Dear Jessica,
The problem is that PYTHONPATH and LD_LIBRARY_PATH are not set for your
IDLE session. This is probably because you set your variables in your
.bashrc and then you are starting IDLE from your GNOME/KDE start menu,
so .bashrc is not sourced. If you start your IDLE session from your
terminal, everything should work. Alternatively, you may set your
PYTHONPATH and LD_LIBRARY_PATH in a place where KDE and GNOME can source
them; check
http://superuser.com/questions/121261/how-can-i-set-environment-variables-for-a-graphical-login-on-linux
for how to do that.
As a (rather awful) workaround, you may echo $LD_LIBRARY_PATH in your
terminal, and add the following in your Python script:
sys.path.append('/opt/rdkit-Release_2016_03_1')
os.environ['LD_LIBRARY_PATH'] = 'value of LD_LIBRARY_PATH shown in the
terminal'
But it would be far better to fix your environment variables before
starting IDLE.
Cheers,
p.
On 07/20/16 09:51, Jessica Krause wrote:
> Hello David,
>
> it shows:
>
> >>> import os
> >>> os.environ["PYTHONPATH"]
>
> Traceback (most recent call last):
> File "<pyshell#4>", line 1, in <module>
> os.environ["PYTHONPATH"]
> File "/usr/lib/python2.7/UserDict.py", line 40, in __getitem__
> raise KeyError(key)
> KeyError: 'PYTHONPATH'
>
>
> And Paolo gave me yesterday the hint to add the following:
>
> import sys
> sys.path.append('/opt/rdkit-Release_2016_03_1')
>
>
> but then I get the following error:
>
> >>> import sys
> >>> sys.path.append('/opt/rdkit-Release_2016_03_1')
> >>> from rdkit import Chem
>
> Traceback (most recent call last):
> File "<pyshell#7>", line 1, in <module>
> from rdkit import Chem
> File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line 18,
> in <module>
> from rdkit import rdBase
> ImportError: libRDBoost.so.1: cannot open shared object file: No such
> file or directory
>
> But in Terminal and IPython console/notebook everything works fine. I
> don't know what exactly is set wrong or installed wrong.
>
>
> On 19.07.2016 18:42, David Hall wrote:
>> what does os.environ["PYTHONPATH”] show when you are in IDLE?
>>
>>
>>> On Jul 19, 2016, at 12:26 PM, Jessica Krause <jessica.kra...@tu-bs.de>
>>> wrote:
>>>
>>> Dear All,
>>>
>>> I installed the new release of Rdkit in Ubunutu 16.04. I am not able to
>>> import rdkit module in my IDLE and Spyder after installing the new
>>> release 2016.
>>> It works in terminal and Ipython Notebook but shows error in IDLE and
>>> Spyder.
>>>
>>> In Terminal:
>>>
>>> Python 2.7.12 (default, Jul 1 2016, 15:12:24)
>>> [GCC 5.4.0 20160609] on linux2
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>> from rdkit import rdBase
>>>>>> print rdBase.rdkitVersion
>>> 2016.03.1
>>>>>> import os
>>>>>> os.environ["PYTHONPATH"]
>>> '/opt/rdkit-Release_2016_03_1:'
>>> In IDLE/Spyder:
>>>
>>> Python 2.7.12 (default, Jul 1 2016, 15:12:24)
>>> [GCC 5.4.0 20160609] on linux2
>>> Type "copyright", "credits" or "license()" for more information.
>>>>>> from rdkit import rdBase
>>> Traceback (most recent call last):
>>> File "<pyshell#0>", line 1, in <module>
>>> from rdkit import rdBase
>>> ImportError: No module named rdkit
>>>
>>> Can somebody help me with this!
>>>
>>>
>>> Thanks & Regards,
>>>
>>> Jessica
>>>
>>>
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reports.http://sdm.link/zohodev2dev
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