Dear Jean-Marc,
as lactic2.sdf is a 3D structure which does not carry any
stereochemistry information in the SDF file, you will need to perceive
stereochemistry from the 3D structure with
Chem.AssignAtomChiralTagsFromStructure(mol)
before calling Chem.AssignStereochemistry().
It looks like allHsExplicit=True prevents SMILES chirality
specifications from being output:
In [1]: from rdkit import Chem
In [2]: molfilename = "lactic2.sdf"
In [3]: mol = Chem.SDMolSupplier(molfilename, removeHs = False)[0]
In [4]: Chem.AssignAtomChiralTagsFromStructure(mol)
In [5]: Chem.AssignStereochemistry(mol, cleanIt=False, force=False,
flagPossibleStereoCenters=True)
In [6]: chiralAtoms = [a for a in mol.GetAtoms() if
a.HasProp("_ChiralityPossible")]
In [7]: chiralAtomNums = [a.GetIdx()+1 for a in chiralAtoms]
In [8]: chiralAtomNums
Out[8]: [4]
In [9]: configs = [a.GetProp("_CIPCode") for a in chiralAtoms]
In [10]: configs
Out[10]: ['S']
In [11]: smi = Chem.MolToSmiles(mol, isomericSmiles=True)
In [12]: smi
Out[12]: '[H]OC(=O)[C@@]([H])(O[H])C([H])([H])[H]'
In [13]: smi = Chem.MolToSmiles(mol, isomericSmiles=True,
allHsExplicit=True)
In [14]: smi
Out[14]: '[H][O][C](=[O])[C]([H])([O][H])[C]([H])([H])[H]'
Cheers,
p.
On 12/18/2016 11:29 PM, Jean-Marc Nuzillard wrote:
Hi again,
When I run:
#------------
from rdkit import Chem
molfilename = "lactic2.sdf"
mol = Chem.SDMolSupplier(molfilename, removeHs = False)[0]
Chem.AssignStereochemistry(mol, cleanIt=False, force=False,
flagPossibleStereoCenters=True)
chiralAtoms = [a for a in mol.GetAtoms() if
a.HasProp("_ChiralityPossible")]
chiralAtomNums = [a.GetIdx()+1 for a in chiralAtoms]
print "chiral centers: ",
print chiralAtomNums
configs = [a.GetProp("_CIPCode") for a in chiralAtoms]
print configs
smi = Chem.MolToSmiles(mol, isomericSmiles=True, allHsExplicit=True)
print smi
#------------
Two (related?) problems arise.
First, _CIPCode rises a KeyError, even for atoms for which
_ChiralityPossible is defined.
When I comment the lines that define and print the configs variable,
the second problem arises.
The string smi does not contain any '@' or '@@', something I expected
from a chiral molecule
for an isomeric smiles string.
The attached lactic2.sdf file comes from PubChem. I removed (set to 0)
the parity flag for atom 4 (index 3)
because there are no parity flags in the files I will have to deal
with later.
Keeping the parity flag does not change anything.
What did I miss?
All the best,
Jean-Marc
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