├── .gitblameignore ├── .github └── workflows │ ├── build.yml │ ├── gh_pages.yml │ ├── jscpd.json │ ├── pypi.yml │ ├── style.yml │ └── suggest.yml ├── .gitignore ├── LICENSE ├── README.md ├── bin └── pytoda-filter-invalid-smi ├── conda.yml ├── dev_requirements.txt ├── docs ├── Makefile ├── _static │ └── logo.png ├── _templates │ ├── module.rst │ └── package.rst ├── app.py ├── conf.py ├── index.md └── make.bat ├── examples ├── README.md ├── smiles_to_fingerprints.py ├── smiles_vocab_creator.py ├── split_csv_data.py └── vocab_from_legacy_language.py ├── pyproject.toml ├── pytoda ├── __init__.py ├── data_splitter.py ├── datasets │ ├── __init__.py │ ├── _cache_datasource.py │ ├── _csv_eager_dataset.py │ ├── _csv_lazy_dataset.py │ ├── _csv_statistics.py │ ├── _fasta_eager_dataset.py │ ├── _fasta_lazy_dataset.py │ ├── _smi_eager_dataset.py │ ├── _smi_lazy_dataset.py │ ├── _table_dataset.py │ ├── annotated_dataset.py │ ├── base_dataset.py │ ├── dataframe_dataset.py │ ├── distributional_dataset.py │ ├── drug_affinity_dataset.py │ ├── drug_sensitivity_dataset.py │ ├── drug_sensitivity_dose_dataset.py │ ├── gene_expression_dataset.py │ ├── polymer_dataset.py │ ├── protein_protein_interaction_dataset.py │ ├── protein_sequence_dataset.py │ ├── set_matching_dataset.py │ ├── smiles_dataset.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_annotated_dataset.py │ │ ├── test_base_dataset.py │ │ ├── test_distributional_dataset.py │ │ ├── test_drug_affinity_dataset.py │ │ ├── test_drug_sensitivity_dataset.py │ │ ├── test_drug_sensitivity_dose_dataset.py │ │ ├── test_gene_expression_dataset.py │ │ ├── test_polymer_dataset.py │ │ ├── test_protein_protein_interaction_dataset.py │ │ ├── test_protein_sequence_dataset.py │ │ ├── test_set_matching_dataset.py │ │ └── test_smiles_datasets.py │ └── utils │ │ ├── __init__.py │ │ ├── background_tensors.py │ │ ├── factories.py │ │ ├── utils.py │ │ └── wrappers.py ├── files.py ├── preprocessing │ ├── __init__.py │ ├── crawlers.py │ ├── smi.py │ └── tests │ │ ├── __init__.py │ │ ├── test_crawlers.py │ │ └── test_smi.py ├── proteins │ ├── __init__.py │ ├── metadata │ │ ├── __init__.py │ │ └── kinase_activesite_alignment.smi │ ├── processing.py │ ├── protein_feature_language.py │ ├── protein_language.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_processing.py │ │ ├── test_protein_feature_language.py │ │ ├── test_protein_language.py │ │ └── test_utils.py │ ├── transforms.py │ └── utils.py ├── smiles │ ├── __init__.py │ ├── metadata │ │ ├── ATTRIBUTION │ │ ├── README.md │ │ ├── __init__.py │ │ ├── spe_chembl.txt │ │ └── tokenizer │ │ │ ├── README.txt │ │ │ ├── token_count.json │ │ │ ├── tokenizer_config.json │ │ │ └── vocab.json │ ├── polymer_language.py │ ├── processing.py │ ├── smiles_language.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_polymer_language.py │ │ ├── test_processing.py │ │ ├── test_smiles_language.py │ │ └── test_transforms.py │ └── transforms.py ├── tests │ ├── __init__.py │ ├── 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