#include <gcu/atom.h>

Inheritance diagram for gcu::Atom:

Public Member Functions
	Atom ()
	Atom (int Z, double x, double y, double z=0.)
	Atom (Atom &a)
Atom &	operator= (Atom &a)
virtual	~Atom ()
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 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)
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 Attributes
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 ()
Protected Member Functions inherited from gcu::Object
virtual Dialog *	BuildPropertiesDialog ()

Detailed Description

This class is used to represent atoms.

Definition at line 46 of file gcu/atom.h.

Constructor & Destructor Documentation

gcu::Atom::Atom ( )

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

Reimplemented in gcp::Atom, and gcr::Atom.

gcu::Atom::Atom	(	int	Z,
		double	x,
		double	y,
		double	z = `0.`
	)

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 in gcp::Atom, and gcr::Atom.

gcu::Atom::Atom ( Atom & a )

Parameters

a	the Atom to duplicate.

Creates a new atom identical to a without any bond.

virtual gcu::Atom::~Atom ( )

virtual

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

Reimplemented in gcp::Atom, and gcr::Atom.

Member Function Documentation

virtual void gcu::Atom::AddBond ( Bond * pBond )

virtual

Parameters

pBond a pointer to the new Bond to this Atom.

Adds a Bond.

Reimplemented in gcp::Atom.

double gcu::Atom::Distance ( Atom * pAtom )

Parameters

pAtom a pointer to an Atom.

Returns: the distance between the Atom at pAtom and this Atom.

Bond* gcu::Atom::GetBond ( Atom * pAtom ) const

Parameters

pAtom a pointer to an Atom instance.

Returns: a pointer to the Bond shared by pAtom and this Atom if it exists or NULL.

int gcu::Atom::GetBondsNumber ( ) const

inline

Returns: the number of Bond instances shared by this Atom. It does not take multiplicity of bonds into account.

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

References m_Bonds.

char gcu::Atom::GetCharge ( )

inline

Returns: the formal charge of this Atom.

Definition at line 128 of file gcu/atom.h.

References m_Charge.

bool gcu::Atom::GetCoords	(	double *	x,
		double *	y,
		double *	z = `NULL`
	)		const

virtual

Parameters

x	a pointer to the double value which will receive the x coordinate of the Atom.
y	a pointer to the double value which will receive the y coordinate of the Atom.
z	a pointer to the double value which will receive the z coordinate of the Atom or NULL for 2D representations.

Retrieves the coordinates of this Atom.

Returns: true if successful and false if an error occurs (if x or y is NULL).

Reimplemented from gcu::Object.

Bond* gcu::Atom::GetFirstBond ( std::map< Atom *, Bond * >::iterator & i )

Parameters

i	a C++ std::map iterator.

Use this function to retrieve the first Bond of this Atom and initialize the iterator.

Returns: the first Bond of this Atom or NULL if the Atom has is not bonded.

Bond const* gcu::Atom::GetFirstBond ( std::map< Atom *, Bond * >::const_iterator & i ) const

Parameters

i	a C++ std::map constant iterator.

Use this function to retrieve the first Bond of this constant Atom and initialize the iterator.

Returns: the first Bond of this Atom or NULL if the Atom has is not bonded.

Bond* gcu::Atom::GetNextBond ( std::map< Atom *, Bond * >::iterator & i )

Parameters

i	a C++ std::map iterator initialized by Atom::GetFirstBond.

Use this method to iterate through the list of Bond instances of this Atom.

Returns: the next Bond of this Atom or NULL.

Bond const* gcu::Atom::GetNextBond ( std::map< Atom *, Bond * >::const_iterator & i ) const

Parameters

i	a C++ std::map constant iterator initialized by Atom::GetFirstBond(std::map< Atom , Bond >::const_iterator&).

Use this method to iterate through the list of Bond instances of this Atom.

Returns: the next Bond of this Atom or NULL.

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

virtual

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::Object.

Reimplemented in gcr::Atom.

virtual const gchar* gcu::Atom::GetSymbol ( ) const

virtual

Returns: the atomic symbol of this Atom or NULL if the element is unknown.

Reimplemented in gcp::FragmentResidue.

Vector gcu::Atom::GetVector ( ) const

Returns: a Vector with the three Atom space coordinates.

int gcu::Atom::GetZ ( ) const

inline

Returns: the atomic number of the atom.

Definition at line 111 of file gcu/atom.h.

References m_Z.

bool gcu::Atom::IsInCycle ( Cycle * pCycle )

Parameters

pCycle a cycle in which the atom might be.

Returns: true if the atom lies in the cycle, false otherwise.

virtual bool gcu::Atom::Load ( xmlNodePtr node )

virtual

Parameters

node	a pointer to the xmlNode containing the serialized Atom.

Loads an atom from an xmlNode.

Reimplemented from gcu::Object.

Reimplemented in gcp::Atom, gcp::FragmentAtom, and gcp::FragmentResidue.

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

virtual

Parameters

node	a pointer to the xmlNode containing the serialized Atom.

This virtual method is called at the end of the Atom::Load method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the Atom::Load method.

Reimplemented in gcp::Atom, and gcr::Atom.

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

virtual

Parameters

atom	the atom to which the this instance is to be compared.
state	the AtomMatchState representing the current comparison state.

Try to match atoms from two molecules which are compared. This function calls itself recursively until all atoms from the two molecules have been matched or until an difference is found. Overriden methods should call this base function and return its result.

Returns: true if the atoms match, false otherwise.

Reimplemented in gcp::Atom, and gcp::FragmentAtom.

virtual void gcu::Atom::Move	(	double	x,
		double	y,
		double	z = `0.`
	)

virtual

Parameters

x	the x component of the transation vector.
y	the y component of the transation vector.
z	the z component of the transation vector.

Used to move an Atom.

Reimplemented from gcu::Object.

Reimplemented in gcp::Atom.

std::string gcu::Atom::Name ( )

virtual

Returns: the localized object generic name.

Reimplemented from gcu::Object.

void gcu::Atom::NetToCartesian	(	double	a,
		double	b,
		double	c,
		double	alpha,
		double	beta,
		double	gamma
	)

Parameters

a,:	the a parameter of the unit cell.
b,:	the b parameter of the unit cell.
c,:	the c parameter of the unit cell.
alpha,:	the alpha angle of the unit cell.
beta,:	the beta angle of the unit cell.
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.

Atom& gcu::Atom::operator= ( Atom & a )

Parameters

a	the Atom to copy.

Returns: an Atom identical to a without any bond.

virtual void gcu::Atom::RemoveBond ( Bond * pBond )

virtual

Parameters

pBond a pointer to the Bond to remove from this Atom.

Removes a Bond.

Reimplemented in gcp::Atom.

virtual xmlNodePtr gcu::Atom::Save ( xmlDocPtr xml ) const

virtual

Parameters

xml	the xmlDoc used to save the document.

Returns: a pointer to the xmlNode representing this Atom or NULL if an error occured.

Reimplemented from gcu::Object.

Reimplemented in gcp::Atom, gcp::FragmentAtom, and gcp::FragmentResidue.

virtual bool gcu::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.

This virtual method is called at the end of the Atom::Save method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the Atom::Save method.

Reimplemented in gcr::Atom.

virtual void gcu::Atom::SetCharge ( char Charge )

inlinevirtual

Parameters

Charge the new formal charge of the Atom.

Changes the formal charge of this Atom.

Definition at line 124 of file gcu/atom.h.

References m_Charge.

void gcu::Atom::SetCoords	(	double	x,
		double	y,
		double	z = `0`
	)

inline

Parameters

x	the new x coordinate of the Atom.
y	the new y coordinate of the Atom.
z	the new z coordinate of the Atom.

Changes the position of this Atom.

Definition at line 107 of file gcu/atom.h.

References m_x, m_y, m_z, x(), y(), and z().

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

virtual

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::Object.

Reimplemented in gcp::Atom, and gcr::Atom.

virtual void gcu::Atom::SetZ ( int Z )

virtual

Parameters

Z	the new atomic number of the Atom.

This method might be overrided by derived class since changing the atomic number generally changes most properties. The default behavior is just to change the atomic number and nothing else.

Reimplemented in gcp::Atom, and gcp::FragmentAtom.

virtual void gcu::Atom::Transform2D	(	Matrix2D &	m,
		double	x,
		double	y
	)

virtual

Parameters

m	the 2D Matrix of the transformation.
x	the x component of the center of the transformation.
y	the y component of the center of the transformation.

Used to move and/or transform an atom.

Reimplemented from gcu::Object.

Reimplemented in gcp::Atom.

double gcu::Atom::x ( ) const

inline

Returns: the x coordinate of this Atom.

Definition at line 148 of file gcu/atom.h.

References m_x.

Referenced by SetCoords().

double gcu::Atom::y ( ) const

inline

Returns: the y coordinate of this Atom.

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

References m_y.

Referenced by SetCoords().

double gcu::Atom::z ( ) const

inline

Returns: the z coordinate of this Atom.

Definition at line 158 of file gcu/atom.h.

References m_z.

Referenced by SetCoords().

void gcu::Atom::zoom ( double ZoomFactor )

Parameters

ZoomFactor the zoom factor.

Multiplies all three coordinates of this Atom by ZoomFactor.

Member Data Documentation

std::map<Atom*, Bond*> gcu::Atom::m_Bonds

protected

The Bond instances of the Atom. The index of the map is a pointer to the other end of the Bond.

Definition at line 323 of file gcu/atom.h.

Referenced by GetBondsNumber().

char gcu::Atom::m_Charge

protected

The charge of the Atom.

Definition at line 319 of file gcu/atom.h.

Referenced by GetCharge(), gcp::Atom::GetCharge(), and SetCharge().

double gcu::Atom::m_x

protected

The x coordinate of the Atom.

Definition at line 307 of file gcu/atom.h.

Referenced by SetCoords(), and x().

double gcu::Atom::m_y

protected

The x coordinate of the Atom.

Definition at line 311 of file gcu/atom.h.

Referenced by SetCoords(), and y().

int gcu::Atom::m_Z

protected

The atomic number of the Atom.

Definition at line 303 of file gcu/atom.h.

Referenced by GetZ().

double gcu::Atom::m_z

protected

The x coordinate of the Atom.

Definition at line 315 of file gcu/atom.h.

Referenced by SetCoords(), and z().

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

gcu/atom.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation