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bio-pdb-structure-navigation

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

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Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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

Source Doc

Excerpt From SKILL.md

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}')

Use cases

Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

Not for

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

Upstream Related Skills

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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