Bio.PDB.PDBMLParser module

This module contains a parser for PDBML (PDB XML) files.

PDBML is a representation of PDB data in XML format.

See https://pdbml.wwpdb.org/.

class Bio.PDB.PDBMLParser.PDBMLParser

Bases: object

A parser for PDBML (PDB XML) files. See https://pdbml.wwpdb.org/.

This parser is based on the mmCIF parser also provided in the PDB package in the sense that the structure object returned by this parser is equal to the structure returned by the mmCIF parser for any given PDB structure.

__init__()

Initialize a PDBML parser.

get_structure(source: int | str | bytes | PathLike | TextIO) → Structure

Parse and return the PDB structure from XML source.

Parameters:

source (Union[int, str, bytes, PathLike, TextIO]) – The XML representation of the PDB structure

Returns:

the PDB structure

Return type:

Bio.PDB.Structure.Structure