def test_isomer_scoring_function_returns_one_for_correct_molecule():
c11h24 = IsomerScoringFunction('C11H24')
# all those smiles fit the formula C11H24
smiles1 = 'CCCCCCCCCCC'
smiles2 = 'CC(CCC)CCCCCC'
smiles3 = 'CCCCC(CC(C)CC)C'
assert c11h24.score(smiles1) == 1.0
assert c11h24.score(smiles2) == 1.0
assert c11h24.score(smiles3) == 1.0
def test_isomer_scoring_function_penalizes_incorrect_number_atoms():
c11h24 = IsomerScoringFunction('C12H24')
# all those smiles fit the formula C11H24O
smiles1 = 'CCCCCCCCOCCC'
smiles2 = 'CC(CCOC)CCCCCC'
smiles3 = 'COCCCC(CC(C)CC)C'
# the penalty corresponds to a deviation of 1.0 from the gaussian modifier in the number of C atoms
penalty_tot_num_atoms = 1.0 - GaussianModifier(mu=0, sigma=1)(1.0)
expected_score = 1.0 - penalty_tot_num_atoms / 3.0
assert c11h24.score(smiles1) == pytest.approx(expected_score)
assert c11h24.score(smiles2) == pytest.approx(expected_score)
assert c11h24.score(smiles3) == pytest.approx(expected_score)
def test_isomer_scoring_function_returns_one_for_correct_molecule():
c11h24_arithmetic = IsomerScoringFunction('C11H24',
mean_function='arithmetic')
c11h24_geometric = IsomerScoringFunction('C11H24',
mean_function='geometric')
# all those smiles fit the formula C11H24
smiles1 = 'CCCCCCCCCCC'
smiles2 = 'CC(CCC)CCCCCC'
smiles3 = 'CCCCC(CC(C)CC)C'
assert c11h24_arithmetic.score(smiles1) == 1.0
assert c11h24_arithmetic.score(smiles2) == 1.0
assert c11h24_arithmetic.score(smiles3) == 1.0
assert c11h24_geometric.score(smiles1) == 1.0
assert c11h24_geometric.score(smiles2) == 1.0
assert c11h24_geometric.score(smiles3) == 1.0
def test_isomer_scoring_function_penalizes_incorrect_number_atoms():
c11h24_arithmetic = IsomerScoringFunction('C12H24',
mean_function='arithmetic')
c11h24_geometric = IsomerScoringFunction('C12H24',
mean_function='geometric')
# all those smiles fit the formula C11H24O
smiles1 = 'CCCCCCCCOCCC'
smiles2 = 'CC(CCOC)CCCCCC'
smiles3 = 'COCCCC(CC(C)CC)C'
# the penalty corresponds to a deviation of 1.0 from the gaussian modifier in the number of C atoms
c_score = GaussianModifier(mu=0, sigma=1)(1.0)
n_atoms_score = 1.0
h_score = 1.0
expected_score_arithmetic = (n_atoms_score + c_score + h_score) / 3.0
expected_score_geometric = (n_atoms_score * c_score * h_score)**(1 / 3)
assert c11h24_arithmetic.score(smiles1) == pytest.approx(
expected_score_arithmetic)
assert c11h24_arithmetic.score(smiles2) == pytest.approx(
expected_score_arithmetic)
assert c11h24_arithmetic.score(smiles3) == pytest.approx(
expected_score_arithmetic)
assert c11h24_geometric.score(smiles1) == pytest.approx(
expected_score_geometric)
assert c11h24_geometric.score(smiles2) == pytest.approx(
expected_score_geometric)
assert c11h24_geometric.score(smiles3) == pytest.approx(
expected_score_geometric)
def test_isomer_scoring_function_invalid_molecule():
sf = IsomerScoringFunction('C60')
assert sf.score('CCCinvalid') == sf.corrupt_score