Re: [Rdkit-discuss] Incorrect Aromaticity?

2019-10-30 Thread Hao
@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 <

Re: [Rdkit-discuss] Incorrect Aromaticity?

2019-10-30 Thread Ivan Tubert-Brohman
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.

Re: [Rdkit-discuss] Incorrect Aromaticity?

2019-10-30 Thread Dan Nealschneider
You've specified that the ring is aromatic in your smiles input. Did you mean "C1CCC2C(C1)OC(N2)=O"? *dan nealschneider* | senior developer [image: Schrodinger Logo] On Wed, Oct 30, 2019 at 12:00 PM Hao wrote: > Hello, > > It seems like RDKit is making my