mmCIF Validator: a comprehensive validation tool for structural biology data files

The PDBx/macromolecular crystallographic information file (PDBx/mmCIF) framework is the standard for representing macromolecular structure data in the Protein Data Bank (PDB) and has been mandatory for crystallographic depositions since 2019. The PDBx/mmCIF dictionary, maintained by the PDBx/mmCIF working group established by the Worldwide PDB (wwPDB) consortium, defines the schema, data types, enumerations and relationships that govern the structure and content of mmCIFs. Pre-deposition validation of mmCIFs enables researchers to identify and correct errors, ensuring both dictionary compliance and that data values are meaningful and appropriate for their dataset. This validation step can significantly streamline the deposition process in the wwPDB OneDep system, when depositing to the PDB and Electron Microscopy Data Bank archives or using the PDB-IHM deposition system for integrative/hybrid structures, reducing delays and improving data quality. We present the mmCIF Validator, a comprehensive validation tool available in two complementary implementations: a Visual Studio Code extension for real-time interactive validation during file editing; and a standalone Python script for command-line use, batch processing, and integration into automated workflows and CI/CD (continuous integration and continuous delivery/deployment) pipelines. The validator performs comprehensive checks including item-definition validation, mandatory-item presence (with category-aware checking), enumeration-value validation, data-type validation (including automatic regex-based validation extracted from OneDep deposition-specific categories in the dictionary for types like email, phone, ORCID ID and PDB ID), range constraints with distinction between strictly allowed and advisory boundary conditions, parent/child category relationships, foreign-key integrity, composite-key validation for relationships defined by multiple items, duplicate category and item detection, and complex operation-expression parsing. The tool requires Python 3.7+ and uses only the Python standard library (no pip packages required). It works out of the box with automatic dictionary downloading from the official wwPDB repository, or users can employ a custom distant or local dictionary file. The two implementations share the same validation engine, ensuring consistent results across different usage scenarios. The validator is particularly valuable for structural biologists preparing structures for deposition, biocurators ensuring data quality and software developers building automated quality-control workflows.