Merge pull request #1752 from RosettaCommons/roccomoretti/dun_binary_log
Attempt to address some issues with Dunbrack binary generation.
Per the rosetta-devel discussion, it seems we have issues with reproducability of Dunbrack binary file generation. These are some simple fixes to help with avoiding/debugging them.
Specifically, adding a tracer output statement to the validate_database integration test to print the SHA1 of the Dunbrack binary, as well as code to delete the Dunbrack binaries on the Benchmark server prior to running the integration test.
@lyskov
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Merge pull request #1750 from RosettaCommons/aleaverfay/sjq_with_more_read_access
The SJQ now keeps track of the job index ranges for preliminary job nodes so that derived job queens can determine what jobs have been output and what jobs have not been output yet. She also provides read access to the DIETs that track which jobs have completed (at all), completed successfully, failed, and which have been output.
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Merge pull request #1748 from RosettaCommons/jadolfbr/nbr_selector
Fix NeighborhoodResidueSelector to properly not include subset in selection if passed the boolean. Thanks Yang Hsai for the find.
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Merge pull request #1747 from RosettaCommons/aleaverfay/jd3_job_geneologist
Protocols in JD3 are responsible for keeping track of indices for jobs that they have created, and it is a tedious task. The class being created in this pull request, the JobGeneologist, will keep track of the parent(s) for each batch of jobs for each node in the JobDAG. It helps by assigning ranges of jobs to different nodes so that job-index-ranges do not overlap, and the JobQueen never makes the mistake of assigning the same index to two separate jobs.
The JobGeneologist also is capable of deducing which ancestral jobs no longer have any living descendants. Imagine this scenario. There's a multi stage protocol where, at the final stage when you're outputting the top structures generated by the protocol, you want to be able to output the intermediate structures from early stages that led to the final structures. Say Job 10 from stage 1 is promising, and serves as the "parent" (i.e. its output is the input to another job) to jobs 100-200 in stage 2. Of those jobs, only job 199 was not discarded, the others failed to pass some threshold. Then Job 199 is parent to jobs 1000-1100 in round 3, and of these jobs none were fruitful - they are all discarded. If the job queen for this protocol is going to avoid having unneeded results piling up, then she needs an algorithm to figure out that jobs 10 and 199 can now be discarded. This algorithm is actually really tedious! It would be a shame to force it on every JD3-protocol writer. The JobGeneologist manages the data and the logic needed for this task.
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Merge pull request #1086 from RosettaCommons/JWLabonte/enzymatic_movers
EnzymaticMovers: GlycosyltransferaseMover example
This merge introduces a framework for a new concept in Rosetta for `EnzymaticMover`s, `Mover`s that simulate enzymatic reactions of post-translational modifications to `Pose`s, which I introduced at Winter RosettaCON2016.
(If interested, view my presentation, which should be available from the Rosetta Commons wiki, or contact me. In short, and `EnzymaticMover` moves "`ResidueType` space" in a `Pose` instead of torsion space and creates starting structures for modeling rather than ending decoys from modeling.)
This is a work-in-progress.
In its current stage, it only uses sequence information, but it will be expanded to include structural information for the determination of which sites on a `Pose` will be modified.
Currently, I have only added a generic, human, glycosyltransferase as an example, which modifies NXS/T sites.
This merge includes unit and integration tests.
It also, as an aside, includes a sorting of the init files for `Mover`s as a bonus. (Please keep those files clean!)
All tests pass.
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