Merge pull request #3179 from RosettaCommons/jadolfbr/simple_metrics
Fix SM features integration test + various bug fixes
Also fix:
- The cdr length metric output for RAbD
- A bug in GlycanTreeRelax when using multiple apply calls, round=1, or when window=1.
- AnchoredGraftMover XSD
- AnchoredGraftMover copy constructor from changes to the way rosetta numbering was parsed.
- Fix rare FoldTree crash for grafting by using `set_reasonable_foldtree`, which is generally reliable.
- Add integration test for RS-interface of CCDEndsGraftMover, which calls the AnchoredGraftMover XSD
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Merge pull request #3199 from CyrusBiotechnology/forcommons/3195-refactor_pdb_diagnostic
Refactor pdb diagnostic - resolves #3195 for the scientific tests drive
Cosmetic itest changes expected in pdb_diagnostic and some of the jd2 mmCIF tests
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Merge pull request #2923 from RosettaCommons/frankdt/frankdt/smart_sewing
This pull request introduces the new SEWING refactor and its associated applications.
This new refactor introduces a number of changes and new features into SEWING, including but not limited to:
· SEWING can now be run without generating an edge file (formerly known as a score file). This “unhashed” mode is default and is recommended for most helical proteins. It also avoids the onerous memory requirements of generating an edge file.
· Legacy SEWING only stored one possible overlap for each pair of matching helices, limiting the number of possible designs. SEWING is now able to sample all alignments that pass a user-specified minimum overlap residue cutoff, which greatly increases the sampling space.
· Legacy SEWING input files contained large amounts of data which could not be held in memory simultaneously; therefore, SEWING had to read from disk periodically throughout the protocol, which led to significant slowdowns. SEWING now reads the entire file from disk at the start.
· SEWING now recovers and outputs the lowest-scoring structure encountered during the assembly process. Legacy SEWING did not store and recover the lowest-scoring assembly during a Monte Carlo protocol, instead outputting whichever structure was present at the end of the run. Users can return to this old behavior by setting the new recover_lowest Boolean option to false.
· SEWING now performs temperature ramping between user-specified minimum and maximum temperature values.
· Users can choose not to include binding partners in their output structures via the output_partner Boolean option.
· SEWING now reads all input information at the beginning of a run.
· SEWING score terms and their weights can now be customized by users in their RosettaScript XML files using the AssemblyScorers subtag. Previously, all scorers and their weights were hard-coded.
· SEWING is now compatible with ligands. Users can specify which residue in their starting structure is the ligand and can either specify its protein contacts manually or, in the case of metals and covalently bound ligands, those contacts can be detected automatically. All ligand contacts and the ligand itself will be preserved as vital residues during the SEWING run.
· The new LigandBindingAssemblyMover allows users to introduce new contacts to existing ligands during the assembly process using user-provided specifications of the ligand’s binding geometry.
· Both vital residues and ligands can now be specified using residue selectors.
· Vital residue information can now be written into the output PDB file; whichever residues so identified in the starting structure will be listed, renumbered, in the output structure as "VITAL" and can be extracted with a ResiduePDBInfoHasLabel ResidueSelector.
· Several new score terms and requirements have been introduced, including terms that allow users to more closely control their assembly’s interactions
with binding partners as well as scorers and requirements that provide compatibility with ligand molecules.
· In AppendAssemblyMover, users can either allow SEWING to automatically detect the boundaries of segments by DSSP (a new feature) or can specify the segments and their secondary structures manually. Manual setting of pose segment starts and ends now occurs in the mover tag rather than via command-line options.
· AppendAssemblyMover can now be set to simply extend the starting helix without adding more helices via the extend_mode Boolean option.
Note that the new SEWING refactor does not currently support discontinuous SEWING. For those cases, users will still need to use Legacy SEWING.
Integration test change to simple_metric_features expected due to old changes in ModelFeatures (associated with LegacySEWING).
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Merge pull request #3178 from CyrusBiotechnology/forcommons/213_62chains
Simple test to ensure that Rosetta is cool with all 62 officially legal chain characters [a-zA-z0-9].
Changes to unit tests only.
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Merge pull request #3186 from RosettaCommons/roccomoretti/fix_make_centroid
Fix silly issue with make_centroid
When checking if an atom has been deleted from a residue, it helps to check the residue for which you've deleted the atom. Checking the original that still has the atom doesn't work as well.
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Merge pull request #3184 from RosettaCommons/sergey/binder
PyRosetta update. Updating LLVM build procedure so it track compiler family and gcc-install-prefix as dependency for Binder deployment.
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Merge pull request #3185 from RosettaCommons/roccomoretti/fixClangSAparsing
Fix breakage in ClangSA test parsing.
Python3.6 requires that a file be opened in binary mode (where Python2.7 was fine with text mode). Update this so the clang_analysis test no longer fails. Also, add additional checks such that such parsing errors show up in the log.
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Merge pull request #3180 from RosettaCommons/roccomoretti/fix_pymol_cif
(Partially) Fix from-Pymol CIF reading
Pymol's mmCIF output is apparently less extensive than from-RCSB ones, and this is causing the Rosetta CIF reader to choke.
Note that Pymol CIF input still has an issue - apparently CIFPARSE-OBJ (the external library from the RCSB which we use to parse CIF files) completely ignores the last table in the CIF file. For from-Pymol output this is the atom_site table, which means that you lose all the coordinate data, resulting in an empty pose. The way to fix it is for you to add a dummy line to the end of the CIF file. As I'm not keen on debugging the external library, I've added a warning message to highlight how to get around the issue.
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