Download anaconda/miniconda if needed
Create a rdkit environment that directly contains rdkit:
conda create -c conda-forge -n digress rdkit=2023.03.2 python=3.9
conda activate digress
Check that this line does not return an error:
python3 -c 'from rdkit import Chem'
Install graph-tool:
conda install -c conda-forge graph-tool=2.45
Check that this line does not return an error:
python3 -c 'import graph_tool as gt'
Install the nvcc drivers for your cuda version. For example:
conda install -c "nvidia/label/cuda-11.8.0" cuda
Install a corresponding version of pytorch, for example:
pip3 install torch==2.0.1 --index-url https://download.pytorch.org/whl/cu118
Install other packages using the requirement file:
pip install -r requirements.txt
Run:
pip install -e .
Navigate to the ./src/analysis/orca directory and compile orca.cpp:
g++ -O2 -std=c++11 -o orca orca.cpp
Please download the zip files via here and unzip it into the folder in the root folder
- graphsseed
cd src
Pre-training: Train on QM9Topo and evaluate on all other domains, Training on {Domain} and Evaluate on all wo {Domain}
bash run_train_seed_marginal.sh
bash run_test_seed_marginal.sh
bash run_test_qm9topo_others_seed_marginal.sh
bash run_train_ft_seed_marginal.sh
bash run_train_qm9topo_ft_seed_marginal.sh
bash run_test_ft_seed_marginal.sh
bash run_test_qm9topo_ft_seed_marginal.sh
run_train_seed_marginal_direct.sh
run_test_seed_marginal_direct.sh
run_test_qm9topo_qm9topo_seed_marginal.sh
run_train_ft_marginal_analysis.sh
run_test_ft_marginal_analysis.sh
bash run_train_seed_marginal_direct_analysis.sh
bash run_test_seed_marginal_direct_analysis.sh
bash run_train_marginal_all.sh
bash run_test_marginal_all.sh
Pre-training: Train on QM9Topo and evaluate on all other domains, Train on {Domain} and Evaluate on all wo {Domain}
bash run_train_seed_uniform.sh
bash run_test_seed_uniform.sh
bash run_test_qm9topo_others_seed_uniform.sh
bash run_train_ft_seed_uniform.sh
bash run_train_qm9topo_ft_seed_uniform.sh
bash run_test_ft_seed_uniform.sh
bash run_test_qm9topo_ft_seed_uniform.sh
run_train_seed_uniform_direct.sh
run_test_seed_uniform_direct.sh
run_test_qm9topo_qm9topo_seed_uniform.sh
run_train_ft_uniform_analysis.sh
run_test_ft_uniform_analysis.sh
bash run_train_seed_uniform_direct_analysis.sh
bash run_test_seed_uniform_direct_analysis.sh
bash run_train_uniform_all.sh
bash run_test_uniform_all.sh
Note that this repository is heavily built upon a public GitHub repository DiGress.