[80a6a52] | 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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