README.md
pyproject.toml
src/shellde/__init__.py
src/shellde/acquisition.py
src/shellde/advisor.py
src/shellde/campaign.py
src/shellde/candidates.py
src/shellde/cli.py
src/shellde/colab.py
src/shellde/conformal.py
src/shellde/consensus.py
src/shellde/design_space.py
src/shellde/funclib.py
src/shellde/gating.py
src/shellde/holo.py
src/shellde/hotspots.py
src/shellde/loop.py
src/shellde/msa.py
src/shellde/naturalness.py
src/shellde/oracle.py
src/shellde/plm.py
src/shellde/prereg.py
src/shellde/protocols.py
src/shellde/rank.py
src/shellde/report.py
src/shellde/selector.py
src/shellde/sitefinder.py
src/shellde/structure.py
src/shellde/surrogate.py
src/shellde/types.py
src/shellde/zero_shot.py
src/shellde.egg-info/PKG-INFO
src/shellde.egg-info/SOURCES.txt
src/shellde.egg-info/dependency_links.txt
src/shellde.egg-info/entry_points.txt
src/shellde.egg-info/requires.txt
src/shellde.egg-info/top_level.txt
src/shellde/bench/__init__.py
src/shellde/bench/falsification.py
src/shellde/bench/harness.py
src/shellde/bench/stats.py
src/shellde/embeddings/__init__.py
src/shellde/embeddings/esm2.py
src/shellde/embeddings/esmc.py
src/shellde/embeddings/provider.py
src/shellde/features/__init__.py
src/shellde/features/base.py
src/shellde/features/defaults.py
src/shellde/features/embedding.py
src/shellde/features/inverse_folding.py
src/shellde/features/matrix.py
src/shellde/features/naturalness.py
src/shellde/features/onehot.py
src/shellde/features/pairwise.py
tests/test_acquisition.py
tests/test_advisor.py
tests/test_anchor.py
tests/test_bench.py
tests/test_campaign.py
tests/test_candidates.py
tests/test_cli.py
tests/test_colab.py
tests/test_conformal.py
tests/test_consensus.py
tests/test_defaults.py
tests/test_design_space.py
tests/test_embeddings.py
tests/test_encode_fast.py
tests/test_falsification.py
tests/test_features.py
tests/test_funclib.py
tests/test_gating.py
tests/test_heldout.py
tests/test_holo.py
tests/test_hotspots.py
tests/test_msa.py
tests/test_naturalness.py
tests/test_oracle_loop.py
tests/test_pairwise.py
tests/test_plm.py
tests/test_prereg.py
tests/test_rank_report.py
tests/test_selector.py
tests/test_sitefinder.py
tests/test_structure.py
tests/test_surrogate.py
tests/test_zero_shot.py