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Agent skill

Chem React Ot

by learningmatter-mit in learningmatter-mit/AtomisticSkills

Generate transition state structures for chemical reactions using React-OT.

MITAuto-check passed

Install Chem React Ot

skills CLI
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot -a claude-code

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

GitHub CLI
$ gh skill install learningmatter-mit/AtomisticSkills chem-react-ot --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/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/chem-react-ot .claude/skills/chem-react-ot && 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/

Facts

Skill name
chem-react-ot
GitHub stars
175
Token cost
~914 tokens
SKILL.md length
340 words
Files
10 (incl. scripts)
Skills in repo
129
Repo updated
First seen
Licence
MIT

At a glance

Generate transition state structures for chemical reactions using React-OT.

  • Works in 2 steps: Fetch React-OT and the model → Generate Transition State
  • SKILL.md covers Goal, Key Features, Usage and Example, plus 2 more sections
  • Runs Python scripts from its folder

What it does

Chem React Ot is an agent skill from learningmatter-mit/AtomisticSkills. Generate transition state structures for chemical reactions using React-OT.

Its SKILL.md is about 910 tokens, which your agent loads only when the skill is triggered. The skill folder holds 13 other files, including scripts (for example `examples/oxadiazole_isomerization/README.md`, `scripts/download_models.py` and `scripts/generate_ts.py`).

It works with React. The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.

Example prompts

  • “/chem-react-ot”

Requirements

  • Python 3

Workflow steps

2 steps, taken from the step headings in SKILL.md.

  1. Fetch React-OT and the model
  2. Generate Transition State

What it can do on your machine

Read from SKILL.md and the folder at commit 7f2d86d. 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

    Ships 3 files in scripts/ (Python), which the agent can run.

    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
    • doi.org

    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

Chem React Ot loads about 914 tokens when it runs. Until then it costs about 22 tokens; SKILL.md has 340 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~22
When it runs · the whole SKILL.md, loaded when a task matches
~914

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); the scripts in this folder are not scanned.

SKILL.md

The full file from learningmatter-mit/AtomisticSkills at commit 7f2d86d, republished under its MIT licence (© learningmatter-mit). 340 words, ~914 tokens.

Download SKILL.mdSave it as .claude/skills/chem-react-ot/SKILL.md (or your agent's skills folder). This skill also uses 9 other files; get the full folder from GitHub.
name
chem-react-ot
description
Generate transition state structures for chemical reactions using React-OT.
metadata.category
chemistry
metadata.venv
reactot

chem-react-ot — React-OT Transition State Generation

Goal

Generate transition state (TS) structures given reactant and product structures using the React-OT model (Optimal Transport). React-OT is a generative model that predicts TS geometries directly without requiring an initial guess path (like NEB).

Category: chemistry Environment: reactot (commands run through venv/run reactot ...)

Key Features

  • Generative TS Prediction: Predicts 3D transition state structures from 3D reactants and products.
  • Fast Inference: Uses an ODE solver for generation, typically much faster than DFT-based NEB.
  • No Path Guess Required: Directly generates the TS structure.

Usage

1. Fetch React-OT and the model

React-OT runs in its own uv environment, reactot (torch 2.2.1, created on first use). Its source is not a package: fetch the pinned version, with the fixes it needs, once, then download the pre-trained weights:

bash
${CLAUDE_SKILL_DIR}/../../venv/run reactot python ${CLAUDE_SKILL_DIR}/scripts/setup_react_ot.py
${CLAUDE_SKILL_DIR}/../../venv/run reactot python ${CLAUDE_SKILL_DIR}/scripts/download_models.py

The source goes to ~/.cache/atomisticskills/react-ot (or $REACT_OT_DIR).

The checkpoint is saved to ~/.cache/react-ot/checkpoints/sb-pretrained.ckpt.

2. Generate Transition State

Run the generation script with reactant and product files (xyz, cif, pdb, etc. - anything ASE reads).

bash
${CLAUDE_SKILL_DIR}/../../venv/run reactot python ${CLAUDE_SKILL_DIR}/scripts/generate_ts.py \
    --reactants reactant.xyz \
    --products product.xyz \
    --output_dir results/ts_search

Arguments:

  • --reactants: Path to reactant structure file(s). Can be a single file with multiple molecules or a list of files.
  • --products: Path to product structure file(s).
  • --output_dir: Directory to save the generated TS structure (ts_generated.xyz) and trajectory (generation_traj.xyz).
  • --nfe: Number of function evaluations for the ODE solver (default: 10). Higher values might be more accurate but slower.
  • --checkpoint: Path to custom model checkpoint (optional, defaults to downloaded one).

Example

bash
${CLAUDE_SKILL_DIR}/../../venv/run reactot python ${CLAUDE_SKILL_DIR}/scripts/generate_ts.py \
    --reactants ${CLAUDE_SKILL_DIR}/examples/oxadiazole_isomerization/reactant.xyz \
    --products ${CLAUDE_SKILL_DIR}/examples/oxadiazole_isomerization/product.xyz \
    --output_dir ${CLAUDE_SKILL_DIR}/examples/oxadiazole_isomerization/output

Constraints

  • Environment: reactot (x86_64: CUDA 12.1 build of torch 2.2.1, driver >= 525; aarch64: CPU). On aarch64 the PyG extensions are compiled on first use, which needs a C++ compiler.
  • Input Format: Reactant and product structures must be in any format readable by ASE (XYZ, CIF, PDB, etc.).
  • Atom Ordering: Reactant and product structures must have the same number of atoms with consistent atom ordering.
  • Model Checkpoint: The pre-trained checkpoint must be downloaded before first use (see step 1).

References

  • React-OT GitHub
  • Duan, C., Liu, G.-H., Du, Y. et al., "Optimal transport for generating transition states in chemical reactions", Nature Machine Intelligence, 2025. DOI

Author: Bowen Deng Contact: GitHub @learningmatter-mit

© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 9 other files (scripts) in skills/chem-react-ot of learningmatter-mit/AtomisticSkills.

  • SKILL.md
  • examples/oxadiazole_isomerization/README.md
  • examples/oxadiazole_isomerization/output/reaction_rxn.xyz
  • examples/oxadiazole_isomerization/output/ts_generated.xyz
  • examples/oxadiazole_isomerization/product.xyz
  • examples/oxadiazole_isomerization/reactant.xyz
  • examples/oxadiazole_isomerization/reference_ts.xyz
  • scripts/download_models.py
  • scripts/generate_ts.py
  • scripts/setup_react_ot.py

Open the folder on GitHubat commit 7f2d86d

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Works with

Questions about Chem React Ot

What does Chem React Ot do?

Generate transition state structures for chemical reactions using React-OT. Chem React Ot is an agent skill from learningmatter-mit/AtomisticSkills. Generate transition state structures for chemical reactions using React-OT.

How do I install Chem React Ot in Claude Code?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot -a claude-code`. Or copy the skill folder (skills/chem-react-ot in learningmatter-mit/AtomisticSkills) into .claude/skills/chem-react-ot in your project. Claude Code loads it when a task matches its description.

How do I install Chem React Ot in Codex?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot -a codex`. Or copy the skill folder (skills/chem-react-ot in learningmatter-mit/AtomisticSkills) into .agents/skills/chem-react-ot in your project. Codex loads it when a task matches its description.

Can I use Chem React Ot 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 learningmatter-mit/AtomisticSkills --skill chem-react-ot -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chem-react-ot, .gemini/skills/chem-react-ot, .github/skills/chem-react-ot and .opencode/skills/chem-react-ot in your project.

What does Chem React Ot need to run?

Going by SKILL.md and its folder, Chem React Ot needs Python for the scripts in its folder. Our summary lists: Python 3.

Does Chem React Ot access the network?

SKILL.md names 2 domains. As links in the text: github.com and doi.org. This is read from the text; nothing was executed.

Is Chem React Ot 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Chem React Ot use?

Chem React Ot is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Chem React Ot use?

About 914 tokens (SKILL.md is roughly 3.7k 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 Chem React Ot?

Skills that share tags, products or a category with Chem React Ot: Web Artifacts Builder (anthropics/skills, 180k stars), React Doctor (makeplane/plane, 60k stars), React Composition Patterns (vercel-labs/openreview, 1.7k stars) and React Router Development (remix-run/react-router, 57k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Chem React Ot?

learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 175 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 6, 2026.

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