If your file has 3D coordinates, AssignAtomChrialTagsFromStructure may help you.
Ling On Fri, Sep 9, 2016 at 3:40 PM, Paolo Tosco <paolo.to...@unito.it> 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 > listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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