def test_one_left_to_right_reaction_set_positive_ub(self):
model = Model("Toy Model")
m1 = Metabolite("M1")
d1 = Reaction("ex1")
d1.add_metabolites({m1: -1})
d1.upper_bound = 0
d1.lower_bound = -1000
model.add_reactions([d1])
self.assertEqual(d1.reverse_variable.lb, 0)
self.assertEqual(d1.reverse_variable.ub, 1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._upper_bound, 0)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1.forward_variable.lb, 0)
self.assertEqual(d1.forward_variable.ub, 0)
d1.upper_bound = .1
self.assertEqual(d1.forward_variable.lb, 0)
self.assertEqual(d1.forward_variable.ub, .1)
self.assertEqual(d1.reverse_variable.lb, 0)
self.assertEqual(d1.reverse_variable.ub, 1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, .1)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, .1)
def test_one_left_to_right_reaction_set_positive_ub(self):
model = Model("Toy Model")
m1 = Metabolite("M1")
d1 = Reaction("ex1")
d1.add_metabolites({m1: -1})
d1.upper_bound = 0
d1.lower_bound = -1000
model.add_reactions([d1])
self.assertEqual(d1.reverse_variable.lb, 0)
self.assertEqual(d1.reverse_variable.ub, 1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._upper_bound, 0)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1.forward_variable.lb, 0)
self.assertEqual(d1.forward_variable.ub, 0)
d1.upper_bound = .1
self.assertEqual(d1.forward_variable.lb, 0)
self.assertEqual(d1.forward_variable.ub, .1)
self.assertEqual(d1.reverse_variable.lb, 0)
self.assertEqual(d1.reverse_variable.ub, 1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, .1)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, .1)
def test_weird_left_to_right_reaction_issue(self):
model = Model("Toy Model")
m1 = Metabolite("M1")
d1 = Reaction("ex1")
d1.add_metabolites({m1: -1})
d1.upper_bound = 0
d1.lower_bound = -1000
# print d1.reaction, d1.lower_bound, d1.upper_bound
model.add_reactions([d1])
self.assertFalse(d1.reversibility)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
with TimeMachine() as tm:
d1.knock_out(time_machine=tm)
self.assertEqual(d1.lower_bound, 0)
self.assertEqual(d1._lower_bound, 0)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
def test_weird_left_to_right_reaction_issue(self):
model = Model("Toy Model")
m1 = Metabolite("M1")
d1 = Reaction("ex1")
d1.add_metabolites({m1: -1})
d1.upper_bound = 0
d1.lower_bound = -1000
# print d1.reaction, d1.lower_bound, d1.upper_bound
model.add_reactions([d1])
self.assertFalse(d1.reversibility)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
with TimeMachine() as tm:
d1.knock_out(time_machine=tm)
self.assertEqual(d1.lower_bound, 0)
self.assertEqual(d1._lower_bound, 0)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
self.assertEqual(d1.lower_bound, -1000)
self.assertEqual(d1._lower_bound, -1000)
self.assertEqual(d1.upper_bound, 0)
self.assertEqual(d1._upper_bound, 0)
def test_make_lhs_irreversible_reversible(self):
model = self.model
rxn = Reaction('test')
rxn.add_metabolites({model.metabolites[0]: -1., model.metabolites[1]: 1.})
rxn.lower_bound = -999999.
rxn.upper_bound = -100
model.add_reaction(rxn)
self.assertEqual(rxn.lower_bound, -999999.)
self.assertEqual(rxn.upper_bound, -100.)
self.assertEqual(rxn.forward_variable.lb, 0.)
self.assertEqual(rxn.forward_variable.ub, 0.)
self.assertEqual(rxn.reverse_variable.lb, 100.)
self.assertEqual(rxn.reverse_variable.ub, 999999.)
rxn.upper_bound = 666.
self.assertEqual(rxn.lower_bound, -999999.)
self.assertEqual(rxn.upper_bound, 666.)
self.assertEqual(rxn.forward_variable.lb, 0.)
self.assertEqual(rxn.forward_variable.ub, 666)
self.assertEqual(rxn.reverse_variable.lb, 0.)
self.assertEqual(rxn.reverse_variable.ub, 999999.)
def test_make_lhs_irreversible_reversible(self):
model = self.model
rxn = Reaction('test')
rxn.add_metabolites({
model.metabolites[0]: -1.,
model.metabolites[1]: 1.
})
rxn.lower_bound = -999999.
rxn.upper_bound = -100
model.add_reaction(rxn)
self.assertEqual(rxn.lower_bound, -999999.)
self.assertEqual(rxn.upper_bound, -100.)
self.assertEqual(rxn.forward_variable.lb, 0.)
self.assertEqual(rxn.forward_variable.ub, 0.)
self.assertEqual(rxn.reverse_variable.lb, 100.)
self.assertEqual(rxn.reverse_variable.ub, 999999.)
rxn.upper_bound = 666.
self.assertEqual(rxn.lower_bound, -999999.)
self.assertEqual(rxn.upper_bound, 666.)
self.assertEqual(rxn.forward_variable.lb, 0.)
self.assertEqual(rxn.forward_variable.ub, 666)
self.assertEqual(rxn.reverse_variable.lb, 0.)
self.assertEqual(rxn.reverse_variable.ub, 999999.)