Somehow when I pulled master before pushing to sync changes, ResetBaselineMover.cc was changed and ResetBaselineMover.hh was not, leading to two inconsistent solutions to the unused parameter in its parse_my_tag function. Whoops!
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Support for homocysteine and D-homocysteine disulfides.
Earlier, I implemented params files for a disulfide bonded homocystine and D-homocystine, and I further made it so that Conformation could conceive of these residue connections. That didn't mean that they would be scored, though, or that a variety of protocols that might
have been primed to think of disulfides strictly in terms of SG atoms and comparisons to aa::cys and such were any more prepared.
Now they are: every protocol I could find that had a special disulfide behavior that was specifically about cysteine disulfides (and shouldn't be) no longer makes that assumption.
Now, some caveats. There still aren't centroid files for NCAAs, which include homocysteine and D-homocysteine. I didn't implement them. That said, whenever they're implemented, disulfides formed from them will work, so that's nice. Essentially, I didn't bend over backwards to implement new protocols or new functionality, but my aim was that--for protocols that ought to be agnostic to cysteine type but that for some reason were married to tepid ol' cysteine, now they aren't. Importantly, since there really isn't a wealth of e.g. D-homocy
stine disulfide structural data, it's not easy to empirically validate these structures, but we're expanding our capabilities.
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Renaming/cleanup of variables to better match conventions. Mostly affects stepwise stuff, but I have always been annoyed PDBInfo -- acronyms should be separated by underscores -- so this is now PDB_Info. Merge of master and rhiju/swm_cleanup. Integration tests checked -- all changes cosmetic.
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Update the RestrictToLoops task operations.
This commit adds a RestrictToLoops task operation, which is closely
related to the RestrictToLoopsAndNeighbors task operation. Support for
rosetta scripts was implemented for both task operations, although the
documentation has not been updated to reflect this.
Unit tests were added for RestrictToLoops. No integration test changes
expected.
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[update of SandwichFeatures]
- added 'min_dis_between_sheets_by_all_res' column to see a relationship
between 'min_dis_between_sheets_by_all_res' and 'holes' (surprisingly,
no relationship found)
- refactored SandwichFeatures much more by introducing WriteToDBFromSandwichFeatures.cc
- should not change any integration tests other than (expected) features and features_database_schema (if any)
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Fix Segfault with RestrictToInterfaceVectorOperation and nonexistant chains.
If you passed a chain number or jump to
RestrictToInterfaceVectorOperation which didn't exist in the pose, your
run would segfault. Look for the error and utility exit appropriately.
Fixes bug 0000039
Meiler lab powercoding with Alyssa Lokits.
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Make usage of boost::uint64_t explicit
Certain compiler/platforms get confused about uint64_t - make it explicit
that Rosetta is using the boost version (as it's more portable).
This fixes bug 0000332
Meiler lab powercoding with Alyssa Lokits
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ResidueType: Residue properties are now stored in a separate class.
This push is first in a series of major refactorings of how proeprties for
ResidueTypes are handled in Rosetta. I will be discussing more about WHY and
what I did at the developer meeting, but the highlights are thus:
* Properties, such as POLAR, TERMINUS, LIPID, METALBINDING, etc., are no
longer stored in a vector of strings AND a series of is_foo_ bools in
ResidueType; instead, they are stored in a ResidueProperties class, to which
ResidueType has an OP.
* Within ResidueProperties, the properties are stored in a vector of bools
keyed by a ResidueProperty enum.
* enum values are auto-generated by a script, found in core/chemical/
residue_properties.
* The script auto-runs at compile (like update_options) and the generated
code files are not tracked by git. (I modified Scons, cmake, & xcode.)
* To add new properties, simply add a new line to the core/chemical/
residue_properties/general_properties.list file.
* Any property can be accessed by
ResidueType.properties().has_property( PROPERTY ).
* Wrappers still exist in Residue and ResidueType to access current properties
indirectly, (such as is_protein(),) but those could be deprecated if we
decide on that.
----------------------------------------
Unit test status: Pass
Integration test status: 2 changes
rings & carbohydrates: intentional output changes
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[update of SandwichFeatures]
- refactored SandwichFeatures by introducing CheckForSandwichFeatures.cc
- better comments
- should not change any integration tests other than (expected) features and features_database_schema (if any)
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