Merge pull request #5759 from RosettaCommons/roccomoretti/interactive_improve_ligand_validation
[Foldit] Attempt to address a number of the soft crashes.
We're getting a large number of "soft" crashes reported for the ligand puzzles. (Molecules which are being rejected for internal issues.) This PR should address the bulk of them, or at least set us up for handling them later.
* A large number of the reports are for "texas" carbons, nitrogens, oxygens, etc. We have valence checking code, but it wasn't being run in at least one location before passing to RDKit - fix that.
* RDKit can handle some odd valences of iodine, which we're not considering (and which lead to issues later). Add iodine to the list of things we explicitly check for.
* We're getting some issues related to the reprotonation of aromatic nitrogen and phosphorus. I'm not sure where these are coming from, and I haven't been able to reproduce this locally. Add annotations of the starting molecule to the soft crash, which will allow me to better debug the issues later.
No Release Notes. (These changes are only internally relevant.)
Merge pull request #5761 from RosettaCommons/roccomoretti/interactive_address_waterbuilder_crashes
[Foldit] Attempt to address issues with LK_Ball crashes.
We're seeing a fair number of crashes with Stub building in LK_Ball evaluation in the ligand design puzzles. Best I can tell from the traceback, this is happening due to coincident atoms. Adjust the LKBall and Stub code to be more robust to these sorts of situations. (This may result in non-ideal energies for the system, but it won't cause the client to crash.)
RELEASE NOTES:
* Address crashes in scoring for ligand design puzzles.
Merge pull request #5762 from RosettaCommons/roccomoretti/interactive_ligand_crash_fixes
[Foldit] Bundle of ligand-related crash fixes.
A few fixes related to issues seen commonly in the small molecule design crash reports.
* Tracer output in conformer generator manager destructor is unneeded (there's some crash reports related to this, probably due to object destruction order at program shutdown.)
* With ligand generation, we can sometimes get large atom names - don't crash in ICoord parsing if we do generate those. (We may crash/mess up PDBs later, but crashing outright here is unnecessary.)
* There's some crashes related to ElementsPanel::disabled_elements() and FragmentsPanel::get_disabled_fragments() Not entirely sure what's causing this, but add in a soft-crash check for atom index issues (which is my current theory.)
RELEASE NOTES:
* Address issue causing crash-on-exit bugs.
* Made small molecule design more robust to certain causes of crashes.
Merge pull request #5760 from RosettaCommons/roccomoretti/interactive_fix_hbond_filter
[Foldit] Fix bug in the HBondFilter
It looks like a typo can cause a crash due to off-the-end access.
RELEASE NOTES:
* Fix bug in HBond Objective that was causing crashes in VHL puzzles.
Merge pull request #5757 from RosettaCommons/rocccomoretti/interactive_fix_tips
[Foldit] Fix the loading tips for the updated GUI.
(No release notes on this one -- it's not really something we need to draw attention to.)
Merge pull request #5710 from RosettaCommons/koepnick/hbnet_buns_display
[Foldit] Highlight unsatisfied atoms in HBNetFilterGeom
Release Notes:
- Show H-Bond Network Objective now highlights unsatisfied atoms in a network
Merge pull request #5745 from RosettaCommons/roccomoretti/interactive_float_menu_wrap_layout_change
[Foldit] Adjust Action Float Menu wrapping
Adjust how the Action Menu wrapping works. Several changes:
1 Icons now wrap left to right, bottom to top, rather than the old way of filling out the second and third rows back to front. (Where the second row started with the last icon of the all-in-one-row and filled in reverse order from the all-in-one-row, and the third row was the middle of the action bar. We got comments, so hopefully this is a bit more intuitive, even if they move around a bit more on a window resize.
2 Sub-float menus (like the secondary structure and the manual mutation panel) base their position dynamically on the action float menu, so will automatically move down/up if they're open when the window resizes.
3 We now query the actual size of the chat tab, rather than the almost-but-apparently-not-quite hard coded value we were using. This fixes some overlap issues.
4 As a consequence of 3), in offline mode (and Standalone) we can now make use of the full bottom bar, rather than having an empty spot where the char bar would be.
A future goal would be to shrink the chat windows for small screen sizes, to keep more real estate for the action bar, but that change isn't part of this PR.
(For completeness, I should point out I changed how the animation of the FloatMenu button positions work. This now supports Y movement as well as X movement. -- We don't actually use the animations anymore, though, as the menus should come in in their completed form, and icon movement on resize is distracting.)
Merge pull request #5746 from RosettaCommons/roccomoretti/interactive_center_score
[Foldit] Center Score in Score Panel.
The score is not centered within the score panel, which leads to slightly off scores, particularly when they get long (see the starting score for the current AlphaFold design puzzle). Part of the reason for this is the attempt at support for the fractional score progress gauge.
We don't ever use this anymore (we have "advanced" mode permanently turned on, except for some tutorial puzzles, which have their own score display.) Rip out the fractional score support, and just put the full score directly in the score panel, which allows us to center it better.
Merge pull request #5740 from RosettaCommons/roccomoretti/interactive_fix_gui_toggle
[Foldit] Fix logic bug for GUI toggle.
As part of PR #5733 I added a convenience function to re-enable the GUI elements if you clicked on the menu button.
This was only supposed to be active if you had the GUI hide enabled, but I messed up the logic a bit, and turned the main icon into a general GUI Hide toggle. This should fix it.
Merge pull request #5719 from RosettaCommons/jtscott/interactive_puzzle_expiration
[Foldit] Display Puzzle Expiration
The puzzle expiration for the new UI was removed, but due to player requests, I have added it in two places:
Display puzzle expiration on title tool tip
When the player hovers over the title, the full title, and the puzzle expiration will now be displayed
Display puzzle expiration on the Score Panel when one day is remaining
One of the design choices for the Score Panel was to keep it as clutter free as possible.
To help with this the puzzle expiration will only be displayed on the Score Panel when one day remains.