gcu/molecule.h

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// -*- C++ -*-

/*
 * Gnome Chemistry Utils
 * libs/gcu/molecule.h
 *
 * Copyright (C) 2001-2012 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_MOLECULE_H
#define GCU_MOLECULE_H

#include "object.h"
#include "structs.h"

namespace gcu {

class Atom;
class Bond;
class Chain;
class Cycle;
class Formula;

class Molecule: public Object
{
friend class Chain;
public:
        Molecule (TypeId Type = MoleculeType, ContentType ct = ContentType3D);
        Molecule (Atom* pAtom, ContentType ct = ContentType3D);
        virtual ~Molecule ();

        void AddChild (Object* object);
        virtual void AddAtom (Atom* pAtom);
        virtual void AddBond (Bond* pBond);
        virtual void Remove (gcu::Object* pObject);
        void UpdateCycles (Bond* pBond);
        void UpdateCycles ();
        bool operator== (Molecule const& molecule) const;
        virtual unsigned GetAtomsNumber () const {return m_Atoms.size ();}
        static Molecule *MoleculeFromFormula (Document *Doc, Formula const &formula, bool add_pseudo = true);

        void Clear ();
        Atom const *GetFirstAtom (std::list<Atom*>::const_iterator &i) const;
        Atom *GetFirstAtom (std::list<Atom*>::iterator &i);
        Atom const *GetNextAtom (std::list<Atom*>::const_iterator &i) const;
        Atom *GetNextAtom (std::list<Atom*>::iterator &i);
        Bond const *GetFirstBond (std::list<Bond*>::const_iterator &i) const;
        Bond const *GetNextBond(std::list<Bond*>::const_iterator &i) const;
        void SetName (char const *name, char const *convention);
        char const *GetName (char const *convention = NULL);
        std::string Name ();

        void ResetIndentifiers ();

        std::string const &GetCML ();

        void ClearCycles ();

        std::string const &GetInChI ();

        std::string const &GetInChIKey ();

        std::string const &GetSMILES ();
        virtual std::string GetRawFormula () const;

protected:
        std::list<Cycle*> m_Cycles;
        std::list<Chain*> m_Chains;
        std::list<Atom*> m_Atoms;
        std::list<Bond*> m_Bonds;

private:
        std::map <std::string, std::string> m_Names;
        std::string m_CML;
        std::string m_InChI;
        std::string m_InChIKey;
        std::string m_SMILES;
        ContentType m_Content;
};

}       //      namespace gcu

#endif  //      GCU_MOLECULE_H