def test_properties(pubchem_cassette):
results = get_properties("tris-(1,10-phenanthroline)ruthenium", ["IsomericSMILES", "InChIKey"], "name")
assert len(results) > 0
for result in results:
assert "CID" in result
assert "IsomericSMILES" in result
assert "InChIKey" in result
def test_properties_dataframe(pubchem_cassette):
df = get_properties("1,2,3,4", ["IsomericSMILES", "XLogP", "InChIKey"],
"cid",
as_dataframe=True)
assert df.ndim == 2
assert df.index.names == ["CID"]
assert len(df.index) == 4
assert df.columns.values.tolist() == [
"IsomericSMILES", "InChIKey", "XLogP"
]
def test_underscore_properties(pubchem_cassette):
"""
Properties can also be specified as underscore-separated words, rather than CamelCase.
"""
results = get_properties("tris-(1,10-phenanthroline)ruthenium", ["IsomericSMILES", "MolecularWeight"], "name")
assert len(results) > 0
for result in results:
assert "CID" in result
assert "IsomericSMILES" in result
assert "MolecularWeight" in result
def test_comma_string_properties(pubchem_cassette): """ Properties can also be specified as a comma-separated string, rather than a list. """ results = get_properties( "tris-(1,10-phenanthroline)ruthenium", "IsomericSMILES,InChIKey,MolecularWeight", "name", ) assert len(results) > 0 for result in results: assert "CID" in result assert "IsomericSMILES" in result assert "MolecularWeight" in result assert "InChIKey" in result
def from_tuple(cls, compound: Tuple[str, Optional[str]]) -> "PCDLCompound":
"""
Construct a :class:`~.PCDLCompound` from a tuple of ``(name, cas)``.
:param compound:
"""
pubchem_id: Optional[str]
try:
name = get_common_name(compound[0])
pubchem_id = get_compound_id(compound[0])
except NotFoundError:
name = compound[0]
pubchem_id = None
cas = compound[1]
try:
properties = get_properties(name, "IUPACName, MolecularFormula")[0]
iupac_name = properties["IUPACName"]
formula = properties["MolecularFormula"]
exact_mass = formula.monoisotopic_mass
except NotFoundError:
# print(compound[0])
iupac_name = name
formula = None
exact_mass = None
return cls(
name=name,
iupac_name=iupac_name,
cas=cas,
formula=formula,
exact_mass=exact_mass,
pubchem_id=pubchem_id,
)