def test_filter_by_name(
elastic_repository_molecule: ElasticRepository,
indigo_fixture: Indigo,
loaded_sdf: IndigoRecordMolecule,
resource_loader,
):
mol = indigo_fixture.loadMoleculeFromFile(
resource_loader("molecules/composition1.mol"))
elastic_repository_molecule.index_record(
IndigoRecordMolecule(indigo_object=mol))
time.sleep(1)
result = elastic_repository_molecule.filter(name="Composition1")
for item in result:
assert item.name == "Composition1"
result = elastic_repository_molecule.filter(
similarity=TanimotoSimilarityMatch(
IndigoRecordMolecule(indigo_object=mol), 0.1))
i = 0
for _ in result:
i += 1
assert i == 10
result = elastic_repository_molecule.filter(
similarity=TanimotoSimilarityMatch(
IndigoRecordMolecule(indigo_object=mol), 0.1),
name="Composition1",
)
for item in result:
assert item.name == "Composition1"
def depict_smile(genecluster, structuresfolder):
indigo = Indigo()
renderer = IndigoRenderer(indigo)
query = indigo.loadMoleculeFromFile("genecluster" + str(genecluster) +
".smi")
indigo.setOption("render-coloring", True)
renderer.renderToFile(query, "genecluster" + str(genecluster) + ".png")
indigo.setOption("render-image-size", 200, 150)
renderer.renderToFile(query,
"genecluster" + str(genecluster) + "_icon.png")
dircontents = os.listdir(os.getcwd())
geneclusterstring = "genecluster" + str(genecluster) + ".png"
if geneclusterstring in dircontents:
shutil.copy("genecluster" + str(genecluster) + ".png",
structuresfolder)
shutil.copy("genecluster" + str(genecluster) + "_icon.png",
structuresfolder)
shutil.copy("genecluster" + str(genecluster) + ".smi",
structuresfolder)
os.remove("genecluster" + str(genecluster) + ".png")
os.remove("genecluster" + str(genecluster) + "_icon.png")
os.remove("genecluster" + str(genecluster) + ".smi")
smiles_input = path.join('SMILES', 'input')
if path.exists(smiles_input):
os.remove(smiles_input)
return "success"
else:
return "failed"
def load_molecule(
file_: Union[str, Path], session: Indigo
) -> IndigoRecordMolecule:
"""
Helper for loading molecules from file into IndigoRecordMolecule object
"""
molecule = session.loadMoleculeFromFile(file_)
return IndigoRecordMolecule(indigo_object=molecule)
def test_wildcard_search(
elastic_repository: ElasticRepository,
indigo_fixture: Indigo,
loaded_sdf: IndigoRecord,
resource_loader: Callable[[str], str],
):
mol = indigo_fixture.loadMoleculeFromFile(
resource_loader("resources/composition1.mol"))
elastic_repository.index_record(IndigoRecord(indigo_object=mol))
time.sleep(1)
result = elastic_repository.filter(name=WildcardQuery("Comp*"))
for item in result:
assert item.name == "Composition1"
def test_custom_fields(
elastic_repository: ElasticRepository,
indigo_fixture: Indigo,
loaded_sdf: IndigoRecord,
resource_loader: Callable[[str], str],
):
mol = indigo_fixture.loadMoleculeFromFile(
resource_loader("resources/composition1.mol"))
rec = IndigoRecord(indigo_object=mol,
PUBCHEM_IUPAC_INCHIKEY="RDHQFKQIGNGIED-UHFFFAOYSA-N")
elastic_repository.index_record(rec)
time.sleep(1)
result = elastic_repository.filter(
PUBCHEM_IUPAC_INCHIKEY="RDHQFKQIGNGIED-UHFFFAOYSA-N")
for item in result:
assert item.PUBCHEM_IUPAC_INCHIKEY == "RDHQFKQIGNGIED-UHFFFAOYSA-N"
