pidibble

Pidibble is a Python package for parsing Protein Data Bank (PDB) files in both legacy PDB and modern PDBx/mmCIF formats. It conforms to the most recent standard (v.3.3 Atomic Coordinate Entry Format, ca. 2011).

Unlike parsers like that found in packages like BioPython, pidibble provides meaningfully parsed objects from all standard PDB record types, not just ATOM and CONECT records.

Once installed, the user has access to the PDBParser class in the pidibble.pdbparse module.

Pidibble can fetch coordinate files from the RCSB PDB and from the AlphaFold model database.

Pidibble can handle hexadecimal serial numbers in all record types.

New to pidibble? Start with the Quickstart, then work through the User Guide. See Installation to install the package.

Note

Pidibble is under active development.

Note

Pidibble is used in pestifer

Contents

• Installation
• Quickstart
  • Where to go next
• User Guide
  • Loading structures
  • The parsed data model
  • Working with records
  • Biological assemblies and symmetry
  • PDBx/mmCIF parsing
  • Large structures and hexadecimal serials
  • Nonconformant files and logging
  • Advanced usage and customization
  • Supported record types
• API
  • pidibble package
• Changelog
  • Changelog