def test_MACCS(mol_list, mol_single):
rdfp = RDKitFingerprint(fingerprint_type='maccs', vector='bit')
df = rdfp.represent(mol_list)
assert df.shape == (2, 167)
assert rdfp.n_molecules_ == 2
df = rdfp.represent(mol_single)
assert df.shape == (1, 167)
assert rdfp.n_molecules_ == 1
def test_Morgan_int(mol_list, mol_single):
rdfp = RDKitFingerprint(fingerprint_type='Morgan', vector='int')
df = rdfp.represent(mol_list)
assert df.shape == (2, 84)
assert rdfp.n_molecules_ == 2
df = rdfp.represent(mol_single)
assert df.shape == (1, 44)
assert rdfp.n_molecules_ == 1
def test_hap_bit(mol_list, mol_single):
rdfp = RDKitFingerprint(fingerprint_type='hap',vector='bit')
df = rdfp.represent(mol_list)
assert df.shape == (2, 1024)
assert rdfp.n_molecules_ == 2
df = rdfp.represent(mol_single)
assert df.shape == (1, 1024)
assert rdfp.n_molecules_ == 1
def test_tt_int(mol_list, mol_single):
rdfp = RDKitFingerprint(fingerprint_type='tt', vector='int')
df = rdfp.represent(mol_list)
assert df.shape == (2, 42)
assert rdfp.n_molecules_ == 2
df = rdfp.represent(mol_single)
assert df.shape == (1, 22)
assert rdfp.n_molecules_ == 1
def test_molecules_exception(mol_list):
with pytest.raises(ValueError):
rdfp = RDKitFingerprint()
rdfp.represent(tuple(mol_list))
with pytest.raises(ValueError):
rdfp = RDKitFingerprint()
rdfp.represent('fake molecule')
def test_Morgan_bit(mol_list, mol_single):
rdfp = RDKitFingerprint(fingerprint_type='Morgan', vector='bit')
df = rdfp.represent(mol_list)
assert df.shape == (2, 1024)
assert rdfp.n_molecules_ == 2
df = rdfp.represent(mol_single)
assert df.shape == (1, 1024)
assert rdfp.n_molecules_ == 1
# kwargs
rdfp = RDKitFingerprint(fingerprint_type='Morgan', vector='bit', radius = 3,
useChirality=True, useBondTypes=True, useFeatures=True)
df = rdfp.represent(mol_list)
assert df.shape == (2, 1024)
df = rdfp.represent(mol_single)
assert df.shape == (1, 1024)
assert rdfp.n_molecules_ == 1
def test_MACCS_exception(mol_list, mol_single):
with pytest.raises(ValueError):
rdfp = RDKitFingerprint(fingerprint_type='maccs', vector='int')
df = rdfp.represent(mol_list)
def test_type_exception(mol_single):
with pytest.raises(ValueError):
rdfp = RDKitFingerprint(fingerprint_type='fake')
rdfp.represent(mol_single)
def test_vector_exception():
with pytest.raises(ValueError):
_ = RDKitFingerprint(vector='Integer')
def test_store_sparse(mol_list, setup_teardown):
rdfp = RDKitFingerprint(fingerprint_type='morgan', vector='bit')
df = rdfp.represent(mol_list)
temp_file = os.path.join(setup_teardown, 'temp.nzp')
rdfp.store_sparse(temp_file, df)
def test_tt_bit_exception(mol_single):
with pytest.raises(ValueError):
cls = RDKitFingerprint(fingerprint_type='tt', vector='bit')
cls.represent(mol_single)