rdkit.Chem.Scaffolds.MurckoScaffold module — The RDKit 2016.09.1 documentation

# 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'