Merge pull request #375 from RosettaCommons/tlinsky/remodelmover_accumulator
Remodel mover now returns without further computation if accumulator is ...
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Merge pull request #384 from RosettaCommons/rpache/KIC_outer_cycles_bugfix
Loop modeling outer cycles refactoring
This commit makes perturb_outer_cycles and refine_outer_cycles the flags
to control the number of outer cycle iterations in the centroid and fullatom stages,
respectively, for all loop modeling protocols.
The default values for those two options are now being read directly from the
Rosetta options system instead of using hard-coded values.
The old loops:outer_cycles flag is now deprecated.
Cosmetic splice and antibody loop modeling integration test changes.
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Merge pull request #380 from RosettaCommons/roccomoretti/fixhbonds
Fix uninitialized variable issue in HBEvalType table.
Add a hbe_UNKNOWN as an uninitialized variable sentinel
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Merging master into branch aleaverfay/map_to_etables_from_etable_options
This commit changes the behavior of the ScoringManager so that now
fewer Etables get created. The ScoringManager stores only a single
data structure for holding etables: a map from the EtableOptions object
to EtableOPs.
This change means fewer etables get constructed -- this is a very good thing,
since Etables (especially the pre-analytic ones) occupy a good chunk of memory.
It does however produce copious cosmetic integration test changes, as the
integration tests now report fewer etable constructions.
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Merge pull request #381 from RosettaCommons/vmullig/bin_prob
vmullig/bin_prob
Adding functions to the BinTransitionCalculator class to calculate the probability of seeing residue i+1 in whichever bin it's in given that residue i is in whichever bin that it's in (and vice versa), if that makes sense. This is needed for a bin transition based energy term.
No unit test failures. Expect integration tests in all tests that use bin transition probabilities (bin_initialization, bin_perturbation, genkic_bin_setting, genkic_bin_sampling, genkic_bin_perturbing). This is due to reduction in default verbosity of BinTransitionCalculator and BinTransitionData objects (switching a number of tracers to debug tracers).
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Merge pull request #360 from RosettaCommons/justinrporter/env_release
Justinrporter/env release; fixing an issue with EnvMover::apply's use of Environment::end.
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Merge pull request #378 from RosettaCommons/vmullig/fix_omega
Vmullig/fix omega
Fixes behaviour of omega score term for beta-amino acids. (Thanks to Andy for pointing out the problem, and for ultimately coming up with the solution.) No integration test changes expected; all unit tests pass (including newly-added one).
Tasks:
Switches the test for beta-amino acids to the is_beta_aa() function in ResidueType (instead of my earlier kludge of looking for a "CM" atom).
Fixes the behaviour for beta-amino acids.
Moves all of the code for figuring out which mainchain torsion is omega to one place.
Adds a unit test for beta-amino acids.
Alters the derivative calculation WRT phi and psi in the special case of beta-amino acids to use mainchain torsions 2 and 3 instead of 1 and 2.
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Merge pull request #370 from RosettaCommons/vmullig/genkic_sampling
Fixing an issue with GenKIC
Since GenKIC now respects the exit status of the pre-selection mover, it is possible for there to be no valid solutions after applying the pre-selection mover despite having a number of candidtates beforehand. This was causing GenKIC to fail, but should be handled gracefully, now. No test changes expected.
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