Thanks Noel, Sure I agree and thanks for answering the original question. For Dimitri and I that are looking for assigning R and S your original answer was also the correct one since this winding property bears no relation to R/S because there are no guarantees that atom 1 is the smallest in priority. If 1 was the smallest in priority then clockwise would correspond to S because we are looking in the direction from 1 to 2.
I apologise to Craig and Geoff and to the readers for my contribution to the confusion. On 4 December 2013 04:32, Noel O'Boyle [via Open Babel] <ml-node+s957263n4657010...@n4.nabble.com> wrote: > 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 <[hidden email]> 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 <[hidden email]> wrote: >>> On Tue, Dec 3, 2013 at 1:11 PM, Yoel <[hidden email]> 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 >> [hidden email] >> 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 > [hidden email] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > ________________________________ > If you reply to this email, your message will be added to the discussion > below: > http://forums.openbabel.org/stereo-config-question-tp4656879p4657010.html > To unsubscribe from stereo config question, click here. > NAML -- View this message in context: http://forums.openbabel.org/stereo-config-question-tp4656879p4657012.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ 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
