Merge pull request #1897 from RosettaCommons/everyday847/fix_uninitialized_variable
Initialized variable in AddMover (added for pH simulation) by default…
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Merge pull request #1888 from RosettaCommons/Cyrus/mergetarget
From Steven Lewis:
Cyrus PR: HELIX and SHEET records in PDBs
Many moons ago, @yfsong wrote a code snippet in Cyrus's application to print HELIX and SHEET records in PDB files. It depended on the late, much-abused FileData, so I found myself needing to convert it to StructFileRep. I decided to go ahead and just rewrite all the code into core, into the SFR machinery, instead of handling it unshareably at app level.
You get:
- with PDB output, you can print PDB-formatted HELIX and SHEET records, using the flag -out:file:output_secondary_structure
- SFR contains HELIXInformation and SHEETInformation structs to track the data
- integration test (trivially)
- unit test on both the SFR internals and the string output, checking formatting (note this is bundled as one unit test, because I do not understand the existing structure of the unit tests in this area of Rosetta)
You do not get:
- Rosetta is not reading the records IN, just printing them
- I'm pretty sure having the PDB writer run DSSP breaks some encapsulation rules: the system only works if your code fills the Pose secstruct string somehow (such as DSSPMover)
- TURNs are not recorded, because TURN does not mean loop, and our DSSP does not distinguish beyond H/E/L, so the data are not there to interpret
- SHEET records are actually quite complex because sheets are multiple-element. This code just outputs each single strand as a one-membered sheet, which is sufficient to get viewers like PyMOL and PV displaying secondary structure correctly.
- StructFileRepOptions has an unimplemented provide_XML_schema...I left it that way for now
This will be of interest to @aleaverfay because it's his job to approve and recreate cyrus PRs, and @JWLabonte and @jadolfbr and other chemXRW attendees as it is the SFR I am extending.
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Merge pull request #1855 from RosettaCommons/jadolfbr/random_start
This changes the default of Glycan Relax to randomly sample on each dihedral of each glycan in order to start with a random conformation of the glycans (including any AA-glycan linkage torsions which are technically part of the glycan). This has been shown to improve model diversity and enrich for low-energy models.
-Removes the sugar_bb_start option, which is not really used, sans for the initial testing.
-Adds a 'refine' option, which turns the starting sampling off and keeps the starting conformation of the glycans passed in. We can then use this option down the line to further 'refinement-specific' code.
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Merge pull request #1856 from RosettaCommons/aleaverfay/close_contact_selector
New neighborhood selector using atom-pair distances
My other residue selector, the NeighborhoodResidueSelector, uses the same logic that the packer uses to decide neighbor relationships. Namely: under any rotamer assignment for two residues, would they interact? It does this by considering each residue as a sphere centered at the neighbor atom (e.g. cbeta), and then asking are the spheres get within the interaction cutoff. Modeling residues as spheres, however, is not always what you want.
This new neighborhood selector, the "CloseContactResidueSelector" identifies residues that have atoms within a certain distance cutoff -- that is, it's using the current atomic coordinates to make the neighborhood decision, instead of "any possible rotamer assignment," which often includes residues that couldn't realistically move into contact distance because there are other residues in the way.
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Merge pull request #1882 from RosettaCommons/rhiju/farna_cleanup
Rhiju/farna cleanup
+ integration test changes are just due to removal of NWC output by default for stepwise.
+ integration.mpi was broken by previous commit into master, http://benchmark.graylab.jhu.edu/test/230501.
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Merge pull request #1868 from RosettaCommons/vmullig/xsd_info
Add an "info" option to rosetta_scripts
I often find, when I'm working in RosettaScripts, that I can't remember the details of the syntax of particular movers, filters, task operations, or residue selectors. Is it "filename" or "file_name" in ReadResfile? Do filters typically have a "cutoff" or a "threshold" option? This typically means that I either have to search the web documentation, or I have to find the right .cc file in the codebase and read the parse_my_tag() function. If I'm on a train or a plane, the former is often not an option, which only leaves the latter -- and that's an awfully slow way to check user input syntax.
Wouldn't it be nice if Rosetta had in-app help? Well, thanks to the hard work of the XSD XRW team, it pretty much does -- all it needs is an interface.
So this pull request adds the "-parser:info" (or just "-info") option to RosettaScripts. If you provide the option with the name of a mover, filter, task operation, or residue selector (e.g. `./bin/rosetta_scripts.default.linuxiccrelease -info FastDesign`) you can get a list of all of the XML-accessible options for that mover/filter/task operation/residue selector, with a description of each. (The app will print out help information and exit _in lieu_ of running a script with this option.)
This is not meant to be a substitute for the web documentation, of course; unlike the documentation, this is only useful if you already know what Rosetta component you need, and just want details of syntax. But it should be a time-saver for those in that boat.
Tasks:
- [x] Add the "-parser:info" option.
- [x] Support for movers.
- [x] Support for filters.
- [x] Support for task operations.
- [x] Support for residue selectors.
- [x] Make the output a bit more human-readable.
- [x] Documentation.
- [x] Beauty.
- [x] Integration test.
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