CIF Format

Read Crystallographic Information File (CIF) _atom_site loop rows as flat dictionaries.

Overview

Property	Value
Format id	cif
Class	CIFIterable
Extensions	.cif
Read	Yes
Write	No
Extra	none (stdlib)
Maturity	experimental

Record shape

Column names are stripped of the _atom_site. prefix:

{"type_symbol": "O", "label_atom_id": "O1", "Cartn_x": 0.0, "Cartn_y": 0.0, "Cartn_z": 0.0}

Only loop_ blocks whose columns all start with _atom_site. are yielded. . / ? become None; numeric fields are coerced when possible.

Usage

from iterable import open_iterable

with open_iterable("structure.cif") as source:
    for atom in source:
        print(atom["type_symbol"], atom["Cartn_x"], atom["Cartn_y"], atom["Cartn_z"])

See also

• XYZ — molecular coordinate tables
• PDB — Protein Data Bank atoms
• Supported formats