molex

Molecular exchange — a Rust library for parsing, analyzing, and serializing molecular structure data.

Features

• Parse PDB, mmCIF, BinaryCIF, MRC/CCP4 density maps, and DCD trajectories
• Entity model — proteins, nucleic acids, ligands, ions, waters, and cofactors as typed entities
• Analyze — DSSP secondary structure, hydrogen bonds, covalent bonds, disulfide bridges
• Transform — Kabsch alignment, CA extraction, backbone segments
• Serialize — compact binary formats (COORDS01, ASSEM01) for FFI and IPC
• Python bindings — PyO3 module with AtomWorks/Biotite interop

Quick start

use molex::adapters::pdb::pdb_file_to_entities;

let entities = pdb_file_to_entities("1ubq.pdb".as_ref())?;
for e in &entities {
    println!("{}: {} atoms", e.label(), e.atom_count());
}

Python

pip install molex

import molex

coords_bytes = molex.pdb_to_coords(open("1ubq.pdb").read())
pdb_string = molex.coords_to_pdb(coords_bytes)

Optional features

Documentation

• Guide — architecture, modules, and examples
• API reference — generated rustdoc

License

MIT