Update argument handling in PDBList.py, possibly by creating a new module.

[JoaoRodrigues]

The command-line interface for the PDBList.py module is quite clunky, using a series of complicated ifs and sys.argv calls to parse input from the user. It would be super nicer to simply use argparse, although this will break compatibility with previous versions.

The solution here might pass through copying the code to a new module and along with other issues (#3988, #3987) upgrade PDBList.py and break backwards compability. We could then slap a deprecation warning on PDBList to warn users to move to the new code.