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‎modelseedpy/core/msminimalmedia.py‎

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@@ -60,6 +60,7 @@ def bioFlux_check(model, sol=None, sol_dict=None, min_growth=0.1):
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return sol_dict
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def minimizeFlux_withGrowth(model_util, min_growth, obj):
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print("here", model_util.model.slim_optimize())
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model_util.add_minimal_objective_cons(min_growth, name="min_growth")
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model_util.add_objective(obj, "min")
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sol = model_util.model.optimize()
@@ -96,16 +97,20 @@ def _influx_objective(model_util, interacting, minExchanges=1e-5):
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def minimize_flux(org_model, min_growth=None, environment=None, interacting=True, pfba=True,
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climit=None, o2limit=None, printing=True, minExchange=None):
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"""minimize the total in-flux of exchange reactions in the model"""
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print("start", org_model.slim_optimize())
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if org_model.slim_optimize() == 0:
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raise ObjectiveError(f"The model {org_model.id} possesses an objective value of 0 in complete media, "
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"which is incompatible with minimal media computations.")
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model_util = MSModelUtil(org_model, True, environment or org_model.medium, climit, o2limit)
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# define the MILP
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print("beginning", model_util.model.slim_optimize())
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sol_growth = model_util.run_fba(None, pfba).fluxes[model_util.biomass_objective]
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print("mid", model_util.model.slim_optimize())
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## some models can't grow at min_growth and therefore are limited by their max_growth
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min_growth = sol_growth if min_growth is None else min(min_growth, sol_growth)
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minExchange = minExchange or min_growth/1000
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media_exchanges, model_util = MSMinimalMedia._influx_objective(model_util, interacting, minExchange)
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print("towards end", model_util.model.slim_optimize())
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# for cons in model_util.model.constraints:
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# if "min" in cons.name and "EX_" in cons.name:
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# print(cons.name, cons.ub, cons.expression, cons.lb)

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