1 | #include "chemelem.h"
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2 |
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3 | #include <string.h>
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4 |
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5 | namespace geoworld
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6 | {
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7 | PeriodicTable periodicity;
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8 |
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9 | PeriodicTable::PeriodicTable ()
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10 | {
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11 | #define ASSIGN_CHEM(x) _name2num[#x] = x
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12 | ASSIGN_CHEM(H);
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13 | ASSIGN_CHEM(He);
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14 | ASSIGN_CHEM(Li);
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15 | ASSIGN_CHEM(Be);
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16 | ASSIGN_CHEM(B);
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17 | ASSIGN_CHEM(C);
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18 | ASSIGN_CHEM(N);
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19 | ASSIGN_CHEM(O);
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20 | ASSIGN_CHEM(F);
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21 | ASSIGN_CHEM(Ne);
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22 | ASSIGN_CHEM(Na);
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23 | ASSIGN_CHEM(Mg);
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24 | ASSIGN_CHEM(Al);
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25 | ASSIGN_CHEM(Si);
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26 | ASSIGN_CHEM(P);
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27 | ASSIGN_CHEM(S);
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28 | ASSIGN_CHEM(Cl);
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29 | ASSIGN_CHEM(Ar);
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30 | ASSIGN_CHEM(K);
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31 | ASSIGN_CHEM(Ca);
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32 | ASSIGN_CHEM(Sc);
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33 | ASSIGN_CHEM(Ti);
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34 | ASSIGN_CHEM(V);
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35 | ASSIGN_CHEM(Cr);
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36 | ASSIGN_CHEM(Mn);
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37 | ASSIGN_CHEM(Fe);
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38 | ASSIGN_CHEM(Co);
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39 | ASSIGN_CHEM(Ni);
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40 | ASSIGN_CHEM(Cu);
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41 | ASSIGN_CHEM(Zn);
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42 | ASSIGN_CHEM(Ga);
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43 | ASSIGN_CHEM(Ge);
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44 | ASSIGN_CHEM(As);
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45 | ASSIGN_CHEM(Se);
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46 | ASSIGN_CHEM(Br);
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47 | ASSIGN_CHEM(Kr);
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48 | ASSIGN_CHEM(Rb);
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49 | ASSIGN_CHEM(Sr);
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50 | ASSIGN_CHEM(Y);
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51 | ASSIGN_CHEM(Zr);
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52 | ASSIGN_CHEM(Nb);
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53 | ASSIGN_CHEM(Mo);
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54 | ASSIGN_CHEM(Tc);
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55 | ASSIGN_CHEM(Ru);
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56 | ASSIGN_CHEM(Rh);
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57 | ASSIGN_CHEM(Pd);
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58 | ASSIGN_CHEM(Ag);
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59 | ASSIGN_CHEM(Cd);
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60 | ASSIGN_CHEM(In);
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61 | ASSIGN_CHEM(Sn);
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62 | ASSIGN_CHEM(Sb);
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63 | ASSIGN_CHEM(Te);
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64 | ASSIGN_CHEM(I);
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65 | ASSIGN_CHEM(Xe);
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66 | ASSIGN_CHEM(Cs);
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67 | ASSIGN_CHEM(Ba);
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68 | ASSIGN_CHEM(La);
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69 | ASSIGN_CHEM(Ce);
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70 | ASSIGN_CHEM(Pr);
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71 | ASSIGN_CHEM(Nd);
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72 | ASSIGN_CHEM(Pm);
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73 | ASSIGN_CHEM(Sm);
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74 | ASSIGN_CHEM(Eu);
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75 | ASSIGN_CHEM(Gd);
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76 | ASSIGN_CHEM(Tb);
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77 | ASSIGN_CHEM(Dy);
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78 | ASSIGN_CHEM(Ho);
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79 | ASSIGN_CHEM(Er);
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80 | ASSIGN_CHEM(Tm);
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81 | ASSIGN_CHEM(Yb);
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82 | ASSIGN_CHEM(Lu);
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83 | ASSIGN_CHEM(Hf);
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84 | ASSIGN_CHEM(Ta);
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85 | ASSIGN_CHEM(W);
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86 | ASSIGN_CHEM(Re);
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87 | ASSIGN_CHEM(Os);
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88 | ASSIGN_CHEM(Ir);
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89 | ASSIGN_CHEM(Pt);
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90 | ASSIGN_CHEM(Au);
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91 | ASSIGN_CHEM(Hg);
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92 | ASSIGN_CHEM(Tl);
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93 | ASSIGN_CHEM(Pb);
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94 | ASSIGN_CHEM(Bi);
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95 | ASSIGN_CHEM(Po);
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96 | ASSIGN_CHEM(At);
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97 | ASSIGN_CHEM(Rn);
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98 | ASSIGN_CHEM(Fr);
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99 | ASSIGN_CHEM(Ra);
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100 | ASSIGN_CHEM(Ac);
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101 | ASSIGN_CHEM(Th);
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102 | ASSIGN_CHEM(Pa);
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103 | ASSIGN_CHEM(U);
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104 | ASSIGN_CHEM(Np);
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105 | ASSIGN_CHEM(Pu);
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106 | ASSIGN_CHEM(Am);
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107 | ASSIGN_CHEM(Cm);
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108 | ASSIGN_CHEM(Bk);
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109 | ASSIGN_CHEM(Cf);
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110 | ASSIGN_CHEM(Es);
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111 | ASSIGN_CHEM(Fm);
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112 | ASSIGN_CHEM(Md);
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113 | ASSIGN_CHEM(No);
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114 | ASSIGN_CHEM(Lr);
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115 | ASSIGN_CHEM(Rf);
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116 | ASSIGN_CHEM(Db);
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117 | ASSIGN_CHEM(Sg);
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118 | ASSIGN_CHEM(Bh);
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119 | ASSIGN_CHEM(Hs);
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120 | ASSIGN_CHEM(Mt);
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121 | ASSIGN_CHEM(Ds);
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122 | ASSIGN_CHEM(Rg);
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123 | ASSIGN_CHEM(Uub);
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124 | ASSIGN_CHEM(Uut);
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125 | ASSIGN_CHEM(Uuq);
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126 | ASSIGN_CHEM(Uup);
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127 | ASSIGN_CHEM(Uuh);
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128 | ASSIGN_CHEM(Uus);
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129 | ASSIGN_CHEM(Uuo);
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130 | #undef ASSIGN_CHEM
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131 | }
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132 |
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133 | ChemicalFormulaParser::Token::Token( const std::string & formula, const unsigned s0 )
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134 | : type(typeOf(formula[s0])), _s0(s0), _formula(formula), _s(s0)
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135 | {
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136 | switch (type)
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137 | {
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138 | case TNum:
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139 | while (++_s < formula.length() && typeOf(formula[_s]) == TNum);
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140 | break;
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141 | case TWord:
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142 | while (++_s < formula.length() && (formula[_s] >= 'a' && formula[_s] <= 'z'));
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143 | break;
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144 | case TSep:
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145 | while (++_s < formula.length() && typeOf(formula[_s]) == TSep);
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146 | break;
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147 | default:
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148 | ++_s;
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149 | break;
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150 | }
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151 | }
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152 |
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153 | ChemicalFormulaParser::Token & ChemicalFormulaParser::Token::operator = ( const ChemicalFormulaParser::Token & a )
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154 | {
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155 | _s0 = a._s0;
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156 | _s = a._s;
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157 | if (_formula != a._formula)
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158 | throw Ex();
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159 |
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160 | return *this;
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161 | }
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162 |
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163 | ChemicalFormulaParser::TokenType ChemicalFormulaParser::Token::typeOf( const char ch )
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164 | {
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165 | if ((ch >= '0' && ch <= '9') || ch == '.')
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166 | return TNum;
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167 | else if (ch >= 'A' && ch <= 'Z')
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168 | return TWord;
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169 | else if (ch == ' ' || ch == '.')
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170 | return TSep;
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171 | else if (ch == '(')
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172 | return TOpen;
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173 | else if (ch == ')')
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174 | return TClose;
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175 | else if (ch == ',')
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176 | return TAlt;
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177 | else
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178 | throw Ex();
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179 | }
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180 |
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181 | void ChemicalFormulaParser::Token::operator >> ( unsigned & num ) const
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182 | {
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183 | num = atoi (_formula.substr(_s0, _s - _s0).c_str());
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184 | }
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185 |
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186 | void ChemicalFormulaParser::Token::operator >> ( AtomicNumber & atom ) const
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187 | {
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188 | atom = periodicity[_formula.substr(_s0, _s - _s0)];
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189 | }
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190 |
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191 | void ChemicalFormulaParser::Token::operator >> ( float & f ) const
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192 | {
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193 | f = static_cast <float> (atof(_formula.substr(_s0, _s - _s0).c_str()));
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194 | }
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195 |
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196 | unsigned ChemicalFormulaParser::Token::length() const
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197 | {
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198 | return _s - _s0;
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199 | }
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200 |
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201 |
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202 | bool ChemicalFormulaParser::lookAhead( const std::vector <ChemicalFormulaParser::Token>::const_iterator & i, const ChemicalFormulaParser::TokenType tok ) const
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203 | {
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204 | return ((i + 1) != _tokens.end() && (i + 1)->type == tok);
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205 | }
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206 |
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207 | bool ChemicalFormulaParser::lookBehind( const std::vector <ChemicalFormulaParser::Token>::const_iterator & i, const ChemicalFormulaParser::TokenType tok ) const
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208 | {
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209 | return (i != _tokens.begin() && (i - 1)->type == tok);
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210 | }
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211 |
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212 | void ChemicalFormulaParser::quantities (ChemicalFormulaParser::IQuantityCallback * cb)
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213 | {
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214 | float mqty = 1, gqty = 1, gdqty = 1;
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215 | AtomicNumber atom;
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216 | std::vector <Token>::const_iterator i = _tokens.begin();
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217 | float quantiteas[NUM_CHEM_ELEMENTS];
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218 |
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219 | memset(quantiteas, 0, sizeof(quantiteas));
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220 | while (i != _tokens.end())
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221 | {
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222 | // Do nothing, skip, group quantifiers were processed in-advance while processing 'TOpen'
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223 | if (lookBehind(i, TClose) && i->type == TNum) {}
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224 |
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225 | else if (i->type == TNum)
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226 | {
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227 | *i++ >> mqty;
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228 |
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229 | if (i == _tokens.end())
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230 | throw Ex(); // Molecular quantifiers cannot terminate a formula
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231 |
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232 | if (i->type == TWord)
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233 | {
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234 | unsigned aqty = 1;
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235 |
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236 | *i >> atom;
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237 |
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238 | // If we're at the end of the word, we expect an atomic quantifier here
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239 | if (lookAhead(i, TNum))
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240 | {
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241 | *++i >> aqty;
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242 | }
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243 |
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244 | quantiteas[atom] += mqty * aqty * (gqty / gdqty);
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245 | } else
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246 | throw Ex(); // A chemical element name must immediately follow a molecular quantifier
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247 | } else if (i->type == TWord)
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248 | {
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249 | unsigned aqty = 1;
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250 |
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251 | *i >> atom;
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252 |
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253 | // If we're at the end of the word, we expect an atomic quantifier here
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254 | if (lookAhead(i, TNum))
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255 | {
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256 | *++i >> aqty;
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257 | }
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258 |
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259 | quantiteas[atom] += mqty * aqty * (gqty / gdqty);
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260 |
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261 | // Process a group including the suffixes after the group terminator
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262 | } else if (i->type == TOpen)
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263 | {
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264 | std::vector <Token>::const_iterator i2 = i;
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265 |
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266 | // Scan to the end of the group
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267 | while (i2->type != TClose && i2 != _tokens.end())
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268 | {
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269 | // If we encounter a comma, then we increase the group quantity dividend (Q = Qm * Qa * Qg / Qd)
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270 | if (i->type == TAlt)
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271 | gdqty++;
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272 | i2++;
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273 | }
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274 |
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275 | // Check for an unbalanced group (no closing brace found)
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276 | if (i2 == _tokens.end())
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277 | throw Ex(); // No closing brace found
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278 |
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279 | // We hope the next token after the group terminator is a number, it becomes our group quantity
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280 | if (lookAhead(i2, TNum))
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281 | *++i2 >> gqty;
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282 | } else if (i->type == TClose)
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283 | {
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284 | gqty = 1;
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285 | gdqty = 1;
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286 | }
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287 | i++;
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288 | }
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289 |
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290 | for (unsigned c = 0; c < NUM_CHEM_ELEMENTS; c++)
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291 | {
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292 | if (quantiteas[c] > 0)
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293 | cb->setChemicalQuantity(static_cast <AtomicNumber> (c), quantiteas[c]);
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294 | }
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295 | }
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296 | ChemicalFormulaParser::ChemicalFormulaParser (const std::string & formula) : _formula(formula)
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297 | {
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298 | unsigned c = 0;
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299 |
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300 | while (c < _formula.length())
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301 | {
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302 | _tokens.push_back(Token(_formula, c));
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303 | c += _tokens.back().length();
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304 | }
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305 | }
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306 | }
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