Hi George, On Mon, Mar 12, 2012 at 5:58 PM, George Papadatos <[email protected]> wrote: > > Could anyone please explain this: > > In [21]: Chem.CanonSmiles('C1=CC=C2C(=C1)NC=S2') > Out[21]: 'c1[nH]c2ccccc2s1' > > In [22]: Chem.MolFromSmiles(Out[21]) > [16:47:14] Can't kekulize mol > > In other words, how is it possible that a valid RDKit SMILES output fails to > be converted to molecule again?
I'm sure the general answer isn't a surprise: it's a bug It may actually be more than one bug. The SMILES 'C1=CC=C2C(=C1)NC=S2' probably shouldn't produce a legal molecule. It certainly shouldn't produce one with an aromatic ring. That's not really a valid/reasonable resonance structure for benzothiazole. This would be ok: S1C=NC2=CC=CC=C12 o The output smiles: 'c1[nH]c2ccccc2s1' is also not a reasonable molecule, which the RDKit recognizes when it tries to read it back in. I'm going to have to think about where the right place to fix this is. -greg ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
