Release replica docking (#3684)
This PR moves the code for the replica docking protocol published in 2013 from devel/ into protocols/ so that it can be released.
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Merge pull request #3726 from RosettaCommons/georgkuenze/fix_nmr_code_quality_issues
Fixing some uninitialized and unread variable errors in RosettaNMR code which were not detected in my previous commit to master.
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Merge pull request #3448 from RosettaCommons/vmullig/qpacker_io
Add I/O modules to allow experimentation with external annealers for packing
Half of the packer is easy to parallelize; the other half is hard. Interaction graph setup can be split over many threads or processes, but the simulated annealing trajectory is inherently difficult to parallelize, since each step depends on completion of the previous step. Of course, one could use completely new annealing or optimization strategies -- but that being the case, we shouldn't limit ourselves, especially when experimenting with different optimization strategies. It would be convenient to have an easy way to export the precomputed interaction graph from Rosetta so that an external optimization strategy can be attempted, and then to re-import the external optimizer's result into Rosetta to generate a final structure. To that end, this pull request adds:
- A new `StringMetric` that allows output of a precomputed interaction graphs from Rosetta, in a convenient ASCII format that it should be easy to get an external optimizer to read.
- A new `ExternalPackerResultLoader` mover that allows the output of an external optimizer to be read back into Rosetta, again using a simple ASCII format that it should be easy to get an external optimizer to write.
TODO:
- [x] Switch the COPs to COP instances to make Andy happy.
- [x] Option to also dump short version of file, without information needed to reconstruct long version.
- [x] Integration test.
- [x] Documentation.
@weitzner, you'll be interested in this.
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Merge pull request #3710 from RosettaCommons/vmullig/add_fullname_support
Add more output options to the SequenceMetric
Currently, the SequenceMetric supports writing sequences as one-letter codes or three-letter codes. This is inconvenient for certain noncanonicals, which are best represented either by their basenames (e.g. DORN for D-ornithine), or by their full names (e.g. DORN:NtermProteinFull). This pull request adds support for writing:
one-letter codes
three-letter codes
base names
full names
Tasks:
Deprecate the three_letter Boolean option with an informative error message.
Implement the output_mode enum option in its place.
Have it do something.
Unit tests.
Beauty.
Documentation.
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Merge pull request #3701 from RosettaCommons/jadolfbr/fix_rabd_nanobody
Fix RAbD nanobody compatibility
========================
Addresses https://www.rosettacommons.org/node/10411
Adds a check for comments in cdr instructions
Adds ability to specify `NONE` for neighbor minimization for speed.
Adds an integration test for nano body, expands AntibodyInfo unit tests.
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Merge pull request #3538 from RosettaCommons/roccomoretti/move_parse_tag_checks_to_apply
Move pose-dependent initializations from parse_my_tag() to apply()
Another sub-PR of the parse_my_tag interface change PR #2466
There's a number of Movers/Filters which do work (initialization/sanity checks) in their parse_my_tag which can be deferred to apply().
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Merge pull request #3704 from RosettaCommons/roccomoretti/fix_cmake_unit
Fix Unit tests on CMake.
The unit tests for the CMake build run in a different directory than the Scons ones. This means that attempts to access the Rosetta/main/source/test directory from the unit test running directory
will fail if attempted from the CMake unit tests.
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