Optimize molecule class

[kainszs]

As described in the issues #454 and #459, the molecule class can be optimized and unified with the AtomGroupInBlender class.

Goals:

• [x] clean up s. #454
• [x] write molecule class, with atomarraystruc as data object
• [x] write molecule class, with mda.atomgroup as data object
• [x] write MoleculeInBlender class

Further steps:

• test implementation
• optimize code, reduce redundancies
• integrate in code base

Regarding the Molecule class. Currently when structures are imported, a 3D model is created inside of Blender. The idea is that the Molecule will contain information about the file that this model came from, and provide an interface that the user can change the associated style and edit the underlying information of the structure through this class. The currently existing python API isn't setup well for interacting with molecular structures, or changing the Geometry Nodes tress that are associated with the models. The class will hopefully provide a neater interface for loading, editing and styling the model, in a way that is nice to script with inside of a Jupyter Notebook or similar script.

Originally posted by @BradyAJohnston in https://github.com/BradyAJohnston/MolecularNodes/issues/459#issuecomment-2028547718