├── .github ├── dependabot.yml └── workflows │ ├── ci.yml │ ├── docker-publish.yml │ ├── pypi-publish.yml │ └── stale.yml ├── .gitignore ├── .howfairis.yml ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── README.md ├── benchmark ├── README.md ├── Table_BM5.5.xlsx ├── bm5_benchmark.csv ├── create_benchmark_set.py └── execute_arctic_bm5.py ├── docs ├── arctic3d.modules.rst ├── arctic3d.rst ├── conf.py ├── examples.md ├── imgs │ └── arctic3d.png └── index.rst ├── example ├── 1ppe_E.fasta ├── 1ppe_E.pdb ├── 1ppe_E_example_interfaces.txt └── clustered_interfaces.out ├── install_blast_deps.sh ├── pyproject.toml ├── src └── arctic3d │ ├── __init__.py │ ├── cli.py │ ├── cli_blast.py │ ├── cli_localise.py │ ├── cli_resclust.py │ ├── cli_restraints.py │ ├── functions.py │ ├── modules │ ├── __init__.py │ ├── blast.py │ ├── cluster_interfaces.py │ ├── clustering.py │ ├── example_clustering.py │ ├── example_get_interface.py │ ├── example_interface_matrix.py │ ├── input.py │ ├── interface.py │ ├── interface_matrix.py │ ├── log.py │ ├── output.py │ ├── pdb.py │ ├── sequence.py │ └── url.py │ └── version.py └── tests ├── __init__.py ├── conftest.py ├── golden_data ├── 1crn.fasta ├── 1ej8-A.pdb ├── 1ej8_updated.cif ├── 1jk9-B.pdb ├── 1jk9-D.pdb ├── 1jk9_updated.cif ├── 1qup-A.pdb ├── 1qup-B.pdb ├── 1qup_updated.cif ├── 1rypB_r_b.pdb ├── 3psg_updated.cif ├── 5u9m-B.pdb ├── 5u9m-D.pdb ├── 5u9m_updated.cif ├── blast.xml ├── clustered_interfaces_empty.out ├── clustered_residues_probs.out ├── interface_data_P40202.json ├── interface_data_P40202_ligand.json ├── interface_file.txt ├── interface_matrix.txt ├── pdb3psg.pdb ├── pdb4xoj.pdb └── pdb_data_P40202.json ├── test_apis.py ├── test_blast.py ├── test_cli.py ├── test_cli_localise.py ├── test_cli_resclust.py ├── test_cli_restraints.py ├── test_clustering.py ├── test_interface.py ├── test_interface_matrix.py ├── test_modules_dummy.py ├── test_output.py └── test_pdb.py /.github/dependabot.yml: 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