Agent skill

Reaction Atom Mapping

by PKU-YuanGroup in PKU-YuanGroup/OpenAI4S

Map atoms and changed bonds for a complete reaction with RXNMapper.

MITAuto-check passed

Install Reaction Atom Mapping

skills CLI

$ npx skills add PKU-YuanGroup/OpenAI4S --skill reaction-atom-mapping -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install PKU-YuanGroup/OpenAI4S reaction-atom-mapping --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4S.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/reaction-atom-mapping .claude/skills/reaction-atom-mapping && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "reaction-atom-mapping" agent skill from https://github.com/PKU-YuanGroup/OpenAI4S/tree/main/skills/reaction-atom-mapping into .claude/skills/reaction-atom-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reaction-atom-mapping", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/PKU-YuanGroup/OpenAI4S/tree/main/skills/reaction-atom-mapping

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add PKU-YuanGroup/OpenAI4S --skill reaction-atom-mapping -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install PKU-YuanGroup/OpenAI4S reaction-atom-mapping --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4S.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/reaction-atom-mapping .agents/skills/reaction-atom-mapping && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "reaction-atom-mapping" agent skill from https://github.com/PKU-YuanGroup/OpenAI4S/tree/main/skills/reaction-atom-mapping into .agents/skills/reaction-atom-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reaction-atom-mapping", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add PKU-YuanGroup/OpenAI4S --skill reaction-atom-mapping -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install PKU-YuanGroup/OpenAI4S reaction-atom-mapping --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4S.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/reaction-atom-mapping .cursor/skills/reaction-atom-mapping && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "reaction-atom-mapping" agent skill from https://github.com/PKU-YuanGroup/OpenAI4S/tree/main/skills/reaction-atom-mapping into .cursor/skills/reaction-atom-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reaction-atom-mapping", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/PKU-YuanGroup/OpenAI4S.git --path skills/reaction-atom-mapping

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add PKU-YuanGroup/OpenAI4S --skill reaction-atom-mapping -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install PKU-YuanGroup/OpenAI4S reaction-atom-mapping --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4S.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/reaction-atom-mapping .gemini/skills/reaction-atom-mapping && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "reaction-atom-mapping" agent skill from https://github.com/PKU-YuanGroup/OpenAI4S/tree/main/skills/reaction-atom-mapping into .gemini/skills/reaction-atom-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reaction-atom-mapping", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install PKU-YuanGroup/OpenAI4S reaction-atom-mapping

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add PKU-YuanGroup/OpenAI4S --skill reaction-atom-mapping -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4S.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/reaction-atom-mapping .github/skills/reaction-atom-mapping && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "reaction-atom-mapping" agent skill from https://github.com/PKU-YuanGroup/OpenAI4S/tree/main/skills/reaction-atom-mapping into .github/skills/reaction-atom-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reaction-atom-mapping", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add PKU-YuanGroup/OpenAI4S --skill reaction-atom-mapping -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install PKU-YuanGroup/OpenAI4S reaction-atom-mapping --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4S.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/reaction-atom-mapping .opencode/skills/reaction-atom-mapping && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "reaction-atom-mapping" agent skill from https://github.com/PKU-YuanGroup/OpenAI4S/tree/main/skills/reaction-atom-mapping into .opencode/skills/reaction-atom-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reaction-atom-mapping", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: reaction-atom-mapping
GitHub stars: 622
Token cost: ~1.2k tokens
SKILL.md length: 528 words
Files: 3
Skills in repo: 17
Repo updated: Oct 9, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Map atoms and changed bonds for a complete reaction with RXNMapper.

Reactant/product correspondence and reaction-centre audits
SKILL.md covers Install and run, Scenario 3 benchmark contract, Derive the reaction centre and Acceptance checks, plus 2 more sections
Calls conda
Not target-only retrosynthesis

What it does

Reaction Atom Mapping is an agent skill from PKU-YuanGroup/OpenAI4S. Map atoms and changed bonds for a complete reaction with RXNMapper. Use for reactant/product correspondence and reaction-centre audits, not target-only retrosynthesis or feasibility.

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files (for example `README.md` and `README_zh.md`).

It works with Python. The repository describes itself as: Open-source AI agent for scientific research. Analyze data in Python/R with Claude, GPT, Gemini, and more. The licence is MIT.

When your agent uses it

Reactant/product correspondence and reaction-centre audits
Not target-only retrosynthesis

Example prompts

“/reaction-atom-mapping”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 4a72e87. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- conda
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- github.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Reaction Atom Mapping loads about 1.2k tokens when it runs. Until then it costs about 51 tokens; SKILL.md has 528 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~51
When it runs · the whole SKILL.md, loaded when a task matches: ~1.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from PKU-YuanGroup/OpenAI4S at commit 4a72e87, republished under its MIT licence (© PKU-YuanGroup). 528 words, ~1,208 tokens.

Download SKILL.mdSave it as .claude/skills/reaction-atom-mapping/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.

name: reaction-atom-mapping
description: Map atoms and changed bonds for a complete reaction with RXNMapper. Use for reactant/product correspondence and reaction-centre audits, not target-only retrosynthesis or feasibility.
license: MIT
origin: openai4s

Reaction atom mapping

Answer one scientific question: for a reaction whose reactant and product sides are already specified, which atoms correspond across the transformation? Changed bonds derived from that mapping define a machine-readable reaction centre. This task does not propose precursors and does not establish feasibility.

Use RXNMapper, an attention-guided ALBERT mapper distributed with a local Python API and a mapping confidence value.

Install and run

Install it in the optional chemistry environment:

bash

conda create -n rxnmapper python=3.11 -y
conda run -n rxnmapper python -m pip install "rxnmapper[rdkit]==0.4.3"

Select that interpreter in its own OpenAI4S Python Cell. The switch is applied before the following Cell, so do not combine this call with the import:

python

host.env.use("rxnmapper")

After the switch succeeds, run the mapping code in a new Cell:

python

from rxnmapper import BatchedMapper

mapper = BatchedMapper(batch_size=32)
reaction = "CCBr.OCC>>CCOCC"
record = next(mapper.map_reactions_with_info([reaction]))
print(record["mapped_rxn"], record["confidence"])

Outside a Web session, where host.env.use(...) is unavailable, save the same code as a workspace script and execute it with conda run -n rxnmapper python. Do not run the bare import in the original kernel after installing into another environment.

Use BatchedMapper for campaigns because it handles invalid records without aborting the whole batch. Keep the original reaction string alongside the mapped result.

For OpenAI4S, create a manifest from the reviewed RXNMapper 0.4.3 wheel SHA in reaction_model_deployment.UPSTREAM_DISTRIBUTIONS, then call ReactionModelBackend("rxnmapper", ...) with a python_command that uses the external prefix. The foreign worker emits mapped reactions, confidence, stable atom correspondences, failures, runtime package versions, and the exact manifest fingerprint. It never downloads a model during inference.

Scenario 3 benchmark contract

Use ../retrosynthesis_planning/atom_mapping_benchmark.py for curated blind evaluation. Public inputs must be map-free. The adapter must emit the mapped reaction plus explicit stable reactant/product atom correspondences; the normalizer checks conservation, duplicate/unmapped atoms and changed bonds. Private scoring accepts pre-frozen symmetry-equivalent correspondences and excludes explicitly ambiguous reactions from whole-reaction exact accuracy, while still reporting changed-bond F1 for them.

Show full SKILL.md (244 more words)Show less

Derive the reaction centre

Parse the mapped reactant and product sides with RDKit. Build bond dictionaries keyed by sorted atom-map-number pairs, with bond type as the value. Report:

bonds present only on the reactant side as broken;
bonds present only on the product side as formed;
pairs present on both sides with a changed bond order;
mapped atoms missing from either side;
unmapped atoms and duplicate map numbers.

Do not silently repair unbalanced reactions, strip reagents, or move molecules between reaction fields. Those choices change the scientific object being mapped and must be recorded as preprocessing.

Acceptance checks

Both >> sides are present and parseable.
Atom-map numbers are unique within each side after mapping.
Every changed bond references mapped atoms.
Mapping confidence is preserved as the model's own score, not converted to a probability that the proposed reaction is correct.
For evaluation, use atom-mapping and bond-change ground truth only after the predicted mapping is fixed.

Output contract

Return original reaction SMILES, mapped reaction SMILES, mapper confidence, formed/broken/order-changed bonds, parse warnings, unmapped atoms, model version, and environment provenance.

Failure modes

Symptom	Action
input contains only a product	Stop and use `single-step-retrosynthesis`; atom mapping requires both sides.
mapper returns `>>` or an empty record	Mark the reaction invalid and preserve the original input.
confidence is low	Keep the mapping for review but do not use its reaction centre as an unquestioned label.
atom conservation fails	Report imbalance separately; do not force a cosmetically balanced mapping.

Primary source: https://github.com/rxn4chemistry/rxnmapper.

Files

SKILL.md and 2 other files in skills/reaction-atom-mapping of PKU-YuanGroup/OpenAI4S.

SKILL.md
README.md
README_zh.md

Open the folder on GitHubat commit 4a72e87

Compare with similar skills

Reaction Atom Mapping next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Reaction Atom Mapping compared with similar skills
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Reaction Atom Mapping this skillPKU-YuanGroup/OpenAI4S	622	—	~1.2k	Automated safety check: Pass	MIT	yesterday
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PDF Processinganthropics/skills	180k	47 repos	~2k	Automated safety check: Pass	Proprietary	yesterday
NotebookLM Research AssistantPleasePrompto/notebooklm-skill	7.8k	14 repos	~2.4k	Automated safety check: Notes	MIT	1 mo ago
Manim Video Productionbrowser-use/video-use	29k	6 repos	~3k	Automated safety check: Pass	MIT	2 days ago
PPT Masterhugohe3/ppt-master	59k	1 repos	~2.5k	Automated safety check: Pass	MIT	3 days ago

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Works with

Python

Questions about Reaction Atom Mapping

What does Reaction Atom Mapping do?

Map atoms and changed bonds for a complete reaction with RXNMapper. Reaction Atom Mapping is an agent skill from PKU-YuanGroup/OpenAI4S. Map atoms and changed bonds for a complete reaction with RXNMapper.

When should I use Reaction Atom Mapping?

Reaction Atom Mapping fits situations like: reactant/product correspondence and reaction-centre audits; not target-only retrosynthesis.

How do I install Reaction Atom Mapping in Claude Code?

Run `npx skills add PKU-YuanGroup/OpenAI4S --skill reaction-atom-mapping -a claude-code`. Or copy the skill folder (skills/reaction-atom-mapping in PKU-YuanGroup/OpenAI4S) into .claude/skills/reaction-atom-mapping in your project. Claude Code loads it when a task matches its description.

How do I install Reaction Atom Mapping in Codex?

Run `npx skills add PKU-YuanGroup/OpenAI4S --skill reaction-atom-mapping -a codex`. Or copy the skill folder (skills/reaction-atom-mapping in PKU-YuanGroup/OpenAI4S) into .agents/skills/reaction-atom-mapping in your project. Codex loads it when a task matches its description.

Can I use Reaction Atom Mapping in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add PKU-YuanGroup/OpenAI4S --skill reaction-atom-mapping -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/reaction-atom-mapping, .gemini/skills/reaction-atom-mapping, .github/skills/reaction-atom-mapping and .opencode/skills/reaction-atom-mapping in your project.

What does Reaction Atom Mapping need to run?

Going by SKILL.md and its folder, Reaction Atom Mapping needs the command-line tools its instructions call (conda). Our summary lists: Python 3.

Does Reaction Atom Mapping access the network?

SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.

Is Reaction Atom Mapping safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Reaction Atom Mapping use?

Reaction Atom Mapping is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Reaction Atom Mapping use?

About 1.2k tokens (SKILL.md is roughly 4.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Reaction Atom Mapping?

Skills that share tags, products or a category with Reaction Atom Mapping: MCP Server Builder (anthropics/skills, 180k stars), PDF Processing (anthropics/skills, 180k stars), NotebookLM Research Assistant (PleasePrompto/notebooklm-skill, 7.8k stars) and Manim Video Production (browser-use/video-use, 29k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Reaction Atom Mapping?

PKU-YuanGroup (a GitHub organization) maintains it in PKU-YuanGroup/OpenAI4S, which has 622 GitHub stars. The repository holds 17 skills in this directory. The repository was last updated on October 9, 2026.

Source: PKU-YuanGroup/OpenAI4S on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Reaction Atom Mapping

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Reaction atom mapping

Install and run

Scenario 3 benchmark contract

Derive the reaction centre

Acceptance checks

Output contract

Failure modes

Files

Compare with similar skills

Similar skills

More from PKU-YuanGroup/OpenAI4S

Related

Questions about Reaction Atom Mapping