On 6 April 2014 05:36, Greg Landrum <[email protected]> wrote: >> 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... >> > > I would certainly be interested to see this. I'm not sure what can be done, > but it's interesting to have the examples.
Try this one with random coordinate generation: Cc1cc(cc3c1c2ccc(cc2C3(C)C)c4ccc(c(C)c4C)c5ccc(s5)c7ccc8c6ccc(cc6C(C)(C)c8c7)c%14ccc(c9ccc(s9)c%10cc%12c(cc%10CC)c%11ccccc%11C%12(C)C)c%13cc(C)ccc%13%14)c%15ccc(s%15)c%17ccc(c%16ccccc%16%17)c%18cc%20c(cc%18)c%19c(C)c(C)c(cc%19C%20(C)C)c%21sc(cc%21C)c%23ccc%24c%22ccc(cc%22C(C)(C)c%24c%23)c%25ccc(s%25)c%31ccc(c%27ccc%28c%26c(C)cc(cc%26C(C)(C)c%28c%27)c%29ccc(s%29)c%30cccs%30)c(C)c%31C AllChem.EmbedMolecule(mol,useRandomCoords=True); AllChem.MMFFOptimizeMolecule(mol,maxIters=100) I have just run it 3 times and each time it produced a knot, which cannot be disentangled by optimization. This example is completely artificial, but I got similar results in a few % of "real" cases. It is not an issue for me, actually, as I now use Corina to get the starting conformations and then optimize them with MMFF in RDKit. >> and KNIME. > Which conformation generator in knime? None, I was using knime just to browse 2D structures. Best wishes, Michal ------------------------------------------------------------------------------ Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees_APR _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
