def test_flux_variability_unbounded(self):
self.model.limits['rxn_7'].upper = float('inf')
self.model.limits['rxn_8'].upper = float('inf')
if self.solver.properties['name'] == 'qsoptex':
# QSopt_ex returns status code 100 for this example. It seems that
# it is unable to determine whether the problem is unbounded.
self.skipTest('Skipping because of known issue with QSopt_ex')
fluxes = dict(
fluxanalysis.flux_variability(self.model,
self.model.reactions, {'rxn_6': 200},
tfba=False,
solver=self.solver))
for bounds in itervalues(fluxes):
self.assertEqual(len(bounds), 2)
self.assertAlmostEqual(fluxes['rxn_6'][0], 200)
self.assertAlmostEqual(fluxes['rxn_7'][0], 0)
self.assertEqual(fluxes['rxn_7'][1], float('inf'))
self.assertAlmostEqual(fluxes['rxn_8'][0], 0)
self.assertEqual(fluxes['rxn_8'][1], float('inf'))
def test_flux_variability_thermodynamic(self):
fluxes = dict(fluxanalysis.flux_variability(
self.model, self.model.reactions, {'rxn_6': 200},
tfba=True, solver=self.solver))
self.assertAlmostEqual(fluxes['rxn_1'][0], 100)
self.assertAlmostEqual(fluxes['rxn_2'][0], 0)
self.assertAlmostEqual(fluxes['rxn_2'][1], 0)
self.assertAlmostEqual(fluxes['rxn_5'][0], 0)
self.assertAlmostEqual(fluxes['rxn_5'][1], 100)
self.assertAlmostEqual(fluxes['rxn_6'][0], 200)
self.assertAlmostEqual(fluxes['rxn_7'][1], 0)
self.assertAlmostEqual(fluxes['rxn_8'][1], 0)
def test_flux_variability(self):
fluxes = dict(fluxanalysis.flux_variability(
self.model, self.model.reactions, {'rxn_6': 200},
tfba=False, solver=self.solver))
self.assertEqual(fluxes['rxn_1'][0], 100)
self.assertEqual(fluxes['rxn_2'][0], 0)
self.assertEqual(fluxes['rxn_2'][1], 0)
self.assertEqual(fluxes['rxn_5'][0], 0)
self.assertEqual(fluxes['rxn_5'][1], 100)
self.assertEqual(fluxes['rxn_6'][0], 200)
self.assertGreater(fluxes['rxn_7'][1], 0)
self.assertGreater(fluxes['rxn_8'][1], 0)
def test_flux_variability_thermodynamic(self):
fluxes = dict(
fluxanalysis.flux_variability(self.model,
self.model.reactions, {'rxn_6': 200},
tfba=True,
solver=self.solver))
self.assertAlmostEqual(fluxes['rxn_1'][0], 100)
self.assertAlmostEqual(fluxes['rxn_2'][0], 0)
self.assertAlmostEqual(fluxes['rxn_2'][1], 0)
self.assertAlmostEqual(fluxes['rxn_5'][0], 0)
self.assertAlmostEqual(fluxes['rxn_5'][1], 100)
self.assertAlmostEqual(fluxes['rxn_6'][0], 200)
self.assertAlmostEqual(fluxes['rxn_7'][1], 0)
self.assertAlmostEqual(fluxes['rxn_8'][1], 0)
def test_flux_variability(self):
fluxes = dict(fluxanalysis.flux_variability(
self.model, self.model.reactions, {'rxn_6': 200},
tfba=False, solver=self.solver))
for bounds in itervalues(fluxes):
self.assertEqual(len(bounds), 2)
self.assertAlmostEqual(fluxes['rxn_1'][0], 100)
self.assertAlmostEqual(fluxes['rxn_2'][0], 0)
self.assertAlmostEqual(fluxes['rxn_2'][1], 0)
self.assertAlmostEqual(fluxes['rxn_5'][0], 0)
self.assertAlmostEqual(fluxes['rxn_5'][1], 100)
self.assertAlmostEqual(fluxes['rxn_6'][0], 200)
self.assertGreater(fluxes['rxn_7'][1], 0)
self.assertGreater(fluxes['rxn_8'][1], 0)
def test_flux_variability(self):
fluxes = dict(
fluxanalysis.flux_variability(self.model,
self.model.reactions, {'rxn_6': 200},
tfba=False,
solver=self.solver))
for bounds in itervalues(fluxes):
self.assertEqual(len(bounds), 2)
self.assertAlmostEqual(fluxes['rxn_1'][0], 100)
self.assertAlmostEqual(fluxes['rxn_2'][0], 0)
self.assertAlmostEqual(fluxes['rxn_2'][1], 0)
self.assertAlmostEqual(fluxes['rxn_5'][0], 0)
self.assertAlmostEqual(fluxes['rxn_5'][1], 100)
self.assertAlmostEqual(fluxes['rxn_6'][0], 200)
self.assertGreater(fluxes['rxn_7'][1], 0)
self.assertGreater(fluxes['rxn_8'][1], 0)
def test_flux_variability_unbounded(self):
self.model.limits['rxn_7'].upper = float('inf')
self.model.limits['rxn_8'].upper = float('inf')
if self.solver.properties['name'] == 'qsoptex':
# QSopt_ex returns status code 100 for this example. It seems that
# it is unable to determine whether the problem is unbounded.
self.skipTest('Skipping because of known issue with QSopt_ex')
fluxes = dict(fluxanalysis.flux_variability(
self.model, self.model.reactions, {'rxn_6': 200},
tfba=False, solver=self.solver))
for bounds in itervalues(fluxes):
self.assertEqual(len(bounds), 2)
self.assertAlmostEqual(fluxes['rxn_6'][0], 200)
self.assertAlmostEqual(fluxes['rxn_7'][0], 0)
self.assertEqual(fluxes['rxn_7'][1], float('inf'))
self.assertAlmostEqual(fluxes['rxn_8'][0], 0)
self.assertEqual(fluxes['rxn_8'][1], float('inf'))