def test_uniqueInsertion(self):
db = setupDB()
data_scheme = registration.MolDocScheme()
assert 200 == write.WriteFromSDF(db.molecules,
'data/test_data/first_200.props.sdf',
data_scheme)
assert 0 == write.WriteFromSDF(db.molecules,
'data/test_data/first_200.props.sdf',
data_scheme)
def test_hashes(self):
db = setupDB()
data_scheme = registration.MolDocScheme()
data_scheme.set_index("CanonicalSmiles")
assert 200 == write.WriteFromSDF(db.molecules,
'data/test_data/first_200.props.sdf',
data_scheme)
data_scheme.set_index("inchikey_standard")
assert 200 == write.WriteFromSDF(db.molecules,
'data/test_data/first_200.props.sdf',
data_scheme)
def test_writeLimit(self):
db = setupDB()
data_scheme = registration.MolDocScheme()
assert 10 == write.WriteFromSDF(db.molecules,
'data/test_data/first_200.props.sdf',
data_scheme,
limit=10)
def test_SubSearchAccuracy():
db_mock = utils.setupMockDB()
write.WriteFromSDF(db_mock.molecules, 'data/test_data/first_200.props.sdf')
substructure.AddPatternFingerprints(db_mock.molecules)
db_python = utils.setupPythonDB('data/test_data/first_200.props.sdf')
for i in range(200):
moldoc = db_python[i]
pattern = Chem.Mol(moldoc['rdmol'])
results_python = utils.SubSearchPython(pattern, db_python)
results = substructure.SubSearch(pattern, db_mock.molecules)
assert sorted(results_python) == sorted(results)
def test_zeroThreshold():
"""
If we search the database with a Tanimoto threshold of zero, we should get
the entire contents of the database back.
"""
db_python = utils.setupPythonDB('data/test_data/first_200.props.sdf')
db_mongo = utils.setupMockDB()
write.WriteFromSDF(db_mongo.molecules, 'data/test_data/first_200.props.sdf')
similarity.AddMorganFingerprints(db_mongo.molecules, db_mongo.mfp_counts)
mol = Chem.Mol(db_python[0]['rdmol'])
assert 200 == len(utils.similaritySearchPython(mol, db_python, 0))
assert 200 == len(similarity.SimSearchAggregate(mol, db_mongo.molecules, db_mongo.mfp_counts, 0))
assert 200 == len(similarity.SimSearch(mol, db_mongo.molecules, db_mongo.mfp_counts, 0))
def test_similarityAccuracy():
"""
Tests for basic accuracy against a brute-force constructed Python 'database'
at thresholds 0.2, 0.4, 0.6, 0.8, and 1. This test is implemented using MongoMock.
"""
db_python = utils.setupPythonDB('data/test_data/first_200.props.sdf')
db_mongo = utils.setupMockDB()
write.WriteFromSDF(db_mongo.molecules, 'data/test_data/first_200.props.sdf')
similarity.AddMorganFingerprints(db_mongo.molecules, db_mongo.mfp_counts)
thresholds = [0.2, 0.4, 0.6, 0.8, 1]
for t in thresholds:
for i in range(200):
mol = Chem.Mol(db_python[i]['rdmol'])
search_python = utils.similaritySearchPython(mol, db_python, t)
search_mongo = similarity.SimSearch(mol, db_mongo.molecules, db_mongo.mfp_counts, t)
assert sorted(search_python) == sorted(search_mongo)
def test_similarityProgression():
"""
Tests that decreasing similarity thresholds return increasing result lists.
This test is implemented using MongoMock.
"""
db_python = utils.setupPythonDB('data/test_data/first_200.props.sdf')
db_mongo = utils.setupMockDB()
write.WriteFromSDF(db_mongo.molecules, 'data/test_data/first_200.props.sdf')
similarity.AddMorganFingerprints(db_mongo.molecules, db_mongo.mfp_counts)
thresholds = [1, 0.8, 0.6, 0.4, 0.2]
for i in range(200):
mol = Chem.Mol(db_python[i]['rdmol'])
last = []
for t in thresholds:
search_mongo = similarity.SimSearch(mol, db_mongo.molecules, db_mongo.mfp_counts, t)
assert len(search_mongo) >= len(last)
assert (all(l in search_mongo for l in last))
last = search_mongo
def test_similarityAggregateProgression(mongoURI):
"""
Tests that decreasing similarity thresholds return increasing result lists. This
test will modify your local MongoDB instance.
"""
db_python = utils.setupPythonDB('data/test_data/first_200.props.sdf')
if mongoURI == 'local':
db_mongo = utils.setupMongoDB()
else:
db_mongo = utils.setupMongoDB(mongoURI)
write.WriteFromSDF(db_mongo.molecules, 'data/test_data/first_200.props.sdf')
similarity.AddMorganFingerprints(db_mongo.molecules, db_mongo.mfp_counts)
thresholds = [1, 0.8, 0.6, 0.4, 0.2]
for i in range(200):
mol = Chem.Mol(db_python[i]['rdmol'])
last = []
for t in thresholds:
search_mongo = similarity.SimSearchAggregate(mol, db_mongo.molecules, db_mongo.mfp_counts, t)
assert len(search_mongo) >= len(last)
assert (all(l in search_mongo for l in last))
last = search_mongo
def test_similarityAccuracyAggregate(mongoURI):
"""
Tests for basic accuracy against a brute-force constructed Python 'database'
at thresholds 0.2, 0.4, 0.6, 0.8, and 1. This test is relatively long and
will modify your local MongoDB instance.
"""
db_python = utils.setupPythonDB('data/test_data/first_200.props.sdf')
if mongoURI == 'local':
db_mongo = utils.setupMongoDB()
else:
db_mongo = utils.setupMongoDB(mongoURI)
write.WriteFromSDF(db_mongo.molecules, 'data/test_data/first_200.props.sdf')
similarity.AddMorganFingerprints(db_mongo.molecules, db_mongo.mfp_counts)
thresholds = [0.2, 0.4, 0.6, 0.8, 1]
counter = 0
for t in thresholds:
for i in range(200):
mol = Chem.Mol(db_python[i]['rdmol'])
search_python = utils.similaritySearchPython(mol, db_python, t)
search_mongo_aggregate = similarity.SimSearchAggregate(mol, db_mongo.molecules, db_mongo.mfp_counts, t)
assert sorted(search_python) == sorted(search_mongo_aggregate)
print(counter)
counter += 1
def test_similarity_accuracy_LSH(mongoURI):
db_python = utils.setupPythonDB('data/test_data/first_200.props.sdf')
if mongoURI == 'local':
db_mongo = utils.setupMongoDB()
else:
db_mongo = utils.setupMongoDB(mongoURI)
write.WriteFromSDF(db_mongo.molecules, 'data/test_data/first_200.props.sdf')
similarity.AddMorganFingerprints(db_mongo.molecules, db_mongo.mfp_counts)
similarity.AddRandPermutations(db_mongo.permutations)
similarity.AddLocalityHashes(db_mongo.molecules, db_mongo.permutations, 25)
similarity.AddHashCollections(db_mongo, db_mongo.molecules)
thresholds = [1, 0.8, 0.6, 0.4, 0.2]
counter = 0
for t in thresholds:
for i in range(200):
mol = Chem.Mol(db_python[i]['rdmol'])
smiles = Chem.MolToSmiles(mol)
search_python = [result[1] for result in utils.similaritySearchPython(mol, db_python, t)]
search_mongo_LSH = [result[1] for result in
similarity.SimSearchLSH(mol, db_mongo, db_mongo.molecules, db_mongo.permutations, db_mongo.mfp_counts, t)]
assert set(search_mongo_LSH).issubset(search_python)
print(counter)
counter += 1
def test_addPatternFingerprints():
db = utils.setupMockDB()
write.WriteFromSDF(db.molecules, 'data/test_data/first_200.props.sdf')
substructure.AddPatternFingerprints(db.molecules)
counter = 0
assert db.molecules.count_documents({"fingerprints.pattern_fp": {"$exists": True}}) == 200