> A bit off topic but it would be great if a new kekulizer had an option to > preserve existing hydrogens. This is the only blocker to applying the > respective valence models on reading for smiles and molfile. It also of > course makes the problem a lot easier.
That’s a given, actually. I’ve sat down and thought out the aromaticity detection and Kekule code and how to explain it to CS undergrads. While I’m sure there will be some initial bugs, I think the results will be strong. The base concept will be to keep atoms as-is when specified and apply bit masks as constraints. That is, there will be a pass to remove atoms/nodes and edges from the graph for Kekule assignment (e.g., aromatic S in thiophene or -NH in pyrrole). I also have the beginnings of an aromaticity detection code that does not use SSSR or LSSR assignments - simply doing a BFS path to count electrons, inspired by recent discussion on OpenSMILES. The students also seem eager to attempt a more efficient, likely OpenMP enabled ConnectTheDots implementation. Again, I’m looking for a good test set. -Geoff ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
