atomium

atomium parses, manipulates, and serializes macromolecular structure files (PDB, PDBML, mmCIF, MMTF) to enable programmatic handling and conversion of structural biology data.

Key Features:

• Comprehensive Format Support: Supports PDB, PDBML, mmCIF, and MMTF file formats for macromolecular structures.
• Parsing, Manipulation, and Serialization: Parses structure files, enables programmatic manipulation of structural entities, and writes updated structures back to supported formats.
• Performance Parity with BioPython: Provides performance comparable to BioPython for relevant parsing and serialization tasks.
• Programmatic API: Exposes an API for structured access and complex data manipulation of macromolecular models and their components.
• pdb2json Web Service: Integrates with the pdb2json service to produce consistent JSON representations for all Protein Data Bank (PDB) entries.

Scientific Applications:

• Structure Parsing and Analysis: Parsing and manipulation of macromolecular coordinates and metadata for structural biology studies.
• Data Conversion and Interoperability: Conversion of PDB entries to consistent JSON for integration with web-based tools and downstream pipelines.
• Pipeline Compatibility: Use in bioinformatics workflows that require support for PDB, PDBML, mmCIF, or MMTF file formats.

Methodology:

Implemented in Python; performs parsing, manipulation, and writing of PDB, PDBML, mmCIF, and MMTF files and integrates with pdb2json to output JSON representations.