def test_formal_charge(self):
"""Test formal charge"""
mol_1 = chemi.smiles_to_oemol('c1cc(c[nH+]c1)c2ccncn2')
charge = chemi.get_charge(mol_1)
self.assertEqual(charge, 1)
mol_2 = chemi.smiles_to_oemol('C[NH+]1CC[NH+](CC1)Cc2ccccc2')
charge = chemi.get_charge(mol_2)
self.assertEqual(charge, 2)
mol_3 = chemi.smiles_to_oemol('CCC(C)(C)C(=O)[O-]')
charge = chemi.get_charge(mol_3)
self.assertEqual(charge, -1)
def test_expand_tautomers():
from openeye import oechem
imidazol_smiles = 'CC1=CN=CN1'
oemol = oechem.OEMol()
oechem.OESmilesToMol(oemol, imidazol_smiles)
tautomers = fragmenter.states._enumerate_tautomers(oemol)
assert len(tautomers) == 2
for tau in tautomers:
assert chemi.get_charge(tau) == 0
salsalate = 'OC(=O)C1=CC=CC=C1OC(=O)C1=CC=CC=C1O'
oemol = oechem.OEMol()
oechem.OESmilesToMol(oemol, salsalate)
tautomers = fragmenter.states._enumerate_tautomers(oemol)
assert len(tautomers) == 1
assert chemi.get_charge(tautomers[0]) == -1
]
if max(scores[b]) > 0.001:
selected_bond = utils.deserialize_bond(b)
selected_bonds.append(selected_bond)
with open('validation_set/{}/{}_oe_wbo_with_score.json'.format(name, name),
'r') as f:
frags = json.load(f)
for bo in frags:
for f in frags[bo]:
if 'parent' in f:
parent_smiles = frags[bo][f]["map_to_parent"]
# parent_smiles = f.split('_')[0]
parent_mol = oechem.OEMol()
oechem.OESmilesToMol(parent_mol, parent_smiles)
# Get charge
charge = chemi.get_charge(parent_mol)
parent_mol.SetTitle(name)
break
break
max_scores.append(
(max_score, name, charge, parent_mol, selected_bonds, parent_smiles))
print(len(max_scores))
# sort mol and visualize top 50 molecules.
sorted_scores = sorted(max_scores, reverse=True)
sorted_mols = [i[3] for i in sorted_scores[:100]]
sorted_bonds = [i[4] for i in sorted_scores[:100]]
sorted_smiles = [i[5] for i in sorted_scores[:100]]
chemi.to_pdf(sorted_mols,
fname='selected_validation_set.pdf',
def test_get_charge(smiles, charge):
mol = chemi.smiles_to_oemol(smiles)
assert chemi.get_charge(mol) == charge