George
Thanks for the course and for the RDkit advice. I was having a few issues,
which I traced down to the PYTHONPATH environment variables. I made the
mistake of setting them within .bashrc in the following form
export RDBASE=/home/chemuser/apps/rdkit/RDKit_2013_09_1
export PYTHONPATH=$PYTHONPATH:$RDBASE:$RDBASE/lib
Since PYTHONPATH was not initially set I ended up with an environment
variable that started with : and seemed not to work. If I put $PYTHONPATH
at the end with the following line, it all seems OK.
export PYTHONPATH=$RDBASE:$RDBASE/lib:$PYTHONPATH
For my Debian based system (Crunchbang Linux 32 bit VM) I documented the
installation for RDKit and the ipython notebook as completely as I could.
I will send these notes shortly, just in case they are useful to other
users.
Mark
On Mon, Dec 23, 2013 at 2:09 PM, George Papadatos <gpapada...@gmail.com>wrote:
> Hi Mark,
>
> Good to hear the workshop was effective!
> Not sure what OS you use or how your python is set up but try adding the
> RDKit folder path to your PYTHONPATH. Then launch a python prompt and type:
> >>from rdkit import rdBase
> >>print rdBase.rdkitVersion
>
> if this works fine, then you'd be able to use RDKit with ipython and
> ipython notebook.
>
> Hope this helps.
>
> George
>
> ---------------------------
> George Papadatos
> EMBL-EBI
>
>
>
>
> On 23 December 2013 12:42, Mark Forster <markf.opensou...@gmail.com>wrote:
>
>> RDkit team and users
>>
>> I have just joined the RDkit discuss mailing list and as a newbie to
>> RDkit I have some entry level questions.
>> I did a quick search of the mailing list and some google searching, but
>> no clear solution popped up.
>> Can I get some pointers to this simple question?
>>
>> If the RDkit tools are installed as described here:
>> http://rdkit.readthedocs.org/en/latest/Install.html
>>
>> What additional steps are required to get the RDkit functionality working
>> in an ipython notebook?
>>
>> Experience suggests it might be something like setting PYTHONPATH but
>> does a step by step guide exist?
>> I saw the functionality demonstrated and used extensively at a recent EBI
>> training workshop. Fantastic stuff.
>> It is available with the MyCHEMBL virtual machine download, but at 18GB
>> this is a network hog.
>> Hence I would just like to get the installation steps needed to get RDkit
>> and iPython NB working in harmony.
>>
>> regards
>>
>> Mark Forster
>>
>>
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