Merge pull request #2713 from RosettaCommons/orlypolo/enable_ignore_unrecognized_res
If not specified by user, set ignore_unrecognized_res to default to t…
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Merge pull request #2757 from RosettaCommons/aleaverfay/beautify_after_trycatch_and_template_initlist_beautifier_changes
Committing the new beautified files after fixing ~~two~~ three bugs in the beautifier:
1. the processing of comments at the end of try/catch blocks,
2. the handling of initializer lists for the constructors of templated classes, and
3. the indentation for lambda functions
The first one I only noticed this morning when I broke the beautification test
on master; the second one I've known about for a while, but haven't sat down to
fix. Well. I just did.
The final one I have not wanted to try and worry about because lambda functions are somewhat hard to detect. You can't grep for them; they're [](){}'s. I think I've written ok lambda-function-detection code now. It took a day and a half that I wanted to spend on the ResourceManager, but it's done.
Testing on the server for this PR was fine for everything except the beautification status of course.
The testing server updates the tools/ repo ahead of every test execution, so I don't need a commit freeze. I'm closing out this PR now.
You will need to update your version of the tools repository before you next run the beautifier from your local machine. The testing server's "beautify" button, however, will work swimmingly.
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Merge pull request #2753 from RosettaCommons/vmullig/correct_DAP_DAB
Fixing a few noncanonical params files.
Adding rama_prepro information to params files for DAP, DAB, and penicillamine.
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Merge pull request #2709 from RosettaCommons/aleaverfay/jd3_fix_mpi_hang_in_distributed_output
Fix hang in JD3+MPI distributed output
I was treating MPI like an asynchronous communication system, but in fact, MPI_Send will block until the buffer that it's using can be reused. What happened was, node0 would send out messages to all the archives saying "Hey, here's an output that you should write to disk" and then after they were all sent, then it would return to its listening loop. The archives would take these messages one at a time, write an output, and then send a "hey, boss, just finished that output you told me to do" message back to node0 before going back and seeing if node0 had any more output messages that it had sent. What would happen is that the MPI_Send calls would buffer the messages to a certain point, and then it would block until the messages from the remote node were processed -- which they couldn't be, because the remote nodes would also be blocking waiting for node0 to read their "hey boss" messages. Thus, deadlock.
New plan.
* Node0 sends output work to the archives one at a time
* Node0 does not output itself
* Worker nodes can be given output tasks (in addition to their regular output)
* Worker nodes can relieve the archive nodes of some of their output tasks (so the archive nodes don't block computation, because the worker nodes often need to talk to the archive nodes!)
Users can now say "I want X% of my nodes to perform output" so that by the time you're up at 100%, then all nodes except the head node are outputting and output is basically the same in JD3 as it was in JD2. Except in JD2, there was no option to have only 10% of the nodes perform output.
@JackMaguire @jadolfbr
Andrew Leaver-Fay 7 years I'm perplexed -- I beautified this branch more than a few times.
Andrew Leaver-Fay 7 years I am pretty sure we cannot beautify on the testing server with the new code-reviewed+PR-only commits to master restriction we just enabled. I'll open a PR.
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Merge pull request #2712 from RosettaCommons/everyday847/kalli_master_merge
Updates to RNA-protein modeling in FARFAR: modeling with density, high-res refinement of RNPs, RNP low-res score function updates, and an optional new method for setting up fold trees.
All integration test changes are expected due to new RNA-protein score terms, new residue types (noncanonical RNA residues), and a new energy function tag (exclude_RNA_RNA_fa_elec).
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Merge pull request #2745 from RosettaCommons/vmullig/code_quality_issues
Fixing a few things flagged by clang analysis
I didn't get through everything, and left a few things alone that seemed to be spurious flaggings.
Some change observed in vip integration test, attributable to bugfix to gauss score term (used for packing by this application). No other changes.
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Merge pull request #2740 from RosettaCommons/vmullig/netcharge
Adding a score term that penalizes deviation from a desired net charge in a pose or region
This is to complement @dougrenfrew's refactoring of the Supercharge application (pull request #2721 and #2737). The term, called `netcharge` will be analogous to `aa_composition`, but instead of letting a user control amino acid composition, it will let him or her control regional or global net charge in any context that calls the packer. (Used in conjunction with `aa_composition`, it can also control total number of charged residues. It will also be usable with the `hbnet` score term to create hydrogen bond networks with a desired net charge.)
Tasks:
- [x] Copy `aa_composition` files to create the score term.
- [x] Add `netcharge` score term to score terms list.
- [x] Modify to penalize deviation from a desired net charge rather than a desired amino acid composition.
- [x] Set up suitable interface for controlling the score term.
- [x] Flags for control from commandline.
- [x] Document this.
- [x] Options for control from RosettaScripts/PyRosetta/C++ code. (Modify `ScoreFunctionLoader` for this.)
- [x] Document this.
- [x] Add `NetChargeConstraint` (a type of `SequenceConstraint`) to control desired net charge on either a pose level or a region level.
- [x] Mover to add constraints to pose or region selected by a ResidueSelector.
- ~~Options in mover so that I don't have to pass in a file if I don't want to.~~ --> for a future pull request.
- [x] Test this.
- [x] Document this.
- [x] Unit tests.
- [x] For symmetric case, too.
- [x] Add more unit tests for out-of-bounds functions. I'm not 100% sure that my logic is correct.
- [x] Good thing I checked. Correct the tailfunction behaviour.
- [x] Integration tests.
- [x] For symmetric case, too.
- [x] Beauty.
- [x] Documentation.
Possibly in a future pull request:
- Modify the `AddHelixSequenceConstraintsMover` to add net charge constraints to helix termini instead of amino acid constraints.
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Merge pull request #2632 from RosettaCommons/everyday847/erraser2
ERRASER 2.0: stepwise refinement of just about anything
All integration test changes are either spurious (related to rna_partition) or expected (bugfixes to rna_design and test_energy_method_options).
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