Merge pull request #4524 from RosettaCommons/JackMaguire/auto_ig
This PR adds simple logic to prevent new users from spending a preventably-large amount of time precomputing 2-body energies.
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Merge pull request #2466 from RosettaCommons/roccomoretti/parse_tag_interface_change
Change the interface to parse_my_tags
This is the final merge in a series of merges to reduce the interface of parse_my_tag(). This PR removes the Pose parameter from the parse_my_tag() function on Movers and Filters, leaving it as `void parse_my_tag( utility::tag::TagCOP tag, basic::datacache::DataMap &)` (like most other RosettaScripts objects.).
The Movers map and Filters map parameters have been merged into the DataMap object, and the Pose parameter has been removed completely. -- In general, there's no reason to rely on the state of the Pose at parse time. There's no guarantee that the state of the Pose at parse time will match that at apply time. Instead, you should cache the information (residue selections, chain designations, etc.) and then evaluate it on the pose passed to apply. There are various objects which allow you to do this deferral more generally.
Correspondingly, APPLY_TO_POSE has been removed. An empty APPLY_TO_POSE section is fine, but any content in that section will result in an error. See https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Updating-RosettaScripts for more information about how to convert an XML using APPLY_TO_POSE to something that will work with the new scheme.
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Merge pull request #4642 from RosettaCommons/vmullig/helical_bundle_predict_sequences
Add support to helical_bundle_predict for arbitrary heteropolymer building-blocks.
This is mainly an input issue. This PR lets you put in a sequence file containing a whitespace-separated list of residue type names in lieu of a FASTA file.
This pull request also updates the EnvPairPotential so that it properly handles D-amino acids.
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Merge pull request #4641 from RosettaCommons/vmullig/add_centroid_ncaas
Add centroid params files for AIB, ORN, DAB, and DAP.
This adds centroid-mode params files for commonly-used noncanonicals, plus a unit test confirming that they work as expected.
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Merge pull request #4562 from RosettaCommons/mlnance/sugar/add_more_sugar_codes
Adding more "easy" sugar PDB codes from the ligand list of the ProCarb database
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Merge pull request #4619 from RosettaCommons/dimaio/bbi_init_from_pdb
Two changes for design of crystal lattices:
* add the ability to supply a reference pose to BuildingBlockInterface
* add the ability to add named symmetric DOFs to TaskAwareSymmMinMover
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Merge pull request #4631 from RosettaCommons/benchmark
Updating benchmark scripts so they can be run on Windows. Updating PyMOL mover, reducing max-packet-size lower bounds.
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python_cc_reader module to python3 (#4590)
Submodule update for the tools repository which includes a large structural change to the `python_cc_reader` module and its conversion to python3.
The directory structure for the `python_cc_reader` module is now as follows:
```
tools/
python_cc_reader/
python_cc_reader/
beauty/
code_improvement/
cpp_parser/
external/
inclusion_removal/
library_splitting/
tests/
utility/
```
The rationale for this dirname-within-dirname structure was given on this page:
https://docs.python-guide.org/writing/structure/
At the top level `python_cc_reader`directory live the user-level scripts such as `library_levels.py` and `beautify_changed_files_in_branch.py.` Within the lower level `python_cc_reader/python_cc_reader` directories live the modules that actually do all the heavy lifting.
These scripts are imported by a number of other scripts in the `tools` repository, and I have updated all of these scripts.
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Merge pull request #4316 from RosettaCommons/roccomoretti/mover_filter_map_remove
Remove Movers_map and Filters_map from the Mover/Filter parse_my_tag interface.
There's no actual reason to have a Movers_map and Filters_map separate from the DataMap we pass to parse_my_tag(), it's simply a historical artifact. Removing them (and placing their data into the DataMap) allows us to reduce the importance of Filters in RosettaScripts, and also will allow us to use Movers/Filters as parameters in setting up more complex ResidueSelectors, SimpleMetrics, etc.
This PR removes the Mover & Filters map from the main interface for parse_my_tag(), going from 5 parameters to 3.
This is merge one of a two part merge, where the second merge removes the pose parameter. That should hopefully be merged in shortly.
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Merge pull request #4635 from RosettaCommons/roccomoretti/master_fixes
Fix some master tests.
The alpine build test seems to have issues with public virtual inheritance of VirtualBase - we can just remove that.
Also fix some unused usings issues with clang-tidy.
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Merge pull request #4611 from RosettaCommons/roccomoretti/database_md5
Add a database_md5 integration test.
Going off a suggestion by Sergey, have an integration test which dumps the MD5 hashes of all the database files. This should hopefully help us debug situations in the future where test server databases get 'dirty' with state.
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