I had a similar experience on that, and it seems the Open Babel has a problem
with
adamantane in general (i.e., unsubstituted):
obabel -:'C1C3CC2CC(CC1C2)C3' -oinchi
==============================
*** Open Babel Warning in InChI code
#1 :Omitted undefined stereo
InChI=1S/C10H16/c1-7-2-9-4-8(1)5-10(3-7)6-9/h7-10H,1-6H2
1 molecule converted
In my code, I had to blacklist the adamantane group to be analyzed for
chirality purposes.
On 03/09/2016 10:28 AM, Geoffrey Hutchison wrote:
>> On Mar 9, 2016, at 11:53 AM, John M <john.wilkinson...@gmail.com
>> <mailto: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
>> <mailto: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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Structural and Computational Biology,
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112A
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