def test_preserve_H():
smiles = "[H]C([H])([H])Oc1ccccc1"
mol = Molecule(smiles)
assert mol.smiles == "COc1ccccc1"
mol = Molecule(smiles, preserve_H=True)
assert mol.smiles == smiles
def test_mol_from_smiles():
mol = Molecule(CANONICAL_SMILES)
assert mol.smiles == CANONICAL_SMILES
mol = Molecule(SMILES)
assert mol.smiles == CANONICAL_SMILES
def test_get_substructure_match():
mol = Molecule("OC1=CC2=C(NC=C2)C=C1")
mol.get_substructure_match("c1ccccc1")
assert mol._rdkit.__sssAtoms == [1, 2, 3, 4, 8, 9]
assert mol._rdkit.__sssBonds == [1, 2, 3, 7, 8, 9]
def test_highlight_aromatics():
mol = Molecule("OC1=CC2=C(NC=C2)C=C1")
mol.highlight_aromatics()
assert mol._rdkit.__sssAtoms == [9, 1, 8, 9, 4, 8, 3, 4, 2, 3, 1, 2, 3, 4]
assert mol._rdkit.__sssBonds == [9, 8, 7, 3, 2, 1, 3]
def test__repr_svg_(shared_datadir):
svg = Molecule(CANONICAL_SMILES)._repr_svg_()
assert svg == (shared_datadir / "mol.svg").read_text()
def test_smiles_kekulized():
mol = Molecule(CANONICAL_SMILES)
assert mol.smiles_kekulized == "OC1=CC=C2NC=CC2=C1"
def test_aromaticity():
mol_default = Molecule(CANONICAL_SMILES)
mol_aromat_simple = Molecule(CANONICAL_SMILES, aromaticity="simple")
assert mol_default != mol_aromat_simple
def test_mol_from_rdkit():
mol_rdkit = Chem.MolFromSmiles(SMILES)
mol = Molecule.from_rdkit(mol_rdkit)
assert mol.smiles == CANONICAL_SMILES
def test_equal():
assert Molecule(CANONICAL_SMILES) == Molecule(SMILES)
assert Molecule(CANONICAL_SMILES) != Molecule(OTHER_SMILES)
assert Molecule(SMILES) != SMILES