Changing the ignore_list to ignore changes to the number of MM paramerters and and ResidueTypes
Unit test status: [Pass]
Integration test status: [210]
210 tests will fail as a result of the cosmetic changes.
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Merging vmullig/ncaas into master to alter the way rama handles nonstandard connections.
--Eliminated the rama_score_nonstandard_connections option. This is now the default behaviour. (That is, if a residue is connected to something that is not the i+1 or i-1 residue, or if the connection is not a traditional C->N connection, rama can still score the residue).
--Fixed a few problems with Ramachandran.cc that were causing unit tests to fail with the new behaviour.
--Added connect_map_size() method to the Residue object (useful for a quick check in Ramachandran.cc to fix one of the afore-mentioned bugs).
Unit test status: All pass (EXCEPT for DdgFilter:test_filter_parsing and DdgFilter:test_use_filter, which were failing before.)
Integration test status: 4 changed tests
--These are all expected changes, due to backbone-to-sidechain connections in which the terminal backbone residue is now scoring with rama.
--The changed tests are:
UBQ_E2_thioester_extra_bodies
UBQ_Gp_LYX-Cterm
UBQ_E2_thioester
UBQ_E2_thioester_two_ubiquitins
--Note that some of the above tests seem to be failing to run sometimes. I couldn't reproduce this on my system, but it seems to happen on the test server, and might be related to my earlier changes to the CYX residue type. I'll try to diagnose and fix this at some point in the future.
On branch master
Changes to be committed:
(use "git reset HEAD <file>..." to unstage)
new file: source/src/apps/pilot/vmullig/ncaa_notes.txt
modified: source/src/basic/options/options_rosetta.py
modified: source/src/core/conformation/Residue.hh
modified: source/src/core/scoring/Ramachandran.cc
modified: source/src/core/scoring/methods/RamachandranEnergy.cc
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Refactor GraftMover classes
Refactor GraftMoverBase, AnchoredGraftMover, and utility functions in protocols/grafting to be more extendable. Separate logic for cartesian-space fixed insert protocol into its own class, CCDEndsGraftMover.
This logic of this GraftMover's apply is as follows (Based off of AnchoredGraftMover):
/// 1) superimposes the insert onto the scaffold using any overhang residues,
/// 2) Inserts the pose piece into the scaffold pose, deleting any overhang residues.
/// 3) Cycles of:
/// a) SmallMover for sampling (Can be disabled))
/// b) CCD of both terminal ends of the scaffold using flexibility settings or movemap
/// to close the graft.
/// c) MinMover to help close the graft through chainbreak terms
/// d) Closure check - will return if closed (Can be disabled)
/// d) MonteCarlo Boltzmann criterion
///
/// 4) Repack flexible residues, insert residues, and neighbors (can be disabled)
Make smooth centroid scoreterms default in both classes
Have AnchoredPDBCreator use dfpmin_armijo_nonmonotone mintype
Update unit tests, add unit test for RestrictToMoveMapChiOperation.
Rename two antibody design movers
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Integration test status: [ 2 ]
AnchoredPDBCreator: Will fail from change in mintype and centroid scorefxn
antibody_designer: Will fail from a number of changes, but this is fine.
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Attempt to fix UBQ integration tests
I'm not entirely sure why this issue just recently started showing up.
(It looks like it should have occured a long time ago.)
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Minor changes to GeneralizedKICfilter.cc. No integration test or unit test changes expected.
--Also made changes to the design_cycpeptide_MPI.cc pilot app.
--This commit turns off an app in pilot_apps.src.settings.all; the previous one is the actual merge commit.
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Updating gitignore to ignore the Xcode project .oirig file. For some reason we have both .orig and .template, but the project file generation script only looks for .template. This should help with some confusion.
Also, removing project.pbxproj.orig
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