molex 0.7.2

Parse, analyze, and transform molecular structure data (PDB, mmCIF, BinaryCIF, MRC)

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 other small molecules as typed entities
• Analyze: DSSP secondary structure, hydrogen bonds, covalent bonds, disulfide bridges, SASA, contacts
• Transform: Kabsch alignment and superposition RMSD
• Serialize: compact binary wire format 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

The Python API is object-centric: parse a structure into an Assembly, walk its entities and residues, and read atoms as numpy columns.

import molex

asm = molex.Assembly.from_pdb(open("1ubq.pdb").read())
for e in asm.entities():
    print(e.kind, e.chain_id, e.residue_count)

asm.recompute_ss()       # opt-in DSSP secondary structure

# Per-atom numpy columns (no Biotite required) come from PyAtomTable:
table = molex.PyAtomTable.from_assembly_bytes(asm.to_assembly_bytes())
coords = table.coords    # (N, 3) float32

Atom completion (filling missing heavy atoms) happens at parse time, during file ingest; the default is Completion.Heavy. from_mmcif and from_bcif parse the other formats. The *_to_assembly_bytes / assembly_bytes_to_* free functions are transport helpers for the wire protocol, not the default path. Type stubs (molex.pyi) ship with the wheel.

Optional features

Feature	Description
python	PyO3 bindings for use from Python

Documentation

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

License

MIT