Adapters — Format I/O

The adapters module provides parsers and serializers for common molecular structure file formats.

PDB / mmCIF (adapters::pdb)

The primary entry point for structure files:

// Auto-detect format from extension
let coords = structure_file_to_coords("path/to/file.pdb")?;

// Explicit format
let bytes = pdb_to_coords(pdb_string)?;      // PDB → COORDS01 bytes
let bytes = mmcif_to_coords(cif_string)?;     // mmCIF → COORDS01 bytes
let pdb = coords_to_pdb(&coords_bytes)?;      // COORDS01 → PDB string

Backed by the pdbtbx crate for robust PDB/mmCIF parsing.

BinaryCIF (adapters::bcif)

RCSB’s compressed binary CIF format. Handles gzip-compressed files automatically.

let bytes = bcif_to_coords(&bcif_bytes)?;
let bytes = bcif_file_to_coords("path/to/file.bcif")?;

DCD Trajectories (adapters::dcd)

CHARMM/NAMD trajectory format — a sequence of coordinate frames sharing the same topology.

let frames: Vec<DcdFrame> = dcd_file_to_frames("trajectory.dcd")?;
// Each frame: Vec<f32> positions (x,y,z interleaved)

Also provides streaming via DcdReader for large trajectories.

MRC / CCP4 Density (adapters::mrc)

Electron density maps:

let density = mrc_to_density(&bytes)?;
let density = mrc_file_to_density("map.mrc")?;
// density: DensityMap with 3D grid + cell parameters

AtomWorks (adapters::atomworks)

Bidirectional conversion between molex entities and Biotite AtomArray objects (via PyO3). Used by ML model pipelines (RF3, RFdiffusion3, LigandMPNN).

import molex

# molex → AtomArray (for model inference)
atom_array = molex.entities_to_atom_array(assembly_bytes)

# AtomArray → molex (after prediction)
assembly_bytes = molex.atom_array_to_entities(atom_array)

Feature-gated behind python.