I'm sorry, it's been a very hectic few weeks and I have not had much time for e-mail, much less coding.
As you suspect the problem is not with GAFF or SMARTS but the aromatic detection and Kekulization of the molecules. I'm not 100% certain where the problem is. The first question is this.. you're going from Gaussian and asking for bond detection. If you translate from the Gaussian output to SDF, do you think the bond orders (e.g., double bonds) are assigned correctly? Next off, it seems like the problems are with charged molecules. Is the positive charge assigned at all to one of the nitrogens? If not, if you take an SDF file and assign the positive charge, does that aromatize correctly (e.g, when saved to SMILES the lower case letters appear). Basically the question is where in the chain is the bug occurring. For example, if I take that file, I see this as a SMILES: [CH]1N(C=CN1C)CC 1-ethyl-3-methylimidazolium3-esp.log.gz So I see the double bond appear, but not the charges.. This is how to break down the problem — what part of the translation is failing? -Geoff ------------------------------------------------------------------------------ Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
