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'