Introducing coarse-grained molecular dynamics simulations and updates to training

[datagato]

High-level updates from this PR:

• Introduce coarse grained MD simulations using the Martini 3 force field (with solvent subtraction) for faster Proteogram generation (5-10x faster than atomistic)
• Fixes to atomistic Proteogram creation for more consistent channel logic and stacking
• New training script that does train/test split on-the-fly with seed argument for reproducibility (this can be used for k-fold cross-validation later on by simply changing the seed); also introduces use of focal loss (a flag on the command line) for the training loss function
• PDB download script by date cutoff for future data pulls (when going beyond SCOPe)
• Annotation script updates (want a "GO slim" as a future label for Proteograms for classification according to the Gene Ontology annotations (biological process, molecular function and cellular component)
• Documentation updates