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structure-io

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Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB. Use when choosing a format (mmCIF/PDBx vs legacy PDB vs BinaryCIF) for a structure that may exceed PDB's ~62-chain / 99,999-atom limits; when residue numbers do not match the paper because of auth_* vs label_* numbering (MMCIFParser defaults auth_residues=True); when metadata (resolution, method, R-free) is missing because Bio.PDB drops it and MMCIF2Dict is needed; when the deposited coordinates are the asymmetric unit and the biological assembly must be downloaded separately; when downloading from RCSB (files.rcsb.org, PDBList); and when a legacy MMTF path is dead (RCSB retired MMTF July 2024, use BinaryCIF).

When to use

• Reading structure files
• Writing structure files
• Downloading structures from RCSB
• Converting between mmCIF, PDB, and BinaryCIF
• Handling auth vs label residue numbering
• Extracting metadata like resolution and R-free
• Retrieving biological assemblies
• Parsing large macromolecular structures

When not to use

• Using retired MMTF format for live downloads
• Applying assembly operators with Bio.PDB
• Processing structures exceeding PDB format limits with legacy PDB parser

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