I think what you're looking for is matched molecular pair finding.  What you 
have described I think is encoding a transformation that captures the local 
chemical environment.

There are open source scripts for RDKit, and also proprietary methods. 

There are some sublties on all pair finding code which may need adjusting, as 
the configuration can make a significant difference.

If you would like to discuss more, mail me directly, we have a huge amount of 
experience in the area.

Best regards,


Dr Ed Griffen,
Technical Director,
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> On 3 Nov 2017, at 13:15, Jens Kristian Munk <> 
> wrote:
> Hi list,
> I’ve searched far and wide for an answer to this; I apologize if the answer 
> is obvious...
> I can use rdFMCS 
> ( 
> <>) to find the 
> maximum common substructure of a set of molecules... But how do I find the 
> difference(s) between two (or more) molecules?
> I work with lipids a lot, so for example, the difference between palmitoic 
> acid (C16:0) and stearic acid (C18:0) is SMILES ‘CC’. I would like RDkit to 
> tell me just that, as well as tell me where on the maximum common 
> substructure (which in this example is palmitoic acid) to add the ‘CC’ to get 
> stearic acid – i.e. on the terminus of the fatty chain.
> Any ideas?
> The example above is just the first step. After that comes identifying and 
> locating double bonds in the fatty chains... And then jump to phospholipids, 
> with two fatty chains and a head group... J
> Med venlig hilsen
> Jens Kristian Munk
> Kemiker, Cand. Scient., Ph.D.
> Telefon: 3862 0398
> Mobil: 5142 3483
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