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_matches(self):
molecule = Molecule(
name="Dimethyl Phthalate",
matches={
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
)
assert molecule.matches == {
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
}
with pytest.raises(TypeError, match="'matches' must be a dictionary, not"):
Molecule(name="Dimethyl Phthalate", matches="Hello World") # type: ignore
def test_repr():
molecule = Molecule(
name="Dimethyl Phthalate",
formula="C10 H10 O4",
matches={
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
)
assert str(molecule) == "Molecule(Dimethyl Phthalate, C10H10O4)"
assert repr(molecule) == "<Molecule(Dimethyl Phthalate, Formula({'C': 10, 'H': 10, 'O': 4}))>"
def expected_compound(fbf_spectrum, tof_spectrum):
score = Score(99.79)
return Compound(
algo="FindByFormula",
location={'m': 169.0893, "rt": 13.649, 'a': 29388223, 'y': 3377289},
compound_scores={"fbf": score},
results=[
Molecule(
name="Diphenylamine", formula="C12 H11 N", matches={
"overall": score,
"tgt": score,
}
)
],
spectra=[fbf_spectrum, tof_spectrum],
)
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 molecule(): return Molecule(name="Dimethyl Phthalate", formula="C10 H10 O4")
def test_from_xml(raw_xml, expects): tree = lxml.objectify.fromstring(raw_xml) spec = Molecule.from_xml(tree) assert spec == expects
def test_name(self): assert Molecule(name="Dimethyl Phthalate").name == "Dimethyl Phthalate"
assert repr(molecule) == "<Molecule(Dimethyl Phthalate, Formula({'C': 10, 'H': 10, 'O': 4}))>"
raw_xml = """
<Molecule name="Dimethyl Phthalate" formula="C10 H10 O4">
<MatchScores>
<Match algo="overall" score="62.90" />
<Match algo="tgt" score="62.90" tgtFlagsString="low score" tgtFlagsSeverity="2" />
</MatchScores>
</Molecule>
"""
expects = Molecule(
name="Dimethyl Phthalate",
formula="C10 H10 O4",
matches={
"overall": Score(62.90),
"tgt": Score(62.90, flag_string="low score", flag_severity=2),
},
)
@pytest.mark.parametrize("raw_xml, expects", [(raw_xml, expects)])
def test_from_xml(raw_xml, expects):
tree = lxml.objectify.fromstring(raw_xml)
spec = Molecule.from_xml(tree)
assert spec == expects
raw_xml_1 = '<MatchScores><Match algo="fbf" score="86.30" /></MatchScores>'
raw_xml_2 = '<MatchScores><Match algo="fbf" score="56.24" tgtFlagsString="low score; No H adduct" tgtFlagsSeverity="2" /></MatchScores>'
raw_xml_3 = '<MatchScores><Match algo="fbf" score="82.53" tgtFlagsString="No H adduct" tgtFlagsSeverity="2" /></MatchScores>'