commit 7111c54c14ba9a53c012a524f8f1438a8e3fb020 Merge: 3bdfef3 417903e Date: Mon Aug 13 11:33:52 2018 -0700 Merge pull request #3392 from RosettaCommons/jkleman/sci_bench_move prep for scientific benchmarking: moved old stuff into before2018 folder commit 3bdfef3c7a2a3ca71f1f0e6082441dae890f3331 Merge: 3135d32 e3e5648 Date: Mon Aug 13 07:32:33 2018 -0700 Merge pull request #3387 from RosettaCommons/bioragul/addtcr added templates for TCR modeling into additional protocol data commit 3135d32229f5ebd35c8a716af00dcdfbbfa81805 Merge: 1b022a3 55967c9 Date: Wed Aug 8 16:02:18 2018 -0700 BindingSiteConstraint bugfixes 1. site_constraint is an orphaned ScoreType. BindingSiteConstraint is a functioning constraint that uses atom_pair_constraint as its ScoreType, but optionally uses whichever ScoreType you request. I have added site_constraint to the list in ConstraintsEnergy so that you may use site_constraint with BindingSiteConstraint. 2. BindingSiteConstraint's Tracer was mislabled (copy paste error) 3. BindingSiteConstraint's clone() function was missing an argument in its dispatch to the copy ctor and thus forced cloned copies into the default ScoreType instead of an assigned ScoreType. commit 1b022a38c8d6cbc7dd8acb8f5da357c475b43d25 Merge: 9dda2bf 9dc0f70 Date: Wed Aug 8 15:52:14 2018 -0700 Merge pull request #3375 from RosettaCommons/smlewis/fix_noe_assignment should fix unstable noe_assignment itest by grepping out the offending log lines commit 9dda2bfc26b328e408c346d988865f7356939d2f Merge: 04840f0 47f7472 Date: Wed Aug 8 12:14:38 2018 -0700 Merge pull request #3381 from RosettaCommons/vmullig/eliminate_std_rand Removing an instance of std::rand in protocols, and updating a function signature to pass a vector by const reference instead of by copy. Flipping tests flip (the same integration tests that changed in the revision in which I did nothing but beautify). No other test changes observed. commit 04840f002fbaea286034f92c892ab90134b6578e Date: Tue Aug 7 06:52:29 2018 -0400 beautifying commit 882cef3e7b60e2ab5b0d7019ee8e12b9690c67c9 Merge: aa13a17 1f27b6c Date: Tue Aug 7 01:06:53 2018 -0700 Merge pull request #2573 from RosettaCommons/vmullig/refactor_parametric_code Refactor the Parametric code Merged from my phone. This somehow feels wrong... This will simplify the code considerably, and make it easier to add additional parameters or new parameterizations. It will also simplify the parameter-space minimizer that I have working in a branch (and which I really need to get back to at some point). Tasks: - [x] Add a Parameter abstract base class. - [x] Derived classes for Real, Size, or Boolean-valued Parameters. - [x] Store parameter name, type, value. - [x] Setters and getters for these. - [x] Value-parsing functions. - [x] XSD functions. - [x] Serialization. - [x] Ensure that default values can be specified (e.g. 1.0 for `epsilon`). - [x] Add means of copying parameters. - [x] Have this do something. - [x] Override the default "copies_from" to say "copies_helix" (_e.g._ "r0_copies_helix"). - [x] Special case of omega -- add means of copying pitch. - [x] Means of converting degrees->radians. - [x] Ensure that sampling and perturbing options are reset before storing in the Conformation. - [x] Add a ParametrizationCalculator abstract base class. - [x] Add a BundleParametrizationCalculator class. - [x] Tie in to MakeBundleHelix mover. - [x] Tie in to MakeBundle. - [x] Add default BundleParametrizationCalculator, and have it parse its options. - [x] Have the individual helix BundleParametrizationCalculators start off as clones of the default one (with cloning _after_ setup). - [x] Have them then override their options by parsing sub-tags. - [x] Check MakeBundle function (existing tests). - [x] Think about non-RosettaScripts interface, too. (What if defaults are set _after_ individual helices?) - [x] Fix the helical_bundle_nonideal integration test. (The second pose should be identical to the first. There's currently a problem with the bundle symmetry option in degrees mode.) - [x] Tie in to PerturbBundle. - [x] Deprecate PerturbBundleOptions class. - [x] Simplify PerturbBundleHelix mover. - [x] Simplify parse_my_tag(). - [x] Simplify apply(). - [x] Simplify perturb_values(). - [x] Check tests. - [x] Simplify XSD function. - [x] Tie in to BundleGridSampler. - [x] Check tests. - [x] Update parametric design GUI. - [x] Refactor the BundleParameters class to reduce the hardcoding of parameters. - ~~Maybe deprecate the BundleParametersSet class, too.~~ --> No, I like having a specialized class for this. _Right now_ it's not doing anything special, but it could conceivably in the future, and I don't want to have to subclass at that point. - [x] Fix integration test failures-to-run. - [x] Debug pitch copying with perturbation. It's currently not working. - [x] Check pitch copying with the BundleGridSampler. - [x] Check integration test changes. - [x] Debug changes seen when delta_t is nonzero. - Caused by ambiguity in rotation direction for beta-strands with omega1 ~ 180 degrees. Not a big cause for concern, though integration tests have been updated. - [x] Fix unit tests. - [x] Check `perturb_helical_bundle` integration test failure. It was the only one showing a real failure, and I think I've fixed it, now. Put off to another pull request: - Fix the longstanding residue vector problem in the Parameters object. commit aa13a17b3a2934dbaa09d6e4df887a95ecb96140 Merge: b148bd2 5bbf762 Date: Mon Aug 6 19:03:53 2018 -0700 Merge pull request #3371 from RosettaCommons/guangfeng/cryst_dock Several bugfixes in 3D-lattice docking. Addresses issue #3363. Minor outputting changes expected in small_molecule_lattice_dock integration test. commit b148bd26d6ff74a4263c77d62c7d6adcec40a788 Merge: 9582d5c 8363ba1 Date: Mon Aug 6 11:10:41 2018 -0700 Merge pull request #3370 from RosettaCommons/everyday847/never_stop_fighting_pdb_input Continued PDB input fixes commit 9582d5cc133ff34e2c69c9b5db300b995a78fcb9 Merge: beb7bad cfd50b3 Date: Sat Aug 4 20:37:54 2018 -0500 Merge pull request #3372 from RosettaCommons/roccomoretti/fix_integration_output Fix integration test run output redirection. Some integration tests were dumping output to stdout, rather than redirecting to a file. Fix this. commit beb7bad41bdf7aff3f890d51f0dc94da39578ae0 Merge: 4bc0e55 0b58323 Date: Sat Aug 4 18:18:52 2018 -0500 Merge pull request #3369 from RosettaCommons/roccmoretti/backrubdd_options Fix XML parsing for BackrubDD. The documentation and reality of BackrubDD were at odds. Attempt to fix/coordinate them. commit 4bc0e55ac44ce2433cb7042396ea41dd5e318f21 Merge: 231d1f3 6b87c90 Date: Fri Aug 3 16:47:40 2018 -0500 Merge pull request #3134 from RosettaCommons/roccomoretti/ResourceManager_unit_fix Fix the ResourceManagerTests with CMake. The CMake builds contain the full path to source files in error messages. Adjust unit tests to ignore the file path.