#include <gcu/chain.h>

Inheritance diagram for gcu::Chain:

Public Member Functions
	Chain (Bond pBond, Atom pAtom=NULL, TypeId Type=ChainType)
	Chain (Molecule molecule, Bond pBond, TypeId Type=ChainType)
	Chain (Molecule molecule, Atom pAtom, TypeId Type=ChainType)
virtual	~Chain ()
void	FindCycles (Atom *pAtom)
bool	FindCycle (Atom pAtom, Bond pBond)
virtual void	Erase (Atom pAtom1, Atom pAtom2)
virtual void	Insert (Atom pAtom1, Atom pAtom2, Chain &chain)
void	Extract (Atom pAtom1, Atom pAtom2, Chain &chain)
void	Reverse ()
void	AddBond (Atom start, Atom end)
unsigned	GetUnsaturations ()
unsigned	GetHeteroatoms ()
bool	Contains (Atom *pAtom)
bool	Contains (Bond *pBond)
unsigned	GetLength ()
double	GetMeanBondLength ()
Atom *	GetNextAtom (Atom *pAtom)
std::string	Name ()
unsigned	BuildLength (unsigned cycle_size=NULL, unsigned cycle_pos=NULL)
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)
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 Object *	GetAtomAt (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 ()
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
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

Protected Attributes
std::map< Atom *, ChainElt >	m_Bonds
Molecule *	m_Molecule

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 gcu::Object
virtual Dialog *	BuildPropertiesDialog ()

Detailed Description

This class is used to represent chains of atoms.

Definition at line 59 of file chain.h.

Constructor & Destructor Documentation

gcu::Chain::Chain	(	Bond *	pBond,
		Atom *	pAtom = `NULL`,
		TypeId	Type = `ChainType`
	)

Parameters

pBond	a bond.
pAtom	an atom.
Type	an optional type id used when constructing a derived type (i. e. a cycle).

Constructs a Chain starting from a bond and an optional atom. Choosing the atom forces the direction of the chain, otherwise, the first atom will be the first atom of the bond.

gcu::Chain::Chain	(	Molecule *	molecule,
		Bond *	pBond,
		TypeId	Type = `ChainType`
	)

Parameters

molecule	a molecule.
pBond	a bond in the molecule or NULL.
Type	an optional type id used when constructing a derived type

Explores a molecule and find all cycles, starting from pBond or an empty chain if pBond is NULL.

gcu::Chain::Chain	(	Molecule *	molecule,
		Atom *	pAtom,
		TypeId	Type = `ChainType`
	)

Parameters

molecule	a molecule.
pAtom	an atom in the molecule.
Type	an optional type id used when constructing a derived type

Explores a molecule and find all cycles, starting from pAtom or an empty chain if pAtom is NULL.

virtual gcu::Chain::~Chain ( )

virtual

The destructor.

Member Function Documentation

void gcu::Chain::AddBond	(	Atom *	start,
		Atom *	end
	)

Parameters

start	an atom.
end	an atom.

Adds the two atoms and the bond between them to the chain. The two atoms must be bonded.

unsigned gcu::Chain::BuildLength	(	unsigned *	cycle_size = `NULL`,
		unsigned *	cycle_pos = `NULL`
	)

Parameters

cycle_size	where to store a cycle size if a cycle is encountered
cycle_pos	where to store a cycle position if a cycle is encountered

Finds the longest chani starting from first bond and ending when a cycle is found or at the chain end.

Returns: the evaluated chain length.

bool gcu::Chain::Contains ( Atom * pAtom )

Parameters

pAtom an atom.

Returns: true if pAtom is in the chain.

bool gcu::Chain::Contains ( Bond * pBond )

Parameters

pBond a bond.

Returns: true if pBond is in the chain.

virtual void gcu::Chain::Erase	(	Atom *	pAtom1,
		Atom *	pAtom2
	)

virtual

Parameters

pAtom1	an atom in the source chain.
pAtom2	an atom in the source chain.

Erases a sub-chain. One of the atoms must already be one of the chain ends.

Reimplemented in gcu::Cycle.

void gcu::Chain::Extract	(	Atom *	pAtom1,
		Atom *	pAtom2,
		Chain &	chain
	)

Parameters

pAtom1	an atom in the chain.
pAtom2	an atom in the chain.
chain	the target chain.

Extracts a sub-chain to the chain variable which should be empty before the call.

bool gcu::Chain::FindCycle	(	Atom *	pAtom,
		Bond *	pBond
	)

Parameters

pAtom	an atom.
pBond	a bond.

Searches for a cycle containing the atom pAtom and the bond pBond. pAtom must be one of the ends of pBond. If a cycle is found, it is added to the molecule cycles list.

Returns: true on success, false otherwise.

void gcu::Chain::FindCycles ( Atom * pAtom )

Parameters

pAtom an atom.

Searches all cycles in a molecule starting from Atom pAtom. Found cycles are added to the molecule cycles list.

unsigned gcu::Chain::GetHeteroatoms ( )

Returns: the number of heteroatoms in the chain.

unsigned gcu::Chain::GetLength ( )

Returns: the number of bonds in the chain

double gcu::Chain::GetMeanBondLength ( )

Returns: the mean bond length in the chain.

Atom* gcu::Chain::GetNextAtom ( Atom * pAtom )

Parameters

pAtom an atom in the chain.

Returns: the next atom in the chain or NULL if pAtom is the last one.

unsigned gcu::Chain::GetUnsaturations ( )

Returns: the number of multiple bonds in the chain so not really the unsaturations number.

virtual void gcu::Chain::Insert	(	Atom *	pAtom1,
		Atom *	pAtom2,
		Chain &	chain
	)

virtual

Parameters

pAtom1	an atom in the source chain.
pAtom2	an atom in the source chain.
chain	the source chain.

Inserts a chain. One of the atoms must already be in the target chain.

Reimplemented in gcu::Cycle.

std::string gcu::Chain::Name ( )

virtual

Returns: the localized object generic name.

Reimplemented from gcu::Object.

Reimplemented in gcu::Cycle.

void gcu::Chain::Reverse ( )

Reverses the chain order.

Member Data Documentation

std::map<Atom*, ChainElt> gcu::Chain::m_Bonds

protected

The gcu::ChainElt elements in the chain indexed by their common atom.

Definition at line 201 of file chain.h.

Molecule* gcu::Chain::m_Molecule

protected

The molecule which owns the chain.

Definition at line 205 of file chain.h.

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

chain.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation