def test_enzyme(self):
"""One-substrate enzyme kinetics."""
filename = path.join(input_sbml, "enzyme.xml")
crn = from_sbml(filename)
crn.save_sbml(path.join(input_sbml, "enzyme_original.xml"))
crn = from_sbml(path.join(input_sbml, "enzyme_original.xml"))
rate = parse_expr("comp*E*vcat_kcat*veq_kon*S/(vcat_kcat + veq_koff)")
crn.qss('ES')
self.assertEqual((crn.rates[0] - rate).simplify(), 0)
crn.save_sbml(path.join(input_sbml,
"enzyme_simplified_qss_with_e.xml"))
crn.remove_constant('E')
self.assertEqual((crn.rates[0] - rate).simplify(), 0)
crn.save_sbml(path.join(input_sbml, "enzyme_simplified_qss.xml"))
# Michaelis-Menten
crn = from_sbml(filename)
enzyme_cons_law = ConsLaw('E + ES', 'Et')
crn.qss(cons_law=('E', enzyme_cons_law))
rate = parse_expr(
"comp*Et*vcat_kcat*veq_kon*S/(vcat_kcat + veq_koff + veq_kon*S)")
self.assertEqual((crn.rates[0] - rate).simplify(), 0)
crn.save_sbml(path.join(input_sbml, "enzyme_simplified_MM.xml"))
crn.save_reaction_file(
path.join(input_reactions, "enzyme_simplified_MM"))
# Reading Michaelis-Menten model
crn = from_sbml(path.join(input_sbml, "enzyme_simplified_MM.xml"))
def enzyme_kinetics():
"""One-substrate enzyme kinetics."""
print("One-substrate enzyme kinetics.")
filename = os.path.join(input_sbml, "enzyme.xml")
crn = from_sbml(filename)
rate = parse_expr("comp*E*vcat_kcat*veq_kon*S/(vcat_kcat + veq_koff)")
crn.qss('ES')
fail_if_not_equal((crn.rates[0] - rate).factor(), 0)
crn.remove_constant('E')
fail_if_not_equal((crn.rates[0] - rate).factor(), 0)
# Michaelis-Menten
crn = from_sbml(filename)
enzyme_cons_law = ConsLaw('E + ES', 'Et')
crn.qss(cons_law=('E', enzyme_cons_law))
rate = parse_expr(
"comp*Et*vcat_kcat*veq_kon*S/(vcat_kcat + veq_koff + veq_kon*S)")
fail_if_not_equal((crn.rates[0] - rate).factor(), 0)
# Rapid equilibrium
filename = os.path.join(input_sbml, "enzyme.xml")
crn = from_sbml(filename)
enzyme_cons_law = ConsLaw('E + ES', 'Et')
crn.rapid_eq('ES', 'S + E', cons_law=('E', enzyme_cons_law))
fail_if_not_equal(
(crn.kinetic_params[0] -
parse_expr("Et*vcat_kcat*comp/(S + veq_koff/veq_kon)")).factor(), 0)
def test_crn_from_sbml(self):
filename = path.join(input_sbml, "BIOMD0000000001.xml")
output = path.join(input_sbml, "out_BIOMD0000000001.xml")
crn = from_sbml(filename)
success = libsbml.writeSBMLToFile(crn.document, output)
self.assertTrue(success)
def test_crn_from_react_file(self):
reactions = parse_reaction_file(path.join(input_reactions, "allosteric_activation"))
filename = path.join(input_sbml, "allosteric_activation.xml")
model, document, _ = model_from_reacts(reactions)
success = libsbml.writeSBMLToFile(document, filename)
self.assertTrue(success)
crn = from_sbml(filename)
crn.inspect()
def test_enzyme_rapid_eq(self):
"""One-substrate enzyme kinetics: rapid equilibrium."""
# Rapid equilibrium
filename = path.join(input_sbml, "enzyme.xml")
crn = from_sbml(filename)
enzyme_cons_law = ConsLaw('E + ES', 'Et')
crn.rapid_eq('ES', 'S + E', cons_law=('E', enzyme_cons_law))
self.assertEqual((
crn.kinetic_params[0] -
parse_expr("Et*vcat_kcat*comp/(S + veq_koff/veq_kon)")).simplify(),
0)
def test_crn_from_reacts(self):
reactions = [
("r1", {"A": 1, "B": 1}, {"C": 1}, "k1 * A * B"),
("r2", {"A": 1, "B": 1}, {"D": 1}, "k2 * A * B"),
("r3", {"C": 1}, {"E": 1, "F": 1}, "k3 * C"),
("r4", {"C": 1, "D": 1}, {"A": 1, "D": 1}, "k4 * C * D")]
filename = path.join(input_sbml, "test_model1.xml")
model, document, _ = model_from_reacts(list(map(lambda x: Reaction(x[0], \
Complex(x[1]), \
Complex(x[2]), \
rate = parse_expr(x[3])), reactions)))
success = libsbml.writeSBMLToFile(document, filename)
self.assertTrue(success)
crn = from_sbml(filename)
crn.inspect(True)