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 = `[AllChem.ReactionFromSmarts('[*:1]-[!#1;D1]`...``
| murckoQ = `Chem.MolFromSmarts(murckoQ)`
| murckoPatts = `[Chem.MolFromSmarts(x) for x in murckoPatts]`
| aromaticNTransform = `AllChem.ReactionFromSmarts('[n:1]-[D1]>>[`...``

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:

      [AllChem.ReactionFromSmarts('[*:1]-[!#1;D1]>>[*:1][H]'), AllChem.React
      ionFromSmarts('[*:1]-[!#1;D2]#[AD1]>>[*:1][H]'), AllChem.ReactionFromS
      marts('[*:1]-[!#1;D2]=[AD1]>>[*:1][H]'), AllChem.ReactionFromSmarts('[
      *:1]-[!#1;D3](=[AD1])=[AD1]>>[*:1][H]')]

### aromaticNTransform

Value:

      AllChem.ReactionFromSmarts('[n:1]-[D1]>>[nH:1]')