def test_most_probable_isotopic_composition():
assert (Formula.from_string('F').most_probable_isotopic_composition() == (
Formula({
"F[19]": 1,
"F[18]": 0
}), 1.0))
Br2 = Formula.from_string("Br2")
assert Br2.most_probable_isotopic_composition()[0] == Formula({
"Br[79]": 1,
"Br[81]": 1
})
assert rounders(Br2.most_probable_isotopic_composition()[1],
"0.000") == decimal.Decimal("0.5")
C6Br6 = Formula.from_string("C6Br6")
assert C6Br6.most_probable_isotopic_composition()[0] == Formula({
"C[12]": 6,
"C[13]": 0,
"Br[79]": 3,
"Br[81]": 3
})
assert rounders(C6Br6.most_probable_isotopic_composition()[1],
"0.000") == decimal.Decimal("0.293")
assert (
Formula.from_string("F10").most_probable_isotopic_composition() == (
Formula({
"F[19]": 10,
}), 1.0))
assert Formula.from_string("CF4").most_probable_isotopic_composition(
elements_with_isotopes=['F'],
) == (Formula({'C': 1, "F[19]": 4}), 1.0) # yapf: disable
def test_formula_sum():
# Test sum of Formula objects.
assert Formula.from_string("C6H12O6") + Formula.from_string("H2O") == {
'C': 6,
'H': 14,
'O': 7
}
def test_formula(self):
assert Molecule(
name="Dimethyl Phthalate", formula="C10 H10 O4"
).formula == Formula({'C': 10, 'H': 10, 'O': 4})
assert Molecule(
name="Dimethyl Phthalate", formula=Formula({'C': 10, 'H': 10, 'O': 4})
).formula == Formula({'C': 10, 'H': 10, 'O': 4})
assert Molecule(name="Dimethyl Phthalate").formula == Formula()
def test_iter_isotopologues():
iter_isotopologues = Formula.from_string("C6Br6").iter_isotopologues()
assert len(list(iter_isotopologues)) == 49
iter_isotopologues = Formula.from_string("C6Br6").iter_isotopologues(
elements_with_isotopes="Br")
assert len(list(iter_isotopologues)) == 7
def test_isotope_formula():
# from dict
f3 = Formula({"C[12]": 10, "C[13]": 2, 'H': 11, 'N': 1})
assert dict(f3) == {"[12C]": 10, "[13C]": 2, 'H': 11, 'N': 1}
# from composition
f5 = Formula(f3)
assert f5 == f3
def test_properties():
f = Formula.from_string("C6H12O6") # Sugar
assert f.hill_formula == "C6H12O6"
assert f.empirical_formula == "CH2O"
assert f.n_atoms == 24
assert f.n_elements == 3
f = Formula.from_string("D2O") # heavy water
assert f.hill_formula == "D2O"
assert f.empirical_formula == "D2O"
assert f.monoisotopic_mass == 20.02311817516
assert f.mass == 20.0276085556
assert f.n_atoms == 3
assert f.n_elements == 2
assert D.nominalmass == 2
assert O.nominalmass == 16
def test_calculate_mz(charge):
# Calculate m/z of an ion.
assert Formula.from_string("C12H13N+").exact_mass == Formula.from_string(
"C12H13N", charge=1).exact_mass
# perhaps math.isclose()
# assert Formula.from_string("C12H13N+").mass == Formula.from_string("C12H13N", charge=1).exact_mass
# assert Formula.from_string("C12H13N+").exact_mass == Formula.from_string("C12H13N", charge=1).mass
# assert Formula.from_string("C12H13N+").mass == Formula.from_string("C12H13N", charge=1).mass
assert Formula.from_string("C12H13N+").get_mz() == Formula.from_string(
"C12H13N", charge=1).get_mz()
assert Formula.from_string("C12H13N+").average_mz == Formula.from_string(
"C12H13N", charge=1).get_mz()
assert Formula.from_string("C12H13N+").mz == Formula.from_string(
"C12H13N", charge=1).get_mz(average=False)
assert Formula.from_string("C12H13N+").get_mz() == Formula.from_string(
"C12H13N", charge=1).average_mz
def test_charged_formula():
# From string
f1 = Formula.from_string("(C6H5)2NH+")
f2 = Formula.from_string("C12H11N", charge=1)
assert f1 == f2
# from dict
f3 = Formula({'C': 12, 'H': 11, 'N': 1}, charge=1)
assert f3 == {'C': 12, 'H': 11, 'N': 1}
assert f1 == f3
assert f2 == f3
# from kwargs
f4 = Formula.from_kwargs(C=12, H=11, N=1, charge=1)
assert f1 == f4
assert f2 == f4
assert f3 == f4
# from composition
f5 = Formula(f1)
assert f5 == f1
assert f5 == f2
for charge in [1, 2, 3]:
with pytest.raises(
ValueError,
match=
"Cannot supply 'charge' when the formula already has a charge!",
):
Formula.from_string(f"BCHFKOH+{charge:d}", charge + 1)
def test_formula():
# From string
f1 = Formula.from_string("(C6H5)2NH")
f2 = Formula.from_string("C12H11N")
assert f1 == f2
# from dict
f3 = Formula({'C': 12, 'H': 11, 'N': 1})
assert f1 == f3
assert f2 == f3
# from kwargs
f4 = Formula.from_kwargs(C=12, H=11, N=1)
assert f1 == f4
assert f2 == f4
assert f3 == f4
# from composition
f5 = Formula(f1)
assert f5 == f1
assert f5 == f2
s = Formula.from_string("H+")
assert s.charge == 1
assert s.mass == 1.007941
def __init__(
self,
name: str,
formula: Union[str, Formula, None] = None,
matches: Optional[Dict[str, "Score"]] = None,
):
super().__init__()
self.name = str(name)
if isinstance(formula, Formula):
self.formula = formula
elif formula is not None:
self.formula = Formula.from_string(formula)
else:
self.formula = Formula()
if isinstance(matches, dict):
self.matches = matches
elif matches is None:
self.matches = {}
else:
raise TypeError(
f"'matches' must be a dictionary, not {type(matches)}")
def test_dict():
assert dict(
Molecule(
name="Dimethyl Phthalate",
formula="C10 H10 O4",
matches={
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
)
) == {
"name": "Dimethyl Phthalate",
"formula": Formula({'C': 10, 'H': 10, 'O': 4}),
"matches": {
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
}
def test_calculate_mass():
# Calculate mass by a formula.
mass = rounders(
Formula.from_string("(C6H5)2NH").monoisotopic_mass, "0.000000")
assert mass == decimal.Decimal("169.089149")
# Calculate average mass / molecular weight by a formula.
assert rounders(Formula.from_string("(C6H5)2NH").average_mass,
"0.00") == decimal.Decimal("169.22")
assert Formula.from_string(
"(C6H5)2NH").average_mass == Formula.from_string(
"(C6H5)2NH").average_mass
# mz
assert Formula.from_string("C12H13N+").get_mz() == Formula.from_string(
"C12H13N", charge=1).average_mass
def test_parsing(formula, data):
assert Formula.from_string(formula) == data
def test_invalid_formulae_unknown_element(formula):
with pytest.raises(
ValueError,
match=f"Unknown chemical element with symbol {formula}"):
Formula.from_string(formula)
def test_invalid_formulae(formula):
pattern = f"Unrecognised formula: {re.escape(formula.replace(' ', ''))}"
with pytest.raises(ValueError, match=pattern):
Formula.from_string(formula)
def test_empirical_formula(formula_1, formula_2):
f1 = Formula.from_string(formula_1)
f2 = Formula.from_string(formula_2)
assert f1.empirical_formula == f2.empirical_formula
assert f1.empirical_formula == formula_2
def test_equivalent(formula_1, formula_2):
f1 = Formula.from_string(formula_1)
f2 = Formula.from_string(formula_2)
assert f1 == f2
def test_masses(formula, mass, exact_mass):
f = Formula.from_string(formula)
print(f)
assert rounders(f.mass, "0.00000") == decimal.Decimal(mass)
assert rounders(f.exact_mass, "0.00000") == decimal.Decimal(exact_mass)
def C6Br6():
return Formula.from_string("C6Br6")
def Br2():
return Formula.from_string("Br2")
def test_iter_isotopologues_with_abundances():
for state, abundance in Formula.from_string("BCHFKO").iter_isotopologues(
elements_with_isotopes='F', report_abundance=True):
assert state
assert abundance
def test_Composition_sub():
# Test subtraction of Composition objects
assert {} - Formula.from_string("C6H12O6") == {'C': -6, 'H': -12, 'O': -6}
def test_Composition_mul():
# Test multiplication of Composition by integers
f1 = Formula.from_string("H2O2")
assert f1 == {'H': 2, 'O': 2}
assert 2 * f1 == {'H': 4, 'O': 4}
assert f1 * 2 == {'H': 4, 'O': 4}