Add missing variable

[amorehead]

• Adds a missing variable
• Also, should the following values be True or False by default?

add_atom_ids: bool = False
add_atompair_ids: bool = False
directed_bonds: bool = False

[lucidrains]

@amorehead probably good to have the network know about the first two, and directed bonds is probably less essential

[lucidrains]

these two hyperparameters will have to be correspondingly set (if turned on)