How to handle post atomtyping adjustments?

[jennyfothergill]

A summary of the question or discussion topic.
Sorry if this has been discussed elsewhere and please feel free to link me to another issue, but I'd like to open discussion about how to handle modifications to a structure (gmso or parmed) after grammar-based atom typing.

This would be useful for UA forcefields (e.g., use smarts to type all the atoms, then remove the hydrogen atoms) or for the conjugated pairs in GAFF (same smarts environment but the pairs alternate to define double and single bonds rsdefever/GAFF-foyer#12).

I like to hear your thoughts about this! How would this work as a foyer plugin?