Thank you Greg, It was that simple!
export PYTHONPATH=/usr/lib/python2.7/dist-packages/:$PYTHONPATH
On 20 October 2016 at 14:40, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Thomas,
>
> The first thing I would check is that you are actually running the system
> version of Python and that you PYTHONPATH is not set.
>
> -greg
>
>
> _____________________________
> From: Thomas Evangelidis <teva...@gmail.com>
> Sent: Wednesday, October 19, 2016 8:10 AM
> Subject: [Rdkit-discuss] installation issues
> To: <rdkit-discuss@lists.sourceforge.net>
>
>
>
> Greetings everyone,
>
> I use Ubuntu 14.04.4 LTS and first I tried to install RDkit through Conda.
> After getting a strange segmentation fault when invoking USRCAT functions
> that imported scipy, I managed to fix it by installing accelerate
> libraries:
>
> conda install accelerate
>
>
> However, in order to use RDkit from my own programs, I 'll have to
> install every python package I need inside the rdkit environment that I
> created ("my-rdkit-env"), which is tedious and disk space consuming.
> Therefore I 'd prefer to use the Ubuntu repository RDkit version. So I
> did:
>
> sudo apt-get install python-rdkit librdkit1 rdkit-data
>
>
> But python2.7 cannot find it:
>
> from rdkit import Chem
>> ImportError: No module named rdkit
>
>
> So my questions are, do I also need to set the environment variables
>
> RDBASE,
>
> LD_LIBRARY_PATH and
>
> PYTHONPATH in order to run RDkit? In that case how should I set
> LD_LIBRARY_PATH,
> since there is no lib/ folder in the installation directory?
>
> $ ll /usr/lib/python2.7/dist-packages/rdkit/
>> total 1096
>> drwxr-xr-x 2 root root 4096 ott 19 00:34 Avalon
>> drwxr-xr-x 17 root root 4096 ott 19 00:34 Chem
>> drwxr-xr-x 3 root root 4096 ott 19 00:34 DataManip
>> drwxr-xr-x 2 root root 4096 ott 19 00:34 DataStructs
>> drwxr-xr-x 3 root root 4096 ott 19 00:34 Dbase
>> drwxr-xr-x 2 root root 4096 ott 19 00:34 DistanceGeometry
>> -rw-r--r-- 1 root root 436 nov 2 2013 epydoc.config
>> drwxr-xr-x 2 root root 4096 ott 19 00:34 ForceField
>> drwxr-xr-x 2 root root 4096 ott 19 00:34 Geometry
>> -rw-r--r-- 1 root root 0 nov 2 2013 __init__.py
>> -rw-r--r-- 1 root root 137 ott 19 00:34 __init__.pyc
>> drwxr-xr-x 2 root root 4096 ott 19 00:34 Logger
>> drwxr-xr-x 16 root root 4096 ott 19 00:34 ML
>> drwxr-xr-x 2 root root 4096 ott 19 00:34 Numerics
>> -rw-r--r-- 1 root root 1000464 dic 29 2013 rdBase.so
>> -rw-r--r-- 1 root root 2049 nov 2 2013 RDConfig.py
>> -rw-r--r-- 1 root root 2026 ott 19 00:34 RDConfig.pyc
>> -rw-r--r-- 1 root root 1536 nov 2 2013 RDLogger.py
>> -rw-r--r-- 1 root root 2654 ott 19 00:34 RDLogger.pyc
>> -rw-r--r-- 1 root root 394 dic 29 2013 RDPaths.py
>> -rw-r--r-- 1 root root 463 ott 19 00:34 RDPaths.pyc
>> -rw-r--r-- 1 root root 803 nov 2 2013 RDRandom.py
>> -rw-r--r-- 1 root root 680 ott 19 00:34 RDRandom.pyc
>> drwxr-xr-x 2 root root 4096 ott 19 00:34 SimDivFilters
>> drwxr-xr-x 15 root root 4096 ott 19 00:34 sping
>> -rw-r--r-- 1 root root 5737 nov 2 2013 TestRunner.py
>> -rw-r--r-- 1 root root 5029 ott 19 00:34 TestRunner.pyc
>> drwxr-xr-x 2 root root 4096 ott 19 00:34 utils
>> drwxr-xr-x 3 root root 4096 ott 19 00:34 VLib
>
>
>
> Thanks in advance for any advice.
> Thomas
>
>
>
>
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