The Gnome Chemistry Utils 0.13.3
chain.h
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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