数据与复现蛋白结构与设计FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-pdb-structure-navigation

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

OpenClawNanoClaw分析处理复现实验bio-pdb-structure-navigation🧬 bioinformatics (gptomics bio-* suite)bioinformatics — structural biology & cheminformaticsnavigate

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-navigation

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

Python：structure[0][' '][100]['CA'].get_vector() ，用于 direct access。
访问 residues 、 atoms in PDB structure" → Navigate Structure-Model-Chain-Residue-Atom hierarchy to iterate over components，extract sequences，、 access atomic coordinates. Python：structure[0][' '][100]['CA'].get_vector() ，用于 direct access。
Navigate Structure-Model-Chain-Residue-Atom (SMCRA) hierarchy to access 、 iterate over structure components。
model = structure[0] # First model chain = model[' '] # Chain residue = chain[100] # Residue 100 (simple numbering) residue = chain[(' '，100，' ')] # Full residue ID (hetfield，resseq，icode) atom = residue['CA'] # C-alpha atom。

原始文档

SKILL.md 摘录

Accessing Hierarchy Levels

from Bio.PDB import PDBParser

parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')

## Iterate all levels

for model in structure:
    for chain in model:
        for residue in chain:
            for atom in residue:
                print(f'{chain.id}:{residue.id[1]}:{atom.name}')

## Shortcut iterators (all levels below current)

for chain in structure.get_chains():
    print(f'Chain: {chain.id}')

for residue in structure.get_residues():
    print(f'Residue: {residue.resname}')

for atom in structure.get_atoms():
    print(f'Atom: {atom.name} at {atom.coord}')

适用场景

适合在accessing models，chains，residues，、 atoms，iterating over structure levels，或 extracting sequences ，面向 PDB files时使用。

不适用场景

Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

structure-io - Parse and write structure files
geometric-analysis - Measure distances, angles, RMSD
structure-modification - Modify coordinates and properties
sequence-manipulation/seq-objects - Work with extracted sequences

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