Merged origin/master with balej/2comp_devel.
Merged origin/master with balej/2comp_devel. Fixed conflict with ResidueCountFilter.
All tests passed, except for the following integration test changes which are either expected or due to an unstable test.
Integration test status: All 7 changes are due either to previous issues or expected logfile changes. See below for details.
Differences in translation are observed and expected in each of the 5 following tests due to setting default for ddG filter back to 1000 for all cases except those where PB calculations are being done. No differences in the resulting ddG values are observed or expected:
hotspot_hashing
hotspot_graft
place_simultaneously
rotamer_probability
dock_with_hotspot_place_simultaneously
Failed to run, as with other recent commits:
metropolis_hastings
This test is known to be unstable and the observed very slight changes in output are similar to those observed previously:
ligand_dock_script
More information on previous commits since the last merge with master are provided below.
source/src/core/pose/symmetry/util.cc:
Commit Message:
The FArray1D_bool for partitioning the pose was not actually being set in the get_symdof_subunits function and was causing a segfault when this function is used. Fixed this so that an initial array is created in which each residue number is set to false.
source/src/devel/matdes/AverageInterfaceEnergyFilter.cc
source/src/devel/matdes/AverageInterfaceEnergyFilter.fwd.hh
Commit Message:
Added functionality to permit filtering individual residues (which can be defined by task operations) for individual score terms. Removed the "return_total" option, which has been replaced with the "mode" option in which the user specifies whether they want to have the average score per residue returned, the total score, or the number of residues failing the user specified threshold; these modes are specified by the user as "average", "total", and "individual", respectively.
source/src/devel/matdes/BuildingBlockInterfaceOperation.cc
source/src/devel/matdes/ClashCheckFilter.cc
source/src/devel/matdes/ClashCheckFilter.hh
source/src/devel/matdes/MutationsFilter.cc
source/src/devel/matdes/MutationsFilter.hh
source/src/devel/matdes/OligomericAverageDegreeFilter.cc
source/src/devel/matdes/OligomericAverageDegreeFilter.hh
source/src/devel/matdes/StoreCompoundTaskMover.cc
source/src/devel/matdes/StoreCompoundTaskMover.hh
source/src/devel/matdes/TaskAwareAlaScan.cc
source/src/devel/matdes/TaskAwareAlaScan.hh
source/src/protocols/toolbox/task_operations/RestrictNativeResiduesOperation.cc
source/src/protocols/toolbox/task_operations/SelectBySASAOperation.cc
Commit Message:
Modified the output pymol selection strings and info from the write_to_pdb functions such that if the user does not set out::file::renumber_pdb to true, then the output residue numbers are retrieved from pose.pdb_info() to ensure that they will match with the output pdb even if there are missing residues that cause the Rosetta numbering to be shifted.
source/src/devel/matdes/SymUnsatHbondFilter.cc
source/src/devel/matdes/SymUnsatHbondFilter.hh
Commit Message:
Added functionality to permit four different modes: bound_vs_unbound, unbound_design_vs_reference, unbound_mutated_sidechains, or all. The default mode is bound_vs_unbound, which yeilds the same behavior as before.
1) bound_vs_unbound: Report buriedunsatpolars that exist in bound state, but not in unbound state. Currently no repacking is done in either state.
2) unbound_design_vs_reference: For bb polars and non-mutated sidechains, compare same atoms design vs reference, identifying those that are now unsatisfied and were not before.
3) unbound_mutated_sidechains: For mutated sidechains in the unbound designed state, simply report any buried unsat polar sidechain atoms and don't compare back to the reference.
source/src/protocols.3.src.settings
source/src/protocols/init/init.TaskOperationCreators.ihh
source/src/protocols/init/init.TaskOperationRegistrators.ihh
source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperation.cc
source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperation.hh
source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperation.fwd.hh
source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperationCreator.hh
Commit Message:
Added the SelectByDeltaScoreOperation in src/protocols/toolbox/task_operations/. This new task allows one to select residues to be designable or packable based on the difference in score for a user-defined score term compared to the score for that residue in a user-defined reference pose. For instance, one can use this task to prevent repacking at all residues that have a difference in fa_atr between the current pose and user-defined reference pose of greater than or equal to 4.0 REU. This could be useful for instance in restricting design to those positions that have lost a significant amount of packing compared to the native scaffold (ie, that now have "holes"). It could also be used in conjuction with the DesignableResidues filter for instance simply to output the number and position of residues that have lost a significant amount of packing compared to the native scaffold.