rust-simulation-tools 0.2.0

Fast algorithms for MD trajectories

Rust Simulation Tools

Fast MD trajectory processing and analysis in Rust with a Python API.

Installation

pip install rust-simulation-tools

Features

• Kabsch alignment with SIMD optimizations
• Fragment-based periodic boundary unwrapping
• SASA calculation (Shrake-Rupley with KD-tree acceleration)
• Interaction energy fingerprinting (LJ + electrostatic)
• AMBER file readers (prmtop, inpcrd)
• DCD trajectory reader with streaming support

Quick Examples

Trajectory Alignment

from rust_simulation_tools import kabsch_align

aligned = kabsch_align(trajectory, reference, align_indices)

SASA Calculation

from rust_simulation_tools import calculate_sasa, get_radii_array

radii = get_radii_array(elements)  # ['C', 'N', 'O', ...]
result = calculate_sasa(coords, radii, residue_indices)
# result['total'], result['per_atom'], result['per_residue']

AMBER Topology + DCD Trajectory

from rust_simulation_tools import read_prmtop, DcdReader

topo = read_prmtop("system.prmtop")
charges, sigmas, epsilons = topo.charges(), topo.sigmas(), topo.epsilons()

dcd = DcdReader("trajectory.dcd")
for i in range(dcd.n_frames):
    coords, box = dcd.read_frame()

Interaction Fingerprints

from rust_simulation_tools import compute_fingerprints, read_prmtop

topo = read_prmtop("system.prmtop")
resmap_indices, resmap_offsets = topo.build_resmap()

lj_fp, es_fp = compute_fingerprints(
    positions, topo.charges(), topo.sigmas(), topo.epsilons(),
    resmap_indices, resmap_offsets, binder_indices
)

API Reference

# Alignment & unwrapping
kabsch_align(trajectory, reference, align_idx) -> aligned_trajectory
unwrap_system(trajectory, box_dimensions, fragment_idx) -> unwrapped_trajectory

# SASA
calculate_sasa(coords, radii, residue_indices, probe_radius=1.4) -> dict
calculate_sasa_trajectory(trajectory, radii, residue_indices) -> dict
calculate_total_sasa(coords, radii, probe_radius=1.4) -> float
get_vdw_radius(element) -> float
get_radii_array(elements) -> np.ndarray

# Fingerprinting
compute_fingerprints(positions, charges, sigmas, epsilons,
                     resmap_indices, resmap_offsets, binder_indices) -> (lj, es)

# File I/O
read_prmtop(path) -> AmberTopology
read_inpcrd(path) -> (positions, box_dimensions)
DcdReader(path)   # .n_frames, .n_atoms, .read_frame(), .seek(n), .read_all()

Development

git clone https://github.com/msinclair-py/rust-simulation-tools.git
cd rust-simulation-tools
pip install maturin pytest pytest-cov numpy
maturin develop --release
pytest tests/ -v --cov

License

MIT License