Inconsistencies between reactions in universe file and in model generated from it

[Brunokemon]

Hi
I'm using a curated universe file and I noticed some changes in the model generated from it, specifically changes in chemical formulas.
Is this related to the optimization method cited in this previous issue or is this another thing?

          - There is a new optimization method that tries to automatically balance reactions when the formulae are incorrect or inconsistent. It assumes that some formulae are incorrect and minimizes the number of formulae that it needs to change. 
           
          This is mostly an heuristic approach, so it is possible that it will also introduce mistakes in some formulae.

Originally posted by @cdanielmachado in #136 (comment)

[cdanielmachado]

Hi,

This curation happens during the creation of the universal model, not during the carving process, so there shouldn't be differences at the level of metadata between the universal model and the generated models... It is a bit strange that this is happening.

[arpacheco]

Hi all, I've also run into an issue recently that might be related to this. After updating to the latest version (having previously used 1.5.0), I noticed substantial changes in the model generated from the same genome file. As an example, in the new model there are a lot of transport reactions that are only connected to single periplasmic metabolites causing them to be interpreted by COBRA as exchanges. I'm not sure if this could be related to changes in how the formulas are balanced or otherwise. Happy to provide model outputs for more context - thank you!