af_plotter processes the AlphaFold3 JSON files it finds using the --glob search
in the target directories and/or the target JSON files listed. Optionally, the
-R (--recursive) flag allows af_plotter to descend through the given directories
applying the --glob search pattern.
By default both PAE and pLDDT plots are produced. These can be individually
disabled by passing --nopae and --noplddt, respectively.