I have put 'os.environ["SDL_VIDEO_X11_WMCLASS"] = "name of .desktop
file"' to my Python code (before pygame.init() statement) and created
.desktop file in ~/.local/share/applications. It works fine for my game
now. Thanks for your advice - it helped my game to look better in Unity.

It would be better to implement this in Pygame of course. I can't
suggest better solution for this. Good luck with solving this problem.

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https://bugs.launchpad.net/bugs/777417

Title:
  Unity launcher doesn't work well with Python Pygame apps

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