Hello Greg,
>>> Chem.MolToSmiles(Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2nccc2)NC1=O'))
[14:25:55] Can't kekulize molThis smiles was generated from ChemSketch. OpenBabel converts it to O=C1NC=CC1=C1C=C(c2[nH]ccc2)NC1=O which is correctly interpreted by RDKit (no problems with kekulization). But IMHO both representations are correct, am I wrong? Best wishes, Michal On 5 December 2013 12:19, Greg Landrum <greg.land...@gmail.com> wrote: > Hi Michal, > > On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec <michal.kromp...@gmail.com> > wrote: >> >> Hello, >> Is it possible to suppress kekulization by SDWriter? I get the >> following error on a call to SDWriter.write: >> ValueError: Sanitization error: Can't kekulize mol >> But some molecules can't be kekulized using RDKit's algorithm, even >> though they are otherwise 'correct'. > > > hmm, I'd love to see examples of those if you can share them. > >> >> I browsed the sources and it seems that SDWriter calls MolToMolBlock >> with the default parameter kekulize=True. Can this parameter be >> exposed in SDWriter? > > > Yep, I'll get it in for the next release. > > -greg > ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
