> So I thought about changing the fragment to be composed of C atoms and > using that to derive the canonical representation.
The problem is that if you change the fragment to C atoms, you have lots of un-filled valence. Consider, changing the "N" in pyrrole (or S in thiophene) to carbon. It's no longer aromatic. So with that approach (making fragments, changing atoms to carbon, writing output), the resulting SMARTS patterns weren't I see your point. Perhaps the "best" solution is to look for similar SMARTS in the post-processing step and merge them? Craig, do you have another solution? Is there a wild-card or dummy atom for the canonical SMILES? -Geoff ------------------------------------------------------------------------------ Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
