Modify Pydantic classes for ttsim3d

[mgiammar]

Overview

This PR adds new pydantic classes Simulator and SimulatorConfig to simplify and standardize input for the ttsim3d program.

The Simulator class does the following:

• Stores the pixel size and volume shape of the simulation.
• Stores and loads atoms from a provided PDB file path.
• Defines additional b-factor and b-factor scaling for a model.
• Holds intermediate calculation tensors, if requested.
• Defines run and export_to_mrc methods.

The SimulatorConfig class does the following:

• Defines parameters for the dose weighting and dqe filters.
• Holds the requested upsampling for the simulation.
• Additional configuration attributes for storing intermediate results.

To do before merging

• Implementing new classes
• Implement CLI program for simulating 3D structure from PDB
• Adding tests for validating new classes and associated methods
• Complete docstrings
• Add basic documentation (including usage examples)