Welcome to Pidibble’s documentation!

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.pdbparser module.

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

Pidibble can handle hexadecimal serial numbers in all record types.

Check out the Usage section for further information, including on Installation of the package.

Note

Pidibble is under active development.

Note

Pidibble is used in pestifer

Contents

• Installation
• Usage
  • Usage Example
• API
  • pidibble package
• Changelog
  • Changelog