The Gnome Chemistry Utils  0.14.12
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
 Molecule (TypeId Type=MoleculeType, ContentType ct=ContentType3D)
 
 Molecule (Atom *pAtom, ContentType ct=ContentType3D)
 
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)
 
- 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 ObjectCreateObject (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 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.

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.

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: