user-set partial charge warning

[JenkeScheen]

With the current setup in openfe every time a molecule gets loaded with user-set partial charges the user receives a warning Partial charges have been provided, these will preferentially be used instead of generating new partial charges. This becomes a bit much when we're loading hundreds of molecules in production, especially when we load/de-load the set of molecules multiple times during prep and setup steps ahead of simulations.

Is there a way to log this more elegantly, or potentially expose a flag for users to disable this warning?

We've now gotten around this by just ignoring this warning but an openfe-side solution would be preferable: https://github.com/asapdiscovery/asapdiscovery/blob/main/asapdiscovery-alchemy/asapdiscovery/alchemy/cli/cli.py

[IAlibay]

Thanks @JenkeScheen , we'll give it a think - possibly shifting to logging rather than warnings. I'm going to triage this as "low prioirity", but please do let me know if you feel it isn't.

[IAlibay]

Just coming back to this, we are definitely not removing the warning, the best we can do is change to a logging.warning instead of a userwarning.

[JenkeScheen]

sure - as long as it's mutable then that works.

[IAlibay]

@atravitz as part of the CLI 1.x "partial charge assignment early" push, we should try to make the switch to logger.INFO or similar here.

[atravitz]

closed by #468