LICENSE
MANIFEST.in
README.md
conda-lock.yml
environment.yml
pyproject.toml
uv.lock
data/scripts/_dataset_provenance.py
data/scripts/build_easy_negatives_from_pisces_cath.py
data/scripts/mpstruc_download_and_classify.py
examples/A0A2R4ALS6.cif
examples/M4QT10.cif
examples/manifest.json
scripts/annotate_bfvd_candidates_blastp.py
scripts/nested_grouped_decision_experiment.py
scripts/perturbation_eval.py
scripts/setup_env.sh
src/cooper_beta/__init__.py
src/cooper_beta/__main__.py
src/cooper_beta/_version.py
src/cooper_beta/bootstrap.py
src/cooper_beta/chain_analysis.py
src/cooper_beta/cli.py
src/cooper_beta/config.py
src/cooper_beta/constants.py
src/cooper_beta/decision.py
src/cooper_beta/dssp_adapter.py
src/cooper_beta/exceptions.py
src/cooper_beta/execution.py
src/cooper_beta/integrity.py
src/cooper_beta/loader.py
src/cooper_beta/logging_config.py
src/cooper_beta/models.py
src/cooper_beta/output_artifacts.py
src/cooper_beta/pipeline.py
src/cooper_beta/polymer_sequence.py
src/cooper_beta/preparation.py
src/cooper_beta/prepare_cache.py
src/cooper_beta/provenance.py
src/cooper_beta/py.typed
src/cooper_beta/results.py
src/cooper_beta/runtime.py
src/cooper_beta/strand_contacts.py
src/cooper_beta/strand_graph.py
src/cooper_beta.egg-info/PKG-INFO
src/cooper_beta.egg-info/SOURCES.txt
src/cooper_beta.egg-info/dependency_links.txt
src/cooper_beta.egg-info/entry_points.txt
src/cooper_beta.egg-info/requires.txt
src/cooper_beta.egg-info/top_level.txt
src/cooper_beta/conf/__init__.py
src/cooper_beta/conf/config.yaml
src/cooper_beta/evaluation/__init__.py
src/cooper_beta/evaluation/__main__.py
src/cooper_beta/evaluation/app.py
src/cooper_beta/evaluation/metrics.py
src/cooper_beta/evaluation/runner.py
tests/test_chain_analysis.py
tests/test_cli_help.py
tests/test_config_validation.py
tests/test_dataset_builders.py
tests/test_decision.py
tests/test_dssp_adapter.py
tests/test_evaluation.py
tests/test_examples.py
tests/test_execution.py
tests/test_integrity.py
tests/test_loader.py
tests/test_logging_config.py
tests/test_models.py
tests/test_nested_grouped_decision_experiment.py
tests/test_output_artifacts.py
tests/test_perturbation_eval.py
tests/test_prepare_cache.py
tests/test_prepare_cache_integrity.py
tests/test_provenance.py
tests/test_public_scripts.py
tests/test_results.py
tests/test_runtime_pipeline.py
tests/test_smoke.py
tests/test_strand_contacts.py
tests/test_strand_graph.py