1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
|
"""Test functionalities of cobra component validation functions."""
import pytest
from cobra.core import Metabolite, Model, Reaction
from cobra.manipulation import check_mass_balance, check_metabolite_compartment_formula
def test_validate_mass_balance(model: Model) -> None:
"""Test reaction mass balance validation."""
assert len(check_mass_balance(model)) == 0
# if we remove the SBO term which marks the reaction as
# mass balanced, then the reaction should be detected as
# no longer mass balanced
EX_rxn = model.reactions.query(lambda r: r.boundary)[0]
EX_rxn.annotation.pop("sbo")
balance = check_mass_balance(model)
assert len(balance) == 1
assert EX_rxn in balance
m1 = Metabolite("m1", formula="()")
r1 = Reaction("r1")
r1.add_metabolites({m1: 1})
with pytest.raises(ValueError), pytest.warns(UserWarning):
r1.check_mass_balance()
def test_validate_formula_compartment(model: Model) -> None:
"""Test metabolite formulae validation."""
model.metabolites[1].formula = "(a*.bcde)"
errors = check_metabolite_compartment_formula(model)
assert len(errors) == 1
|
