Write a notebook on the use of the atomic_models.py module

[ninamiolane]

What?

• Write a tutorial notebook on the use of the ioSPI/atomic_models.py module.
• Add details in the docstrings of the atomic_models.py module, and complete the "TODO".
• Add corresponding unit-tests.
• Use pre-commit (see README) to make sure that your code follows style guidelines.

Optionally:

• If needed, modify the atomic_models.py module to improve user experience.
• Add visualizations.

Why?

Atomic models are the heart of cryo-EM research.

Being able to manipulate representations of atomic models is crucial for the field and its community.

Where?

• The notebook should go in the notebooks folder with the title atomic_models.ipynb.
• The test of the notebook should go in a new file test_notebooks.py in the tests folder, inspired by this file.

How?

Get data for the following atomic models by downloading their .cif at the url below:

• bacterial Ribosome
• pre-catalytic spliceosome: 5nrl
• human GABA(B) receptor-Gi protein
  Get inspiration on how to write your notebook, look at:
• other notebooks, e.g. here.
• the test file for the atomic_models.py module.