On 6/22/11 9:18 AM, Noel O'Boyle wrote: >> I dont really understand this limitation, why should 4=aromatic be only used >> for queries, its not ambigious like the others? (maybe its a typo, and it >> should be '5 though 8' ;-) ). > > In general, it's not clear which bonds should be marked aromatic.
To elaborate on Noel's answer, the real problem is that aromaticity isn't well defined for cheminformatics in general. It's only well defined within the rules for a particular file format. For the SMILES language, there is a specific set of rules. For InChI, there is another set of rules. For SDF, there is no rule. If the OpenBabel project tried to write out aromatic bonds for SD Files, we'd have to make up a new set of rules. Would we use the SMILES or the InChI rules, or some new set? It would be a mistake to do this. A project like OpenBabel needs to stay within the definition of each file type, and the SD File doesn't define how to decide which bonds are aromatic and which bonds are not. The only solution is to write out the molecule in Kekule form. Craig ------------------------------------------------------------------------------ Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Data protection magic? Nope - It's vRanger. Get your free trial download today. http://p.sf.net/sfu/quest-sfdev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
