00001 // -*- C++ -*- 00002 00003 /* 00004 * Gnome Chemistry Utils 00005 * libs/gcu/molecule.h 00006 * 00007 * Copyright (C) 2001-2010 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_MOLECULE_H 00026 #define GCU_MOLECULE_H 00027 00028 #include "object.h" 00029 00031 namespace gcu { 00032 00033 class Atom; 00034 class Bond; 00035 class Chain; 00036 class Cycle; 00037 class Formula; 00038 00042 class Molecule: public Object 00043 { 00044 friend class Chain; 00045 public: 00052 Molecule (TypeId Type = MoleculeType); 00059 Molecule (Atom* pAtom); 00063 virtual ~Molecule (); 00064 00070 void AddChild (Object* object); 00076 virtual void AddAtom (Atom* pAtom); 00082 virtual void AddBond (Bond* pBond); 00088 virtual void Remove (gcu::Object* pObject); 00094 void UpdateCycles (Bond* pBond); 00098 void UpdateCycles (); 00104 bool operator== (Molecule const& molecule) const; 00108 virtual unsigned GetAtomsNumber () const {return m_Atoms.size ();} 00119 static Molecule *MoleculeFromFormula (Document *Doc, Formula const &formula, bool add_pseudo = true); 00120 00124 void Clear (); 00130 Atom const *GetFirstAtom (std::list<Atom*>::const_iterator &i) const; 00136 Atom const *GetNextAtom (std::list<Atom*>::const_iterator &i) const; 00142 Bond const *GetFirstBond (std::list<Bond*>::const_iterator &i) const; 00148 Bond const *GetNextBond(std::list<Bond*>::const_iterator &i) const; 00159 void SetName (char const *name, char const *convention); 00165 char const *GetName (char const *convention = NULL); 00169 std::string Name (); 00170 00171 protected: 00175 std::list<Cycle*> m_Cycles; 00179 std::list<Chain*> m_Chains; 00183 std::list<Atom*> m_Atoms; 00187 std::list<Bond*> m_Bonds; 00188 00189 private: 00190 std::map <std::string, std::string> m_Names; 00191 }; 00192 00193 } // namespace gcu 00194 00195 #endif // GCU_MOLECULE_H