Merge pull request #609 from RosettaCommons/roccomoretti/cartbonded_auto_torsion
Cart_bonded: automatically add torsion parameters if missing
The cart_bonded term can automatically pull bond lengths and angles from the ResidueType if there isn't values listed in the database. It didn't, however, do anything about constrained improper torsions (e.g. for planar systems).
These changes take the existing improper torsion parameter generation code from molfile_to_params.py that @yfsong added and puts it into Rosetta to allow autogeneration of torsional restraints for planar systems (aromatic bonds, double bonds to carbon) for ResidueTypes which don't already have any data listed in the database. -- It doesn't change anything for other sorts of impropers (e.g. aniline protons) that might also have a constrained geometry, though those should be easy enough to add later, if someone figures out what needs to be added.
Potential User Facing Change: While the autogeneration of parameters should be turned off if you feed manual parameters for the residue to -score::extra_improper_file, the behavior of the residue identifier for that file (and for the Rosetta database files) has changed. For non-protein, non-nucleic acid residue types, the residue identifier is the full name, rather than the name3. In most cases this shouldn't be an issue (as normally for ligands and the like name3 == full name), but it might catch someone out on edge cases.
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Merge pull request #2260 from RosettaCommons/roccomoretti/fix_ligand_database_io
Attempt to fix ligand_database_io test
I think I've tracked the instability in this test to the use of a std::set< ConstraintOP > in
ResidueTorsionRestraints. This was used in removing/re-adding constraints, such that the order of
the constraint addition was different run-to-run, as the address layout
is different. Different constraint orders means that there are slight
differences in energy summing (due to machine precision rounding),
which snowball during minimization. Changing the set to a vector1 appears to fix the instability issue.
Integration test changes in ligand docking tests expected, as they settle down to their (hopefully) stable trajectories.
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Merge pull request #2098 from RosettaCommons/roccomoretti/Transform_reporting_additions
Fixes to ligand scoring grid caching
While docking large ligands with multiple starting locations, I realized the ligand docking scoring grid caching wasn't working appropriately.
* Only the conformation and not the grid center was being hashed, which means for multiple starting locations you could get a grid from the cache that wasn't over any of your ligand.
* Const-correctness was not a thing in the scoring grid hierarchy, which meant that even if you get the correct caching key, the cached grid might not be what you want, as it might have been modified in the meantime. -- I attempted to impose const-correctness and proper copy-before-modifying semantics on the scoring grid.
While I was at it, I added more reporting functionality to the Transform mover, to recognize when the grid size is inadequate, and to recommend a grid size that's hopefully better. (Grid size recommendation are still somewhat "beta".)
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Merge pull request #2206 from RosettaCommons/csykang/retro_inverso
Adding a pilot app: This pilot app will take a pose and generate a retroinverso version of it.
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Merge pull request #2247 from RosettaCommons/roccomoretti/asst_test_fixes
Two quick test fixes
* ResidueType::delete_atom() was using atom data after deleting, which the unit.addsan tests was tripping over.
* There was an uninitialized member variable in NPDHBondInteractionGraph that unit.ubsan was tripping over.
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Merge pull request #2251 from RosettaCommons/vmullig/fix_select_by_layer_bug
Caught a bug in SelectResiduesByLayer
DSSP was being called even when explicitly disabled.
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More annotation of ligand_database_io integration test.
I can't replicate the test server changes locally, so hopefully more loging output will help track down the instability.
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Merge pull request #2239 from RosettaCommons/aleaverfay/faster_lkball_rpe
LK_Ball performance improvements
Two speedups for lk_ball in anticipation of it becoming part of the default score function.
First: Avoid construction/destruction of a count_pair object in the LK_BallEnergy evaluation
by using the "invoker" scheme where a stack-allocated object with the virtual function
"invoke" is handed a stack-allocated count-pair object by the CountPairFactory. This avoids
a call to new and delete. Stack allocation is much much faster than heap allocation. (The same thing could be done with the FA_ElecEnergy.)
This speeds up the off-rotamer packer by 1.18x when using lk_ball.
Second: Speed up lk-ball when using the linear-memory interaction graph by splitting RPE calculations for LK_BallEnergy into bb/bb, bb/sc, sc/bb, and sc/sc interactions. This drops LK-ball evaluation from being the largest single expense in the packer's deltaE calculation, to being the smallest of the atom-wise energy calculations. This is surely the result of the tighter bounding sphere pruning that allows the calculation to skip interaction calculations that it can prove are out of range.
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Merge pull request #2249 from RosettaCommons/everyday847/RT_count
Update ignore_list to ignore RT # change
P. Douglas Renfrew 7 years I like this commit in spirit...but, you need to make an exception for the "number_of_residuetypes" integration test
Andy Watkins 7 years We discussed this on Slack -- for everyone else watching, there's still a differently-formatted line in that integration test that will still change.
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Merge pull request #2100 from RosettaCommons/roccomoretti/RosettaScripts_empty_sfxn
A few small, unrelated administrative changes.
* Tell git to ignore the DAlphaBall executable if it's built (in main/source/external/DAlpahBall/)
* Update the naive/default runtimes for integration tests.
This was originally going to add "empty" to the list of pre-defined scorefunctions in RosettaScripts -- I dropped that plan, as it conflicts with the manual definition of "empty" within the XML, which a number of scripts are using.
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