formula.h
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00025 #ifndef GCU_FORMULA_H
00026 #define GCU_FORMULA_H
00027
00028 #include <string>
00029 #include <map>
00030 #include <list>
00031 #include <stdexcept>
00032 #include "isotope.h"
00033 #include "macros.h"
00034 #include "value.h"
00035
00037 namespace gcu
00038 {
00039
00052 typedef enum {
00053 GCU_FORMULA_PARSE_GUESS,
00054 GCU_FORMULA_PARSE_ATOM,
00055 GCU_FORMULA_PARSE_RESIDUE,
00056 GCU_FORMULA_PARSE_ASK,
00057 GCU_FORMULA_PARSE_NO_CASE=8
00058 } FormulaParseMode;
00059
00065 class parse_error: public std::exception
00066 {
00067 public:
00071 explicit
00072 parse_error (const std::string& __arg, int start, int length);
00073
00074 virtual
00075 ~parse_error () throw ();
00076
00080 virtual const char*
00081 what () const throw ();
00085 const char*
00086 what (int& start, int& length) const throw ();
00087
00091 void add_offset (int offset) {m_start += offset;}
00092
00093 private:
00094 std::string m_msg;
00095 int m_start, m_length;
00096
00097 };
00098
00103 class FormulaElt
00104 {
00105 public:
00109 FormulaElt ();
00113 virtual ~FormulaElt ();
00117 virtual std::string Markup ();
00121 virtual std::string Text ();
00128 virtual void BuildRawFormula (std::map<int, int> &raw) = 0;
00132 virtual int GetValence () = 0;
00136 int stoich;
00140 unsigned start;
00144 unsigned end;
00145 };
00146
00151 class FormulaAtom: public FormulaElt
00152 {
00153 public:
00157 FormulaAtom (int Z);
00161 virtual ~FormulaAtom ();
00165 std::string Markup ();
00169 std::string Text ();
00175 void BuildRawFormula (std::map<int, int> &raw);
00179 int GetValence ();
00182 int elt;
00183 };
00184
00189 class FormulaBlock: public FormulaElt
00190 {
00191 public:
00194 FormulaBlock ();
00198 virtual ~FormulaBlock ();
00202 std::string Markup ();
00206 std::string Text ();
00213 void BuildRawFormula (std::map<int, int> &raw);
00217 int GetValence ();
00221 std::list<FormulaElt *> children;
00225 int parenthesis;
00226 };
00227
00228 class Residue;
00229
00236 class FormulaResidue: public FormulaElt
00237 {
00238 public:
00244 FormulaResidue (Residue const *res, char const *symbol, int Z);
00248 virtual ~FormulaResidue ();
00252 std::string Markup ();
00256 std::string Text ();
00263 void BuildRawFormula (std::map<int, int> &raw);
00267 int GetValence ();
00271 Residue const *residue;
00275 std::string Symbol;
00279 GCU_RO_PROP (int, Z);
00280 };
00281
00282
00288 class Formula
00289 {
00290 public:
00297 Formula (std::string entry, FormulaParseMode mode = GCU_FORMULA_PARSE_GUESS) throw (parse_error);
00298
00302 virtual ~Formula ();
00303
00307 char const *GetMarkup ();
00311 std::map<int,int> &GetRawFormula ();
00315 char const *GetRawMarkup ();
00322 void SetFormula (std::string entry) throw (parse_error);
00326 void Clear ();
00332 DimensionalValue GetMolecularWeight (bool &artificial);
00338 void CalculateIsotopicPattern (IsotopicPattern &pattern);
00339
00343 std::list<FormulaElt *> const &GetElements () const {return Details;}
00344
00345 private:
00346 bool BuildConnectivity ();
00347 void Parse (std::string &formula, std::list<FormulaElt *>&result) throw (parse_error);
00348 bool AnalString (char *sz, std::list<FormulaElt *> &result, bool &ambiguous, int offset);
00349 bool TryReplace (std::list<FormulaElt *> &result, std::list<FormulaElt *>::iterator it);
00350
00351 private:
00352 std::string Entry, Markup, RawMarkup;
00353 std::map<int,int> Raw;
00354 std::list<FormulaElt *> Details;
00355 DimensionalValue m_Weight;
00356 bool m_WeightCached;
00357 bool m_Artificial;
00358 bool m_ConnectivityCached;
00359
00371 GCU_PROP (FormulaParseMode, ParseMode);
00372 };
00373
00374 }
00375
00376 #endif // GCU_FORMULA_H