The Gnome Chemistry Utils  0.14.0
Public Member Functions | List of all members
gcugtk::Molecule Class Reference

#include <gcugtk/molecule.h>

Inheritance diagram for gcugtk::Molecule:
gcu::Molecule gcu::Object gcp::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
ObjectGetMolecule () const
ObjectGetReaction () const
ObjectGetGroup () const
DocumentGetDocument () const
ApplicationGetApplication () const
ObjectGetParentOfType (TypeId Id) const
ObjectGetChild (const gchar *Id) const
ObjectGetFirstChild (std::map< std::string, Object * >::iterator &i)
ObjectGetNextChild (std::map< std::string, Object * >::iterator &i)
ObjectGetDescendant (const char *Id) const
ObjectGetParent () 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 ObjectGetAtomAt (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 ()
ObjectGetFirstLink (std::set< Object * >::iterator &i)
ObjectGetNextLink (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 MoleculeMoleculeFromFormula (Document *Doc, Formula const &formula, bool add_pseudo=true)
- Protected Member Functions inherited from gcu::Object
virtual DialogBuildPropertiesDialog ()
- 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
Typethe type id of a derived class
ctthe 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
ctthe 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
UIManagera GtkUIManager.
paththe path to insert before each new action entry.
path_endthe path to insert after each new action entry.

Adds menu entry for databases access.


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