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Installation

Python environment

1. Download pyenv

git clone https://github.com/yyuu/pyenv.git $HOME/.pyenv

2. Setup environment for pyenv

  • Add the following lines to $HOME/.bash_profile
# Setting for pyenv and pyenv-virtualenv
export PYENV_ROOT="$HOME/.pyenv"
export PATH="$PYENV_ROOT/bin:$PATH"
if command -v pyenv 1>/dev/null 2>&1; then
    eval "$(pyenv init -)"
fi

3. Update your environment (pyenv will be installed)

source $HOME/.bash_profile

4. Install pyenv-virtualenv

git clone https://github.com/pyenv/pyenv-virtualenv.git $(pyenv root)/plugins/pyenv-virtualenv
echo 'eval "$(pyenv virtualenv-init -)"' >> $HOME/.bash_profile
source $HOME/.bash_profile

Create ReTReK implementation environment in pyenv

  • Install miniconda3.
pyenv install miniconda3-4.3.27
  • Create virtual environment using conda
conda create -n home python=3.7
pyenv global miniconda3-4.2.12/envs/home
# (Only for Ubuntu18.04 users)
# If you create the environment using environment.yml, you don't need to install the dependency libraries.
conda env create -f environment.yml
# (For NOT Ubuntu18.04 users)
conda create -n retrek python=3.7
pyenv shell miniconda3-4.2.12/envs/retrek
  • Install the dependency libraries.
conda install py4j=10.8.1 tqdm oddt mendeleev
conda install -c rdkit rdkit=2020.03.2.0
conda install keras-gpu=2.3.1 tensorflow-gpu=1.13.1 cudatoolkit=10.0
pip install --upgrade git+https://github.com/clinfo/kGCN.git

Java environment (for Ubuntu18.04)

1. Download jenv

git clone https://github.com/jenv/jenv.git ~/.jenv

2. Setup environment for jenv

  • Add the following lines to $HOME/.bash_profile
# Jenv
export PATH=${PATH}:$HOME/.jenv/bin
eval "$(jenv init -)"

3. Update your environment (pyenv will be installed)

source $HOME/.bash_profile

4. Install Java8.0

sudo apt install openjdk-8-jdk
jenv add /usr/lib/jvm/java-8-openjdk-amd64/

5. Switch the java version to 1.8

jenv global 1.8

6. Download the dependency libraries

7. Install

mkdir -p $HOME/opt/jar
sh jchem_unix_20.13.sh  # install in $HOME/opt
# put args4j-2.33.jar and commons-collections4-4.3 in $HOME/opt/jar

8. Add the path for the libralies to CLASSPATH environment variable

# ChemAxon
export PATH=$PATH:$HOME/opt/chemaxon/jchemsuite/bin
export CLASSPATH=$CLASSPATH:$HOME/opt/chemaxon/jchemsuite/lib/jchem.jar
# Jar
export CLASSPATH=$CLASSPATH:$HOME/opt/jar/commons-collections4-4.3/commons-collections4-4.3.jar:$HOME/.pyenv/versions/miniconda3-4.3.27/envs/retro/share/py4j/py4j0.10.8.1.jar:$HOME/opt/jar/args4j-2.33.jar

9. Get the ChemAxon license and its installation

For the license and instllation, please refer to the following instructions.