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"])
Error Handling
- Missing dependency: optional libraries raise
ImportErrorwith an install hint (pip install 'iterabledata[<extra>]'when an extra exists). - Read-only: opening with
mode="w"raisesWriteNotSupportedErrororValueError. - Bad or unsupported input: may raise
ValueError,OSError, or library-specific errors. - See Troubleshooting for decoding, detection, and engine issues.
See also
- XYZ — molecular coordinate tables
- PDB — Protein Data Bank atoms
- Supported formats
Parameters
| Parameter | Type | Default | Required | Description |
|---|---|---|---|---|
encoding | str | 'utf-8' | No | Passed via iterableargs. |