The Gnome Chemistry Utils 0.13.3
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00001 // -*- C++ -*- 00002 00003 /* 00004 * Gnome Chemistry Utils 00005 * libs/gcu/chain.h 00006 * 00007 * Copyright (C) 2001-2011 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_CHAIN_H 00026 #define GCU_CHAIN_H 00027 00028 #include "object.h" 00029 #include <map> 00030 00032 namespace gcu { 00033 00034 class Atom; 00035 class Bond; 00036 class Molecule; 00037 00043 typedef struct 00044 { 00048 Bond *fwd; 00052 Bond *rev; 00053 } ChainElt; 00054 00059 class Chain: public Object 00060 { 00061 public: 00072 Chain (Bond* pBond, Atom* pAtom = NULL, TypeId Type = ChainType); 00081 Chain (Molecule* molecule, Bond* pBond, TypeId Type = ChainType); 00090 Chain (Molecule* molecule, Atom* pAtom, TypeId Type = ChainType); 00094 virtual ~Chain(); 00095 00102 void FindCycles (Atom* pAtom); 00112 bool FindCycle (Atom* pAtom, Bond* pBond); 00119 virtual void Erase (Atom* pAtom1, Atom* pAtom2); 00127 virtual void Insert (Atom* pAtom1, Atom* pAtom2, Chain& chain); 00135 void Extract (Atom* pAtom1, Atom* pAtom2, Chain& chain); 00139 void Reverse (); 00140 void Append (Chain& chain); 00147 void AddBond (Atom* start, Atom* end); 00151 unsigned GetUnsaturations (); 00155 unsigned GetHeteroatoms (); 00161 bool Contains (Atom* pAtom); 00167 bool Contains (Bond* pBond); 00171 unsigned GetLength (); 00175 double GetMeanBondLength (); 00180 Atom* GetNextAtom (Atom* pAtom); 00181 00185 std::string Name (); 00186 unsigned BuildLength (unsigned *cycle_size = NULL, unsigned *cycle_pos = NULL); 00187 00188 protected: 00192 std::map<Atom*, ChainElt> m_Bonds; 00196 Molecule* m_Molecule; 00197 }; 00198 00199 } // namespace gcu 00200 00201 #endif // GCHEMPAINT_CHAIN_H