kalngyk for doing all the work porting calibur into Rosetta and @everyday847 for getting the main PR merged in, I believe using the external upgrades the @roccomoretti put into place. Cheers!

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Disabling release as-git-repository for PyRosetta debug builds

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Merge pull request #1853 from RosettaCommons/everyday847/l_nas L-RNA implementation

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Merge pull request #1852 from RosettaCommons/aleaverfay/undo_schema_short_circuit Reverting 72915a0

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Merge pull request #1847 from RosettaCommons/hahnbeom/hxl_tors_fix fixing multiple db load issue with hxl_tors (part of beta-nov16)

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Merge pull request #1833 from RosettaCommons/hssnzdh2/UnsatSelector UnsatSelector

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Merge pull request #1849 from RosettaCommons/sergey/binder Adding test/test-release support for Mac Python-3 platform for PyRosetta-4

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Merge pull request #1834 from RosettaCommons/JWLabonte/sugars/branching PDB Input: Making Rosetta a little bit less picky about LINK records This merge will fix a problem with loading `.pdb` files where `LINK` records are not sorted like any sensible human would sort them. In cases where such files include a `LINK` record from a branch point residue to a higher-numbered residue before a lower-numbered residue, Rosetta would crash, because one cannot build a branch before a main chain is complete. (This still does not fix cases where people list `LINK` records backwards or where they number residues in branches in non-nonsensical ways.) I also want to say that I fixed this using a lambda function, so yay, C++11. FYI: @jadolfbr, @raemisch @smlewis: Will you be able to run this branch with your XRW read-all-the-pdbs script? This should give us better numbers. All tests pass.

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Merge pull request #1838 from RosettaCommons/vmullig/identify_cycpep_symm Add a filter for identifying cyclic peptides with internal symmetry The CycpepSymmetryFilter can pick out peptides with c2, c3, c4, etc. symmetry, or with c2/m, c4/m, c6/m, etc. symmetry. Should be useful for organometallic frameworks. @twcraven @hssnzdh2 @atom-moyer @gbhardwaj Tasks: - Implement the filter. - Unit test -- confirm that it correctly picks out a c2 peptide and a c2/m peptide from a group. - Integration test. - Beauty. - New flag to skip XML validation. (TEMPORARY -- will be removed once parse order is fixed.) - Documentation.

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Merge pull request #1784 from RosettaCommons/jadolfbr/sugars/omega_sugar_bb GlycanRelax upgrades This PR adds the following: - [x] Phi SugarBB sampling for exocyclic carbons in GlycanRelax using @JWLabonte 's Implementation of this in the sugar_bb energy term (from PR #1635) - [x] Enable Omega sampling from OmegaPreferencesFunction (from PR #1635) in a similar manner to what we are doing for the ChiEnergyFunction. Integrate this new sampling ability into GlycanRelax as another BB torsional selection of the BBDihedralSamplerMover. - [x] Enable CartMin in GlycanRelax. For both cmd-line and RS, the boolean option is _cartmin_ - [x] Integrate GlycanTree-based sampling for minimization and packing into GlycanRelax - Write _GlycanTreeMinMover_ and _RandomGlycanFoliageSelector_ - This is a subclass of the MinMover which uses the _RandomGlcyanFoliageSelector_ select a random residue from it, and then select the rest of the downstream branch (which is also ON in the movemap/task). Integrate this for Minimization and Packing. - This will make GlycanRelax speed increase linearly with the number of glycan residues instead of non-linearly as is the case now. - This will be an option that is on by default, as this enables more efficient sampling of large forests of glycans instead of wasting a great amount of time minimizing and packing ALL of the glycans as was the default. @JWLabonte @raemisch

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Merge pull request #1831 from RosettaCommons/weitzner/pyrosetta_py3 Expanding the configurability of the PyRosetta build script

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Merge pull request #1837 from RosettaCommons/dimaio/beta_fixes_1 A small bugfix to beta: intra_elec crashed when nblist_autoupdate is specified. Fixing this.

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Updating the beta_nov15_patch score test to reflect the new flag.

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Merge pull request #1830 from RosettaCommons/hssnzdh2/MutateResidue_Selector Add Selector Option to MutateResidue

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Merge pull request #1832 from RosettaCommons/dimaio/cryst_refine_post_xrw_fixes Update XMLs and a few misc. bugfixes

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