bio-pdb-structure-navigation - Navigate PDB structure hierarchy
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model to access models, chains, residues, and atoms
Tags
Updated: 2026-05-28Typical Inputs
Typical Outputs
What this skill does
- parse PDB file
- access structure models
- access structure chains
- access structure residues
- access structure atoms
- iterate over models
- iterate over chains
- iterate over residues
- iterate over atoms
- get atom coordinates
- get atom properties
- extract polypeptide sequences
- filter residues by type
- filter atoms by name
- handle disordered atoms
- handle disordered residues
- count structure entities
- navigate parent entities
- convert residue names
Inputs
- PDB file
- Residue ID
- Chain ID
- Atom name
- Residue type
Outputs
- Structure object
- Model object
- Chain object
- Residue object
- Atom object
- Atom coordinates
- Polypeptide sequence
- Residue name conversion
Requirements
- BioPython 1.83+
- Python environment