If you just want to know which atoms have defined stereo, write it out as CML and look at the bondStereo and atomParity sections, e.g.:
C:\Users\Noel>obabel -:Br[C@](Cl)(I)C/C=C/Cl -ocml <?xml version="1.0"?> <molecule xmlns="http://www.xml-cml.org/schema";> <atomArray> <atom id="a1" elementType="Br"/> <atom id="a2" elementType="C"> <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity> </atom> <atom id="a3" elementType="Cl"/> <atom id="a4" elementType="I"/> <atom id="a5" elementType="C"/> <atom id="a6" elementType="C"/> <atom id="a7" elementType="C"/> <atom id="a8" elementType="Cl"/> </atomArray> <bondArray> <bond atomRefs2="a1 a2" order="1"/> <bond atomRefs2="a2 a3" order="1"/> <bond atomRefs2="a2 a4" order="1"/> <bond atomRefs2="a2 a5" order="1"/> <bond atomRefs2="a5 a6" order="1"/> <bond atomRefs2="a6 a7" order="2"> <bondStereo atomRefs4="a5 a6 a7 a8">T</bondStereo> </bond> <bond atomRefs2="a7 a8" order="1"/> </bondArray> </molecule> 1 molecule converted On 21 August 2012 10:53, Tim Vandermeersch <tim.vandermeer...@gmail.com> wrote: > Hi, > > On Tue, Aug 21, 2012 at 9:38 AM, Alejandro Speck Planche > <alejspivanov...@gmail.com> wrote: >> Dear colleagues >> My name is Alejandro. I've been using it several times OpenBabel program >> (version 2.3.1) for conversion to multiple molecular formats. Right now I'm >> particularly interested in how to print the atoms and / or bonds with a >> defined stereochemistry (R or S, Z or E). If there is any way to do >> OpenBabel, could someone please explain? On the other hand, if there is any >> information regarding the use of a command line, someone could explain step >> by step how to enter that command line? > > OpenBabel does not have any algorithm for determining the > Cagn-Ingold-Prelog (CIP) priorities of atoms so is not able to assign > R/S and E/Z labels. Implementing the CIP algorithm is hard to do > efficiently and there are other superior algorithm to assign unique > labels to atoms to decide if an atom is stereogenic (i.e. symmetry > classes + rules). Also, CIP does not identify some cases of > stereogenic enters. CIP priorities are mostly used for naming purposes > only. > > Tim > >> Thanks in advance, >> >> Alejandro. >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
