Possible fix to stochastic failure in HRFDyamicsEnergyTests (#4910)
The one thing that I can see is that there's no check that the data read from each line of the initialization file can actually be interpreted as an int and a float (which the code expects). If this fails, the int and the float _should_ be set to 0 and 0.0, respectively, under the cxx11 standard, but earlier standards left the container variables unchanged. I'm wondering if that's what we're seeing here, resulting in stochastic behaviour since the int and the float are uninitialized.
I'm adding a check that the line was properly parsed, and taking out the blank line in the config file. I don't know that this will fix the stochastic failure, but it can't hurt.
Tasks:
- [x] Add the check.
- [x] Confirm that the unit test now fails consistently due to the blank line.
- [x] Remove the blank line in the config file.
- [x] Ensure that test passes.
* Remove blank line in test.
* Update tools repo to point at latest master.
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Merge pull request #4896 from RosettaCommons/dpaoliello/UseNonFwdHeader
Ensure the non-forward declaration headers are included for types used in standard library containers
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Merge pull request #4904 from RosettaCommons/JackMaguire/ParsedProtocolUtil_cherry
Tracking the number of filters passed in ParsedProtocol
Thanks for the review, Jared!
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Merge pull request #4667 from RosettaCommons/jadolfbr/parser_logic
Enable Residue Selector logic across RosettaScripts
This PR does one main thing, it allows most classes to use selector logic through their `selector=` option in a tag. It does this through using the logic in `parse_residue_selector` and `get_residue_selector` after checking if the selector exists in the DataMap first. (I was going to roll my own parsing logic/etc. before @ajasja pointed me to use the already-present logic - so thank you @ajasja for that - saved a lot of time!)
A lot of selectors have been updated to use the util - I was frankly shocked at how much pure copy-paste happened in getting selectors.
**This functionality has been extensively tested, has a unit test, and we have a few bonuses.**
1) You no longer need to use `!` and can use the actual word not. Why not eh? (courtesy goes to @ajasja for this)
2) You no longer have to have everything caps.
3) A disulfide container crash has been properly wrapped in an exit instead of a vector segfault
4) The `SelectedResiduesPyMOLMetric` now uses the custom type IN the selection. I Should have done that a long time ago.
5) Logic works when doing `selectors=` for each selector in between commas
I hope this will be as beneficial to everyone as it has to me the past week. My 150 lines of selectors have been cut to only a select important few.
**The caveat to this is as follows**: I tried to find all the classes where selectors were being pulled straight from the `DataMap` (which, honestly, I didn't know people actually did when I started this) and fixed as many as I could through a few searches. I may have missed some. Due to the inconsistent use of the `residue_selector` name and inconsistencies when using multiple selectors, I cannot envision a way to test this exhaustively. If you have ideas, please let me know!
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Merge pull request #4895 from RosettaCommons/dpaoliello/MatchDefinition
Change `look_up` to match the type of the `tensor_index` variables it is initialized with
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Merge pull request #4881 from CyrusBiotechnology/smlewis/fix_disulfidizer_detection_copybranch
DisulfidizeMover fails when you have disulfide sets like [(3, 21), (10, 24), (20, 29)] in the input because it erroneously pairs 20-21.
See this comment from the middle of the code:
//this check alone determines if two residues are bonded to each other, (and their presence in the set means they are disulfide bonded in general), but as written this does not work properly with vicinal reisudes polymer bonded to each other, but not disulfide bonded to each other.
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