Merge pull request #3815 from RosettaCommons/vmullig/fix_xcode_yet_again
Fix the xcode build after the xrw_packer_palette merge.
Minor mistake in an iterator of the sort that xcode flags.
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Merge pull request #3711 from RosettaCommons/roccomoretti/normalize_enzdes_scitest_format
Update the output format of the enzyme_design scientific test for consistency with standard format.
Also add per-protein result graphs to the output html.
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Merge pull request #3813 from RosettaCommons/vmullig/clean_up_deprecated
Removing a few references to NC from comments and information strings.
The NC resfile command has been deprecated. This PR just makes sure that protocols aren't still making reference to it.
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Merge pull request #1047 from RosettaCommons/xrw_packer_palette
XRW -- PackerPalettes: Let noncanonicals share the TaskOperation conventions of canonicals
After three years, this PR is finally in master!
This pull request was originally part of the 2016 Chemical XRW, which aimed to expand Rosetta's chemical functionality greatly, with the goal of letting Rosetta read in and operate on the entire PDB (including all noncanonical entries.)
~~This pull request uses stuff developed for the MirrorSymmetry branch, and must be merged after pull request #1104.~~ (Merged a long time ago.)
- [x] <b>THIS PULL REQUEST NEEDS TO HAVE `vmullig/xrw_packer_palette` MERGED INTO IT AFTER COMPILATION ERRORS ARE FIXED IN THAT BRANCH.</b>
<b>Background and Rationale:</b>
TaskOperations modify the default packer behaviour, and are commutative (i.e. the order of application doesn't matter). This means, though, that in order to have the default behaviour be that one designs with all twenty canonical amino acids (and nothing else), TaskOperations can only turn canonical amino acids OFF and noncanonical amino acids ON. This makes it a real pain in the neck to do any mixed canonical/noncanonical design -- indeed, it has required the addition of some commutativity-breaking resfile commands. We'd like to remedy that.
<b>Description of Pull Request</b>:
This pull request changes the convention for noncanonicals, so that they share the convention for canonicals (i.e. TaskOperations can only turn ResidueTypes OFF, be they canonical or noncanonical). However, we want to preserve (a) commutativity, and (b) the default behaviour of Rosetta for users who are not using noncanonicals.
We are therefore introducing the concept of a <b>PackerPalette</b>. The PackerPalette tells the packer, "These are all of the possible ResidueTypes and VariantTypes that you're allowed to use for design. All of these are ON by default, unless you're passed TaskOperations that turn some of these OFF at some positions." If a user does not provide a PackerPalette, the default palette is the twenty canonical amino acids, preserving the classic behaviour of Rosetta (so the only people who have to learn new rules are noncanonical designers, and the new rules are nicer for them).
<b>[Packer?]Tasks:</b>
- [x] Create the PackerPalette class (in same core level as TaskOperation class?).
- [x] Write the default apply() function.
- [x] Let actual PackerPalettes derive from the base class -- so create a ~~BasicPackerPalette~~ CustomBaseTypePackerPalette class.
- [x] Implement the ~~BasicPackerPalette~~ CustomBaseTypePackerPalette parse_my_tag() function.
- [x] Integration test for the ~~BasicPackerPalette~~ CustomBaseTypePackerPalette class.
- [x] Documentation for the ~~BasicPackerPalette~~ CustomBaseTypePackerPalette class.
- [x] Create DefaultPackerPalette class, too (no options for that).
- ~~Integration test for the DefaultPackerPalette class.~~ --> Not necessary. Every integration test that calls the packer now invokes the DefaultPackerPalette.
- [x] Documentation for the DefaultPackerPalette class.
- [x] Implement factory architecture for PackerPalettes.
- [x] Finish PackerPalette::decide_what_to_do_with_base_type().
- [x] Check how I'm using ResidueTypeFinder::variants() and ResidueTypeFinder::disallow_variants(). I fear that the two calls to it (one for terminal variant types, one for non-terminal) step on one another, with the second one overwriting the first.
- Think about the AND/OR logic here a bit. If I'm designing with N-methyl-phosphotyrosine (i.e. with two variants), do I want to allow all four possible combinations of those variants (tyrosine, N-methyl-tyrosine, phosphotyrosine, and N-methyl-phosphotyrosine)? --> Put off for the next pull request, which will add a `CustomVariantTypePackerPalette`.
- [x] Create a RosettaScripts-accessible user interface for setting up PackerPalettes.
- [x] A PACKER_PALETTE section in a RosettaScript.
- [x] Utility functions for parsing defined PackerPalettes in mover or filter parse_my_tag functions.
- [x] Document this!
- [x] Add this to the template-printing function in the RosettaScripts app.
- [x] Create a commandline-accessible user interface for setting up a default CustomBaseTypePackerPalette.
- [x] Document this.
- [x] Modify the appropriate packer initialization functions to accept a PackerPalette.
- [x] Ensure that they default to a PackerPalette that preserves the old default Rosetta behaviour.
- [x] Continue at the TODO FIRST lines in ResidueLevelTask_.cc. Move all of the commented-out logic to the initialization function in the PackerPalette base class.
- [x] Modify movers and filters that invoke the packer so that they accept (and parse from XML) a PackerPalette.
- [x] Deprecate the RESET resfile command.
- [x] Refine the EMPTY resfile command to be a non-commutativity-breaking command.
- [x] Deprecate the NC resfile command.
- [x] Deprecate the PIKRNA resfile command.
- [x] Ensure that deprecated commands (RESET, EMPTY, NC, PIKRNA) produce an appropriate, <i>informative</i> error message explaining what the user needs to do to get his/her protocol working again.
- [x] Remove NCAA support from LayerDesign (too hard to maintain).
- [x] Remove this in the LayerDesign documentation, too.
- [x] Update other protocols that need NCAA packing to use the new convention.
- [x] Ensure that all canonical design continues to work as before, with no modification.
- [x] Unit tests for `PackerPalette` functions.
- [x] Integration tests for new noncanonical design workflow.
- ~~Add base ResidueType lookup to ResidueType class. (Make it fast at the expense of memory by storing the string for the base ResidueType).~~ -> Moved to pull request #1050.
- [x] Tweak the PIKAA syntax to allow restricting to canonicals plus noncanonicals. (Syntax is, for example, "PIKAA FAMILYVWX[601]X[ORN]", where the brackets contain full base names).
- [x] Integration test.
- [x] Documentation.
- [x] Beauty.
- [x] Documentation.
- [x] Delete temporary text file with pull request description.
- [x] Switch temporary output to debug output, or delete it outright.
- [x] XSD functions for PackerPalettes.
- [x] Add PackerPalette behaviors for carbohydrates (provided by @JWLabonte).
- [x] ~~Add general way to check that backbones are compatible. (@JWLabonte).~~ We will do this later, but see #3744.
- [x] Read default base `ResidueType`s from the database and remove hardcoding of names. (@JWLabonte).
- Write a `CustomVariantTypePackerPalette`. --> Put off to a future pull request.
- Add support for selecting residues with certain properties to the `CustomBaseTypePackerPalette`. --> Put off to a future pull request.
- Re-enable unit test for peptoid design from sarcosine (in `core/pack/PeptoidDesignTests.cxxtest.hh`) and ensure that this is possible. --> Put off to a future pull request.
- [x] Debug the small subset of performance tests that get slower. --> Done. They no longer get slower.
- [x] Debug the subset of integration tests that get slower.
- [x] Serialize.
The above task list will be expanded and fleshed out as we figure out exactly how to do what we want to do, here. Documentation is in pull request RosettaCommons/documentation#2.
Vikram K. Mulligan 6 years And I broke the xcode build. Of course. *Sigh*. Will fix.
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Merge pull request #3791 from RosettaCommons/JackMaguire/Allocations
Refactoring RamaPrePro Function Signature
The RamaPrePro energy has a lot of unneeded heap allocations because it is implemented as a single function that serves two purposes. This PR splits it into two functions and reduces the number of heap allocations, especially for L-amino acids.
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Merge pull request #3795 from RosettaCommons/jadolfbr/shear_in_sampler
This merge does a few things to the glycan modeling code:
1) Adds optional `ShearMover` to the sampler that was developed by Jason Labonte, with a final shear/min/pack
2) Changes name of `GlycanTreeSampler` to `GlycanSampler`
3) Fixes all virtual residues in the sampler
4) Removes large/medium bb movements (other than conformers) for refinement
4) Adds an option to turn off randomization in beginning of glycan sampler outside of refinement
5) Adds an inner cycle for BB movements within the glycan sampler with MonteCarlo to further drive the energy down. This adds about 15% of time into the protocol, but results in significantly lower energies than just generally increasing the number of cycles.
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Merge pull request #3647 from RosettaCommons/bioragul/TCRmodel
TCRmodel contains the protocol for modeling T cell receptors (TCR). The ‘tcrmodel’ application is used for modeling TCRs. The protocol uses the template structures present in "Rosetta/main/database/additional_protocol_data/tcr/". The template files are updated separately. The TCRseqInfo class handles the parsing/numbering of TCR sequences. The TCRmodel class handles the actual grafting/modeling of TCRs. TCRloopRefine class handles the post-modeling refinement of CDR loops. Two unit tests and an integration test were added. A demo of this protocol is included in the tutorials. The documentation link for this protocol is https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/TCRmodel.
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Merge pull request #3792 from RosettaCommons/aleaverfay/jd3_fix_archive_crosstalk_deadlock
Fix deadlock bug in archive-to-archive communication in JD3
Previously, if archive 1 finished outputting all of its results,
the master node could assign it to retrieve a result from
archive 2, which was not done outputting all of its results.
Archive 1 would then go and send a message to archive 2: an
MPI_Send request. Archive 1 would block until archive 2
responded. While it was waiting, output work could get
assigned to archive 1. When archive 2 would get back to
the master node, the master node would assign it to retrieve
the result from archive 1. Then archives 1 and 2 are both
sending MPI_Send requests.
This is deadlock.
MPI_Send requests do not exit until the corresponding MPI_Recv
has been called on the remote host.
Oops.
The solution is simple: do not allow archives to talk to each
other until the very end of the simulation when it is possible
to guarantee that no work will arrive for Archive 1 while it
waits to hear from Archive 2.
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Merge pull request #3798 from RosettaCommons/jadolfbr/sm_in_xmlobjects
This PR adds functions to access individual `SimpleMetrics` from the `XmlObject` class - which is useful for PyRosetta. The SM can call the apply function of the base SM, which will add the data to the pose. With #3797 it should now be easy to access the calculated SM data as a dict.
It should be noted that some functions, like `cached_calculate` and `calculate`, are not in the base class, and so, cannot be accessed in this way in PyRosetta without knowing which type of SM you are obtaining ahead of time. In C++, you can cast it.
Unit tests are updated to fully test these additions.
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