On 2014-03-07 22:16, Geoffrey Hutchison wrote: > I'm sorry, it's been a very hectic few weeks and I have not had much time for > e-mail, much less coding. > No worries, that's life. > 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? > There should be an additional double bond N=C (on either of the N), so the answer is no. One of the ring carbons is detected as c3 and the whole ring designated AL (aliphatic?).
> 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). > Positive charge does not help, and adding the extra double bond in addition to that does not help either. > 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 > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ 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
