gcu/atom.h

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00001 // -*- C++ -*-
00002 
00003 /* 
00004  * Gnome Chemistry Utils
00005  * atom.h 
00006  *
00007  * Copyright (C) 2002-2008 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 
00045 class Atom: public Object
00046 {
00047 public:
00051         Atom ();
00060         Atom (int Z, double x, double y, double z = 0.);
00066         Atom (Atom& a);
00072         Atom& operator= (Atom& a);
00076         virtual ~Atom ();
00077 
00078 public :
00083         double Distance (Atom* pAtom);
00089         void zoom (double ZoomFactor);
00098         virtual bool GetCoords (double *x, double *y, double *z = NULL) const;
00106         void SetCoords (double x, double y, double z = 0) {m_x = x; m_y = y; m_z = z;}
00110         int GetZ () const {return m_Z;}
00117         virtual void SetZ (int Z);
00123         virtual void SetCharge (char Charge) {m_Charge = Charge;}
00127         char GetCharge () {return m_Charge;}
00131         virtual const gchar* GetSymbol () const;
00137         virtual void AddBond (Bond* pBond);
00143         virtual void RemoveBond (Bond* pBond);
00147         double x () const {return m_x;}
00151         double y () const {return m_y;}
00155         double z () const {return m_z;}
00162         Bond* GetFirstBond (std::map<Atom*, Bond*>::iterator& i);
00169         Bond* GetNextBond (std::map<Atom*, Bond*>::iterator& i);
00174         Bond* GetBond (Atom* pAtom) const;
00178         int GetBondsNumber () const {return m_Bonds.size();}
00183         virtual xmlNodePtr Save (xmlDocPtr xml) const;
00189         virtual bool Load (xmlNodePtr node);
00196         virtual bool LoadNode (xmlNodePtr node);
00204         virtual bool SaveNode (xmlDocPtr xml, xmlNodePtr node) const;
00212         virtual void Move (double x, double y, double z = 0.);
00220         virtual void Transform2D (Matrix2D& m, double x, double y);
00221 
00229         bool SetProperty (unsigned property, char const *value);
00230 
00237         std::string GetProperty (unsigned property) const;
00238 
00244         bool IsInCycle (Cycle* pCycle);
00245 
00256         virtual bool Match (Atom *atom, AtomMatchState &state);
00257 
00258 protected:
00262         int m_Z;
00266         double m_x;
00270         double m_y;
00274         double m_z;
00278         char m_Charge;
00282         std::map<Atom*, Bond*> m_Bonds;
00283 };
00284 
00290 class AtomPair {
00291 public:
00292 
00299         AtomPair (Atom *at1, Atom *at2) {atom1 = at1; atom2 = at2;}
00300 
00304         Atom *atom1;
00305 
00309         Atom *atom2;
00310 };
00311 
00317 class AtomMatchState
00318 {
00319 public:
00320 
00324         std::map <Atom*, int> mol1;
00325 
00329         std::map <Atom*, int> mol2;
00330 
00334         std::vector <AtomPair> atoms;
00335 };
00336 
00337 } //namespace gcu
00338 #endif // GCU_ATOM_H

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