#include <atom.h>

Inheritance diagram for gcp::Atom:

Public Member Functions
	Atom ()
	Atom (int Z, double x, double y, double z)
virtual	~Atom ()
virtual void	SetZ (int Z)
void	AddBond (gcu::Bond *pBond)
void	RemoveBond (gcu::Bond *pBond)
virtual void	Update ()
int	GetTotalBondsNumber () const
int	GetAttachedHydrogens () const
HPos	GetBestSide ()
virtual gccv::Anchor	GetChargePosition (unsigned char &Pos, double Angle, double &x, double &y)
virtual int	GetAvailablePosition (double &x, double &y)
virtual bool	GetRelativePosition (double angle, double &x, double &y)
virtual bool	GetPosition (double angle, double &x, double &y)
virtual xmlNodePtr	Save (xmlDocPtr xml) const
virtual bool	Load (xmlNodePtr node)
virtual bool	LoadNode (xmlNodePtr node)
void	AddItem ()
void	SetSelected (int state)
virtual bool	AcceptNewBonds (int nb=1)
virtual bool	AcceptCharge (int charge)
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)
virtual void	AddToMolecule (Molecule *Mol)
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 ()
bool	Match (gcu::Atom *atom, gcu::AtomMatchState &state)
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 ()
virtual void	UpdateItem ()
Item *	GetItem (void)

Protected Member Functions
void	BuildSymbolGeometry (double width, double height, double ascent)
bool	SetProperty (unsigned property, char const *value)

Protected Attributes
double	m_CHeight
Protected Attributes inherited from gcu::Atom
int	m_Z
double	m_x
double	m_y
double	m_z
char	m_Charge
std::map< Atom , Bond >	m_Bonds
Protected Attributes inherited from gccv::ItemClient
Item *	m_Item

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 ()

Detailed Description

Represents atoms in GChemPaint.

Definition at line 113 of file gcp/atom.h.

Constructor & Destructor Documentation

gcp::Atom::Atom ( )

Default construtor.

Reimplemented from gcu::Atom.

gcp::Atom::Atom	(	int	Z,
		double	x,
		double	y,
		double	z
	)

Parameters

Z	the atomic number.
x	the x coordinate.
y	the y coordinate.
z	the z coordinate.

Reimplemented from gcu::Atom.

virtual gcp::Atom::~Atom ( )

virtual

The destructor.

Reimplemented from gcu::Atom.

Member Function Documentation

virtual bool gcp::Atom::AcceptCharge ( int charge )

virtual

Parameters

charge the charge that might be set.

Returns: true if the charge is acceptable.

Reimplemented in gcp::FragmentAtom.

virtual bool gcp::Atom::AcceptNewBonds ( int nb = 1 )

virtual

Parameters

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

Returns: true if the operation is allowed, false if the new bonds would exceed the maximum valence for the element.

Reimplemented in gcp::FragmentAtom.

void gcp::Atom::AddBond ( gcu::Bond * pBond )

virtual

Parameters

pBond a bond.

Adds a bond to the atom.

Reimplemented from gcu::Atom.

void gcp::Atom::AddElectron ( Electron * electron )

Parameters

electron a pointer to an Electron instance.

Adds the Electron (representing either a single electron or a pair) to the Atom.

void gcp::Atom::AddItem ( )

virtual

Used to add a representation of the atom in the view.

Reimplemented from gccv::ItemClient.

Reimplemented in gcp::FragmentAtom.

virtual void gcp::Atom::AddToMolecule ( Molecule * Mol )

virtual

Parameters

Mol,: a pointer to a molecule

Adds the atom to the molecule calling gcpMolecule::AddAtom()

Reimplemented in gcp::FragmentAtom.

bool gcp::Atom::BuildContextualMenu	(	gcu::UIManager *	UIManager,
		Object *	object,
		double	x,
		double	y
	)

Parameters

UIManager,:	the gcu::UIManager to populate.
object	the atom on which occured the mouse click.
x	x coordinate of the mouse click.
y	y coordinate of the mouse click.

This method is called to build a contextual menu for the atom.

void gcp::Atom::BuildSymbolGeometry	(	double	width,
		double	height,
		double	ascent
	)

protected

Parameters

width	the witdh of the atomic symbol.
height	the height of the atomic symbol.
ascent	the ascent of the atomic symbol.

Evaluates where lines representing bonds should end to not overload the symbol.

void gcp::Atom::ForceChanged ( )

inline

Forces an update.

Definition at line 348 of file gcp/atom.h.

int gcp::Atom::GetAttachedHydrogens ( ) const

inline

Returns: the number of implicit hydrogens lnked to the atom.

Definition at line 164 of file gcp/atom.h.

virtual int gcp::Atom::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 or electrons 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 in gcp::FragmentAtom.

HPos gcp::Atom::GetBestSide ( )

Returns: the position of the attached hydrogen atoms symbol when automatically arranged.

Bond* gcp::Atom::GetBondAtAngle ( double angle )

Parameters

angle the angle from the east direction in the trigonometric convention.

Returns: the bond at or near the direction given by angle.

int gcp::Atom::GetCharge ( ) const

inline

Returns: the current formal local charge.

Definition at line 344 of file gcp/atom.h.

References gcu::Atom::m_Charge.

gcp::Atom::GetChargeItem ( void )

inline

Returns: the gccv::Item used to represent the formal charge of the atom.

Definition at line 503 of file gcp/atom.h.

virtual gccv::Anchor gcp::Atom::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 in gcp::FragmentAtom.

char gcp::Atom::GetChargePosition	(	double *	Angle,
		double *	Dist
	)		const

Parameters

Angle	where to store the angle from east direction in the trigonometric convention.
Dist	where to store the distance from the center of the atom.

Returns: the charge position as one of POSITION_E, POSITION_N,...

gcp::Atom::GetHPosStyle ( void ) const

inline

Returns: the position of attached hydrogen atoms symbol.

Definition at line 491 of file gcp/atom.h.

Bond* gcp::Atom::GetNewmanBond ( ) const

Returns: the axial bond in a Newman projection if the atom has one. If the atom has more than one (as in an allene) one of them is returned.

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

virtual

Parameters

angle	the angle at which a charge sign or an electron 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 in gcp::FragmentAtom.

gcp::Atom::GetRefHPosStyle ( void )

inline

Returns: the position of attached hydrogen atoms symbol as a reference.

Definition at line 491 of file gcp/atom.h.

gcp::Atom::GetRefShowSymbol ( void )

inline

Returns: whether the symbol of a carbon atom is displayed or not as a reference.

Definition at line 478 of file gcp/atom.h.

virtual bool gcp::Atom::GetRelativePosition	(	double	angle,
		double &	x,
		double &	y
	)

virtual

Parameters

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

Updates x and y so that they become the position corresponding to the angle when the position is available, the origin being the position of the atom.

Returns: true on success, false otherwise.

gcp::Atom::GetShowCharge ( void ) const

inline

Returns: whether the local charge is displayed.; whether the local charge is displayed as a reference.

Definition at line 515 of file gcp/atom.h.

gcp::Atom::GetShowSymbol ( void ) const

inline

Returns: whether the symbol of a carbon atom is displayed or not.

Definition at line 478 of file gcp/atom.h.

void gcp::Atom::GetSymbolGeometry	(	double &	width,
		double &	height,
		double &	angle,
		bool	up
	)		const

Parameters

width	where to store the width.
height	where to store the height.
angle	where to store the limit angle.
up	whether considering the top half or the bottom half

Used to retrieve the size of the ink rectangle of the atom symbol (if displayed). angle is absolute value of the angle between an horizontal line and the line joining the center and the top left or the bottom left vertex. The returned width value is actually half the full width. Height is the height. This method is used to avoid bonds lines extending over their atoms symbols.

int gcp::Atom::GetTotalBondsNumber ( ) const

Returns: the bonds number for this atom taking bond order into account

virtual double gcp::Atom::GetYAlign ( )

virtual

Returns: the y coordinate at half height of the atom symbol if it was carbon.

Reimplemented from gcu::Object.

bool gcp::Atom::HasAvailableElectrons ( bool paired )

Parameters

paired whether to ask for a pair of electrons or a single electron.

Returns: true if non-bonding valence electrons are available.

bool gcp::Atom::HasImplicitElectronPairs ( )

Returns: true if the atom has implicit electron pairs, false otherwise.

bool gcp::Atom::HasStereoBond ( ) const

Returns: true if the bond is a stereocenter.

virtual bool gcp::Atom::Load ( xmlNodePtr node )

virtual

Parameters

node	a pointer to the xmlNode containing the serialized atom.

Used to load an atom in memory. The Atom must already exist.

Returns: true on succes, false otherwise.

Reimplemented from gcu::Atom.

Reimplemented in gcp::FragmentAtom, and gcp::FragmentResidue.

virtual bool gcp::Atom::LoadNode ( xmlNodePtr node )

virtual

Parameters

node	a pointer to the xmlNode containing the serialized Atom.

Used in this class to correctly set the atomic number.

Reimplemented from gcu::Atom.

bool gcp::Atom::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.

Returns: true if the atoms match, false otherwise.

Reimplemented from gcu::Atom.

Reimplemented in gcp::FragmentAtom.

bool gcp::Atom::MayHaveImplicitUnpairedElectrons ( )

Returns: true if the atom has implcit electrons that might be unpaired.

virtual void gcp::Atom::Move	(	double	x,
		double	y,
		double	z = `0.`
	)

virtual

Parameters

x	the x component of the transation vector.
y	the y component of the transation vector.
z	the z component of the transation vector.

Used to move an Atom.

Reimplemented from gcu::Atom.

void gcp::Atom::NotifyPositionOccupation	(	unsigned char	pos,
		bool	occupied
	)

Parameters

pos	one of POSITION_E, POSITION_N,...
occupied	true if occupied, false otherwise.

Notifies if a position is occupied or not.

void gcp::Atom::RemoveBond ( gcu::Bond * pBond )

virtual

Parameters

pBond a bond.

Removes a bond from the atom.

Reimplemented from gcu::Atom.

void gcp::Atom::RemoveElectron ( Electron * electron )

Parameters

electron a pointer to an Electron instance.

Removes the Electron (representing either a single electron or a pair) from the Atom.

virtual xmlNodePtr gcp::Atom::Save ( xmlDocPtr xml ) const

virtual

Parameters

xml	the xmlDoc used to save the document.

Used to save the Atom to the xmlDoc.

Returns: the xmlNode containing the serialized atom.

Reimplemented from gcu::Atom.

Reimplemented in gcp::FragmentAtom, and gcp::FragmentResidue.

void gcp::Atom::SetCharge ( int charge )

Parameters

charge the charge to set.

Sets the formal local charge of an atom.

gcp::Atom::SetChargeItem ( gccv::Item * item )

inline

Parameters

item	a gccv::Item.

Sets the gccv::Item used to represent the formal charge of the atom, might be NULL.

Definition at line 503 of file gcp/atom.h.

void gcp::Atom::SetChargePosition	(	unsigned char	Pos,
		bool	def,
		double	angle = `0.`,
		double	distance = `0.`
	)

Parameters

Pos	one of POSITION_E, POSITION_N,...
def	true if the position is automatic.
angle	the angle from the east direction in the trigonometric convention.
distance	the distance from the center of the atom, or 0. if automatic.

Sets the relative position of a charge sign.

gcp::Atom::SetHPosStyle ( HPos val )

inline

Parameters

val	the new position.

Sets the position of attached hydrogen atoms symbol.

Definition at line 491 of file gcp/atom.h.

bool gcp::Atom::SetProperty	(	unsigned	property,
		char const *	value
	)

protectedvirtual

Parameters

property	the identity of the property as defined in objprops.h.
value	the value of the property as a string.

Used by the gcu::Loader mechanism to load properties of atoms.

Returns: true on success.

Reimplemented from gcu::Atom.

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

virtual

Parameters

state the selection state of the atom.

Used to set the selection state of the atom inside the widget. The values of state might be gcp::SelStateUnselected, gcp::SelStateSelected, gcp::SelStateUpdating, or gcp::SelStateErasing.

Reimplemented from gccv::ItemClient.

Reimplemented in gcp::FragmentAtom.

gcp::Atom::SetShowCharge ( bool show )

inline

Parameters

show	whether to display the local charge.

Shows or hides the atom local charge.

Definition at line 515 of file gcp/atom.h.

gcp::Atom::SetShowSymbol ( bool ShowSymbol )

inline

Parameters

ShowSymbol whether the symbol of a carbon atom is to be displayed or not.

Sets the visibility of a carbon atom symbol in a chain.

Definition at line 478 of file gcp/atom.h.

virtual void gcp::Atom::SetZ ( int Z )

virtual

Parameters

Z	the new atomic number.

Changes the atomic number of the atom.

Reimplemented from gcu::Atom.

Reimplemented in gcp::FragmentAtom.

virtual void gcp::Atom::Transform2D	(	gcu::Matrix2D &	m,
		double	x,
		double	y
	)

virtual

Parameters

m	the Matrix2D of the transformation.
x	the x component of the center of the transformation.
y	the y component of the center of the transformation.

Used to move and/or transform an object.

Reimplemented from gcu::Atom.

virtual void gcp::Atom::Update ( )

virtual

Updates the atom after changing its bonds, charge or explicit electrons.

Reimplemented in gcp::FragmentAtom.

bool gcp::Atom::UpdateStereoBonds ( )

Infers which bonds should be displayed as stereobonds given the known parity and molecular structure.

Member Data Documentation

double gcp::Atom::m_CHeight

protected

Half the height of the "C" character.

Definition at line 465 of file gcp/atom.h.

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

gcp/atom.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation