@Dan The issue I meant was in the first line, where it writes the 5 membered ring as aromatic. Thanks for the response Ivan. I thought each atom in an aromatic ring must contribute but I guess not. Very cool!
On Wed, Oct 30, 2019 at 3:08 PM Ivan Tubert-Brohman < ivan.tubert-broh...@schrodinger.com> wrote: > It is aromatic according to the RDKit aromaticity model described here: > https://www.rdkit.org/docs/RDKit_Book.html#aromaticity > > The O and N each contribute 2 electrons. Each of the carbons shared with > the 6-member ring contribute one electron. The carbonyl is sp2 and > contributes zero electrons. The total is 6, which satisfies the 4n+2 rule. > > Ivan > > On Wed, Oct 30, 2019 at 3:00 PM Hao <shenha...@gmail.com> wrote: > >> Hello, >> >> It seems like RDKit is making my molecule aromatic when I don't think it >> should it. Here's the original smiles: c1ccc2c(c1)OC(N2)=O. A snippet of >> the workflow: >> [image: image.png] >> As you can see it makes the 5 membered ring aromatic. My chemistry isn't >> strong, so if someone can elucidate what I'm seeing, that would be >> very helpful. >> >> Thanks! >> Hao >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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