I am happy to send you the entire test set if you are interested. Just reply to me off list.
Tom -- Dr. Thomas C. Allison, NIST thomas.alli...@nist.gov 301-975-2216 On Apr 17, 2012, at 10:11 AM, Geoffrey Hutchison wrote: >> Let me start with a little more background on the problem. I am using Pybel >> to extract the information I need about a set of ~875 PAH molecules >> (including alkyl substituted and radical PAHs). > ... >> "signature" of an error is typically that a C atom is labelled as sp3 >> hybridized when it only has three atoms attached. (I have since learned that >> I can correct the labeling of one of the molecules by reordering the C >> atoms.) > > Quick question -- can we turn this data set into a unit test to distribute > with Open Babel? I wrote up a few fused aromatics into one of the tests, and > we've added through bug reports. But this is definitely the most systematic > torture test of Kekulization that I've seen. > >> I have worked quite a bit with two of the molecules, azulene and 2175908. I >> have tried to reorder the atoms, convert to 2d, create a mol file using >> openbabel, remove hydrogens and then convert to 2d, etc. None of these >> things has helped. However, when I create the same molecule in ChemDraw, >> openbabel does label the aromaticity correctly. > > Right. The problem with XYZ format is that Open Babel has to work out all the > bond orders from scratch, while in ChemDraw, it just has to detect that it's > an aromatic system. > > As Noel can tell you, we've worked through plenty of rare, subtle Kekule bugs > across versions, so this will definitely help us stomp out more of them. > > If no one else goes for it, I should have some time on Thursday to sift > through the code and fix this. > > Thanks, > -Geoff ------------------------------------------------------------------------------ Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
