Install RDKit 2015-03 Build on Ubuntu 14.04 / Linux Mint 17

Share Tweet

RDKit is an open source toolkit for cheminformatics. It has many functionalities to work with chemical files.

RDKit Logo

Follow the below guide to install RDKit 2015-03 build on an Ubuntu 14.04 / Linux Mint 17 computer. Since Ubuntu packages don’t have the latest RDKit for trusty, you have to build RDKit from its source.

Install Dependencies

sudo apt-get install flex bison build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev libboost1.54-all-dev

Download the Build

cd /usr/local
sudo wget http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2015/RDKit_2015_03_1.tgz
sudo tar -xzf RDKit_2015_03_1.tgz
sudo mv rdkit-Release_2015_03_1/ rdkit
cd rdkit/
sudo mkdir build

Set Environment Variables

vim ~/.bashrc

Enter following three lines at the end of .bashrc

export RDBASE="/usr/local/rdkit"
export PYTHONPATH="$RDBASE:$PYTHONPATH"
export LD_LIBRARY_PATH="$RDBASE/lib"
source ~/.bashrc

Download InChi API

Optional, remove the argument -DRDK_BUILD_INCHI_SUPPORT=ON in the next step if you skip.

cd $RDBASE/External/INCHI-API
sudo bash download-inchi.sh

Build

cd $RDBASE/build
sudo cmake -DRDK_BUILD_INCHI_SUPPORT=ON ..
sudo make
sudo make install

Verify

python
>>> import rdkit
>>> rdkit.rdBase.rdkitVersion
'2015.03.1'

Please comment if you have any issue with this installation.

Share Tweet

Questions?

Please start a discussion down below or send me an email!