def detect_mixtures(mol, *args, **kwargs):
"""Detects mixtures.
Generates a SMILES out of the entered mol for validation, performs fragment
removal, turns the changed mol into another SMILES and validates it with the
first SMILES created.
Parameters
----------
mol: rdkit.Chem.Mol
The molecule which has to be searched for non-organic
substructures.
Returns
-------
boolean: bool
Returns if the stucture contains a mixture (True),
or not (False).
"""
smiles_before = _validation_smiles(mol)
mol_without_fragment = rdMolStandardize.FragmentRemover().remove(mol)
smiles_after = _validation_smiles(mol_without_fragment)
if smiles_before == smiles_after:
return False
else:
return True
def test7Fragment(self):
fragremover = rdMolStandardize.FragmentRemover()
mol = Chem.MolFromSmiles("CN(C)C.Cl.Cl.Br")
nm = fragremover.remove(mol)
self.assertEqual(Chem.MolToSmiles(nm), "CN(C)C")
lfragchooser = rdMolStandardize.LargestFragmentChooser()
mol2 = Chem.MolFromSmiles("[N+](=O)([O-])[O-].[CH3+]")
nm2 = lfragchooser.choose(mol2)
self.assertEqual(Chem.MolToSmiles(nm2), "O=[N+]([O-])[O-]")
lfragchooser2 = rdMolStandardize.LargestFragmentChooser(
preferOrganic=True)
nm3 = lfragchooser2.choose(mol2)
self.assertEqual(Chem.MolToSmiles(nm3), "[CH3+]")
fragremover = rdMolStandardize.FragmentRemover(skip_if_all_match=True)
mol = Chem.MolFromSmiles("[Na+].Cl.Cl.Br")
nm = fragremover.remove(mol)
self.assertEqual(nm.GetNumAtoms(), mol.GetNumAtoms())
def remove_fragments(mol):
"""Filters out fragments.
A predefined list contains numerous known fragments which can be
filtered out.
Parameters
----------
mol: rdkit.Chem.Mol
A molecule with various fragments.
Returns
-------
mol: rdkit.Chem.Mol
Returns a molecule filtered from known fragments.
Notes
-----
The predefined list containing fragments is a list REMOVE_FRAGMENTS
saved in rdkit/Chem/MolStandardize/fragments.py
"""
return rdMolStandardize.FragmentRemover().remove(mol)
def test7Fragment(self):
fragremover = rdMolStandardize.FragmentRemover()
mol = Chem.MolFromSmiles("CN(C)C.Cl.Cl.Br")
nm = fragremover.remove(mol)
self.assertEqual(Chem.MolToSmiles(nm), "CN(C)C")
lfragchooser = rdMolStandardize.LargestFragmentChooser()
mol2 = Chem.MolFromSmiles("[N+](=O)([O-])[O-].[CH3+]")
nm2 = lfragchooser.choose(mol2)
self.assertEqual(Chem.MolToSmiles(nm2), "O=[N+]([O-])[O-]")
lfragchooser2 = rdMolStandardize.LargestFragmentChooser(
preferOrganic=True)
nm3 = lfragchooser2.choose(mol2)
self.assertEqual(Chem.MolToSmiles(nm3), "[CH3+]")
fragremover = rdMolStandardize.FragmentRemover(skip_if_all_match=True)
mol = Chem.MolFromSmiles("[Na+].Cl.Cl.Br")
nm = fragremover.remove(mol)
self.assertEqual(nm.GetNumAtoms(), mol.GetNumAtoms())
smi3 = "CNC[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O.c1cc2c(cc1C(=O)O)oc(n2)c3cc(cc(c3)Cl)Cl"
lfParams = rdMolStandardize.CleanupParameters()
lfrag_params = rdMolStandardize.LargestFragmentChooser(lfParams)
mol3 = Chem.MolFromSmiles(smi3)
lfrag3 = lfrag_params.choose(mol3)
self.assertEqual(Chem.MolToSmiles(lfrag3),
"CNC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO")
lfParams = rdMolStandardize.CleanupParameters()
lfParams.largestFragmentChooserCountHeavyAtomsOnly = True
lfrag_params = rdMolStandardize.LargestFragmentChooser(lfParams)
mol3 = Chem.MolFromSmiles(smi3)
lfrag3 = lfrag_params.choose(mol3)
self.assertEqual(Chem.MolToSmiles(lfrag3),
"O=C(O)c1ccc2nc(-c3cc(Cl)cc(Cl)c3)oc2c1")
lfParams = rdMolStandardize.CleanupParameters()
lfParams.largestFragmentChooserUseAtomCount = False
lfrag_params = rdMolStandardize.LargestFragmentChooser(lfParams)
mol3 = Chem.MolFromSmiles(smi3)
lfrag3 = lfrag_params.choose(mol3)
self.assertEqual(Chem.MolToSmiles(lfrag3),
"O=C(O)c1ccc2nc(-c3cc(Cl)cc(Cl)c3)oc2c1")
smi4 = "CC.O=[Pb]=O"
lfParams = rdMolStandardize.CleanupParameters()
lfrag_params = rdMolStandardize.LargestFragmentChooser(lfParams)
mol4 = Chem.MolFromSmiles(smi4)
lfrag4 = lfrag_params.choose(mol4)
self.assertEqual(Chem.MolToSmiles(lfrag4), "CC")
lfParams = rdMolStandardize.CleanupParameters()
lfParams.largestFragmentChooserCountHeavyAtomsOnly = True
lfrag_params = rdMolStandardize.LargestFragmentChooser(lfParams)
mol4 = Chem.MolFromSmiles(smi4)
lfrag4 = lfrag_params.choose(mol4)
self.assertEqual(Chem.MolToSmiles(lfrag4), "O=[Pb]=O")
lfParams = rdMolStandardize.CleanupParameters()
lfParams.largestFragmentChooserUseAtomCount = False
lfrag_params = rdMolStandardize.LargestFragmentChooser(lfParams)
mol4 = Chem.MolFromSmiles(smi4)
lfrag4 = lfrag_params.choose(mol4)
self.assertEqual(Chem.MolToSmiles(lfrag4), "O=[Pb]=O")
lfParams = rdMolStandardize.CleanupParameters()
lfParams.largestFragmentChooserCountHeavyAtomsOnly = True
lfParams.preferOrganic = True
lfrag_params = rdMolStandardize.LargestFragmentChooser(lfParams)
mol4 = Chem.MolFromSmiles(smi4)
lfrag4 = lfrag_params.choose(mol4)
self.assertEqual(Chem.MolToSmiles(lfrag4), "CC")
lfParams = rdMolStandardize.CleanupParameters()
lfParams.largestFragmentChooserUseAtomCount = False
lfParams.preferOrganic = True
lfrag_params = rdMolStandardize.LargestFragmentChooser(lfParams)
mol4 = Chem.MolFromSmiles(smi4)
lfrag4 = lfrag_params.choose(mol4)
self.assertEqual(Chem.MolToSmiles(lfrag4), "CC")