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

[Ling C. <lin...@gm...>]

If your file has 3D coordinates, AssignAtomChrialTagsFromStructure may help
you.

Ling

On Fri, Sep 9, 2016 at 3:40 PM, Paolo Tosco <pao...@un...> wrote:

> 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/abbab6e39f9d3bd03676f06ecd331b
> d9#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,
>
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Rdkit-discuss mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>