molex

Molecular exchange — a Rust library for parsing, transforming, and serializing molecular structure data. Provides a unified type system for proteins, nucleic acids, ligands, and other biomolecules across multiple file formats.

Features

• Parse PDB, mmCIF, BinaryCIF, DCD trajectory, and MRC density files
• Convert between formats via a canonical intermediate representation
• Transform coordinates: Kabsch alignment, filtering, interpolation
• Analyze secondary structure (DSSP), bond inference, validation
• Extract render-ready geometry (backbone chains, sidechains, bonds)
• Serialize to compact binary formats for IPC and storage

Quick start

use molex::{MoleculeEntity, MoleculeType};
use molex::adapters::pdb::structure_file_to_entities;

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

Optional features

Documentation

• API docs: cargo doc --open
• Book: cd docs && mdbook serve

License

MIT