On 10/8/10 4:22 PM, Geoffrey Hutchison wrote: >> c12=c3c(c4c(c5c(c1csc2)csc5)csc4)csc3 5860502 >> C12C(C3C(C4C(C5C1CSC5)CSC4)CSC3)CSC2 5860502 > >> c12=c(nn2)ssnc1S 6137697 >> c12c(nn2)ssnc1S 6137697 > > I've been looking at very similar SMILES for the kekulize code. As a general > question -- is it ever OK to output a '=' between two aromatic atoms? > > I haven't thought of a good example yet.
The original purpose of aromaticity was to avoid Kekule' structures so that databases could use SMILES as an indexable, unique identifier. That is still the main purpose. A secondary purpose is the SMILES-as-SMARTS problem: Every SMILES should match itself as a SMARTS (it's not 100% true, but pretty close). With those in in mind ... there's probably never a good reason to put an '=' in an aromatic ring. Would c=c match? No. Is there a canonical form? Maybe, but it would require some pretty tricky rules. My two cents. 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
