One more interesting (and related) case: pleiadene Carbons 3 and 8 are labelled as radical centers. Clearly this is a consequence of the xyz format as you point out below.
Tom ----- 30 C 0.0308731391 1.4691736561 0.0066435902 C 0.0509994911 -0.0014052265 0.0004118536 C -1.0544454244 -0.8154062097 0.0066876805 C 1.3146087833 2.1555452458 0.0001056644 C 2.4992117439 1.4900795222 -0.0121747070 C 2.5190062915 0.0457290997 -0.0191977233 C 1.3531630314 -0.6521604111 -0.0133075993 C -1.0964428571 2.2525514971 0.0172188150 C -2.5239134092 1.9877760473 0.0260044273 C -3.1740364827 0.6898505184 0.0271818776 C -2.4886916064 -0.5897886310 0.0207008914 C -3.2524029094 -1.7678927921 0.0265434655 C -4.6551311259 -1.7641470501 0.0371229601 C -5.3281205504 -0.5648513566 0.0406686159 C -4.6189588836 0.6703298311 0.0361869478 C -5.3614844180 1.8858011321 0.0409545398 C -4.7212716178 3.1029764590 0.0400976105 C -3.3192614397 3.1447207650 0.0334229041 H -0.8147137403 -1.8834328100 0.0001296390 H 1.2979955944 3.2484583218 0.0054060708 H 3.4420366473 2.0416713369 -0.0170114240 H 3.4767524835 -0.4794266519 -0.0290532764 H 1.3660076449 -1.7450868610 -0.0184670434 H -0.8849996717 3.3265460165 0.0194033504 H -2.7247137217 -2.7239142474 0.0222087477 H -5.2013640634 -2.7102775522 0.0421629600 H -6.4203095423 -0.5356360910 0.0484892059 H -6.4524785701 1.8271634369 0.0456015763 H -5.2932921446 4.0337736135 0.0447939229 H -2.8173697700 4.1145653417 0.0330998246 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
