A bit of cleanup and using self.*_named_attribute

[BradyAJohnston]

I've gone through and done a bit of cleanup, but it was mostly how it it should be I think!

I'll leave individual comments on sections, but mostly what I have changed is moving to using self.store_named_attribute() as MolecularEntity already subclasses BlenderObject and thus gets those methods. I lead you a bit astray with my example in the original thread, but thanks for doing it all!

[BradyAJohnston]

If you accept this PR it should then be reflected in the other PR. I wanted to do it this way so I could comment everything change-wise :)

[MartinBaGar]

Thanks a lot for your reviews, I'm glad it is going in the right direction :)
No worries with the example, thanks to it I could dig into databpy and have a more in depth understanding of Molecular Nodes ecosystem, I hope I am not going to slow on this project.
If you have other suggestions of functionalities, let me know ! I will propose the next steps on the other PR.