def test_stereochem():
parser = parse_smiles('N[C@](Br)(O)C')
parser_coords = np.array([atom.coord for atom in parser.atoms][:5])
desired_coords = np.array([[1.26597, 0.60740, -0.09729],
[-0.26307, 0.59858, -0.07141],
[-0.91282, 2.25811, 0.01409],
[-0.72365, -0.12709, 1.01313],
[-0.64392, 0.13084, -1.00380]])
assert calc_rmsd(parser_coords, desired_coords) < 0.5
parser = parse_smiles('N[C@@H](Br)(O)')
parser_coords = np.array([atom.coord for atom in parser.atoms][:4]
+ [parser.atoms[6].coord])
desired_coords = np.array([[1.26597, 0.60740, -0.09729],
[-0.26307, 0.59858, -0.07141],
[-0.72365, -0.12709, 1.01313],
[-0.91282, 2.25811, 0.01409],
[-0.64392, 0.13084, -1.00380]])
assert calc_rmsd(parser_coords, desired_coords) < 0.5
parser = parse_smiles('F/C=C/F')
parser_coords = np.array([atom.coord for atom in parser.atoms])
desired_coords = np.array([[-4.14679, 1.36072, 0.92663],
[-3.58807, 1.44785, -0.00000],
[-2.26409, 1.31952, 0.00000],
[-1.70538, 1.40665, -0.92663],
[-4.11965, 1.64066, -0.92663],
[-1.73251, 1.12671, 0.92663]])
assert calc_rmsd(parser_coords, desired_coords) < 0.5
def test_charge():
parser = parse_smiles('C[O-]')
assert parser.charge == -1
parser = parse_smiles('[O-]S(=O)([O-])=O')
assert parser.charge == -2
parser = parse_smiles('C[N-2]')
assert parser.charge == -2
def test_parse_smiles():
parser = parse_smiles('CC')
assert len(parser.atoms) == 8
assert len(parser.bonds) == 7
assert parser.stereocentres == []
assert parser.charge == 0
assert parser.n_radical_electrons == 0
with pytest.raises(InvalidSmilesString):
_ = parse_smiles('CC1')
def init_smiles(molecule, smiles):
"""
Initialise a molecule from a SMILES string
Arguments:
molecule (autode.molecule.Molecule):
smiles (str): SMILES string
"""
# Assume that the RDKit conformer generation algorithm is not okay for
# metals
molecule.rdkit_conf_gen_is_fine = False
parser = parse_smiles(smiles)
molecule.charge = parser.charge
molecule.mult = calc_multiplicity(
molecule=molecule, n_radical_electrons=parser.n_radical_electrons)
molecule.set_atoms(atoms=parser.atoms)
make_graph(molecule, bond_list=parser.bonds)
for stereocentre in parser.stereocentres:
molecule.graph.nodes[stereocentre]['stereo'] = True
for bond_index in parser.bond_order_dict.keys():
bond = parser.bonds[bond_index]
molecule.graph.edges[bond]['pi'] = True
molecule.set_atoms(atoms=get_simanl_atoms(molecule))
check_bonds(molecule, bonds=parser.bonds)
return None
def test_alt_ring_branch():
smiles = ('[H][Rh]12([C]=O)([P+](C3=CC=CC4=C3OC5=C([P+](C6=CC=CC=C6)2C7='
'CC=CC=C7)C=CC=C5C4(C)C)(C8=CC=CC=C8)C9=CC=CC=C9)CC1')
parser = parse_smiles(smiles)
# Should be valid and not raise InvalidSmilesString
assert len(parser.atoms) == 84
def test_alkene_stereochem():
parser = parse_smiles('C/C=C/C')
assert len(parser.alkene_stero_dict.keys()) > 0
parser = parse_smiles('C/C=C/C#C')
assert len(parser.alkene_stero_dict.keys()) > 0
def test_double_bonds_in_ring():
parser = parse_smiles('C1=C=C=1')
assert len(parser.bonds) == 3
assert parser.charge == 0
