Struct Topology 

pub struct Topology { /* private fields */ }

Bond graph overlay for a Structure.

A Topology pairs structural coordinates with explicit bonds, enabling neighbor queries, validation routines, and format writers that require connectivity information.

Implementations

impl Topology

pub fn new(structure: Structure, bonds: Vec<Bond>) -> Self

Builds a topology from a structure and its associated bonds.

Indices are assumed to reference atoms within the provided structure. A debug assert validates this assumption in development builds to catch mismatched templates.

Arguments

• structure - Fully instantiated structure containing all atoms.
• bonds - Canonical bond list describing connectivity.

Returns

A Topology ready for neighbor queries and downstream processing.

pub fn structure(&self) -> &Structure

Exposes the underlying structure.

Returns

Immutable reference to the wrapped Structure.

pub fn bonds(&self) -> &[Bond]

Returns all bonds present in the topology.

Returns

Slice containing every Bond, preserving insertion order.

pub fn bond_count(&self) -> usize

Counts the number of stored bonds.

Returns

Total number of bonds in the topology.

pub fn atom_count(&self) -> usize

Counts the atoms tracked by the underlying structure.

Returns

Number of atoms derived from the wrapped structure.

pub fn bonds_of(&self, atom_idx: usize) -> impl Iterator<Item = &Bond>

Iterates over all bonds incident to a specific atom.

Arguments

• atom_idx - Index of the atom whose incident bonds should be returned.

Returns

Iterator yielding references to Bond instances connected to atom_idx.

pub fn neighbors_of(&self, atom_idx: usize) -> impl Iterator<Item = usize> + '_

Enumerates the neighboring atom indices for the provided atom.

Arguments

• atom_idx - Index of the atom whose neighbors will be traversed.

Returns

Iterator producing the indices of atoms bonded to atom_idx.

Trait Implementations

impl Clone for Topology

fn clone(&self) -> Topology

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Topology

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Display for Topology

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the topology by reporting the atom and bond counts.

This user-friendly summary is leveraged in logs and debugging output.