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 ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
