#include <gcu/bond.h>

Inheritance diagram for gcu::Bond:

Public Member Functions
	Bond ()
	Bond (Atom first, Atom last, unsigned char order)
virtual	~Bond ()
virtual Atom *	GetAtom (int which) const
virtual Atom *	GetAtom (Atom *pAtom, int which=0) const
virtual Atom const *	GetAtom (Atom const *pAtom, int which=0) const
unsigned char	GetOrder () const
void	SetOrder (unsigned char Order)
virtual xmlNodePtr	Save (xmlDocPtr xml) const
virtual bool	Load (xmlNodePtr node)
virtual void	IncOrder (int n=1)
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
virtual void	AddCycle (Cycle *pCycle)
virtual void	RemoveCycle (Cycle *pCycle)
virtual void	RemoveAllCycles ()
unsigned	IsCyclic ()
Cycle *	GetFirstCycle (std::list< Cycle * >::iterator &i, Cycle *pCycle)
Cycle *	GetNextCycle (std::list< Cycle * >::iterator &i, Cycle *pCycle)
bool	IsInCycle (Cycle *pCycle)
double	Get2DLength ()
double	GetAngle2DRad (Atom *pAtom)
bool	ReplaceAtom (Atom oldAtom, Atom newAtom)
void	OnLoaded ()
std::string	Name ()
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)
virtual bool	GetCoords (double x, double y, double *z=NULL) const
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
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
unsigned char	m_order
Atom *	m_Begin
Atom *	m_End
std::list< Cycle * >	m_Cycles

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 bonds.

Definition at line 42 of file gcu/bond.h.

Constructor & Destructor Documentation

gcu::Bond::Bond ( )

The default constructor. Creates a bond with order set to 0.

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

gcu::Bond::Bond	(	Atom *	first,
		Atom *	last,
		unsigned char	order
	)

Parameters

first	a pointer to the first Atom instance of the bond.
last	a pointer to the last Atom instance of the bond.
order	the order of the new bond.

The distinction between first and last is important mostly for stereobonds. The Bond instance is created and adds itself to the two atoms calling Atom::AddBond.

virtual gcu::Bond::~Bond ( )

virtual

The destructor of Bond.

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

Member Function Documentation

virtual void gcu::Bond::AddCycle ( Cycle * pCycle )

virtual

Parameters

pCycle a cycle to add to the list.

Reimplemented in gcp::Bond.

double gcu::Bond::Get2DLength ( )

Returns: the length of the bond when projected to the xy plane.

double gcu::Bond::GetAngle2DRad ( Atom * pAtom )

Parameters

pAtom one of the atoms of the bond.

Returns: the direction of the bond starting from the atom.

virtual Atom* gcu::Bond::GetAtom ( int which ) const

virtual

Parameters

which the index of the Atom instance to be returned.

Returns: a pointer to the Atom instance: first Atom if which is 0, last if which is 1 or NULL.

virtual Atom* gcu::Bond::GetAtom	(	Atom *	pAtom,
		int	which = `0`
	)		const

virtual

Parameters

pAtom	a pointer to an Atom instance.
which	an index which might be used for multicentered bonds (not supported); the default value should always be used even if the implementation does not use it in this version.

Returns: the last atom if pAtom is the first, the first if pAtom is the last or NULL if pAtom is not concerned by this Bond.

virtual Atom const* gcu::Bond::GetAtom	(	Atom const *	pAtom,
		int	which = `0`
	)		const

virtual

Parameters

pAtom	a pointer to a constant Atom instance.
which	an index which might be used for multicentered bonds (not supported); the default value should always be used even if the implementation does not use it in this version.

The const version of the method.

Returns: the last atom if pAtom is the first, the first if pAtom is the last or NULL if pAtom is not concerned by this Bond.

Cycle* gcu::Bond::GetFirstCycle	(	std::list< Cycle * >::iterator &	i,
		Cycle *	pCycle
	)

Parameters

i	a C++ std::map iterator.
pCycle	a cycle.

Returns: the first cycle to which the bond belongs, excluding the one passed as second argument.

Cycle* gcu::Bond::GetNextCycle	(	std::list< Cycle * >::iterator &	i,
		Cycle *	pCycle
	)

Parameters

i	a C++ std::map iterator initialized by Bond::GetFirstCycle.
pCycle	a cycle.

Returns: the next cycle to which the bond belongs, excluding the one passed as second argument.

unsigned char gcu::Bond::GetOrder ( ) const

Returns: the Bond order.

std::string gcu::Bond::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 bonds.

Returns: the value of the property as a string.

Reimplemented from gcu::Object.

Reimplemented in gcp::Bond.

virtual void gcu::Bond::IncOrder ( int n = 1 )

virtual

Parameters

n	the increment to add to the bond order

If the resulting bond order is greater than 4, the remainder of the division by 4 is retained.

Reimplemented in gcp::Bond.

unsigned gcu::Bond::IsCyclic ( )

inline

Returns: the number of cycles to which the bond belongs.

Definition at line 183 of file gcu/bond.h.

References m_Cycles.

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

Parameters

pCycle a cycle in which the bond might be.

Returns: true if the bond is in the cycle.

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

virtual

Parameters

node	a pointer to the xmlNode containing the serialized Bond.

Loads a bond from an xmlNode.

Reimplemented from gcu::Object.

Reimplemented in gcr::Bond.

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

virtual

Parameters

node	a pointer to the xmlNode containing the serialized Bond.

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

Reimplemented in gcp::Bond.

virtual void gcu::Bond::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.

Does nothing. Just a slight optimization to avoid execution of Object::Move

Reimplemented from gcu::Object.

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

std::string gcu::Bond::Name ( )

virtual

Returns: the localized object generic name.

Reimplemented from gcu::Object.

void gcu::Bond::OnLoaded ( )

virtual

This method should be called when a bond has been fully loaded.

Reimplemented from gcu::Object.

Reimplemented in gcp::Bond.

virtual void gcu::Bond::RemoveAllCycles ( )

virtual

Clears the bond cycles list.

Reimplemented in gcp::Bond.

virtual void gcu::Bond::RemoveCycle ( Cycle * pCycle )

virtual

Parameters

pCycle a cycle to remove from the list.

Reimplemented in gcp::Bond.

bool gcu::Bond::ReplaceAtom	(	Atom *	oldAtom,
		Atom *	newAtom
	)

Parameters

oldAtom	the atom to replace.
newAtom	the new atom.

To sucess, this needs that the new atom can accept all the bonds from the old one.

Returns: true on success.

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

virtual

Parameters

xml	the xmlDoc used to save the document.

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

Reimplemented from gcu::Object.

virtual bool gcu::Bond::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 Bond is serialized.

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

Reimplemented in gcp::Bond.

void gcu::Bond::SetOrder ( unsigned char Order )

Parameters

Order the new bond order.

The value used is not checked. Should be a significant value (1 to 3, exceptionally 4).

bool gcu::Bond::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 bonds.

Returns: true on success.

Reimplemented from gcu::Object.

Reimplemented in gcp::Bond.

virtual void gcu::Bond::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.

Does nothing. Just a slight optimization to avoid execution of Object::Transform2D

Reimplemented from gcu::Object.

Reimplemented in gcp::Bond.

Member Data Documentation

Atom* gcu::Bond::m_Begin

protected

A pointer to the first Atom instance of the Bond.

Definition at line 249 of file gcu/bond.h.

std::list<Cycle*> gcu::Bond::m_Cycles

protected

The gcu::Cycle instnces to which the bond pertains.

Definition at line 258 of file gcu/bond.h.

Referenced by IsCyclic().

Atom* gcu::Bond::m_End

protected

A pointer to the last Atom instance of the Bond.

Definition at line 253 of file gcu/bond.h.

unsigned char gcu::Bond::m_order

protected

The order of the bond.

Definition at line 245 of file gcu/bond.h.

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

gcu/bond.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation