GChemPaint molecule class. More...

#include <gcp/molecule.h>

Inheritance diagram for gcp::Molecule:

Public Member Functions
	Molecule (gcu::TypeId Type=gcu::MoleculeType)
	Molecule (Atom *pAtom)
virtual	~Molecule ()
void	AddChild (gcu::Object *object)
void	AddAtom (gcu::Atom *pAtom)
void	AddFragment (Fragment *pFragment)
void	AddBond (gcu::Bond *pBond)
void	Remove (gcu::Object *pObject)
bool	Merge (Molecule *pMolecule, bool RemoveDuplicates=false)
bool	Load (xmlNodePtr node)
xmlNodePtr	Save (xmlDocPtr xml) const
void	Clear ()
void	Transform2D (gcu::Matrix2D &m, double x, double y)
Object *	GetAtomAt (double x, double y, double z=0.)
double	GetYAlign ()
bool	BuildContextualMenu (gcu::UIManager UIManager, gcu::Object object, double x, double y)
bool	OnSignal (gcu::SignalId Signal, gcu::Object *Child)
void	SelectAlignmentItem (gcu::Object *child)
std::string	GetAlignmentId ()
void	OpenCalc ()
void	CheckCrossings (Bond *pBond)
std::string	GetRawFormula () const
void	OnLoaded ()
unsigned	GetAtomsNumber () const
double	GetMeanBondLength () const
void	AddChiralAtom (Atom *atom)
bool	AtomIsChiral (Atom *atom) const
Public Member Functions inherited from gcugtk::Molecule
	Molecule (gcu::TypeId Type=gcu::MoleculeType, gcu::ContentType ct=gcu::ContentType3D)
	Molecule (gcu::Atom *pAtom, gcu::ContentType ct=gcu::ContentType3D)
void	BuildDatabasesMenu (GtkUIManager UIManager, char const path, char const *path_end)
Public Member Functions inherited from gcu::Molecule
void	UpdateCycles (Bond *pBond)
void	UpdateCycles ()
bool	operator== (Molecule const &molecule) const
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 ()
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 bool	GetCoords (double x, double y, double *z=NULL) const
virtual void	Move (double x, double y, double z=0.)
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 bool	Build (std::set< Object * > const &Children) throw (std::invalid_argument)
void	EmitSignal (SignalId Signal)
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
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

GChemPaint molecule class.

Definition at line 45 of file gcp/molecule.h.

Constructor & Destructor Documentation

gcp::Molecule::Molecule ( gcu::TypeId Type = gcu::MoleculeType )

The default constructor. Builds a new empty molecule.

gcp::Molecule::Molecule ( Atom * pAtom )

Parameters

pAtom an atom.

Constructs a new molecule containing pAtom and all atoms which might be bonded to it, and the corresponding bonds.

virtual gcp::Molecule::~Molecule ( )

virtual

The destructor.

Reimplemented from gcugtk::Molecule.

Member Function Documentation

void gcp::Molecule::AddAtom ( gcu::Atom * pAtom )

virtual

Parameters

pAtom an atom.

Adds an atom to the molecule.

Reimplemented from gcu::Molecule.

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

virtual

Parameters

pBond a bond.

Adds a bond to the molecule.

Reimplemented from gcu::Molecule.

void gcp::Molecule::AddChild ( gcu::Object * object )

virtual

Parameters

object the object to add to the molecule.

Adds an object (atom, bond, or fragment) to the molecule.

Reimplemented from gcu::Molecule.

void gcp::Molecule::AddChiralAtom ( Atom * atom )

inline

Parameters

atom	a chiral atom

Adds atom to the list of chiral atoms.

Definition at line 214 of file gcp/molecule.h.

void gcp::Molecule::AddFragment ( Fragment * pFragment )

Parameters

pFragment an atoms group.

Adds a fragment to the molecule.

bool gcp::Molecule::AtomIsChiral ( Atom * atom ) const

Parameters

atom an atom

Returns: true if atom is a chirality center.

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

virtual

Parameters

UIManager	the gcu::UIManager to populate.
object	the Object 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 the contextual menu for the molecule.

Returns: true if something is added to the UIManager, false otherwise.

Reimplemented from gcu::Object.

void gcp::Molecule::CheckCrossings ( Bond * pBond )

Parameters

pBond a bond in the molecule.

Checks if any other bond in the molecule crosses pBond, and notify both bonds that they are crossing.

void gcp::Molecule::Clear ( )

virtual

Removes all children from the molecule, resulting in a empty molecule.

Reimplemented from gcu::Molecule.

std::string gcp::Molecule::GetAlignmentId ( )

inline

Returns: the id string of the child used for alignment if any, or an empty string.

Definition at line 176 of file gcp/molecule.h.

References gcu::Object::GetId().

Object* gcp::Molecule::GetAtomAt	(	double	x,
		double	y,
		double	z = `0.`
	)

virtual

Parameters

x	the x coordinate
y	the y coordinate
z	the z coordinate (not used)

Returns: a pointer to n atom at or near position defined by the coordinates passed as parameters or NULL if none is found in the molecule.

Reimplemented from gcu::Object.

unsigned gcp::Molecule::GetAtomsNumber ( ) const

virtual

Returns: the number of atoms in the molecule. Atoms groups are counted for one only, whatever their real atomic composition.

Reimplemented from gcu::Molecule.

double gcp::Molecule::GetMeanBondLength ( ) const

Returns: the mean of the bond lengths for the molecule.

std::string gcp::Molecule::GetRawFormula ( ) const

virtual

Returns: the raw formula as a string. Molecules with fragments are not currently supported.

Reimplemented from gcu::Molecule.

double gcp::Molecule::GetYAlign ( )

virtual

Used to retrieve the y coordinate for alignment.

Returns: y coordinate used for the molecule alignment.

Reimplemented from gcu::Object.

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

virtual

Parameters

node	a pointer to the xmlNode containing the serialized molecule.

Used to load a molecule in memory. The Mlecule instance must already exist.

Returns: true on succes, false otherwise.

Reimplemented from gcu::Object.

bool gcp::Molecule::Merge	(	Molecule *	pMolecule,
		bool	RemoveDuplicates = `false`
	)

Parameters

pMolecule	a molecule.
RemoveDuplicates	whether duplicate atoms should be unififed or not.

Adds all children from pMolecule in this instance, and removes one of the atoms for each pair of duplicates (atoms with same atomic number and position) if RemoveDuplicates is true. This might fail when it would end with hypervalent atoms. On success pMolecule is deleted.

Returns: true on success, false otherwise.

void gcp::Molecule::OnLoaded ( )

virtual

Updates all cycles after loading.

Reimplemented from gcu::Object.

bool gcp::Molecule::OnSignal	(	gcu::SignalId	Signal,
		gcu::Object *	Child
	)

virtual

Parameters

Signal	the appropriate SignalId
Child	the child which emitted the signal or NULL

Signals the molecule that at least one of its children changed.

Returns: true to propagate the signal to the parent.

Reimplemented from gcu::Object.

void gcp::Molecule::OpenCalc ( )

Opens GChemCalc with the formula for the molecule. Molecules with fragments are not currently supported.

void gcp::Molecule::Remove ( gcu::Object * pObject )

virtual

Parameters

pObject an atom, a bond, or a fragment in the molecule.

Removes an atom, a bond, or a fragment from a molecule.

Reimplemented from gcu::Molecule.

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

virtual

Parameters

xml	the xmlDoc used to save the document.

Used to save the molecule to the xmlDoc.

Returns: the xmlNode containing the serialized molecule.

Reimplemented from gcu::Object.

void gcp::Molecule::SelectAlignmentItem ( gcu::Object * child )

Parameters

child the child used for alignment.

Selects the child used for alignment, which might be an atom or group of atoms, or a bond. For bonds, the center of the bonds is used, a while for the others a call to their gcu::Object::GetYAlign() method will be used.

void gcp::Molecule::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 the molecule taking care of hydrogen atoms positions around heteroatoms.

Reimplemented from gcu::Object.

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

gcp/molecule.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation