Thanks for comments. When I print out files from Avogadro that we use for
input to our program, the atoms are in a given sequence. After going through
OpenBabel, the atom numbering and sequence is totally different from the files
that were read as evidenced by the numbering that appears in our displays and
the input files for the MO program. I don't think we're doing anything to
reorder the atoms just to display.
For example, for a Cyclobutene, the Avogadro output has 4 carbons listed first
than all the hydrogens because than is how it was drawn. Our display
(after OpenBabel) then shows carbons are #s 1, 4, 7, 9 instead of the original
sequence 1, 2, 3, 4 -- the hydrogens are numbered so the first two (# 2 & 3)
are attached to C-1, 5&6 to C-4 and so forth. I can check that further ---
although the resequencing is not really an issue for us. Intuitively I would
think SMILES might have to resequence atoms to get the most efficient
description.
I'm just saying what we observe. Perhaps there is another explanation.
Per Noel's note about Isaromatic , I realized after reading it that I may have
made an assumption about how OpenBabel designates bond types. I assumed
aromatic is a distinct bond type (0, 1, 2, 3, aromatic) However, if we can
ignore the "Isaromatic" bonds, I interpret that to indicate that OpenBabel
designates a bond order (1, 2,3) between two atoms plus whether that bond is
also aromatic. If that is true, then it now becomes obvious (wasn't before)
that ignoring the "Isaromatic" bonds should leave the 1, 2, 3 type bond
information intact that our program will still be able to use. Do I
understand that correctly?
The reason we have included PDB files (which work fine from Avogadro) is that
the Spartan ab initio program can generate such 3d files and their PDB files
work ok. Oddly, the MOL files generated by Spartan don't work. We are trying
to allow file types from other programs besides Avogadro that can generate 3d
structure files.
I appreciate your comment about aromaticity. For the
5,6-diaza-1,3-cyclohexadiene [DACHD] case, there is a single bond between
the Nitrogens (the N-Hs might be hard to see in my screenshots). It is a
dihydropyridazine (C4H4N2 + H2 --> C4H6N2). Since pyridazine is
definitely(?😉) delocalized, difficult for me to see how the hydrogenated
derivative could also be aromatic. In any case, for our reactant/product
analysis, using aromatic bonds for DACHD doesn't work properly.
Thanks to you both for suggestions. I'm hoping either ignoring the Isaromatic
bonds or using the development version will solve our issues.
Best regards,
Don
On Aug 29, 2018, at 2:08 PM, Geoffrey Hutchison <geoff.hutchi...@gmail.com>
wrote:
>> 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!)
>
> There's absolutely no way that's happening. Sorry to sound so emphatic, but
> Avogadro v1 directly uses Open Babel. Unless you're removing hydrogens,
> there's never any atom reordering occurring inside the Open Babel code. And
> if you're deleting hydrogens - you don't need to do that to depict 2D
> diagrams, since they can ignore hydrogens themselves.
>
>> 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).
>
> If you get X chemists in a room, chances are that you'll have X+1 definitions
> of "what is aromatic" after not too long. As Noel indicated, an aromaticity
> model for cheminformatics (Daylight, previous Open Babel aromaticity models,
> etc.) may not match your intuition.
>
> If you have MOL and CML formats from Avogadro or other programs, these will
> have 1, 2, 3 bond orders without aromaticity. You're done. PDB is a whole
> different ball of wax and I'd suggest you avoid that format as much as you
> can.
>
> Hope that helps,
> -Geoff
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