Bonding

Structure::bond_graph() perceives distance-based bonds on the P1 cell with BondRules::default(): a bond exists when the distance is at least 0.4 A and at most 1.15 times the sum of the two covalent radii. Dummy X atoms and metal-metal pairs never bond. Each Bond carries i, j, the lattice image, distance, order and the explicit flag.

let graph = structure.bond_graph()?;
for bond in &graph.bonds {
    println!("{} - {} at {:.3} A", bond.i, bond.j, bond.distance);
}
let components = graph.components();

BondGraph exposes bonds, n_atoms, degree, bonds_of and components. The graph is built over the expanded P1 cell, so periodic bonds keep their image. perceive_bonds(structure, rules) is the configurable entry point.

Explicit and topology bonds

ExplicitBond { i, j, image, order, remove } is applied after perception: a removal deletes the matching perceived bond, and an addition inserts it (or updates its order) and marks it explicit. TopologyBond { i, j, image } is stored separately in Structure::topology_bonds(); it is a network edge, not chemistry, and never enters the chemical bond graph. Both types are serialized with the structure.

Status

Distance perception, explicit additions/removals, topology edges and the connectivity graph are complete. The full golden corpus comparison of bond sets and coordination numbers is in crates/xtalforge-io/tests/golden_bonds.rs (Task 1.11.5). Bond symmetry propagation to every image (1.11.2) remains a later refinement.