> 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
