On Mon, 3 Mar 2014 15:41:43 +0000 Toby Wright <toby.wri...@inhibox.com> wrote:
> If I have a five membered ring with 2 consecutive Ns and alternating single > and double bonds expressed by the smiles: N1N=CC=C1 RDKit gives me a > molecule in which every atom is aromatic. If I give it: N1=NC=CC1 it gives > me a molecule in which every atom is aliphatic. If I give it: n1nccc1 it > gives me a kekulization error. I, possibly naively, thought the forms would > be all aromatic or all aliphatic. Am I missing something or is this a bug? I would say that the behavior you described is rather due to Daylight's specification of aromaticity-detection algorithm in SMILES which I assume RDKit follows. For more details see, section 3.4.2 "Aromaticity" of the document below http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html Following it, I think to make RDKit recognized your aromatic heterocycle properly, its SMILES should read e.g. [nH]1nccc1. Hope it helps. -- MikoĊaj Kowalik ------------------------------------------------------------------------------ Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss