Looking at the first one, C1(=C)C(=C)NN1 has an aromatic ring according to
the Daylight aromaticity model. This is according to Open Babel but also
the CDK (and anyone else that implements it correctly). The atom
contributions are described at
https://figshare.com/articles/Daylight_Aromatic_Atoms/3370945
Since you say that Kekule structures are perfectly fine, then there is no
need to call IsAromatic() - just use the bond orders as provided. I forget
if this will work correctly with the released version, but it certainly
does with the development version.
Regards,
- Noel
On Wed, 29 Aug 2018 at 04:54, Don Kelsey <kel...@ucmo.edu> wrote:
> Hello, Thanks to you both for your prompt reply. Perhaps I should
> mention that this project is a joint project between chemistry and computer
> science. I'm the "chemistry" guy and I'm working with a professor and
> students who are doing the actual programming. My experience with
> programming is very long ago, so I'm a bit naive about some details.
>
> That being said, we are using OpenBabel to read MOL (MDL), PDB and CML
> formats generated by Avogadro (or other programs), which all have a bonding
> table with 1, 2, or 3 bond orders (no aromatic designations).
>
> We need the bond orders because we are displaying the molecules in
> rotatable 2D structures (I think we use OxyPlot) but also because we are
> comparing the bonding parameters between reactants and products, which is
> important. With, say, benzene rings, the aromatic bonds that OpenBabel
> generates are OK. But other structures, they create havoc. I will attach
> examples.
>
> For reasons too lengthy to go into, when OpenBabel generates an improper
> aromatic bond, it not only creates errors in the display but also creates
> errors in our reactant/product comparison analysis.
>
> I'm reasonably sure it is OpenBabel that is changing the input bonding (0,
> 1, 2, 3) between atom pairs to aromatic: In our Folder "OpenBabel
> Integration", there is are three files, one of which for example has code:
> "if bond.Isaromatic
> bondType = BondType.Aromatic_Bond"
>
> where I'm pretty sure the "Isaromatic" comes from a term in OpenBabel and
> this code is just telling our program to then set the bond type as
> "Aromatic_Bond" (which separately we also set as 1.5 bond order --- sorry,
> I might have confused you by mentioning this in my first note).
>
> Since OpenBabel is designating aromatic bonds, we have to go along with
> that for use in our program. (If we knew the original bond -- from
> Avogadro input -- between the pertinent atoms, we could just use that info
> but OpenBabel rearranges the atom sequences ----- which we don't really
> need to have done, either!)
>
> Your suggestion that using the development version maybe very useful ----
> I will have to ask the computer guys to see if they can use it so I can
> test to see if the errors go away. Right now, I can't send examples using
> the release version ---- I have to defer to the computer guys to alter our
> program first.
>
> Another solution would be to prevent the release version OpenBabel from
> generating any aromatic bonds and, in fact, they really aren't necessary
> --- Kekule structures are perfectly fine for our program.
>
> In case it is useful for correcting the release version,
> I have attached 4 screen shots of our graphics showing examples of
> molecules where aromatic bonds (double dashed bonds) should not occur. It
> appears the program thinks that the electron pairs on oxygen and nitrogen
> (also phosphorus) should be combined with the double bonds or aromatic ring
> to make delocalized "aromatic" structures. The heteroatoms don't have to
> be adjacent (e.g. a similar case occurs with P in the 1,3 positions of the
> cyclobutane ring).
> I would guess it may happen with sulphur, too. It doesn't happen with C
> or Si (at least neutral). I haven't found an example with B or Al but that
> doesn't mean it might occur.
>
> Other than trying the development version, do you have any other
> suggestions of possible solutions or work arounds? Solving this is
> important to us since there are potentially many reactions of interest
> where inappropriate aromatic bonds ruin our analyses.
>
> Thanks much for your help,
>
> Don
>
> On 8/24/2018 9:11 AM, Noel O'Boyle wrote:
>
> 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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