rust-simulation-tools 0.1.3

Fast algorithms for MD trajectories

Rust Simulation Tools

Fast Kabsch alignment for MD trajectories using Rust.

Installation

pip install rust-simulation-tools

Features

• ⚡ Fast: Rust implementation with SIMD optimizations
• 🔧 Easy to use: Simple Python API compatible with MDAnalysis
• 🧪 Well tested: Comprehensive test suite with >80% coverage
• 🎯 Accurate: Numerically stable Kabsch algorithm

Usage

import MDAnalysis as mda
from rust_simulation_tools import kabsch_align

# Load trajectory
u = mda.Universe("topology.pdb", "trajectory.dcd")

# Select alignment atoms
align_selection = u.select_atoms("backbone")
align_indices = align_selection.indices.astype(np.uintp)

# Get coordinates
reference = u.atoms.positions.copy().astype(np.float64)
trajectory = np.array([ts.positions for ts in u.trajectory], dtype=np.float64)

# Align
aligned = kabsch_align(trajectory, reference, align_indices)

Development

# Clone repository
git clone https://github.com/msinclair-py/rust-simulation-tools.git
cd rust-simulation-tools

# Install development dependencies
pip install maturin pytest pytest-cov numpy

# Build and install in development mode
maturin develop --release

# Run tests
pytest test_kabsch.py -v --cov

License

MIT License