def check_2d_coords(mol, force=False):
"""Check if a mol has 2D coordinates and if not, calculate them."""
try:
mol.GetConformer()
except ValueError:
force = True # no 2D coords... calculate them
if force:
if USE_AVALON:
pyAv.Generate2DCoords(mol)
else:
mol.Compute2DCoords()
def testGitHub1062(self):
s0 = 'C/C=C\C'
m1 = Chem.MolFromSmiles(s0)
s1 = Chem.MolToSmiles(m1)
pyAvalonTools.Generate2DCoords(m1)
mb = Chem.MolToMolBlock(m1)
m2 = Chem.MolFromMolBlock(mb)
s2 = Chem.MolToSmiles(m2)
self.assertEqual(s1, s2)
# repeat the test with an input smiles that is not canonical
# to verify that the implementation is not sensitive to the
# ordering of atoms
s0 = 'C/C=C(F)\C'
m1 = Chem.MolFromSmiles(s0)
s1 = Chem.MolToSmiles(m1)
self.assertNotEqual(s1, s0)
pyAvalonTools.Generate2DCoords(m1)
mb = Chem.MolToMolBlock(m1)
m2 = Chem.MolFromMolBlock(mb)
s2 = Chem.MolToSmiles(m2)
self.assertEqual(s1, s2)
def test6(self):
mb = pyAvalonTools.Generate2DCoords('c1ccccc1C1(CC1)N', True)
m = Chem.MolFromMolBlock(mb)
self.assertEqual(m.GetNumConformers(), 1)
self.assertTrue(m.GetConformer(0).Is3D() == False)
def test5(self):
m = Chem.MolFromSmiles('c1ccccc1C1(CC1)N')
pyAvalonTools.Generate2DCoords(m)
self.assertEqual(m.GetNumConformers(), 1)
self.assertTrue(m.GetConformer(0).Is3D() == False)
