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: CCD, ProtOr, NACCESS, and 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

Project links

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Credits

Author: Tsubasa Nagae

GitHub Statistics

Data verified by PyPI on Jul 28, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

MIT
View SPDX License List

Requires

Python >=3.11

Provides Extra

all biopython biotite dev gemmi mdanalysis mdtraj

Classifiers

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