On Sun, Nov 24, 2019 at 6:42 PM Benjamin Datko <benjamin.datko....@gmail.com> wrote:
> > Digging around within the documentation the imidazole example I shared is > yet another example on how RDKit defines aromaticity. I know there might be > a lot of nuance here since RDKit already makes it clear aromaticity is > difficult, but here is what I don't understand. > > RDKit gives examples of their aromaticity model, found [here]( > https://www.rdkit.org/docs/RDKit_Book.html#the-rdkit-aromaticity-model). > Applying the examples given in the table possibly would explain the > behavior I am observing, but the nomenclature is going over my head. > > For example the table shows an atomic environment 'c(a)a' contributing one > pi-electron. Breaking down the terms, 'a' is any aromatic atom (this is > given in the footnote of the table), and I assume 'c' is a carbon atom. > Using the daylight nomenclature I would read the parenthesized expression > as a branch containing any aromatic atom. Is that correct? > > Also, if the atomic environment of 'c(a)a' is showing at most three atoms > (one carbon, one branching aromatic atom, and then another aromatic atom), > which atom is contributing the single pi-electron. > Now that you point it out, that table is not a great example of clear documentation. Each row in that table shows the number of pi electrons a single atom contributes to a possibly aromatic ring system. The table does not, however, tell you *which* atom it means. If you know the answer, it's completely obvious though! ;-) Sorry about that. That example is intended to tell you that a "c" atom that has two aromatic neighbors contributes one pi electron to a possibly aromatic ring system. I will try and figure out some way to underline the atom being described in that table. I'll reply to the other bit separately. -greg > >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
