├── .gitignore ├── LICENSE ├── README.md ├── pdb_toolkit ├── __init__.py ├── constants.py ├── editor │ ├── __init__.py │ ├── fix_pdb.py │ ├── keep_only_atoms.py │ ├── protonate_pdb.py │ ├── renumber_pdb.py │ ├── sort_atoms.py │ └── unprotonate_pdb.py ├── generic │ ├── __init__.py │ ├── align.py │ ├── concat_pdbs.py │ ├── download_pdb.py │ ├── extract_chains_from_pdb.py │ └── split_chains.py └── parser │ ├── __init__.py │ ├── get_atoms_residues.py │ ├── get_pdb_centroid.py │ ├── get_pdb_sequence.py │ ├── split_residues_surface_boundary_core.py │ └── steric_clashes.py ├── setup.py └── tests ├── all_in_one.sh ├── test_editor.py ├── test_generic.py ├── test_parser.py └── testing_data └── 7vyt ├── 7vyt.pdb ├── 7vyt_fixed.pdb ├── 7vyt_fixed_HL.pdb ├── 7vyt_fixed_HL_T.pdb ├── 7vyt_fixed_T.pdb ├── 7vyt_only_atoms.pdb ├── 7vyt_protonated.pdb ├── 7vyt_renumbered.pdb ├── 7vyt_sorted.pdb ├── 7vyt_unprotonated.pdb ├── antibody_7vyt.pdb ├── complex_7vyt.pdb ├── splitted_chains ├── 7vyt_A.pdb ├── 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