Package rdkit :: Package Chem
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Package Chem

source code

A module for molecules and stuff

see Chem/index.html in the doc tree for documentation

Submodules [hide private]

Functions [hide private]
 
QuickSmartsMatch(smi, sma, unique=True, display=False) source code
 
CanonSmiles(smi, useChiral=1) source code
 
SupplierFromFilename(fileN, delim='', **kwargs) source code
 
FindMolChiralCenters(mol, force=True, includeUnassigned=False)
>>> from rdkit import Chem >>> mol = Chem.MolFromSmiles('[C@H](Cl)(F)Br') >>> FindMolChiralCenters(mol) [(0, 'R')] >>> mol = Chem.MolFromSmiles('[C@@H](Cl)(F)Br') >>> FindMolChiralCenters(mol) [(0, 'S')]
source code
 
_test() source code
Variables [hide private]
  _HasSubstructMatchStr = rdchem._HasSubstructMatchStr

Imports: rdBase, RDConfig, DataStructs, rdGeometry, pyPeriodicTable, rdchem


Function Details [hide private]

FindMolChiralCenters(mol, force=True, includeUnassigned=False)

source code 

>>> from rdkit import Chem
>>> mol = Chem.MolFromSmiles('[C@H](Cl)(F)Br')
>>> FindMolChiralCenters(mol)
[(0, 'R')]
>>> mol = Chem.MolFromSmiles('[C@@H](Cl)(F)Br')
>>> FindMolChiralCenters(mol)
[(0, 'S')]

>>> FindMolChiralCenters(Chem.MolFromSmiles('CCC'))
[]

By default unassigned stereo centers are not reported:
>>> mol = Chem.MolFromSmiles('C[C@H](F)C(F)(Cl)Br')
>>> FindMolChiralCenters(mol,force=True)
[(1, 'S')]

but this can be changed:
>>> FindMolChiralCenters(mol,force=True,includeUnassigned=True)
[(1, 'S'), (3, '?')]

The handling of unassigned stereocenters for dependent stereochemistry is not correct:
>>> Chem.FindMolChiralCenters(Chem.MolFromSmiles('C1CC(C)C(C)C(C)C1'),includeUnassigned=True)
[(2, '?'), (6, '?')]
>>> Chem.FindMolChiralCenters(Chem.MolFromSmiles('C1C[C@H](C)C(C)[C@H](C)C1'),includeUnassigned=True)
[(2, 'S'), (4, '?'), (6, 'R')]