├── .gitattributes ├── .github ├── dependabot.yml └── workflows │ ├── publish_to_pypi.yaml │ └── tests.yaml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _static │ └── css │ │ └── colours.css ├── api.rst ├── citing.rst ├── conf.py ├── graphical_abstract.png ├── index.rst ├── installation.rst ├── make.bat ├── sceptr.rst ├── sceptr_model.rst ├── sceptr_variant.rst ├── troubleshooting.rst └── usage.rst ├── pyproject.toml ├── sceptr.svg ├── src └── sceptr │ ├── __init__.py │ ├── _model_saves │ ├── A_SCEPTR │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── B_SCEPTR │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_BLOSUM │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_CDR3_only │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_CDR3_only_MLM_only │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_MLM_only │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_average_pooling │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_dropout_noise_only │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_finetuned │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_large │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_left_aligned │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_shuffled_data │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_small │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_synthetic_data │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ ├── SCEPTR_tiny │ │ ├── config.json │ │ ├── log.csv │ │ └── state_dict.pt │ └── __init__.py │ ├── model.py │ └── variant.py ├── tests ├── bad_cdr3a.csv ├── bad_trav.csv ├── mock_data.csv ├── mock_data_musmusculus.csv ├── test_errors.py ├── test_functional_api.py ├── test_musmusculus_support.py ├── test_residue_representations.py └── test_variants.py └── tox.ini /.gitattributes: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yutanagano/sceptr/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/workflows/publish_to_pypi.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yutanagano/sceptr/HEAD/.github/workflows/publish_to_pypi.yaml -------------------------------------------------------------------------------- /.github/workflows/tests.yaml: 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