Obtaining all reaction fluxes from grow()

[AlexHoratio]

Hi!

I'm new to this whole field, so please bear with me if I'm getting this wrong, but: Is there any reason why all taxon reaction fluxes are not returned from the grow() method, and it only returns the exchanges?

I've had the thought to modify the function to simply not filter the fluxes list for exchanges, so that it will dump the whole table of fluxes into my GrowthResults object. Is this a terrible thing to do, or is it ok?

I understand there are helper functions that I might not want to use on this 'modified' GrowthResults object, like the micom.measures.production_rates() thing.. but if I just want to look at individual per-taxon reaction fluxes, is this an ok modification to make?

Thanks,
-Alex

[cdiener]

Hi Alex,

Yeah good point, this is planned but has not been added. The reason initially was that (1) it's a lot of fluxes and take quite long to extract and store, and (2) internal fluxes are not unique, so there may be many possible flux distributions yielding a specific set of growth rates and exchanges.

But the idea is to add those as an attribute to GrowthResults (internal_fluxes or similar). The single model API for this is already proposed but the workflow API needs to be overhauled because I don't want to add yet another arg to grow().

[AlexHoratio]

Awesome, thanks for the quick reply!