def setUp(self):
# TODO use mock model instead of actual model
self.database = DictDatabase()
self.database.set_reaction("rxn_1", parse_reaction("=> |A|"))
self.database.set_reaction("rxn_2", parse_reaction("(0.000001) |A| =>"))
self.model = MetabolicModel.load_model(self.database, self.database.reactions)
self.solver = cplex.Solver()
def setUp(self):
# TODO use mock model instead of actual model
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction(
'|A| + |B| => |C|'))
self.database.set_reaction('rxn_2', parse_reaction(
'|C| + |Z| => |A| + |B|'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
self.solver = cplex.Solver()
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
self.database.set_reaction('rxn_7', parse_reaction('|E| => |F|'))
self.database.set_reaction('rxn_8', parse_reaction('|F| => |E|'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
self.solver = cplex.Solver()
def setUp(self):
database1 = DictDatabase()
database1.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
database1.set_reaction('rxn_2', parse_reaction('|B| => |C| + |D|'))
database1.set_reaction('rxn_3', parse_reaction('|D| <=> |E|'))
database1.set_reaction('rxn_4', parse_reaction('|F| => |G|'))
database2 = DictDatabase()
database2.set_reaction('rxn_2', parse_reaction('|B| => |C|'))
database2.set_reaction('rxn_3', parse_reaction('|C| => |D|'))
database2.set_reaction('rxn_4', parse_reaction('|F| <=> |G|'))
database2.set_reaction('rxn_5', parse_reaction('|G| + |I| <=> |H|'))
self.database = ChainedDatabase(database2, database1)
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D[e]|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D[e]|'))
self.database.set_reaction('rxn_6', parse_reaction('|D[e]| =>'))
def setUp(self):
# TODO use mock database instead of actual database
self.database = DictDatabase()
self.database.set_reaction("rxn_1", parse_reaction("=> (2) |A|"))
self.database.set_reaction("rxn_2", parse_reaction("|A| <=> |B|"))
self.database.set_reaction("rxn_3", parse_reaction("|A| => |D[e]|"))
self.database.set_reaction("rxn_4", parse_reaction("|A| => |C|"))
self.database.set_reaction("rxn_5", parse_reaction("|C| => |D[e]|"))
self.database.set_reaction("rxn_6", parse_reaction("|D[e]| =>"))
self.model = MetabolicModel.load_model(self.database, self.database.reactions)
def setUp(self):
# TODO use mock model instead of actual model
self.database = DictDatabase()
self.database.set_reaction("rxn_1", parse_reaction("=> (2) |A|"))
self.database.set_reaction("rxn_2", parse_reaction("|A| <=> |B|"))
self.database.set_reaction("rxn_3", parse_reaction("|A| => |D|"))
self.database.set_reaction("rxn_4", parse_reaction("|A| => |C|"))
self.database.set_reaction("rxn_5", parse_reaction("|C| => |D|"))
self.database.set_reaction("rxn_6", parse_reaction("|D| =>"))
self.model = MetabolicModel.load_model(self.database, self.database.reactions)
self.solver = cplex.Solver()
def setUp(self):
# TODO use mock model instead of actual model
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
self.model = MetabolicModel.load_model(self.database, self.database.reactions)
self.solver = cplex.Solver()
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('ex_A', parse_reaction('|A| <=>'))
self.database.set_reaction('ex_D', parse_reaction('|D| <=>'))
self.database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
self.database.set_reaction('rxn_2', parse_reaction('|B| <=> |C|'))
self.database.set_reaction('rxn_3', parse_reaction('|C| <=> |D|'))
self.database.set_reaction('rxn_4', parse_reaction('|D| <=> |E|'))
self.database.set_reaction('rxn_5', parse_reaction('|E| => |B|'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
self.model.limits['ex_A'].lower = -10 # Low uptake
self.model.limits['ex_D'].lower = 0 # No uptake
self.solver = cplex.Solver()
def test_modelseed_parse_with_decimal(self):
r = modelseed.parse_reaction('|H2| + (0.5) |O2| => |H2O|')
self.assertEquals(r, Reaction(Reaction.Right, [(Compound('H2'), 1), (Compound('O2'), Decimal('0.5'))],
[(Compound('H2O'), 1)]))
def test_get_reaction(self):
reaction = parse_reaction('|A| => |D[e]|')
self.assertEqual(self.database.get_reaction('rxn_3'), reaction)
def test_fastcore_global_inconsistent(self):
self.database.set_reaction("rxn_7", parse_reaction("|E| <=>"))
self.model.add_reaction("rxn_7")
with self.assertRaises(fastcore.FastcoreError):
fastcore.fastcore(self.model, {"rxn_7"}, 0.001, solver=self.solver)
def test_modelseed_parse_raw_compound_id_in_compartment(self):
r = modelseed.parse_reaction('(2) cpd00001 => cpd00002[e]')
self.assertEquals(r, Reaction(Reaction.Right,
[(Compound('cpd00001'), 2)],
[(Compound('cpd00002', 'e'), 1)]))
def test_modelseed_parse_raw_compound_id_with_typo(self):
r = modelseed.parse_reaction('(2) cpd00001 => cdp00002')
self.assertEquals(r, Reaction(Reaction.Right,
[(Compound('cpd00001'), 2)],
[(Compound('cdp00002'), 1)]))
def test_modelseed_parse_with_multichar_compartment(self):
r = modelseed.parse_reaction('(2) |H2[C_c]| + |O2[C_c]| => (2) |H2O[C_e]|')
self.assertEquals(r, Reaction(Reaction.Right, [(Compound('H2', compartment='C_c'), 2),
(Compound('O2', compartment='C_c'), 1)],
[(Compound('H2O', compartment='C_e'), 2)]))
def test_add_reaction_new(self):
self.database.set_reaction("rxn_7", parse_reaction("|D[e]| => |E[e]|"))
self.model.add_reaction("rxn_7")
self.assertIn("rxn_7", set(self.model.reactions))
self.assertIn(Compound("E", "e"), set(self.model.compounds))
def test_modelseed_parse(self):
r = modelseed.parse_reaction('|H2O| + |PPi| => (2) |Phosphate| + (2) |H+|')
self.assertEquals(r, Reaction(Reaction.Right, [(Compound('H2O'), 1), (Compound('PPi'), 1)],
[(Compound('Phosphate'), 2), (Compound('H+'), 2)]))
def test_mass_inconsistent_is_consistent(self):
exchange = { 'rxn_1', 'rxn_6' }
self.database.set_reaction('rxn_7', parse_reaction('|D| => (2) |C|'))
self.model.add_reaction('rxn_7')
self.assertFalse(massconsistency.is_consistent(
self.model, self.solver, exchange, set()))
def test_add_all_database_reactions(self):
self.database.set_reaction("rxn_7", parse_reaction("|D| => |E|"))
added = self.model.add_all_database_reactions()
self.assertEqual(added, {"rxn_7"})
self.assertEqual(set(self.model.reactions), {"rxn_1", "rxn_2", "rxn_3", "rxn_4", "rxn_5", "rxn_6", "rxn_7"})
def test_modelseed_parse_with_compartment(self):
r = modelseed.parse_reaction('(2) |H2| + |O2| => (2) |H2O[e]|')
self.assertEquals(r, Reaction(Reaction.Right, [(Compound('H2'), 2), (Compound('O2'), 1)],
[(Compound('H2O', compartment='e'), 2)]))