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Revisions №58043

branch: master 「№58043」
Commited by: Brian Weitzner
GitHub commit link: 「0e84f3df68b00052」 「№701」
Difference from previous tested commit:  code diff
Commit date: 2015-08-13 09:06:04

Merge pull request #701 from RosettaCommons/weitzner/dock_partners_flag Dock partners in any order ==================== This change set enables docking chains to be specified in any order. The previous functionality required that the dock_partners flag listed the chains in the same order as in the PDB file. For example, if you had a PDB file with the chains A, B and C, you could dock the A–B dimer to C ("AB_C") or A to the B–C dimer ("A_BC"), but not the A–C dimer to B ("AC_B"). To use "AC_B", the user would have to rearrange the chains in the PDB file. Absurd! :angry: This change set fixes that using `ChainSelectors` and representing dock partners as `vector1< bool >`s. There were many flavors of the `setup_foldtree` function, several of which were not called anywhere in the code. These functions have been removed with the author's permission as appropriate. Unit tests: ------------- All unit tests pass. Unit tests that tested functions that were removed were also removed and the `DockingProtocolFunctions.u` file was updated to account for `FoldTree` edges being printed in a different order. A new unit test has been added to demonstrate and test the out-of-order functionality. Integration test changes: --------------------------------- Seventeen integration tests differ (3 were failing on the branched revision, 2 are failing as a result of an unknown bug somewhere else) as a result of this change, but the differences are limited to the order in which `FoldTree` `Edge`s are printed out and do not affect the folding direction of the pose or cause trajectory changes. ### Tests with text-based differences ### These differences are all of the form: < protocols.docking.DockingProtocol: FOLD_TREE EDGE 1 71 -1 EDGE 71 107 -1 EDGE 71 126 1 EDGE 126 193 -1 EDGE 126 108 -1 --- > protocols.docking.DockingProtocol: FOLD_TREE EDGE 1 71 -1 EDGE 71 107 -1 EDGE 71 126 1 EDGE 126 108 -1 EDGE 126 193 -1 1. `docking_local_refine_min` 2. `docking_low_res` 3. `score_only_silence` 4. `fuzzy` 5. `assemble_domains_jd2` 6. `docking_local_refine` 7. `rotamer_probability` 8. `docking_distance_constraints` 9. `docking_site_constraints` 10. `docking_full_protocol` 11. `score12_docking` 12. `docking_ensemble` ### Tests that were failing on the merge base with master: 1. `place_simultaneously` 2. `hotspot_graft` 3. `inverse_rotamer_remodel` ### New test failures: ### 1. `mp_dock_prepack` (does not run) – ***disabled with permission from JKL*** 2. `mp_find_interface` (does not run) – ***disabled with permission from JKL***

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