gcu/residue.h

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// -*- C++ -*-

/*
 * Gnome Chemistry Utils
 * residue.h
 *
 * Copyright (C) 2007-2008 Jean Bréfort <jean.brefort@normalesup.org>
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License as
 * published by the Free Software Foundation; either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301
 * USA
 */

#ifndef GCU_RESIDUE_H
#define GCU_RESIDUE_H

#include "macros.h"
#include <libxml/parser.h>
#include <map>
#include <set>
#include <string>

namespace gcu {

class Application;
class Residue;
class Molecule;
class Document;

typedef struct {
        Residue *res;
        bool ambiguous;
} SymbolResidue;

typedef std::map<std::string, SymbolResidue>::iterator ResidueIterator;

class Residue
{
public:
        Residue ();
        Residue (char const *name, Document *doc = NULL);
        virtual ~Residue ();

        std::map<int,int> const &GetRawFormula () const {return m_Raw;}
        std::map<std::string, bool> const &GetSymbols () const {return m_Symbols;}
        std::map<std::string, std::string> const &GetNames () const {return m_Names;}
        void SetName (char const *name);
        void AddSymbol (char const *symbol);
        void RemoveSymbol (char const *symbol);
        virtual void Load (xmlNodePtr node, Application *app);
        static Residue const *GetResidue (char const *symbol, bool *ambiguous = NULL);
        static Residue const *GetResiduebyName (char const *name);
        static std::string const *GetFirstResidueSymbol (ResidueIterator &i);
        static std::string const *GetNextResidueSymbol (ResidueIterator &i);
        virtual bool operator== (G_GNUC_UNUSED Molecule const &mol) const {return false;}

public:
        static unsigned MaxSymbolLength;

private:
        std::map<int,int> m_Raw;
        std::map<std::string, bool> m_Symbols; // boolean is true if the symbol is ambiguous
        std::map<std::string, std::string> m_Names;

GCU_RO_PROP (char const *, Name)
GCU_PROP (bool, Generic)
GCU_PROT_POINTER_PROP (Document, Document);
GCU_PROT_POINTER_PROP (Molecule, Molecule);
GCU_RO_PROP (Document *, Owner)
};

}       //      namespace gcu

#endif  //      GCU_RESIDUE_H