Struct System 

pub struct System {
    pub atoms: Vec<Atom>,
    pub bonds: Vec<Bond>,
    pub box_vectors: Option<[[f64; 3]; 3]>,
    pub bio_metadata: Option<BioMetadata>,
}

A complete molecular system.

Contains all information needed to represent a molecular structure: atoms with their positions, connectivity through bonds, optional periodic boundary conditions, and optional biological metadata for biomolecular systems.

Fields

• atoms — Vector of atoms with element types and positions
• bonds — Vector of bonds defining molecular connectivity
• box_vectors — Optional 3×3 matrix defining periodic cell vectors
• bio_metadata — Optional biological annotation (residues, chains)

Examples

use dreid_forge::{Atom, Bond, BondOrder, Element, System};

// Build a simple CO molecule
let mut system = System::new();
system.atoms.push(Atom::new(Element::C, [0.0, 0.0, 0.0]));
system.atoms.push(Atom::new(Element::O, [1.128, 0.0, 0.0]));
system.bonds.push(Bond::new(0, 1, BondOrder::Triple));

assert_eq!(system.atom_count(), 2);
assert_eq!(system.bond_count(), 1);
assert!(!system.is_periodic());

Fields

atoms: Vec<Atom>

Atoms in the system with element types and positions.

bonds: Vec<Bond>

Bonds defining molecular connectivity.

box_vectors: Option<[[f64; 3]; 3]>

Periodic cell vectors as row-major 3×3 matrix, if periodic.

bio_metadata: Option<BioMetadata>

Biological metadata (residue info, chains) for biomolecules.

Implementations

impl System

pub fn new() -> Self

Creates a new empty molecular system.

Initializes a system with no atoms, no bonds, no periodic boundaries, and no biological metadata.

Returns

An empty System instance.

pub fn atom_count(&self) -> usize

Returns the number of atoms in the system.

pub fn bond_count(&self) -> usize

Returns the number of bonds in the system.

pub fn is_periodic(&self) -> bool

Returns true if the system has periodic boundary conditions.

A system is periodic if box_vectors is Some.

pub fn has_bio_metadata(&self) -> bool

Returns true if the system has biological metadata attached.

Biological metadata includes residue names, chain IDs, and other annotations from PDB/mmCIF files.

Trait Implementations

impl Clone for System

fn clone(&self) -> System

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for System

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

Formats the value using the given formatter.

impl Default for System

fn default() -> System

Returns the “default value” for a type.