[OpenBabel-Devel] segmentation fault

2013-03-06 Thread david.lagorce
Dear all I am in trouble with some molecules which are ending my script. When I run in a python interpreter with a sample molecule I get that message: Python 2.6.6 (r266:84292, Feb 11 2011, 09:52:37) [GCC 4.3.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>>

Re: [OpenBabel-Devel] segmentation fault

2013-03-06 Thread Noel O'Boyle
Somethings wrong with the SMILES string. Daylight won't accept it for example: http://www.daylight.com/daycgi/depict?5b43405d3132335b4340405d34285b4340485d285b4e5d2843433543433529434333294329436333633163284f5b4340485d3243283d4f29434334296328636333294f294f We should fix the segmentation fault thou

Re: [OpenBabel-Devel] segmentation fault

2013-03-21 Thread david.lagorce
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?5b43

Re: [OpenBabel-Devel] segmentation fault

2013-03-24 Thread Noel O'Boyle
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'