Hi Noel, > I've run into the problem that the current kekulization code (or at least > that invoked by the SMILES reader) does not take into account the location of > implicit Hs, rather it works it out itself independently of anything I do.
I think the problem has been not-quite-kosher SMILES. I'm thinking of things like: c1nncn1 triazole So the aromatic nitrogens have an undefined number of implicit hydrogens. One of them should have an explicit hydrogen, but it's not clear which one does. In the case of "good" SMILES, the Kekule code is moot and might cause more harm than good. I don't know if there's a good way to flag good SMILES vs. "quirky" SMILES. Certainly, I can help walk you through the kekule.cpp code. There's probably a simpler implementation when the implicit and explicit valence is well-defined. Hope that helps, -Geoff ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
