Merge pull request #3224 from RosettaCommons/hahnbeom/iterhyb_update Hahnbeom/iterhyb update

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Merge pull request #3194 from RosettaCommons/revert-3192-guffysl/revert_sewing Revert "Reverting sewing merge to diagnose testing failures" See commit message for pull request #2923 for details. Broken unit and integration tests have been repaired. Changes to continuous_sewing_hasher and discontinuous_sewing_hasher integration tests expected due to new option namespacing.

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Merge pull request #3216 from RosettaCommons/vmullig/add_octahedral_metals Add support for octahedrally-coordinated metals to the CrosslinkerMover and to the simple_cycpep_predict application

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Merge pull request #3219 from RosettaCommons/roccomoretti/clang6 Fix Clang 6.0 issues. Clang 6 has a 'private field is not used' warning (-Wunused-private-field) which was triggering in several places, causing Werror issues.

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Merge pull request #3214 from RosettaCommons/jadolfbr/fix_xcode_project Fix Xcode Project Generation This PR updates the Xcode project generation, post-protocols.3 split. It also adds documentation for how to do it, from much trial-and-error. @weitzner and I will attempt an automated solution - but this is not trivial and will take some generous time to do.

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Merge pull request #2521 from RosettaCommons/vmullig/add_metal_xlinks Allow the CrosslinkerMover to place tetrahedrally-coordinated metals

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Merge pull request #3217 from RosettaCommons/sergey/binder Updating PyRosetta documentation generation procedure so undocumented C++ classes is also listed.

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adding PyMOL-RosettaServer.python3.py into PyRosetta package

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Merge pull request #3215 from RosettaCommons/vmullig/fix_lariat_filtering Fixing a little mistake affecting lariat structure prediction. I had some exclusion logic backwards for filtering. I meant to exclude the cyclization side-chain from Ramachandran filtering, but was actually excluding the terminus involved in the cyclization. Corrected. @stephen-rettie

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Merge pull request #3132 from RosettaCommons/roccomoretti/nan_debugging Fix NaN issue in FastSaxsEnergy, with additional NaN/Inf checking elsewhere I spent a bit of time tracking down a NaN issue coming from the fastsaxs scoreterm. Add diagnostics to better report input file format failure cases. Also, add some helper functions to help do debugging for the source of NaN/Inf. Add a few judicious debug_asserts() to ScoreFunction, Minimizer and AtomTree to help catch NaN/Inf before the propagate too far.

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RosettaAI: Setting rosetta_scripts_scripts submodule to latest origin/master version.

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Merge pull request #3201 from RosettaCommons/bcov/BuriedUnsatDdGStyleFix Adding ddG_style_dont_recalc_surface to BuriedUnsatisfiedHbondFilter

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removing merge conflict markers that was accidentally committed into `master`

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Merge pull request #3203 from RosettaCommons/vmullig/fix_tailless_lariats Fix peptide structure prediction with tailless lariats Problem identified by @stephen-rettie and @deiblerk. Tasks: - [x] Diagnose the problem --> I'm mistakenly trying to randomize backbones of terminal residues. - [x] Integration test the problem. - [x] Fix the problem. - [x] Beauty. Also: - [x] This pull request is branched from #3202, and must be merged after that one.

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Merge pull request #3202 from RosettaCommons/vmullig/fix_lariat_issue Fix an issue affecting correct placement of O and V1 atoms in isopeptide lariats There were a couple of spurious lines in a function that's intended to return connection atom IDs, and this was creating problems with the SidechainConjugation patch. (Come to think of it, this might have worked if we changed the order of patches, but I wanted a less fragile solution.) There was an additional function that I needed to write, too, to preserve backwards compatibility with the old ASX/GLX patches. This also updates a feature in GenKIC. Old behaviour: - You have a residue with two polymeric connections (1, 2) and a sidechain connection (3). - You apply a patch that removes polymeric connection 2. - Sidechain connection 3 is now connection 2. - Atoms whose internal coordinates depended on sidechain connection 3 still depend on sidechain connection 3. - The Residue::inter_residue_connection_partner() function would correct for this by checking whether a residue was an upper terminus or lower terminus type, and subtracting 1 from the connection ID if it was. This was fragile (especially since someone might query the ICOOR records from anywhere, not just from this function). New behaviour: - You have a residue with two polymeric connections (1, 2) and a sidechain connection (3). - You apply a patch that removes polymeric connection 2. - Sidechain connection 3 is now connection 2. - When the patch is applied, we iterate through all atoms and update all ICOORs that depended on connection IDs greater than 2, so that they depend on the N-1 connection ID now. - The ICOOR records for each atom are always correct, now, and the Residue::inter_residue_connection_partner() function doesn't do any silly -1 logic, now.

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Merge pull request #3204 from RosettaCommons/vmullig/fix_app_exception_handling Fix the app_exception_handling integration test. Ensuring that make_motif_tables exits with error status when an exception is thrown.

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