.gitignore
CHANGELOG.rst
CONTRIBUTING.rst
LICENSE.txt
README.rst
nbval_sanitize.cfg
pytest.ini
ruff.toml
setup.py
test_requirements.txt
.github/workflows/test.yaml
docs/.gitignore
docs/.nojekyll
docs/Makefile
docs/RBD_average.nblink
docs/README.rst
docs/acknowledgments.rst
docs/biophysical_model.nblink
docs/concentration_set.nblink
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docs/fit_RBD.nblink
docs/index.rst
docs/installation.rst
docs/library_size.nblink
docs/mutation_rate.nblink
docs/optimization.nblink
docs/package_index.rst
docs/partition_function.nblink
docs/real_LyCoV1404.nblink
docs/real_cocktail.nblink
docs/reference_site_numbering.nblink
docs/regularization.rst
docs/simulate_RBD.nblink
docs/specify_epitopes.nblink
docs/visualize_RBD.nblink
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notebooks/RBD_mean_class_2.pdb
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notebooks/RBD_mean_class_3.pdb
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notebooks/mutation_rate.ipynb
notebooks/optimization.ipynb
notebooks/partition_function.ipynb
notebooks/real_LyCoV1404.ipynb
notebooks/real_cocktail.ipynb
notebooks/reference_site_numbering.ipynb
notebooks/simulate_RBD.ipynb
notebooks/specify_epitopes.ipynb
notebooks/visualize_RBD.ipynb
optimization_benchmarks/.gitignore
optimization_benchmarks/README.md
optimization_benchmarks/Snakefile_opt_settings
optimization_benchmarks/analyze_opt_settings.ipynb
optimization_benchmarks/run_opt_settings.bash
polyclonal/__init__.py
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polyclonal.egg-info/SOURCES.txt
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tests/.gitignore
tests/README.rst
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tests/profile_fitting.ipynb
tests/test_bootstrap.ipynb
tests/test_epitope_harmony.ipynb
tests/test_gradients.ipynb
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