Hi Greg,
Thanks a lot for that, very helpful again. I just need to scratch my head a bit more and do a bit of background reading to understand better the actual delocalization concept - from a chemistry point of view. All the best, George. > Date: Thu, 2 Apr 2009 05:27:15 +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 8:37 PM, George Oakman <[email protected]> wrote: > > > > Can delocalized bonds be represented using SMILES strings? (this might be a > > silly question, please excuse my limited level of understanding of this > > domain). > > It's not a particularly silly question, but the answer is still "not > directly". You need to localize the bonds to represent the molecule > with SMILES. The four bond types supported by SMILES are single, > double, triple, and aromatic (which only applies to ring systems). > > Recognizing that a certain system of single and double bonds is > delocalized would be the job of the cheminformatics system. In the > RDKit you can ask if bonds are conjugated, which might be a first step > in deciding if they are delocalized: > #--------- > [6]>>> m = Chem.MolFromSmiles('CCC(=O)O') > > [7]>>> m.GetBondWithIdx(0).GetIsConjugated() > Out[7] False > > [8]>>> m.GetBondWithIdx(1).GetIsConjugated() > Out[8] False > > [9]>>> m.GetBondWithIdx(2).GetIsConjugated() > Out[9] True > > [10]>>> m.GetBondWithIdx(3).GetIsConjugated() > Out[10] True > > [11]>>> m = Chem.MolFromSmiles('C=CC(=O)O') > > [12]>>> m.GetBondWithIdx(0).GetIsConjugated() > Out[12] True > > [13]>>> m.GetBondWithIdx(1).GetIsConjugated() > Out[13] True > #--------- > > But then this is all determined after the molecule has already been read in. > > -greg _________________________________________________________________ View your Twitter and Flickr updates from one place – Learn more! http://clk.atdmt.com/UKM/go/137984870/direct/01/
