Merge pull request #1954 from RosettaCommons/Cyrus/mergetarget
From Steven Lewis:
three items:
1) @yfsong -sourced bugfixes and updates to Hybridize. This is mostly an update to add a more powerful constructor (previously the class was dependent on parse_my_tag being called). This code is marked as smlewis code because it's a squash-cherrypick from an abandoned poisoned branch.
2) read_topology_file, the function that converts params files into ResidueTypes, previously assumed that the file was coming in from disk (string filename, or izstream from file). The interface has been rearranged to allow a std::istream, for params files not coming from disk (coming in over network communication from some non-Rosetta black box in my case). There has been discussion of unifying the function name read_topology_file and the file names "*.params" to match better - that's been put off to the winter meeting.
3) @roccomoretti pointed out a bug in my last ACTCCMover updates; fixed.
Tests all look fine from my end. There is an added unit test to support read_topology_file.
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Merge pull request #1968 from RosettaCommons/roccomoretti/parse_xsd_desc_fix
Fix documentation on some of the common XSD parsing utilities.
There was a bunch of XRW TODO for documentation in protocols/rosetta_scripts/util.cc -- I changed this to something passable, as well as extending the utility functions to take (optional) descriptions, so you can have "TaskOperations for the low-resolution stage" instead of just a plain "TaskOperations to use" description.
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Merge pull request #1963 from RosettaCommons/roccomoretti/enable_CIF
Attempt to (re)enable mmCIF input on JD2
Update 'PDB'JobInputter to use the auto-detection logic and update the auto-detection logic.
Add usage of mmCIF input to integration tests to catch if we break it (again).
Large number of cosmetic integration test changes expected, as an additional diagnostic line has been added to PDB loading.
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Merge pull request #1958 from RosettaCommons/roccomoretti/chifix
ICOOR/CHI correspondence fixes
There's an implicit assumption in ResidueType that the two terminal bonds of a chi are situated along the ICOOR tree. We get that right most of the time, but there's a couple of examples where it doesn't quite work.
This PR adds a check during finalize() to make sure things are set up appropriately w/r/t CHI and ICOORD trees. It also fixes some of the existing params files which don't get things correct, as well as the SDF/CIF loading code which was ignoring the issue.
Trajectory changes to pna and vancomycin integration tests expected: these use params files that changed.
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Merge pull request #1960 from RosettaCommons/roccomoretti/XML_roundtrip
Add quoting to script outputting.
Now that we have XSD validation, input RosettaScripts XMLs need to have quoted options/attributes. However, the tracer-output of the parsed XML currently omits the quotes. Ideally, the outputted script should be 'round-trip-able' (that is, functional for feeding back into Rosetta as input.)
This change enables quoting of options/attributes by default in the script output, so that the output script looks "proper".
No test changes expected, aside from the obvious integration test log changes.
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Merge pull request #1953 from RosettaCommons/rhiju/recces_bulge
Rhiju/recces bulge
Only tests that really change are
+ `rna_denovo_bps`; due to a different ordering of noncanonical base pairs due to use of Andrew's nice `rna_secstruct.pairings()` function instead of my and Joe's _ad hoc_ flatten of stems.
+ `swm_builld_full_model` restored.
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Merge pull request #1812 from RosettaCommons/vmullig/fix_boinc_mac
Update mac/clang/boinc build and BOINC code for new BOINC API
The move to C++11 broke the BOINC builds, and we've had to move to the latest verison of BOINC, which in turn broke the way in which we were interfacing with BOINC. This corrects all code issues, so that Rosetta can talk to BOINC again.
DONE:
- Fix linking issues, particularly related to the new TrueType libraries that BOINC uses.
- Test font display with the new BOINC libraries and the TrueType libraries; adjust font sizes and spacings appropriately.
@davidekim
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