def check_mol_rdkit(self, clean=False):
"""
Checks validity of rdmol molecule against internal rules
Valence electrons
Bond order
Charge
Fragments
Args:
self: aemol object
rdmol: rdkit molecule object
Returns:
if clean = True: returns cleaned molecule
else: returns null
"""
if self.rdmol == None:
self.to_rdkit()
rdkit_vm = mol_std.RDKitValidation()
molvs_vm = mol_std.MolVSValidation()
rdkit_vm.validate(self.rdmol)
molvs_vm.validate(self.rdmol)
if clean:
lfc = mol_stf.LargestFragmentChooser()
idx = self.rdmol.GetProp('_Name')
self.rdmol = lfc.choose(rself.rdmol)
mol_std.Cleanup(self.rdmol)
self.rdmol.SetProp('_Name', idx)
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_format(mol):
"""Clean up molecule and return in standardized format
"""
mol = rdMolStandardize.Cleanup(mol)
mol = get_biggest_component(mol)
uncharger = rdMolStandardize.Uncharger()
mol = uncharger.uncharge(mol)
remove_isotopes(mol)
return mol
def standardize(mol, neutralize, fragment):
"""
:param mol: The molecule to standardize
:param neutralize: Boolean for whether to neutralize the molecule
:param fragment: The approach for choosing the largest fragment. Either 'hac' or 'mw'. If not specified the whole
molecule is used.
:return: The standardized molecule
"""
mol = rdMolStandardize.Cleanup(mol)
#mol = lfc.choose(mol)
# We use our own largest fragment picker as the RDKit one behaves slightly differently
if fragment:
mol = mol_utils.fragment(mol, fragment)
if neutralize:
mol = uncharger.uncharge(mol)
return mol
def test1Cleanup(self):
mol = Chem.MolFromSmiles("CCC(=O)O[Na]")
nmol = rdMolStandardize.Cleanup(mol)
self.assertEqual(Chem.MolToSmiles(nmol), "CCC(=O)[O-].[Na+]")
def standardize(mol):
mol = rdMolStandardize.Cleanup(mol)
mol = fragment(mol)
mol = uncharger.uncharge(mol)
remove_isotopes(mol)
return mol
