Dear Dimitri,
the MOL reader perceives chirality based on the bond stereo field of the
bond block. Instead the atom stereo parity value of the atom block is
read and stored in the "molParity" atom property, but it is ignored for
the purpose of chirality perception, as per the MOL file specs:
http://c4.cabrillo.edu/404/ctfile.pdf (see in particular Figure 4)
Therefore, if the MOL file lacks the bond stereo information chirality
won't be set.
This Jupyter notebook exemplifies the above:
https://gist.github.com/ptosco/abbab6e39f9d3bd03676f06ecd331bd9#file-bondstereo-ipynb
Hope this helps,
Paolo
On 09/09/2016 22:42, Dimitri Maziuk wrote:
Hi everyone,
m = rdkit.Chem.SupplierFromFilename( filename, removeHs = False ).next()
sts = rdkit.Chem.FindMolChiralCenters( m, includeUnassigned = True )
for s in sts :
lbl = m.GetAtomWithIdx( s[0] ).GetSymbol() + str( s[0] + 1 )
print lbl, ":", s[1]
For L-ALA 3D SDF the output is
C4 : ?
For D-ALA 3D SDF the output is also
C4 : ?
And for ALA 2D SDF the output is also
C4 : ?
If I change includeUnassigned to False, the list returned by
FindMolChiralCenters() is empty.
The SDFs have 1, 2, and 3 in the 7th column in the atom block.
If I use
m = rdkit.Chem.MolFromSmiles( 'C[C@@H](C(=O)O)N' )
instead, the output is
C2 : S
(this is L-ALA from the same PubChem record as the SDF).
So it looks like MOL reader ignores chirality, is that the case?
Thanks,
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