docs/html/c_fragment_ions_8h_source.html

#ifndef _CFRAGMENTIONS_H

#define _CFRAGMENTIONS_H


#include <string>

#include <iostream>

#include <iomanip>

#include <fstream>

#include <map>

#include <vector>

#include <QMetaType>

#include "core/utilities.h"


using namespace std;


// monoisotopic masses

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;


// monoisotopic masses of natural isotopes

const double H1 = H;

const double H2 = D;

//const double H3 = T;

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 C14 = 14.003242;

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;


// probabilities of natural isotope abundances

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;


class cPeriodicTableMap {


    map<string, double> table;

    vector<string> adductElements;


public:


    cPeriodicTableMap();


    double &operator[](string& element);


    int count(string& element);


    map<string, double>& getElements();


    vector<string>& getAdductElements();


};


extern cPeriodicTableMap periodictablemap;


struct isotope {


    double mass;


    double probability;


    isotope() {

        clear();

    }


    void clear() {

        mass = 0;

        probability = 0;

    }


};


class cIsotopeMap {


    map< string, map<string, isotope> > table;


public:


    cIsotopeMap();


    map<string, isotope> &operator[](string& element);


    int count(string& element);


};


extern cIsotopeMap isotopemap;


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;


Q_DECLARE_METATYPE(ePeptideType);


double charge(double neutralmass, int charge);


double uncharge(double mzratio, int charge);


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

};


Q_DECLARE_METATYPE(vector<eFragmentIonType>);


struct cFragmentIonType {


    string name;


    string summary;


    map<string, int> summarymap;


    double massdifference;


    bool nterminal;


    bool cterminal;


    bool positive;


    cFragmentIonType() {

        clear();

    }


    void clear() {

        name = "";

        summary = "";

        summarymap.clear();

        massdifference = 0;

        nterminal = false;

        cterminal = false;

        positive = true;

    }


    void store(ofstream& os);


    void load(ifstream& is);


};


Q_DECLARE_METATYPE(vector<cFragmentIonType>);


class cFragmentIons {


    map<eFragmentIonType, cFragmentIonType> fragmentions;


public:


    cFragmentIons();


    cFragmentIons(bool cyclicnterminus, bool cycliccterminus, string& precursoradduct);


    cFragmentIonType &operator[](eFragmentIonType iontype);


    void recalculateFragments(bool cyclicnterminus, bool cycliccterminus, string& precursoradduct);


    void store(ofstream& os);


    void load(ifstream& is);


};


Q_DECLARE_METATYPE(cFragmentIons);


void initializeFragmentIonsForDeNovoGraphOfCyclicPeptides(vector<eFragmentIonType>& fragmentions);


void initializeFragmentIonsForDeNovoGraphOfLinearPeptides(vector<eFragmentIonType>& fragmentions);


void initializeFragmentIonsForDeNovoGraphOfTPeptides(vector<eFragmentIonType>& fragmentions);


void initializeFragmentIonsForDeNovoGraphOfBranchCyclicPeptides(vector<eFragmentIonType>& fragmentions);


void initializeFragmentIonsForDeNovoGraphOfLinearPolyketide(vector<eFragmentIonType>& fragmentions);


void initializeFragmentIonsForDeNovoGraphOfCyclicPolyketide(vector<eFragmentIonType>& fragmentions);


struct neutralLoss {


    string summary;


    map<string, int> summarymap;


    double massdifference;


    neutralLoss() {

        clear();

    }


    void clear() {

        summary = "";

        summarymap.clear();

        massdifference = 0;

    }


    void store(ofstream& os);


    void load(ifstream& is);


};


class cDefaultNeutralLosses {


    vector<string> neutrallosses;


public:


    cDefaultNeutralLosses();


    vector<string>& getNeutralLosses() {

        return neutrallosses;

    }


};


extern cDefaultNeutralLosses defaultneutrallosses;


int loadModificationsFromPlainTextStream(ifstream &stream, vector<cFragmentIonType>& modifications, string& errormessage, bool ignoreerrors);


void storeModificationsToPlainTextStream(ofstream &stream, vector<cFragmentIonType>& modifications);


#endif


charge
double charge(double neutralmass, int charge)
Get mzratio from neutral mass.
Definition: cFragmentIons.cpp:1435

initializeFragmentIonsForDeNovoGraphOfCyclicPolyketide
void initializeFragmentIonsForDeNovoGraphOfCyclicPolyketide(vector< eFragmentIonType > &fragmentions)
Initialize fragment ion types for the de novo graph of a cyclic polyketide.
Definition: cFragmentIons.cpp:1719

initializeFragmentIonsForDeNovoGraphOfTPeptides
void initializeFragmentIonsForDeNovoGraphOfTPeptides(vector< eFragmentIonType > &fragmentions)
Initialize fragment ion types for the de novo graph of branched peptides.
Definition: cFragmentIons.cpp:1695

isotopemap
cIsotopeMap isotopemap
Global isotope map.
Definition: cFragmentIons.cpp:6

uncharge
double uncharge(double mzratio, int charge)
Get neutral mass from mzratio.
Definition: cFragmentIons.cpp:1440

initializeFragmentIonsForDeNovoGraphOfLinearPeptides
void initializeFragmentIonsForDeNovoGraphOfLinearPeptides(vector< eFragmentIonType > &fragmentions)
Initialize fragment ion types for the de novo graph of linear peptides.
Definition: cFragmentIons.cpp:1688

periodictablemap
cPeriodicTableMap periodictablemap
Global periodic table map.
Definition: cFragmentIons.cpp:5

loadModificationsFromPlainTextStream
int loadModificationsFromPlainTextStream(ifstream &stream, vector< cFragmentIonType > &modifications, string &errormessage, bool ignoreerrors)
Load modifications from a plain text stream.
Definition: cFragmentIons.cpp:1759

Q_DECLARE_METATYPE
Q_DECLARE_METATYPE(ePeptideType)
Register ePeptideType by Qt.

storeModificationsToPlainTextStream
void storeModificationsToPlainTextStream(ofstream &stream, vector< cFragmentIonType > &modifications)
Store modifications into a plain text stream.
Definition: cFragmentIons.cpp:1863

initializeFragmentIonsForDeNovoGraphOfLinearPolyketide
void initializeFragmentIonsForDeNovoGraphOfLinearPolyketide(vector< eFragmentIonType > &fragmentions)
Initialize fragment ion types for the de novo graph of a linear polyketide.
Definition: cFragmentIons.cpp:1708

eFragmentIonType
eFragmentIonType
The types of supported fragment ions.
Definition: cFragmentIons.h:944

initializeFragmentIonsForDeNovoGraphOfCyclicPeptides
void initializeFragmentIonsForDeNovoGraphOfCyclicPeptides(vector< eFragmentIonType > &fragmentions)
Initialize fragment ion types for the de novo graph of cyclic peptides.
Definition: cFragmentIons.cpp:1683

defaultneutrallosses
cDefaultNeutralLosses defaultneutrallosses
Default neutral losses definitions.
Definition: cFragmentIons.cpp:7

initializeFragmentIonsForDeNovoGraphOfBranchCyclicPeptides
void initializeFragmentIonsForDeNovoGraphOfBranchCyclicPeptides(vector< eFragmentIonType > &fragmentions)
Initialize fragment ion types for the de novo graph of branch-cyclic peptides.
Definition: cFragmentIons.cpp:1702

cDefaultNeutralLosses
The class representing a vector of default neutral losses.
Definition: cFragmentIons.h:1233

cDefaultNeutralLosses::cDefaultNeutralLosses
cDefaultNeutralLosses()
The constructor.
Definition: cFragmentIons.cpp:1741

cDefaultNeutralLosses::getNeutralLosses
vector< string > & getNeutralLosses()
Get the vector of neutral losses.
Definition: cFragmentIons.h:1249

cFragmentIons
The detailed definitions of all supported fragment ion types.
Definition: cFragmentIons.h:1070

cFragmentIons::recalculateFragments
void recalculateFragments(bool cyclicnterminus, bool cycliccterminus, string &precursoradduct)
Recalculate all fragment ion types.
Definition: cFragmentIons.cpp:1483

cFragmentIons::store
void store(ofstream &os)
Store the structure into an output stream.
Definition: cFragmentIons.cpp:1656

cFragmentIons::load
void load(ifstream &is)
Load the structure from an input stream.
Definition: cFragmentIons.cpp:1668

cFragmentIons::operator[]
cFragmentIonType & operator[](eFragmentIonType iontype)
Overloaded operator [].
Definition: cFragmentIons.cpp:1478

cFragmentIons::cFragmentIons
cFragmentIons()
The constructor.
Definition: cFragmentIons.cpp:1467

cIsotopeMap
The class representing an isotope map.
Definition: cFragmentIons.h:851

cIsotopeMap::cIsotopeMap
cIsotopeMap()
The constructor.
Definition: cFragmentIons.cpp:159

cIsotopeMap::count
int count(string &element)
Check whether an element occurs in the table.
Definition: cFragmentIons.cpp:1430

cIsotopeMap::operator[]
map< string, isotope > & operator[](string &element)
Overloaded operator [].
Definition: cFragmentIons.cpp:1425

cPeriodicTableMap
The class representing a periodic table.
Definition: cFragmentIons.h:760

cPeriodicTableMap::cPeriodicTableMap
cPeriodicTableMap()
The constructor.
Definition: cFragmentIons.cpp:10

cPeriodicTableMap::getElements
map< string, double > & getElements()
Reference to the map of elements.
Definition: cFragmentIons.cpp:149

cPeriodicTableMap::count
int count(string &element)
Check whether an element occurs in the table.
Definition: cFragmentIons.cpp:144

cPeriodicTableMap::operator[]
double & operator[](string &element)
Overloaded operator [].
Definition: cFragmentIons.cpp:139

cPeriodicTableMap::getAdductElements
vector< string > & getAdductElements()
Vector of elements which are allowed to be adducts.
Definition: cFragmentIons.cpp:154

cFragmentIonType
The struct for definition of a fragment ion type.
Definition: cFragmentIons.h:979

cFragmentIonType::cFragmentIonType
cFragmentIonType()
The default constructor.
Definition: cFragmentIons.h:1026

cFragmentIonType::name
string name
Name of the fragment.
Definition: cFragmentIons.h:984

cFragmentIonType::cterminal
bool cterminal
True when the fragment is C-terminal.
Definition: cFragmentIons.h:1014

cFragmentIonType::positive
bool positive
Charge of the fragment.
Definition: cFragmentIons.h:1020

cFragmentIonType::summarymap
map< string, int > summarymap
A map of atoms corresponding to the formula.
Definition: cFragmentIons.h:996

cFragmentIonType::load
void load(ifstream &is)
Load the structure from an input stream.
Definition: cFragmentIons.cpp:1456

cFragmentIonType::clear
void clear()
Clear the structure.
Definition: cFragmentIons.h:1034

cFragmentIonType::nterminal
bool nterminal
True when the fragment is N-terminal.
Definition: cFragmentIons.h:1008

cFragmentIonType::massdifference
double massdifference
Mass difference of the fragment.
Definition: cFragmentIons.h:1002

cFragmentIonType::store
void store(ofstream &os)
Store the structure into an output stream.
Definition: cFragmentIons.cpp:1445

cFragmentIonType::summary
string summary
Formula of the fragment.
Definition: cFragmentIons.h:990

isotope
Representation of an isotope.
Definition: cFragmentIons.h:815

isotope::probability
double probability
Probability of natural abundance.
Definition: cFragmentIons.h:826

isotope::isotope
isotope()
The default constructor.
Definition: cFragmentIons.h:832

isotope::clear
void clear()
Clear the structure.
Definition: cFragmentIons.h:840

isotope::mass
double mass
Monoisotopic mass.
Definition: cFragmentIons.h:820

neutralLoss
The structure for a detailed definition of a neutral loss.
Definition: cFragmentIons.h:1176

neutralLoss::load
void load(ifstream &is)
Load the structure from an input stream.
Definition: cFragmentIons.cpp:1734

neutralLoss::clear
void clear()
Clear the structure.
Definition: cFragmentIons.h:1207

neutralLoss::summary
string summary
Summary formula of the loss.
Definition: cFragmentIons.h:1181

neutralLoss::neutralLoss
neutralLoss()
The default constructor.
Definition: cFragmentIons.h:1199

neutralLoss::summarymap
map< string, int > summarymap
A map of atoms corresponding to the summary formula.
Definition: cFragmentIons.h:1187

neutralLoss::massdifference
double massdifference
Mass difference of the loss.
Definition: cFragmentIons.h:1193

neutralLoss::store
void store(ofstream &os)
Store the structure into an output stream.
Definition: cFragmentIons.cpp:1727

utilities.h
Auxiliary funtions and structures.

ePeptideType
ePeptideType
The types of peptides supported by the application.
Definition: utilities.h:104