50 : mz(mz), charge(charge)
71 bool has_H2O_loss =
false;
72 bool has_NH3_loss =
false;
176 virtual void addPrecursorPeaks_(std::vector< SimplePeak >& spectrum,
double precursor_mass,
int charge)
const;
186 virtual void addLosses_(std::vector< SimplePeak >& spectrum,
double mono_weight,
int charge,
LossIndex & losses)
const;
273 double loss_H2O_ = 0;
274 double loss_NH3_ = 0;
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
ResidueType
Definition: Residue.h:152
Generates theoretical spectra for cross-linked peptides.
Definition: SimpleTSGXLMS.h:38
bool add_x_ions_
Definition: SimpleTSGXLMS.h:258
bool add_precursor_peaks_
Definition: SimpleTSGXLMS.h:264
bool add_charges_
Definition: SimpleTSGXLMS.h:262
std::vector< LossIndex > getForwardLosses_(AASequence &peptide) const
Calculates sets of possible neutral losses for each position in the given peptide.
bool add_losses_
Definition: SimpleTSGXLMS.h:261
virtual void addLinearPeaks_(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge=1, Size link_pos_2=0) const
Adds cross-link-less ions of a specific ion type and charge to a spectrum.
bool add_a_ions_
Definition: SimpleTSGXLMS.h:256
bool add_b_ions_
Definition: SimpleTSGXLMS.h:254
bool add_abundant_immonium_ions_
Definition: SimpleTSGXLMS.h:265
virtual void addPrecursorPeaks_(std::vector< SimplePeak > &spectrum, double precursor_mass, int charge) const
Adds precursor masses including neutral losses for the given charge.
SimpleTSGXLMS()
default constructor
SimpleTSGXLMS & operator=(const SimpleTSGXLMS &tsg)
assignment operator
bool add_y_ions_
Definition: SimpleTSGXLMS.h:255
bool add_isotopes_
Definition: SimpleTSGXLMS.h:263
SimpleTSGXLMS(const SimpleTSGXLMS &source)
copy constructor
double pre_int_NH3_
Definition: SimpleTSGXLMS.h:269
virtual void addKLinkedIonPeaks_(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, int charge) const
Adds one-residue-linked ion peaks, that are specific to XLMS.
virtual void addLosses_(std::vector< SimplePeak > &spectrum, double mono_weight, int charge, LossIndex &losses) const
Adds neutral losses for an ion to a spectrum.
bool add_k_linked_ions_
Definition: SimpleTSGXLMS.h:270
bool add_first_prefix_ion_
Definition: SimpleTSGXLMS.h:260
~SimpleTSGXLMS() override
destructor
void updateMembers_() override
overwrite
virtual void addXLinkIonPeaks_(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge, Size link_pos_2=0) const
Adds cross-linked ions of a specific ion type and charge to a spectrum.
virtual void getXLinkIonSpectrum(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, int min_charge, int max_charge, Size link_pos_2=0) const
Generates fragment ions containing the cross-linker for one peptide.
std::map< String, LossIndex > loss_db_
Definition: SimpleTSGXLMS.h:272
double pre_int_
Definition: SimpleTSGXLMS.h:267
virtual void getLinearIonSpectrum(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, int charge=1, Size link_pos_2=0) const
Generates fragment ions not containing the cross-linker for one peptide.
Int max_isotope_
Definition: SimpleTSGXLMS.h:266
std::vector< LossIndex > getBackwardLosses_(AASequence &peptide) const
Calculates sets of possible neutral losses for each position in the given peptide.
bool add_c_ions_
Definition: SimpleTSGXLMS.h:257
virtual void addXLinkIonPeaks_(std::vector< SimplePeak > &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, LossIndex &losses_peptide2, int charge) const
Adds cross-linked ions of a specific ion type and charge to a spectrum.
bool add_z_ions_
Definition: SimpleTSGXLMS.h:259
virtual void getXLinkIonSpectrum(std::vector< SimplePeak > &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, int min_charge, int max_charge) const
Generates fragment ions containing the cross-linker for a pair of peptides.
double pre_int_H2O_
Definition: SimpleTSGXLMS.h:268
Definition: SimpleTSGXLMS.h:70
int Int
Signed integer type.
Definition: Types.h:72
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL.
Definition: OPXLDataStructs.h:47
Comparator to sort SimplePeaks by mz.
Definition: SimpleTSGXLMS.h:62
A simple struct to represent peaks with mz and charge and sort them easily.
Definition: SimpleTSGXLMS.h:45
SimplePeak(double mz, int charge)
Definition: SimpleTSGXLMS.h:49
double mz
Definition: SimpleTSGXLMS.h:46
SimplePeak()
Definition: SimpleTSGXLMS.h:53
int charge
Definition: SimpleTSGXLMS.h:47