Getting it into your agent
It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.
git clone --depth 1 https://github.com/InternScience/ChemClawnpx agentmods add skills/internscience/chemclaw/chemical-file-converterWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/internscience/chemclaw/chemical-file-converter)<a href="https://agentmods.dev/skills/internscience/chemclaw/chemical-file-converter"><img src="https://agentmods.dev/badge/skills/internscience/chemclaw/chemical-file-converter/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/internscience/chemclaw/chemical-file-converter"><img src="https://agentmods.dev/badge/skills/internscience/chemclaw/chemical-file-converter.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00076 | $0.03099 |
| Opus 5 | $0.00038 | $0.01550 |
| Sonnet 5 | $0.00015 | $0.00620 |
| Haiku 4.5 | $0.00008 | $0.00310 |
Grade A, and why
chemical-file-converter scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 337 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Chemical File Converter
化学文件格式转换技能，支持多种常见化学文件格式之间的互转。
支持的文件格式
| 格式 | 扩展名 | 说明 |
|---|---|---|
| XYZ | .xyz |
简单坐标格式，包含原子类型和 3D 坐标 |
| Gaussian Input | .gjf, .com |
Gaussian 计算输入文件 |
| MDL Molfile | .mol |
单个分子的 2D/3D 结构 |
| Structure Data | .sdf, .sd |
多个分子的结构数据文件 |
| Protein Data Bank | .pdb |
生物大分子结构 |
| Tripos Mol2 | .mol2 |
Tripos 分子格式 |
| SMILES | .smi, .smiles |
线性分子表示 |
| CML | .cml |
化学标记语言 (XML) |
| MOPAC | .mop, .zmt |
MOPAC 输入文件 |
使用方法
对话框中使用
用户可以直接上传文件并要求转换：
把这个 xyz 文件转成 gjf 格式
将 molecule.mol 转换为 .sdf 格式
帮我生成 Gaussian 输入文件，用 B3LYP/6-31G* 方法
把 pdb 文件转成 xyz 坐标
批量转换这些文件为 .mol2 格式
命令行使用
# 基本转换
python3 scripts/convert_chemical.py input.xyz -o output.gjf
# 指定输出格式
python3 scripts/convert_chemical.py input.mol --format sdf
# 批量转换
python3 scripts/convert_chemical.py *.xyz --output-dir ./converted
# Gaussian 输入文件（指定方法和基组）
python3 scripts/convert_chemical.py input.xyz -o output.gjf \
--method B3LYP --basis 6-31G* --charge 0 --multiplicity 1
# 使用 Open Babel（如果可用）
python3 scripts/convert_chemical.py input.pdb -o output.xyz --use-openbabel
参数说明
| 参数 | 简写 | 说明 | 默认值 |
|---|---|---|---|
--input |
-i |
输入文件路径 | 必需 |
--output |
-o |
输出文件路径 | 自动生成 |
--format |
-f |
输出格式 (xyz/sdf/mol2/pdb/gjf 等) | 从输出文件扩展名推断 |
--output-dir |
-d |
输出目录（批量模式） | 当前目录 |
--method |
-m |
Gaussian 计算方法 | B3LYP |
--basis |
-b |
Gaussian 基组 | 6-31G* |
--charge |
分子电荷 | 0 | |
--multiplicity |
自旋多重度 | 1 | |
--link0 |
Gaussian Link0 命令（如 %mem=4GB） | 自动 | |
--use-openbabel |
强制使用 Open Babel | 自动检测 | |
--use-rdkit |
强制使用 RDKit | 自动检测 |
工作流程
1. 文件上传和识别
用户上传化学文件后，自动识别文件格式：
# 根据扩展名识别格式
.xyz → xyz
.gjf/.com → gaussian
.mol → mdl
.sdf → sdf
.pdb → pdb
.mol2 → mol2
2. 格式转换
根据目标格式选择合适的转换引擎：
| 转换类型 | 推荐引擎 | 说明 |
|---|---|---|
| xyz ↔ mol/sdf | RDKit | 支持 3D 坐标 |
| pdb ↔ xyz | Open Babel | 生物大分子支持好 |
| 任意 → gjf | 内置脚本 | 可自定义 Gaussian 参数 |
| 任意格式互转 | Open Babel | 支持 100+ 格式 |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 11d ago First seen · 337 lines · 76 tokens per session scan A 9aed51537ec8
chemical-file-converter is a skill published in the GitHub repository InternScience/ChemClaw (52 stars, last pushed 5mo ago), licensed MIT. It adds 76 tokens to every session and 3,099 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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