NCBI C++ ToolKit
Classes | Typedefs | Variables
msms.hpp File Reference
#include <list>
#include <iostream>
#include <fstream>
#include <string>
#include <set>
#include <deque>
#include <map>
#include <objects/omssa/MSModSpecSet.hpp>
#include <objects/omssa/MSSearchSettings.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include "Mod.hpp"
#include "SpectrumSet.hpp"
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Classes

class  CMassArray
 
class  CAA
 
class  CMod
 contains information for a post translational modification at a particular sequence site More...
 
class  COMSSAException
 generic exception class for omssa More...
 
class  CCleave
 
class  CCNBr
 
class  CFormicAcid
 
class  CTrypsin
 
class  CArgC
 
class  CChymotrypsin
 
class  CLysC
 
class  CLysCP
 
class  CPepsinA
 
class  CTrypCNBr
 
class  CTrypChymo
 
class  CTrypsinP
 
class  CWholeProtein
 whole protein (no cleavage) More...
 
class  CAspN
 Asp-N, Nterm of D. More...
 
class  CGluC
 Glu-C, Cterm of E. More...
 
class  CGluCAspN
 Glu-C and Asp-N. More...
 
class  CTopDown
 eMSEnzymes_top_down top-down search of ETD spectra More...
 
class  CSemiTryptic
 eMSEnzymes_semi_tryptic semi tryptic search (one end of peptide has to be tryptic) More...
 
class  CNoEnzyme
 eMSEnzymes_no_enzyme search without enzyme (precursor mass only) More...
 
class  CChymoP
 eMSEnzymes_chymotrypsin_p chymotrypsin without proline rule More...
 
class  CAspNDE
 eMSEnzymes_aspn_de Asp-N that cuts at D and E More...
 
class  CGluCDE
 eMSEnzymes_gluc_de Glu-C that cuts at D and E More...
 
class  CLysN
 eMSEnzymes_lysn Cuts N term of lysine More...
 
class  CThermolysinP
 eMSEnzymes_thermolysin_p cuts N terminal at A,F,I,L,M or V More...
 
class  CSemiChymotrypsin
 Chymotrypsin, cuts N terminal at A,F,I,L,M or V. More...
 
class  CSemiGluC
 Glu-C, Cterm of E. More...
 
class  CCleaveFactory
 factory to return back object for enzyme More...
 

Typedefs

typedef std::deque< intTCleave
 

Variables

const int kNumAAIntervals = 19
 
const double kWater = 18.010565
 mass of water More...
 
const double kNeutron = 1.008664904
 neutron mass More...
 
const double MonoMass [] = {0.0, 71.03711, 0.0, 103.00919, 115.02694, 129.04259, 147.06841, 57.02147, 137.05891, 113.08406, 128.09496, 113.08406, 131.04049, 114.04293, 97.05276, 128.05858, 156.10111, 87.03203, 101.04768, 99.06841, 186.07931, 0.0, 163.06333, 0.0, 149.903 , 0.0, 113.08406, 237.14776, 0.0 }
 
const double AverageMass [] = {0.0, 71.08, 0.0, 103.15, 115.09, 129.12, 147.18, 57.05, 137.14, 113.16, 128.17, 113.16, 131.20, 114.10, 97.12, 128.13, 156.19, 87.08, 101.11, 99.13, 186.21, 0.0, 163.18, 0.0, 150.044, 0.0, 113.16, 237.30, 0.0 }
 
const double MonoN15Mass [] = {0.0, 72.034144893, 0.0, 104.006224893, 116.023974893, 130.039624893, 148.065444893, 58.018494893, 140.050014679, 114.081094893, 130.089029786, 114.081094893, 132.037524893, 116.036999786, 98.049794893, 130.052649786, 160.089239572, 88.029064893, 102.044714893, 100.065444893, 188.073379786, 0.0, 164.060364893, 0.0, 150.8964, 0.0, 114.081094893, 240.1388649, 0.0 }
 
const double kTermMass [] = {1.007825, 1.007825, 1.007825, 17.00274, 17.00274, 17.00274, 0, 0, 0, 0, 1.007825, 17.00274, 1.007825}
 
const double kIonTypeMass [] = { -27.994915, 0.0, 17.02655, 27.994915, 2.01565, -14.003075, 0, 0, 0, 0, -26.98709, -15.9994, -70.981405}
 

Typedef Documentation

◆ TCleave

typedef std::deque<int> TCleave

Definition at line 467 of file msms.hpp.

Variable Documentation

◆ AverageMass

const double AverageMass[] = {0.0, 71.08, 0.0, 103.15, 115.09, 129.12, 147.18, 57.05, 137.14, 113.16, 128.17, 113.16, 131.20, 114.10, 97.12, 128.13, 156.19, 87.08, 101.11, 99.13, 186.21, 0.0, 163.18, 0.0, 150.044, 0.0, 113.16, 237.30, 0.0 }

Definition at line 79 of file msms.hpp.

Referenced by CMassArray::x_Init().

◆ kIonTypeMass

const double kIonTypeMass[] = { -27.994915, 0.0, 17.02655, 27.994915, 2.01565, -14.003075, 0, 0, 0, 0, -26.98709, -15.9994, -70.981405}

Definition at line 88 of file msms.hpp.

Referenced by CLadder::CreateLadder().

◆ kNeutron

const double kNeutron = 1.008664904

neutron mass

Definition at line 70 of file msms.hpp.

Referenced by CLadder::CalcDelta(), CSearch< LEGACY, NHITS >::CreateModCombinations(), and CMSPeakSet::SortPeaks().

◆ kNumAAIntervals

const int kNumAAIntervals = 19

Definition at line 62 of file msms.hpp.

◆ kTermMass

const double kTermMass[] = {1.007825, 1.007825, 1.007825, 17.00274, 17.00274, 17.00274, 0, 0, 0, 0, 1.007825, 17.00274, 1.007825}

Definition at line 87 of file msms.hpp.

Referenced by CLadder::CreateLadder().

◆ kWater

const double kWater = 18.010565

mass of water

Definition at line 67 of file msms.hpp.

Referenced by CCleave::CCleave().

◆ MonoMass

const double MonoMass[] = {0.0, 71.03711, 0.0, 103.00919, 115.02694, 129.04259, 147.06841, 57.02147, 137.05891, 113.08406, 128.09496, 113.08406, 131.04049, 114.04293, 97.05276, 128.05858, 156.10111, 87.03203, 101.04768, 99.06841, 186.07931, 0.0, 163.06333, 0.0, 149.903 , 0.0, 113.08406, 237.14776, 0.0 }

Definition at line 77 of file msms.hpp.

Referenced by CPepXML::ConvertFromOMSSA(), and CMassArray::x_Init().

◆ MonoN15Mass

const double MonoN15Mass[] = {0.0, 72.034144893, 0.0, 104.006224893, 116.023974893, 130.039624893, 148.065444893, 58.018494893, 140.050014679, 114.081094893, 130.089029786, 114.081094893, 132.037524893, 116.036999786, 98.049794893, 130.052649786, 160.089239572, 88.029064893, 102.044714893, 100.065444893, 188.073379786, 0.0, 164.060364893, 0.0, 150.8964, 0.0, 114.081094893, 240.1388649, 0.0 }

Definition at line 81 of file msms.hpp.

Referenced by CMassArray::x_Init().

Modified on Wed Feb 21 09:54:08 2024 by modify_doxy.py rev. 669887