Merge pull request #3025 from RosettaCommons/vmullig/update_ncaas
Adding properties and BACKBONE_AA to some NCAAs.
It should now be possible to score all L-alpha-amino acids with ref2015, provided the params files have either BACKBONE_AA lines or mainchain potentials defined. This pull request aims to update some params files with PROPERTIES and BACKBONE_AA lines. It also updates the H and O atoms so that they depend on the lower and upper connections, respectively.
Merge pull request #2979 from RosettaCommons/kalekundert/core_rosetta_scripts_utils
Move parse_task_operations(), parse_score_function(), etc. into core.
Merge pull request #2925 from RosettaCommons/jadolfbr/ab_design_optimize_interface
Jadolfbr/ab_design
Small tweaks to RAbD:
- Remove try/catch for sequence design. It should only be there for graft design.
- Fail if we have caught exceptions the whole time. I had some issues on a cluster that was being hammered hardcore with IO operations of another user and my runs still completed and output a file. We should never have that.
- Improve the speed at which we load structures from the database through a pre-made text file. This is a temporary solution until we have updated databases in raw txt form in the rosetta database. However, this significantly speeds up runs and is up-to-date with the current PyIgClassify db.
Etc:
- Throw exception in ProteinResidueFeatures instead of a utility_exit_with_message.
- Add option, `-read_only_ATOM_entries` to literally only read ATOM records in pdb_reader and cif_reader.
Merge pull request #2899 from CyrusBiotechnology/for_commons/indigo/nmer_refactor
From @indigogo at Cyrus.
* new unit test for core/scoring/methods/NMerSVMEnergy, the scoring method used for tcell epitope prediction. unit test just compares epitope predictions for rosetta's idealized trpcage pose
* refactoring of all 3 tcell epitope scoring terms (NMerSVMEnergy,NMerPSSMEnergy,NMerRefEnergy). no functional changes, just added full constructors like I should have done in the first place, also some new functions to extract model energies before everything is summed/averaged into total residue energy
Merge pull request #2898 from RosettaCommons/vmullig/fix_voids_penalty_config
Fixing a little problem in EnergyMethodsOptions setter functions that was preventing configuration of the voids_penalty energy term from RosettaScripts XML.
Merge pull request #2820 from RosettaCommons/roccomoretti/switch_residue_type_set_fix
Fix issue with crashing SwitchResidueTypeSet
The make_centroid() utility function, which is applied when SwitchResidueTypeSetMover can't find a corresponding type, had a bug where resetting the ResidueType's atom type assumed that it was operating with the same type set with the current and replacement type - which wasn't the case for make_centroid().
Change things such that switching the atom type set on a ResidueType appropriately swaps out the atom types, as much as possible.
Merge pull request #2817 from RosettaCommons/jadolfbr/fix_ff_from_loops
Fix DihedralConstraintGenerator XSD and add option to FoldTreeFromLoopsWrapper to add cutpoint variants for the proper use of the chain break term.
Merge pull request #2769 from RosettaCommons/roccomoretti/icc_scons_fix
Fix compiler autodetection for ICC.
Add os information to pre-load stage, such that the OS-specific ICC commands can be loaded and used for pre-load detection.
Merge pull request #2745 from RosettaCommons/vmullig/code_quality_issues
Fixing a few things flagged by clang analysis
I didn't get through everything, and left a few things alone that seemed to be spurious flaggings.
Some change observed in vip integration test, attributable to bugfix to gauss score term (used for packing by this application). No other changes.