Noel, thanks for the clarification. It makes sense now, but it means that I'm using the wrong tool for what I want to do.
In a previous discussion[1] I was suggested to use this code to alter the chirality of a tetrahedral stereocenter, since OBTetrahedralStereo.Invert() doesn't seem to be available in Python. What would you recommend to identify a chiral center configuration and invert it in Python? Thanks, S [1] http://sourceforge.net/p/openbabel/mailman/message/32475236/ On 02/17/2015 01:50 AM, Noel O'Boyle wrote: > Hi, > > Hope you don't mind but... > > 1. Should GetId() not GetIdx()-1 > 2. Should be "HasTetrahedralStereo(idx)" > > Regarding the main question, the config objects are correct, but the > stereo definition consist of three parts (see the API docs): view, > winding and refs. You were just looking at the winding. The refs are > in a different order in each case. > > Regards, > - Noel > > > On 17 February 2015 at 00:53, Stefano Forli <fo...@scripps.edu> wrote: >> Hi, >> >> I can't understand the way in which chiral winding is handled by OpenBabel. >> I wrote a small test script in Python (attached) to try to clarify the >> concept. The output is: >> >> ClC(I)Br -> WINDING [1->2] -> ClC(I)Br >> Cl[C@H](I)Br -> WINDING [1->2] -> Cl[C@@H](I)Br >> Cl[C@@H](I)Br -> WINDING [1->2] -> Cl[C@H](I)Br >> >> The winding is always perceived as 1, and this is wrong by definition >> (right?) >> Setting the winding to 2 generates the other enantiomer, independently from >> the starting point. >> Both atom.IsClockwise() and atom.IsAntiClockwise() return False, showing >> that chirality is not perceived (uncomment the last line to test it). >> Is this expected, or there is a way to perceive it properly? >> Thanks, >> >> S >> >> >> -- >> Stefano Forli, PhD >> >> Staff Scientist >> Molecular Graphics Laboratory >> Dept. of Integrative Structural >> and Computational Biology, MB-112F >> The Scripps Research Institute >> 10550 North Torrey Pines Road >> La Jolla, CA 92037-1000, USA. >> >> tel: +1 (858)784-2055 >> fax: +1 (858)784-2860 >> email: fo...@scripps.edu >> http://www.scripps.edu/~forli/ >> >> ------------------------------------------------------------------------------ >> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >> with Interactivity, Sharing, Native Excel Exports, App Integration & more >> Get technology previously reserved for billion-dollar corporations, FREE >> http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> -- Stefano Forli, PhD Staff Scientist Molecular Graphics Laboratory Dept. of Integrative Structural and Computational Biology, MB-112F The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
