I'd like to pitch in about the changes in aromaticity perception - it looks like the more recent version of OB (2.3.1) is not recognizing one of the rings in the attached image as aromatic. I set atomic numbers for Z and D to 0. I think the behavior was different before. I would much prefer to see both rings as aromatic for my purposes.
Also, it might be just me but the way to get AliasData for an atom seems to have changed at some point as well? Best regards, Igor On Tue, 2012-04-17 at 11:56 -0400, Craig James wrote: > On Tue, Apr 17, 2012 at 7:56 AM, Noel O'Boyle <baoille...@gmail.com> wrote: > > Well, Geoff, if you're going to be working on this I've recently been > > subjecting ChEMBL to some canonicalisation tests, and can supply a good few > > more test cases. I'll wrap them up and email them to you off list tomorrow. > > Would it be possible to get all of these cases -- both the Kekule' > form and the "correct" canonicalized aromatic versions of them? > > I more-or-less threw up my hands on getting the OpenSMILES definition > of aromaticity nailed down, due in part to the fact that I'm not a > chemist and I was never able to spark a conversation to resolve it. > Now I'm thinking that if we have a comprehensive set of example > structures, it might be possible to do it by spelling out a few fairly > simple rules, and then enumerate a set of exceptions or special cases. > Or maybe given a complete set of examples, someone can actually > create a set of rules that handles every case. > > Craig > > > > > - Noel > > > > On 17 April 2012 15:11, Geoffrey Hutchison <ge...@geoffhutchison.net> 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 > > > > ------------------------------------------------------------------------------ > 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
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