The Gnome Chemistry Utils 0.13.3
formula.h
Go to the documentation of this file.
00001 // -*- C++ -*-
00002 
00003 /* 
00004  * Gnome Chemistry Utils
00005  * formula.h 
00006  *
00007  * Copyright (C) 2005-2010 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 
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