gcu/residue.h

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 
00034 namespace gcu {
00035 
00036 class Residue;
00037 
00038 
00039 typedef struct {
00040         Residue *res;
00041         bool ambiguous;
00042 } SymbolResidue;
00043 
00044 typedef std::map<std::string, SymbolResidue>::iterator ResidueIterator;
00045 
00046 class Residue
00047 {
00048 public:
00049         Residue ();
00050         Residue (char const *name);
00051         virtual ~Residue ();
00052 
00053         std::map<int,int> const &GetRawFormula () const {return m_Raw;}
00054         std::map<std::string, bool> const &GetSymbols () const {return m_Symbols;}
00055         std::map<std::string, std::string> const &GetNames () const {return m_Names;}
00056         void SetName (char const *name);
00057         void AddSymbol (char const *symbol);
00058         void RemoveSymbol (char const *symbol);
00059         virtual void Load (xmlNodePtr node);
00060         static Residue const *GetResidue (char const *symbol, bool *ambiguous = NULL);
00061         static Residue const *GetResiduebyName (char const *name);
00062         static std::string const *GetFirstResidueSymbol (ResidueIterator &i);
00063         static std::string const *GetNextResidueSymbol (ResidueIterator &i);
00064 
00065 public:
00066         static unsigned MaxSymbolLength;
00067 
00068 private:
00069         std::map<int,int> m_Raw;
00070         std::map<std::string, bool> m_Symbols; // boolean is true if the symbol is ambiguous
00071         std::map<std::string, std::string> m_Names; // boolean is true if the symbol is ambiguous
00072 
00073 GCU_RO_PROP (char const *, Name)
00074 GCU_PROP (bool, Generic)
00075 };
00076 
00077 }       //      namespace gcu
00078 
00079 #endif  //      GCU_RESIDUE_H

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