On Tue, Oct 5, 2010 at 2:29 AM, Craig A. James <cja...@emolecules.com> wrote: > 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).
This is why fragments are handled individually :) > Either the charge isn't being taken into account, or else fragments aren't > being written in a canonical order. Charges are included in the symmetry classes which is enough if there is only a single fragment. However, when there are multiple fragments charges must be included in the canonical code. It's a trivial extension and in svn r4153. Thanks, Tim > 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 > ------------------------------------------------------------------------------ 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
