Struct TopologyBuilder 

pub struct TopologyBuilder { /* private fields */ }

Builder responsible for creating Topology objects from a Structure.

The builder can augment the internal template database with additional hetero templates and tweak geometric cutoffs for disulfide, peptide, and nucleic bonds before running TopologyBuilder::build.

Implementations

impl TopologyBuilder

pub fn new() -> Self

Creates a builder that uses default cutoffs and no extra templates.

Default cutoffs were chosen to capture typical covalent geometry in Ångström. They can be overridden through the builder-style setters.

pub fn add_hetero_template(self, template: Template) -> Self

Registers a new template that will be used for hetero residues.

Arguments

• template - Template describing atoms and bonds for a residue that is classified as ResidueCategory::Hetero.

pub fn disulfide_cutoff(self, cutoff: f64) -> Self

Configures the maximum SG···SG distance allowed for disulfide bonds.

Arguments

• cutoff - Maximum distance in Ångström for connecting cysteine SG atoms.

pub fn build(self, structure: Structure) -> Result<Topology, Error>

Builds a Topology for the provided structure.

All intra-residue bonds are taken from templates and terminal rules, while inter-residue bonds rely on distance checks using the configured cutoffs.

Arguments

• structure - Structure for which to build the bond topology.

Returns

A Result containing the built Topology or an Error.

Errors

Returns Error when a required template or atom is missing.

Trait Implementations

impl Default for TopologyBuilder

fn default() -> Self

Returns the “default value” for a type.