Merge pull request #2307 from RosettaCommons/arubenstein/enzscore_defaults
Added defaults to EnzScore filter to fix bug regarding the setting of data variables resnum and whole_pose
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Merge pull request #2546 from RosettaCommons/everyday847/better_align_pdb
A better align_pdb
Andy Watkins 7 years I'm getting
Encounter error while executing: /scratch/local-benchmark/T/T/59696.master/linux.clang.python36/scripts.pyrosetta/ve/bin/pip install pytest pytest-json
because it can't find pip. I don't think this could be due to me, right?
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Merge pull request #2545 from RosettaCommons/roccomoretti/utf_decode_replace
Be more robust with UTF parsing.
Add errors=replace to the UTF decode statements in Python scripts. Instead of crashing when input contains non-parsable data, replace it with the codepoint-missing character.
Doesn't completely solve the issue, as Python2 will still crash when redirecting Unicode-containing characters. -- That's not really something we can fix from within the script, though. You need to set the `PYTHONIOENCODING` environment variable in the launching shell to `utf_8` or equivalent.
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Merge pull request #2537 from RosettaCommons/roccomoretti/fix_missing_with_make_from_annotated
Fix bug with nullptr in make_pose_from_sequence.
ResidueTypeSet::name_mapOP can return a nullptr. This is an issue within make_pose_from_sequence(), if the sequence requires a residue that is unknown. With current master, this results in a segfault. This PR should fix that.
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Merge pull request #2536 from RosettaCommons/roccomoretti/vector_normalize_issue
Metal constraint fixes & better diagnostics.
* In a recent master, there's an issue with the Enzdes/metal constraint code when the constraints add additional virtual tracking atoms. Fix this such that when we replace_residue_keeping_all_atom_positions() we don't crash if the new residue has more virtual atoms than the starting residue.
* Normalizing a zero-length vector isn't necessarily bad user input, so we shouldn't throw an exception which will result in all nstruct for this input to be canceled. Also provide better diagnostic info in certain conditions.
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Merge pull request #2541 from RosettaCommons/roccomoretti/ligand_rmsd_native_ensemble_best
Add ability to get an 'ensemble best' from the ligand docking RMSD.
If you enable the 'native_ensemble_best' option in the InterfaceScoreCalculator, you can provide a native with multiple residues in the given chain. The native comparisons (e.g. ligand_rmsd) will then be reported for the best (i.e. lowest rmsd) structure.
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Merge pull request #2530 from RosettaCommons/Cyrus/mergetarget
Cyrus/mergetarget
Two code packets from Steven Lewis from Cyrus:
a) IndependentLoopMover internally tracks the status of the loops it is trying to close, but does not REPORT that status (or perhaps it reports it to a checkpointing file, which is useless to non-BOINC clients). Changes to that class are to expose that loop status so calling code can check closure status.
b) SingleLigandRotamerLibrary previously accepted rotamers only via the PDB_ROTAMERS line in a params file, or rotamers generated within Rosetta. I have rearranged this functionality so that a PDB-formatted set of rotamers (the same data that might come in from disk via PDB_ROTAMERS) can come in from a more generic input stream object. In other words SingleLigandRotamerLibrary no longer requisitely reads from disk to initialize itself. This class, and also StoredRotamerLibrarySpecification, gain unit tests.
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Merge pull request #2534 from RosettaCommons/aleaverfay/rename_just_parse_a_script
Aleaverfay/rename just parse a script
As part of the get-out-the-scripts drive, I'm adding two public apps:
* validate_rosetta_script, and
* parse_rosetta_script
based on Andy Watkins' prior just_parse_a_script pilot app. The purpose of these two applications is to validate an XML file against Rosetta's internally-generated XSD (validate_rosetta_script) and to create all of the Movers/Filters/TaskOperations/etc. in the XML file ensuring that their parse-my-tag functions all run smoothly (parse_rosetta_script). In both cases, if the input XML file is ok, then the applications print out a short success message and exit with a zero exit status. If either fail, then they print out the message of any exception that was thrown and then exit with a non-zero (1) exit status.
I have written application-level documentation for them in the documentation/ repository.
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