Types — Core Data Structures

The types module contains molex’s canonical data representations.

`types::coords` — Atom-Level Data

`Coords`

Flat parallel arrays representing atoms in a molecular structure. Every atom has a position (CoordsAtom), chain ID, residue name, residue number, atom name, and element type.

This is the lowest-level representation — no hierarchy, no classification. Use split_into_entities() to get grouped molecules.

`CoordsAtom`

pub struct CoordsAtom {
    pub x: f32, pub y: f32, pub z: f32,
    pub occupancy: f32,
    pub b_factor: f32,
}

`Element`

Chemical element enum with methods for covalent radius, VDW radius, and CPK color. Supports lookup by symbol or by atom name heuristics.

Binary serialization

serialize(&coords) → Vec<u8> — COORDS01 format (26 bytes/atom)
deserialize(&bytes) → Coords — inverse
serialize_assembly(&entities) → Vec<u8> — ASSEM01 multi-entity format
deserialize_assembly(&bytes) → Vec<MoleculeEntity> — inverse

`types::entity` — Molecule Classification

`MoleculeEntity`

A classified molecule with its atom data:

entity_id: u32 — unique identifier
molecule_type: MoleculeType — Protein, DNA, RNA, Ligand, Ion, etc.
kind: EntityKind — Polymer(PolymerData) or AtomSet(AtomSet)

`MoleculeType`

pub enum MoleculeType {
    Protein, DNA, RNA, Ligand, Ion, Water, Lipid, Cofactor, Solvent,
}

Key functions

split_into_entities(&coords) → Vec<MoleculeEntity> — classify and group
merge_entities(&[MoleculeEntity]) → Coords — flatten back to atoms
classify_residue(name) → MoleculeType — single residue lookup

`types::density` — Electron Density

`DensityMap`

3D grid of electron density values from MRC/CCP4 files:

Grid dimensions, cell parameters, origin
f32 voxel data
Methods for coordinate-to-grid mapping

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