On 5 April 2014 19:11, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote:
> On 05/04/14 19:04, Michal Krompiec wrote:
>
>
>> For example, it does not work well
>> for long conjugated oligomers - sometimes it produces molecular knots
>> instead of straight strands, and is quite slow for large systems.
>
> Can you expand on that? What sort of long conjugated oligomers were you
> looking at?

Some substituted oligoarenes with at least 8 rings in the chain, not
particularly fancy (I think the problem is related more to the length
of the molecule than to the nature of the repeat units). I tried
various options in the EmbedMolecule function, but without success.
This error occured in less than 10% tested structures. If anyone is
interested in correcting this, I think I can produce a
non-confidential input example...

> What was the nature of the input from which you were making
> rdkit molecules?

SMILES. The same input worked 100% fine with CORINA (which was, btw,
approx. 5-20x faster on the same computer) and KNIME.

Regards,
Michal

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