Data & ReproProtein Structure & DesignFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-pdb-structure-io

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-pdb-structure-io🧬 bioinformatics (gptomics bio-* suite)bioinformatics — structural biology & cheminformaticsparse

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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

Source Doc

Excerpt From SKILL.md

Supported Formats

Format	Parser	Writer	Description
PDB	`PDBParser`	`PDBIO`	Legacy format, limited to 99999 atoms
mmCIF	`MMCIFParser`	`MMCIFIO`	Modern standard, full metadata
MMTF	`MMTFParser`	-	Compact binary (read-only in Biopython)
BinaryCIF	`BinaryCIFParser`	-	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()

Use cases

Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

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