Source: https://github.com/aipoch/medical-research-skills

biopython-structure

When to Use

• You need to parse PDB or mmCIF files and access the structure hierarchy (model → chain → residue → atom).
• You want to compute geometric measurements such as distances, bond angles, and dihedral angles between atoms/residues.
• You need neighbor searches (e.g., find residues/atoms within a cutoff) for contact analysis or local environment inspection.
• You want to perform structural comparison, including alignment/superposition and RMSD-style evaluation.
• You need to extract, modify, and save structures (e.g., subset chains/residues and write back to PDB/mmCIF).

Key Features

• Structure parsing for PDB/mmCIF using Bio.PDB parsers.
• Hierarchical traversal and selection of models, chains, residues, and atoms.
• Geometry calculations: distance, angle, and dihedral computations using Bio.PDB utilities.
• Neighbor search via spatial indexing (NeighborSearch) for efficient cutoff queries.
• Structural operations: extraction, saving, and superposition (e.g., Superimposer).
• Quality/annotation hooks: optional integration with DSSP (external executable) for secondary structure and accessibility.