def test_add_fingerprint_no_smiles_no_inchi():
"""Test if fingerprint it generated correctly."""
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={})
spectrum = add_fingerprint(spectrum_in)
assert spectrum.get("fingerprint", None) is None, "Expected None."
def test_add_fingerprint_from_smiles():
"""Test if fingerprint it generated correctly."""
pytest.importorskip("rdkit")
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"smiles": "[C+]#C[O-]"})
spectrum = add_fingerprint(spectrum_in, nbits=16)
expected_fingerprint = numpy.array([0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0])
assert numpy.all(spectrum.get("fingerprint") == expected_fingerprint), "Expected different fingerprint."
def test_add_fingerprint_from_inchi():
"""Test if fingerprint it generated correctly."""
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"inchi": "InChI=1S/C2O/c1-2-3"})
spectrum = add_fingerprint(spectrum_in, nbits=16)
expected_fingerprint = numpy.array(
[0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0])
assert numpy.all(spectrum.get("fingerprint") ==
expected_fingerprint), "Expected different fingerprint."
def test_add_fingerprint_no_smiles_no_inchi():
"""Test if fingerprint it generated correctly."""
set_matchms_logger_level("INFO")
spectrum_in = SpectrumBuilder().with_metadata({"compound_name": "test name"}).build()
with LogCapture() as log:
spectrum = add_fingerprint(spectrum_in)
assert spectrum.get("fingerprint", None) is None, "Expected None."
log.check(
("matchms", "INFO", "No fingerprint was added (name: test name).")
)
reset_matchms_logger()
def test_add_fingerprint_empty_spectrum():
"""Test if empty spectrum is handled correctly."""
spectrum = add_fingerprint(None)
assert spectrum is None, "Expected None."
def test_add_fingerprint(metadata, expected):
pytest.importorskip("rdkit")
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = add_fingerprint(spectrum_in, nbits=16)
assert numpy.all(spectrum.get("fingerprint") == expected), "Expected different fingerprint."