> As you mentioned, openbabel goes over gaff.prm from simple patterns to the > complex ones. But, it seems the problem is to distinguish aliphatic > conjugated rings from aromatic rings, particularly for 5- and 6- membered > rings. Because, it uses “ca” atom types very often for aliphatic conjugated > ring systems rather than “cc” or “cd”. > > Therefore, even if we have correct SMARTS pattern for aliphatic conjugated > rings, it does not use them because of the failure of the matching process.
I don’t know what you mean by “failure of the matching process.” You can come up with arbitrarily precise SMARTS patterns. As I indicated, you can specifically type out a carbon in a 5-membered furan ring: atom [cR5]o cc "correct conjugated carbon in furans” That’s a carbon atom detected by Open Babel to be aromatic, but in a 5-membered ring next to an aromatic oxygen (i.e., furan or similar). Then you declare whatever GAFF type you want. I’m not at all sure what an “aliphatic conjugated ring” that’s not aromatic. I *think* you mean that GAFF determines some conjugated ring-systems as non-aromatic. That’s fine. You’ll just need to have separate SMARTS rules for carbons in those types of ring systems (e.g., furan). If you want to take this off-list, I can probably give you more specific atom typing suggestions using SMARTS. But it’s absolutely possible to construct a set of SMARTS that will do whatever atom typing you want - regardless of how Open Babel determines aromaticity. -Geoff ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
