zsasa 0.6.0

Fast SASA calculation using Zig

zsasa Python Bindings

Python bindings for zsasa — a high-performance SASA calculator in Zig.

Full Documentation

Installation

pip install zsasa
# or
uv add zsasa

Optional Dependencies

pip install zsasa[gemmi]      # Gemmi integration
pip install zsasa[biopython]  # BioPython integration
pip install zsasa[biotite]    # Biotite integration
pip install zsasa[all]        # All integrations

Quick Start

import numpy as np
from zsasa import calculate_sasa

coords = np.array([[0.0, 0.0, 0.0], [3.0, 0.0, 0.0]])
radii = np.array([1.5, 1.5])
result = calculate_sasa(coords, radii)
print(f"Total SASA: {result.total_area:.2f} Ų")

# With structure file (gemmi)
from zsasa.integrations.gemmi import calculate_sasa_from_structure
result = calculate_sasa_from_structure("protein.cif")
print(f"Total: {result.total_area:.1f} Ų")

Features

• Two algorithms: Shrake-Rupley and Lee-Richards, with bitmask LUT optimization
• Selectable precision: f64 (default) or f32
• Multi-threading: Automatic parallelization
• Atom classification: NACCESS, ProtOr, OONS classifiers
• Analysis: Per-residue aggregation, RSA, polar/nonpolar classification
• Batch processing: process_directory() for proteome-scale datasets
• MD trajectory: MDTraj and MDAnalysis integrations; use pyztraj for direct trajectory-file I/O
• Integrations: Gemmi, BioPython, Biotite

See the full API reference for details.

Development

cd python
uv run --with pytest pytest tests/ -v    # Tests
ruff format . && ruff check --fix .      # Lint

License

MIT