Merge pull request #445 from RosettaCommons/vmullig/fix_remodel_AP_issue
Fixing an issue with the RemodelMover
Fixing an owning pointers issue where an owning pointer was being requested from an object created as a reference on the stack in the RemodelMover.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #443 from RosettaCommons/rfalford12/turn_off_mp_scorejd2
Turning off mp_score_jd2 integration test until stability issues are resolved
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #442 from RosettaCommons/rfalford12/add_ligand_mover
Basic support for ligands in the membrane framework
Adding basic support for working with ligands in the membrane framework. This support will add a ligand to the desired place in the foldtree, while also preserving the membrane jump required for modeling. The following components were added:
AddMPLigandMover: A mover that runs after AddMembraneMover and rearranges the foldtree to accommodate the membrane residue and a single ligand
Unit test for AddMPLigandMover: Checks membrane framework invariants are still in check after running and the foldtree is reasonable
Integration test: Integration test for this mover in combination with the membrane relax protocol - runs a short version (relax repeats = 1 instead of 8)
Integration Test Changes: mp_relax_w_ligand
Unit Test Changes: None Expected
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #427 from RosettaCommons/rfalford12/membrane_bugs
Lots of bug fixes in the membrane framework. Also, adding new unit and integration tests to prevent current and catch future bugs in critical functions.
Bug Fixes:
- Adding additional error checking, demonstrating to the user
SetupForSymmetry is required to run before SymmetricAddMembraneMover. This is clear in C++, but the error is more difficult to track in RosettaScripts
- Fixed the RosettaMPRelax (new) RosettaScript that was previously
not scoring final models with the specified membrane scoring function
by adding an <OUTPUT ...> line in the script. Corrected in the
integration test and in Rosetta/demos
- Fix bug in AddMembraneMover that skipped setting the membrane position
from an existing membrane residue
- Fixed weird logic that seemed to allow multiple membrane residues? This
is not currently allowed in the membrane framework. If you need multiple, add EMB residues
- Fixing messy implementation of membrane-depth dependent hydrogen
bonding for the framework and previous code. Cleaning this up - will do an object-oriented implementation soon.
New Integration/Unit Tests:
- Add Integration test for rescoring a pose output by the membrane
framework with score_jd2 app (mp_score_jd2)
- Added new scorefxn fingerprint test for pH-aware membrane scoring
function (membrane_fa_pH)
- Updated existing membrane score fingerprint tests:
- Removed previous resource manager dependence
- Removed spanfiles with extra files, created by bug in old code
- Adding integration test for previous version of membrane relax (Barth
2007) which includes the membrane depth-dependent hydrogen bonding
correction. Needed to check this code is compatible with both
frameworks and for some future code updates
- Added unit test for reading in a membrane residue using a position
provided in the constructor or searching for one in the PDB. The
membrane residue has a non-trivial position to check for an edge case
previously causing trouble
- Add integration test for just loading in a pose using the symmetry
and membrane frameworks using RosettaScripts (reason described above)
Expected Sfxn Regression Test Changes:
- membrane_cen_scorefxn
- membrane_fa_pH
- membrane_fa_scorefxn
- menv_smooth_scorefxn
* Nothing numeric: just due to addition/deletion of files
Expected Integration Test Changes:
- mp_symmetry_load
- membrane_relax
- membrane_relax_hbond
- mp_relax
- mp_score_jd2
* Nothing numeric: just due to addition/deletion of files
Thank you to Amanda for identifying the bug in the symmetry RosettaScripts hook!
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #439 from RosettaCommons/justinrporter/env_release
Hard to tell exactly if things are broken or not based on the currents state of master, but an additional test of these commits gave changes that don't make any sense. Will revert if changes persist. No unit test failures.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #426 from RosettaCommons/JWLabonte/sugars/scoring
Carbohydrates: 1st Scoring Method for Sugars -- Woo!
NEWS: The "CHI energy function", developed by Woods Lab, has been (partially) integrated into Rosetta as the `sugar_bb` term of the scoring function. If the `-include_sugars` flag is used, the weight is set to 1 by default. It has no effect on non-saccharide residues. It acts very similarly to the Ramachandran score term, granting lower scores for phi and psi torsion angles known to be favorable experimentally. The function is thoroughly unit tested.
Currently, it only works for the phi angle of sugars, and it doesn't work on branches. Moreover, it is only accurate if the rings are in the 4C1 state. Adding these functionalities will require some additional coding, which I'll include in future pull requests.
The carbohydrate integration test now includes testing of the `score_bb` term and shows that it scores and minimizes phi properly.
All unit tests pass.
carbohydrates integration test changes expected, as they have been expanded.
Changes also seen in the database_jd2, database_jd2_io, and features tests, where the `sugar_bb` weight has been added. sweep_respair_energies also changes; I assume it is because of the addition of `sugar_bb`.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #433 from RosettaCommons/justinrporter/env_release
Improved error reporting in RigidChunkCM, fixed a minor bug in the way disulfides are handled by the broker, and modified the internal security interfaces in ProtectedConformation. Break out EnvExcn into .hh and .cc files and improve the way it reports errors.
notify author
notify list [rosetta-logs@googlegroups.com]