def test_gecko_adjustment_sanchez_etal():
mmol_gdw = pd.read_csv(
os.path.join(os.path.dirname(__file__),
'../../src/mewpy/model/data/sanchez-mmol_gdw.csv'))
PROTEIN_PROPERTIES = ModelList().protein_properties()
ggdw = pd.Series(PROTEIN_PROPERTIES.loc[mmol_gdw.index, 'mw'] /
1000.) * pd.Series(mmol_gdw)
model = GeckoModel('multi-pool')
simulation = GeckoSimulation(model)
result = simulation.simulate()
growth_rate_unlimited_protein = result.objective_value
model.limit_proteins(ggdw=pd.Series(ggdw))
result = simulation.simulate()
growth_rate_limited_protein = result.objective_value
# should be smaller, but how much..
assert growth_rate_limited_protein < 0.8 * growth_rate_unlimited_protein
measured_in_model = set(mmol_gdw.index).intersection(model.proteins)
assert sum(model.concentrations[p] - ggdw[p]
for p in measured_in_model) < 1e-10
def test_basic_gecko_adjustment():
"""Tests basic adjustments
"""
in_model = {
'P00549': 0.1,
'P31373': 0.1,
'P31382': 0.1,
'P39708': 0.1,
'P39714': 0.1,
'P39726': 0.1,
'Q01574': 0.1
}
not_in_model = {'P10591': 0.1, 'P31383': 0.1, 'P32471': 0.1}
measurements = pd.concat([pd.Series(in_model), pd.Series(not_in_model)])
model = GeckoModel('multi-pool')
model.limit_proteins(fractions=pd.Series(measurements))
simul = GeckoSimulation(model)
sol = simul.simulate()
assert sol.objective_value > 0.05
assert len(model.proteins) - len(model.pool_proteins) - len(in_model) == 0
assert all(model.reactions[rxn].ub > 0
for rxn in model.individual_protein_exchanges)