.gitignore
.readthedocs.yaml
CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
README.md
pyproject.toml
pytest.ini
.github/workflows/publish.yml
.github/workflows/tests.yml
docs/api.md
docs/benchmark.md
docs/calibration.md
docs/circular.md
docs/cli_reference.md
docs/conf.py
docs/config.md
docs/different_molecules.md
docs/examples.md
docs/getting_started.md
docs/index.md
docs/installation.md
docs/metrics.md
docs/order_parameters.md
docs/performance.md
docs/references.md
docs/statistics.md
docs/validate.md
docs/_static/.gitkeep
legacy/Prothon.py
legacy/README.md
legacy/prothon_example_script.py
recipes/prothon/recipe.yaml
scripts/calibration.py
scripts/circular_cost.py
scripts/convergence.py
scripts/figures.py
scripts/floor_scaling.py
scripts/parallel_speedup.py
scripts/scale_envelope.py
scripts/ubiquitin_rerun.py
src/Prothon.py
src/prothon/__init__.py
src/prothon/_version.py
src/prothon/cli.py
src/prothon/quiet.py
src/prothon/utils.py
src/prothon/batch/__init__.py
src/prothon/batch/benchmark.py
src/prothon/config/__init__.py
src/prothon/config/schema.py
src/prothon/config/study.py
src/prothon/core/__init__.py
src/prothon/core/correlation.py
src/prothon/core/dissimilarity.py
src/prothon/core/ensemble_metrics.py
src/prothon/core/metrics.py
src/prothon/core/plotting.py
src/prothon/core/precision_recall.py
src/prothon/core/prothon_core.py
src/prothon/core/representation.py
src/prothon/ingest/__init__.py
src/prothon/ingest/ensemble.py
src/prothon/ingest/ped.py
src/prothon/ingest/reconcile.py
src/prothon/ingest/sequence.py
src/prothon/ingest/sources.py
src/prothon/validate/__init__.py
src/prothon/validate/observables.py
src/prothon/validate/score.py
src/prothon_ensembles.egg-info/PKG-INFO
src/prothon_ensembles.egg-info/SOURCES.txt
src/prothon_ensembles.egg-info/dependency_links.txt
src/prothon_ensembles.egg-info/entry_points.txt
src/prothon_ensembles.egg-info/requires.txt
src/prothon_ensembles.egg-info/scm_file_list.json
src/prothon_ensembles.egg-info/scm_version.json
src/prothon_ensembles.egg-info/top_level.txt
tests/conftest.py
tests/test_analytic.py
tests/test_benchmark.py
tests/test_chains.py
tests/test_config.py
tests/test_core.py
tests/test_correlation.py
tests/test_dissimilarity.py
tests/test_ensemble_metrics.py
tests/test_figures.py
tests/test_global_parameters.py
tests/test_ingest.py
tests/test_interface.py
tests/test_metadata.py
tests/test_metrics.py
tests/test_ped.py
tests/test_precision_recall.py
tests/test_real_data.py
tests/test_representation.py
tests/test_validate.py