Struct OligoSettings 

pub struct OligoSettings {

    pub opt_size: usize,
    pub min_size: usize,
    pub max_size: usize,
    pub opt_tm: f64,
    pub min_tm: f64,
    pub max_tm: f64,
    pub opt_bound: f64,
    pub min_bound: f64,
    pub max_bound: f64,
    pub opt_gc_content: f64,
    pub min_gc: f64,
    pub max_gc: f64,
    pub conditions: SolutionConditions,
    pub max_self_any: f64,
    pub max_self_end: f64,
    pub max_self_any_th: f64,
    pub max_self_end_th: f64,
    pub max_hairpin_th: f64,
    pub max_repeat_compl: f64,
    pub max_template_mispriming: f64,
    pub max_template_mispriming_th: f64,
    pub must_match_five_prime: Option<String>,
    pub must_match_three_prime: Option<String>,
    pub num_ns_accepted: usize,
    pub max_poly_x: usize,
    pub weights: OligoWeights,
}

Settings for an individual primer or internal oligo.

Controls constraints on size, Tm, GC content, self-complementarity, etc.

Primer-only fields (ignored for internal oligos): max_end_stability, max_template_mispriming, max_template_mispriming_th

Internal-oligo-only fields (ignored for primers): none currently – all fields apply to both, though some constraints may not be meaningful for probes (e.g., max_poly_x is often relaxed).

Fields

opt_size: usize

Optimal primer length in bp (default: 20).

min_size: usize

Minimum primer length in bp (default: 18).

max_size: usize

Maximum primer length in bp (default: 27). Note: primer3-py defaults to 25; we follow the C library v2 default of 27.

opt_tm: f64

Optimal melting temperature in Celsius (default: 60.0).

min_tm: f64

Minimum melting temperature in Celsius (default: 57.0).

max_tm: f64

Maximum melting temperature in Celsius (default: 63.0).

opt_bound: f64

Optimal fraction of primers bound at annealing temp (default: 0.0, unset).

min_bound: f64

Minimum bound fraction (default: 0.0).

max_bound: f64

Maximum bound fraction (default: 0.0, unset).

opt_gc_content: f64

Optimal GC content as percentage (default: 50.0).

min_gc: f64

Minimum GC content as percentage (default: 20.0).

max_gc: f64

Maximum GC content as percentage (default: 80.0).

conditions: SolutionConditions

Salt and buffer concentrations for Tm calculations.

max_self_any: f64

Maximum self-complementarity score (default: 8.0).

max_self_end: f64

Maximum 3’ self-complementarity score (default: 3.0).

max_self_any_th: f64

Maximum self-complementarity (thermodynamic) in cal/mol (default: 47.0).

max_self_end_th: f64

Maximum 3’ self-complementarity (thermodynamic) in cal/mol (default: 47.0).

max_hairpin_th: f64

Maximum hairpin stability (thermodynamic) in cal/mol (default: 47.0).

max_repeat_compl: f64

Maximum repeat library complementarity (default: 12.0).

max_template_mispriming: f64

Maximum template mispriming score (default: 12.0).

max_template_mispriming_th: f64

Maximum template mispriming (thermodynamic) (default: 47.0).

must_match_five_prime: Option<String>

IUPAC pattern that the 5’ end of the primer must match (e.g., “NNNNN”). Length must be exactly 5 characters. None means no constraint.

must_match_three_prime: Option<String>

IUPAC pattern that the 3’ end of the primer must match. Length must be exactly 5 characters. None means no constraint.

num_ns_accepted: usize

Maximum number of Ns accepted in a primer (default: 0).

max_poly_x: usize

Maximum homopolymer length (default: 5).

weights: OligoWeights

Penalty weights for scoring this oligo type.

Trait Implementations

impl Clone for OligoSettings

fn clone(&self) -> OligoSettings

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for OligoSettings

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

Formats the value using the given formatter.

impl Default for OligoSettings

fn default() -> Self

Returns the “default value” for a type.