Dear Greg, It seems that all examples I found are in fact incorrect (due to an error during conversion of SDF produced by ISIS Draw with OpenBabel) and contain this bit: c1(sc(c2c1nsn2)) which was meant to be: c1scc2N=S=Nc12. By the way, ChemSketch understands c1(sc(c2c1nsn2)) as N1SNc2cscc12. So it is not a bug in your code, unless you consider the fused thiadiazole ring aromatic. 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 > ------------------------------------------------------------------------------ Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
