def test_divide_smiles():
parser = SmilesParser()
divided_smiles = list(parser.divide_smiles('CCl=[](())/C1=2'))
assert divided_smiles == [('C', 'atom'), ('Cl', 'atom'), ('=', 'bond'),
('[]', 'bracket_atom'), ('(())', 'branch'),
('/', 'double_bond_stereochem'),
('C1=2', 'atom')]
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 = SmilesParser()
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_add_atom():
parser = SmilesParser()
parser.add_atom('C')
assert parser.add_atom('Cl1') == '1'
assert parser.bonds == [(0, 1)]
assert parser.atoms[0].label == 'C'
assert np.allclose(parser.atoms[0].coord, [0, 0, 0])
assert parser.atoms[1].label == 'Cl'
def test_alt_ring_branch():
parser = SmilesParser()
parser.parse_smiles(
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')
# Should be valid and not raise InvalidSmilesString
assert len(parser.atoms) == 84
def test_analyse_atom_details():
parser = SmilesParser()
parser.add_atom('C')
parser.analyse_atom_details('H+2@')
assert parser.charge_dict[0] == 2
assert parser.hydrogen_dict[0] == 1
assert parser.stereochem_dict[0] == '@td'
parser.add_atom('C')
parser.analyse_atom_details('-2@@')
assert parser.charge_dict[1] == -2
assert parser.hydrogen_dict[1] == 0
assert parser.stereochem_dict[1] == '@@td'
def test_parse_smiles():
parser = SmilesParser()
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):
parser.parse_smiles('CC1')
def test_add_hs():
parser = SmilesParser()
parser.add_atom('C')
parser.analyse_atom_details('H2')
parser.add_atom('C')
parser.add_atom('C')
parser.bond_order_dict[1] = 2
parser.add_hs()
assert len(parser.atoms) == 8
assert len(parser.bonds) == 7
assert parser.n_radical_electrons == 1
def test_analyse_bond_ring_string():
parser = SmilesParser()
parser.analyse_bond_ring_string('=1')
assert parser.ring_dict[1] == (0, 2)
parser.prev_atom_no = 2
parser.analyse_bond_ring_string('1')
assert parser.bonds == [(0, 2)]
assert parser.ring_dict == {}
parser.analyse_bond_ring_string('23')
assert parser.ring_dict[2] == (2, None)
assert parser.ring_dict[3] == (2, None)
parser.prev_atom_no = 5
parser.analyse_bond_ring_string('%15')
assert parser.ring_dict[15] == (5, None)
def test_analyse_char():
parser = SmilesParser()
parser.analyse_char('C', 'atom')
assert parser.atoms[0].label == 'C'
assert len(parser.ring_dict) == 0
parser.analyse_char('[C+]', 'bracket_atom')
assert parser.atoms[1].label == 'C'
assert parser.charge_dict[1] == 1
parser.analyse_char('(C)', 'branch')
assert parser.bonds[1] == (1, 2)
assert parser.prev_atom_no == 1
parser.analyse_char('=', 'bond')
assert parser.bond_order_dict[2] == 2
parser.analyse_char('/', 'double_bond_stereochem')
assert parser.alkene_stereochem_dict[3] == '/'
def test_stereochem():
parser = SmilesParser()
parser.parse_smiles('N[C@](Br)(O)C')
parser_coords = [atom.coord for atom in parser.atoms][:5]
desired_coords = [[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 = SmilesParser()
parser.parse_smiles('N[C@@H](Br)(O)')
parser_coords = [atom.coord
for atom in parser.atoms][:4] + [parser.atoms[6].coord]
desired_coords = [[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 = SmilesParser()
parser.parse_smiles('F/C=C/F')
parser_coords = [atom.coord for atom in parser.atoms]
desired_coords = [[-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