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.
>>>
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
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
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'