formula.h

00001 // -*- C++ -*-
00002 
00003 /* 
00004  * Gnome Chemistry Utils
00005  * formula.h 
00006  *
00007  * Copyright (C) 2005-2008 Jean Bréfort <jean.brefort@normalesup.org>
00008  *
00009  * This program is free software; you can redistribute it and/or 
00010  * modify it under the terms of the GNU General Public License as 
00011  * published by the Free Software Foundation; either version 2 of the
00012  * License, or (at your option) any later version.
00013  *
00014  * This program is distributed in the hope that it will be useful,
00015  * but WITHOUT ANY WARRANTY; without even the implied warranty of
00016  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00017  * GNU General Public License for more details.
00018  *
00019  * You should have received a copy of the GNU General Public License
00020  * along with this program; if not, write to the Free Software
00021  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301
00022  * USA
00023  */
00024 
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 
00036 namespace gcu
00037 {
00038 
00039 typedef enum {
00040         GCU_FORMULA_PARSE_GUESS,
00041         GCU_FORMULA_PARSE_ATOM,
00042         GCU_FORMULA_PARSE_RESIDUE,
00043         GCU_FORMULA_PARSE_ASK,
00044         GCU_FORMULA_PARSE_NO_CASE=8
00045 } FormulaParseMode;
00046 
00052 class parse_error: public std::exception
00053 {
00054 public:
00058     explicit 
00059     parse_error (const std::string&  __arg, int start, int length);
00060 
00061     virtual 
00062     ~parse_error () throw ();
00063 
00067     virtual const char* 
00068     what () const throw ();
00072     const char* 
00073     what (int& start, int& length) const throw ();
00074 
00078         void add_offset (int offset) {m_start += offset;}
00079 
00080 private:
00081         std::string m_msg;
00082         int m_start, m_length;
00083 
00084 };
00085 
00086 class FormulaElt
00087 {
00088 public:
00089         FormulaElt ();
00090         virtual ~FormulaElt ();
00091         virtual std::string Markup ();
00092         virtual void BuildRawFormula (std::map<int, int> &raw) = 0;
00093         virtual int GetValence () = 0;
00094         int stoich;
00095         unsigned start, end;
00096 };
00097 
00098 class FormulaAtom: public FormulaElt
00099 {
00100 public:
00101         FormulaAtom (int Z);
00102         virtual ~FormulaAtom ();
00103         std::string Markup ();
00104         void BuildRawFormula (std::map<int, int> &raw);
00105         int GetValence ();
00106         int elt;
00107 };
00108 
00109 class FormulaBlock: public FormulaElt
00110 {
00111 public:
00112         FormulaBlock ();
00113         virtual ~FormulaBlock ();
00114         std::string Markup ();
00115         void BuildRawFormula (std::map<int, int> &raw);
00116         std::list<FormulaElt *> children;
00117         int GetValence ();
00118         int parenthesis;
00119 };
00120 
00121 class Residue;
00122 
00123 class FormulaResidue: public FormulaElt
00124 {
00125 public:
00126         FormulaResidue (Residue const *res, char const *symbol, int Z);
00127         virtual ~FormulaResidue ();
00128         std::string Markup ();
00129         void BuildRawFormula (std::map<int, int> &raw);
00130         int GetValence ();
00131         Residue const *residue;
00132         std::string Symbol;
00133 GCU_RO_PROP (int, Z);
00134 };
00135 
00136 
00142 class Formula
00143 {
00144 public:
00150         Formula (std::string entry, FormulaParseMode mode = GCU_FORMULA_PARSE_GUESS) throw (parse_error);
00151         virtual ~Formula ();
00152 
00156         char const *GetMarkup ();
00160         std::map<int,int> &GetRawFormula ();
00164         char const *GetRawMarkup ();
00171         void SetFormula (std::string entry) throw (parse_error);
00175         void Clear ();
00181         DimensionalValue GetMolecularWeight (bool &artificial);
00187         void CalculateIsotopicPattern (IsotopicPattern &pattern);
00188 
00189         std::list<FormulaElt *> const &GetElements () const {return Details;}
00190 
00191 private:
00192         bool BuildConnectivity ();
00193         void Parse (std::string &formula, std::list<FormulaElt *>&result) throw (parse_error);
00194         bool AnalString (char *sz, std::list<FormulaElt *> &result, bool &ambiguous, int offset);
00195         bool TryReplace (std::list<FormulaElt *> &result, std::list<FormulaElt *>::iterator it);
00196                 
00197 private:
00198         std::string Entry, Markup, RawMarkup;
00199         std::map<int,int> Raw;
00200         std::list<FormulaElt *> Details;
00201         DimensionalValue m_Weight;
00202         bool m_WeightCached;
00203         bool m_Artificial;
00204         bool m_ConnectivityCached;
00205 GCU_PROP (FormulaParseMode, ParseMode);
00206 };
00207         
00208 }
00209 
00210 #endif // GCU_FORMULA_H

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