Fix lowercase atom name encoding

[Tanokri02]

Summary

Fix issue 278 B2. Single line change that ensures all inputs are uppercase for the model.

Changes

Changed a single line from: to atom.GetProp("annot_atom_name").ljust(4) to atom.GetProp("annot_atom_name").upper().ljust(4)

Related Issues

Testing

Ensured the new line gives the model the uppercase text, while the original molecular data is unchanged.

[Tanokri02]

The last commit address issue #278 B3 where two lettered elements needed to be titlecased in order to pass OF3 checks. The new version updates the copy of the CIF that is passed to Biotite, leaving the original CIF file unchanged. One example unit test has also been added.

[Tanokri02]

The last commit updates the assign_entity_ids function to now only accept numeric entity ids. It parses through all the non-numeric entity ids and returns an error highlighting all those that need to be updated. Additionally, 2 tests have been added.