Merge pull request #1881 from RosettaCommons/everyday847/analogue_na
Integration test changes are exclusively from uncommenting the inosine RT we've had for a while but inexplicably had kept commented out.
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Merge pull request #1874 from RosettaCommons/roccomoretti/HighResDocker_resfile_fix
Fix bug with XML resfiles in HighResDocker
Setting a resfile in the XML for ligand docking hasn't worked properly in the past ~5 years, due to a bug.
Thanks to Brian Kuhlman for pointing it out.
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Merge pull request #1873 from RosettaCommons/aleaverfay/fix_abscript_xsd
Ok, AbscriptMover looks like it ought to be able to read multiple
"Fragments" subtags, and not just a single one, and that "Stage" and
"Fragments" subtags can be interleaved. This PR updates the XSD to reflect that.
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Merge pull request #1865 from RosettaCommons/vmullig/fix_beta_disulfidize_test
Fixing disulfidize_beta_cys integration test.
Adding one rotamer library (B3C) needed by integration test. All other noncanonical rotamer libraries remain in the git LFS repository. (That one is still there, too; it's just also in the rotamer libraries directory).
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Merge pull request #1858 from RosettaCommons/everyday847/farfar_metrics
There may be a curious issue with the way division is working with the fractional scores -- but we'll only know for sure after we use it a lot, and we won't be able to until we've got these features to play with. So, merging for now!
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Merge pull request #1817 from RosettaCommons/vmullig/expand_disulfidize
Expand functionality of disulfidize for NCAAs
Tasks:
- [x] In Disulfidize:
- [x] Add options for placing:
- [x] beta-3-cysteine.
- [x] Track down bug in creating beta-3-cysteine disulfides.
- [x] Make dslf_fa13 score beta-cysteine disulfides.
- [x] Unit test for hetero-disulfide bond (alpha-beta).
- [x] Integration test for Disulfidize with beta-3-cysteine.
- [x] Beauty.
- [x] XML schema.
- [x] Fix unit test failures.
- [x] Fix integration test failures.
- [x] Documentation.
Also:
- [x] Tweak params files for cyclic beta-amino acids.
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Merge pull request #1854 from RosettaCommons/aleaverfay/fix_overfrequent_validation
Aleaverfay/fix overfrequent validation
This PR seeks the same goal as PR #1845 (which I inadvertently corrupted): spend less time validating XML files. The way it achieves it is by generating the text contents of the schema only once (which previously took ~half the time) and generating the data structure that can validate an XML file from this schema so that it can be reused (which took ~half the time). The time spent actually validating the XML file once those two steps completed was miniscule.
It still includes Vikram's code for validating a single script only a single time by keeping track of which scripts it has encountered in the past by file name. (This will need to be changed for the JD3 version of RosettaScripts, when it comes eventually comes online, where different jobs may use different script variables (script vars) for the same input XML file.)
This produces expected cosmetic integration test changes in all of the integration tests that rely on rosetta_scripts.
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