On Wed, Mar 27, 2013 at 2:26 PM, David van der Spoel
<sp...@xray.bmc.uu.se>wrote:
> On 2013-03-27 22:04, Craig James wrote:
> >
> >
> > Reinis Danne <rei4...@gmail.com <mailto:rei4...@gmail.com>>wrote:
> >
> > > I think it was the thread where I mentioned I'm working on
> > > kekulization algorithm using graph theory (maximum matching). It
> > > has been quite some time when I last looked at that code and it
> > > is not yet usable.
> >
> >
> > I don't know if this overlaps with your work, but I spent a fair amount
> > of time on the aromaticity-detection algorithm and improved it by orders
> > of magnitude. See the comment in kekulize.cpp around line 887....
>
> Great that a number of solutions are being worked on. At least for
> Carbon based molecules one can relatively easy filter out errors by
> counting the sum of bond orders on the bonds to each carbon (although
> there are pathetic cases like carbon monoxide). I would rather not get
> bond orders from the algorithm than incorrect ones.
>
> It is my impression that the total charge on molecules is not (always)
> taken into account, even if it is present from e.g. quantum chemistry
> files.
>
>
This is a good time to re-raise the issue of plug-in aromaticity
algorithms. SMILES "aromaticity" is very specific to cheminformatics, and
other OpenBabel users need aromaticity definitions that are useful for
pharmacology, chemistry and physics. Those are very different things.
Maybe something like ...
mol.SetAromaticityMethod("smiles");
Craig
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