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

Format	Extension
(Extended) XYZ	.xyz
PDB	.pdb
SDF	.sdf
SMILES	.smi

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.