gcu/residue.h

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00001 // -*- C++ -*-
00002 
00003 /* 
00004  * Gnome Chemistry Utils
00005  * residue.h 
00006  *
00007  * Copyright (C) 2007-2008 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_RESIDUE_H
00026 #define GCU_RESIDUE_H
00027 
00028 #include "macros.h"
00029 #include <libxml/parser.h>
00030 #include <map>
00031 #include <set>
00032 #include <string>
00033 
00035 namespace gcu {
00036 
00037 class Residue;
00038 class Molecule;
00039 class Document;
00040 
00044 typedef struct {
00050         Residue *res;
00054         bool ambiguous;
00055 } SymbolResidue;
00056 
00057 typedef std::map<std::string, SymbolResidue>::iterator ResidueIterator;
00058 
00066 class Residue
00067 {
00068 public:
00072         Residue ();
00079         Residue (char const *name, Document *doc = NULL);
00083         virtual ~Residue ();
00084 
00098         std::map<int,int> const &GetRawFormula () const {return m_Raw;}
00105         std::map<std::string, bool> const &GetSymbols () const {return m_Symbols;}
00110         std::map<std::string, std::string> const &GetNames () const {return m_Names;}
00114         void SetName (char const *name);
00120         void AddSymbol (char const *symbol);
00126         void RemoveSymbol (char const *symbol);
00132         virtual void Load (xmlNodePtr node);
00140         static Residue const *GetResidue (char const *symbol, bool *ambiguous = NULL);
00146         static Residue const *GetResiduebyName (char const *name);
00155         static std::string const *GetFirstResidueSymbol (ResidueIterator &i);
00165         static std::string const *GetNextResidueSymbol (ResidueIterator &i);
00170         virtual bool operator== (G_GNUC_UNUSED Molecule const &mol) const {return false;}
00171 
00172 public:
00177         static unsigned MaxSymbolLength;
00178 
00179 private:
00180         std::map<int,int> m_Raw;
00181         std::map<std::string, bool> m_Symbols; // boolean is true if the symbol is ambiguous
00182         std::map<std::string, std::string> m_Names;
00183 
00187 GCU_RO_PROP (char const *, Name)
00202 GCU_PROP (bool, Generic)
00207 GCU_PROT_POINTER_PROP (Document, Document);
00212 GCU_PROT_POINTER_PROP (Molecule, Molecule);
00217 GCU_RO_PROP (Document *, Owner)
00218 };
00219 
00220 }       //      namespace gcu
00221 
00222 #endif  //      GCU_RESIDUE_H

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