Exchanges not added for all extracellular metabolites #2
Description
Current behavior
If a reconstructed model contains extracellular metabolites that aren't in the medium used for gap-filling, exchange reactions are not added for these metabolItes (unless the exchange reactions are part of the gap-filling solution).
I suspect this behavior is not noticed currently because transport reactions (and subsequently extracellular metabolites) only get added during gap-filling (I think the gene → reaction map that is used to create the initial model draft does not contain any transport reactions).
Expected behavior
Exchange reactions should be added for all extracellular metabolites in the reconstructed model. If these metabolites are not part of the gap-filling medium, their bounds should be (0.0, 1000.0) (i.e., only allow export of the metabolite and not uptake).
Issue originally created here.