pdb_io.PdbFileQuery

class pdb_io.PdbFileQuery(protein_id: str, file_path: str, chain_ids: list[str])[source]

Bases: object

Object representing a specific proteins structure file and the amino protein chain entities that should be parsed from it

protein_id

pdb entity ID of the protein structure

file_path

path to the protein structure file

chain_ids

list of protein chain entities to parse

__init__(protein_id: str, file_path: str, chain_ids: list[str]) → None

Methods

`__init__`(protein_id, file_path, chain_ids)
`add_chain`(chain_id)
`get_polypeptides`(pdb_reader, builder)	Identify contiguous chains of amino acids in the protein chain entity
`get_structure`(pdb_reader)	Parse a protein structure file and return a biopython PDB structure

Attributes

get_polypeptides(pdb_reader: PdbReader, builder: PPBuilder | CaPPBuilder) → Generator[PolypeptideEntry, None, None][source]

Identify contiguous chains of amino acids in the protein chain entity

Parameters:

pdb_reader (PdbReader) – protein structure file parser
builder (PDB.Polypeptide.PPBuilder or PDB.Polypeptide.CaPPBuilder) – polypeptide constructor

Yields:

PolypeptideEntry – contiguous chains of amino acids from the protein chain entry

get_structure(pdb_reader: PdbReader) → Structure | None[source]

Parse a protein structure file and return a biopython PDB structure