OpenMS
OPXLDataStructs::ProteinProteinCrossLink Struct Reference

The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL. More...

#include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>

Collaboration diagram for OPXLDataStructs::ProteinProteinCrossLink:
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Public Member Functions

ProteinProteinCrossLinkType getType () const
 
bool operator== (const ProteinProteinCrossLink &other) const
 

Public Attributes

const AASequencealpha = nullptr
 longer peptide More...
 
const AASequencebeta = nullptr
 shorter peptide (empty for mono-link), tie breaker: mass then lexicographical More...
 
std::pair< SignedSize, SignedSizecross_link_position
 index in alpha, beta or between alpha, alpha in loop-links More...
 
double cross_linker_mass = 0
 
String cross_linker_name
 
ResidueModification::TermSpecificity term_spec_alpha
 
ResidueModification::TermSpecificity term_spec_beta
 
int precursor_correction = 0
 

Detailed Description

The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL.

This struct completely defines a cross-link linking two peptides. It contains the two peptides alpha and beta as AASequences, the positions that are linked in each peptide, the mass and name of the linker and terminal specificities to distinguish linkers attached to side chains of the terminal residues from linkers attached to the termini themselves. The beta peptide can be an empty AASequence object in case of a mono- or loop-link. Used to represent a theoretical candidate for generation of theoretical spectra and matching to experimental spectra.

Member Function Documentation

◆ getType()

ProteinProteinCrossLinkType getType ( ) const
inline

References AASequence::empty().

◆ operator==()

Member Data Documentation

◆ alpha

const AASequence* alpha = nullptr

◆ beta

const AASequence* beta = nullptr

shorter peptide (empty for mono-link), tie breaker: mass then lexicographical

Referenced by OPXLDataStructs::ProteinProteinCrossLink::operator==().

◆ cross_link_position

std::pair<SignedSize, SignedSize> cross_link_position

index in alpha, beta or between alpha, alpha in loop-links

Referenced by OPXLDataStructs::CLSMScoreComparator::operator()(), and OPXLDataStructs::ProteinProteinCrossLink::operator==().

◆ cross_linker_mass

double cross_linker_mass = 0

◆ cross_linker_name

◆ precursor_correction

int precursor_correction = 0

◆ term_spec_alpha

◆ term_spec_beta