Explicit molecule component "to_json" does not have the same behaviour as GufeTokenizable "to_json"

[IAlibay]

I'm not sure if we picked up on this in #368 (sorry if it's a known issue!).

I just realised that calling to_json on an explicit molecule component (SmallMoleculeComponent) actually is a different behaviour than the GufeTokenizable to_json.

The former takes no arguments and only returns a json string whilst the latter can take a filepath and write the string directly there.

I know we rely a lot on the "to/from_json" utility for Components, but my understanding is that we could just directly remove the class method in explicit molecule and it should just give us the same behaviour?

A more immediate / short term concern

I noticed that the explicit molecule component to_json and from_json have no docstring 🙀 ! So they just inherit it from GufeTokenizable which has teh different behaviour.

[dotsdl]

Ah, this was certainly an oversight on our part in #368! As you suggest, I believe we could drop these methods from ExplicitMoleculeComponent and add in the ability to read previously-generated to_dict JSON dumps to the GufeTokenizable.from_json implementation as a fallback on failure.

Although, it looks like the ExplicitMoleculeComponent methods don't use our JSON_HANDLER encoder/decoder, which may mean they never worked right in the first place. 😅

[IAlibay]

they never worked right in the first place

I am able to write an SMC with to_json and manually load it back in (not sure if I just got lucky though!)