Name: structure-conversion
Author: AI4MS

About

Imported from AI4MS/MatCreator (src/matcreator/skills/structure-conversion/SKILL.md). Install upstream with npx skills add AI4MS/MatCreator --skill structure-conversion. Copyright stays with the author.

Overview

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]

Supported Conversions

cif -> extxyz
single-frame extxyz or xyz -> single cif
multi-frame extxyz or xyz -> directory of per-frame cif files
extxyz or xyz -> extxyz

For 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.

Command

`convert`

Convert 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

Recommended Behavior

Prefer directory outputs when converting multi-frame extxyz to cif
Always return absolute paths
Report the output mode, frame count, output directory or file, and all generated paths
Surface exact parsing or conversion errors from ASE

Examples

# 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

Notes

This skill is commonly used after mattergen generation and before downstream property prediction
If output_format is omitted, the script infers it from output_path
If the input contains multiple frames and the target is cif, the result is a directory, not a single file

Use it

Copy one of these into your project. Installing also returns the manifest and these snippets.

yaml

targets:
  - https://api.opensmartroute.ai/api/v1/registry/ai4ms-matcreator-structure-conversion/manifest   # or paste the manifest below

Manifest

An Open Capability Manifest: the router reads it to know what this does, what it costs and when to pick it.

ai4ms-matcreator-structure-conversion.ocm.jsonjson

{
  "ocm": "1",
  "id": "ai4ms-matcreator-structure-conversion",
  "kind": "skill",
  "name": "structure-conversion",
  "description": "Convert crystal structure files between extxyz and CIF, including splitting multi-frame extxyz into per-frame CIF files.",
  "publisher": "AI4MS",
  "version": "1.0.0",
  "capabilities": {
    "domains": [
      "general"
    ],
    "tags": [
      "skill-md",
      "structure",
      "conversion",
      "extxyz",
      "cif",
      "ase",
      "github"
    ],
    "languages": [
      "en"
    ]
  },
  "quality_prior": 0.6,
  "examples": [
    "Convert crystal structure files between extxyz and CIF, including splitting multi-frame extxyz into per-frame CIF files."
  ],
  "primary": false,
  "metadata": {
    "source": {
      "provider": "github",
      "repository": "https://github.com/AI4MS/MatCreator",
      "path": "src/matcreator/skills/structure-conversion/SKILL.md",
      "ref": "cb5dc92f6cbb630aeaab11a6ac1cc791ae6f45c4",
      "url": "https://github.com/AI4MS/MatCreator/blob/cb5dc92f6cbb630aeaab11a6ac1cc791ae6f45c4/src/matcreator/skills/structure-conversion/SKILL.md",
      "key": "AI4MS/MatCreator/src/matcreator/skills/structure-conversion/SKILL.md"
    }
  },
  "instructions": "## Overview\n\nUse 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.\n\nEvery 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\"`.\n\n```bash\npython skills/structure_conversion/structure_conversion_tools.py convert <input_file> <output_path> [options]\n```\n\n",
  "cost": {
    "context_tokens": 608
  }
}

Fetch it by URL: GET /api/v1/registry/ai4ms-matcreator-structure-conversion/manifest?version=1.0.0

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