modifying the xcode project build_util.py to work with the latest master. Pull request #810 removed protocols_f.5 from all src.setting files (it appears to have been an empty library anyway), in order for the xcode make_project tool to work protocols_f.5 must be removed from the KNOWN_PROJECTS dictionary
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Fix inverse_rotamer_remodel integration test.
If you put a tracer output statement that prints object addresses in the code, yeah,
that's going to cause integration tests to fail.
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Merge pull request #756 from RosettaCommons/rhiju/remove_patch_selectors_from_daslab_code
+ Remove patch selectors from daslab code
+ For residue_type_set, name3_map_DO_NOT_USE and
aa_map_DO_NOT_USE calls are still not suggested as best practices, but now run over a set of about 30 patches that were on by default in 2015 rosetta -- this allows unit tests and a few integration tests to not time out. Any new patches (e.g., upcoming metapatches) are not covered.
+ got rid of some legacy code (e.g., for setting up packer jobs for residue types with custom_variants in ResidueLevelTask_) since I could expand ResidueTypeSet to handle them.
Only tests that change are integration -- inverse_rotamer_remodel remains broken; and ligand_motif_design generates fewer FullatomCustomPairDistanceEnergy AtomPairFunc lists, but that does not affect test results. The linux integration_release_debug_no_symbols show some change, but I think that's due to clang versions -- will monitor carefully.
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Merge pull request #842 from RosettaCommons/roccomoretti/inv_rot_remod
Attempt to fix the inverse_rotamer_remodel integration test
Recent changes mean that the inverse_rotamer_remodel integration test has gone from crashing silently to failing with a recognizable error. This provided an opportunity to start picking things apart.
The current cause of failure looks to be an issue with the ReadResfileAndObeyLengthEvents taskoperation.
The ReadResfileAndObeyLengthEvents taskop collects a number of Conformation LengthEvents and combines them to get a mapping of before to after residue numbers. The issue here is that the mapping code was pulling the total size from the stored Conformation (raw) pointer in the LengthEvents. This has two problems.
The first is that it gets the length from the final conformation, rather than the length at the time the LengthEvent occured.
The second is that the raw conformation pointer might have been invalidated, due to copying, etc. resulting in an invalid read.
This pull request fixes that by storing the current value of the Conformation length when the LengthEvent is created, and then using that value (rather than the value from the Conformation pointer) when making the mapping. It does not address the more general issue of long-term storage of a raw Conformation pointer in Event objects, where the underlying Conformation might be invalidated in the meantime.
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Merge pull request #803 from RosettaCommons/rhiju/remove_placeholder_residue_types
*Removing last exponential blow up in ResidueTypeSet*
Reduces setup time for FA_STANDARD residue type set from 1.1 seconds to 0.40 seconds on my machine. Allows activation of all available patches (e.g., ones currently under command-line control; see https://github.com/RosettaCommons/main/pull/756) and new 'metapatches' (see https://github.com/RosettaCommons/main/pull/844) without blowup of setup time & memory.
All Rosetta modes now compatible with refactored ResidueTypeSet and accessor function, including adducts; and lots of code cleanup.
Only tests that change are integration tests:
+ _fiber_diffraction_fad_, _fold_and_dock_ (cosmetic, tracer debug now registers instantiation of D-AA residue types)
+ _inverse_rotamer_remodel_ (broken before at SequenceMapping)
+ _mm_params_ now loops through D-AA residue types, though does not actually check mm parameters for those-- could do so.
+ _dna_interface_design_ changes at late stage; tracked down to a difference in a random number in a SmallMin move -- all the 'physics' of the simulation, including number of adduct rotamers used in design, appears preserved up to that point and later -- may be a sign of a memory leak.
+ _number_of_residuetypes_ now does not report on total number of residue types, which is no longer computed, but on the components of ResidueTypeSet, e.g.:
```
apps.pilot.doug.number_of_residuetypes: The FA_STANDARD ResidueTypeSet contains 364 base ResidueTypes, 71 Patches, and 0 custom ResidueTypes
```
instead of
```
apps.pilot.doug.number_of_residuetypes: The FA_STANDARD ResidueTypeSet contains 42632 ResidueTypes
```
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Merge pull request #843 from RosettaCommons/roccomoretti/mm_params_fix
Attempt to fix issues with the mm_params integration test.
Use Rhiju's ResidueType sorter to fix the order of iteration in mm_params.cc
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Merge pull request #834 from RosettaCommons/vmullig/disulfidize_symmetry
Allow the Disulfidize movers to add disulfides across a symmetric interface.
Tasks:
- Add declare_chemical_bond() function to SymmetricConformation class.
- Add ScoreFunctionOP to DisulfidizeMover class.
- Edit DisulfidizeMover's parse_my_tag to let user set scorefunction.
- Get global scorefunction if user specifies no scorefunction.
- Check symmetric iff symmetric pose.
- Get core::utility::rebuild_disulfide() to work with symmetric poses.
- Use symmetric packer.
- Use symmetric minimizer.
- Fix issue in case where the symmetric copy is the same residue as the original.
- Fix additional strange issue causing rare failure.
- Seems to be caused by independently finding multiple disulfides at equivalent positions.
- Beauty.
- Add integration test.
- Update documentation.
- Set scorefunction.
- Use with symmetric pose.
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