[Rdkit-discuss] installation issues

[Thomas E. <te...@gm...>]

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