Merge pull request #3530 from RosettaCommons/smlewis/pdb_diagnostic_update_lists
For the PDB diagnostic benchmark test: update test dox. update reference results. Fix bugs
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Merge pull request #3391 from CyrusBiotechnology/bfrenz/cartesian_ddg
Test changes appear to be timeout problems unrelated to the PR. Given Hahnboem's approval I am merging.
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Merge pull request #3499 from RosettaCommons/vmullig/penalize_only_reachable_bunsats
Ensure that the buried_unsatisfied_penalty works with packing problems in which there are unsatisfiable "native" buried unsats.
Kale Kundert identified a problem with the buried_unsatisfied_penalty scoreterm in pull request #3498: when used for partial redesign of a pose that contains "native" buried unsats (e.g. when doing binder design to a target from the PDB), the buried unsats that can't be designed out are penalized, resulting in ridiculously high penalty values and penalty deltas, and causing the term to dominate unreasonably. The solution is to take a page from the voids_penalty, and to ensure that, during packing, only those buried unsats that are (a) part of packable rotamers, or (b) on unpackable rotamers, but reachable by at least one hbond to a packable rotamer, are the only ones counted and penalized. This is arguably the best solution (and thanks to Andy Watkins and Rocco Moretti for the suggestions), since it will mean that the term will "just work" on all problems without users having to do anything. This pull request aims to implement this solution.
@kalekundert @everyday847 @roccomoretti
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Merge pull request #3517 from RosettaCommons/jadolfbr/simple_metric_overrides
- Print a good error message if one tries to set SimpleMetric data that already exists.
- Enable an off-by-default option in RunSimpleMetrics (and the base classes) that will override data.
- Fix Glycan Tree Relax integration test by lowering the number of glycans to model
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Merge pull request #3521 from RosettaCommons/mlnance/sugar/get_new_chainIDs_bug
Fixed chain numbering issue so that branches in glycans get their own unique chain ID
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Merge pull request #3529 from RosettaCommons/bcov/FixApprox2
Fixed bug in approximate_buried_unsat_energy where packing with 0 rotamers caused a freeze
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Merge pull request #3520 from RosettaCommons/orlypolo/change_default_dslf_energy_threshold
Change DisulfideInsertion test to allow a more linient threshold for …
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Merge pull request #3524 from RosettaCommons/vmullig/add_ppi_params
Adding Crick parameters for a type 1 polyproline helix.
This is only a database addition. No test changes expected (or possible).
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