A set of walkthrough notes for RDKit and iPython notebook installation on a
Debian based Linux machine.
Build RDkit from source.
Instructions take from page
http://www.rdkit.org/docs/Install.html#building-from-source
[1] First Install these dependencies on Debian based Linux system.
apt-get update
apt-get install flex bison build-essential python-numpy cmake
python-dev sqlite3 libsqlite3-dev libboost-dev libboost-python-dev
libboost-regex-dev
=> boost libraries installed to /usr/lib
[2] Download rdkit 2013 Q3 release from
Download RDkit source from
http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2013/
Unzip and untar to ~/apps/rdkit/
=> Directory ~/apps/rdkit/RDKit_2013_09_1
Ensure these lines in ~/.bashrc file to set environment variables
export RDBASE=/home/chemuser/apps/
rdkit/RDKit_2013_09_1
export LD_LIBRARY_PATH=$RDBASE/lib:/usr/lib/:$LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$RDBASE/lib/:$PYTHONPATH
Open new bash shell, then build source.
cd $RDBASE
mkdir build
cd build
cmake ..
make
sudo make install
Run RDkit build tests
cd $RDBASE/build
ctest
=> 77 out of 78 tests passed (99%)
=> only test number 78 failed - pythonTestDirChem
[3] Install ipython notebook
(as root)
apt-get install ipython-notebook
[4] Run simple python script test for presence of RDkit
Create script ~/code/rdkit/test-rdkit.py with 2 lines of code
from rdkit import rdBase
print rdBase.rdkitVersion
=> prints version 2013.09.1
[5] Start ipython notebook with command line
ipython notebook
Select option to create new notebook, paste two lines of code from above
into input box.
Use shift-enter to run code
=> prints version 2013.09.1
The ipython notebook and RDkit are installed and ready for use.
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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>>
>>
>
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