I would just add that while there are known problems with aromatic SMILES
written by the release version, I'm not aware of any problems with the
development version. Those SMILES should be read without any trouble by any
other toolkit.
Could you give a specific example as Geoff says, but using the development
version. Internally, we don't have bond order 1.5 or even "aromatic bonds".
Every bond has a discrete bond order; but in addition to this, the aromatic
model may mark some bonds as aromatic.
Regards,
- Noel
On Fri, 24 Aug 2018 at 08:45, Geoffrey Hutchison <geoff.hutchi...@gmail.com>
wrote:
> > An issue is that for some molecules, the translation process introduces
> improper aromatic (delocalized) bonds (e.g. Bond Oder 1.5). For our use,
> we don't need display of aromatic bonds nor for input into the MO program
> (which needs only xyz coordinates).
>
> Well, I'm obviously curious to know your examples where the aromatic bonds
> are "improper" but I'd point out that the issue is the "display" there.
> Usually most programs let you turn off display of multiple bonds. So my
> question would be what program you're using for display.
>
> Moreover, if you're only using XYZ coordinates - the bonds are irrelevant.
>
> Perhaps you could tell us more about your workflow? How are you getting
> your 3D molecular structure files, what are you using to display, and what
> files give you the problem?
>
> Thanks,
> -Geoff
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geo...@pitt.edu
> twitter: @ghutchis
> web: https://hutchison.chem.pitt.edu/
>
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