Merge pull request #2532 from RosettaCommons/jadolfbr/unused_sugar_options Remove antiquated option that simply gives a warning now for sugars. (Integration tests are cosmetic as expected)

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Merge pull request #2526 from RosettaCommons/jadolfbr/carb_params_talaris Talaris Glycan Params Updates the Talaris glycan params with those from REF2015 to prepare for benchmarking.

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Merge pull request #2413 from RosettaCommons/aleaverfay/jd3_multithreaded_jd_take3 I've extracted the rather complex logic of asking the JobQueen for the next job to run out of the MPIWorkPoolJobDistributor and into a new class, the JobExtractor. I've replaced the original logic from the MPIWorkPoolJobDistributor with the JobExtractor class, and that looks like it works just fine. So writing the (single-process) MultiThreadedJobDistributor then becomes very easy: pop a job from the Extractor, put it into a work-queue, let a thread pool get to it when the next thread becomes available. This implementation makes use of the Apache2-licensed C++ Thread Pool Library (CTPL); it works incredibly smoothly.

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Merge pull request #2531 from RosettaCommons/jadolfbr/update_vax_settings Updating SchiefLab cluster site.settings

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Merge pull request #2518 from RosettaCommons/jadolfbr/code_template_dir Add robustness to Code Template outdir option. More robustly fail with not using correct dir options full paths or not-quite-relative paths. Add ability to use slashes with options just in case by splitting them. We won't fail, but we also prefer lists due to complete relative paths. Should help new users as found in BootCamp.

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Merge pull request #2529 from RosettaCommons/vmullig/correct_nomenclature Correct my nomenclature in certain movers, filters, and protocols that work with mirror symmetry. I incorrectly had "cN/m" instead of "sN".

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Merge pull request #2512 from RosettaCommons/mlnance/Me_glycoside_fix Carbohydrates: Update to Me-glycoside patch to assume pyranose

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Merge pull request #2505 from RosettaCommons/JackMaguire/monte_carlo_hbnet Monte Carlo HBNet

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Merge pull request #2511 from RosettaCommons/orlypolo/FPD_PhiPsi_check Orlypolo/fpd check for phi & psi defined residue types before calculating phi psi rmsd

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Merge pull request #2510 from RosettaCommons/sboyken/updated_holes Adding options to HolesFilter to only calculate holes score for a residue selection. The holes calculation is performed on the Pose as whole (ignoring the ResidueSelector), but when the time comes to report the score, only the atoms in the residue selector are summed. The Holes score is a sum of individual atoms/residues anyway (technically "PoseBalls"), so by only reporting a specific selection, we should be able to get location-specific data.

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Merge pull request #2523 from RosettaCommons/sergey/binder Refactoring install_llvm_tool so it now perform clean rebuild of LLVM when configuration options has changed. This will also speedup PyRosetta rebuild by avoiding unnecessary Binder rebuilds.

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Merge pull request #2520 from RosettaCommons/vmullig/refactor_crosslinkermover Refactor the CrosslinkerMover a bit for generality Needed for planned work with metals and for other crosslinkers. Ideally, this should cause no test changes, beyond minor cosmetic changes due to a changed input. Tasks: - [x] Update documentation ("threefold_symmetric" option is now "symmetry").

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Update crystal refinement XMLs for ref15 as default

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Merge pull request #2517 from RosettaCommons/jadolfbr/code_templates_py35 Add Python3 compatibility to the Code Template Generators Enable Python 2/3 running of code_templates using python-modernize. Found during Bootcamp! Woot! Thanks for the patience everyone!

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Merge pull request #2309 from RosettaCommons/vmullig/fix_cutpoint_variant Fix up the cutpoint code a bit to support cis-peptide bonds, peptoids, and N-methylation properly When I started working on cyclic peptides, the cutpoint energy had problems associated with it (_e.g._ hardcoded assumptions about i->i+1 connections) that made me want to avoid it. Today, these problems have largely been solved, and I've come around to the idea that this is one of the better ways to enforce cyclic geometry in peptides. To this end, this pull request aims to tweak the cutpoint code a bit, mainly to make it compatible with _cis_-peptide bonds and with non-ideal geometry. **Update**: This pull request has expanded. It now fixes a number of issues associated with peptoids, and has also had the glycan changes from pull request #2321 merged into it. **Tasks** - ~~Allow Calpha-C-V1-V2 and V2-V1-N-Ca dihedrals to move. The omega energy now enforces planarity.~~ --> Already happens. - [x] Check how chainbreak energy works and make sure that there's no i->i+1 hardcoding. - [x] Unit test for cyclic geometry and chainbreak energy. - [x] Correct expected energy in unit test. - [x] Add a function that moves virtual atoms around to ensure that _if_ cutpoint variants exist, then: - [x] C-OVL1 distance of lower matches LOWER-N distance of upper. - [x] V1-OVL2 distance of lower matches N-CA distance of upper. - [x] C-OVL1-OVL2 angle matches LOWER-N-CA angle. - [x] OVU1-N distance of upper matches C-UPPER distance of lower. - [x] Unit test. - [x] Call the above function from `core::pose::correctly_add_cutpoint_variants_to_pose()`. - [x] Unit test. - [x] Call the above from `core::conformation::Conformation::declare_bond`. - [x] Unit test. - [x] Call the above with conditional logic from `core::pose::add_variant_type_to_pose_residue()`. - [x] Unit test. - [x] Drop deletion of cutpoint types in `DeclareBondMover` and in `simple_cycpep_predict`. - [x] Add support for peptoids. - [x] Unit test. - [x] Add support for N-methylation. - [x] Unit test - [x] Unit test: cyclic scoring when the terminal types are cutpoint variants. - [x] For beta_nov16, too. - [x] Unit test: mirror symmetric scoring when the terminal types are cutpoint variants. - [x] For beta_nov16, too. - [x] Add support for: - [x] DNA. - [x] RNA. - [x] Sugars. - [x] Delete the NtermConnect and CtermConnect patches. - [x] Remove from patches.txt. - [x] Remove the patches. - [x] Remove the variant types, and all mentions in the code. - [x] Remove the variant types from the older residue type sets, too. - [x] Update PoseFromSFRBuilder, pass 4 --> add proper logic for determining if there are link records for mainchain connections, and set up cutpoints. - [x] Unit test for importing a cyclic peptide with LINK records. - [x] Fix the unit test breakages. - [x] Fix the integration test breakages. - [x] Fix updating of polymer bond-dependent geometry for peptoids. - [x] Correct peptoid params files: carbonyl oxygens are polymer-dependent. - [x] Fix updating of cutpoint virtuals (polymer-dependent). - [x] Debug test/core/scoring/cyclic_geometry_headers.hh. - [ ] Documentation. - [ ] Include documentation on when to use linear_chainbreak and when to use (quadratic) chainbreak. - [x] Fix peptoid geometry issue in Residue::place(). - [x] Beauty. Also: - [x] Fix bug in hxl_torsion code: basing the potential on atom indices creates problems with variants that renumber atom indices. - [x] Fix rama_prepro code for compatibility with cutpoint variants. Down the road: - We might switch `simple_cycpep_predict` and the `PeptideCyclizeMover` to use the chainbreak approach. This will require some explicit tweaks to set virtual atom _cis_ conformations in cases of _cis_-peptide bonds. - Unit test: GenKIC with cutpoint. - Unit test: GenKIC with _cis_-omega cutpoint. - Unit test: GenKIC with peptoid cutpoint. Lots of trajectory changes are expected, as well as additional, cosmetic integration test changes. A small scoring change is expected due to a bugfix to the hydroxyl torsion energy.

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Merge pull request #2514 from RosettaCommons/vmullig/andy_thread_issue Fixing thread-safety issue in ChainbreakUtil.cc, and ensuring that the has_chainbreak function actually does something. This was identified as an issue (#2447) by Andy Watkins. This fully addresses the issue, I think.

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