Struct Structure 

pub struct Structure {
    pub box_vectors: Option<[[f64; 3]; 3]>,
    /* private fields */
}

High-level biomolecular assembly composed of zero or more chains.

A Structure wraps individual chains, tracks optional periodic box vectors, and offers convenience iterators for traversing chains, residues, and atoms alongside contextual metadata. Builders and operations mutate the structure to clean, solvate, or analyze biological systems.

Fields

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

Optional periodic box represented as crystallographic basis vectors.

Implementations

impl Structure

pub fn new() -> Self

Creates an empty structure with no chains or box vectors.

Returns

A new Structure identical to Structure::default().

pub fn add_chain(&mut self, chain: Chain)

Appends a chain to the structure, asserting unique chain IDs in debug builds.

The chain is inserted at the end of the current collection and becomes visible to iterator methods immediately.

Arguments

• chain - Chain instance whose id must be unique within the structure.

pub fn remove_chain(&mut self, id: &str) -> Option<Chain>

Removes and returns a chain by identifier if it exists.

Arguments

• id - Chain identifier to search for.

Returns

Some(Chain) when a chain with the provided ID is present, otherwise None.

pub fn clear(&mut self)

Drops every chain from the structure, leaving box vectors untouched.

pub fn chain(&self, id: &str) -> Option<&Chain>

Retrieves an immutable chain by identifier.

Arguments

• id - Chain identifier to search for.

Returns

Some(&Chain) if found, otherwise None.

pub fn chain_mut(&mut self, id: &str) -> Option<&mut Chain>

Retrieves a mutable chain by identifier.

Arguments

• id - Chain identifier to search for.

Returns

Some(&mut Chain) if found, otherwise None.

pub fn find_residue( &self, chain_id: &str, residue_id: i32, insertion_code: Option<char>, ) -> Option<&Residue>

Finds a residue using chain ID, residue number, and optional insertion code.

Arguments

• chain_id - Identifier of the chain to search.
• residue_id - Numeric residue index (typically PDB resSeq).
• insertion_code - Optional insertion code differentiating duplicate IDs.

Returns

Some(&Residue) when the residue is located, otherwise None.

pub fn find_residue_mut( &mut self, chain_id: &str, residue_id: i32, insertion_code: Option<char>, ) -> Option<&mut Residue>

Finds a mutable residue reference using chain and residue identifiers.

Arguments

• chain_id - Identifier of the chain to search.
• residue_id - Numeric residue index.
• insertion_code - Optional insertion code to disambiguate residues.

Returns

Some(&mut Residue) when located, otherwise None.

pub fn sort_chains_by_id(&mut self)

Sorts chains lexicographically by their identifier.

pub fn chain_count(&self) -> usize

Returns the number of chains currently stored.

Returns

Chain count as usize.

pub fn residue_count(&self) -> usize

Counts all residues across every chain.

Returns

Total residue count as usize.

pub fn atom_count(&self) -> usize

Counts all atoms across every chain.

Returns

Total atom count as usize.

pub fn is_empty(&self) -> bool

Indicates whether the structure contains zero chains.

Returns

true if no chains are present.

pub fn iter_chains(&self) -> Iter<'_, Chain>

Provides an iterator over immutable chains.

Returns

std::slice::Iter<'_, Chain> spanning all chains in insertion order.

pub fn iter_chains_mut(&mut self) -> IterMut<'_, Chain>

Provides an iterator over mutable chains.

Returns

std::slice::IterMut<'_, Chain> for in-place modification of chains.

pub fn iter_atoms(&self) -> impl Iterator<Item = &Atom>

Iterates over immutable atoms across all chains.

Returns

An iterator yielding &Atom in chain/residue order.

pub fn iter_atoms_mut(&mut self) -> impl Iterator<Item = &mut Atom>

Iterates over mutable atoms across all chains.

Returns

An iterator yielding &mut Atom for direct coordinate editing.

pub fn retain_residues<F>(&mut self, f: F)

where F: FnMut(&str, &Residue) -> bool,

Retains residues that satisfy a predicate, removing all others.

The predicate receives the chain ID and a residue reference, enabling context-sensitive filtering.

Arguments

• f - Closure returning true to keep the residue.

pub fn prune_empty_chains(&mut self)

Removes any chain that became empty after residue pruning.

pub fn iter_atoms_with_context( &self, ) -> impl Iterator<Item = (&Chain, &Residue, &Atom)>

Iterates over atoms while including chain and residue context.

Returns

An iterator yielding triples (&Chain, &Residue, &Atom) for every atom.

pub fn geometric_center(&self) -> Point

Computes the geometric center of all atom coordinates.

Falls back to the origin when the structure contains no atoms.

Returns

A Point located at the unweighted centroid.

pub fn center_of_mass(&self) -> Point

Computes the mass-weighted center of all atoms.

Uses element atomic masses and returns the origin when the total mass is below numerical tolerance.

Returns

A Point representing the center of mass.

Trait Implementations

impl Clone for Structure

fn clone(&self) -> Structure

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Structure

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

Formats the value using the given formatter.

impl Default for Structure

fn default() -> Structure

Returns the “default value” for a type.

impl Display for Structure

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

Formats the value using the given formatter.

impl FromIterator<Chain> for Structure

fn from_iter<T: IntoIterator<Item = Chain>>(iter: T) -> Self

Creates a value from an iterator.