Merge pull request #2710 from RosettaCommons/sergey/binder
PyRosetta update. Adding bindings generation for constructor inherited from base class by 'using' declaration.
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Merge pull request #2693 from RosettaCommons/rhiju/PDB_components
all tests pass
- in integration tests, all changes are cosmetic, except sequence_recovery has slight deviation due to readin of some ligands; they are ignored in design calcs though.
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Merge pull request #2593 from RosettaCommons/roccomoretti/no_pose_get_resnum
Remove Pose dependency from get_resnum*() usage in parse_my_tags()
The functions in core/pose/selection.hh which take a TagOP used to also take a Pose, which is sub-ideal, as the pose at parse_my_tag time is likely different from the pose at apply() time. Fix this by converting things to use ResidueSelectors for deferred parsing (for multi-residue selection), or by storing the resnum string directly and parsing it later (for single residues).
I haven't fixed all Pose-dependent get_resnum usage, but I have eliminated the utility functions which take TagOPs, which is worth a commit so people don't re-introduce usage.
PyRosetta User Alert: Due to the conversion from core::Size specification to std::string for residue specifications, the get/set interface of some classes have changed. This should be a minimal change, as you likely to wrap the inputs with a str() call -- but it does mean a number of scripts may need to be adjusted.
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Merge pull request #2671 from RosettaCommons/guffysl/deprecate_legacy_sewing
This branch deprecates the version of SEWING currently in master to legacy_sewing in preparation for the merge of the SEWING refactor. It also adds accurate xml schema for the legacy SEWING movers so that they can still be accessed through RosettaScripts. Integration test changes to continuous_sewing_hasher and discontinuous_sewing_hasher expected (namespace changes in tracers/options).
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Merge pull request #2707 from RosettaCommons/roccomoretti/reb_insertion_codes
Add insertion code support to per_residue_energies and residue_energy_breakdown.
Uses the antibody-style 123C:I for chain C, residue 123, insertion code I. Omit insertion code if unused.
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Merge pull request #2695 from RosettaCommons/orlypolo/split-peptideDeriverFilter-to-classes
Separating classes that lived under the same PeptideDeriverFilter files
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Merge pull request #2670 from RosettaCommons/aleaverfay/simple_lkball_performance_improvements
Performance improvements for LK_Ball
Performance improvements for LK_Ball that will perhaps improve multithreaded performance
In particular:
LKB_ResidueInfo now holds a pointer to the singleton-managed array of WaterBuilders that it needs to compute the coordinates of the waters in scoring/derivative calculation. Previously, it had to go to the Singleton and obtain a ReadLock on the singleton once per residue per score function evaluation. Yikes! I'm hoping this reduces lock contention.
Unrelatedly, I noticed that a signficant amount of time is spent in setup-for-minimization in the construction of residue-pair atom neighbor lists. The big expense: pushing back atom-index pairs into an array. So I am now reserving space for 100 atom-index pairs.
Also. The water-positional-derivative calculation is somewhat slow and needed only during derivative evaluation, but was being computed at every score function evaluation. So that is another source of speed.
Finally, LKBall was allocating and deallocating lots of small arrays during scoring and derivative evaluation. Those small arrays have been replaced with fixedsizearray1's which can be allocated on the stack. This requires knowing an upper bound on the number of waters per heavyatom, which is now hard coded to 4 in the constant MAX_N_WATERS_PER_ATOM defined in LK_BallInfo.hh. This constant controls the size of these fixedsizearray1s.
In my hands relax_jd3 is performing just as fast in multithreaded mode and MPI mode at a small benchmark of 100 relax trajectories of 1ubq with 40 worker threads.
@fdimaio @vmullig @phbradley
Andrew Leaver-Fay 7 years There's a pretty uniform drop in running times for the profile tests. That's good news.
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Merge pull request #2686 from RosettaCommons/jadolfbr/skip_crap_structures
Enable old databases to load disulfide residues.
With the switch from CYD residue type to a proper patch, old databases could no longer load in. This fixes that with a simple string replace in the res_type table column to the current name with the patch.
Also fix an unimplemented option in RosettaAntibodyDesign, and expand a antibody database unit test.
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