The Gnome Chemistry Utils  0.13.7
gcu/molecule.h
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00001 // -*- C++ -*-
00002 
00003 /*
00004  * Gnome Chemistry Utils
00005  * libs/gcu/molecule.h
00006  *
00007  * Copyright (C) 2001-2012 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 3 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_MOLECULE_H
00026 #define GCU_MOLECULE_H
00027 
00028 #include "object.h"
00029 #include "structs.h"
00030 
00032 namespace gcu {
00033 
00034 class Atom;
00035 class Bond;
00036 class Chain;
00037 class Cycle;
00038 class Formula;
00039 
00043 class Molecule: public Object
00044 {
00045 friend class Chain;
00046 public:
00055         Molecule (TypeId Type = MoleculeType, ContentType ct = ContentType3D);
00064         Molecule (Atom* pAtom, ContentType ct = ContentType3D);
00068         virtual ~Molecule ();
00069 
00075         void AddChild (Object* object);
00081         virtual void AddAtom (Atom* pAtom);
00087         virtual void AddBond (Bond* pBond);
00093         virtual void Remove (gcu::Object* pObject);
00099         void UpdateCycles (Bond* pBond);
00103         void UpdateCycles ();
00109         bool operator== (Molecule const& molecule) const;
00113         virtual unsigned GetAtomsNumber () const {return m_Atoms.size ();}
00124         static Molecule *MoleculeFromFormula (Document *Doc, Formula const &formula, bool add_pseudo = true);
00125 
00129         void Clear ();
00135         Atom const *GetFirstAtom (std::list<Atom*>::const_iterator &i) const;
00141         Atom const *GetNextAtom (std::list<Atom*>::const_iterator &i) const;
00147         Bond const *GetFirstBond (std::list<Bond*>::const_iterator &i) const;
00153         Bond const *GetNextBond(std::list<Bond*>::const_iterator &i) const;
00164         void SetName (char const *name, char const *convention);
00170         char const *GetName (char const *convention = NULL);
00174         std::string Name ();
00175 
00179         void ResetIndentifiers ();
00180 
00184         std::string const &GetCML ();
00185 
00189         void ClearCycles ();
00190 
00194         std::string const &GetInChI ();
00195 
00199         std::string const &GetInChIKey ();
00200 
00204         std::string const &GetSMILES ();
00208         virtual std::string GetRawFormula () const;
00209 
00210 protected:
00214         std::list<Cycle*> m_Cycles;
00218         std::list<Chain*> m_Chains;
00222         std::list<Atom*> m_Atoms;
00226         std::list<Bond*> m_Bonds;
00227 
00228 private:
00229         std::map <std::string, std::string> m_Names;
00230         std::string m_CML;
00231         std::string m_InChI;
00232         std::string m_InChIKey;
00233         std::string m_SMILES;
00234         ContentType m_Content;
00235 };
00236 
00237 }       //      namespace gcu
00238 
00239 #endif  //      GCU_MOLECULE_H