#include <gcr/atom.h>

Inheritance diagram for gcr::Atom:

Public Member Functions
	Atom ()
virtual	~Atom ()
	Atom (int Z, double x, double y, double z)
	Atom (Atom &caAtom)
void	SetColor (float red, float green, float blue, float alpha)
void	SetDefaultColor ()
bool	HasCustomColor ()
void	GetColor (double red, double green, double blue, double alpha)
void	SetSize (double r)
double	GetSize ()
bool	operator== (Atom &caAtom)
void	Cleave ()
double	ScalProd (int h, int k, int l)
double	Distance (double x, double y, double z, bool bFixed)
double	r ()
const GcuAtomicRadius &	GetRadius ()
void	SetRadius (const GcuAtomicRadius &r)
bool	IsCleaved ()
virtual bool	SaveNode (xmlDocPtr xml, xmlNodePtr node) const
virtual bool	LoadNode (xmlNodePtr node)
Public Member Functions inherited from gcu::Atom
	Atom (Atom &a)
Atom &	operator= (Atom &a)
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)
int	GetZ () const
virtual void	SetZ (int Z)
virtual void	SetCharge (char Charge)
char	GetCharge ()
virtual const gchar *	GetSymbol () const
virtual void	AddBond (Bond *pBond)
virtual void	RemoveBond (Bond *pBond)
double	x () const
double	y () const
double	z () const
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
virtual xmlNodePtr	Save (xmlDocPtr xml) const
virtual bool	Load (xmlNodePtr node)
virtual void	Move (double x, double y, double z=0.)
virtual void	Transform2D (Matrix2D &m, double x, double y)
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)
Public Member Functions inherited from gcu::Object
	Object (TypeId Id=OtherType)
virtual	~Object ()
TypeId	GetType () const
void	SetId (gchar const *Id)
char const *	GetId () const
virtual void	AddChild (Object *object)
Object *	GetMolecule () const
Object *	GetReaction () const
Object *	GetGroup () const
Document *	GetDocument () const
Application *	GetApplication () const
Object *	GetParentOfType (TypeId Id) const
Object *	GetChild (const gchar *Id) const
Object *	GetFirstChild (std::map< std::string, Object * >::iterator &i)
Object *	GetNextChild (std::map< std::string, Object * >::iterator &i)
Object *	GetDescendant (const char *Id) const
Object *	GetParent () const
void	SetParent (Object *Parent)
bool	SaveChildren (xmlDocPtr xml, xmlNodePtr node) const
void	SaveId (xmlNodePtr node) const
xmlNodePtr	GetNodeByProp (xmlNodePtr node, char const Property, char const Id)
xmlNodePtr	GetNextNodeByProp (xmlNodePtr node, char const Property, char const Id)
xmlNodePtr	GetNodeByName (xmlNodePtr node, char const *Name)
xmlNodePtr	GetNextNodeByName (xmlNodePtr node, char const *Name)
bool	HasChildren () const
unsigned	GetChildrenNumber () const
virtual Object *	GetAtomAt (double x, double y, double z=0.)
virtual bool	Build (std::set< Object * > const &Children) throw (std::invalid_argument)
virtual double	GetYAlign ()
virtual bool	BuildContextualMenu (UIManager uim, Object object, double x, double y)
void	EmitSignal (SignalId Signal)
virtual bool	OnSignal (SignalId Signal, Object *Child)
void	Lock (bool state=true)
bool	IsLocked ()
Object *	GetFirstLink (std::set< Object * >::iterator &i)
Object *	GetNextLink (std::set< Object * >::iterator &i)
void	Link (Object *object)
void	Unlink (Object *object)
virtual void	OnUnlink (Object *object)
void	GetPossibleAncestorTypes (std::set< TypeId > &types) const
virtual void	OnLoaded ()
void	SetDirty (bool dirty=true)
virtual void	Clear ()
std::string	Identity ()
virtual char const *	HasPropertiesDialog () const
virtual bool	CanSelect () const
virtual void	NotifyEmpty ()
void	ShowPropertiesDialog ()
bool	GetDirty (void) const

Protected Member Functions
bool	SetProperty (unsigned property, char const *value)
std::string	GetProperty (unsigned property) const

Protected Attributes
float	m_fBlue
float	m_fRed
float	m_fGreen
float	m_fAlpha
bool	m_bCustomColor
GcuAtomicRadius	m_Radius
int	m_nCleave
Protected Attributes inherited from gcu::Atom
int	m_Z
double	m_x
double	m_y
double	m_z
char	m_Charge
std::map< Atom , Bond >	m_Bonds

Additional Inherited Members
Static Public Member Functions inherited from gcu::Object
static TypeId	AddType (std::string TypeName, Object (CreateFunc)(), TypeId id=OtherType)
static void	AddAlias (TypeId id, std::string TypeName)
static Object *	CreateObject (const std::string &TypeName, Object *parent=NULL)
static TypeId	GetTypeId (const std::string &Name)
static std::string	GetTypeName (TypeId Id)
static void	AddMenuCallback (TypeId Id, BuildMenuCb cb)
static void	AddRule (TypeId type1, RuleId rule, TypeId type2)
static void	AddRule (const std::string &type1, RuleId rule, const std::string &type2)
static const std::set< TypeId > &	GetRules (TypeId type, RuleId rule)
static const std::set< TypeId > &	GetRules (const std::string &type, RuleId rule)
static void	SetCreationLabel (TypeId Id, std::string Label)
static const std::string &	GetCreationLabel (TypeId Id)
static const std::string &	GetCreationLabel (const std::string &TypeName)
static SignalId	CreateNewSignalId ()

Detailed Description

Used to represent atoms in a crystal.

Definition at line 45 of file gcr/atom.h.

Constructor & Destructor Documentation

gcr::Atom::Atom ( )

The default constructor. Creates an atom with atomic number set to 0.

Reimplemented from gcu::Atom.

virtual gcr::Atom::~Atom ( )

virtual

The destructor of Atom. It removes bonds but do not delete the associated Bond instances.

Reimplemented from gcu::Atom.

gcr::Atom::Atom	(	int	Z,
		double	x,
		double	y,
		double	z
	)

Parameters

Z	the atomic number of the new atom.
x	the x coordinate of the new atom.
y	the y coordinate of the new atom.
z	the z coordinate of the new atom.

Creates an atom.

Reimplemented from gcu::Atom.

gcr::Atom::Atom ( Atom & caAtom )

Parameters

caAtom,: the Atom to duplicate.

Creates a new Atom identical to caAtom.

Member Function Documentation

void gcr::Atom::Cleave ( )

inline

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.

Definition at line 127 of file gcr/atom.h.

References m_nCleave.

double gcr::Atom::Distance	(	double	x,
		double	y,
		double	z,
		bool	bFixed
	)

Parameters

x,:	the x coordinate of the center.
y,:	the y coordinate of the center.
z,:	the z coordinate of the center.
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.

Returns: the distance of the atom to the center of the view or 0 if bFixed is false and the atom cleaved.

void gcr::Atom::GetColor	(	double *	red,
		double *	green,
		double *	blue,
		double *	alpha
	)

Parameters

red,:	a pointer to the red component.
green,:	a pointer to the green component.
blue,:	a pointer to the blue component.
alpha,:	a pointer to the alpha component.

Used to retrieve the color used in the representation of the atom. Mainly useful for user defined colors.

std::string gcr::Atom::GetProperty ( unsigned property ) const

protectedvirtual

Parameters

property the identity of the property as defined in objprops.h.

Used by the gcu::Loader mechanism to retrieve properties of atoms.

Returns: the value of the property as a string.

Reimplemented from gcu::Atom.

const GcuAtomicRadius& gcr::Atom::GetRadius ( void )

inline

Returns: the GcuAtomicRadius containing the caracteristics of the atom radius.

Definition at line 157 of file gcr/atom.h.

References m_Radius.

double gcr::Atom::GetSize ( )

Returns: the value of the radius (in pm).

bool gcr::Atom::HasCustomColor ( )

inline

Returns: : true if the color is user defined and false if it is the default color.

Definition at line 96 of file gcr/atom.h.

References m_bCustomColor.

bool gcr::Atom::IsCleaved ( )

inline

Returns: true if the atom is cleaved by at least one cleavage or false if the atom is not cleaved at all.

Definition at line 165 of file gcr/atom.h.

References m_nCleave.

virtual bool gcr::Atom::LoadNode ( xmlNodePtr node )

virtual

Parameters

node,: a pointer to the xmlNode containing the serialized Atom.

Loads the color and the radius of the atom.

Reimplemented from gcu::Atom.

bool gcr::Atom::operator== ( Atom & caAtom )

Parameters

caAtom,: a Atom instance.

Returns: true if the atoms are at the same position and false if their positions are different.

double gcr::Atom::r ( )

inline

Returns: the value of the radius (in pm).

Definition at line 153 of file gcr/atom.h.

References m_Radius, GcuDimensionalValue::value, and GcuAtomicRadius::value.

virtual bool gcr::Atom::SaveNode	(	xmlDocPtr	xml,
		xmlNodePtr	node
	)		const

virtual

Parameters

xml,:	the xmlDoc used to save the document.
node,:	a pointer to the xmlNode to which this Atom is serialized.

Saves the color and the radius of the atom.

Reimplemented from gcu::Atom.

double gcr::Atom::ScalProd	(	int	h,
		int	k,
		int	l
	)

Parameters

h,:	the h Miller index of a plane.
k,:	the k Miller index of a plane.
l,:	the l Miller index of a plane.

Returns: 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().

void gcr::Atom::SetColor	(	float	red,
		float	green,
		float	blue,
		float	alpha
	)

Parameters

red,:	the red component of the color.
green,:	the green component of the color.
blue,:	the blue component of the color.
alpha,:	the alpha component of the color.

Sets a custom color to the atom.

void gcr::Atom::SetDefaultColor ( )

Gives the atom the default color.

bool gcr::Atom::SetProperty	(	unsigned	property,
		char const *	value
	)

protectedvirtual

Parameters

property	the identity of the property as defined in objprops.h.
value	the value of the property as a string.

Used by the gcu::Loader mechanism to load properties of atoms.

Returns: true on success.

Reimplemented from gcu::Atom.

void gcr::Atom::SetRadius ( const GcuAtomicRadius & r )

Parameters

r,:	a GcuAtomicRadius with the caracteristics of the atom radius.

void gcr::Atom::SetSize ( double r )

Parameters

r,:	the new value of the atomic radius.

Sets the value of the radius (in pm).

Member Data Documentation

bool gcr::Atom::m_bCustomColor

protected

False if the color used is the default color and true if it is a user defined color.

Definition at line 200 of file gcr/atom.h.

Referenced by HasCustomColor().

float gcr::Atom::m_fAlpha

protected

The alpha component of the color of the sphere representing the atom.

Definition at line 196 of file gcr/atom.h.

float gcr::Atom::m_fBlue

protected

The blue component of the color of the sphere representing the atom.

Definition at line 184 of file gcr/atom.h.

float gcr::Atom::m_fGreen

protected

The green component of the color of the sphere representing the atom.

Definition at line 192 of file gcr/atom.h.

float gcr::Atom::m_fRed

protected

The red component of the color of the sphere representing the atom.

Definition at line 188 of file gcr/atom.h.

int gcr::Atom::m_nCleave

protected

When cleavages (see gcr::Cleavage class documentation) are defined, the atom might be cleaved. m_nCleave is the number of gcr::Cleavage instances which remove the atom. If this member is not 0, the atom will not be displayed.

Definition at line 210 of file gcr/atom.h.

Referenced by Cleave(), and IsCleaved().

GcuAtomicRadius gcr::Atom::m_Radius

protected

The GcuAtomicRadius containing the radius caracteristics of the atom.

Definition at line 204 of file gcr/atom.h.

Referenced by GetRadius(), and r().

The documentation for this class was generated from the following file:

gcr/atom.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation