OpenMS
2.5.0
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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 | |
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 | term_spec_beta |
int | precursor_correction = 0 |
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.
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References AASequence::empty().
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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.
const AASequence* alpha = nullptr |
longer peptide
Referenced by OPXLDataStructs::ProteinProteinCrossLink::operator==().
const AASequence* beta = nullptr |
shorter peptide (empty for mono-link), tie breaker: mass then lexicographical
Referenced by OPXLDataStructs::ProteinProteinCrossLink::operator==().
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==().
double cross_linker_mass = 0 |
Referenced by OPXLDataStructs::ProteinProteinCrossLink::operator==().
String cross_linker_name |
Referenced by OPXLDataStructs::ProteinProteinCrossLink::operator==().
int precursor_correction = 0 |
Referenced by OPXLDataStructs::ProteinProteinCrossLink::operator==().
ResidueModification::TermSpecificity term_spec_alpha |
Referenced by OPXLDataStructs::ProteinProteinCrossLink::operator==().
ResidueModification::TermSpecificity term_spec_beta |
Referenced by OPXLDataStructs::ProteinProteinCrossLink::operator==().