Module model 

Analyte-class isotope models: the average composition koth scores an isotope envelope against.

Hill detection and chain assembly assume only that isotopes sit at charge-spaced m/z intervals. Scoring is the single place an analyte class enters, through an “averagine”: an average residue composition scaled to a molecule’s neutral mass (Senko 1995, for peptides). Carrying that composition as data rather than as constants is what lets a non-peptide analyte be scored against its own model.

Phosphorus is deliberately absent. ³¹P is the only stable phosphorus isotope, so a phosphate contributes a delta at offset 0 and cannot shift an isotope pattern. The nucleic-acid models carry their P in residue_mass, which is what sets the scale, and nowhere else — excluding it from the convolution is exact, not an approximation.

Structs

IsotopeModel

Average residue composition of an analyte class, expressed as element counts per residue_mass Da of neutral mass. Scaling these by neutral_mass / residue_mass and rounding gives the composition whose exact isotopologue distribution super::elements convolves.

Enums

IsotopeClass

The built-in analyte classes, selected by name in a config file.

IsotopeModelSpec

What a config file may say for isotope_model: either a class name (isotope_model = "rna") or an explicit composition table (isotope_model = { residue_mass = 321.2916, c = 9.5, h = 11.75, n = 3.75, o = 7.0 }). An unknown class name is a parse error, not a silent fallback.

Constants

DNA

DNA — the same construction over the four deoxyribonucleotide residues (dA C₁₀H₁₂N₅O₅P, dC C₉H₁₂N₃O₆P, dG C₁₀H₁₂N₅O₆P, dT C₁₀H₁₃N₂O₇P): C₉.₇₅ H₁₂.₂₅ N₃.₇₅ O₆ (P₁) per 308.8006 Da.

PEPTIDE

Peptide averagine — Senko’s averaged amino acid, C₄.₉₃₈₄ H₇.₇₅₈₃ N₁.₃₅₇₇ O₁.₄₇₇₃ S₀.₀₄₁₇ per 111.1254 Da. koth’s default and the only model the published benchmark exercises.

RNA

RNA — the mean of the four ribonucleotide chain residues (a nucleoside monophosphate less one water, the unit a phosphodiester chain repeats):