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.gitignore
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LICENSE
README.md
changelog_data.md
codecov.yml
faq.md
limitations.md
mypy.ini
pyproject.toml
pytest.ini
ruff.toml
tox.ini
version.sh
.github/workflows/docs.yaml
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assets/dockq_performance_profile.png
assets/foldseek_alnlen_distribution.png
assets/foldseek_precision_vs_threshold.png
assets/foldseek_recall_vs_threshold.png
assets/interface_length_distribution.png
assets/intermolecular_contacts_distribution_max500.png
assets/loader_abstractions.svg
assets/mmseqs_alnlen_distribution.png
assets/pinder.png
assets/planarity_distribution.png
assets/top_50_ecod_families.png
assets/top_50_pfam_clans.png
docker/frodock/Dockerfile.frodock
docker/hdock/Dockerfile.hdock
docker/patchdock/Dockerfile.patchdock
docs/Makefile
docs/af2_L.pdb
docs/build.sh
docs/changelog.md
docs/conf.py
docs/example_readme.md
docs/examples.rst
docs/faq.md
docs/index.rst
docs/limitations.md
docs/make.bat
docs/methods_readme.md
docs/pinder.rst
docs/readme.md
docs/viewcode.py
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examples/README.md
examples/pinder-eval.ipynb
examples/pinder-index.ipynb
examples/pinder-loader.ipynb
examples/pinder-mlsb.ipynb
examples/pinder-system.ipynb
examples/superposition.ipynb
pinder.egg-info/PKG-INFO
pinder.egg-info/SOURCES.txt
pinder.egg-info/dependency_links.txt
pinder.egg-info/entry_points.txt
pinder.egg-info/requires.txt
pinder.egg-info/top_level.txt
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src/pinder-core/pinder/core/_version.py
src/pinder-core/pinder/core/index/__init__.py
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src/pinder-core/pinder/core/loader/structure.py
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src/pinder-core/pinder/core/loader/writer.py
src/pinder-core/pinder/core/structure/__init__.py
src/pinder-core/pinder/core/structure/atoms.py
src/pinder-core/pinder/core/structure/contacts.py
src/pinder-core/pinder/core/structure/models.py
src/pinder-core/pinder/core/structure/superimpose.py
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src/pinder-data/pinder/data/README.md
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src/pinder-data/pinder/data/_version.py
src/pinder-data/pinder/data/alignment_utils.py
src/pinder-data/pinder/data/apo_utils.py
src/pinder-data/pinder/data/config.py
src/pinder-data/pinder/data/csv_utils.py
src/pinder-data/pinder/data/find_transitive_hits.py
src/pinder-data/pinder/data/foldseek_utils.py
src/pinder-data/pinder/data/get_alignment_similarity.py
src/pinder-data/pinder/data/get_annotations.py
src/pinder-data/pinder/data/get_apo.py
src/pinder-data/pinder/data/get_clusters.py
src/pinder-data/pinder/data/get_data.py
src/pinder-data/pinder/data/get_dimers.py
src/pinder-data/pinder/data/get_splits.py
src/pinder-data/pinder/data/get_test_set.py
src/pinder-data/pinder/data/graph_utils.py
src/pinder-data/pinder/data/rcsb_rsync.py
src/pinder-data/pinder/data/run.py
src/pinder-data/pinder/data/system.py
src/pinder-data/pinder/data/annotation/__init__.py
src/pinder-data/pinder/data/annotation/canonical_apo.py
src/pinder-data/pinder/data/annotation/constants.py
src/pinder-data/pinder/data/annotation/contact_classification.py
src/pinder-data/pinder/data/annotation/detached_components.py
src/pinder-data/pinder/data/annotation/elongation.py
src/pinder-data/pinder/data/annotation/graphql.py
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src/pinder-data/pinder/data/plot/difficulty.py
src/pinder-data/pinder/data/plot/families.py
src/pinder-data/pinder/data/plot/figure_utils.py
src/pinder-data/pinder/data/plot/image.py
src/pinder-data/pinder/data/plot/leaderboards.py
src/pinder-data/pinder/data/plot/leakage.py
src/pinder-data/pinder/data/plot/performance.py
src/pinder-data/pinder/data/plot/plot.py
src/pinder-data/pinder/data/plot/run.py
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src/pinder-data/pinder/data/qc/run.py
src/pinder-data/pinder/data/qc/similarity_check.py
src/pinder-data/pinder/data/qc/uniprot_leakage.py
src/pinder-data/pinder/data/qc/utils.py
src/pinder-eval/pinder/eval/__init__.py
src/pinder-eval/pinder/eval/_version.py
src/pinder-eval/pinder/eval/create_submission.py
src/pinder-eval/pinder/eval/run.py
src/pinder-eval/pinder/eval/clashes/__init__.py
src/pinder-eval/pinder/eval/dockq/__init__.py
src/pinder-eval/pinder/eval/dockq/biotite_dockq.py
src/pinder-eval/pinder/eval/dockq/method.py
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tests/conftest.py
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