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:

Public Member Functions
ProteinProteinCrossLinkType	getType () const
bool	operator== (const ProteinProteinCrossLink &other) const

Public Attributes
const AASequence *	alpha = nullptr
	longer peptide More...
const AASequence *	beta = nullptr
	shorter peptide (empty for mono-link), tie breaker: mass then lexicographical More...
std::pair< SignedSize, SignedSize >	cross_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::ANYWHERE
ResidueModification::TermSpecificity	term_spec_beta = ResidueModification::TermSpecificity::ANYWHERE
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==()

bool operator== ( const ProteinProteinCrossLink &  other ) const

inline

References OPXLDataStructs::ProteinProteinCrossLink::alpha, OPXLDataStructs::ProteinProteinCrossLink::beta, OPXLDataStructs::ProteinProteinCrossLink::cross_link_position, OPXLDataStructs::ProteinProteinCrossLink::cross_linker_mass, OPXLDataStructs::ProteinProteinCrossLink::cross_linker_name, OPXLDataStructs::ProteinProteinCrossLink::precursor_correction, OPXLDataStructs::ProteinProteinCrossLink::term_spec_alpha, and OPXLDataStructs::ProteinProteinCrossLink::term_spec_beta.

Member Data Documentation

alpha

const AASequence* alpha = nullptr

longer peptide

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

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

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

cross_linker_name

String cross_linker_name

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

precursor_correction

int precursor_correction = 0

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

term_spec_alpha

ResidueModification::TermSpecificity term_spec_alpha = ResidueModification::TermSpecificity::ANYWHERE

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

term_spec_beta

ResidueModification::TermSpecificity term_spec_beta = ResidueModification::TermSpecificity::ANYWHERE

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