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Convert crystal structure files between extxyz and CIF, including splitting multi-frame extxyz into per-frame CIF files.
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| name | structure-conversion |
| description | Convert crystal structure files between extxyz and CIF, including splitting multi-frame extxyz into per-frame CIF files. |
| metadata | {"tools":["run_python_file"],"tags":["structure","conversion","extxyz","cif","ASE"]} |
Use the CLI script structure_conversion_tools.py (located alongside this file) to convert structure files between extxyz and cif. It mirrors the behavior of the former ase_structure_convert_tool and is especially useful for turning MatterGen multi-frame extxyz outputs into per-frame cif files.
Every command writes a JSON object to stdout and exits 0 on success or 1 on error. Always parse the JSON output and confirm "status": "success".
python skills/structure_conversion/structure_conversion_tools.py convert <input_file> <output_path> [options]
cif -> extxyzextxyz or xyz -> single cifextxyz or xyz -> directory of per-frame cif filesextxyz or xyz -> extxyzFor multi-frame extxyz input, never collapse all frames into one cif. Write one cif file per frame using stable names such as frame_000001.cif.
convertConvert a structure file and return output metadata.
Positional arguments
| Argument | Description |
|---|---|
input_file | Source structure path. Supported: .extxyz, .xyz, .cif |
output_path | Output file path or output directory |
Optional arguments
| Flag | Type | Description |
|---|---|---|
--output-format | str | Explicit target format: cif or extxyz. If omitted, infer from output_path |
JSON response fields
status, message, output_mode, output_format, frame_count, output_path, output_paths
extxyz to cif# Multi-frame extxyz to per-frame CIF directory
python skills/structure_conversion/structure_conversion_tools.py convert \
generated.extxyz converted_cifs --output-format cif
# Single CIF to extxyz
python skills/structure_conversion/structure_conversion_tools.py convert \
structure.cif structure.extxyz
mattergen generation and before downstream property predictionoutput_format is omitted, the script infers it from output_pathcif, the result is a directory, not a single file