├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _templates │ └── layout.html ├── api │ ├── drugex.data.corpus.rst │ ├── drugex.data.rst │ ├── drugex.logs.rst │ ├── drugex.molecules.converters.rst │ ├── drugex.molecules.rst │ ├── drugex.parallel.rst │ ├── drugex.rst │ ├── drugex.training.explorers.rst │ ├── drugex.training.generators.rst │ ├── drugex.training.rst │ ├── drugex.training.scorers.rst │ ├── drugex.utils.rst │ └── modules.rst ├── conf.py ├── index.rst ├── install.rst ├── make.sh ├── requirements.txt ├── upload.sh └── use.rst ├── drugex ├── __init__.py ├── about.py ├── data │ ├── __init__.py │ ├── corpus │ │ ├── __init__.py │ │ ├── corpus.py │ │ ├── interfaces.py │ │ ├── tests.py │ │ └── vocabulary.py │ ├── datasets.py │ ├── fragments.py │ ├── interfaces.py │ ├── processing.py │ ├── tests.py │ └── utils.py ├── dataset.py ├── download.py ├── generate.py ├── logs │ ├── __init__.py │ ├── config.py │ └── utils.py ├── molecules │ ├── __init__.py │ ├── converters │ │ ├── __init__.py │ │ ├── default.py │ │ ├── dummy_molecules.py │ │ ├── fragmenters.py │ │ ├── interfaces.py │ │ ├── standardizers.py │ │ └── tests.py │ ├── interfaces.py │ ├── mol.py │ └── suppliers.py ├── parallel │ ├── __init__.py │ ├── collectors.py │ ├── evaluator.py │ ├── interfaces.py │ ├── test_files │ │ └── test.tsv │ └── tests.py ├── train.py ├── training │ ├── __init__.py │ ├── environment.py │ ├── explorers │ │ ├── __init__.py │ │ ├── frag_graph_explorer.py │ │ ├── frag_sequence_explorer.py │ │ ├── interfaces.py │ │ └── sequence_explorer.py │ ├── generators │ │ ├── __init__.py │ │ ├── graph_transformer.py │ │ ├── interfaces.py │ │ ├── sequence_rnn.py │ │ ├── sequence_transformer.py │ │ └── utils.py │ ├── interfaces.py │ ├── monitors.py │ ├── rewards.py │ ├── scorers │ │ ├── __init__.py │ │ ├── fpscores.pkl.gz │ │ ├── interfaces.py │ │ ├── modifiers.py │ │ ├── properties.py │ │ ├── qsprpred.py │ │ ├── ra_scorer.py │ │ ├── sascorer.py │ │ ├── similarity.py │ │ └── smiles.py │ ├── test_data │ │ ├── A2AR_RF_cls │ │ │ ├── A2AR_RF_cls.json │ │ │ └── A2AR_RF_cls_meta.json │ │ ├── A2AR_RF_multicls │ │ │ ├── A2AR_RF_multicls.json │ │ │ └── A2AR_RF_multicls_meta.json │ │ ├── A2AR_RF_reg │ │ │ ├── A2AR_RF_reg.json │ │ │ └── A2AR_RF_reg_meta.json │ │ ├── A2AR_raw_small.txt │ │ ├── AR_RF_cls │ │ │ ├── AR_RF_cls.json │ │ │ └── AR_RF_cls_meta.json │ │ ├── AR_RF_reg │ │ │ ├── AR_RF_reg.json │ │ │ └── AR_RF_reg_meta.json │ │ ├── ZINC_raw_small.txt │ │ └── create_test_qsar.py │ └── tests.py └── utils │ ├── __init__.py │ ├── download.py │ ├── fingerprints.py │ ├── gcmol.py │ ├── optim.py │ └── pareto.py ├── figures ├── TOC_figure.png ├── fig_1.png ├── fig_2.png ├── fig_3.png └── logo.png ├── pyproject.toml ├── scripts └── drugex ├── testing ├── clitest │ ├── README.md │ ├── data │ │ ├── A2AR_raw_small.tsv │ │ ├── ZINC_raw_small.tsv │ │ ├── pyrazines.tsv │ │ ├── voc_graph.txt │ │ └── voc_smiles.txt │ ├── env.sh │ ├── qsar │ │ └── A2AR_RandomForestClassifier │ │ │ ├── A2AR_RandomForestClassifier.json │ │ │ └── A2AR_RandomForestClassifier_meta.json │ ├── test.sh │ ├── test_graph_trans.sh │ ├── test_seq_rnn.sh │ └── test_seq_trans.sh ├── modeltest │ ├── .gitignore │ ├── README.md │ ├── __init__.py │ ├── graph │ │ ├── __init__.py │ │ ├── pretrain.py │ │ ├── processing.py │ │ └── run.py │ ├── plot.py │ ├── qsub.sh │ ├── requirements.txt │ ├── rnn │ │ ├── __init__.py │ │ ├── pretrain.py │ │ ├── processing.py │ │ └── run.py │ ├── run.py │ ├── run.sh │ ├── seq_trans │ │ ├── __init__.py │ │ ├── pretrain.py │ │ ├── processing.py │ │ └── run.py │ └── settings.py └── runner │ ├── .gitignore │ ├── Dockerfile │ ├── README.md │ ├── docker-compose.yml │ ├── entrypoint.sh │ ├── runner.sh │ └── tests.sh └── tutorial ├── CLI └── README.md ├── Graph-Transformer.ipynb ├── README.md ├── Sequence-RNN.ipynb ├── advanced ├── __init__.py ├── extending_api.ipynb ├── multitask_scorers.ipynb └── scaffold_based.ipynb ├── colab.sh ├── images 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