diff --git a/etfl/data/ecoli.py b/etfl/data/ecoli.py index ad0e454..33b8851 100644 --- a/etfl/data/ecoli.py +++ b/etfl/data/ecoli.py @@ -317,7 +317,7 @@ def remove_from_biomass_equation(model, nt_dict, aa_dict, essentials_dict): expression_mets = list(nt_dict.values()) + list(aa_dict.values()) - # For ATP correction (see lower) + # For ATP correction (see below) n_aa = 0 for m,stoich in model.growth_reaction.metabolites.items(): @@ -361,15 +361,7 @@ def remove_from_biomass_equation(model, nt_dict, aa_dict, essentials_dict): # ppi: 1*n_aa, # h: 4*n_aa, # }) - # model.growth_reaction.add_metabolites({atp: -1*atp_recovery - 2*n_aa , - # h2o: -2*n_aa, # h2o consumed less (n_aa is negative), - # adp: 2 * n_aa, - # amp: 0 * n_aa, - # pi: 2*n_aa, - # ppi: 0*n_aa, - # h: 2*n_aa, - # }) - model.growth_reaction.add_metabolites({atp: -1*atp_recovery - 3*n_aa , + model.growth_reaction.add_metabolites({atp: -1*atp_recovery - 2*n_aa , h2o: -2*n_aa, # h2o consumed less (n_aa is negative), adp: 2 * n_aa, amp: 0 * n_aa, @@ -377,6 +369,14 @@ def remove_from_biomass_equation(model, nt_dict, aa_dict, essentials_dict): ppi: 0*n_aa, h: 2*n_aa, }) + # model.growth_reaction.add_metabolites({atp: -1*atp_recovery - 3*n_aa , + # h2o: -2*n_aa, # h2o consumed less (n_aa is negative), + # adp: 2 * n_aa, + # amp: 0 * n_aa, + # pi: 2*n_aa, + # ppi: 0*n_aa, + # h: 2*n_aa, + # })