def test_get_atom_map_mapped_smiles(toolkit):
smiles_1 = '[H]C([H])(C([H])([H])O[H])O[H]'
smiles_2 = '[H:5][C:1]([H:6])([C:2]([H:7])([H:8])[O:4][H:10])[O:3][H:9]'
mol_1 = utils.load_molecule(smiles_1, toolkit=toolkit)
if not utils.has_explicit_hydrogen(mol_1):
mol_1 = utils.add_explicit_hydrogen(mol_1)
mol_2 = utils.load_molecule(smiles_2, toolkit=toolkit)
if not utils.has_explicit_hydrogen(mol_2):
mol_2 = utils.add_explicit_hydrogen(mol_2)
def test_n_valence():
from openeye import oechem
json_molecule = {
'symbols': [
'C', 'C', 'C', 'C', 'C', 'C', 'N', 'N', 'N', 'N', 'N', 'H', 'H',
'H', 'H'
],
'geometry':
np.array([
11.02088236, 0.30802536, 2.96687012, 10.37270642, 2.8383686,
2.75522059, 9.32012957, -1.48532476, 2.09948562, 8.06346176,
3.48843435, 1.68941515, 6.98820713, -0.772898, 1.02801107,
5.21186447, -2.73065435, 0.12850138, 5.70508328, -5.1797392,
0.28345893, 6.45152507, 1.7536658, 0.86549457, 2.97820833,
-2.31491455, -0.90706852, 3.71709131, -6.31357514, -0.68408084,
2.05980154, -4.57124733, -1.40784597, 12.76887939, -0.24566439,
3.77189345, 11.61992628, 4.26322222, 3.39583795, 9.76610505,
-3.43174262, 2.23743576, 7.53811768, 5.41217579, 1.50989122
]),
'connectivity':
[[0, 1, 1], [0, 2, 2], [0, 11, 1], [1, 3, 2], [1, 12, 1], [2, 4, 1],
[2, 13, 1], [3, 7, 1], [3, 14, 1], [4, 5, 1], [4, 7, 2], [5, 6, 1],
[5, 8, 2], [6, 9, 1], [8, 10, 1], [9, 10, 2]]
}
mol = utils.load_molecule(json_molecule)
assert utils.has_explicit_hydrogen(mol)
assert oechem.OEMolToSmiles(mol) == 'c1ccnc(c1)c2[n-]nnn2'
def test_atom_order_in_mol_copy(toolkit, smiles):
"""Test that atom orders do not change when copying molecule"""
import copy
mol = utils.load_molecule(smiles, toolkit=toolkit)
if not utils.has_explicit_hydrogen(mol):
mol = utils.add_explicit_hydrogen(mol)
molcopy = copy.deepcopy(mol)
for a1, a2 in zip(mol.GetAtoms(), molcopy.GetAtoms()):
if toolkit == 'openeye':
assert a1.GetIdx() == a2.GetIdx()
assert a1.GetName() == a2.GetName()
assert a1.GetMapIdx() == a2.GetMapIdx()
if toolkit == 'rdkit':
assert a1.GetIdx() == a2.GetIdx()
assert a1.GetAtomMapNum() == a2.GetAtomMapNum()
assert a1.GetSmarts() == a2.GetSmarts()
def test_atom_map(smiles):
"""Test that atom map orders geometry the same way every time no matter the SMILES used to create the molecule"""
import cmiles
mapped_smiles = '[H:5][C:1]([H:6])([C:2]([H:7])([H:8])[O:4][H:10])[O:3][H:9]'
mol_id_oe = cmiles.get_molecule_ids(mapped_smiles, toolkit='openeye')
oemol = utils.load_molecule(mapped_smiles, toolkit='openeye')
mapped_symbols = ['C', 'C', 'O', 'O', 'H', 'H', 'H', 'H', 'H', 'H']
mapped_geometry = [
-1.6887193912042044, 0.8515190939276903, 0.8344587822904272,
-4.05544806361675, -0.3658269566455062, -0.22848169646448416,
-1.6111611950422127, 0.4463128276938808, 3.490617694146934,
-3.97756355964586, -3.0080934853087373, 0.25948499322223956,
-1.6821252026076652, 2.891135395246369, 0.4936556190978574, 0.0, 0.0,
0.0, -4.180315034973438, -0.09210893239246959, -2.2748227320305525,
-5.740516456782416, 0.4115539217904015, 0.6823267491485907,
-0.07872657410528058, 1.2476492272884379, 4.101615944163073,
-5.514569080545831, -3.7195945404657222, -0.4441653010509862
]
mol = cmiles.utils.load_molecule(smiles, toolkit='openeye')
if not utils.has_explicit_hydrogen(mol):
mol = utils.add_explicit_hydrogen(mol)
atom_map = utils.get_atom_map(mol, mapped_smiles=mapped_smiles)
# use the atom map to add coordinates to molecule. First reorder mapped geometry to order in molecule
mapped_coords = np.array(mapped_geometry, dtype=float).reshape(
int(len(mapped_geometry) / 3), 3)
coords = np.zeros((mapped_coords.shape))
for m in atom_map:
coords[atom_map[m]] = mapped_coords[m - 1]
# flatten
coords = coords.flatten()
# convert to Angstroms
coords = coords * utils.BOHR_2_ANGSTROM
# set coordinates in oemol
mol.SetCoords(coords)
mol.SetDimension(3)
# Get new atom map
atom_map = utils.get_atom_map(mol, mapped_smiles)
symbols, geometry = _cmiles_oe.get_map_ordered_geometry(mol, atom_map)
assert geometry == mapped_geometry
assert symbols == mapped_symbols
def test_explicit_h_oe(input, output):
"""Test input SMILES for explicit H"""
mol = utils.load_molecule(input, toolkit='openeye')
assert utils.has_explicit_hydrogen(mol) == output
def test_explicit_h(input, output, toolkit_name):
"""Test input SMILES for explicit H"""
mol = utils.load_molecule(input, toolkit=toolkit_name)
assert utils.has_explicit_hydrogen(mol) == output
