Re: [Rdkit-discuss] installation issues

[Greg L. <gre...@gm...>]

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 <te...@gm...>
Sent: Wednesday, October 19, 2016 8:10 AM
Subject: [Rdkit-discuss] installation issues
To:  <rdk...@li...>


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