Struct DigestConfig 

pub struct DigestConfig {

    pub missed_cleavages: u8,
    pub min_len: usize,
    pub max_len: usize,
    pub cleave_at: String,
    pub restrict: String,
    pub c_terminal: bool,
    pub peptide_min_mass: f32,
    pub peptide_max_mass: f32,
    pub static_mods: HashMap<String, f32>,
    pub variable_mods: HashMap<String, Vec<f32>>,
    pub max_variable_mods: usize,
    pub decoy_tag: String,
    pub generate_decoys: bool,
    pub decoy_mass_shift: f64,
    pub decoy_shuffle: bool,
    pub decoy_method: String,
    pub decoy_order: usize,
    pub decoy_seed: u64,
}

Digestion + modification configuration. Mirrors Sage’s database block.

Fields

missed_cleavages: u8

min_len: usize

max_len: usize

cleave_at: String

Residues to cleave at (trypsin = “KR”).

restrict: String

Residues that block cleavage when following a cleavage site (“P”).

c_terminal: bool

peptide_min_mass: f32

peptide_max_mass: f32

static_mods: HashMap<String, f32>

Fixed modifications, e.g. {“C”: 57.02146}.

variable_mods: HashMap<String, Vec<f32>>

Variable modifications, e.g. {“M”: [15.9949]}.

max_variable_mods: usize

decoy_tag: String

generate_decoys: bool

decoy_mass_shift: f64

Mass (Da) added to every decoy peptide so decoys are NOT mass twins of their targets. A real feature then never competes against its own decoy; decoys match only by random mass coincidence, giving an honest MS1 null where retention time has full discriminating power. (koth uses 11 Da.)

decoy_shuffle: bool

Generate decoys by SHUFFLING the peptide interior (same mass as the target) instead of reversing + mass-shifting. Shuffled same-mass decoys model the random mass-coincidence background honestly (unlike mass-shifted decoys, which sample a different mass region and underestimate the false rate), while randomized order keeps them from being RT-twins (unlike plain reversal). When true, decoy_mass_shift is ignored.

decoy_method: String

Protein-level decoy generator (experimental). When set to anything other than “shuffle”, whole decoy proteins are synthesized from the target proteome and digested by the same enzyme, overriding decoy_shuffle. One of: “shuffle” (default), “reverse”, “random_uniform”, “random_freq”, “markov”, “debruijn”. See crate::decoy.

decoy_order: usize

Order k for “markov” / “debruijn” decoy methods (ignored otherwise).

decoy_seed: u64

Seed for the decoy shuffle (0 = the shipped default stream; see crate::seed_mix). Set with uno --seed.

Trait Implementations

impl Clone for DigestConfig

fn clone(&self) -> Self

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for DigestConfig

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

Formats the value using the given formatter.

impl Default for DigestConfig

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for DigestConfig

where DigestConfig: Default,

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.