Here's another problem case: [Cl].[Cl-].[Cl+]
There are six ways to write this SMILES, and the canonicalizer doesn't distinguish them: [Cl-].Cl.[Cl+] Cl.[Cl-].[Cl+] [Cl-].[Cl+].Cl Cl.[Cl+].[Cl-] [Cl+].[Cl-].Cl [Cl+].Cl.[Cl-] If you add another fragment, you get 24 choices, and so on (N! combinations, where N is the number of fragments). Either the charge isn't being taken into account, or else fragments aren't being written in a canonical order. Craig ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel