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.
- 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
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