Usage for structure prediction tasks

[padix-key]

Biotite is integrated in workflows of many structure prediction models. Hence we could add an example script that serves as loose collection of possible uses of Biotite in this context.

Input topics:

• One-hot sequence encoding (using ProteinSequence.code)
• Getting the assembly (structure.io.pdbx.get_assembly())
• Filtering high-quality structures from AFDB as training samples
• Secondary structure as feature (DsspApp, structure.annotate_sse())

Output topics:

• Structure superimposition, including methods that are robust with respect to missing residues
• Evaluation of pose against ground truth (rmsd(), lddt() (Add support for lDDT computation #699), tm_score() (Implement structural superimposition and TM-score #705))

This list is probably not exhaustive, so if anyone has additional ideas, please add them to the issue!

Notably this script should not run any model itself. It is only about preparing features for a hypothetical model and evaluating the output structure poses (e.g. taken from AlphaFold DB).