Hi,
I think this is pretty easy to explain but just to clarify, you converted
SMILES to SDF/CML with 3D coordinates? If you're input didn't have
stereochemistry before this conversion it will always have it defined
after. A simpler example of butan-2-ol demonstrates this:
> obabel -:'CCC(C)O' -osdf --gen3d | obabel -isdf -osmi
> 1 molecule converted
> CC[C@@H](C)O
> obabel -:'CCC(C)O' -osdf | obabel -isdf -oinchikey
> ==============================
> *** Open Babel Warning in WriteMolecule
> No 2D or 3D coordinates exist. Stereochemical information will be stored
> using an Open Babel extension. To generate 2D or 3D coordinates instead use
> --gen2D or --gen3D.
> 1 molecule converted
> ==============================
> *** Open Babel Warning in InChI code
> #1 :Omitted undefined stereo
> BTANRVKWQNVYAZ-*UHFFFAOYSA*-N
> > obabel -:'CCC(C)O' -osdf --gen3d | obabel -isdf -oinchikey
> 1 molecule converted
> BTANRVKWQNVYAZ-*SCSAIBSYSA*-N
What's more fun is I can get a different key by changing the input order:
> obabel -:'CCC(O)C' -osdf --gen3d | obabel -isdf -oinchikey
> 1 molecule converted
> BTANRVKWQNVYAZ-*BYPYZUCNSA*-N
John
Regards,
John W May
john.wilkinson...@gmail.com
On 8 March 2016 at 11:55, M.D. Driver <md...@cam.ac.uk> wrote:
> Hi,
>
> I've got a problem with the InChIKeys being generated from CML for a
> series of adamantanes. The structures attached in the cml were generated in
> torch (from a smiles string) and then converted from and sdf to CML using
> open babel. I'm trying to use the function in the python script to add the
> InChIKey of the CML to the attributes (the function takes an
> lxml.etree.Element representation of the molecule CML block as input, and
> adds the generated InChIKey). I want to be able to match these 3D
> structures to experimental data for them that is stored in xml, which uses
> the InChIKey as an id for the molecule.
>
> From the csv file the expected InChIKey and the canonicalised smiles used
> to generate it (in the columns exp_inchikey and exp_smiles respectively).
> The InChIKey that was actually generated for the cml is in the cml_inchikey
> column. The second part of the inchikey is different, and I was wondering
> why this is the case? Is it to do with some unseen stereo-chemistry that
> isn't in the smiles used to generate it, or is it to do with the options
> I'm using for the conversion or something else that I haven't thought of?
>
> Note: the expected inchikey is taken from the chemspider entry for the
> molecule.
>
> Thanks,
>
> Mark Driver
>
> PhD student
>
> University of Cambridge
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://makebettercode.com/inteldaal-eval
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
