gcu/atom.h

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// -*- C++ -*-

/*
 * Gnome Chemistry Utils
 * atom.h
 *
 * Copyright (C) 2002-2011 Jean Bréfort <jean.brefort@normalesup.org>
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License as
 * published by the Free Software Foundation; either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301
 * USA
 */

#ifndef GCU_ATOM_H
#define GCU_ATOM_H

#include "object.h"
#include <glib.h>
#include <map>
#include <vector>

namespace gcu
{

class Bond;
class Cycle;
class AtomMatchState;
class Vector;

class Atom: public Object
{
public:
        Atom ();
        Atom (int Z, double x, double y, double z = 0.);
        Atom (Atom& a);
        Atom& operator= (Atom& a);
        virtual ~Atom ();

public :
        double Distance (Atom* pAtom);
        void zoom (double ZoomFactor);
        bool GetCoords (double *x, double *y, double *z = NULL) const;
        void SetCoords (double x, double y, double z = 0) {m_x = x; m_y = y; m_z = z;}
        int GetZ () const {return m_Z;}
        virtual void SetZ (int Z);
        virtual void SetCharge (char Charge) {m_Charge = Charge;}
        char GetCharge () {return m_Charge;}
        virtual const gchar* GetSymbol () const;
        virtual void AddBond (Bond* pBond);
        virtual void RemoveBond (Bond* pBond);
        double x () const {return m_x;}
        double &x () {return m_x;}
        double y () const {return m_y;}
        double &y () {return m_y;}
        double z () const {return m_z;}
        double &z () {return m_z;}
        Vector GetVector () const;
        Bond *GetFirstBond (std::map < Atom *, Bond * >::iterator& i);
        Bond const *GetFirstBond (std::map< Atom *, Bond * >::const_iterator& i) const;
        Bond *GetNextBond (std::map<Atom*, Bond*>::iterator& i);
        Bond const *GetNextBond (std::map< Atom *, Bond * >::const_iterator& i) const;
        Bond* GetBond (Atom* pAtom) const;
        int GetBondsNumber () const {return m_Bonds.size();}
        virtual xmlNodePtr Save (xmlDocPtr xml) const;
        virtual bool Load (xmlNodePtr node);
        virtual bool LoadNode (xmlNodePtr node);
        virtual bool SaveNode (xmlDocPtr xml, xmlNodePtr node) const;
        virtual void Move (double x, double y, double z = 0.);
        virtual void Transform2D (Matrix2D& m, double x, double y);

        bool SetProperty (unsigned property, char const *value);

        std::string GetProperty (unsigned property) const;

        bool IsInCycle (Cycle* pCycle);

        virtual bool Match (Atom *atom, AtomMatchState &state);

        std::string Name ();

        void NetToCartesian (double a, double b, double c, double alpha, double beta, double gamma);

protected:
        int m_Z;
        double m_x;
        double m_y;
        double m_z;
        char m_Charge;
        std::map<Atom*, Bond*> m_Bonds;
};

class AtomPair {
public:

        AtomPair (Atom *at1, Atom *at2) {atom1 = at1; atom2 = at2;}

        Atom *atom1;

        Atom *atom2;
};

class AtomMatchState
{
public:

        std::map <Atom*, int> mol1;

        std::map <Atom*, int> mol2;

        std::vector <AtomPair> atoms;
};

} //namespace gcu
#endif // GCU_ATOM_H