The Gnome Chemistry Utils 0.13.3
gcu/atom.h
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00001 // -*- C++ -*-
00002 
00003 /* 
00004  * Gnome Chemistry Utils
00005  * atom.h 
00006  *
00007  * Copyright (C) 2002-2011 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_ATOM_H
00026 #define GCU_ATOM_H
00027 
00028 #include "object.h"
00029 #include <glib.h>
00030 #include <map>
00031 #include <vector>
00032 
00034 namespace gcu
00035 {
00036         
00037 class Bond;
00038 class Cycle;
00039 class AtomMatchState;
00040 class Vector;
00041 
00046 class Atom: public Object
00047 {
00048 public:
00052         Atom ();
00061         Atom (int Z, double x, double y, double z = 0.);
00067         Atom (Atom& a);
00073         Atom& operator= (Atom& a);
00077         virtual ~Atom ();
00078 
00079 public :
00084         double Distance (Atom* pAtom);
00090         void zoom (double ZoomFactor);
00099         bool GetCoords (double *x, double *y, double *z = NULL) const;
00107         void SetCoords (double x, double y, double z = 0) {m_x = x; m_y = y; m_z = z;}
00111         int GetZ () const {return m_Z;}
00118         virtual void SetZ (int Z);
00124         virtual void SetCharge (char Charge) {m_Charge = Charge;}
00128         char GetCharge () {return m_Charge;}
00132         virtual const gchar* GetSymbol () const;
00138         virtual void AddBond (Bond* pBond);
00144         virtual void RemoveBond (Bond* pBond);
00148         double x () const {return m_x;}
00152         double y () const {return m_y;}
00156         double z () const {return m_z;}
00160         Vector GetVector () const;
00167         Bond *GetFirstBond (std::map < Atom *, Bond * >::iterator& i);
00168         Bond const *GetFirstBond (std::map< Atom *, Bond * >::const_iterator& i) const;
00175         Bond *GetNextBond (std::map<Atom*, Bond*>::iterator& i);
00176         Bond const *GetNextBond (std::map< Atom *, Bond * >::const_iterator& i) const;
00181         Bond* GetBond (Atom* pAtom) const;
00185         int GetBondsNumber () const {return m_Bonds.size();}
00190         virtual xmlNodePtr Save (xmlDocPtr xml) const;
00196         virtual bool Load (xmlNodePtr node);
00203         virtual bool LoadNode (xmlNodePtr node);
00211         virtual bool SaveNode (xmlDocPtr xml, xmlNodePtr node) const;
00219         virtual void Move (double x, double y, double z = 0.);
00227         virtual void Transform2D (Matrix2D& m, double x, double y);
00228 
00236         bool SetProperty (unsigned property, char const *value);
00237 
00244         std::string GetProperty (unsigned property) const;
00245 
00251         bool IsInCycle (Cycle* pCycle);
00252 
00263         virtual bool Match (Atom *atom, AtomMatchState &state);
00264 
00268         std::string Name ();
00269 
00270 protected:
00274         int m_Z;
00278         double m_x;
00282         double m_y;
00286         double m_z;
00290         char m_Charge;
00294         std::map<Atom*, Bond*> m_Bonds;
00295 };
00296 
00302 class AtomPair {
00303 public:
00304 
00311         AtomPair (Atom *at1, Atom *at2) {atom1 = at1; atom2 = at2;}
00312 
00316         Atom *atom1;
00317 
00321         Atom *atom2;
00322 };
00323 
00329 class AtomMatchState
00330 {
00331 public:
00332 
00336         std::map <Atom*, int> mol1;
00337 
00341         std::map <Atom*, int> mol2;
00342 
00346         std::vector <AtomPair> atoms;
00347 };
00348 
00349 } //namespace gcu
00350 #endif // GCU_ATOM_H