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test_optmdfpathway_with_toymodel.py
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test_optmdfpathway_with_toymodel.py
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import cobra
from fba import get_fba_base_problem, perform_fba_flux_maximization
from optmdfpathway import get_optmdfpathway_base_problem, get_thermodynamic_bottlenecks, perform_concentration_variability_analysis, perform_concentration_variability_analysis_multi, perform_optmdfpathway_mdf_maximization
from helper import json_load
import time
test_model = cobra.io.read_sbml_model("./resources/astheriscToymodelDouble_irreversible.xml")
test_model.reactions.get_by_id("EX_C_S_exchg_REV").upper_bound = 3.14
R = 8.314e-3 # kJ⋅K⁻1⋅mol⁻1 (standard value is in J⋅K⁻1⋅mol⁻1)
T = 298.15 # K
test_model.objective = "EX_C_P_exchg_FWD"
# test_model.reactions.get_by_id("EXCHG_strain1_B_c_to_B_FWD").upper_bound = float("inf")
# test_model.reactions.get_by_id("EXCHG_strain2_B_c_to_B_REV").upper_bound = float("inf")
test_model.optimize()
print("~~~ORIGINAL FBA~~~")
print(test_model.objective.value)
print("")
print("~~~OWN FBA~~~")
fba_base_problem = get_fba_base_problem(cobra_model=test_model, extra_constraints=[{}])
print(perform_fba_flux_maximization(fba_base_problem, "EX_C_P_exchg_FWD"))
print("")
print("~~~OptMDFpathway~~~")
concentration_values = {
"DEFAULT": {
"min": 1.0,
"max": 10.0,
},
"P_exchg": {
"min": 5.0,
"max": 10.0,
}
}
dG0_values = json_load("resources/dG0_astheriscToymodelDouble.json")
for key in [x for x in dG0_values.keys()]:
dG0_values[key+"_FWD"] = dG0_values[key]
dG0_values[key+"_REV"] = dG0_values[key]
optmdfpathway_base_problem = get_optmdfpathway_base_problem(
cobra_model=test_model,
extra_constraints=[
{
"EX_C_P_exchg_FWD": 1,
"ub": 1,
"lb": 1,
}
],
dG0_values=dG0_values,
metabolite_concentration_values=concentration_values,
ratio_constraint_data=[],
R=R,
T=T,
)
print("A) OptMDFpathway")
optmdfpathway_result = perform_optmdfpathway_mdf_maximization(
optmdfpathway_base_problem=optmdfpathway_base_problem,
)
print(optmdfpathway_result)
print(optmdfpathway_result["values"]["var_B"])
print("\nB1) Concentration variability analysis - single-threaded")
variability_results = perform_concentration_variability_analysis(
cobra_model=test_model,
min_mdf=optmdfpathway_result["values"]["var_B"],
optmdfpathway_base_problem=optmdfpathway_base_problem,
)
print(variability_results)
print(optmdfpathway_result["values"]["var_B"])
"""
print("\nB2) Concentration variability analysis - multi-processed")
variability_results = perform_concentration_variability_analysis_multi(
cobra_model=test_model,
min_mdf=optmdfpathway_result["values"]["var_B"],
optmdfpathway_base_problem=optmdfpathway_base_problem,
)
print(variability_results)
"""
print("\nC) Check for thermodynamic bottlenecks")
bottlenecks, report = get_thermodynamic_bottlenecks(
cobra_model=test_model,
optmdfpathway_result=optmdfpathway_result,
optmdfpathway_base_problem=optmdfpathway_base_problem
)
print(report)