Merge pull request #6587 from RosettaCommons/roccomoretti/tetrazole
[Foldit] Fix protonation state of tetrazoles.
Tetrazoles have a pKa of 4.9 and are a carboxylate mimic.
Right now we're not properly deprotonating them, change the charge state heuristics to better capture their physiologic state.
RELEASE NOTES: Better handling of tetrazole protonation states.
Merge pull request #6582 from RosettaCommons/roccomoretti/fix_lua_score_upweighting
[Foldit] Fix GetSegmentEnergyScore for reweighted residues.
Ligand design puzzles upweight residues. This is properly accounted for in the GetSegmentEnergySubscore lua functions, but not for the GetSegmentEnergyScore function. Correct this oversight. (Reported in https://fold.it/forum/bugs/ligand-scoring-mismatch)
RELEASE NOTES: Fix incorrect values sometimes reported by the GetSegmentEnergyScore Lua function
Merge pull request #6584 from RosettaCommons/interactive/petrides/keep_untrimmed_trunc_variants
[Foldit] Fix Excessive Removal of Trunc Variants on Untrim
Merge pull request #6573 from RosettaCommons/roccomoretti/ligand_filter
[Foldit] Update Objectives & Compound Library Panel
One feature that was requested was the ability to filter Compound Library compounds by their matching of objectives. This PR adds a checkbox to the Load Library Compound panel which allows you to do this.
To enable this functionality, I needed to rework all the ligand-based filters. Specifically, I made a new base class from which all of the Filters which act on ligand identities (versus location in the pose) now derive. This allows me to iterate through the current filters and specifically test the RDKit molecules in the compound list. I took the opportunity to do an extensive refactor of how those Objectives were constructed & worked to enable this.
This also reworked/centralized the residue identification parsing code (allowing easy updates later) and also added a "multi" setting to the filter, to possibly change how the objective operates over multiple ligands. Given that all puzzles to date have had a single ligand, I changed the defaults to what I think will be the best approach going forward with the anticipated future ability to split ligands: the filters will sum the settings across all ligands before providing thresholds. (Note that this is possibly at odds with the filtering, which works at a single ligand level. There may be adjustments needed later. I tried to make the interface amenable to that change)
I also added the parent query molecule to the list of molecules presented. This requires support from crowdgames/foldit-server-rails#676 to work, though. (The code is robust to it not being present.)
RELEASE NOTES: Added checkbox to filter Compound Library compounds by (some) Objectives
RELEASE NOTES: Added 'Query' compound to the Compound Library compound list.
Merge pull request #6564 from RosettaCommons/GreenTomato5/interactive_clear_params_cache
[Foldit] Clears Params File Cache for Puzzles Loaded With Secret Buttons
This PR clears the cached params file for puzzles loaded with secret buttons. Currently, puzzles loaded with secret buttons have the same ID of 1, so when a puzzle is first loaded with secret buttons ChemicalManager will use its params file and associate it with a specific tag based on puzzle ID. Because successive puzzles loaded with secret buttons also have the same ID of 1, new params files don't replace the old ones.
Merge pull request #6560 from RosettaCommons/GreenTomato5/interactive_camera_config_on_puzzle_init
[Foldit] Configuration for Camera Starting Position in non-campaign/intro Puzzles
This pr adds support for configuring the starting position of the camera in non intro/campaign puzzles. To configure the starting position the following should be added anywhere in .puzzle_setup fiies:
```
"cam_center" : "x y z"
"cam_eye" : "x y z"
"cam_up" : "x y z"
```
Where x, y, and z for each component are replaced by a position an individual making a puzzle can obtain by using the CTRL+SHIFT+ALT+V keybind and checking their log file. Not adding in these fields to a puzzle_setup file will produce the previous behavior where the camera looks at/goes to a constant position.
Merge pull request #6567 from RosettaCommons/roccomoretti/load_save_tooltips
[Foldit] Make working with saved solutions descriptions easier.
Right now the interface for dealing with saved solutions with descriptions isn't great. There isn't a convenient way of viewing larger descriptions (the display in the LoadSaveDialog cuts it off at 5 lines), and it's not all that convenient to enter the description in the first place.
This PR adds a tooltip in the LoadSaveDialog which displays the full description (inartfully wrapped, if necessary).
It also adjusts the keyboard behavior of the Save Solution panel. Right now, if you hit enter on either the Name or Description, it immediately saves the solution. This disincentivizes adding a description or a longer (multi-line) description. (Which may be why practically no save-with-scientists have a description entry.) Change that such that an enter on the Name moves to the Description field, and an enter on the Description simply adds a line. -- This may or may not be popular with some, as it does slow down the process of saving a bit.
RELEASE NOTES: Show full solution descriptions in Open/Share Solutions panel.
RELEASE NOTES: Adjust how enter and tab keys behave on Save Solutions panel.
Merge pull request #6569 from RosettaCommons/roccomoretti/fix_compound_library_error
[Foldit] Fix issue with Compound Library Objective
It looks like the current stereochemical enumeration we're using with the compound library doesn't work for all molecules. This means that the annotated stored library compound smiles doesn't match what the (post-3D embedding) compound smiles is like.
In particular, a shared-with-scientist molecule from Puzzle 2602 was showing the issue. This particular issue has been fixed in upstream RDKit python code, we can just crib the changes.
Additionally, I've cleaned up a bunch of the code related to CompoundDataStore, which hopefully should make sure that the related functionality (particularly the Compound Library Objective) are more consistent.
RELEASE NOTES: Fix issue where certain compound library compounds weren't getting the bonus.
Merge pull request #6570 from RosettaCommons/roccomoretti/fix_ThreadedRDKitRotamerLibrarySpecification_crash
[Foldit] Fix crash reported for some entries.
Crashes were reported which looked to trace to ThreadedRDKitRotamerLibrarySpecification and its embedding. Make that process more robust. (If we can't get a conformation for the ligands, just skip it.)
RELEASE NOTES: Fix crashes in ligand puzzles.
Merge pull request #6572 from RosettaCommons/roccomoretti/resize_ligand_puzzles
[Foldit] Some initial baseline reworking to help support multiple ligands/resizing.
The list of ligand designable positions in the SessionConfig is a mal-feature. If the pose changes size (e.g. if there's insertions or deletions, or if we fragment the designable ligands), then this numbering can become wrong. The proper place for this information is the ReferenceInfo, which gets properly resized when the structure is resized. We already have this info present, so make sure we use it.
This also cleans up a bunch of direct usage of the ReferenceInfo variables, in favor of the get_ligand_designable_positions() utility function.
(No release notes: internal cleanup only.)