Package rdkit :: Package Chem :: Package Scaffolds :: Module MurckoScaffold

Module MurckoScaffold


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]')