Can you confirm that you're using OB 2.3.2? It works fine for me on Windows:
C:\Users\Noel>python Python 2.7.1 (r271:86832, Nov 27 2010, 18:30:46) [MSC v.1500 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> import pybel >>> pybel.readstring('smi','[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C(=O)CC 4)c(cc3)O)O') <pybel.Molecule object at 0x02807810> >>> mol = pybel.readstring('smi','[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C >>> mol.write("smi") '[C@]123[C@@]4([C@H](N(CC1)CC=C)Cc1c2c(O[C@H]3C(=O)CC4)c(cc1)O)O\t\n' >>> On 21 March 2013 14:43, david.lagorce <david.lago...@univ-paris-diderot.fr> wrote: > Dear Noel, > > > I am still searching what is wrong with that kind of molecules. > I wrote the problematic molecule in "bug.sdf" and the smiles generated by > pybel (the same by babel -i bug.sdf -o bug2.smi) in "bug.smi > > > The smiles is ok in depiction by Daylight: > http://www.daylight.com/daycgi/depict?5b43405d3132335b4340405d34285b4340485d284e284343332943433d4329436333633163284f5b4340485d3243283d4f29434334296328636333294f294f > > > > > Python 2.7.3 (default, Mar 21 2013, 14:15:19) > [GCC 4.3.2] on linux2 > Type "help", "copyright", "credits" or "license" for more information. >>>> import pybel >>>> mol = pybel.readfile("sdf","bug.sdf").next() >>>> mol.write() > '[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C(=O)CC4)c(cc3)O)O\tNALOXONE\n' >>>> >>>> >>>> pybel.readstring('smi','[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C(=O)CC4)c(cc3)O)O') > Segmentation fault >>>> mol = pybel.readfile("smi","bug.smi").next() > Segmentation fault > > > Do you have an idea? > > Thanks for all > > > > > > -- > View this message in context: > http://forums.openbabel.org/segmentation-fault-tp4656023p4656087.html > Sent from the openbabel-devel mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel