commit 757388b0ca57a08035e4f6c87472fab29b1cd1c4 Date: Wed Jun 27 18:00:43 2018 -0400 beautifying commit a3ecb20a8222352a113fc0250b00a861e6145741 Merge: 08584b1 e000c0d Date: Wed Jun 27 11:37:36 2018 -0500 Merge pull request #3274 from RosettaCommons/jadolfbr/simple_metrics_custom_type_ Add additional custom_type setting to SimpleMetrics This adds a `custom_type` option to the `SimpleMetric` framework, which can be set in code or in RosettaScripts. The `custom_type` allows one to define multiple SimpleMetrics, each with different settings, and have them all be output through a single `RunSimpleMetric` run or reused in multiple. For example, you can calculate rmsd for three different atom sets and use `custom_type` to tag them as `BBONLY` `HEAVY`, and `ALL` for example, and output them at the same time using a single mover. Before this PR, you would need three different RunSimpleMetric movers to change the prefix/suffix in the output. This reduces the number of times we need to define SMs in RosettaScripts. The output name in the scorefile or features db will now be `prefix + custom_type + "_"+ type + suffix` where the type is the name output by the Metric (such as RMSD, SASA, etc.). If no custom_type is given, we use the same output as before: `prefix + type + suffix` commit 08584b1392cd95e7ac82810a4c2f035dee39e8c9 Merge: 4e38af7 b60a022 Date: Tue Jun 26 23:48:57 2018 -0400 Merge pull request #3284 from RosettaCommons/JWLabonte/sugars/scoring Carbohydrate Scoring: Fixing bug in TorsionID query functions for glycosidic torsions beyond omega This merge will fix in bug in pose::carbohydrates::is_glycosidic_torsion() that was causing minimization to segfault in cases involving linkages with more than a single omega angle, such as glycolipids, phosphodiester-linked sugars, and polysialic acids. Integration test coverage has been expanded for scoring and minimizing such cases. carbohydrates and glycan_anomers test changes expected; cyclization and ddG_of_mutation test changes are cosmetic. All unit tests pass. commit 4e38af7b2c776fc414d218ef890f48464b821503 Merge: c4c4368 bd86b05 Date: Tue Jun 26 23:46:13 2018 -0400 Merge pull request #3246 from RosettaCommons/everyday847/update_lores_potential Set lores base pairing potential file from options commit c4c4368947c280f310e5c9bd64fb02d7366a4f14 Merge: ccae93d 155bd26 Date: Mon Jun 25 11:14:21 2018 -0500 Merge pull request #3278 from RosettaCommons/roccomoretti/PDB_load_fix_header Fix two PDB loading error classes In the PDB loading scientific test, there are two failure cases related to parsing headers: unrecognized_experimental_technique and unrecognized_compound. Dying for this is silly, as we rarely (never) use the information contained in these records, anyway. commit ccae93d7719aeadd86ddc754c726b2bf65644cce Merge: e1d272e 417e9de Date: Mon Jun 25 11:07:51 2018 -0500 Merge pull request #3283 from RosettaCommons/roccomoretti/PDB_loading_connect_detail Add more information to unrecognized residue message. Residues can now be unrecognized because of missing connection points. Add details about this to the warning message. (So you don't get obtuse 'unrecognized residue: LYS' style messages.) commit e1d272e79550f4d4a7c13dc0697b91a4ea096348 Merge: 13ea9dc 3be9293 Date: Fri Jun 22 17:36:58 2018 -0500 Merge pull request #3282 from RosettaCommons/roccomoretti/PDB_zero_coord_H Fix one unrecognized res issue in PDB components loading. When a PDB component is L-PEPTIDE LINKING, the H atom is special cased. Although the coordinates for H are reset later, at the time we check for too many zero coordinate atoms, it's still zero coordinates. Special case it, such that the hydrogen doesn't count against the 'too many missing coordinate' count. commit 13ea9dc1bb0f9f6c0ed9515eb7341a1719423af4 Date: Fri Jun 22 18:29:45 2018 -0400 beautifying commit 07ed2f40d646193fe204378a50b80276d9daec9c Merge: 427a800 ecf6375 Date: Fri Jun 22 14:54:52 2018 -0700 Merge pull request #3281 from RosettaCommons/bcov/InterfaceHydrophobicResidueContacts Adding InterfaceHydrophobicResidueContactsFilter commit 427a800f033302a89141424e3178fd629efb9151 Merge: 10ae62d d8c0337 Date: Fri Jun 22 17:51:45 2018 -0400 Merge pull request #3273 from RosettaCommons/lqtza/fix-snugdock-integration-test Fix SnugDock Integration Instability commit 10ae62d6eb4ca580c82c8a186d736c0bb8cfd8e4 Merge: 0d056a2 f1611fe Date: Thu Jun 21 18:56:19 2018 -0500 Merge pull request #3280 from RosettaCommons/roccomoretti/PDB_loading_segfaults Fix segfaults occurring in PDB loading scientific test Two classes of segfaults were happening in the PDB loading tests * When building a Foldtree, we were checking if a residue was in an empty foldtree. This lead to a crash instead of just saying it wasn't. * Some PDB components have hydrogens with two bonds to them. This violates some assumptions Rosetta has about hydrogens and only belonging to a single atom. Catch this earlier. There's four PDBs which now are failures which used to be "successes" - turns out they were suffering from the same issues which were causing segfaults, but weren't actually triggering a segfault for some reason. commit 0d056a2e35ffe67bbf63ac361d61d9ff6ac7055d Merge: fc93460 4cd3a13 Date: Thu Jun 21 14:40:04 2018 -0500 Merge pull request #3277 from RosettaCommons/roccomoretti/PDB_xyzvector_fix Fixes for xyzVector normalization in PDB loading There's two main issues here, both related to Stub::from_four_points(). * With the PDB components, there's a number of (perfectly) colinear residues. These fail in Icoor assignment, as we attempt to grab a cross-product of two colinear vectors * I fixed this by tweaking Stub::from_four_points() itself. The docs just guarantee that the second stub coordinate is within the a/b/c plane. When a/b/c are colinear, any arbitrary orthogonal vector will satisfy this requirement, so I pull out an arbitrary one. * When there are co-incident adjacent atoms, fill_missing_atoms can choke when it tries to build based on a zero length vector. * I fixed this by altering AtomICoor::build() -- we're already tweaking things slightly here, and I'm of the opinion that an arbitrarily build atom is better than a hard crash. Note that in both cases I've taken the approach of applying arbitrary (small) tweaks to the vectors, rather than crashing with a zero-length error. commit fc934606e1208c8ccfbfb4d2669d7bdae2ebd71c Merge: b189021 02cdf9f Date: Thu Jun 21 11:24:12 2018 -0600 Merge pull request #3271 from RosettaCommons/sergey/ui Fixing Workbench UI app commit b189021a5eebcf01af7a69f6908cd61f016e82b7 Merge: 236dfd6 e2127c6 Date: Thu Jun 21 12:08:36 2018 -0400 Merge pull request #3279 from RosettaCommons/JWLabonte/sugars/branching Glycosylation: Allowing glycosylation of lipids and nucleotide diphosphates This merge will allow one to glycosylate an appropriate lipid or nucleotide diphosphate (e.g., UDP) using the glycosylate_pose() functions. For example: make_pose_from_sequence( pose, "Z[UDP:non-conjugated]", *residue_set ); pose::carbohydrates::glycosylate_pose( pose, 1, "a-D-Glcp-" ); carbohydrates integration test changes expected. rosetta_scripts_jd3 and simple_glycosylation test changes are cosmetic. All unit tests pass. commit 236dfd6b67dd7cd06d47e8893dd3809def806ab9 Merge: 9d22951 cbfbd31 Date: Thu Jun 21 11:10:58 2018 -0400 Merge pull request #3247 from RosettaCommons/everyday847/odd_error Add functionality to rna_minimizer plus fix a patching bug This branch cannot be beautified, so we'll just have to beautify master. commit 9d229517e1cc14cb8022c21a853ba0ede9ee089b Merge: 24060e4 8a36129 Date: Tue Jun 19 11:24:31 2018 -0400 Merge pull request #3270 from RosettaCommons/smlewis/pdb_diagnostic_test_language New language for the PDB diagnostic test, to make its results more interpretable to the community. Example run here: http://benchmark.graylab.jhu.edu/test/418571. commit 24060e44a755d555bd27953e618f1ba97b94aa2c Merge: de50085 d1e078e Date: Mon Jun 18 14:24:33 2018 -0700 Merge pull request #3269 from RosettaCommons/vmullig/fix_clang6_werror Fix a couple of unused variable warnings-as-errors preventing compilation with clang 6 on Ubuntu 18.04. commit de5008505edb36c4ade6288516ea3dfb91b4cd2f Merge: cb135ef adfef8a Date: Mon Jun 18 11:26:50 2018 -0400 protein_data_bank_diagnostic: updating blacklist, slightly increase timeout for fast mode commit cb135ef0d2ac15e253d317a47d256e20425b67b6 Merge: 780410f dfee89d Date: Sun Jun 17 13:44:48 2018 -0600 Merge pull request #3236 from RosettaCommons/sergey/scientific adding protein_data_bank_diagnostic.full test commit 780410f4e1f74c00a0faa075e6aa8e0b1481bc0a Merge: 7230771 c2208fd Date: Sat Jun 16 10:27:36 2018 -0600 Merge pull request #3267 from RosettaCommons/benchmark Fixing PyRosetta release script commit 723077125378041680a39b936be7211217f6a871 Merge: eace349 c8e7ebb Date: Fri Jun 15 10:46:32 2018 -0700 Merge pull request #3266 from RosettaCommons/dimaio/cryst_gen_mirrorsyms Updating a pilot app. Making one small change in numeric (changing absolute float check to a tolerance check). commit eace34955a8893a9a732f5d67d72930575875216 Merge: 450949e 3f44e3b Date: Thu Jun 14 20:54:31 2018 -0700 Merge pull request #3190 from RosettaCommons/vmullig/fix_peptidestubmover The PeptideStubMover is kinda crappy. Fix it. This pull request adds proper unit tests for the PeptideStubMover, and fixes the currently super-twitchy behaviour of the mover. (The problem was diagnosed by Andrew Leaver-Fay, and fixed by Brian Wetizner, so thanks to both of those fellows!) @weitzner @aleaverfay Tasks: - [x] Add unit test for Append. - [x] With repeat. - [x] Add unit test for Prepend. - [x] With repeat. - [x] Fix aberrant behaviour in all of the above. Not in this pull request, but possibly in future: - Add unit test for Insert. - With repeat. - Add unit test for sidechain conjugation. commit 450949e481542459ae6534e867a61fe9709846be Merge: 95fe019 50cc62d Date: Wed Jun 13 13:16:10 2018 -0400 Merge pull request #3258 from RosettaCommons/JWLabonte/sugars/output Pose IO: Providing option to force Rosetta to assign ligands unique .pdb chainIDs This merge will provide an option, `-output_ligands_as_separate_chains`, that will cause Rosetta to reassign the `.pdb` `chainID` of a ligand when it shares the same `chainID` as one of the peptide chains. Very often in `.pdb` structures, there might be, for example, a homodimeric protein with chains A and B in addition to a cofactors or product molecules, _etc.,_ that are also labeled as chains A and B. Using this option forces Rosetta to output them instead as belonging to separate chains, for example, C, D, _etc._ This new option will _not_ reassign a chain to a PTM, such as glycosylation; that is, saccharide or other residues that are attached covalently to a peptide chain will maintain the same `chainID` as the peptide chain to which they are attached. All tests pass. commit 95fe0192661940c18dc9e7adb1786fe01a6669d4 Merge: 090bbee 07de9e7 Date: Tue Jun 12 15:25:29 2018 -0600 Merge pull request #3259 from RosettaCommons/revert-3242-revert-3240-smlewis_for_gideonla/add_additional_protocol_data_submodule adding `additional_protocol_data` as a submodule, on Gideon's behalf commit 090bbeec96c0b4985b58b1522a69ac2f3bd4a709 Merge: 12896f7 8ae9d4f Date: Mon Jun 11 11:04:39 2018 -0700 Merge pull request #3255 from RosettaCommons/dimaio/beta_nov16_ramatable_bug Fix accidentally reverted line that points beta_nov16 to wrong database. commit 12896f74527c5d51f9fcf2fcf75d4346addb3cd9 Merge: b70b136 004a73e Date: Mon Jun 11 13:38:58 2018 -0400 Merge pull request #2480 from RosettaCommons/JWLabonte/sugars/database Carbohydrates: Ensuring that all sugars in the database have their anomeric forms also This merge adds about 20 new .params files to the database, such that all current sugars have their anomeric forms present. All unit tests pass; integration test changes expected in a few carbohydrate-related tests. Output change in c-term-conjugation test because of additional residue types being added. commit b70b13686cd9f8299ae1fd575afc589fe8ed583b Merge: 2c4ae17 ef20488 Date: Mon Jun 11 18:45:27 2018 +0300 Merge pull request #3256 from RosettaCommons/gideonla/splice_filtered Gideonla/splice filtered commit 2c4ae1785ec09e312edfaefa28b75fe1fa0dd82c Merge: 45eb559 d153d71 Date: Sat Jun 9 09:08:15 2018 -0400 Merge pull request #2122 from RosettaCommons/lqtza/snugdock_foldtree_update A frequent complaint of SnugDock users is the requirement for PDB chain order to be LH_A. I'm not sure why this was hard-coded at a point, but it shouldn't be the case. This pull request will update the SnugDock code to use a single FoldTree for docking and loop remodeling. This "universal" FoldTree is shown below. ![snugdock_foldtree](https://user-images.githubusercontent.com/6910140/41170084-f2148f38-6b18-11e8-8808-fc7cc4d8ddcc.png) It will be set once by setup_ab_ag_foldtree in the apply() function of SnugDockProtocol. This new function will also set up the FoldTree with the appropriate Loops for the CDRs. The universal FoldTree will also set the MoveMap and PackerTask for docking. All these objects will be passed along to the various movers involved in SnugDock, so no additional modification is made, whereas previously the FoldTree would be altered at each step depending. Future work will involve generalizing the new functions and moving them to AntibodyInfo as there might be some other code that will benefit from this FoldTree. commit 45eb559bac4f37ac00cc5ea2a5c0f135ad496f40 Merge: 345becc a1767d8 Date: Thu Jun 7 16:28:45 2018 -0400 Merge pull request #3238 from RosettaCommons/JWLabonte/sugars/sampling2 ShearMover: Refactoring BackboneMover code to allow for shearing of non-peptide linkages This merge refactors and simplifies the archaic code of `BackboneMover` to remove most of the hard-coded assumptions and setup a much simpler framework for moves of NCAAs and non-peptides. I am doing this primarily to introduce shear moving of sugars, which was impossible with the previous framework, but it should be much easier to code up shearing for other systems now. FWIW, historical shear moving of a standard peptide linkage only works because a trans peptide bond (omega) forces the two bonds on either side [psi(n-1) and phi(n)] to be nearly parallel. To make a shearing motion, minimizing downstream effects, the two twisting bonds must be near-parallel, and the bond twists must occur in opposite directions with equal magnitude. If the bonds are not near parallel, the chain will spiral. In non-peptide cases, there is no guarantee of any particular bonds being near-parallel to each other, so functions had to be written to search for nearby bonds with similar directional/3D orientations. In the setup phase of the `BackboneMover`s, a list of moving `TorsionID`s is now stored for every "position", removing any hardcoding of which torsions are moving and allowing for shearing of any system. This major change to shearing code means that Rosetta no longer will be guaranteed to pick the previous residue as the counter-moving residue for peptides; it may now also choose the next residue for the counter move. However, it also means that shearing should work for NCAAs with only very minor modifications. Some pedantic notes: in this new implementation, the selected counter move is the nearest to parallel, but no cut-off is used, so it is hypothetically possible that a near-orthogonal counter-move is chosen if there are no better options. However, I think that this case should be exceptionally rare, since most systems are going to be extended, and I require that a counter move be at least a bond away. Even if not so, such a "defective" shear move would effectively be like a small move. It could also be noted that a "less-parallel" bond that is a bond away may be less disruptive than a "more-parallel" bond that is three bonds away. I don't think the difference is worth the extra complexity involved to check for this, again, since a shear move is a small move to begin with. That is, if a move has two shearing counter-move options, the system doesn't test for the least disruptive; it tests for the closest to parallel bond, but both options would at least be shearing and therefore not as disruptive as other options. A large number of integration test changes are expected, from any tests that use glycans, `SmallMover`, `ShearMover` or any torsion-moving across branches, such as ubiquitin tests. All unit tests pass, and old tests were expanded and new ones written to ensure that shearing is behaving as expected. To the best of my knowledge, things work differently but they still work as they should. If this causes anyone problems, please let me know. commit 345becc78256af375e94103c682fda5e6e6f2913 Merge: 0831787 d40fa31 Date: Wed Jun 6 10:59:03 2018 -0700 Merge pull request #3241 from RosettaCommons/everyday847/accelerate_bfm Build full model now 15-20x faster commit 0831787c75bba750254e86f55acf8b6fe314a7b9 Merge: c635639 755b863 Date: Tue Jun 5 11:31:29 2018 -0600 Merge pull request #3242 from RosettaCommons/revert-3240-smlewis_for_gideonla/add_additional_protocol_data_submodule Revert "Add additional_protocol_data as a submodule, on Gideon's behalf" Reverts RosettaCommons/main#3240 because submodule contain LFS files (see https://github.com/RosettaCommons/additional_protocol_data/blob/master/motif_dock/.gitattributes) so it make impossible for ppl to clone it commit c63563914d0de668d8dd5c5c347417b6aeb4b3ee Merge: 5b7637c e3797e7 Date: Tue Jun 5 16:03:10 2018 +0300 Merge pull request #3240 from RosettaCommons/smlewis_for_gideonla/add_additional_protocol_data_submodule Add additional_protocol_data as a submodule, on Gideon's behalf commit 5b7637c16756bac2fc5daec5bc70c9946c6b4cb3 Merge: 3b2286a 7914b0d Date: Mon Jun 4 20:11:12 2018 -0700 Merge pull request #3237 from RosettaCommons/vmullig/add_square_planar_or_square_pyramidal_metals Vmullig/add square planar or square pyramidal metals This pull request will allow the `CrosslinkerMover` to place square pyramidal or square planar metals. - [x] This is branched off of pull request #3222, so that must be merged first. @srgerb Tasks: - [x] Add parameters for nickel. - [x] Add new helpers. - [x] Square planar helper. - [x] Delete std::cout line. - [x] Square pyramidal helper. - [x] Delete std::cout line. - [x] Update them to do something. - [x] Square planar helper. - [x] Square pyramidal helper (have it call the square planar helper functions, and inherit from the square planar helper class). - [x] Link to `CrosslinkerMover`. - [x] Link to `simple_cycpep_predict`. - [x] Integration tests: - [x] Square planar case, asymmetric. - [x] Square planar case, d2 symmetric. - [x] Square pyramidal case, asymmetric. - [x] Shorten this test. - [x] Square planar case with `simple_cycpep_predict`, with s6 quasi-symmetry. (The two unoccupied positions break symmetry.) - [x] Check this and add expected results. - [x] Square pyramidal case with `simple_cycpep_predict`, with s6 quasi-symmetry. (Note that 5th position breaks symmetry.) - [x] Check this and add expected results. - [x] Documentation for `CrosslinkerMover`(see https://github.com/RosettaCommons/documentation/pull/22 in the documentation repository). - [x] Documentation for `simple_cycpep_predict`(see https://github.com/RosettaCommons/documentation/pull/22 in the documentation repository). - [x] Beauty. commit 3b2286a7b511fd5d81d43e80afbeb0889f606983 Merge: d217306 2ba918d Date: Sun Jun 3 22:17:59 2018 -0400 Merge pull request #3239 from RosettaCommons/BYachnin/enzdes_preverse_header_errorhandling The enzdes constraint machinery relies on a set of REMARK headers in the pdb file. If the -run:preserve header option is NOT set, these remarks get discarded when Rosetta reads in the PDB. If the user tries to apply enzdes constraints, the error message that is produced indicates that there are no REMARKs in the PDB file. I have added a quick check to see if -run:preserve_header is set, and if not, add additional tracer output to inform the user that they probably need to turn it on. commit d21730674410d87996e8a77de75365626ca9ce8f Merge: 4e66e58 ec68ba3 Date: Fri Jun 1 22:46:54 2018 -0500 Merge pull request #3233 from RosettaCommons/jadolfbr/cart_glycan_min Add per-atom Cartesian Minimization Control This PR adds the ability to control specific atoms in cartesian minimization through a new `set_atom( AtomID, bool`) function and associated map in the `MoveMap` Additionally, a boolean option is added to the `MoveMapFactory`, `cartesian`, in order to allow us to set specific behavior for `cartesian` vs `dihedral` movemaps. This option is available in code or through RosettaScripts, and currently is only in use for glycans. It could be expanded in the future for lipids or other polymeric systems. This PR addresses issue #3181, allowing cartesian minimization of glycans to match dihedral minimization and standard IUPAC nomenclature of residues and torsions. This PR will also allow refinement of specific glycan residues in cartesian space, or per-atom refinement for ligands. However, since we do not yet have an `AtomSelector`, this functionality is only currently accessible via code. Unit tests for the `MoveMapFactory` and glycan-specific movemap creation have been added. An integration test for the full functionality has also been added. Finally, this fixes GlycanRelax and GlycanTreeRelax to use the new settings for cartesian. commit 4e66e589974641d9cced5c8dedc593a7623c5bc7 Merge: bc3bcf3 6169b46 Date: Fri Jun 1 17:17:42 2018 -0700 Merge pull request #3222 from RosettaCommons/vmullig/add_trigonal_pyramidal_or_planar_metals Add support for trigonal planar and trigonal pyramidal metal coordination to the CrosslinkerMover This pull request will allow the `CrosslinkerMover` to place trigonal pyramidal or trigonal planar metals. Tasks: - [x] This pull request is branched off of pull request #3216, so that one must be merged first. - [x] Add new helpers (`TrigonalPlanarMetal_Helper` and `TrigonalPyramidalMetal_Helper`). - [x] Update names. - [x] Update `TrigonalPlanarMetal_Helper`'s bond angles, expected symmetries, _etc._ - [x] Add improper dihedrals for planarity. - [x] Update `TrigonalPyramidalMetal_Helper`'s bond angles, expected symmetries, _etc._ - [x] Tie in to `CrosslinkerMover`. - [x] Tie in to `SimpleCycpepPredictApplication`. - [x] Integration tests: - [x] For `TrigonalPlanarMetal_Helper`: - [x] Asymmetric case - [x] Update this. - [x] C3-symmetric case - [x] Fix this. - [x] With `simple_cycpep_predict`, quasi-C3-symmetric case. - [x] For `TrigonalPyramidalMetal_Helper`: - [x] Asymmetric case - [x] C3-symmetric case - [x] With `simple_cycpep_predict`, quasi-C3-symmetric case. - [x] Caught a little bug in the filtering steps performed by the `Metal_HelperBase` class. - [x] Remove temporary `std::cout` line in `TrigonalPlanarMetal_Helper`. - [x] Beauty. - [x] Update `CrosslinkerMover` documentation. - [x] Update `simple_cycpep_predict` application documentation. @csykang @ralphcacho @srgerb commit bc3bcf3f3fcfe026c6700b53e6cdf14eb1c3b189 Merge: 99b36fe 497b000 Date: Thu May 31 16:46:58 2018 -0600 Merge pull request #3232 from RosettaCommons/sergey/scientific adding protein_data_bank_diagnostic script and switching Benchmark execute to use PTY commit 99b36feae433b8844356edc437c1c2e16e55540b Merge: 599586d a76f13a Date: Thu May 31 13:59:26 2018 -0700 Merge pull request #3234 from RosettaCommons/vmullig/shush_noisy_tests Switch some unit tests from std::cout or TS_TRACE to proper tracers Tests can't be muted unless they use tracers. commit 599586d4ebf8515b723c0ef8c99d4483f888fd45 Merge: fe7d6ed 2d51fd9 Date: Wed May 30 22:45:24 2018 -0700 Merge pull request #1636 from RosettaCommons/vmullig/cyclic_cart Making cart_bonded compatible with cyclic geometry, D-amino acids, and symmetric gly tables. Most of this pull request was already merged. This corrects symmetric glycine scoring and minimization with cart_bonded, and should also fix a bug with cyclic geometry and cart_bonded minimization. Tiny cart_bonded scoring changes are expected, and changes to cart_bonded minimization trajectories in several integration tests are likely. commit fe7d6edbed85cfbf21488775ed8a164ed3d2f565 Merge: 6102a80 0abb73c Date: Wed May 30 14:20:15 2018 -0400 Merge pull request #3231 from CyrusBiotechnology/231-forcommons-options-order-test Unit test to ensure that the order in which options are interpreted it as-intended and remains stable. This checks a vector option to make sure it appends and a single-valued option to make sure the "last" one always dominates. commit 6102a80f66d31c7fbfc4e884ea4cbfc9fb2e0d50 Merge: a13beee fa4fc96 Date: Tue May 29 21:38:12 2018 -0700 Merge pull request #3028 from RosettaCommons/vmullig/exclude_from_rms Add option to exclude user-specified residues from RMSD calculation in simple_cycpep_predict application This is useful, for example, when predicting structures of lariats with "tails", where the ring RMSD matters more than the tail RMSD. Requested by @deiblerk. Tasks: - [x] This branch is branched from pull request #3000. That pull request must be merged first. - [x] Add option. - [x] Have it do something. - [x] Integration test. - [x] Documentation. - [x] Beauty. commit a13beee2e35354cd3519dc416f6964185cd3c710 Merge: b9be90b 6183e6a Date: Tue May 29 15:01:52 2018 -0700 Merge pull request #3221 from RosettaCommons/bfrenz/anomeric_pseudotorsion Bfrenz/anomeric pseudotorsion commit b9be90b1ee12ab8165ca0c0fd7c1d18dd9a31fd9 Merge: 1d0cc3e e5008e9 Date: Mon May 28 11:16:46 2018 -0700 Merge pull request #3223 from RosettaCommons/rpavlovicz/water_ddg This commit is a major refactor of PR #2825, removing a lot of code from core into protocols. * all the point-water code, including generation and packing, now lives in WaterBoxMover. This mover is parsable with only 3 options: Mode is one of (remove, append, replace), and the mover carries out all steps of the protocol. * water overlap code logic is rewritten to be faster * bunch of options removed (where default values were generally reasonable); option system calls centralized to one function There are many expected integration test failures: * 20 result from changing RestrictToInterface (removing dependency on interaction graph) * 49 result from showing EnergyMethodOptions on stdout (several defaults changed) commit 1d0cc3eb6f10af8b9620bfb3261bea8d7636c56d Merge: 1348d15 09c59a3 Date: Fri May 25 12:25:42 2018 -0700 Merge pull request #3224 from RosettaCommons/hahnbeom/iterhyb_update Hahnbeom/iterhyb update commit 1348d15fc464efe3bae325ffcb9a4f03f04aeeb9 Merge: 2678f85 82baa44 Date: Thu May 24 10:23:47 2018 -0400 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.