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
