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Gemmi Integration

Fast mmCIF and PDB parsing with gemmi.

Installation​

pip install zsasa[gemmi]
# or
uv add zsasa[gemmi]

Import​

from zsasa.integrations.gemmi import (
    calculate_sasa_from_structure,
    calculate_sasa_from_model,
    extract_atoms_from_model,
)

Supported Formats​

  • mmCIF (.cif, .cif.gz)
  • PDB (.pdb, .pdb.gz)

Example​

from zsasa.integrations.gemmi import calculate_sasa_from_structure

# From file
result = calculate_sasa_from_structure("protein.cif")

# From gemmi Structure
import gemmi
structure = gemmi.read_structure("protein.pdb")
result = calculate_sasa_from_structure(structure)

# Access results
print(f"Total: {result.total_area:.1f} Ų")
print(f"Polar: {result.polar_area:.1f} Ų")
print(f"Apolar: {result.apolar_area:.1f} Ų")

Why Gemmi?​

  • Fast: C++ backend, optimized for large files
  • Memory efficient: Streaming parser
  • Comprehensive: Full mmCIF dictionary support