pdb_io.PdbReader

class pdb_io.PdbReader(pdb_directory: str, pdb_type: str = 'cif', gzipped: bool = True)[source]

Bases: object

Object for parsing protein structures in pdb or cif format from a specific directory

Parameters:

  • pdb_directory (str) – a directory containing protein structure files

  • pdb_type (str) – the format of the protein structure files. Default “cif”

  • gzipped (bool) – true if the protein structure files are compressed with gzip, false if uncompressed

directory_queries
pdb_directory

path to the directory containing protein structure files

Type:

pathlib.Path

text_handler

method for opening text stream

Type:

Callable

parser
Type:

PDB.MMCIFParser or PDB.PDBParser

__init__(pdb_directory: str, pdb_type: str = 'cif', gzipped: bool = True)[source]

Object for parsing protein structures in pdb or cif format from a specific directory

Parameters:

  • pdb_directory (str) – a directory containing protein structure files

  • pdb_type (str) – the format of the protein structure files. Default “cif”

  • gzipped (bool) – true if the protein structure files are compressed with gzip, false if uncompressed

directory_queries
pdb_directory

path to the directory containing protein structure files

Type:

pathlib.Path

text_handler

method for opening text stream

Type:

Callable

parser
Type:

PDB.MMCIFParser or PDB.PDBParser

Methods

__init__(pdb_directory[, pdb_type, gzipped])

Object for parsing protein structures in pdb or cif format from a specific directory

read_file(protein_id, file_name)

Parse a protein structure file and return a biopython PDB structure

Attributes

directory_queries

read each file in the directory and get the protein chain IDs and each protein structure file
property directory_queries

read each file in the directory and get the protein chain IDs and each protein structure file

Returns:

the path to each protein structure file and the IDs of the polypeptide chains in that protein

Return type:

PdbQueries

read_file(protein_id: str, file_name: str) → Structure | None[source]

Parse a protein structure file and return a biopython PDB structure

Parameters:

  • protein_id (str) – pdb entity ID of the protein structure

  • file_name (str) – name of the protein structure file

Returns:

Biopython structure entity

Return type:

PDB.Structure.Structure or None