DiffDock Molecular Docking
K-Dense-AI/scientific-agent-skills
Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.
Agent skill
Bio Reaction Enumeration
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Enumerates chemical libraries through reaction SMARTS transformations using RDKit.
Install Bio Reaction Enumeration
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-reaction-enumeration --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-reaction-enumeration .claude/skills/bio-reaction-enumeration && rm -rf skills-srcUse ~/.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/
Install the "bio-reaction-enumeration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-reaction-enumeration into .claude/skills/bio-reaction-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-reaction-enumeration", 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 install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-reaction-enumerationType 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.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-reaction-enumeration --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-reaction-enumeration .agents/skills/bio-reaction-enumeration && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-reaction-enumeration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-reaction-enumeration into .agents/skills/bio-reaction-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-reaction-enumeration", 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.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-reaction-enumeration --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-reaction-enumeration .cursor/skills/bio-reaction-enumeration && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bio-reaction-enumeration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-reaction-enumeration into .cursor/skills/bio-reaction-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-reaction-enumeration", 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 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-reaction-enumeration--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-reaction-enumeration --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-reaction-enumeration .gemini/skills/bio-reaction-enumeration && rm -rf skills-srcUse ~/.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/
Install the "bio-reaction-enumeration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-reaction-enumeration into .gemini/skills/bio-reaction-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-reaction-enumeration", 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.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-reaction-enumerationInstalls 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).
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-reaction-enumeration .github/skills/bio-reaction-enumeration && rm -rf skills-srcUse ~/.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/
Install the "bio-reaction-enumeration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-reaction-enumeration into .github/skills/bio-reaction-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-reaction-enumeration", 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.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-reaction-enumeration --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-reaction-enumeration .opencode/skills/bio-reaction-enumeration && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bio-reaction-enumeration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-reaction-enumeration into .opencode/skills/bio-reaction-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-reaction-enumeration", 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
bio-reaction-enumeration- GitHub stars
- 3.1k
- Token cost
- ~1.9k tokens
- SKILL.md length
- 232 words
- Files
- 3
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Enumerates chemical libraries through reaction SMARTS transformations using RDKit.
- Creating combinatorial libraries
- SKILL.md covers Version Compatibility, Reaction SMARTS Basics, Common Reaction SMARTS and Combinatorial Library…, plus 4 more sections
- Runs Python scripts from its folder; calls pip
- Enumerating products from synthetic routes
What it does
Bio Reaction Enumeration is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with product validation. Use when creating combinatorial libraries or enumerating products from synthetic routes.
Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/enumerate_reactions.py` and `usage-guide.md`).
It sits in Research & Science, covering Drug discovery and cheminformatics. It works with RDKit. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Creating combinatorial libraries
- Enumerating products from synthetic routes
Example prompts
- “Use the bio-reaction-enumeration skill to enumerate chemical libraries through reaction SMARTS transformations using RDKit”
- “/bio-reaction-enumeration”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. 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 script files (Python), which the agent can run.
Shell commands in SKILL.md call:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
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
Bio Reaction Enumeration loads about 1.9k tokens when it runs. Until then it costs about 78 tokens; SKILL.md has 232 words of instructions outside code blocks.
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
Without a licence we can't republish the file, so here is its outline and opening line. It has 232 words (~1,933 tokens).
“Reference examples tested with: RDKit 2024.03+”
- name
- bio-reaction-enumeration
- tool_type
- python
- primary_tool
- RDKit
Files
SKILL.md and 2 other files in skills/bio-reaction-enumeration of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/enumerate_reactions.py
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Compare with similar skills
Bio Reaction Enumeration 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bio Reaction Enumeration this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~1.9k | Automated safety check: Pass | None | |
| DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3k | Automated safety check: Notes | MIT | |
| Edu Chem Reactionwy51ai/edulab | 1.4k | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Biopipelineslocbp-uzh/biopipelines | 109 | — | ~2.4k | Automated safety check: Pass | MIT | |
| RDKit Cheminformatics Practicesaiming-lab/AutoResearchClaw | 15k | — | ~708 | Automated safety check: Pass | MIT | |
| Rowanlamm-mit/scienceclaw | 244 | 4 repos | ~3.1k | Automated safety check: Warn | Proprietary |
Similar skills
Edu Chem Reaction
wy51ai/edulab
把一个化学反应做成自包含的微观 3D 交互演示网页：左/上为 Three.js 可交互分子动画 （拖滑块看断键·成键·原子重组，分步高亮），右为 KaTeX 反应方程 + 分步讲解 + 原子守恒计数 + 可选能量-反应进程曲线。支持三入口——给定文字反应/方程、随机出题、上传图片识别后演示。
Biopipelines
locbp-uzh/biopipelines
Design and run computational protein and ligand workflows on a GPU: binder and enzyme design, de novo backbone generation, inverse folding and sequence redesign, structure prediction, protein-ligand…
RDKit Cheminformatics Practices
aiming-lab/AutoResearchClaw
Reference guide for working with molecules in RDKit: reading SMILES and SDF files, computing descriptors and fingerprints, and searching substructures.
Rowan
lamm-mit/scienceclaw
Cloud-based quantum chemistry platform with Python API. An agent skill from lamm-mit/scienceclaw.
Coot Rdkit
pemsley/coot
RDKit molecular manipulation and visualization within Coot's Python environment.
More from FreedomIntelligence/OpenClaw-Medical-Skills
All 279 skills in this repoSingle Cell Rna Qc
FreedomIntelligence/OpenClaw-Medical-Skills
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations.
Differentiation Schemes
FreedomIntelligence/OpenClaw-Medical-Skills
Select and apply numerical differentiation schemes for PDE/ODE discretization.
Fhir Developer Skill
FreedomIntelligence/OpenClaw-Medical-Skills
FHIR API development guide for building healthcare endpoints.
Linear Solvers
FreedomIntelligence/OpenClaw-Medical-Skills
Select and configure linear solvers for systems Ax=b in dense and sparse problems.
Medical Research Toolkit
FreedomIntelligence/OpenClaw-Medical-Skills
Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research.
Mesh Generation
FreedomIntelligence/OpenClaw-Medical-Skills
Plan and evaluate mesh generation for numerical simulations.
Related
Works with
Categories
Questions about Bio Reaction Enumeration
What does Bio Reaction Enumeration do?
Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Bio Reaction Enumeration is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Enumerates chemical libraries through reaction SMARTS transformations using RDKit.
When should I use Bio Reaction Enumeration?
Bio Reaction Enumeration fits situations like: creating combinatorial libraries; enumerating products from synthetic routes.
How do I install Bio Reaction Enumeration in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration -a claude-code`. Or copy the skill folder (skills/bio-reaction-enumeration in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-reaction-enumeration in your project. Claude Code loads it when a task matches its description.
How do I install Bio Reaction Enumeration in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration -a codex`. Or copy the skill folder (skills/bio-reaction-enumeration in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-reaction-enumeration in your project. Codex loads it when a task matches its description.
Can I use Bio Reaction Enumeration 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-reaction-enumeration, .gemini/skills/bio-reaction-enumeration, .github/skills/bio-reaction-enumeration and .opencode/skills/bio-reaction-enumeration in your project.
What does Bio Reaction Enumeration need to run?
Going by SKILL.md and its folder, Bio Reaction Enumeration needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Reaction Enumeration access the network?
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Bio Reaction Enumeration 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 Bio Reaction Enumeration use?
No licence was found for Bio Reaction Enumeration or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Reaction Enumeration use?
About 1.9k tokens (SKILL.md is roughly 7.7k 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 Bio Reaction Enumeration?
Skills that share tags, products or a category with Bio Reaction Enumeration: DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars), Edu Chem Reaction (wy51ai/edulab, 1.4k stars), Biopipelines (locbp-uzh/biopipelines, 109 stars) and RDKit Cheminformatics Practices (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Reaction Enumeration?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 279 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.