Let me just answer the original question as this is getting somewhat out of hand. :-)
Open Babel stores tetrahedral stereochemistry in a Config object. A typical Config object associated with a tetrahedral center may have the following fields and values: winding: "Clockwise" center: 2 from: 1 refs: 3 4 5 This means that looking from atom 1 towards 2, the atoms 3, 4, 5 should be arranged clockwise. I hope you agree that this perfectly specifies the stereochemistry at atom 2. - Noel On 4 December 2013 03:44, Yoel <yoe...@gmail.com> wrote: > 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 ------------------------------------------------------------------------------ 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
