Hi,
Thanks for the clearAromatic tip, that's very helpful. Are there any ways to deal with delocalized bonds at all? I can see why, and it's a good thing, the RDKit needs to be picky about these though. Can delocalized bonds be represented using SMILES strings? (this might be a silly question, please excuse my limited level of understanding of this domain). Thanks. > Date: Wed, 1 Apr 2009 20:19:54 +0200 > Subject: Re: [Rdkit-discuss] Aromatic and conjugated bonds to singles and > doubles > From: [email protected] > To: [email protected] > CC: [email protected] > > On Wed, Apr 1, 2009 at 8:10 PM, George Oakman <[email protected]> wrote: > > > > I would like to explore the possiblilty of transforming aromatic bonds into > > single and double bonds, for example: > > > > c1ccccc1 into C1=CC=CC=C1 into > > > > [9]>>> m = Chem.MolFromSmiles('c1ccccc1') > > [10]>>> Chem.MolToSmiles(m) > Out[10] 'c1ccccc1' > > [11]>>> Chem.Kekulize(m,clearAromaticFlags=True) > > [12]>>> Chem.MolToSmiles(m) > Out[12] 'C1=CC=CC=C1' > > > > and similarly, transform conjugated bonds into single and doubles, for > > example: > > > > N:C:O into NC=O > > This kind of structure won't be read in in the first place, it will fail: > > [13]>>> m = Chem.MolFromSmiles('N:C:O') > [20:17:58] Kekulization somehow did not convert bond 0 > > > ":" in a SMILES does not mean delocalized, it means aromatic and that > is a concept that only applies to rings. > > The RDKit is, by design, exceedingly picky about these things. > > -greg _________________________________________________________________ View your Twitter and Flickr updates from one place – Learn more! http://clk.atdmt.com/UKM/go/137984870/direct/01/
