On Fri, Mar 29, 2013 at 7:33 AM, Reinis Danne <rei4...@gmail.com> wrote:
> On Wed, Mar 27, 2013 at 02:04:00PM -0700, Craig James wrote:
> > Reinis Danne <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 -- copied
> below.
> >
>
> Still there are situations (even not that complex ones) where
> the current algorith fails to find correct kekule form of
> aromatic system and that is one of the main reasons I'm looking
> into another algorithm.
>
This is why I raised the issue yesterday in this forum of pluggable
algorithms. SMILES has very specific rules that are based on chemistry but
are NOT chemically correct in every situation. That's not an accident --
the rules for SMILES have to remain fixed over time.
> Also, I'm looking into this, because it is just interesting :)
>
An excellent reason. I think OpenBabel needs a really good aromaticity
algorithm that's useful for real chemistry.
Craig
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