Result of NuXLModificationsGenerator::initModificationMassesNA — empirical formulas with their monoisotopic mass and the disambiguating nucleotide-composition lookup. More...

#include <OpenNuXL/include/NuXLModificationsGenerator.h>

Classes
struct	MyStringLengthCompare
	Comparator that orders strings primarily by length (shortest first) and lexicographically within the same length. More...

struct	PrecursorAdduct
	Sum formula and precursor adduct (nucleotide composition) returned by findPrecursorAdduct. More...

Public Types
using	NucleotideFormulas = std::set< std::string, MyStringLengthCompare >
	Length-ordered set of nucleotide-composition strings producing the same empirical formula.

using	MapSumFormulaToNucleotideFormulas = std::map< std::string, NucleotideFormulas >
	Empirical formula → NucleotideFormulas.

Public Member Functions
PrecursorAdduct	findPrecursorAdduct (Size NA_mod_index, Size NA_adduct_amb_index) const
	Looks up the precursor adduct that a hit refers to by its indices.

Public Attributes
std::map< std::string, double >	formula2mass
	Empirical formula → monoisotopic mass.

MapSumFormulaToNucleotideFormulas	mod_combinations
	Empirical formula → all nucleotide compositions yielding that formula (kept as a set because mutations / losses can make the mapping ambiguous).

Detailed Description

Result of NuXLModificationsGenerator::initModificationMassesNA — empirical formulas with their monoisotopic mass and the disambiguating nucleotide-composition lookup.

Two parallel maps keyed by the same empirical-formula string:

formula2mass — empirical formula → monoisotopic mass.
mod_combinations — empirical formula → set of nucleotide-composition strings that produce that formula. A set rather than a single value because different oligos can share a chemical formula, e.g. C18H22N4O16P2 → {CU-H3N1, UU-H2O1}.

The nested MyStringLengthCompare comparator orders the composition strings primarily by length and lexicographically within the same length so the shortest (most likely) composition appears first when iterating a value.

Class Documentation

◆ OpenMS::NuXLModificationMassesResult::PrecursorAdduct

struct OpenMS::NuXLModificationMassesResult::PrecursorAdduct

Sum formula and precursor adduct (nucleotide composition) returned by findPrecursorAdduct.

Class Members
const string *	adduct = nullptr	Entry in the set of nucleotide compositions with that sum formula, `nullptr` if not found.
const string *	sum_formula = nullptr	Key in `mod_combinations`, `nullptr` if not found.

Member Typedef Documentation

◆ MapSumFormulaToNucleotideFormulas

using MapSumFormulaToNucleotideFormulas = std::map<std::string, NucleotideFormulas>

Empirical formula → NucleotideFormulas.

◆ NucleotideFormulas

using NucleotideFormulas = std::set<std::string, MyStringLengthCompare>

Length-ordered set of nucleotide-composition strings producing the same empirical formula.

Member Function Documentation

◆ findPrecursorAdduct()

PrecursorAdduct findPrecursorAdduct	(	Size	NA_mod_index,
		Size	NA_adduct_amb_index
	)		const

inline

Looks up the precursor adduct that a hit refers to by its indices.

Parameters

[in]	NA_mod_index	Index of the sum formula in `mod_combinations`.
[in]	NA_adduct_amb_index	Index of the adduct in the set of nucleotide compositions with that sum formula (e.g., 0 for C-H3N1 and 1 for U-H2O1).