├── .github └── workflows │ ├── publish_release.yaml │ └── tests.yaml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.rst ├── docs ├── Makefile └── source │ ├── _autosummary │ ├── pywindow.DLPOLY.rst │ ├── pywindow.Input.rst │ ├── pywindow.MolecularSystem.rst │ ├── pywindow.Molecule.rst │ ├── pywindow.PDB.rst │ ├── pywindow.XYZ.rst │ ├── pywindow.compare_properties_dict.rst │ ├── pywindow.make_supercell.rst │ └── pywindow.rst │ ├── _static │ ├── EPIRUR_no_solvent.pdb │ ├── EPIRUR_no_solvent_rebuild.pdb │ ├── EPIRUR_no_solvent_rebuild_mol_0.pdb │ ├── EPIRUR_no_solvent_rebuild_mol_1.pdb │ ├── EPIRUR_no_solvent_rebuild_mol_2.pdb │ ├── PUDXES.xyz │ ├── PUDXES_out.json │ ├── PUDXES_out.pdb │ └── pyWINDOW_logo.png │ ├── _templates │ ├── class.rst │ └── module.rst │ ├── conf.py │ ├── examples.rst │ ├── index.rst │ ├── modules.rst │ └── multi_examples.rst ├── examples ├── Example1_StructuralPropertiesOfMolecularPores.ipynb ├── Example2_LoadingRDKitMolecule.ipynb ├── Example3_CalculatingAverageDiameter.ipynb ├── Example4_AnalyseMOF.ipynb ├── Example5_AnalyseMetalOrganicCage.ipynb ├── Example6_PeriodicSystemMultipleMolecules.ipynb ├── Example7_AnalysingTrajectorySingleMol.ipynb ├── Example8_AnalysingTrajectoryPeriodic.ipynb ├── README.md ├── __init__.py ├── data │ ├── input │ │ ├── BATVUP.xyz │ │ ├── EPIRUR_no_solvent.pdb │ │ ├── HISTORY_periodic │ │ ├── HISTORY_singlemol │ │ ├── HISTORY_singlemol_short │ │ ├── MIBQAR.pdb │ │ ├── NUXHIZ.xyz │ │ ├── PUDXES.mol2 │ │ ├── PUDXES.xyz │ │ ├── PUDXES_no_solvent.pdb │ │ ├── REYMAL.xyz │ │ ├── SAYGOR.pdb │ │ ├── TATVER_no_solvent.pdb │ │ └── YAQHOQ.xyz │ └── output │ │ ├── BATVUP_out.json │ │ ├── BATVUP_out.pdb │ │ ├── EPIRUR_no_solvent_rebuild.pdb │ │ ├── EPIRUR_no_solvent_rebuild_mol_0.pdb │ │ ├── EPIRUR_no_solvent_rebuild_mol_1.pdb │ │ ├── EPIRUR_no_solvent_rebuild_mol_2.pdb │ │ ├── HISTORY_out.json │ │ ├── MIBQAR_out.pdb │ │ ├── NUXHIZ_out.json │ │ ├── NUXHIZ_out.pdb │ │ ├── PUDXES_no_solvent_rebuild.pdb │ │ ├── PUDXES_no_solvent_rebuild_mol_0.pdb │ │ ├── PUDXES_no_solvent_rebuild_mol_1.pdb │ │ ├── PUDXES_no_solvent_rebuild_mol_2.pdb │ │ ├── PUDXES_no_solvent_rebuild_mol_3.pdb │ │ ├── PUDXES_no_solvent_rebuild_mol_4.pdb │ │ ├── PUDXES_no_solvent_rebuild_mol_5.pdb │ │ ├── PUDXES_no_solvent_rebuild_mol_6.pdb │ │ ├── PUDXES_no_solvent_rebuild_mol_7.pdb │ │ ├── PUDXES_out.json │ │ ├── PUDXES_out.pdb │ │ ├── REYMAL_out.json │ │ ├── REYMAL_out.pdb │ │ ├── SAYGOR_out.pdb │ │ ├── TATVER_no_solvent_rebuild.pdb │ │ ├── TATVER_no_solvent_rebuild_mol_0.pdb │ │ ├── TATVER_no_solvent_rebuild_mol_1.pdb │ │ ├── YAQHOQ_out.json │ │ └── YAQHOQ_out.pdb ├── example_1.py ├── example_2.py ├── example_3.py ├── example_4.py ├── example_5.py ├── example_6.py ├── example_7.py └── example_8.py ├── justfile ├── pyproject.toml ├── src └── pywindow │ ├── __init__.py │ ├── _internal │ ├── __init__.py │ ├── io_tools.py │ ├── molecular.py │ ├── tables.py │ ├── trajectory.py │ └── utilities.py │ └── py.typed ├── tests ├── __init__.py ├── data │ ├── mol_system.pdb │ ├── mol_system_rebuild.pdb │ ├── system.pdb │ ├── system_periodic.pdb │ └── system_periodic_rebuild.pdb ├── test_io.py ├── test_molecular.py ├── test_validate_average_diameter.py ├── test_validate_cc3.py └── test_validate_windows.py └── uv.lock /.github/workflows/publish_release.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marcinmiklitz/pywindow/HEAD/.github/workflows/publish_release.yaml -------------------------------------------------------------------------------- /.github/workflows/tests.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marcinmiklitz/pywindow/HEAD/.github/workflows/tests.yaml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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