Assembly
Assembly (source: src/assembly.rs) is the host-owned structural source of truth. It bundles a Vec<MoleculeEntity> with eagerly-computed derived data:
- per-entity DSSP secondary structure (
ss_types) - backbone H-bonds (Kabsch-Sander)
- cross-entity covalent bonds (currently disulfides)
- a monotonic
generationcounter
Every &mut Assembly mutation bumps generation and recomputes the full derived-data set before returning, so any consumer holding a snapshot sees consistent state.
use molex::{Assembly, CoordinateSnapshot};
let assembly = Assembly::new(entities); // runs disulfide + DSSP + H-bond detectionRead accessors
| Method | Returns | Description |
|---|---|---|
entities() | &[MoleculeEntity] | All entities in declaration order |
entity(id) | Option<&MoleculeEntity> | Look up an entity by id |
generation() | u64 | Monotonic counter, bumps on mutation |
hbonds() | &[HBond] | Backbone H-bonds across all proteins (flat sequence) |
ss_types(id) | &[SSType] | DSSP classification per residue for an entity |
cross_entity_bonds() | &[CovalentBond] | Cross-entity bonds (disulfides today) |
bonds_touching(atom) | impl Iterator<Item=AtomId> | Far endpoints of bonds touching atom (intra + cross) |
disulfides() | impl Iterator<Item=&CovalentBond> | CYS SG-SG cross-entity bonds |
Mutations
All mutations recompute derived data:
assembly.add_entity(new_entity);
assembly.remove_entity(entity_id);
assembly.update_positions(entity_id, &new_coords); // skipped if atom counts mismatch
assembly.set_coordinate_snapshot(snapshot); // bulk position updateCoordinateSnapshot
CoordinateSnapshot captures per-entity positions for a “save / restore” workflow:
let saved = CoordinateSnapshot::from_assembly(&assembly);
// ... run mutations ...
assembly.set_coordinate_snapshot(saved); // restoreEntities present in the snapshot but missing from the assembly are ignored; entities in the assembly missing from the snapshot keep their current positions.