Merge pull request #1987 from RosettaCommons/dougrenfrew/nterm_proline_hydrogens
Change ICOOR for Nterminal hydrogens for proline and proline-analogs.
This results in quite a few integration test changes, 35 on my machine and 38 on the test server. All of them are either cosmetic changes from the modified patches, trajectory changes as a result of having Nterminal prolines in input files or allowing them during the trajectory (e.g. during design), or are round off differences.
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Merge pull request #2638 from RosettaCommons/bfrenz/no_lower_glycan_term_w_MissingDensityToJump
don't add lower terminus types glycans when using missing density to jump.
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Merge pull request #2639 from RosettaCommons/sergey/binder
Refactoring PyRosetta build so it now avoid copying database files. Updating PyRosetta package, adding symlink creation for pyrosetta and rosetta dirs so PyRosetta and scripts(like self-test.py) could be run in package unpacked location in-place, without need to install PyRosetta first.
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Merge pull request #2528 from RosettaCommons/vmullig/oligourea
Add support for oligoureas in Rosetta peptide design and structure prediction
These resemble beta-amino acids, but with a urea linkage to the next amino acid instead of a simple amide bond.
@twcraven
Tasks:
- [x] Add `OLIGOUREA` property.
- [x] Convenience functions in `ResidueType` class.
- [x] Torsion specifications in `Pose` class.
- [x] Add to the horrible `Conformation::backbone_torsion_angle_atoms()` function... ugh. (At least I'll have it call another function for oligoureas, so that it's not more mess in that function.)
- [x] Some new unit tests for `Conformation`.
- [x] Update relevant patches:
- [x] NtermProteinFull.
- [x] CtermProteinFull.
- [x] N-terminal acetylation.
- [x] C-terminal methylation.
- [x] Cutpoint variants.
- [x] Update `SmallMover` to support oligoureas.
- [x] Unit test.
- [x] Document this.
- [x] Update `pro_close` energy to support OU3_PRO.
- [x] Unit test.
- [x] Document this.
- [x] Update `OmegaTetherEnergy` to support oligoureas.
- [x] Unit test.
- [x] Unit test: minimization.
- [x] Document this.
- [x] Update CycpepSymmetryFilter to support oligoureas.
- [x] Document this.
- [x] Add oligourea mainchain potentials.
- [x] Update mainchain potential class so that it can be applied to a subset of mainchain torsions.
- [x] Unit test.
- [x] Add oligourea params files.
- [x] OU3_ALA.
- [x] Update peptide bond geometry.
- [x] OU3_PHE.
- [x] OU3_ILE.
- [x] OU3_LEU.
- [x] OU3_PRO.
- [x] OU3_VAL.
- [x] Update peptide bond geometry in all of the above.
- [x] Add oligourea mainchain potentials.
- [x] For OU3_ALA.
- [x] Unit tests for mainchain potential with 3 mainchain torsions.
- [x] For OU3_PRO.
- [x] Add oligourea rotamer libraries to Git LFS repository.
- [x] Update `simple_cycpep_predict` to allow oligourea prediction.
- [x] Integration test: `simple_cycpep_predict`.
- [x] Integration test: oligourea design.
- [x] Address points in comments below: make it possible for rotamer libraries to be dependent on a subset of mainchain torsions.
- [x] Documentation: `simple_cycpep_predict`.
- [x] Beauty.
Put off to a future pull request:
- Unit test: cyclic geometry.
- Unit test: mirroring.
- Add additional oligourea params files.
- OU3_AIB.
- OU3_CYS.
- OU3_ASP.
- OU3_GLU.
- OU3_GLY.
- OU3_HIS.
- OU3_LYS.
- OU3_MET.
- OU3_ASN.
- OU3_ORN.
- OU3_DAB.
- OU3_DAP.
- OU3_GLN.
- OU3_ARG.
- OU3_SER.
- OU3_THR.
- OU3_TRP.
- OU3_TYR.
- Update peptide bond geometry in all of the above.
- Add additional oligourea mainchain potentials.
- For OU3_AIB.
- For OU3_GLY.
- Symmetry unit tests for OU3_GLY, OU3_AIB.
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Merge pull request #2627 from RosettaCommons/sergey/binder
Adding function to set/get Path* options in PyRosetta. Refactoring PyJobDistributor so it works more reliably on filesystem with caching. Adding option to write compressed PDB files. Adding JD unit tests.
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Merge pull request #2633 from RosettaCommons/xingjiepan/fix_loop_modeling_build_levels_problem
Quick and ugly fix of the build level bug caused by loop modeler
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Merge pull request #2628 from RosettaCommons/aleaverfay/fix_invrottree_atom_indexing_bug
PDB I/O from the InvrotTree indexing-from-0 bug
The InvrotTree code was constructing a PDB file counting from atom index 0,
but large sections of PDB writing assumes that atom indices start from 1.
This bug was recently uncovered by the (several) fixes to the behavior of
CONECT record creation in PDB writing with PR #2595 and disrupted the behavior
of the cstfile_to_theozyme_pdb integration test
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