Re: [Rdkit-discuss] ImportError: No module named rdkit

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

Hi Loris,

On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett <lor...@fu...>
wrote:

>
> I am trying to install RDKit on a university cluster running Linux from
> source.  The build seem to go OK and 'make install' copied the
> directories
>
>   lib
>   rdkit
>
> to the NFS share where the software should reside.  I then do
>
>   export RDBASE=/cm/shared/apps/rdkit/rdkit_2017_03_3
>   export PYTHONPATH=$PYTHONPATH:$RDBASE
>   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib
>
> However when I then run Python (2.6.6) and try
>

Just to do some expectation management: python 2.6 is pretty ancient and
there's no guarantee that all of the RDKit code will work with it. Python
2.7 is the minimum version that we "officially" support. It's a very good
idea to update.


>   import rdkit
>
> I get
>
>   ImportError: No module named rdkit
>
> I am not a Python person and my naive expectation was that there should
> be a file called
>
>   rdkit.py
>

Based on the info provided so far, there should be a directory called rdkit
in the directory:
/cm/shared/apps/rdkit/rdkit_2017_03_3
That directory should contain a number of sub dirs, other files, and a file
called __init__.py (this is the one that tells Python that it can import
the directory as a package).
What do you see there?



> which has to be on my PYTHONPATH.  However, since the unpacked sources
> together with the build don't seem to contain such a file, either
> something is broken or the rdkit module should be found by some other
> mechanism.
>

Again, based on the info above, I would expect that you want "make install"
to copy the "rdkit" and "lib" directories (as well as a couple others) to
/cm/shared/apps/rdkit/rdkit_2017_03_3. Once we figure out what actually
happened I can maybe help you figure out how to fix it.

best.
-greg



> Any ideas what I'm doing wrong or what initialisation file I should
> ensure is on my PYTHONPATH?
>
> Cheers,
>
> Loris
>
> --
> Dr. Loris Bennett (Mr.)
> ZEDAT, Freie Universität Berlin         Email lor...@fu...
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>