Basic definitions of fragment ions occurring in the mass spectra. More...

#include <string>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <map>
#include <vector>
#include <QMetaType>
#include "core/utilities.h"

Classes
class	cPeriodicTableMap
	The class representing a periodic table. More...

struct	isotope
	Representation of an isotope. More...

class	cIsotopeMap
	The class representing an isotope map. More...

struct	cFragmentIonType
	The struct for definition of a fragment ion type. More...

class	cFragmentIons
	The detailed definitions of all supported fragment ion types. More...

struct	neutralLoss
	The structure for a detailed definition of a neutral loss. More...

class	cDefaultNeutralLosses
	The class representing a vector of default neutral losses. More...

Enumerations
enum	eFragmentIonType { a_ion = 1 , b_ion , c_ion , x_ion , y_ion , z_ion , precursor_ion , cyclic_precursor_ion , l0h_ion , l1h_ion , l2h_ion , r1h_ion , r2h_ion , l1oh_ion , l2oh_ion , r1oh_ion , r2oh_ion , linear_polyketide_precursor_ion_h_h , linear_polyketide_precursor_ion_h_oh , linear_polyketide_precursor_ion_oh_oh , cyclic_polyketide_precursor_ion , fragmentIonTypeEnd }
	The types of supported fragment ions.

Functions
	Q_DECLARE_METATYPE (ePeptideType)
	Register ePeptideType by Qt.

double	charge (double neutralmass, int charge)
	Get mzratio from neutral mass. More...

double	uncharge (double mzratio, int charge)
	Get neutral mass from mzratio. More...

	Q_DECLARE_METATYPE (vector< eFragmentIonType >)
	Register vector<eFragmentIonType> by Qt.

	Q_DECLARE_METATYPE (vector< cFragmentIonType >)
	Register vector<cFragmentIonType> by Qt.

	Q_DECLARE_METATYPE (cFragmentIons)
	Register cFragmentIons by Qt.

void	initializeFragmentIonsForDeNovoGraphOfCyclicPeptides (vector< eFragmentIonType > &fragmentions)
	Initialize fragment ion types for the de novo graph of cyclic peptides. More...

void	initializeFragmentIonsForDeNovoGraphOfLinearPeptides (vector< eFragmentIonType > &fragmentions)
	Initialize fragment ion types for the de novo graph of linear peptides. More...

void	initializeFragmentIonsForDeNovoGraphOfTPeptides (vector< eFragmentIonType > &fragmentions)
	Initialize fragment ion types for the de novo graph of branched peptides. More...

void	initializeFragmentIonsForDeNovoGraphOfBranchCyclicPeptides (vector< eFragmentIonType > &fragmentions)
	Initialize fragment ion types for the de novo graph of branch-cyclic peptides. More...

void	initializeFragmentIonsForDeNovoGraphOfLinearPolyketide (vector< eFragmentIonType > &fragmentions)
	Initialize fragment ion types for the de novo graph of a linear polyketide. More...

void	initializeFragmentIonsForDeNovoGraphOfCyclicPolyketide (vector< eFragmentIonType > &fragmentions)
	Initialize fragment ion types for the de novo graph of a cyclic polyketide. More...

int	loadModificationsFromPlainTextStream (ifstream &stream, vector< cFragmentIonType > &modifications, string &errormessage, bool ignoreerrors)
	Load modifications from a plain text stream. More...

void	storeModificationsToPlainTextStream (ofstream &stream, vector< cFragmentIonType > &modifications)
	Store modifications into a plain text stream. More...

Variables
const double	H = 1.0078250321

const double	D = 2.014102

const double	T = 3.016049

const double	He = 4.002606

const double	Li = 7.016004

const double	Be = 9.012182

const double	B = 11.009306

const double	C = 12.0

const double	N = 14.0030740052

const double	O = 15.9949146221

const double	F = 18.998404

const double	Ne = 19.992439

const double	Na = 22.989771

const double	Mg = 23.985043

const double	Al = 26.981539

const double	Si = 27.976927

const double	P = 30.97376151

const double	S = 31.97207069

const double	Cl = 34.968853

const double	Ar = 39.962383

const double	K = 38.963707

const double	Ca = 39.962589

const double	Sc = 44.95591

const double	Ti = 47.947948

const double	V = 50.943962

const double	Cr = 51.940514

const double	Mn = 54.938049

const double	Fe = 55.93494

const double	Co = 58.933201

const double	Ni = 57.935349

const double	Cu = 62.9296

const double	Zn = 63.929146

const double	Ga = 68.925583

const double	Ge = 73.921181

const double	As = 74.921600

const double	Se = 79.916519

const double	Br = 78.918327

const double	Kr = 83.911507

const double	Rb = 84.911789

const double	Sr = 87.905617

const double	Y = 88.905846

const double	Zr = 89.904701

const double	Nb = 92.906403

const double	Mo = 97.905411

const double	Tc = 97.907219

const double	Ru = 101.904388

const double	Rh = 102.905502

const double	Pd = 105.903481

const double	Ag = 106.905090

const double	Cd = 113.903358

const double	In = 114.903877

const double	Sn = 119.902199

const double	Sb = 120.903824

const double	Te = 129.906219

const double	I = 126.904457

const double	Xe = 131.904160

const double	Cs = 132.905441

const double	Ba = 137.905243

const double	La = 138.906342

const double	Ce = 139.905441

const double	Pr = 140.907593

const double	Nd = 141.907700

const double	Pm = 144.912750

const double	Sm = 151.919693

const double	Eu = 152.921204

const double	Gd = 157.924103

const double	Tb = 158.925293

const double	Dy = 163.929199

const double	Ho = 164.930298

const double	Er = 165.930298

const double	Tm = 168.934204

const double	Yb = 173.938904

const double	Lu = 174.940796

const double	Hf = 179.946503

const double	Ta = 180.947998

const double	W = 183.950897

const double	Re = 186.955597

const double	Os = 191.961502

const double	Ir = 192.962906

const double	Pt = 194.964798

const double	Au = 196.966507

const double	Hg = 201.970596

const double	Tl = 204.974396

const double	Pb = 207.976593

const double	Bi = 208.980392

const double	Po = 208.982422

const double	At = 209.987137

const double	Rn = 222.017563

const double	Fr = 209.996399

const double	Ra = 226.025406

const double	Ac = 227.027740

const double	Th = 232.038055

const double	Pa = 231.035904

const double	U = 238.050781

const double	Np = 237.048172

const double	Pu = 242.058746

const double	Am = 243.061371

const double	Cm = 247.070343

const double	Bk = 247.070297

const double	Cf = 251.079575

const double	Es = 252.082977

const double	Fm = 257.095093

const double	Md = 258.098419

const double	No = 259.101044

const double	Lr = 262.109802

const double	R = 0

const double	X = 0

const double	e = H - 1.00727645

const double	H1 = H

const double	H2 = D

const double	He3 = 3.016029

const double	He4 = He

const double	Li6 = 6.015122

const double	Li7 = Li

const double	Be9 = Be

const double	B10 = 10.012937

const double	B11 = B

const double	C12 = C

const double	C13 = 13.003355

const double	N14 = N

const double	N15 = 15.000109

const double	O16 = O

const double	O17 = 16.999132

const double	O18 = 17.999160

const double	F19 = F

const double	Ne20 = Ne

const double	Ne21 = 20.993847

const double	Ne22 = 21.991386

const double	Na23 = Na

const double	Mg24 = Mg

const double	Mg25 = 24.985837

const double	Mg26 = 25.982593

const double	Al27 = Al

const double	Si28 = Si

const double	Si29 = 28.97649

const double	Si30 = 29.973770

const double	P31 = P

const double	S32 = S

const double	S33 = 32.971458

const double	S34 = 33.967867

const double	S36 = 35.967081

const double	Cl35 = Cl

const double	Cl37 = 36.965903

const double	Ar36 = 35.967546

const double	Ar38 = 37.962732

const double	Ar40 = Ar

const double	K39 = K

const double	K40 = 39.963999

const double	K41 = 40.961825

const double	Ca40 = Ca

const double	Ca42 = 41.958618

const double	Ca43 = 42.958767

const double	Ca44 = 43.955481

const double	Ca46 = 45.953693

const double	Ca48 = 47.952534

const double	Sc45 = Sc

const double	Ti46 = 45.952629

const double	Ti47 = 46.951764

const double	Ti48 = Ti

const double	Ti49 = 48.947871

const double	Ti50 = 49.944792

const double	V50 = 49.947163

const double	V51 = V

const double	Cr50 = 49.946046

const double	Cr52 = Cr

const double	Cr53 = 52.940651

const double	Cr54 = 53.938885

const double	Mn55 = Mn

const double	Fe54 = 53.939612

const double	Fe56 = Fe

const double	Fe57 = 56.935399

const double	Fe58 = 57.933280

const double	Co59 = Co

const double	Ni58 = Ni

const double	Ni60 = 59.930788

const double	Ni61 = 60.931060

const double	Ni62 = 61.928346

const double	Ni64 = 63.927970

const double	Cu63 = Cu

const double	Cu65 = 64.927793

const double	Zn64 = Zn

const double	Zn66 = 65.926034

const double	Zn67 = 66.927129

const double	Zn68 = 67.924846

const double	Zn70 = 69.925325

const double	Ga69 = Ga

const double	Ga71 = 70.9247

const double	Ge70 = 69.924250

const double	Ge72 = 71.922076

const double	Ge73 = 72.923459

const double	Ge74 = Ge

const double	Ge76 = 75.921403

const double	As75 = As

const double	Se74 = 73.922477

const double	Se76 = 75.919214

const double	Se77 = 76.919915

const double	Se78 = 77.917310

const double	Se80 = Se

const double	Se82 = 81.9167

const double	Br79 = Br

const double	Br81 = 80.916291

const double	Kr78 = 77.920386

const double	Kr80 = 79.916378

const double	Kr82 = 81.913485

const double	Kr83 = 82.914136

const double	Kr84 = Kr

const double	Kr86 = 85.910610

const double	Rb85 = Rb

const double	Rb87 = 86.909183

const double	Sr84 = 83.913425

const double	Sr86 = 85.909262

const double	Sr87 = 86.908879

const double	Sr88 = Sr

const double	Y89 = Y

const double	Zr90 = Zr

const double	Zr91 = 90.905645

const double	Zr92 = 91.90504

const double	Zr94 = 93.906316

const double	Zr96 = 95.908276

const double	Nb93 = Nb

const double	Mo92 = 91.906810

const double	Mo94 = 93.905088

const double	Mo95 = 94.905841

const double	Mo96 = 95.904679

const double	Mo97 = 96.906021

const double	Mo98 = Mo

const double	Mo100 = 99.907477

const double	Tc98 = Tc

const double	Ru96 = 95.907598

const double	Ru98 = 97.905287

const double	Ru99 = 98.905939

const double	Ru100 = 99.904220

const double	Ru101 = 100.905582

const double	Ru102 = Ru

const double	Ru104 = 103.90543

const double	Rh103 = Rh

const double	Pd102 = 101.905608

const double	Pd104 = 103.904035

const double	Pd105 = 104.905084

const double	Pd106 = Pd

const double	Pd108 = 107.903894

const double	Pd110 = 109.905152

const double	Ag107 = Ag

const double	Ag109 = 108.904756

const double	Cd106 = 105.906458

const double	Cd108 = 107.904183

const double	Cd110 = 109.903006

const double	Cd111 = 110.904182

const double	Cd112 = 111.902757

const double	Cd113 = 112.904401

const double	Cd114 = Cd

const double	Cd116 = 115.904755

const double	In113 = 112.904061

const double	In115 = In

const double	Sn112 = 111.904821

const double	Sn114 = 113.902782

const double	Sn115 = 114.903346

const double	Sn116 = 115.901744

const double	Sn117 = 116.902954

const double	Sn118 = 117.901606

const double	Sn119 = 118.903309

const double	Sn120 = Sn

const double	Sn122 = 121.90344

const double	Sn124 = 123.905275

const double	Sb121 = Sb

const double	Sb123 = 122.904216

const double	Te120 = 119.90402

const double	Te122 = 121.903047

const double	Te123 = 122.904273

const double	Te124 = 123.902819

const double	Te125 = 124.904425

const double	Te126 = 125.903306

const double	Te128 = 127.904461

const double	Te130 = Te

const double	I127 = I

const double	Xe124 = 123.905896

const double	Xe126 = 125.904269

const double	Xe128 = 127.90353

const double	Xe129 = 128.904779

const double	Xe130 = 129.903508

const double	Xe131 = 130.905082

const double	Xe132 = Xe

const double	Xe134 = 133.905395

const double	Xe136 = 135.90722

const double	Cs133 = Cs

const double	Ba130 = 129.906310

const double	Ba132 = 131.905056

const double	Ba134 = 133.904503

const double	Ba135 = 134.905683

const double	Ba136 = 135.90457

const double	Ba137 = 136.905821

const double	Ba138 = Ba

const double	La138 = 137.907107

const double	La139 = La

const double	Ce136 = 135.907144

const double	Ce138 = 137.905986

const double	Ce140 = Ce

const double	Ce142 = 141.90924

const double	Pr141 = Pr

const double	Nd142 = Nd

const double	Nd143 = 142.90981

const double	Nd144 = 143.910083

const double	Nd145 = 144.912569

const double	Nd146 = 145.913112

const double	Nd148 = 147.916889

const double	Nd150 = 149.920887

const double	Pm145 = Pm

const double	Sm144 = 143.911995

const double	Sm147 = 146.914893

const double	Sm148 = 147.914818

const double	Sm149 = 148.917180

const double	Sm150 = 149.917271

const double	Sm152 = Sm

const double	Sm154 = 153.922205

const double	Eu151 = 150.919846

const double	Eu153 = Eu

const double	Gd152 = 151.919788

const double	Gd154 = 153.920862

const double	Gd155 = 154.922619

const double	Gd156 = 155.92212

const double	Gd157 = 156.923957

const double	Gd158 = Gd

const double	Gd160 = 159.927051

const double	Tb159 = Tb

const double	Dy156 = 155.924278

const double	Dy158 = 157.924405

const double	Dy160 = 159.925194

const double	Dy161 = 160.926930

const double	Dy162 = 161.926795

const double	Dy163 = 162.928728

const double	Dy164 = Dy

const double	Ho165 = Ho

const double	Er162 = 161.928775

const double	Er164 = 163.929197

const double	Er166 = Er

const double	Er167 = 166.932045

const double	Er168 = 167.932368

const double	Er170 = 169.935460

const double	Tm169 = Tm

const double	Yb168 = 167.933894

const double	Yb170 = 169.934759

const double	Yb171 = 170.936322

const double	Yb172 = 171.936378

const double	Yb173 = 172.938207

const double	Yb174 = Yb

const double	Yb176 = 175.942568

const double	Lu175 = Lu

const double	Lu176 = 175.942682

const double	Hf174 = 173.94004

const double	Hf176 = 175.941402

const double	Hf177 = 176.94322

const double	Hf178 = 177.943698

const double	Hf179 = 178.945815

const double	Hf180 = Hf

const double	Ta180 = 179.947466

const double	Ta181 = Ta

const double	W180 = 179.946706

const double	W182 = 181.948206

const double	W183 = 182.950224

const double	W184 = W

const double	W186 = 185.954362

const double	Re185 = 184.952956

const double	Re187 = Re

const double	Os184 = 183.952491

const double	Os186 = 185.953838

const double	Os187 = 186.955748

const double	Os188 = 187.955836

const double	Os189 = 188.958145

const double	Os190 = 189.958445

const double	Os192 = Os

const double	Ir191 = 190.960591

const double	Ir193 = Ir

const double	Pt190 = 189.95993

const double	Pt192 = 191.961035

const double	Pt194 = 193.962664

const double	Pt195 = Pt

const double	Pt196 = 195.964935

const double	Pt198 = 197.967876

const double	Au197 = Au

const double	Hg196 = 195.965815

const double	Hg198 = 197.966752

const double	Hg199 = 198.968262

const double	Hg200 = 199.968309

const double	Hg201 = 200.970285

const double	Hg202 = Hg

const double	Hg204 = 203.973476

const double	Tl203 = 202.972329

const double	Tl205 = Tl

const double	Pb204 = 203.973029

const double	Pb206 = 205.974449

const double	Pb207 = 206.975881

const double	Pb208 = Pb

const double	Bi209 = Bi

const double	Po209 = Po

const double	At210 = At

const double	Rn222 = Rn

const double	Fr223 = Fr

const double	Ra226 = Ra

const double	Ac227 = Ac

const double	Th232 = Th

const double	Pa231 = Pa

const double	U234 = 234.040946

const double	U235 = 235.043923

const double	U238 = U

const double	Np237 = Np

const double	Pu244 = Pu

const double	Am243 = Am

const double	Cm247 = Cm

const double	Bk247 = Bk

const double	Cf251 = Cf

const double	Es252 = Es

const double	Fm257 = Fm

const double	Md258 = Md

const double	No259 = No

const double	Lr262 = Lr

const double	Pr_H1 = 0.999885

const double	Pr_H2 = 0.000115

const double	Pr_He3 = 0.00000137

const double	Pr_He4 = 0.99999863

const double	Pr_Li6 = 0.0759

const double	Pr_Li7 = 0.9241

const double	Pr_Be9 = 1

const double	Pr_B10 = 0.00199

const double	Pr_B11 = 0.00801

const double	Pr_C12 = 0.9893

const double	Pr_C13 = 0.0107

const double	Pr_N14 = 0.99632

const double	Pr_N15 = 0.00368

const double	Pr_O16 = 0.99757

const double	Pr_O17 = 0.00038

const double	Pr_O18 = 0.00205

const double	Pr_F19 = 1

const double	Pr_Ne20 = 0.9048

const double	Pr_Ne21 = 0.0027

const double	Pr_Ne22 = 0.0925

const double	Pr_Na23 = 1

const double	Pr_Mg24 = 0.7899

const double	Pr_Mg25 = 0.1

const double	Pr_Mg26 = 0.1101

const double	Pr_Al27 = 1

const double	Pr_Si28 = 0.922297

const double	Pr_Si29 = 0.046832

const double	Pr_Si30 = 0.030872

const double	Pr_P31 = 1

const double	Pr_S32 = 0.9493

const double	Pr_S33 = 0.0076

const double	Pr_S34 = 0.0429

const double	Pr_S36 = 0.0002

const double	Pr_Cl35 = 0.7578

const double	Pr_Cl37 = 0.2422

const double	Pr_Ar36 = 0.003365

const double	Pr_Ar38 = 0.000632

const double	Pr_Ar40 = 0.996003

const double	Pr_K39 = 0.932581

const double	Pr_K40 = 0.000117

const double	Pr_K41 = 0.067302

const double	Pr_Ca40 = 0.96941

const double	Pr_Ca42 = 0.00647

const double	Pr_Ca43 = 0.00135

const double	Pr_Ca44 = 0.02086

const double	Pr_Ca46 = 0.00004

const double	Pr_Ca48 = 0.00187

const double	Pr_Sc45 = 1

const double	Pr_Ti46 = 0.0825

const double	Pr_Ti47 = 0.0744

const double	Pr_Ti48 = 0.7372

const double	Pr_Ti49 = 0.0541

const double	Pr_Ti50 = 0.0518

const double	Pr_V50 = 0.0025

const double	Pr_V51 = 0.9975

const double	Pr_Cr50 = 0.04345

const double	Pr_Cr52 = 0.83789

const double	Pr_Cr53 = 0.09501

const double	Pr_Cr54 = 0.02365

const double	Pr_Mn55 = 1

const double	Pr_Fe54 = 0.05845

const double	Pr_Fe56 = 0.91754

const double	Pr_Fe57 = 0.02119

const double	Pr_Fe58 = 0.00282

const double	Pr_Co59 = 1

const double	Pr_Ni58 = 0.680769

const double	Pr_Ni60 = 0.262231

const double	Pr_Ni61 = 0.011399

const double	Pr_Ni62 = 0.036345

const double	Pr_Ni64 = 0.009256

const double	Pr_Cu63 = 0.6917

const double	Pr_Cu65 = 0.3083

const double	Pr_Zn64 = 0.4863

const double	Pr_Zn66 = 0.2790

const double	Pr_Zn67 = 0.0410

const double	Pr_Zn68 = 0.1875

const double	Pr_Zn70 = 0.0062

const double	Pr_Ga69 = 0.60108

const double	Pr_Ga71 = 0.39892

const double	Pr_Ge70 = 0.2084

const double	Pr_Ge72 = 0.2754

const double	Pr_Ge73 = 0.0773

const double	Pr_Ge74 = 0.3628

const double	Pr_Ge76 = 0.0761

const double	Pr_As75 = 1

const double	Pr_Se74 = 0.0089

const double	Pr_Se76 = 0.0937

const double	Pr_Se77 = 0.0763

const double	Pr_Se78 = 0.2377

const double	Pr_Se80 = 0.4961

const double	Pr_Se82 = 0.0873

const double	Pr_Br79 = 0.5069

const double	Pr_Br81 = 0.4931

const double	Pr_Kr78 = 0.0035

const double	Pr_Kr80 = 0.0228

const double	Pr_Kr82 = 0.1158

const double	Pr_Kr83 = 0.1149

const double	Pr_Kr84 = 0.57

const double	Pr_Kr86 = 0.173

const double	Pr_Rb85 = 0.7217

const double	Pr_Rb87 = 0.2783

const double	Pr_Sr84 = 0.0056

const double	Pr_Sr86 = 0.0986

const double	Pr_Sr87 = 0.07

const double	Pr_Sr88 = 0.8258

const double	Pr_Y89 = 1

const double	Pr_Zr90 = 0.5145

const double	Pr_Zr91 = 0.1122

const double	Pr_Zr92 = 0.1715

const double	Pr_Zr94 = 0.1738

const double	Pr_Zr96 = 0.028

const double	Pr_Nb93 = 1

const double	Pr_Mo92 = 0.1484

const double	Pr_Mo94 = 0.0925

const double	Pr_Mo95 = 0.1592

const double	Pr_Mo96 = 0.1668

const double	Pr_Mo97 = 0.0955

const double	Pr_Mo98 = 0.2413

const double	Pr_Mo100 = 0.0963

const double	Pr_Tc98 = 1

const double	Pr_Ru96 = 0.0554

const double	Pr_Ru98 = 0.0187

const double	Pr_Ru99 = 0.1276

const double	Pr_Ru100 = 0.126

const double	Pr_Ru101 = 0.1706

const double	Pr_Ru102 = 0.3155

const double	Pr_Ru104 = 0.1862

const double	Pr_Rh103 = 1

const double	Pr_Pd102 = 0.0102

const double	Pr_Pd104 = 0.1114

const double	Pr_Pd105 = 0.2233

const double	Pr_Pd106 = 0.2733

const double	Pr_Pd108 = 0.2646

const double	Pr_Pd110 = 0.1172

const double	Pr_Ag107 = 0.51839

const double	Pr_Ag109 = 0.48161

const double	Pr_Cd106 = 0.0125

const double	Pr_Cd108 = 0.0089

const double	Pr_Cd110 = 0.1249

const double	Pr_Cd111 = 0.128

const double	Pr_Cd112 = 0.2413

const double	Pr_Cd113 = 0.1222

const double	Pr_Cd114 = 0.2873

const double	Pr_Cd116 = 0.0749

const double	Pr_In113 = 0.0429

const double	Pr_In115 = 0.9571

const double	Pr_Sn112 = 0.0097

const double	Pr_Sn114 = 0.0066

const double	Pr_Sn115 = 0.0034

const double	Pr_Sn116 = 0.1454

const double	Pr_Sn117 = 0.0768

const double	Pr_Sn118 = 0.2422

const double	Pr_Sn119 = 0.0859

const double	Pr_Sn120 = 0.3258

const double	Pr_Sn122 = 0.0463

const double	Pr_Sn124 = 0.0579

const double	Pr_Sb121 = 0.5721

const double	Pr_Sb123 = 0.4279

const double	Pr_Te120 = 0.0009

const double	Pr_Te122 = 0.0255

const double	Pr_Te123 = 0.0089

const double	Pr_Te124 = 0.0474

const double	Pr_Te125 = 0.0707

const double	Pr_Te126 = 0.1884

const double	Pr_Te128 = 0.3174

const double	Pr_Te130 = 0.3408

const double	Pr_I127 = 1

const double	Pr_Xe124 = 0.0009

const double	Pr_Xe126 = 0.0009

const double	Pr_Xe128 = 0.0192

const double	Pr_Xe129 = 0.2644

const double	Pr_Xe130 = 0.0408

const double	Pr_Xe131 = 0.2118

const double	Pr_Xe132 = 0.2689

const double	Pr_Xe134 = 0.1044

const double	Pr_Xe136 = 0.0887

const double	Pr_Cs133 = 1

const double	Pr_Ba130 = 0.00106

const double	Pr_Ba132 = 0.00101

const double	Pr_Ba134 = 0.02417

const double	Pr_Ba135 = 0.06592

const double	Pr_Ba136 = 0.07854

const double	Pr_Ba137 = 0.11232

const double	Pr_Ba138 = 0.71698

const double	Pr_La138 = 0.0009

const double	Pr_La139 = 0.9991

const double	Pr_Ce136 = 0.00185

const double	Pr_Ce138 = 0.00251

const double	Pr_Ce140 = 0.8845

const double	Pr_Ce142 = 0.11114

const double	Pr_Pr141 = 1

const double	Pr_Nd142 = 0.272

const double	Pr_Nd143 = 0.122

const double	Pr_Nd144 = 0.238

const double	Pr_Nd145 = 0.083

const double	Pr_Nd146 = 0.172

const double	Pr_Nd148 = 0.057

const double	Pr_Nd150 = 0.056

const double	Pr_Pm145 = 1

const double	Pr_Sm144 = 0.0307

const double	Pr_Sm147 = 0.1499

const double	Pr_Sm148 = 0.1124

const double	Pr_Sm149 = 0.1382

const double	Pr_Sm150 = 0.0738

const double	Pr_Sm152 = 0.2675

const double	Pr_Sm154 = 0.2275

const double	Pr_Eu151 = 0.4781

const double	Pr_Eu153 = 0.5219

const double	Pr_Gd152 = 0.002

const double	Pr_Gd154 = 0.0218

const double	Pr_Gd155 = 0.148

const double	Pr_Gd156 = 0.2047

const double	Pr_Gd157 = 0.1565

const double	Pr_Gd158 = 0.2484

const double	Pr_Gd160 = 0.2186

const double	Pr_Tb159 = 1

const double	Pr_Dy156 = 0.0006

const double	Pr_Dy158 = 0.001

const double	Pr_Dy160 = 0.0234

const double	Pr_Dy161 = 0.1891

const double	Pr_Dy162 = 0.2551

const double	Pr_Dy163 = 0.249

const double	Pr_Dy164 = 0.2818

const double	Pr_Ho165 = 1

const double	Pr_Er162 = 0.0014

const double	Pr_Er164 = 0.0161

const double	Pr_Er166 = 0.3361

const double	Pr_Er167 = 0.2293

const double	Pr_Er168 = 0.2678

const double	Pr_Er170 = 0.1493

const double	Pr_Tm169 = 1

const double	Pr_Yb168 = 0.0013

const double	Pr_Yb170 = 0.0304

const double	Pr_Yb171 = 0.1428

const double	Pr_Yb172 = 0.2183

const double	Pr_Yb173 = 0.1613

const double	Pr_Yb174 = 0.3183

const double	Pr_Yb176 = 0.1276

const double	Pr_Lu175 = 0.9741

const double	Pr_Lu176 = 0.0259

const double	Pr_Hf174 = 0.0016

const double	Pr_Hf176 = 0.0526

const double	Pr_Hf177 = 0.186

const double	Pr_Hf178 = 0.2728

const double	Pr_Hf179 = 0.1362

const double	Pr_Hf180 = 0.3508

const double	Pr_Ta180 = 0.00012

const double	Pr_Ta181 = 0.99988

const double	Pr_W180 = 0.0012

const double	Pr_W182 = 0.265

const double	Pr_W183 = 0.1431

const double	Pr_W184 = 0.3064

const double	Pr_W186 = 0.2843

const double	Pr_Re185 = 0.374

const double	Pr_Re187 = 0.626

const double	Pr_Os184 = 0.0002

const double	Pr_Os186 = 0.0159

const double	Pr_Os187 = 0.0196

const double	Pr_Os188 = 0.1324

const double	Pr_Os189 = 0.1615

const double	Pr_Os190 = 0.2626

const double	Pr_Os192 = 0.4078

const double	Pr_Ir191 = 0.373

const double	Pr_Ir193 = 0.627

const double	Pr_Pt190 = 0.00014

const double	Pr_Pt192 = 0.00782

const double	Pr_Pt194 = 0.32967

const double	Pr_Pt195 = 0.33832

const double	Pr_Pt196 = 0.25242

const double	Pr_Pt198 = 0.07163

const double	Pr_Au197 = 1

const double	Pr_Hg196 = 0.0015

const double	Pr_Hg198 = 0.0997

const double	Pr_Hg199 = 0.1687

const double	Pr_Hg200 = 0.231

const double	Pr_Hg201 = 0.1318

const double	Pr_Hg202 = 0.2986

const double	Pr_Hg204 = 0.0687

const double	Pr_Tl203 = 0.29524

const double	Pr_Tl205 = 0.70476

const double	Pr_Pb204 = 0.014

const double	Pr_Pb206 = 0.241

const double	Pr_Pb207 = 0.221

const double	Pr_Pb208 = 0.524

const double	Pr_Bi209 = 1

const double	Pr_Po209 = 1

const double	Pr_At210 = 1

const double	Pr_Rn222 = 1

const double	Pr_Fr223 = 1

const double	Pr_Ra226 = 1

const double	Pr_Ac227 = 1

const double	Pr_Th232 = 1

const double	Pr_Pa231 = 1

const double	Pr_U234 = 0.000055

const double	Pr_U235 = 0.0072

const double	Pr_U238 = 0.992745

const double	Pr_Np237 = 1

const double	Pr_Pu244 = 1

const double	Pr_Am243 = 1

const double	Pr_Cm247 = 1

const double	Pr_Bk247 = 1

const double	Pr_Cf251 = 1

const double	Pr_Es252 = 1

const double	Pr_Fm257 = 1

const double	Pr_Md258 = 1

const double	Pr_No259 = 1

const double	Pr_Lr262 = 1

cPeriodicTableMap	periodictablemap
	Global periodic table map.

cIsotopeMap	isotopemap
	Global isotope map.

const double	H2O = 2 * H + O

const double	NH3 = 3 * H + N

const double	CO = C + O

const double	A_ION = H - e - C - O

const double	B_ION = H - e

const double	C_ION = H - e + NH3

const double	X_ION = H - e + 2 * O + C

const double	Y_ION = H - e + H2O

const double	Z_ION = H - e + O - N - H

const double	PRECURSOR_ION = H - e + H2O

const double	PRECURSOR_ION_CYCLIC = H - e

const double	L0H_ION = H - e - 2 * H

const double	L1H_ION = H - e

const double	L2H_ION = H - e + 2 * H

const double	R1H_ION = H - e

const double	R2H_ION = H - e + 2 * H

const double	L1OH_ION = H - e + O

const double	L2OH_ION = H - e + H2O

const double	R1OH_ION = H - e + O

const double	R2OH_ION = H - e + H2O

const double	PRECURSOR_ION_LINEAR_POLYKETIDE_H_H = H - e + 2 * H

const double	PRECURSOR_ION_LINEAR_POLYKETIDE_H_OH = H - e + H2O

const double	PRECURSOR_ION_LINEAR_POLYKETIDE_OH_OH = H - e + 2 * H + 2 * O

cDefaultNeutralLosses	defaultneutrallosses
	Default neutral losses definitions.

Detailed Description

Basic definitions of fragment ions occurring in the mass spectra.

Function Documentation

◆ charge()

double charge	(	double	neutralmass,
		int	charge
	)

Get mzratio from neutral mass.

Parameters

neutralmass	neutral mass
charge	charge

Return values

double mzratio

◆ initializeFragmentIonsForDeNovoGraphOfBranchCyclicPeptides()

void initializeFragmentIonsForDeNovoGraphOfBranchCyclicPeptides ( vector< eFragmentIonType > & fragmentions )

Initialize fragment ion types for the de novo graph of branch-cyclic peptides.

Parameters