Fixing the simple_cycpep_predict_terminal_disulfide integration tests. Note that the enumerative_sampling tests also have the same problem (beta_nov15 in the flags), but they have additional problems, too -- bad paths in the run script. I'm not fixing those.
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Merge pull request #2290 from RosettaCommons/sergey/binder
PyRosetta, adding name simplification for std:: container classes
This should make Python names for set, map, vector, list, deque, forward_list, unordered_set, unordered_map, multiset, multimap, unordered_multiset and unordered_multimap classes considerably more readable.
Vikram K. Mulligan 7 years For unknown reasons, this merge seems to have broken all of the MPI-mode integration tests. (Note that some were already broken by the beta_nov15 merge, but now ALL are broken.)[list]
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Merge pull request #2278 from RosettaCommons/rhiju/rna_denovo2017_stage2
more RNA denovo/stepwise updates. Tests look fine, with minor changes in integration that are expected from changes in flag names, except very latest test run where the `beta_nov15` merge has broken some tests.
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Merge pull request #2283 from RosettaCommons/everyday847/stepwise_submovers_rs
Allow the sub-movers of StepWiseMonteCarlo to be accessed through RosettaScripts
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Merge pull request #2012 from RosettaCommons/hahnbeom/beta_nov15_as_default
Merging beta_nov15 as default energy function into master
Vikram K. Mulligan 7 years Three of the integration test breakages (symple_cycpep_predict*) are mine; they're integration tests that are newer than the most recent test of the beta_nov15 branch. I'll fix these right away.[list]
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Merge pull request #2284 from RosettaCommons/fordas/feature/vim_ymc_ninja_support
Update ninja_build.py path support and YouCompleteMe compilation db support.
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Merge pull request #2250 from RosettaCommons/vmullig/tweak_perturb_bundle
Add options to PerturbBundle mover to allow parameter values to be set directly.
This allows the PerturbBundle mover to set the absolute value of a parameter if the user so wishes, instead of perturbing a parameter value.
Tasks:
- [x] Add the options.
- [x] Update `parse_my_tag()`.
- [x] Update `provide_xml_schema()`.
- [x] Update `apply()`.
- [x] Integration test.
- [x] Beauty.
- [x] Documentation.
Also:
- [x] Fix current problems with `provide_xml_schema()` function.
Note that the new integration test is set to use the current default scorefunction, be that talaris2014 or ref2015. This test shouldn't change significantly (except for the score line in the output PDB file) with the switch to ref2015, and I want it to continue to use whatever the current default Rosetta scorefunction is in the future.
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Merge pull request #2253 from RosettaCommons/Cyrus/mergetarget
From Indigo King at Cyrus:
RandomResidueSelector: option to select random residue clusters
RandomResidueSelector currently has an option to select >1 residue at a time. This PR adds new option to ensure that, when multiple residues are selected, they are all close to each other (within N angstroms, where N is also an option)
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Merge pull request #2280 from RosettaCommons/dougrenfrew/fix_eusec
The change to the MPIWorkPoolJD job index a while ago caused an issue for the the explicit unfolded state energy calculator JD which derives from it.
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