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OpenMS
2.5.0
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72 bool has_H2O_loss =
false;
73 bool has_NH3_loss =
false;
108 virtual void getLinearIonSpectrum(
PeakSpectrum & spectrum,
AASequence & peptide,
Size link_pos,
bool frag_alpha,
int charge = 1,
Size link_pos_2 = 0)
const;
133 virtual void getXLinkIonSpectrum(
PeakSpectrum & spectrum,
AASequence & peptide,
Size link_pos,
double precursor_mass,
bool frag_alpha,
int mincharge,
int maxcharge,
Size link_pos_2 = 0)
const;
157 void updateMembers_()
override;
175 virtual void addLinearPeaks_(
PeakSpectrum & spectrum,
DataArrays::IntegerDataArray & charges,
DataArrays::StringDataArray & ion_names,
AASequence & peptide,
Size link_pos,
bool frag_alpha,
Residue::ResidueType res_type, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses,
int charge = 1,
Size link_pos_2 = 0)
const;
275 virtual void addXLinkIonPeaks_(
PeakSpectrum& spectrum,
DataArrays::IntegerDataArray & charges,
DataArrays::StringDataArray & ion_names,
AASequence & peptide,
Size link_pos,
double precursor_mass,
bool frag_alpha,
Residue::ResidueType res_type, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses,
int charge,
Size link_pos_2 = 0)
const;
304 std::vector< LossIndex > getForwardLosses_(
AASequence & peptide)
const;
313 std::vector< LossIndex > getBackwardLosses_(
AASequence & peptide)
const;
342 double loss_H2O_ = 0;
343 double loss_NH3_ = 0;
Integer data array class.
Definition: DataArrays.h:52
bool add_x_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:319
std::map< String, LossIndex > loss_db_
Definition: TheoreticalSpectrumGeneratorXLMS.h:341
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGeneratorXLMS.h:326
bool add_charges_
Definition: TheoreticalSpectrumGeneratorXLMS.h:324
A more convenient string class.
Definition: String.h:58
Int max_isotope_
Definition: TheoreticalSpectrumGeneratorXLMS.h:334
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double rel_loss_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:335
double x_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:331
bool add_y_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:316
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
bool add_b_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:315
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGeneratorXLMS.h:321
bool add_isotopes_
Definition: TheoreticalSpectrumGeneratorXLMS.h:325
double z_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:333
The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL.
Definition: OPXLDataStructs.h:72
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:327
bool add_z_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:320
ResidueType
Definition: Residue.h:150
String data array class.
Definition: DataArrays.h:59
double a_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:328
bool add_a_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:317
bool add_c_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:318
double y_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:332
bool add_losses_
Definition: TheoreticalSpectrumGeneratorXLMS.h:322
double pre_int_NH3_
Definition: TheoreticalSpectrumGeneratorXLMS.h:338
double c_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:330
double b_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:329
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
Generates theoretical spectra for cross-linked peptides.
Definition: TheoreticalSpectrumGeneratorXLMS.h:65
double pre_int_H2O_
Definition: TheoreticalSpectrumGeneratorXLMS.h:337
bool add_metainfo_
Definition: TheoreticalSpectrumGeneratorXLMS.h:323
double pre_int_
Definition: TheoreticalSpectrumGeneratorXLMS.h:336
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Definition: TheoreticalSpectrumGeneratorXLMS.h:70
bool add_k_linked_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:339