Biopython Bioinformatics
aiming-lab/AutoResearchClaw
Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.
Agent skill
Bio Pdb Structure Io
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Parse and write protein structure files using Biopython Bio.PDB.
Install Bio Pdb Structure Io
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-io -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-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-pdb-structure-io .claude/skills/bio-pdb-structure-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-pdb-structure-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-io into .claude/skills/bio-pdb-structure-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-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-pdb-structure-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-pdb-structure-io -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-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-pdb-structure-io .agents/skills/bio-pdb-structure-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-pdb-structure-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-io into .agents/skills/bio-pdb-structure-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-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-pdb-structure-io -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-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-pdb-structure-io .cursor/skills/bio-pdb-structure-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-pdb-structure-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-io into .cursor/skills/bio-pdb-structure-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-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-pdb-structure-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-pdb-structure-io -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-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-pdb-structure-io .gemini/skills/bio-pdb-structure-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-pdb-structure-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-io into .gemini/skills/bio-pdb-structure-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-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-pdb-structure-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-pdb-structure-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-pdb-structure-io .github/skills/bio-pdb-structure-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-pdb-structure-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-io into .github/skills/bio-pdb-structure-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-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-pdb-structure-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-pdb-structure-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-pdb-structure-io .opencode/skills/bio-pdb-structure-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-pdb-structure-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-io into .opencode/skills/bio-pdb-structure-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-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-pdb-structure-io- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~1.9k tokens
- SKILL.md length
- 211 words
- Files
- 5
- Skills in repo
- 170
- Repo updated
- First seen
- Licence
- None found
At a glance
Parse and write protein structure files using Biopython Bio.PDB.
- Downloading structures from RCSB PDB
- SKILL.md covers Version Compatibility, Required Imports, Supported Formats and Parsing PDB Files, plus 16 more sections
- Runs Python scripts from its folder; calls pip
- Writing structures to various formats
What it does
Bio Pdb Structure Io is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.
Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files (for example `examples/download_structure.py`, `examples/extract_chain.py` and `examples/parse_pdb.py`).
It sits in Research & Science, covering Bioinformatics and Protein structure and design. It works with Biopython. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Downloading structures from RCSB PDB
- Writing structures to various formats
Example prompts
- “/bio-pdb-structure-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 Pdb Structure Io loads about 1.9k tokens when it runs. Until then it costs about 53 tokens; SKILL.md has 211 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 211 words (~1,924 tokens).
“Reference examples tested with: BioPython 1.83+, scanpy 1.10+”
- name
- bio-pdb-structure-io
- tool_type
- python
- primary_tool
- Bio.PDB
Files
SKILL.md and 4 other files in skills/bio-pdb-structure-io of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/download_structure.py
- examples/extract_chain.py
- examples/parse_pdb.py
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Bio Pdb Structure 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 Pdb Structure Io this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.9k | Automated safety check: Pass | None | |
| Biopython Bioinformaticsaiming-lab/AutoResearchClaw | 15k | — | ~810 | Automated safety check: Pass | MIT | |
| Ggetdavila7/claude-code-templates | 32k | 11 repos | ~6.3k | Automated safety check: Pass | MIT | |
| Bio Entrez LinkGPTomics/bioSkills | 1.2k | 2 repos | ~3.8k | Automated safety check: Pass | MIT | |
| Bio Structural Biology Geometric AnalysisGPTomics/bioSkills | 1.2k | 1 repos | ~4.9k | Automated safety check: Pass | MIT | |
| Bio Structural Biology Structure IoGPTomics/bioSkills | 1.2k | 1 repos | ~4k | Automated safety check: Pass | MIT |
Similar skills
Gget
davila7/claude-code-templates
CLI/Python toolkit for rapid bioinformatics queries. An agent skill from davila7/claude-code-templates.
Bio Entrez Link
GPTomics/bioSkills
Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink).
Bio Structural Biology Geometric Analysis
GPTomics/bioSkills
Measures geometric properties of protein structures with Biopython Bio.PDB - interatomic distances, distance matrices, bond and dihedral angles (phi/psi/chi, Ramachandran), superposition and RMSD…
Bio Structural Biology Structure Io
GPTomics/bioSkills
Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB.
Bio Structural Biology Structure Modification
GPTomics/bioSkills
Modifies protein structures in place with Biopython Bio.PDB - transforms coordinates, strips waters/heteroatoms, overloads the B-factor column, renumbers, and builds entities.
More from FreedomIntelligence/OpenClaw-Medical-Skills
All 170 skills in this repoDifferentiation Schemes
FreedomIntelligence/OpenClaw-Medical-Skills
Select and apply numerical differentiation schemes for PDE/ODE discretization.
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.
Numerical Integration
FreedomIntelligence/OpenClaw-Medical-Skills
Select and configure time integration methods for ODE/PDE simulations.
Ontology Explorer
FreedomIntelligence/OpenClaw-Medical-Skills
Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy).
Ontology Mapper
FreedomIntelligence/OpenClaw-Medical-Skills
Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties.
Related
Works with
Categories
Questions about Bio Pdb Structure Io
What does Bio Pdb Structure Io do?
Parse and write protein structure files using Biopython Bio.PDB. Bio Pdb Structure Io is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.PDB.
When should I use Bio Pdb Structure Io?
Bio Pdb Structure Io fits situations like: downloading structures from RCSB PDB; writing structures to various formats.
How do I install Bio Pdb Structure Io in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-io -a claude-code`. Or copy the skill folder (skills/bio-pdb-structure-io in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-pdb-structure-io in your project. Claude Code loads it when a task matches its description.
How do I install Bio Pdb Structure Io in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-io -a codex`. Or copy the skill folder (skills/bio-pdb-structure-io in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-pdb-structure-io in your project. Codex loads it when a task matches its description.
Can I use Bio Pdb Structure 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-pdb-structure-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-pdb-structure-io, .gemini/skills/bio-pdb-structure-io, .github/skills/bio-pdb-structure-io and .opencode/skills/bio-pdb-structure-io in your project.
What does Bio Pdb Structure Io need to run?
Going by SKILL.md and its folder, Bio Pdb Structure 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 Pdb Structure 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 Pdb Structure 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 Pdb Structure Io use?
No licence was found for Bio Pdb Structure Io or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Pdb Structure Io 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 Pdb Structure Io?
Skills that share tags, products or a category with Bio Pdb Structure Io: Biopython Bioinformatics (aiming-lab/AutoResearchClaw, 15k stars), Gget (davila7/claude-code-templates, 32k stars), Bio Entrez Link (GPTomics/bioSkills, 1.2k stars) and Bio Structural Biology Geometric Analysis (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Pdb Structure Io?
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.