Merge pull request #2091 from RosettaCommons/rfalford12/enumerate-polar-rotamers
Dump Rotamers into PDB files at a single position
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At a given residue position, this mover dumps the rotamers for the residue into individual PDB files and prints rotamer probabilities to standard output. I'm using it for other analyses, but Jeff may want to use it in class on Monday so it would be great to add to PyRosetta.
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Merge pull request #2128 from RosettaCommons/roccomoretti/auto_rebuild_dunbrack_binaries
Add autogeneration of Dunbrack binaries as part of the build process
Coming off a comment by Vikram:: put (re)generation of the Dunbrack binaries into the build process.
* A new application (generate_database_cache) has been added which runs through the major Dunbrack libraries and loads them, generating the Dunbrack binaries if they don't already exist.
- Associated with this are a number of de-globalization changes to the dunbrack::RotamerLibrary and associated code to allow for loading multiple RotamerLibraries in the same program from different OptionCollections
- The normal usage (packing, etc.) still uses a single global object constructed from the default option set -- the alternate ones are really only useful for direct usage at this point.
* Add a hook to Scons to run the generate_database_cache application for release mode compiles
The hook only runs on release mode compiles (and only on Scons), and only if bin/generate_database_cache.etc link is being (re)generated. So it should run with most standard "installation" compiles (./scons.py mode=release bin) but will not be triggered for many of the time-sensitive testing compiles (e.g. unit test compiles, or compiles of just specific executables). That said, the no-regeneration-needed run of the release mode generate_database_cache application only takes about a second or so on my machine, which is dwarfed by the overhead of scons scanning.
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Merge pull request #2138 from RosettaCommons/roccomoretti/chain_in_InterfaceScoreCalculator
InterfaceScoreCalculator fixes
Previously, the ligand docking InterfaceScoreCalculator, while it takes a set of chain letters as the specification of the chain to use, instead bounced the chain specification through chain IDs, jump numbers, and even residue numbers. This resulted in difficulties when attempting to score poses which aren't set up with precise chain letter/chain ID/jump number/residue number correspondence, particularly with RMSD calculations on structures with differing numbers of (non-ligand) residues.
Rework the InterfaceScoreCalculator associate functions, so they work directly on chain letters (what the user is specifying). As an added bonus, reduce (but don't eliminate yet) the dependence on JD2.
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Merge pull request #2143 from RosettaCommons/vmullig/tweak_genkic
Decrease verbosity of GenKIC backbone_bin filter
The backbone_bin GeneralizedKICFilter is a bit too verbose. Switching its output to the debug tracer.
Cosmetic changes expected to the genkic_bin_setting integration test.
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Merge pull request #2124 from RosettaCommons/rhiju/rna_denovo_master_mover
Rhiju/rna denovo master mover
all test changes are cosmetic due to change in Tracer name.
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Merge pull request #2130 from RosettaCommons/roccomoretti/split_by_selection
Add utility functions for jump/residue selection correspondence.
One utility function ( core::kinematics::jump_which_partitions() ) to test if a jump splits a pose according to a defined set of residues. Another function ( core::kinematics::get_foldtree_which_partitions() ) to (minimally) rearrange a FoldTree such that a single jump does split the pose.
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JumpDownstreamSelector bug fix
So, for a FoldTree such as: FOLD_TREE EDGE 1 115 -1 EDGE 1 116 1 EDGE 116 221 -1, a call like:
ResidueSelectorCOP jump( new JumpDownstreamSelector( 1 ) );
ResidueRanges ranges( jump->apply( pose ) );
will create a ResidueRanges[1] of 116-220, missing the last residue of the chain.
This change should solve this issue.
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Merge pull request #2132 from RosettaCommons/vmullig/fix_aib
Fix AIB structure prediction for BOINC. I missed a few MAL->AIB renamings in the database patches.
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Merge pull request #2121 from RosettaCommons/rhiju/reorganize_rna_denovo
reorganize directory/namespace structure for rna_denovo/farna
test changes are cosmetic.
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