FragmentIndex.h File Reference

#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/Peak1D.h>
#include <array>
#include <mutex>
#include <vector>
#include <functional>
#include <algorithm>

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Classes
class	FragmentIndex
	Generates from a set of Fasta files a 2D-datastructure which stores all theoretical masses of all b and y ions from all peptides generated from the Fasta file. The datastructure is build such that on one axis the fragments are sorted by their own mass and the axis by the mass of their precursor/protein. The FI has two options: Bottom-up and Top Down. In later digestion is skiped and the fragments have a direct reference to the mass of the proteins instead of digested peptides. More...
struct	FragmentIndex::Peptide
	Compact descriptor of a peptide instance held by the FragmentIndex. More...
struct	FragmentIndex::SpectrumMatch
	Match between a query peak and an entry in the DB. More...
struct	FragmentIndex::SpectrumMatchesTopN
	container for SpectrumMatch. Also keeps count of total number of candidates and total number of matches. More...
struct	FragmentIndex::Hit
struct	FragmentIndex::Fragment
	One entry in the fragment index. More...
struct	FragmentIndex::VarModEntry
	Entry in the per-AA variable modification lookup table. More...
struct	FragmentIndex::ModSlot
	A candidate modification slot for a specific peptide. More...
struct	FragmentIndex::IonOffsets
	Precomputed ion-type mass offsets (from Residue::getInternalTo*Ion formulas) More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::FragmentIndex::SpectrumMatch

struct OpenMS::FragmentIndex::SpectrumMatch

Match between a query peak and an entry in the DB.

Collaboration diagram for FragmentIndex::SpectrumMatch:

Class Members
int16_t	isotope_error_ {}
uint32_t	num_matched_ {}	Number of peaks-fragment hits.
size_t	peptide_idx_ {}	< The isotope_error used for the performed search The idx this struct belongs to
uint16_t	precursor_charge_ {}	The precursor_charged used for the performed search.

OpenMS::FragmentIndex::VarModEntry

struct OpenMS::FragmentIndex::VarModEntry

Entry in the per-AA variable modification lookup table.

Collaboration diagram for FragmentIndex::VarModEntry:

Class Members
double	delta_mass	mass delta from this modification
const ResidueModification *	mod_ptr	pointer to the modification (for AASequence reconstruction)
TermSpecificity	term_spec	where this mod can be applied

OpenMS::FragmentIndex::IonOffsets

struct OpenMS::FragmentIndex::IonOffsets

Precomputed ion-type mass offsets (from Residue::getInternalTo*Ion formulas)

Collaboration diagram for FragmentIndex::IonOffsets:

Class Members
double	a_offset {0.0}
double	b_offset {0.0}
double	c_offset {0.0}
double	x_offset {0.0}
double	y_offset {0.0}
double	z_offset {0.0}