"[protein]-" tags go missing from metabolite names

[johan-gson]

I think I have found a bug in the human ec model (which does not exist in Human1).
In Human-GEM, reaction HMR_7197 looks like this:
[protein][c] + serine[c] => [protein]-L-serine[c] + H2O[c]
But, in the ec model, it looks like this when I do constructEquations:
[protein][c] + serine[c] => L-serine[c] + H2O[c]
So, the [protein]- part of the L-serine seems to have gone missing. We suspect that it has something to do with the square brackets, or potentially the word "protein".

[johan-gson]

I have fixed this issue in GeckoLight, you should be able to use the same approach. The problem is that the pipeline renames the metabolites, which in my mind it shouldn't, so I simply restore the metabolite names after running the pipeline. This also messes up the metabolite names in for example the biomass_human reaction.