├── .gitattributes ├── .github └── workflows │ └── python-package.yml ├── .gitignore ├── .pylintrc ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── _templates │ └── autosummary │ │ └── module.rst │ ├── api.rst │ ├── changelog.rst │ ├── command.rst │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── quickstart.rst │ └── references.rst ├── propka ├── __init__.py ├── __main__.py ├── _version.py ├── atom.py ├── bonds.py ├── calculations.py ├── conformation_container.py ├── coupled_groups.py ├── determinant.py ├── determinants.py ├── energy.py ├── group.py ├── hybrid36.py ├── hydrogens.py ├── input.py ├── iterative.py ├── lib.py ├── ligand.py ├── ligand_pka_values.py ├── molecular_container.py ├── output.py ├── parameters.py ├── propka.cfg ├── protein_bonds.json ├── protonate.py ├── py.typed ├── run.py ├── vector_algebra.py └── version.py ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── .gitignore ├── README.md ├── __init__.py ├── pdb │ ├── 1FTJ-Chain-A.pdb │ ├── 1HPX-warn.pdb │ ├── 1HPX.pdb │ ├── 3SGB-subset.pdb │ ├── 3SGB.pdb │ ├── 4DFR.pdb │ ├── conf-alt-AB-mutant.pdb │ ├── conf-alt-AB.pdb │ ├── conf-alt-BC.pdb │ ├── conf-model-missing-atoms.pdb │ ├── conf-model-mutant.pdb │ └── sample-issue-140.pdb ├── results │ ├── 1FTJ-Chain-A.dat │ ├── 1HPX-warn.dat │ ├── 1HPX.json │ ├── 3SGB-subset.dat │ ├── 3SGB.dat │ ├── 4DFR.dat │ └── sample-issue-140.dat ├── test_basic_regression.py ├── test_hybrid36.py ├── test_input.py ├── test_lib.py ├── test_molecular_container.py ├── test_protonate.py ├── test_run.py ├── test_streamio.py ├── test_vector_algebra.py └── test_version.py └── versioneer.py /.gitattributes: -------------------------------------------------------------------------------- 1 | propka/_version.py export-subst 2 | -------------------------------------------------------------------------------- /.github/workflows/python-package.yml: 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