def test_equation_double_stoichiometry(self):
""" Test Equation. """
eq_string = '3.0 atp + 2.0 phos + ki <-> 16.98 tet'
eq = Equation(eq_string)
self.assertTrue(eq.reversible)
test_res = eq_string.replace('<->', REV_SEP)
self.assertEqual(eq.toString(), test_res)
def test_equation_2(self):
""" Test Equation. """
eq_string = 'e__h2oM <-> c__h2oM'
eq = Equation(eq_string)
self.assertTrue(eq.reversible)
test_res = eq_string.replace('<->', REV_SEP)
self.assertEqual(eq.to_string(), test_res)
def test_equation_double_stoichiometry(self):
""" Test Equation. """
eq_string = '3.0 atp + 2.0 phos + ki <-> 16.98 tet'
eq = Equation(eq_string)
self.assertTrue(eq.reversible)
test_res = eq_string.replace('<->', REV_SEP)
self.assertEqual(eq.to_string(), test_res)
def test_equation_double_stoichiometry() -> None:
""" Test Equation. """
eq_string = "3.0 atp + 2.0 phos + ki <-> 16.98 tet"
eq = Equation(eq_string)
assert eq.reversible
test_res = eq_string.replace("<->", REV_SEP)
assert eq.to_string() == test_res
def test_equation_2(self):
""" Test Equation. """
eq_string = 'e__h2oM <-> c__h2oM'
eq = Equation(eq_string)
self.assertTrue(eq.reversible)
test_res = eq_string.replace('<->', REV_SEP)
self.assertEqual(eq.toString(), test_res)
def test_equation_2() -> None:
""" Test Equation. """
eq_string = "e__h2oM <-> c__h2oM"
eq = Equation(eq_string)
assert eq.reversible
test_res = eq_string.replace("<->", REV_SEP)
assert eq.to_string() == test_res
def test_equation_examples(self):
equations = [
'1.0 S1 + 2 S2 => 2.0 P1 + 2 P2 [M1, M2]',
'c__gal1p => c__gal + c__phos',
'e__h2oM <-> c__h2oM',
'3 atp + 2.0 phos + ki <-> 16.98 tet',
'c__gal1p => c__gal + c__phos [c__udp, c__utp]',
'A_ext => A []',
'=> cit',
'acoa =>',
]
for eq_str in equations:
eq = Equation(eq_str)
assert eq
def test_equation_examples() -> None:
equations = [
"1.0 S1 + 2 S2 => 2.0 P1 + 2 P2 [M1, M2]",
"c__gal1p => c__gal + c__phos",
"e__h2oM <-> c__h2oM",
"3 atp + 2.0 phos + ki <-> 16.98 tet",
"c__gal1p => c__gal + c__phos [c__udp, c__utp]",
"A_ext => A []",
"=> cit",
"acoa =>",
]
for eq_str in equations:
eq = Equation(eq_str)
assert eq
def __init__(
self,
sid,
equation,
formula=None,
pars=None,
rules=None,
name=None,
compartment=None,
fast=False,
reversible=None,
sboTerm=None,
metaId=None,
annotations=None,
notes=None,
lowerFluxBound=None,
upperFluxBound=None,
uncertainties=None,
port=None,
):
super(Reaction, self).__init__(
sid=sid,
name=name,
sboTerm=sboTerm,
metaId=metaId,
annotations=annotations,
notes=notes,
port=port,
uncertainties=uncertainties,
)
if pars is None:
pars = list()
if rules is None:
rules = list()
self.equation = Equation(equation)
self.compartment = compartment
self.reversible = reversible
self.pars = pars
self.rules = rules
self.formula = formula
if formula is not None:
self.formula = Formula(*formula)
self.fast = fast
self.lowerFluxBound = lowerFluxBound
self.upperFluxBound = upperFluxBound
def test_equation_empty_modifier() -> None:
""" Test Equation. """
eq_string = "A_ext => A []"
eq = Equation(eq_string)
assert len(eq.modifiers) == 0
def test_equation_modifier() -> None:
""" Test Equation. """
eq_string = "c__gal1p => c__gal + c__phos [c__udp, c__utp]"
eq = Equation(eq_string)
assert eq.to_string(modifiers=True) == eq_string
def test_equation_1() -> None:
""" Test Equation. """
eq_string = "c__gal1p => c__gal + c__phos"
eq = Equation(eq_string)
assert eq.to_string() == eq_string
def test_equation_no_products(self):
""" Test Equation. """
eq_string = 'B => '
eq = Equation(eq_string)
test_res = eq_string.replace('=>', IRREV_SEP)
self.assertEqual(eq.to_string(), test_res)
def test_equation_empty_modifier(self):
""" Test Equation. """
eq_string = 'A_ext => A []'
eq = Equation(eq_string)
self.assertEqual(len(eq.modifiers), 0)
def test_equation_modifier(self):
""" Test Equation. """
eq_string = 'c__gal1p => c__gal + c__phos [c__udp, c__utp]'
eq = Equation(eq_string)
self.assertEqual(eq.to_string(modifiers=True), eq_string)
def test_equation_1(self):
""" Test Equation. """
eq_string = 'c__gal1p => c__gal + c__phos'
eq = Equation(eq_string)
self.assertEqual(eq.to_string(), eq_string)
def test_equation_no_reactants():
""" Test Equation. """
eq_string = " => A"
eq = Equation(eq_string)
test_res = eq_string.replace("=>", IRREV_SEP)
assert eq.to_string() == test_res
def test_equation_no_products(self):
""" Test Equation. """
eq_string = 'B => '
eq = Equation(eq_string)
test_res = eq_string.replace('=>', IRREV_SEP)
self.assertEqual(eq.toString(), test_res)
def test_equation_modifier(self):
""" Test Equation. """
eq_string = 'c__gal1p => c__gal + c__phos [c__udp, c__utp]'
eq = Equation(eq_string)
self.assertEqual(eq.toString(modifiers=True), eq_string)
def test_equation_no_products() -> None:
""" Test Equation. """
eq_string = "B => "
eq = Equation(eq_string)
test_res = eq_string.replace("=>", IRREV_SEP)
assert eq.to_string() == test_res
def test_equation_1(self):
""" Test Equation. """
eq_string = 'c__gal1p => c__gal + c__phos'
eq = Equation(eq_string)
self.assertEqual(eq.toString(), eq_string)
