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. I thought that was what Dimitri was asking. Clearly if one start from a notation where chiraility is already represented then CIP has already been applied and therefore there is no need to do that again.
I keep the reference in mind. I’m sure that at one point I’m going to want to understand more about smile representation. Cheers Yoel On 3 December 2013 15:51, Craig James-2 [via Open Babel] <ml-node+s957263n4656995...@n4.nabble.com> wrote: > > > > On Tue, Dec 3, 2013 at 11:43 AM, Dimitri Maziuk <[hidden email]> wrote: >> >> On 12/03/2013 01:28 PM, Yoel wrote: >> > Dimitri, >> > >> > In this case you do know which way you are looking. For brevity let's >> > consider a tetrahedral carbon atom with four different substituents... >> > the >> > first thing you do is to assign them priorities based on there atomic >> > numbers then you place the smallest priority backward... this gives you >> > the >> > point of reference you need to say clockwise and anticlockwise... >> > >> > The algorithm may take a different form but these are the general rules. >> > >> > I hope it helps. >> >> No it doesn't, sorry. >> >> I have a message from Craig James here: >> http://forums.openbabel.org/stereo-config-td4656861.html that says it's >> based on "local connectivity around a single atom or bond". Please >> define "atomic numbers" in terms of "local connectivity around a single >> atom or bond". > > > Try this; the section entitled "Tetrahedral Centers" has an explanation of > the concept of an atom-centered stereochemistry specification. > > http://opensmiles.org/opensmiles.html#_tetrahedral_centers > > 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 > > > ________________________________ > If you reply to this email, your message will be added to the discussion > below: > http://forums.openbabel.org/stereo-config-question-tp4656879p4656995.html > To unsubscribe from stereo config question, click here. > NAML -- View this message in context: http://forums.openbabel.org/stereo-config-question-tp4656879p4656997.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
