RDKit installation in Virtual environment

Here are the steps to install RDKit in the Virtual environment. I used Ubuntu 16.04

• Create virtual environment, for which a create directory and make VM on it.

mkdir VM1

python -m virtualenv VM1 (python3 -m virtualenv VM1 )

• Activate the virtual environment

source ~/VEs/VM1/bin/activate

• Requisites of RDKit from pip

pip install numpy matplotlib boost yapf coverage cmake pandas
(pip3 install numpy matplotlib boost yapf coverage cmake pandas)

• Packages needed for the installation of boost

sudo apt install build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev libboost-dev libboost-system-dev libboost-thread-dev libboost-serialization-dev libboost-python-dev libboost-regex-dev
(sudo apt install build-essential python3-numpy cmake python3-dev sqlite3 libsqlite3-dev libboost-dev libboost-system-dev libboost-thread-dev libboost-serialization-dev libboost-python-dev libboost-regex-dev)

• Download boost library
• Installation of boost in virtual environment

tar zxvf boost_1_66_1.tar.gz

cd boost_1_66_1

• Bootstrapping boost in the VE location

./bootstrap.sh --prefix=/home/CD/CLPB/VEs/VM1 (here prefix path is location where lib directory exists in VE)

• Building boost

./b2 (this step takes a while to complete)

• SWIG installation, download it from here (into tools directory under VE - used this option just to keep all the tools together).

tar zxvf swig-3.0.12.tar.gz

cd swig-3.0.12

./configure --prefix=/home/CD/CLPB/VEs/VM1 (here prefix path is location where lib directory exists in VE)

make -j 6 (to let use the process 6 cpus)

make check (check will take a while as it checks multiple languages compatibility)

make install

• Packages need for RDKit in ubuntu

sudo apt install doxygen

• Download latest RDKit from tags

cp rdkit-Release_2017_09_3.tar.gz /home/CD/CLPB/VEs/VM1/
cd /home/CD/CLPB/VEs/VM1/

tar zxvf rdkit-Release_2017_09_3.tar.gz

mv rdkit-Release_2017_09_3 RDKit

• Paths are set in /home/CD/CLPB/VEs/VM1/bin/activate file where the Virtual environment activate file exists.

########## Paths for RDKit
export RDBASE="/home/CD/CLPB/VEs/VM1/RDKit"
export PYTHONPATH="$RDBASE:/home/CD/CLPB/VEs/VM1/lib:/home/CD/CLPB/VEs/VM1/local/lib:/home/CD/CLPB/VEs/VM1/bin/python2.7"
export LD_LIBRARY_PATH="$RDBASE/lib"
export LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"

• Building RDKit

cd RDKit

mkdir build

cd build

• cmake options to install in VE and use the Boost libraries which are installed in VE

cmake -DBOOST_ROOT=/home/CD/CLPB/VEs/VM1/lib -DCMAKE_INSTALL_PREFIX=/home/CD/CLPB/VEs/VM1 .. (cmake command is complete one command at a time)

• Make the RDKit installation

make -j 6 (to let use the process 6 cpus)

make install

• Test the installation with ctest

ctest