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
> 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
> 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
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
Since I didn't do the integration with OpenBabel, I'll have to check with the
programmers perhaps they assumed they had to invoke SMILES. Possible they
didn't understand the programming needed for simply reading in and translating
files OR more likely, perhaps I suggested it would be
