> On Mar 9, 2016, at 11:53 AM, John M <john.wilkinson...@gmail.com> wrote:
> 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:
No, I think the question is "why is there stereochemistry in these modified
adamantanes, which don't look chiral."
Indeed, Open Babel is declaring that the SMILES have undefined stereochemistry:
obabel -:'CC(C)(C)C(=O)C12CC3CC(CC(C3)C1)C2' -oinchi
==============================
*** Open Babel Warning in InChI code
#1 :Omitted undefined stereo
The key to debugging this is not in the InChI Key but in the InChI itself. I
don't know where the supposedly "undefined" stereo center is.
-Geoff
> On Mar 8, 2016, at 6:55 AM, 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
>
> <adamantaneInChIKeys.csv><obabelInchKeyfunction.py><adamantaneexamples.cml>------------------------------------------------------------------------------
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