#include <gcp/fragment-residue.h>

Inheritance diagram for gcp::FragmentResidue:

Public Member Functions
	FragmentResidue ()
	FragmentResidue (Fragment fragment, char const symbol)
virtual	~FragmentResidue ()
xmlNodePtr	Save (xmlDocPtr xml) const
bool	Load (xmlNodePtr node)
void	SetResidue (Residue const res, char const symbol=NULL)
const gchar *	GetSymbol () const
Residue const *	GetResidue (void) const
std::string	GetAbbrev (void) const
Public Member Functions inherited from gcp::FragmentAtom
	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)
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 ()
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 a residue inside a atoms group (see gcp::Fragment class).

Definition at line 38 of file fragment-residue.h.

Constructor & Destructor Documentation

gcp::FragmentResidue::FragmentResidue ( )

The default constructor.

gcp::FragmentResidue::FragmentResidue	(	Fragment *	fragment,
		char const *	symbol
	)

Parameters

fragment	the fragment containing the residue symbol.
symbol	the residue symbol.

Constructs a FragmentResidue as a child of fragment.

virtual gcp::FragmentResidue::~FragmentResidue ( )

virtual

The destructor.

Member Function Documentation

gcp::FragmentResidue::GetAbbrev ( void ) const

inline

Returns: the used symbol for the residue.

Definition at line 90 of file fragment-residue.h.

gcp::FragmentResidue::GetResidue ( void ) const

inline

Returns: the associated residue.

Definition at line 86 of file fragment-residue.h.

const gchar* gcp::FragmentResidue::GetSymbol ( ) const

virtual

Returns: the symbol of this Residue.

Reimplemented from gcu::Atom.

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

virtual

Parameters

node	an XML node.

Loads the symbol and associated resdue from node.

Returns: true on success, false otherwise.

Reimplemented from gcp::FragmentAtom.

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

virtual

Parameters

xml	the xmlDoc used to save the document.

Builds an XML node representing this instance.

Returns: the new XML node or NULL on error.

Reimplemented from gcp::FragmentAtom.

void gcp::FragmentResidue::SetResidue	(	Residue const *	res,
		char const *	symbol = `NULL`
	)

Parameters

res	the residue corresponding to the symbol.
symbol	the symbol to use, or NULL to use the default symbol.

Sets the associated residue.

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

fragment-residue.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation