ports//science/gchemutils/work/gnome-chemistry-utils-0.8.5/gcu/crystalatom.h

// -*- C++ -*-

/* 
 * Gnome Chemistry Utils
 * crystalatom.h 
 *
 * Copyright (C) 2002-2004 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 2 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 CRYSTAL_ATOM_H
#define CRYSTAL_ATOM_H

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

using namespace std;

namespace gcu
{

/*! \class CrystalAtom gcu/crystalatom.h
Used to represent atoms in a crystal.
*/
class CrystalAtom : public Atom
{
public:
/*
The default constructor.
*/
	CrystalAtom ();
/*
The destructor of CrystalAtom.
*/
	virtual ~CrystalAtom ();

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.
*/
	CrystalAtom (int Z, double x, double y, double z);
/*!
@param caAtom: the CrystalAtom to duplicate.

Creates a new CrystalAtom identical to caAtom.
*/
	CrystalAtom (CrystalAtom& caAtom);
/*
@param caAtom: the Atom to copy.

@return a CrystalAtom identical to caAtom.
*/
	CrystalAtom& operator= (CrystalAtom& caAtom);

/*!
Draws the atom inside the active OpenGL window.
*/
	void Draw ();
/*!
@param red: the red component of the color.
@param green: the green component of the color.
@param blue: the blue component of the color.
@param alpha: the alpha component of the color.

Sets a custom color to the atom.
*/
	void SetColor (float red, float green, float blue, float alpha);
/*!
Gives the atom the default color.
*/
	void SetDefaultColor ();
/*!
@return: true if the color is user defined and false if it is the default color.
*/
	bool HasCustomColor () {return m_bCustomColor;}
/*!
@param red: a pointer to the red component.
@param green: a pointer to the green component.
@param blue: a pointer to the blue component.
@param alpha: a pointer to the alpha component.

Used to retreive the color used in the representation of the atom. Mainly useful for user defined
colors.
*/
	void GetColor (double *red, double *green, double *blue, double *alpha);
/*!
@param r: the new value of the atomic radius.

Sets the value of the radius (in pm).
*/
	void SetSize (double r);
/*!
@return the value of the radius (in pm).
*/
	double GetSize ();
/*!
@param caAtom: a CrystalAtom instance.
@return true if the atoms are at the same position and false if their positions are different.
*/
	bool operator== (CrystalAtom& caAtom);
/*!
Method used to cleave an atom. The inverse operation does not exist since the whole crystal must be recalculated
after a change in the definition.
*/
	void Cleave () {m_nCleave++;}
/*!
@param h: the h Miller index of a plane.
@param k: the k Miller index of a plane.
@param l: the l Miller index of a plane.

@return the product hx+ky+lz where x, y and z are the coordinates of the atom. This makes sense only if coordinates
are related to the net and are not the cartesian coordinates. This method should not be called after NetToCartesian().
*/
	double ScalProd (int h, int k, int l);
/*!
@param a: the a parameter of the unit cell.
@param b: the b parameter of the unit cell.
@param c: the c parameter of the unit cell.
@param alpha: the alpha angle of the unit cell.
@param beta: the beta angle of the unit cell.
@param gamma: the gamma angle of the unit cell.

Converts the coordinates of the atom from net related ones to cartesian. Initially, atoms are defined by their
position relative to the unit cell and the coordinates must be transformed to the cartesian ones before
displaying the atom.
*/
	void NetToCartesian (double a, double b, double c, double alpha, double beta, double gamma);
/*!
@param x: the x coordinate of the center.
@param y: the y coordinate of the center.
@param z: the z coordinate of the center.
@param bFixed: tells if cleaved atoms are taken into account.

This helper method is called when searching for the size of the crystal. When some cleavages are defined,
the procedure cn take into account atoms cleaved to get the same position in the view for the cleaved crystal
than for the whole crystal. If bFixed is true, all atoms are taken into account.

@return the distance of the atom to the center of the view or 0 if bFixed is false and the atom cleaved. 
*/
	double Distance (double x, double y, double z, bool bFixed);
/*!
@return the value of the radius (in pm).
*/
	double r () {return m_Radius.value.value;}
/*!
@return the GcuAtomicRadius containing the caracteristics of the atom radius.
*/
	const GcuAtomicRadius& GetRadius () {return m_Radius;}
/*!
@param r: a GcuAtomicRadius with the caracteristics of the atom radius.
*/
	void SetRadius (const GcuAtomicRadius& r);
/*!
@return true if the atom is cleaved by at least one cleavage or false if the atom is not cleaved at all.
*/
	bool IsCleaved () {return m_nCleave != 0;}
/*!
@param xml: the xmlDoc used to save the document.
@param node: a pointer to the xmlNode to which this Atom is serialized.

Saves the color and the radius of the atom.
*/
	virtual bool SaveNode (xmlDocPtr xml, xmlNodePtr node);
/*!
@param node: a pointer to the xmlNode containing the serialized Atom.

Loads the color and the radius of the atom.
*/
	virtual bool LoadNode (xmlNodePtr node);
	
protected:
/*!
The blue component of the color of the sphere representing the atom.
*/
	float m_fBlue;
/*!
The red component of the color of the sphere representing the atom.
*/
	float m_fRed;
/*!
The green component of the color of the sphere representing the atom.
*/
	float m_fGreen;
/*!
The alpha component of the color of the sphere representing the atom.
*/
	float m_fAlpha;
/*!
False if the color used is the default color and true if it is a user defined color.
*/
	bool m_bCustomColor;
/*!
The GcuAtomicRadius containing the radius caracteristics of the atom.
*/
	GcuAtomicRadius m_Radius;
/*!
When cleavages (see CrystalCleavage class documentation) are defined, the atom might be cleaved. m_nCleave is
the number of CrystalCleavage instances which remove the atom. If this member is not 0, the atom will
not be displayed.
*/
	int m_nCleave; //0 if not cleaved
};

/*!
a list of pointers to CrystalAtom instances derived from std::list.
*/
typedef list<CrystalAtom*> CrystalAtomList;

}// namespace gcu

#endif // CRYSTAL_ATOM_H
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