def test_overlay_molecules(reference_smiles, fit_smiles, comparator):
"""Compare results to have a TanimotoCombo score bigger or smaller than 1."""
reference_molecule = read_smiles(reference_smiles)
reference_molecule = generate_conformations(reference_molecule,
max_conformations=1)
fit_molecule = read_smiles(fit_smiles)
fit_molecule = generate_conformations(fit_molecule, max_conformations=10)
score, overlay = overlay_molecules(reference_molecule, fit_molecule)
if comparator == ">":
assert score > 1
elif comparator == "<":
assert score < 1
else:
raise ValueError(
"Wrong comparator provided. Only '<' and '>' are allowed.")
def test_generate_reasonable_conformations(smiles, n_conformations_list):
"""Compare results to expected number of isomers and conformations."""
molecule = read_smiles(smiles)
conformations_ensemble = generate_reasonable_conformations(
molecule, max_conformations=5)
assert len(conformations_ensemble) == len(n_conformations_list)
for conformations, n_conformations in zip(conformations_ensemble,
n_conformations_list):
assert conformations.NumConfs() == n_conformations
def test_read_smiles(smiles, add_hydrogens, expectation, n_atoms):
"""Compare results to expected number of atoms."""
with expectation:
molecule = read_smiles(smiles, add_hydrogens)
assert molecule.NumAtoms() == n_atoms
def test_are_identical_molecules(smiles1, smiles2, identical_molecules):
"""Compare results to expected molecular identity."""
molecule1 = read_smiles(smiles1)
molecule2 = read_smiles(smiles2)
assert are_identical_molecules(molecule1, molecule2) == identical_molecules
def test_enumerate_isomeric_smiles(smiles, n_smiles):
"""Compare results to expected number of generated isomeric SMILES strings."""
molecule = read_smiles(smiles)
isomeric_smiles_representations = enumerate_isomeric_smiles(molecule)
assert len(isomeric_smiles_representations) == n_smiles
def test_generate_conformations(smiles, n_conformations):
"""Compare results to expected number of conformations."""
molecule = read_smiles(smiles)
conformations = generate_conformations(molecule, max_conformations=5)
assert conformations.NumConfs() == n_conformations
def test_generate_enantiomers(smiles, n_enantiomers):
"""Compare results to expected number of enantiomers."""
molecule = read_smiles(smiles)
enantiomers = generate_enantiomers(molecule)
assert len(enantiomers) == n_enantiomers
def test_generate_tautomers(smiles, n_tautomers):
"""Compare results to expected number of tautomers."""
molecule = read_smiles(smiles)
tautomers = generate_tautomers(molecule)
assert len(tautomers) == n_tautomers
0,
),
],
)
def test_read_electron_density(package, resource, expectation, n_grid_points):
"""Compare results to expected number of grip points in the interpreted electron density."""
with resources.path(package, resource) as path:
with expectation:
electron_density = read_electron_density(path)
assert electron_density.GetSize() == n_grid_points
@pytest.mark.parametrize(
"molecules, suffix, n_atoms_list",
[
([read_smiles("CCC")], ".sdf", [11]),
([read_smiles("CCC")], ".pdb", [11]),
([read_smiles("COCC"), read_smiles("cccccc")], ".sdf", [12, 14]),
([read_smiles("CCC"), read_smiles("cccccc")], ".pdb", [11, 14]),
],
)
def test_write_molecules(molecules, suffix, n_atoms_list):
"""Compare results to expected number of molecules and atoms in the written file."""
import tempfile
def _count_molecules(path):
with open(path) as rf:
if path.split(".")[-1] == "sdf":
return rf.read().count("\n$$$$\n")
elif path.split(".")[-1] == "pdb":
return rf.read().count("\nEND\n")