#include <gcp/fragment-atom.h>

Inheritance diagram for gcp::FragmentAtom:

Public Member Functions
	FragmentAtom ()
	FragmentAtom (Fragment *fragment, int Z)
virtual	~FragmentAtom ()
void	SetZ (int Z)
bool	AcceptNewBonds (int nb)
void	Update ()
void	AddItem ()
void	UpdateItem ()
void	SetSelected (int state)
xmlNodePtr	Save (xmlDocPtr xml) const
bool	Load (xmlNodePtr node)
gccv::Anchor	GetChargePosition (unsigned char &Pos, double Angle, double &x, double &y)
int	GetAvailablePosition (double &x, double &y)
bool	GetPosition (double angle, double &x, double &y)
bool	AcceptCharge (int charge)
void	AddToMolecule (Molecule *Mol)
bool	Match (gcu::Atom *atom, gcu::AtomMatchState &state)
void	DoBuildSymbolGeometry (View *pView)
Fragment const *	GetFragment (void) const
Public Member Functions inherited from gcp::Atom
	Atom ()
	Atom (int Z, double x, double y, double z)
virtual	~Atom ()
void	AddBond (gcu::Bond *pBond)
void	RemoveBond (gcu::Bond *pBond)
int	GetTotalBondsNumber () const
int	GetAttachedHydrogens () const
HPos	GetBestSide ()
virtual bool	GetRelativePosition (double angle, double &x, double &y)
virtual bool	LoadNode (xmlNodePtr node)
virtual double	GetYAlign ()
virtual void	Move (double x, double y, double z=0.)
virtual void	Transform2D (gcu::Matrix2D &m, double x, double y)
bool	BuildContextualMenu (gcu::UIManager UIManager, Object object, double x, double y)
bool	HasImplicitElectronPairs ()
bool	MayHaveImplicitUnpairedElectrons ()
void	AddElectron (Electron *electron)
void	RemoveElectron (Electron *electron)
void	NotifyPositionOccupation (unsigned char pos, bool occupied)
void	SetChargePosition (unsigned char Pos, bool def, double angle=0., double distance=0.)
char	GetChargePosition (double Angle, double Dist) const
void	SetCharge (int charge)
int	GetCharge () const
void	ForceChanged ()
void	GetSymbolGeometry (double &width, double &height, double &angle, bool up) const
bool	HasAvailableElectrons (bool paired)
Bond *	GetBondAtAngle (double angle)
bool	UpdateStereoBonds ()
bool	HasStereoBond () const
Bond *	GetNewmanBond () const
void	SetShowSymbol (bool val)
bool	GetShowSymbol (void) const
bool &	GetRefShowSymbol (void)
void	SetHPosStyle (HPos val)
HPos	GetHPosStyle (void) const
HPos &	GetRefHPosStyle (void)
void	SetChargeItem (gccv::Item *val)
gccv::Item *	GetChargeItem (void)
void	SetShowCharge (bool val)
bool	GetShowCharge (void) const
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	SetCharge (char Charge)
char	GetCharge ()
virtual const gchar *	GetSymbol () const
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 bool	SaveNode (xmlDocPtr xml, xmlNodePtr node) const
std::string	GetProperty (unsigned property) const
bool	IsInCycle (Cycle *pCycle)
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 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
Public Member Functions inherited from gcu::DialogOwner
	DialogOwner ()
virtual	~DialogOwner ()
Dialog *	GetDialog (std::string name) const
void	ClearDialogs ()
Public Member Functions inherited from gccv::ItemClient
	ItemClient ()
virtual	~ItemClient ()
Item *	GetItem (void)

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 gcp::Atom
void	BuildSymbolGeometry (double width, double height, double ascent)
bool	SetProperty (unsigned property, char const *value)
Protected Attributes inherited from gcp::Atom
double	m_CHeight

Detailed Description

Represents an atom inside a atoms group (see gcp::Fragment class).

Definition at line 40 of file fragment-atom.h.

Constructor & Destructor Documentation

gcp::FragmentAtom::FragmentAtom ( )

The default constructor.

gcp::FragmentAtom::FragmentAtom	(	Fragment *	fragment,
		int	Z
	)

Parameters

fragment	the parent Fragment.
Z	the atomic number.

Constructs a FragmentAtom inside fragment with atomic number Z. This does not add the symbol to the string.

virtual gcp::FragmentAtom::~FragmentAtom ( )

virtual

The destructor.

Member Function Documentation

bool gcp::FragmentAtom::AcceptCharge ( int charge )

virtual

Parameters

charge the charge that might be set.

Currently, these atoms only accept -1, 0, and +1 as charges.

Returns: true if the charge is acceptable.

Reimplemented from gcp::Atom.

bool gcp::FragmentAtom::AcceptNewBonds ( int nb )

virtual

Parameters

nb	the number of bonds to add, taking orders into account.

This atom class does not currently support more than one single bond and no multiple bond at all.

Returns: true if the operation is allowed, false otherwise.

Reimplemented from gcp::Atom.

void gcp::FragmentAtom::AddItem ( )

virtual

Overrided to avoid Atom::AddItem execution. Don't do anything.

Reimplemented from gcp::Atom.

void gcp::FragmentAtom::AddToMolecule ( Molecule * Mol )

virtual

Parameters

Mol,: a pointer to a molecule

Adds the fragment containing the atom to the molecule calling gcpMolecule::AddFragment()

Reimplemented from gcp::Atom.

void gcp::FragmentAtom::DoBuildSymbolGeometry ( View * pView )

Parameters

pView the document view.

Builds the symbol geometry if necessary.

int gcp::FragmentAtom::GetAvailablePosition	(	double &	x,
		double &	y
	)

virtual

Parameters

x	the x position.
y	the y position.

This method finds an available position for drawing a charge sign and returns it as a symbolic value (see POSITION_E, POSITION_N,...). The x and y are updated so that they give the absolute position.

Returns: an available position.

Reimplemented from gcp::Atom.

gccv::Anchor gcp::FragmentAtom::GetChargePosition	(	unsigned char &	Pos,
		double	Angle,
		double &	x,
		double &	y
	)

virtual

Parameters

Pos	the approximate position of the charge.
Angle	the angle from horizontal left.
x	the x position of the charge symbol.
y	the y position of the charge symbol.

On input Pos can be one of POSITION_E, POSITION_N,... or 0xff, in which case, it will be given a default value. x and y are set to the position where the charge sign should be displayed usding the alignment code returned by this method.

Returns: the anchor for the charge symbol. On error, gccv::AnchorCenter is used as the returned value.

Reimplemented from gcp::Atom.

gcp::FragmentAtom::GetFragment ( void ) const

inline

Returns: the Fragment enclosing the FragmentAtom.

Definition at line 176 of file fragment-atom.h.

bool gcp::FragmentAtom::GetPosition	(	double	angle,
		double &	x,
		double &	y
	)

virtual

Parameters

angle	the angle at which a charge sign should be displayed.
x	the x position.
y	the y position.

Updates x and y so that they become the absolute position corresponding to the angle when the position is available.

Returns: true on success, false otherwise.

Reimplemented from gcp::Atom.

bool gcp::FragmentAtom::Load ( xmlNodePtr node )

virtual

param node a pointer to the xmlNode containing the serialized atom.

Used to load the atom specific properties in memory. The FragmentAtom must already exist.

Returns: true on succes, false otherwise.

Reimplemented from gcp::Atom.

Reimplemented in gcp::FragmentResidue.

bool gcp::FragmentAtom::Match	(	gcu::Atom *	atom,
		gcu::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. FragmentAtom instances can't be matched currently.

Returns: always false.

Reimplemented from gcp::Atom.

xmlNodePtr gcp::FragmentAtom::Save ( xmlDocPtr xml ) const

virtual

Parameters

xml	the xmlDoc used to save the document.

Used to save the atome specific data to the xmlDoc.

Returns: the xmlNode containing the serialized atom.

Reimplemented from gcp::Atom.

Reimplemented in gcp::FragmentResidue.

void gcp::FragmentAtom::SetSelected ( int state )

virtual

Parameters

state the selection state of the atom.

Overrided to avoid Atom::SetSelected execution. Just call Fragment::SetSelected method.

Reimplemented from gcp::Atom.

void gcp::FragmentAtom::SetZ ( int Z )

virtual

Parameters

Z	the new atomic number.

Changes the atomic number of the atom.

Reimplemented from gcp::Atom.

void gcp::FragmentAtom::Update ( )

virtual

Overrided to avoid Atom::Update execution. Just call Fragment::Update() method.

Reimplemented from gcp::Atom.

void gcp::FragmentAtom::UpdateItem ( )

virtual

Overrided to avoid Atom::UpdateItem execution. Just call Fragment::UpdateItem().

Reimplemented from gccv::ItemClient.

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

fragment-atom.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation