Allow writing AlphaFold 3 input specification json file

[Tom Goddard]

AlphaFold 3 can take a JSON input file specifing all the molecules and sequences and modifications and seed values. It might be useful if ChimeraX could output this file corresponding to an already open PDB model. This would allow using AlphaFold 3 to complete unresolved parts of the experimental model and to see if AlphaFold 3 predicts alternate binding of ligands for example.

If the open PDB model contains entities that cannot be predicted (e.g. most ligands using limited Google AlphaFold server, waters, ...) then it should warn that those have not been included.