gcugtk::Molecule Class Reference

#include <gcugtk/molecule.h>

Inheritance diagram for gcugtk::Molecule:

Public Member Functions
	Molecule (gcu::TypeId Type=gcu::MoleculeType, gcu::ContentType ct=gcu::ContentType3D)
	Molecule (gcu::Atom *pAtom, gcu::ContentType ct=gcu::ContentType3D)
virtual	~Molecule ()
void	BuildDatabasesMenu (GtkUIManager *UIManager, char const *path, char const *path_end)
Public Member Functions inherited from gcu::Molecule
void	AddChild (Object *object)
virtual void	AddAtom (Atom *pAtom)
virtual void	AddBond (Bond *pBond)
virtual void	Remove (gcu::Object *pObject)
void	UpdateCycles (Bond *pBond)
void	UpdateCycles ()
bool	operator== (Molecule const &molecule) const
virtual unsigned	GetAtomsNumber () const
void	Clear ()
Atom const *	GetFirstAtom (std::list< Atom * >::const_iterator &i) const
Atom const *	GetNextAtom (std::list< Atom * >::const_iterator &i) const
Bond const *	GetFirstBond (std::list< Bond * >::const_iterator &i) const
Bond const *	GetNextBond (std::list< Bond * >::const_iterator &i) const
void	SetName (char const *name, char const *convention)
char const *	GetName (char const *convention=NULL)
std::string	Name ()
void	ResetIndentifiers ()
std::string const &	GetCML ()
void	ClearCycles ()
std::string const &	GetInChI ()
std::string const &	GetInChIKey ()
std::string const &	GetSMILES ()
virtual std::string	GetRawFormula () const
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
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 xmlNodePtr	Save (xmlDocPtr xml) const
virtual bool	Load (xmlNodePtr node)
virtual bool	GetCoords (double *x, double *y, double *z=NULL) const
virtual void	Move (double x, double y, double z=0.)
virtual void	Transform2D (Matrix2D &m, double x, double y)
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 bool	SetProperty (unsigned property, char const *value)
virtual std::string	GetProperty (unsigned property) const
virtual void	OnLoaded ()
void	SetDirty (bool dirty=true)
std::string	Identity ()
virtual char const *	HasPropertiesDialog () const
virtual bool	CanSelect () const
virtual void	NotifyEmpty ()
void	ShowPropertiesDialog ()
bool	GetDirty (void) const

Additional Inherited Members
Static Public Member Functions inherited from gcu::Molecule
static Molecule *	MoleculeFromFormula (Document *Doc, Formula const &formula, bool add_pseudo=true)
Protected Member Functions inherited from gcu::Object
virtual Dialog *	BuildPropertiesDialog ()
Protected Attributes inherited from gcu::Molecule
std::list< Cycle * >	m_Cycles
std::list< Chain * >	m_Chains
std::list< Atom * >	m_Atoms
std::list< Bond * >	m_Bonds

Detailed Description

Provide some uiser interface for molecules.

Definition at line 37 of file gcugtk/molecule.h.

Constructor & Destructor Documentation

gcugtk::Molecule::Molecule	(	gcu::TypeId	Type = gcu::MoleculeType,
		gcu::ContentType	ct = gcu::ContentType3D
	)

Parameters

Type	the type id of a derived class
ct	the content type for the molecule (2d or 3d), defaults to ContentType3D.

The constructor. The type id may be changed in derived classes, otherwise the argument is not needed, since the default value is enough.

Reimplemented from gcu::Molecule.

gcugtk::Molecule::Molecule	(	gcu::Atom *	pAtom,
		gcu::ContentType	ct = gcu::ContentType3D
	)

Parameters

pAtom
ct	the content type for the molecule (2d or 3d), defaults to ContentType3D.

Builds a molecule from an atom. If the atom has bonds, the connectivity will be explored and all atoms and bonds found will be added to the molecule.

Reimplemented from gcu::Molecule.

virtual gcugtk::Molecule::~Molecule ( )

virtual

The destructor.

Reimplemented from gcu::Molecule.

Reimplemented in gcp::Molecule.

Member Function Documentation

void gcugtk::Molecule::BuildDatabasesMenu	(	GtkUIManager *	UIManager,
		char const *	path,
		char const *	path_end
	)

Parameters

UIManager	a GtkUIManager.
path	the path to insert before each new action entry.
path_end	the path to insert after each new action entry.

Adds menu entry for databases access.

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

• gcugtk/molecule.h