OPXLDataStructs::ProteinProteinCrossLink Struct Reference

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

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

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

Public Attributes
AASequence	alpha
AASequence	beta
std::pair< SignedSize, SignedSize >	cross_link_position
double	cross_linker_mass
String	cross_linker_name
ResidueModification::TermSpecificity	term_spec_alpha
ResidueModification::TermSpecificity	term_spec_beta
int	precursor_correction

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().

Referenced by TOPPOpenPepXLLF::main_(), and TOPPOpenPepXL::main_().

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

AASequence alpha

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::ProteinProteinCrossLink::operator==().

beta

AASequence beta

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::ProteinProteinCrossLink::operator==().

cross_link_position

std::pair<SignedSize, SignedSize> cross_link_position

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

cross_linker_mass

double cross_linker_mass

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::ProteinProteinCrossLink::operator==().

cross_linker_name

String cross_linker_name

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

precursor_correction

int precursor_correction

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::ProteinProteinCrossLink::operator==().

term_spec_alpha

ResidueModification::TermSpecificity term_spec_alpha

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

term_spec_beta

ResidueModification::TermSpecificity term_spec_beta

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