Created attachment 1130246 [details]
set the WM_CLASS property on the pymol main window

The main window (the OpenGL one) of pymol doesn't specify the WM_CLASS property for its window. This property is used to match windows to .desktop files in certain desktop environments, such as gnome. Without this matching one can observe several smaller issues in gnome-shell:
- Windows are not grouped by application in Alt+Tab
- Windows are missing the icon in Alt+Tab
- The application title in the top panel differs from the one in the .desktop file
- The application icon is missing from the top panel
- The entry in the dash (the panel on the left) in the activities overview is missing the proper icon
- The entry in the dash can't be marked as favorite
- The entry from the "All Applications" list can be marked as favorite, but when used to launch pymol, entries for each window show up in the dash

Some of those affect the gnome-shell "classic" mode as well. With this additional issues:
- The icon is missing from window list in the bottom

The external GUI component of pymol (the Tk window) is not missing the WM_CLASS property but defaults to a Tk specific WM_CLASS which doesn't match the pymol.desktop file either.

I have written two patches to add this property to both, the main window and the external GUI.

I'm submitting these patches as downstream patches rather than upstream for multiple reasons:
1.) They are only useful in combination with a .desktop file which only gets added downstream
2.) The patch for the main window is a bit hack-ish, but GLUT doesn't allow to do this cleanly. I've tried to keep this very contained and guarded against everything that might break though. A cleaner solution would require to port pymol away from GLUT to something like SDL which would be much more work and I'm not sure if that is even something that would be desirable.
3.) The patches as they are would probably compile on linux only. (That could be fixed with a couple of #ifdefs though)

And one final note about the patch for the external GUI: This doesn't fix every possible dialog of the external GUI but just the window that opens when you start pymol. Fixing everything would basically require patching every call to Tk() and Toplevel() scattered through the code which would make maintaining this patch much harder for very little gain.

I've tested these patches on F24 against the latest pymol package.