Merge pull request #667 from RosettaCommons/rfalford12/membrane_transform2
Rfalford12/membrane transform2
Fixed TransformIntoMembraneMover interface & unit test. Mostly work from Julia (@jkleman) - just fixing some smaller things here.
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Merge pull request #622 from RosettaCommons/everyday847/covalent_hbs
Fun and games with LINK records for covalent HBS sampling and more, now compatible with all tests. Integration tests are all cosmetic (or alterations to the tests themselves)
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Update SetPyRosettaEnvironment.sh
According to Sergey, removing the $PYROSETTA/rosetta directory from the LD_LIBRARY_PATH will break the namespace build so I have restored this to the LD_LIBRARY_PATH (while maintaining the $PYROSETTA in that environment variable).
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Update SetPyRosettaEnvironment.sh
Fixing LD_LIBRARY_PATH from $PYROSETTA/rosetta to $PYROSETTA because as far as I can tell the file libboost_python.so.1.55.0 lives in $PYROSETTA and gives an import error with the previous LD_LIBRARY_PATH.
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Merge pull request #654 from RosettaCommons/vmullig/aa_composition_energy
Add an energy term for penalizing deviations from a desired residue type composition
This is a wholebody energy, which has the disadvantage of being ignored by the packer in its current implementation, but the advantage of permitting nonlinear penalties as the deviation from desired composition increases.
Tasks:
- Add AACompositionEnergy.cc
- Add AACompositionEnergy.hh
- Add AACompositionEnergy.fwd.hh
- Add AACompositionEnergyCreator.hh
- Register with init.cc, core.3.src.settings
- Register scoretype in ScoreType.hh, ScoreTypeManager.cc.
- Rename energy term from aa_composition_energy to aa_composition.
- Write finalize_total_energy() function.
- Write calculate_aa_composition_energy() function.
- Permit penalties for deviation from desired composition by residue type.
- Permit penalties for deviation from desired composition by residue properties (e.g. 40% hydrophobic, 10% aromatic).
- Add PropertiesSet class to allow the above.
- Create a helper class for storing data associated with this energy function.
- Move the data access and data storage functions into this class.
- Permit initialization (desired amino acid composition, penalty function) from a file.
- Option for filename.
- File read from database.
- Parse properties setup, too.
X Add default files to the database. --> Put off to a future pull request. Requires validation. (There are some sample files in the database now, mostly as user templates and for unit tests.)
- Permit desired levels to be set by percentage (e.g. 7% valine) or by absolute number (e.g. I want exactly 1 tryptophan).
- Unit test with initialization file that only penalizes a subset of properties, based on fraction (e.g. just AROMATIC).
- Unit test with initialization file that only penalizes a subset of properties, based on absolute number of residues (e.g. just AROMATIC).
- Unit test with initialization file that only penalizes a subset of residue types, based on absolute number of residues (e.g. just ALA and GLY).
- Unit test with initialization file that only penalizes a subset of residue types, based on fraction (e.g. just ALA and GLY).
- Unit test with noncanonicals.
- Integration test for design. (This should currently do nothing during design, since it's a multibody energy. With Alex's changes, though, it should be very useful for controlling the packer's behaviour.)
- Documentation
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Merge pull request #656 from RosettaCommons/aleaverfay/fix_subversive_place_stub_mover_behavior
Changing the behavior of the PlaceStubMover so that it no longer
changes constraints after they have been placed in a Pose.
Cosmetic integration test changes only -- the hotspot_graft trajectory
is unchanged.
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