Struct Atom 

pub struct Atom {
    pub name: String,
    pub element: Element,
    pub pos: Point,
}

Labeled atom with immutable element identity and mutable position.

The struct is shared across residue, chain, and structure builders. Keeping the element metadata close to the coordinate allows downstream algorithms (e.g., heavy-atom filters or hydrogen placement) to reason locally without traversing additional tables.

Fields

name: String

Atom name as it appears in crystallographic or modeling files (e.g., CA).

element: Element

Chemical element derived from the periodic table definitions.

pos: Point

Cartesian coordinates measured in ångströms.

Implementations

impl Atom

pub fn new(name: &str, element: Element, pos: Point) -> Self

Creates a new atom from a name, element, and position.

Caller controls ownership of the label string while the element enforces chemical consistency. The position is copied as-is; no normalization is performed.

Arguments

• name - Atom label such as "CA" or "OXT".
• element - Element variant describing the chemical identity.
• pos - Point describing the Cartesian coordinates in ångströms.

Returns

A fully initialized Atom instance.

pub fn distance_squared(&self, other: &Atom) -> f64

Computes the squared Euclidean distance to another atom.

Prefer this when comparing relative distances or feeding cutoffs, as it avoids the costly square-root step while remaining in ångström squared units.

Arguments

• other - Reference atom to measure against.

Returns

The squared distance as f64.

pub fn distance(&self, other: &Atom) -> f64

Computes the Euclidean distance to another atom.

This is the fully realized length in ångströms and is suitable for reporting or geometry calculations that require actual bond lengths.

Arguments

• other - Reference atom to measure against.

Returns

The distance in ångströms as f64.

pub fn translate_by(&mut self, vector: &Vector3<f64>)

Translates the atom by an arbitrary vector.

The operation mutates the underlying position and is commonly used during rigid-body transforms or when applying simulation displacements.

Arguments

• vector - Translation expressed as a nalgebra::Vector3<f64> in ångströms.

Trait Implementations

impl Clone for Atom

fn clone(&self) -> Atom

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Atom

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

Formats the value using the given formatter.

impl Display for Atom

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

Formats the value using the given formatter.

impl PartialEq for Atom

fn eq(&self, other: &Atom) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl StructuralPartialEq for Atom