rdkit.Chem.Scaffolds.MurckoScaffold

Package rdkit :: Package Chem :: Package Scaffolds :: Module MurckoScaffold |
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# Module MurckoScaffold

source code

    Generation of Murcko scaffolds from a molecule

Functions | [hide private]
MakeScaffoldGeneric(mol) Makes a Murcko scaffold generic (i.e. | source code
GetScaffoldForMol(mol) Return molecule object containing scaffold of mol | source code
_pyGetScaffoldForMol(mol) | source code
MurckoScaffoldSmilesFromSmiles(smiles, includeChirality=False) Returns MurckScaffold Smiles from smiles | source code
MurckoScaffoldSmiles(smiles=None, mol=None, includeChirality=False) Returns MurckScaffold Smiles from smiles | source code
_test() | source code

Variables | [hide private]
| murckoTransforms = ``[`<rdkit.Chem.rdChemReactions.ChemicalReacti`...``
| murckoQ = `<rdkit.Chem.rdchem.Mol object>`
| murckoPatts = ``[`<rdkit.Chem.rdchem.Mol object>`,` <rdkit.Chem.rdc`...``
| aromaticNTransform = `<rdkit.Chem.rdChemReactions.ChemicalReact`...``
| __package__ = ``'``rdkit.Chem.Scaffolds``'``
| x = ``'``[!#1;D1;$([D1]-[!#1;!n])]``'``

Imports: Chem, AllChem

Function Details | [hide private]

### MakeScaffoldGeneric(mol) | source code
    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'

### GetScaffoldForMol(mol) | source code
    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'

### MurckoScaffoldSmilesFromSmiles(smiles, includeChirality=False) | source code
    Returns MurckScaffold Smiles from smiles

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

### MurckoScaffoldSmiles(smiles=None, mol=None, includeChirality=False) | source code
    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'

Variables Details | [hide private]

  ### murckoTransforms Value:
      [<rdkit.Chem.rdChemReactions.ChemicalReaction object>,
       <rdkit.Chem.rdChemReactions.ChemicalReaction object>,
       <rdkit.Chem.rdChemReactions.ChemicalReaction object>,
       <rdkit.Chem.rdChemReactions.ChemicalReaction object>]

  ### murckoPatts Value:
      [<rdkit.Chem.rdchem.Mol object>,
       <rdkit.Chem.rdchem.Mol object>,
       <rdkit.Chem.rdchem.Mol object>]

  ### aromaticNTransform Value:
      <rdkit.Chem.rdChemReactions.ChemicalReaction object>