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 <[email protected]>
Sent: Wednesday, October 19, 2016 8:10 AM
Subject: [Rdkit-discuss] installation issues
To: <[email protected]>
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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