├── .codecov.yml ├── .codeql.yml ├── .github └── workflows │ ├── _build-package.yml │ ├── build.yml │ ├── ci.yml │ ├── codeql.yml │ ├── formatting_linting.yml │ └── type-check.yml ├── .gitignore ├── .readthedocs.yml ├── CHANGELOG.md ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs ├── conf.py ├── index.rst ├── notebooks │ ├── advanced.ipynb │ ├── docking.ipynb │ ├── md-ligand-protein.ipynb │ ├── md-protein-protein.ipynb │ ├── pdb.ipynb │ └── water-bridge.ipynb └── source │ ├── api.rst │ ├── changelog.md │ ├── citation.rst │ ├── installation.rst │ ├── modules │ ├── input.rst │ ├── interaction-fingerprint.rst │ ├── plotting.rst │ ├── residues.rst │ ├── types.rst │ └── utils.rst │ └── tutorials.rst ├── notebooks ├── prolif ├── __init__.py ├── _version.py ├── data │ ├── acceptor.mol2 │ ├── acceptor_false.mol2 │ ├── anion.mol2 │ ├── benzene.mol2 │ ├── bromine.mol2 │ ├── cation.mol2 │ ├── cation_false.mol2 │ ├── chlorine.mol2 │ ├── donor.mol2 │ ├── edgetoface.mol2 │ ├── facetoface.mol2 │ ├── ligand.mol2 │ ├── metal.mol2 │ ├── metal_false.mol2 │ ├── mol_comment.mol2 │ ├── top.pdb │ ├── traj.xtc │ ├── vina │ │ ├── lig.pdb │ │ ├── rec.pdb │ │ ├── vina_output.mol2 │ │ ├── vina_output.sdf │ │ ├── vina_output_ligand_1.pdbqt │ │ ├── vina_output_ligand_2.pdbqt │ │ ├── vina_output_ligand_3.pdbqt │ │ ├── vina_output_ligand_4.pdbqt │ │ ├── vina_output_ligand_5.pdbqt │ │ ├── vina_output_ligand_6.pdbqt │ │ ├── vina_output_ligand_7.pdbqt │ │ ├── vina_output_ligand_8.pdbqt │ │ └── vina_output_ligand_9.pdbqt │ ├── water_m2.pdb │ ├── water_m2.xtc │ ├── xbond_acceptor.mol2 │ ├── xbond_acceptor_false_axd.mol2 │ ├── xbond_acceptor_false_xar.mol2 │ └── xbond_donor.mol2 ├── datafiles.py ├── exceptions.py ├── fingerprint.py ├── ifp.py ├── interactions │ ├── __init__.py │ ├── base.py │ ├── constants.py │ ├── interactions.py │ ├── utils.py │ └── water_bridge.py ├── molecule.py ├── parallel.py ├── pickling.py ├── plotting │ ├── __init__.py │ ├── barcode.py │ ├── complex3d.py │ ├── network │ │ ├── __init__.py │ │ ├── lignetwork.py │ │ ├── network.css │ │ ├── network.html │ │ └── network.js │ ├── residues.py │ └── utils.py ├── py.typed ├── rdkitmol.py ├── residue.py ├── typeshed.py └── utils.py ├── pyproject.toml ├── scripts ├── check_types.py └── test_build.py ├── tests ├── __init__.py ├── conftest.py ├── plotting │ ├── __init__.py │ ├── test_barcode.py │ ├── test_complex3d.py │ ├── test_network.py │ └── test_residues.py ├── test_fingerprint.py ├── test_ifp.py ├── test_interactions.py ├── test_molecule.py ├── test_pickling.py ├── test_residues.py └── test_utils.py └── uv.lock /.codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chemosim-lab/ProLIF/HEAD/.codecov.yml -------------------------------------------------------------------------------- /.codeql.yml: -------------------------------------------------------------------------------- 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