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Maybe I’m misunderstanding your request, but why not just use pymol? You can make sessions entirely programmatically with python which you can then open in the GUI.
Two similar alternatives you could look at are PyVista which is based on the same framework as Mayavi and VisPy. Mayavi is strongly dependent on the whole Enthought suite which can be a disadvantage if you don’t really use its abilities.
Two similar alternatives you could look at are PyVista which is based on the same framework as Mayavi and VisPy. Mayavi is strongly dependent on the whole Enthought suite which can be a disadvantage if you don’t really use its abilities.
Also I'd take a look through https://github.com/lmmentel/awesome-python-chemistry because I have a hard time believing this isn't a "solved problem" where you just need to find the right existing library.