├── .git-blame-ignore-revs ├── .gitattributes ├── .github ├── PULL_REQUEST_TEMPLATE │ └── release-prep.md ├── pull_request_template.md └── workflows │ ├── check_for_api_break.yaml │ ├── ci.yaml │ ├── clean_cache.yaml │ ├── conda_cron.yaml │ └── mypy.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.md ├── devtools └── raise-or-close-issue.py ├── docs ├── CHANGELOG.rst ├── Makefile ├── _static │ ├── .gitkeep │ ├── alchemical_network_diagram.svg │ ├── gufe_protocol_diagram.svg │ └── ligand_network_diagram.svg ├── api.rst ├── concepts │ ├── included_models.rst │ ├── index.rst │ ├── serialization.rst │ └── tokenizables.rst ├── conf.py ├── environment.yaml ├── how-tos │ ├── atommapper.rst │ ├── atommapping.rst │ ├── component.rst │ ├── componentmapping.rst │ ├── custom_quantities.rst │ ├── index.rst │ ├── protocol.rst │ └── serialization.rst ├── index.rst ├── installation.rst └── make.bat ├── environment.yml ├── gufe ├── __init__.py ├── chemicalsystem.py ├── components │ ├── __init__.py │ ├── component.py │ ├── explicitmoleculecomponent.py │ ├── proteincomponent.py │ ├── smallmoleculecomponent.py │ └── solventcomponent.py ├── compression.py ├── custom_typing.py ├── ligandnetwork.py ├── mapping │ ├── __init__.py │ ├── atom_mapper.py │ ├── atom_mapping.py │ ├── componentmapping.py │ ├── errors.py │ └── ligandatommapping.py ├── molhashing.py ├── network.py ├── protocols │ ├── __init__.py │ ├── errors.py │ ├── protocol.py │ ├── protocoldag.py │ └── protocolunit.py ├── serialization │ ├── __init__.py │ ├── json.py │ └── msgpack.py ├── settings │ ├── __init__.py │ ├── models.py │ └── typing.py ├── storage │ ├── __init__.py │ ├── errors.py │ └── externalresource │ │ ├── __init__.py │ │ ├── base.py │ │ ├── filestorage.py │ │ └── memorystorage.py ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── data │ │ ├── 181l.cif │ │ ├── 181l.pdb │ │ ├── 181l_openmmClean.cif │ │ ├── __init__.py │ │ ├── all_settings.json │ │ ├── benzene_modifications.sdf │ │ ├── ethane.sdf │ │ ├── ligand_network.graphml │ │ ├── lomap_basic │ │ │ ├── 1,3,7-trimethylnaphthalene.mol2 │ │ │ ├── 1-butyl-4-methylbenzene.mol2 │ │ │ ├── 2,6-dimethylnaphthalene.mol2 │ │ │ ├── 2-methyl-6-propylnaphthalene.mol2 │ │ │ ├── 2-methylnaphthalene.mol2 │ │ │ ├── 2-naftanol.mol2 │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── methylcyclohexane.mol2 │ │ │ └── toluene.mol2 │ │ ├── multi_molecule.sdf │ │ ├── offxml_settings.json │ │ └── toluene.mol2 │ ├── dev │ │ ├── __init__.py │ │ └── serialization_test_templates.py │ ├── storage │ │ └── test_externalresource.py │ ├── test_alchemicalnetwork.py │ ├── test_chemicalsystem.py │ ├── test_explicitmoleculecomponent.py │ ├── test_ligand_network.py │ ├── test_ligandatommapping.py │ ├── test_mapping │ ├── test_mapping.py │ ├── test_mapping_visualization.py │ ├── test_models.py │ ├── test_molhashing.py │ ├── test_proteincomponent.py │ ├── test_protocol.py │ ├── test_protocoldag.py │ ├── test_protocolresult.py │ ├── test_protocolunit.py │ ├── test_serialization_json.py │ ├── test_serialization_migration.py │ ├── test_serialization_msgpack.py │ ├── test_smallmoleculecomponent.py │ ├── test_solvents.py │ ├── test_tokenization.py │ ├── test_transformation.py │ └── test_utils.py ├── tokenization.py ├── transformations │ ├── __init__.py │ └── transformation.py ├── utils.py ├── vendor │ ├── __init__.py │ ├── openff │ │ ├── __init__.py │ │ └── interchange │ │ │ ├── __init__.py │ │ │ ├── _annotations.py │ │ │ └── pydantic.py │ └── pdb_file │ │ ├── PdbxContainers.py │ │ ├── PdbxReader.py │ │ ├── __init__.py │ │ ├── data │ │ ├── pdbNames.xml │ │ ├── residues.xml │ │ └── residues_orig.xml │ │ ├── element.py │ │ ├── pdbfile.py │ │ ├── pdbstructure.py │ │ ├── pdbxfile.py │ │ ├── singelton.py │ │ ├── topology.py │ │ └── unitcell.py └── visualization │ ├── __init__.py │ └── mapping_visualization.py ├── news ├── TEMPLATE.rst ├── add-iter.rst ├── 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