Merge pull request #3799 from RosettaCommons/jadolfbr/iam_bugfix
General bug fix from an email - IAM is now chain order independent as of sometime not too long ago. This is now reflected in both `RosettaAntibodyDesign` and Antibody Modeling to protect against failures arising from chain order.
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Merge pull request #3789 from RosettaCommons/JackMaguire/HBNetFlatSet
Replacing HBNet's sorted vectors with boost flat_sets
One of the messiest things I added to HBNet was sorted vectors. They helped with performance but littered the code with `std::lower_bound` and `std::binary_search`. I'm going through and replacing them with boost's flat containers (ordered sets and maps that are built on top of vectors) to keep the performance benefits without all the mess.
Thanks to Brian for the review!
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Merge pull request #3793 from RosettaCommons/vmullig/enforce_generating_function_privacy
Trying to prevent some initialization functions for static const global data from being called from outside the intended context.
Currently, a developer could call these functions from anywhere. This causes two problems. First, it duplicates data that have already been generated and are available globally. Second, it creates possible memory leaks, since the data are allocated on the heap by raw pointer, and a developer will probably not think to call `delete[]` on them after finishing with his or her local copy.
By making the initialization functions into ordinary functions with no prototype outside of the context in which they are used, these functions can't be used for anything but initializing the static const data that they're supposed to initialize.
<b>Edit:</b> This pull request also fixes a memory leak in the ResidueCountFilter, caused by improperly calling one of the initialization functions.
Before merging, I need to do the following:
- [x] Check that the functions to get properties from strings and strings from properties are unit-tested.
- [x] Add some comments to those functions explaining how to use them.
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Merge pull request #3796 from RosettaCommons/roccomoretti/reb_lr_fix
Fix behavior of residue_energy_breakdown w/r/t long range energies.
The residue_energy_breakdown application was accumulating the unweighted energies for long range energy terms, despite accumulating the weighted energies for the one-body and the short-range terms.
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Merge pull request #3784 from RosettaCommons/jadolfbr/residue_property_selector
Add a `ResiduePropertySelector` that selects based off of the ResidueProperty of a residue_type. Can set multiple properties and select and/or logic to simplify complex queries. Unit test suite for both code-level and rosetta_scripts based interfaces to the class.
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Merge pull request #3764 from RosettaCommons/bcov/ReadResfileFromDbSelector
Adding a ResidueSelector to ReadResfileFromDB and a few bug fixes
Rocco Moretti 6 years Whoops, my mistake -- it doesn't seem that the mac.clang unit test failures in pre-merge were timeout related. That possibly means this commit doesn't have significant timing considerations, and the timeout issues are due to on-server variation.
Brian Coventry 6 years Indeed. This pull request just adds an option to a parse_my_tag.
Sergey Lyskov 6 years I have restated this test, - lets see if that will make any difference...
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Merge pull request #3788 from RosettaCommons/JackMaguire/Allocations
There was a needless Residue copy in the inner loop of the FixbbSimAnnealer. It accounted for 54% of all heap allocations and 2% of total runtime (25% of total runtime according to the benchmark server).
Thanks to Vikram for the review!
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Merge pull request #3782 from RosettaCommons/sergey/f
Updating `beautify` test logic so it does not mess-up Git submodules. Thanks to @roccomoretti for valuable feedback!
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Merge pull request #3783 from RosettaCommons/vmullig/fix_octahedral_metal_test
Fix the simple_cycpep_predict_octahedral_metal integration test.
This is unfortunately testing something that has an inherently low success rate. I'm tweaking the test to "cheat" as much as possible, to bias the results to a success.
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