Try circular fingerprints. Open Babel has two: MolPrint2D and MNA. See
http://baoilleach.webfactional.com/site_media/ob-docs/FileFormats/Utility.html

NMRShiftDB uses circular fingerprints (HOSE codes to be exact) for
just this purpose. In fact, it might be worth while implementing HOSE
codes for Open Babel if you're interested in writing a new file
format.

- Noel

On 17 August 2010 12:16, Eiso AB <e...@zobio.com> wrote:
>
> hi,
>
> I'm looking for some convenient standard atom naming scheme that I
> could use for assigning (1H) NMR resonances on a large set of compounds.
>
> Preferably, atoms that are topologically similar and/or are chemically
> and or magnetically equivalent would have similar names (or root names),
> for example the protons of a single methylgroup, equivalent protons
> of rotating aromatic groups (like PHE/TYR HD/HE).
>
> My initial thoughts run in this direction:
>
> * generate cansmi (to be independent of how the input format is specified)
>
> * name heavy atoms numerically or alphabetically following the smiles string 
> or
>   molecular tree from the start, preferably taking symmetries in the molecule
>   into account (but how?).
>
> * name the hydrogens after the attached heavyatom.
>
> First and last point are trivial I guess, but the middle point seems to
> be quite tricky. I'm probably not the first with this problem, so if anyone
> knows software that does something similar or has suggestions how to approach
> this, I would be very grateful.
>
> kind regards - Eiso
>
>
>
>
>
>
>
>
>
>
>
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