├── .dockerignore ├── .github └── workflows │ └── pr.yml ├── .gitignore ├── .gitlab-ci.yml ├── GNN_only.png ├── LICENSE.pdf ├── README.md ├── container ├── Dockerfile └── README.md ├── dfpl ├── __init__.py ├── __main__.py ├── autoencoder.py ├── callbacks.py ├── deepFPlearn-HyperParameterTuning.py ├── deepFPlearn-HyperParameterTuning_single.py ├── dfplmodule.py ├── feedforwardNN.py ├── fingerprint.py ├── history.py ├── options.py ├── plot.py ├── predictions.py ├── settings.py ├── single_label_model.py ├── utils.py └── vae.py ├── environment.yml ├── example ├── predict.json ├── predictgnn.json ├── train.json └── traingnn.json ├── requirements.txt ├── scripts ├── conda_env.rdkit2019.create.sh ├── conda_env.rdkit2019.yml ├── eveuge-batch-job.sh ├── eveuge-sc-job.sh ├── halirutan-batch-job.sh ├── mpcdf-batch-job-AE-sweep.sh ├── mpcdf-batch-job.sh ├── run-all-cases.sh ├── run-all-publication-cases.sh ├── run-feasible-MoleculeNet-cases.sh ├── run-feasible-MoleculeNet-cases2.sh ├── run-one-case.sh ├── submitHPtuning.sh ├── submitTrainingCPU.sh ├── submitTrainingGPU.noAC.sh └── submitTrainingGPU.sh ├── setup.cfg ├── setup.py ├── singularity_container └── environment.yaml └── tests ├── data ├── S_dataset.csv ├── inchi.tsv └── smiles.csv ├── run_autoencoder.py ├── run_fnntraining.py ├── run_predictgnn.py ├── run_prediction.py ├── run_traingnn.py ├── run_vae.py ├── test_fingerprint.py ├── test_fractional_sampling.py └── try_fpcomparison.py /.dockerignore: -------------------------------------------------------------------------------- 1 | .git* 2 | -------------------------------------------------------------------------------- /.github/workflows/pr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yigbt/deepFPlearn/HEAD/.github/workflows/pr.yml -------------------------------------------------------------------------------- /.gitignore: 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