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 > ------------------------------------------------------------------------------ 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
