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 Substructure Search
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit.
Install Bio Substructure Search
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-substructure-search -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-substructure-search --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-substructure-search .claude/skills/bio-substructure-search && 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-substructure-search" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-substructure-search into .claude/skills/bio-substructure-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-substructure-search", 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-substructure-searchType 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-substructure-search -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-substructure-search --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-substructure-search .agents/skills/bio-substructure-search && 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-substructure-search" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-substructure-search into .agents/skills/bio-substructure-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-substructure-search", 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-substructure-search -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-substructure-search --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-substructure-search .cursor/skills/bio-substructure-search && 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-substructure-search" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-substructure-search into .cursor/skills/bio-substructure-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-substructure-search", 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-substructure-search--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-substructure-search -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-substructure-search --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-substructure-search .gemini/skills/bio-substructure-search && 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-substructure-search" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-substructure-search into .gemini/skills/bio-substructure-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-substructure-search", 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-substructure-searchInstalls 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-substructure-search -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-substructure-search .github/skills/bio-substructure-search && 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-substructure-search" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-substructure-search into .github/skills/bio-substructure-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-substructure-search", 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-substructure-search -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-substructure-search --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-substructure-search .opencode/skills/bio-substructure-search && 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-substructure-search" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-substructure-search into .opencode/skills/bio-substructure-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-substructure-search", 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-substructure-search- GitHub stars
- 3.1k
- Token cost
- ~1.6k tokens
- SKILL.md length
- 236 words
- Files
- 3
- Skills in repo
- 170
- Repo updated
- First seen
- Licence
- None found
At a glance
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit.
- Finding compounds containing specific chemical moieties
- SKILL.md covers Version Compatibility, Basic Substructure Search, Common SMARTS Patterns and Library Filtering, plus 5 more sections
- Runs Python scripts from its folder; calls pip
- Filtering libraries by structural features
What it does
Bio Substructure Search is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.
Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/substructure_search.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
- Finding compounds containing specific chemical moieties
- Filtering libraries by structural features
Example prompts
- “Use the bio-substructure-search skill to search molecular libraries for substructure matches using SMARTS patterns with RDKit”
- “/bio-substructure-search”
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 Substructure Search loads about 1.6k tokens when it runs. Until then it costs about 82 tokens; SKILL.md has 236 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 236 words (~1,583 tokens).
“Reference examples tested with: RDKit 2024.03+”
- name
- bio-substructure-search
- tool_type
- python
- primary_tool
- RDKit
Files
SKILL.md and 2 other files in skills/bio-substructure-search of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/substructure_search.py
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Compare with similar skills
Bio Substructure Search 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 Substructure Search this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~1.6k | 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 Conformer Generatorjinzhezenggroup/computational-chemistry-agent-skills | 148 | 1 repos | ~2.4k | Automated safety check: Pass | LGPL-3.0 | |
| RDKit Descriptors and Fingerprintsjinzhezenggroup/computational-chemistry-agent-skills | 148 | 1 repos | ~2.3k | Automated safety check: Pass | LGPL-3.0 |
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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。
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Generates 3D molecular conformers from SMILES strings or files with RDKit, keeps the lowest-energy one per molecule, and falls back to 2D coordinates when embedding fails.
RDKit Descriptors and Fingerprints
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RDKit Cheminformatics Practices
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Related
Works with
Categories
Questions about Bio Substructure Search
What does Bio Substructure Search do?
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Bio Substructure Search is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Searches molecular libraries for substructure matches using SMARTS patterns with RDKit.
When should I use Bio Substructure Search?
Bio Substructure Search fits situations like: finding compounds containing specific chemical moieties; filtering libraries by structural features.
How do I install Bio Substructure Search in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-substructure-search -a claude-code`. Or copy the skill folder (skills/bio-substructure-search in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-substructure-search in your project. Claude Code loads it when a task matches its description.
How do I install Bio Substructure Search in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-substructure-search -a codex`. Or copy the skill folder (skills/bio-substructure-search in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-substructure-search in your project. Codex loads it when a task matches its description.
Can I use Bio Substructure Search 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-substructure-search -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-substructure-search, .gemini/skills/bio-substructure-search, .github/skills/bio-substructure-search and .opencode/skills/bio-substructure-search in your project.
What does Bio Substructure Search need to run?
Going by SKILL.md and its folder, Bio Substructure Search needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Substructure Search 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 Substructure Search 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 Substructure Search use?
No licence was found for Bio Substructure Search or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Substructure Search use?
About 1.6k tokens (SKILL.md is roughly 6.3k 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 Substructure Search?
Skills that share tags, products or a category with Bio Substructure Search: 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 Conformer Generator (jinzhezenggroup/computational-chemistry-agent-skills, 148 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Substructure Search?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 170 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.