├── .DS_Store ├── .github ├── dependabot.yml └── workflows │ ├── code_coverage.yml │ ├── config │ └── grcov.yml │ ├── create_octo_diagram.yml │ └── rust.yml ├── .gitignore ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── Cargo.toml ├── LICENSE ├── README.md ├── benches ├── E_coli.rs ├── benchmark.py ├── benchmark.rs └── transformation.py ├── changelog.md ├── example-pdbs ├── 1BC8.pdb ├── 1htq.pdb ├── 1kmk.pdb ├── 1ubq.cif ├── 1ubq.pdb ├── 1yyf.cif ├── 1yyf.pdb ├── 2btv.pdb ├── 3b5j.pdb ├── 3nig.cif ├── 3nig.pdb ├── 3pdz.cif ├── 6wlb.cif ├── 7az6.pdb ├── eq.pdb ├── insertion_codes.pdb ├── large.pdb ├── liquid.pdb ├── low_b.pdb ├── models.pdb ├── nucleic.pdb ├── pTLS-6484.cif ├── pTLS-6484.pdb ├── refined_1SDB.pdb ├── rosetta_model.cif └── rosetta_model.pdb ├── examples ├── selection.rs ├── sphere.rs └── waterbox.rs ├── src ├── errorlevel.rs ├── general_docs │ └── mod.rs ├── lib.rs ├── read │ ├── general.rs │ ├── mmcif │ │ ├── lexer.rs │ │ ├── lexitem.rs │ │ ├── mod.rs │ │ └── parser.rs │ ├── mod.rs │ ├── pdb │ │ ├── lexer.rs │ │ ├── lexitem.rs │ │ ├── mod.rs │ │ ├── parser.rs │ │ ├── temporary_structs.rs │ │ ├── utils.rs │ │ └── validate.rs │ └── read_options.rs ├── reference │ ├── crystal_transformations.txt │ ├── hall_symbols.txt │ └── hermann_mauguin_symbols.txt ├── reference_tables.rs ├── save │ ├── general.md │ ├── general.rs │ ├── mmcif.rs │ ├── mod.rs │ └── pdb.rs ├── strictness_level.rs ├── structs │ ├── atom.rs │ ├── bond.rs │ ├── chain.rs │ ├── conformer.rs │ ├── database_reference.rs │ ├── elements.rs │ ├── general.md │ ├── helper.rs │ ├── hierarchy.rs │ ├── mod.rs │ ├── model.rs │ ├── mtrix.rs │ ├── pdb.rs │ ├── residue.rs │ ├── search.rs │ ├── symmetry.rs │ └── unit_cell.rs ├── transformation.rs └── validate.rs └── tests ├── atom_serial_number_id.rs ├── atomic_only.rs ├── clipped.rs ├── duplicate_hydrogens.rs ├── ignore_hydrogens.rs ├── insertion_codes.rs ├── low_b.rs ├── multi_model.rs ├── read_write_pdbs.rs ├── wrapping_atom_number.rs └── 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