molio

molio is a Rust library for reading and writing chemistry files used in computational chemistry simulations. It provides a unified interface to access atomic (positions, velocities, atomic symbols) and trajectory (frames, topology) information and other data across various chemical file formats.

Currently supports

This project is a Rust port of chemfiles, a modern C++ library with the same purpose.

Usage

Reading Trajectories

use std::path::Path;
use molio::trajectory::Trajectory;

// Open a trajectory file
let path = Path::new("./src/tests-data/xyz/extended.xyz");
let mut trajectory = Trajectory::open(path).unwrap();

// Read a specific frame
let frame = trajectory.read_at(0).unwrap().unwrap();

// Access frame properties
let energy = frame.properties["ENERGY"].expect_double();

// Access atomic properties
let atom = &frame[0];
let unit_cell = frame.unit_cell;

Writing Trajectories

use std::path::Path;
use molio::{trajectory::Trajectory, frame::Frame, atom::Atom};

// Create a trajectory file for writing
let path = Path::new("output.pdb");
let mut writer = Trajectory::create(path).unwrap();

// Populate Frame with a single C atom with position [1.0, 2.0, 3.0]
let mut frame = Frame::new();
frame.add_atom(Atom::new("C".to_string()), [1.0, 2.0, 3.0]);
// ..add other properties here

// Write frames
writer.write(&frame).unwrap();

// Optionally, explicitly finalize the file (adds END record for PDB)
// If not called explicitly, finalization happens when writer is dropped
writer.finish().unwrap();

Contributions

Contributions are very welcome! Please open an issue to discuss bugs or new features.

Citation

Consider citing the original chemfiles library.