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.
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel.
Install Bio Molecular Io
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-molecular-io -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-molecular-io --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-molecular-io .claude/skills/bio-molecular-io && 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-molecular-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-molecular-io into .claude/skills/bio-molecular-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-molecular-io", 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-molecular-ioType 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-molecular-io -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-molecular-io --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-molecular-io .agents/skills/bio-molecular-io && 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-molecular-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-molecular-io into .agents/skills/bio-molecular-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-molecular-io", 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-molecular-io -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-molecular-io --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-molecular-io .cursor/skills/bio-molecular-io && 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-molecular-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-molecular-io into .cursor/skills/bio-molecular-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-molecular-io", 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-molecular-io--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-molecular-io -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-molecular-io --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-molecular-io .gemini/skills/bio-molecular-io && 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-molecular-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-molecular-io into .gemini/skills/bio-molecular-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-molecular-io", 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-molecular-ioInstalls 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-molecular-io -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-molecular-io .github/skills/bio-molecular-io && 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-molecular-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-molecular-io into .github/skills/bio-molecular-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-molecular-io", 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-molecular-io -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-molecular-io --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-molecular-io .opencode/skills/bio-molecular-io && 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-molecular-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-molecular-io into .opencode/skills/bio-molecular-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-molecular-io", 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-molecular-io- GitHub stars
- 3.1k
- Token cost
- ~1.5k tokens
- SKILL.md length
- 236 words
- Files
- 3
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel.
- Loading chemical libraries
- SKILL.md covers Version Compatibility, Supported Formats, Reading Molecules and Writing Molecules, plus 4 more sections
- Runs Python scripts from its folder; calls pip
- Converting formats
What it does
Bio Molecular Io is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/molecule_io.py` and `usage-guide.md`).
It sits in Research & Science, covering Drug discovery and cheminformatics. It works with RDKit and Python. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Loading chemical libraries
- Converting formats
- Preparing molecules for analysis
Example prompts
- “/bio-molecular-io”
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 Molecular Io loads about 1.5k tokens when it runs. Until then it costs about 91 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 (~1,460 tokens).
“Reference examples tested with: RDKit 2024.03+”
- name
- bio-molecular-io
- tool_type
- python
- primary_tool
- RDKit
Files
SKILL.md and 2 other files in skills/bio-molecular-io of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/molecule_io.py
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Compare with similar skills
Bio Molecular Io 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 Molecular Io this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~1.5k | 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 | |
| Rowanlamm-mit/scienceclaw | 244 | 4 repos | ~3.1k | Automated safety check: Warn | Proprietary | |
| Coot Rdkitpemsley/coot | 168 | — | ~981 | Automated safety check: Pass | GPL-3.0 | |
| RDKit Cheminformaticsdavila7/claude-code-templates | 32k | 14 repos | ~5k | Automated safety check: Pass | MIT |
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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。
Rowan
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Coot Rdkit
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RDKit Cheminformatics
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Guides molecular work with RDKit in Python: reading SMILES and SDF, sanitization, descriptors, fingerprints, substructure and similarity search, reactions and coordinates.
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Related
Categories
Questions about Bio Molecular Io
What does Bio Molecular Io do?
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Bio Molecular Io is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel.
When should I use Bio Molecular Io?
Bio Molecular Io fits situations like: loading chemical libraries; converting formats; preparing molecules for analysis.
How do I install Bio Molecular Io in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-molecular-io -a claude-code`. Or copy the skill folder (skills/bio-molecular-io in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-molecular-io in your project. Claude Code loads it when a task matches its description.
How do I install Bio Molecular Io in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-molecular-io -a codex`. Or copy the skill folder (skills/bio-molecular-io in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-molecular-io in your project. Codex loads it when a task matches its description.
Can I use Bio Molecular Io 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-molecular-io -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-molecular-io, .gemini/skills/bio-molecular-io, .github/skills/bio-molecular-io and .opencode/skills/bio-molecular-io in your project.
What does Bio Molecular Io need to run?
Going by SKILL.md and its folder, Bio Molecular Io needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Molecular Io 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 Molecular Io 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 Molecular Io use?
No licence was found for Bio Molecular Io or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Molecular Io use?
About 1.5k tokens (SKILL.md is roughly 5.8k 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 Bio Molecular Io?
Skills that share tags, products or a category with Bio Molecular Io: DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars), Edu Chem Reaction (wy51ai/edulab, 1.4k stars), Rowan (lamm-mit/scienceclaw, 244 stars) and Coot Rdkit (pemsley/coot, 168 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Molecular Io?
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.