What is mol-image-to-smiles?

A tool that reads a picture of a chemical molecule and converts its structure into a SMILES string, a compact text notation for molecules.

Use it with PNG, JPG, JPEG, GIF or BMP structure images to obtain SMILES, compare predictions from two recognition models and review confidence information.

It saves developers or researchers from manually redrawing a molecule before using it in cheminformatics software.

mol-image-to-smiles — Skill for Claude Code and Codex by InternScience

Install

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.

Clone the repo

git clone --depth 1 https://github.com/InternScience/ChemClaw

agentmods

npx agentmods add skills/internscience/chemclaw/mol-image-to-smiles

Made for: Claude Code, Codex.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/internscience/chemclaw/mol-image-to-smiles/github.svg)](https://agentmods.dev/skills/internscience/chemclaw/mol-image-to-smiles)

Your own site

<a href="https://agentmods.dev/skills/internscience/chemclaw/mol-image-to-smiles"><img src="https://agentmods.dev/badge/skills/internscience/chemclaw/mol-image-to-smiles/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/internscience/chemclaw/mol-image-to-smiles"><img src="https://agentmods.dev/badge/skills/internscience/chemclaw/mol-image-to-smiles.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 34 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 2,847 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

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	$0.00034	$0.02847
Opus 5	$0.00017	$0.01424
Sonnet 5	$0.00007	$0.00569
Haiku 4.5	$0.00003	$0.00285

Measured 11d ago against content hash 8ca9ef95e79b, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

mol-image-to-smiles 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.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/mol_image_to_smiles.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

skills/mol-image-to-smiles/SKILL.md · 354 lines

How it starts

The opening of the file, as written. The whole thing — 354 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Mol Image to SMILES Converter

将分子结构图片转换为 SMILES 字符串，使用 DECIMER 和 MolNextR 模型进行智能识别。

触发条件

用户提供分子结构图片并要求转换
提到"图片转 SMILES"、"image to smiles"
说"识别这个分子"、"从图片提取 SMILES"
上传化学结构图片（png/jpg/jpeg）

功能

✅ 双模型支持 - DECIMER + MolNextR
✅ 自动模型选择 - 优先使用本地模型，失败时自动切换
✅ 高精度识别 - 支持复杂分子结构
✅ 批量处理 - 支持多张图片同时转换
✅ 结果对比 - 可比较不同模型的预测结果
✅ 置信度评估 - 提供预测可靠性信息
✅ 格式支持 - PNG、JPG、JPEG、GIF、BMP

核心模型

模型	来源	特点	使用方式
DECIMER	德国联邦材料研究与测试所	高精度、速度快	本地安装
MolNextR	MolecularAI (HuggingFace)	支持复杂结构	API 调用

DECIMER

版本: 2.8.0
优势:
- 本地运行，无需网络
- 识别速度快
- 对标准化学结构图准确率高
限制:
- 需要安装 decimer 包
- 某些复杂结构可能识别不准确

MolNextR

来源: HuggingFace (MolecularAI/MolNextR)
优势:
- 支持复杂分子结构
- 持续更新
- 无需本地安装模型
限制:
- 需要网络连接
- 依赖 HuggingFace API

使用方法

对话框中使用

把这个分子图片转成 SMILES
识别这张化学结构图
image to smiles: molecule.png
用 DECIMER 识别这个分子

命令行使用

# 基本转换（自动选择模型）
python3 scripts/mol_image_to_smiles.py -i molecule.png

# 指定使用 DECIMER
python3 scripts/mol_image_to_smiles.py -i molecule.png -m decimer

# 指定使用 MolNextR
python3 scripts/mol_image_to_smiles.py -i molecule.png -m molnextr

# 指定输出目录
python3 scripts/mol_image_to_smiles.py -i molecule.png -o ./results

# 批量处理
python3 scripts/mol_image_to_smiles.py -i "*.png" -o ./batch

# 安静模式（输出 JSON）
python3 scripts/mol_image_to_smiles.py -i molecule.png -q

参数说明

参数	简写	说明	默认值
`--input`	`-i`	输入图片路径	-
`--output`	`-o`	输出目录	`~/.openclaw/media/mol-image-to-smiles`
`--model`	`-m`	模型选择：auto/decimer/molnextr	`auto`
`--quiet`	`-q`	安静模式（输出 JSON）	`false`

输出示例

成功转换

{
  "input_image": "/path/to/molecule.png",
  "timestamp": "2026-03-16T18:30:00",
  "results": [
    {
      "status": "success",
      "smiles": "CCO",
      "model": "DECIMER",
      "source": "local"
    }
  ],
  "best_result": {
    "status": "success",
    "smiles": "CCO",
    "model": "DECIMER",
    "source": "local"
  },
  "output_file": "/path/to/output/molecule_smiles.json"
}

Read the full file on GitHub · 354 lines

Files

What ships with it

3 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.

Changes

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 · 354 lines · 34 tokens per session scan A 8ca9ef95e79b

Subscribe to this mod's changes

mol-image-to-smiles is a skill published in the GitHub repository InternScience/ChemClaw (52 stars, last pushed 5mo ago), licensed MIT. It adds 34 tokens to every session and 2,847 once invoked, about $0.0002 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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