Amide N is sp2-hybridised. I guess the concept doesn't really extend to most elements such as Cl.
- Noel On 21 September 2012 15:41, Pascal Muller <pascal.jm.mul...@gmail.com> wrote: > Hi, > > I would like to use the pybel "hyb" attribute (corresponding to > OBAtom::GetHyb() ) > Docs says that it gives the hybridization of the atom: 1 for sp, 2 for sp2, > 3 for sp3, ... > > But some sp3 atoms have 2 or 0 for hyb. (Using Open Babel 2.3.1) > > mol = pybel.readstring( "smi", "C(Cl)NC(=O)C") > for a in mol.atoms: > print "Atom %d" % a.idx, a.OBAtom.GetAtomicNum(), a.hyb > > Output : > Atom 1 6 3 # sp3, correct > Atom 2 17 0 # sp3, incorrect > Atom 3 7 2 # sp3, incorrect > Atom 4 6 2 # sp2, correct > Atom 5 8 2 # sp2, correct > Atom 6 6 3 # sp3, correct > > But with C(Cl)NCC(=O)C : > Atom 1 6 3 > Atom 2 17 0 > Atom 3 7 3 # different, now 3 instead of 2 > Atom 4 6 3 # sp3, correct > Atom 5 6 2 > Atom 6 8 2 > Atom 7 6 3 > > Do I misinterpret something? > > Thanks, > Regards, > Pascal > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Got visibility? Most devs has no idea what their production app looks like. Find out how fast your code is with AppDynamics Lite. http://ad.doubleclick.net/clk;262219671;13503038;y? http://info.appdynamics.com/FreeJavaPerformanceDownload.html _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
