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

bio-pdb-structure-io

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

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.

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

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

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：Bio.PDB.PDBParser().get_structure('id'，'file.pdb')，Bio.PDB.MMCIFParser()。
  • Read PDB file" → Parse protein structure files (PDB，mmCIF，MMTF)，download ，面向 RCSB PDB，、 write structures to various formats. Python：Bio.PDB.PDBParser().get_structure('id'，'file.pdb')，Bio.PDB.MMCIFParser()。
  • 解析，download，、 write protein structure files in PDB，mmCIF，、 MMTF formats。
  • print(f'Structure：{structure.id}')。

原始文档

SKILL.md 摘录

Supported Formats

FormatParserWriterDescription
PDBPDBParserPDBIOLegacy format, limited to 99999 atoms
mmCIFMMCIFParserMMCIFIOModern standard, full metadata
MMTFMMTFParser-Compact binary (read-only in Biopython)
BinaryCIFBinaryCIFParser-Compact binary, RCSB recommended

Parsing mmCIF Files

from Bio.PDB import MMCIFParser

parser = MMCIFParser(QUIET=True)
structure = parser.get_structure('1abc', '1abc.cif')

## Downloading from RCSB PDB

```python
from Bio.PDB import PDBList

pdbl = PDBList()

适用场景

  • 适合在reading PDB，mmCIF，、 MMTF files，downloading structures ，面向 RCSB PDB，或 writing structures to various formats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-navigation - Traverse SMCRA hierarchy to access chains, residues, atoms
  • geometric-analysis - Measure distances, angles, and superimpose structures
  • structure-modification - Modify coordinates and properties before writing
  • database-access/entrez-fetch - Fetch structure metadata from NCBI/UniProt

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