gcr/atom.h

Go to the documentation of this file.

// -*- C++ -*-

/*
 * Gnome Chemistry Utils
 * gcr/atom.h
 *
 * Copyright (C) 2002-2010 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 GCR_ATOM_H
#define GCR_ATOM_H

#include <gcu/atom.h>
#include <gcu/chemistry.h>
#include <gcu/macros.h>
#include <libxml/parser.h>
#include <libxml/parserInternals.h>
#include <libxml/xmlmemory.h>
#include <list>

namespace gcr
{

#define PREC 1e-3

class Atom : public gcu::Atom
{
public:
/*
The default constructor.
*/
        Atom ();
/*
The destructor of Atom.
*/
        virtual ~Atom ();

public :
/*
@param Z: the atomic number of the new atom.
@param x: the x coordinate of the new atom.
@param y: the y coordinate of the new atom.
@param z: the z coordinate of the new atom.

Creates an atom.
*/
        Atom (int Z, double x, double y, double z);
        Atom (Atom& caAtom);
/*
@param caAtom: the Atom to copy.

@return an Atom identical to caAtom.
*/
        Atom& operator= (Atom& caAtom);

        void SetColor (float red, float green, float blue, float alpha);
        void SetDefaultColor ();
        bool HasCustomColor () {return m_bCustomColor;}
        void GetColor (double *red, double *green, double *blue, double *alpha);
        void GetColor (GdkRGBA &rgba);
        void SetSize (double r);
        double GetSize ();
        bool operator== (Atom& caAtom);
        void Cleave () {m_nCleave++;}
        double ScalProd (int h, int k, int l);
        double Distance (double x, double y, double z, bool bFixed);
        double r () {return m_Radius.value.value;}
        const GcuAtomicRadius& GetRadius () {return m_Radius;}
        void SetRadius (const GcuAtomicRadius& r);
        bool IsCleaved () {return m_nCleave != 0;}
        virtual bool SaveNode (xmlDocPtr xml, xmlNodePtr node) const;
        virtual bool LoadNode (xmlNodePtr node);

protected:
        float m_fBlue;
        float m_fRed;
        float m_fGreen;
        float m_fAlpha;
        bool m_bCustomColor;
        GcuAtomicRadius m_Radius;
        int m_nCleave; //0 if not cleaved

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

        std::string GetProperty (unsigned property) const;

GCU_PROP (double, EffectiveRadiusRatio);
};

typedef std::list<Atom*> AtomList;
}// namespace gcr

#endif // GCR_ATOM_H