PDB Format

Read and write Protein Data Bank structure files as ATOM/HETATM records.

Overview

Property	Value
Format id	pdb
Class	PDBIterable
Extensions	.pdb
Read	Yes
Write	Yes
Extra	none (stdlib)
Maturity	stable

Record shape

{
    "record_type": "ATOM",
    "serial": 1,
    "name": "CA",
    "resName": "ALA",
    "chainID": "A",
    "resSeq": 1,
    "x": 1.0,
    "y": 2.0,
    "z": 3.0,
    "element": "C",
    "model": 1,
}

Only ATOM/HETATM lines are yielded. Write emits fixed-width ATOM/HETATM lines.

Parameters

Parameter	Description
model	Optional filter to the N-th MODEL in multi-model files

Usage

from iterable import open_iterable

with open_iterable("protein.pdb") as source:
    for atom in source:
        print(atom["name"], atom["resName"], atom["x"], atom["y"], atom["z"])

with open_iterable("protein.pdb", iterableargs={"model": 1}) as source:
    for atom in source:
        print(atom["model"], atom["serial"])

See also

• CIF — crystallographic atom sites
• XYZ — molecular coordinate tables
• Supported formats