Hum! I’m pretty confident with what I know but the issue here is that you answer isn’t contributing to clarifying the question. The question is how to we determine the chirality of a centre regardless of how you may choose to represent it at a later point. And this problem inevitable will come down to applying the CIP rules. Do you disagree with that?
On 3 December 2013 22:34, Craig James <cja...@emolecules.com> wrote: > On Tue, Dec 3, 2013 at 1:11 PM, Yoel <yoe...@gmail.com> wrote: >> >> Craig, >> >> Thanks a lot for this. I do not know the smile notation in details >> however as a chemist I’m pretty sure I understand chirality. If I >> understood your article I see that explains how chirality is >> represented in smile notations but I still don’t see how do you know >> what chirality to represent starting from a mol file lets say. > > > The reason that Dave Weininger invented SMILES' way of representing > chirality is that it's much more sensible from a > mathematical/graph-theoretical perspective than R/S and E/Z representation. > R/S and E/Z are potentially time-consuming to compute. They are usually > illustrated with trivial examples, such as Cl/C=C/Cl, where it's obvious > that it's trans. But what is CCC/C(\CCO)=C(/CCCl)\CCBr -- E or Z? There is > a formal definition, but most chemists probably couldn't tell you at a > glance whether this molecule should be called E or Z. The same goes for R/S > naming conventions. With SMILES, the algorithm only has to look out one > atom from the chiral center, or one atom out from the double-bonded atoms, > to figure out how to write the SMILES (with the caveat that it first has to > do a symmetry analysis). > > Cheers, > Craig > ------------------------------------------------------------------------------ Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
