tree_based_molecule_generation

1. Setting up the environment

You can set up the environment by following commands. You need to specify cudatoolkit version and torch geometric versions accordinly to your local computing device.

conda create -n mol python=3.7
conda install -y pytorch cudatoolkit=10.1 -c pytorch
conda install -y tqdm
conda install -y -c conda-forge neptune-client
conda install -y -c conda-forge rdkit

pip install pytorch-lightning
pip install neptune-client[pytorch-lightning]

pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.8.1+cu111.html
pip install torch-sparse -f https://pytorch-geometric.com/whl/torch-1.8.1+cu111.html
pip install torch-cluster -f https://pytorch-geometric.com/whl/torch-1.8.1+cu111.html
pip install torch-spline-conv -f https://pytorch-geometric.com/whl/torch-1.8.1+cu111.html
pip install torch-geometric

pip install cython
pip install molsets

2. Executing the scripts

You can execute the scripts in the following order.

CUDA_VISIBLE_DEVICES=${GPU} bash generator_moses_hparam0.sh
CUDA_VISIBLE_DEVICES=${GPU} bash generator_moses_hparam1.sh
CUDA_VISIBLE_DEVICES=${GPU} bash generator_moses_hparam2.sh
CUDA_VISIBLE_DEVICES=${GPU} bash generator_moses_hparam3.sh
CUDA_VISIBLE_DEVICES=${GPU} bash generator_moses_hparam4.sh
CUDA_VISIBLE_DEVICES=${GPU} bash generator_moses_hparam5.sh
CUDA_VISIBLE_DEVICES=${GPU} bash generator_zinc_hparam0.sh
CUDA_VISIBLE_DEVICES=${GPU} bash generator_zinc_hparam1.sh
CUDA_VISIBLE_DEVICES=${GPU} bash generator_qm9_hparam0.sh
CUDA_VISIBLE_DEVICES=${GPU} bash generator_qm9_hparam1.sh
CUDA_VISIBLE_DEVICES=${GPU} bash smiles_generator_moses.sh
CUDA_VISIBLE_DEVICES=${GPU} bash smiles_generator_zinc.sh
CUDA_VISIBLE_DEVICES=${GPU} bash smiles_generator_qm9.sh