rdkit.Chem.Scaffolds.MurckoScaffold module

Generation of Murcko scaffolds from a molecule

rdkit.Chem.Scaffolds.MurckoScaffold.GetScaffoldForMol(mol)

Return molecule object containing scaffold of mol

>>> m = Chem.MolFromSmiles('Cc1ccccc1')
>>> GetScaffoldForMol(m)
<rdkit.Chem.rdchem.Mol object at 0x...>
>>> Chem.MolToSmiles(GetScaffoldForMol(m))
'c1ccccc1'

>>> m = Chem.MolFromSmiles('Cc1cc(Oc2nccc(CCC)c2)ccc1')
>>> Chem.MolToSmiles(GetScaffoldForMol(m))
'c1ccc(Oc2ccccn2)cc1'

rdkit.Chem.Scaffolds.MurckoScaffold.MakeScaffoldGeneric(mol)

Makes a Murcko scaffold generic (i.e. all atom types->C and all bonds ->single

>>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles('c1ccccc1')))
'C1CCCCC1'
>>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles('c1ncccc1')))
'C1CCCCC1'

The following were associated with sf.net issue 246 >>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles(‘c1[nH]ccc1’))) ‘C1CCCC1’ >>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles(‘C1[NH2+]C1’))) ‘C1CC1’ >>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles(‘C1[C@](Cl)(F)O1’))) ‘CC1(C)CC1’

rdkit.Chem.Scaffolds.MurckoScaffold.MurckoScaffoldSmiles(smiles=None, mol=None, includeChirality=False)

Returns MurckScaffold Smiles from smiles

>>> MurckoScaffoldSmiles('Cc1cc(Oc2nccc(CCC)c2)ccc1')
'c1ccc(Oc2ccccn2)cc1'

>>> MurckoScaffoldSmiles(mol=Chem.MolFromSmiles('Cc1cc(Oc2nccc(CCC)c2)ccc1'))
'c1ccc(Oc2ccccn2)cc1'

rdkit.Chem.Scaffolds.MurckoScaffold.MurckoScaffoldSmilesFromSmiles(smiles, includeChirality=False)

Returns MurckScaffold Smiles from smiles

>>> MurckoScaffoldSmilesFromSmiles('Cc1cc(Oc2nccc(CCC)c2)ccc1')
'c1ccc(Oc2ccccn2)cc1'