Re: [Rdkit-discuss] SDF and FindMolChiralCenters()

[Paolo T. <pao...@un...>]

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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