Struct IoContext 

pub struct IoContext { /* private fields */ }

Canonicalization state for residue names used during IO operations.

IoContext stores both the alias-to-canonical mapping as well as the canonical-to-StandardResidue lookup so that structure builders can translate raw residue labels into actionable metadata.

Implementations

impl IoContext

pub fn new_default() -> Self

Creates a context pre-populated with the built-in alias registry.

The registry covers variants for protonation, modifications, and common force-field naming conventions so that raw files parse into consistent structures.

Returns

A context instance ready for use by IO helpers and downstream operations.

pub fn resolve_name<'a>(&'a self, name: &'a str) -> &'a str

Resolves an input residue name to its canonical representative.

When the name is unknown the original string is returned unchanged, preserving user-provided labels for heterogens.

Arguments

• name - Raw residue identifier from an input file.

Returns

A borrowed string slice representing the canonical code, or the original input when no alias mapping exists.

pub fn map_to_standard(&self, name: &str) -> Option<StandardResidue>

Maps a canonical residue name to its StandardResidue entry when possible.

Aliases must be resolved first; the lookup only matches canonical keys that were registered via IoContext::new_default.

Arguments

• name - Canonical residue code returned by resolve_name.

Returns

Some(StandardResidue) when the name matches a known polymer residue, otherwise None for heterogens and custom ligands.

pub fn add_alias( &mut self, alias: impl Into<String>, canonical: impl Into<String>, )

Adds or overrides an alias pointing to a canonical residue name.

This is useful when callers want to supply additional naming conventions without rebuilding the default table.

Arguments

• alias - The alternative label to match within input files.
• canonical - The canonical residue code the alias should resolve to.

pub fn classify_residue( &self, raw_name: &str, ) -> (String, Option<StandardResidue>)

Classifies a residue by returning the canonical name plus optional standard metadata.

This combines resolve_name and map_to_standard to provide a single lookup step for IO pipelines.

Arguments

• raw_name - The residue label read directly from an input structure file.

Returns

A tuple containing the canonical residue name as an owned String and the optional StandardResidue classification.

Trait Implementations

impl Clone for IoContext

fn clone(&self) -> IoContext

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for IoContext

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

Formats the value using the given formatter.

impl Default for IoContext

fn default() -> Self

Constructs the default IO context.

Returns

A direct alias of IoContext::new_default.