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.
>
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