def test20NoneHandling(self):
with self.assertRaises(ValueError):
rdMolStandardize.ChargeParent(None)
with self.assertRaises(ValueError):
rdMolStandardize.Cleanup(None)
with self.assertRaises(ValueError):
rdMolStandardize.FragmentParent(None)
with self.assertRaises(ValueError):
rdMolStandardize.Normalize(None)
with self.assertRaises(ValueError):
rdMolStandardize.Reionize(None)
def standardize_mol(mol):
"""
Standardize molecule.
Parameters
----------
mol : rdkit.Chem.rdchem.Mol
Molecule.
Returns
-------
rdkit.Chem.rdchem.Mol or None
Standardized molecule or None if standardization failed.
"""
try:
# sanitize molecule
Chem.SanitizeMol(mol)
# remove non-explicit hydrogens
mol = Chem.RemoveHs(mol)
# disconnect metals from molecule
mol = rdMolStandardize.MetalDisconnector().Disconnect(mol)
# normalize moleucle
mol = rdMolStandardize.Normalize(mol)
# reionize molecule
mol = rdMolStandardize.Reionize(mol)
# uncharge molecule (this helps to standardize protonation states)
u = rdMolStandardize.Uncharger()
mol = u.uncharge(mol)
# assign stereochemistry
Chem.AssignStereochemistry(mol, force=True, cleanIt=True)
return mol
except Exception as e:
print(f"ERROR in standardization: {e}")
return None
def test4Reionize(self):
mol = Chem.MolFromSmiles("C1=C(C=CC(=C1)[S]([O-])=O)[S](O)(=O)=O")
nmol = rdMolStandardize.Reionize(mol)
self.assertEqual(Chem.MolToSmiles(nmol),
"O=S(O)c1ccc(S(=O)(=O)[O-])cc1")
def test21UpdateFromJSON(self):
params = rdMolStandardize.CleanupParameters()
# note: these actual parameters aren't useful... they are for testing
rdMolStandardize.UpdateParamsFromJSON(
params, """{
"normalizationData":[
{"name":"silly 1","smarts":"[Cl:1]>>[F:1]"},
{"name":"silly 2","smarts":"[Br:1]>>[F:1]"}
],
"acidbaseData":[
{"name":"-CO2H","acid":"C(=O)[OH]","base":"C(=O)[O-]"},
{"name":"phenol","acid":"c[OH]","base":"c[O-]"}
],
"fragmentData":[
{"name":"hydrogen", "smarts":"[H]"},
{"name":"fluorine", "smarts":"[F]"},
{"name":"chlorine", "smarts":"[Cl]"}
],
"tautomerTransformData":[
{"name":"1,3 (thio)keto/enol f","smarts":"[CX4!H0]-[C]=[O,S,Se,Te;X1]","bonds":"","charges":""},
{"name":"1,3 (thio)keto/enol r","smarts":"[O,S,Se,Te;X2!H0]-[C]=[C]"}
]}""")
m = Chem.MolFromSmiles("CCC=O")
te = rdMolStandardize.TautomerEnumerator(params)
tauts = [Chem.MolToSmiles(x) for x in te.Enumerate(m)]
self.assertEqual(tauts, ["CC=CO", "CCC=O"])
self.assertEqual(
Chem.MolToSmiles(rdMolStandardize.CanonicalTautomer(m, params)),
"CCC=O")
# now with defaults
te = rdMolStandardize.TautomerEnumerator()
tauts = [Chem.MolToSmiles(x) for x in te.Enumerate(m)]
self.assertEqual(tauts, ["CC=CO", "CCC=O"])
self.assertEqual(
Chem.MolToSmiles(rdMolStandardize.CanonicalTautomer(m)), "CCC=O")
m = Chem.MolFromSmiles('ClCCCBr')
nm = rdMolStandardize.Normalize(m, params)
self.assertEqual(Chem.MolToSmiles(nm), "FCCCF")
# now with defaults
nm = rdMolStandardize.Normalize(m)
self.assertEqual(Chem.MolToSmiles(nm), "ClCCCBr")
m = Chem.MolFromSmiles('c1cc([O-])cc(C(=O)O)c1')
nm = rdMolStandardize.Reionize(m, params)
self.assertEqual(Chem.MolToSmiles(nm), "O=C([O-])c1cccc(O)c1")
# now with defaults
nm = rdMolStandardize.Reionize(m)
self.assertEqual(Chem.MolToSmiles(nm), "O=C([O-])c1cccc(O)c1")
m = Chem.MolFromSmiles('C1=C(C=CC(=C1)[S]([O-])=O)[S](O)(=O)=O')
nm = rdMolStandardize.Reionize(m, params)
self.assertEqual(Chem.MolToSmiles(nm), "O=S([O-])c1ccc(S(=O)(=O)O)cc1")
# now with defaults
nm = rdMolStandardize.Reionize(m)
self.assertEqual(Chem.MolToSmiles(nm), "O=S(O)c1ccc(S(=O)(=O)[O-])cc1")
m = Chem.MolFromSmiles('[F-].[Cl-].[Br-].CC')
nm = rdMolStandardize.RemoveFragments(m, params)
self.assertEqual(Chem.MolToSmiles(nm), "CC.[Br-]")
# now with defaults
nm = rdMolStandardize.RemoveFragments(m)
self.assertEqual(Chem.MolToSmiles(nm), "CC")
