Bob, The CORINA documentation that I sent in my last email made me start thinking about an old problem. At the end of the CORINA documentation there is an extensive list of SMILES and stereochemistry input errors that CORINA throws. Over the years, the Jmol SMILES Resolver input problems that I have seen resulted from edited models - it’s a model kit! I encounter them when I want to clean up an edited structure with Resolver.
Some of these edited structures are a geometric mess. For example if I break the single C-C bond on the para carbon of toluene, I get a geometric mess and this SMILES after correcting H and using an MMFF94 hit: C(\C)/1=C/C=C.C\1=C Resolver cannot read this, and I’m now thinking that it’s, understandably, geometry confused. I don’t know how to read these things, so I’m not sure. Interestingly, if I send the molfile to the new inchi.js, it creates an inchi, but NIST reports the resulting structure as being geometry ambiguous. That’s the nice thing about NIST. It fails gracefully with a valid inchi, simply showing connectivity structures with links to NIST possibilities. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
