Binding_affinity

Drug design, Machine learning, MPNN

Installing libraries

• Install Anaconda
• Create conda environment

  * $ conda create --name <env_name> python={3.6 or 3.7}
  * $ conda activate <env_name>

• RDKit conda install -q -y -c conda-forge rdkit
• Pytorch+cpu conda install pytorch torchvision cpuonly -c pytorch
• Pytorch geometric

  python3 -m pip install torch-scatter==latest+cu101 -f https://pytorch-geometric.com/whl/torch-1.4.0.html
  python3 -m pip install torch-sparse==latest+cu101 -f https://pytorch-geometric.com/whl/torch-1.4.0.html
  python3 -m pip install torch-cluster==latest+cu101 -f https://pytorch-geometric.com/whl/torch-1.4.0.html
  python3 -m pip install torch-spline-conv==latest+cu101 -f https://pytorch-geometric.com/whl/torch-1.4.0.html
  python3 -m pip install torch-geometric
  

Execution

python data_prep.py -d data.csv -s sampling -t train_size
python model.py @arguments.txt >> result.txt