On 7 October 2010 16:41, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: >> The majority of these are errors in determination of the number of >> implicit Hs. Basically, I call DeleteHydrogens and then AddHydrogens > > Well, implicit valence is controlled in atomtyp.txt by a bunch of SMARTS > patterns. You can add more specific rules to the bottom of the list -- the > last pattern matched will "win." > > So there's definitely an easy way to fix these in the short term.
I've spent a little while on this, but it's all new to me and a bit tricky. About half of the failings are caused by -N3, the azide moiety, as exemplified by HN3 in the sdf file. (3 more are caused by its cousin -N2.) > -Geoff > > > ------------------------------------------------------------------------------ > 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
