#include <gcu/molecule.h>

Inheritance diagram for gcu::Molecule:

Public Member Functions
	Molecule (TypeId Type=MoleculeType, ContentType ct=ContentType3D)
	Molecule (Atom *pAtom, ContentType ct=ContentType3D)
virtual	~Molecule ()
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
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)
std::string	Identity ()
virtual char const *	HasPropertiesDialog () const
virtual bool	CanSelect () const
virtual void	NotifyEmpty ()
void	ShowPropertiesDialog ()
bool	GetDirty (void) const

Static Public Member Functions
static Molecule *	MoleculeFromFormula (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 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 Attributes
std::list< Cycle * >	m_Cycles
std::list< Chain * >	m_Chains
std::list< Atom * >	m_Atoms
std::list< Bond * >	m_Bonds

Additional Inherited Members
Protected Member Functions inherited from gcu::Object
virtual Dialog *	BuildPropertiesDialog ()

Detailed Description

Represents molecules.

Definition at line 43 of file gcu/molecule.h.

Constructor & Destructor Documentation

gcu::Molecule::Molecule	(	TypeId	Type = `MoleculeType`,
		ContentType	ct = `ContentType3D`
	)

Parameters

Type	the type id of a derived class
ct	the 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.

Reimplemented in gcugtk::Molecule.

gcu::Molecule::Molecule	(	Atom *	pAtom,
		ContentType	ct = `ContentType3D`
	)

Parameters

pAtom
ct	the 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.

Reimplemented in gcugtk::Molecule.

virtual gcu::Molecule::~Molecule ( )

virtual

The destructor.

Reimplemented in gcp::Molecule, and gcugtk::Molecule.

Member Function Documentation

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

virtual

Parameters

pAtom an atom.

Adds an atom to the molecule.

Reimplemented in gcp::Molecule.

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

virtual

Parameters

pBond a bond.

Adds a bond to the molecule.

Reimplemented in gcp::Molecule.

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

virtual

Parameters

object an object, generally an atom or a bond.

Adds an object (which might be an atom or a bond) to the molecule.

Reimplemented from gcu::Object.

Reimplemented in gcp::Molecule.

void gcu::Molecule::Clear ( )

virtual

Clears cycles and chains and call gcu::Object::Clear().

Reimplemented from gcu::Object.

Reimplemented in gcp::Molecule.

void gcu::Molecule::ClearCycles ( )

Clears all information related to cycles.

virtual unsigned gcu::Molecule::GetAtomsNumber ( ) const

inlinevirtual

Returns: the number of atoms in the molecule.

Reimplemented in gcp::Molecule.

Definition at line 113 of file gcu/molecule.h.

References m_Atoms.

Referenced by gcu::Chem3dDoc::IsEmpty().

std::string const& gcu::Molecule::GetCML ( )

Returns: a CML representation of the molecule.

Atom const* gcu::Molecule::GetFirstAtom ( std::list< Atom * >::const_iterator & i ) const

Parameters

i	an uninitialized iterator.

Returns: the first atom of the molecule.

Bond const* gcu::Molecule::GetFirstBond ( std::list< Bond * >::const_iterator & i ) const

Parameters

i	an uninitialized iterator.

Returns: the first bond of the molecule.

std::string const& gcu::Molecule::GetInChI ( )

Returns: the InChI.

std::string const& gcu::Molecule::GetInChIKey ( )

Returns: the InChIKey.

char const* gcu::Molecule::GetName ( char const * convention = NULL )

Parameters

convention a naming convention.

Returns: the molecule name using convention if known.

Atom const* gcu::Molecule::GetNextAtom ( std::list< Atom * >::const_iterator & i ) const

Parameters

i	an iterator initialized by a call to GetFirstAtom().

Returns: the next atom of the molecule or NULL if all atoms have been previously returned.

Bond const* gcu::Molecule::GetNextBond ( std::list< Bond * >::const_iterator & i ) const

Parameters

i	an iterator initialized by a call to GetFirstBond().

Returns: the next bond of the molecule or NULL if all bonds have been previously returned.

virtual std::string gcu::Molecule::GetRawFormula ( ) const

virtual

Returns: the raw formula as a string.

Reimplemented in gcp::Molecule.

std::string const& gcu::Molecule::GetSMILES ( )

Returns: the canonical SMILES for the molecule.

static Molecule* gcu::Molecule::MoleculeFromFormula	(	Document *	Doc,
		Formula const &	formula,
		bool	add_pseudo = `true`
	)

static

Parameters

Doc	a document.
formula	a formula
add_pseudo	tells if a pseudo atom (with Z = 0) has to be added (used when building a gcu::Residue instance).

Tries to build a molecule from a formula, adding bonds between atoms. Atoms coordinates are not calculated.

Returns: a molecule on success or NULL.

std::string gcu::Molecule::Name ( )

virtual

Returns: the localized object generic name.

Reimplemented from gcu::Object.

bool gcu::Molecule::operator== ( Molecule const & molecule ) const

Parameters

molecule a molecule.

Returns: true if the molecules have identical atoms and the connection framework between the atoms.

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

virtual

Parameters

pObject an atom or a bond in the molecule.

Removes an atom or a bond from a molecule.

Reimplemented in gcp::Molecule.

void gcu::Molecule::ResetIndentifiers ( )

Reinitialize all chemical identifiers for the molecule (InChI, InChIKey, and SMILES

void gcu::Molecule::SetName	(	char const *	name,
		char const *	convention
	)

Returns: the localized object generic name.

Parameters

name	a name.
convention	a naming convention, might be NULL.

Adds a molecule name following convention. Only one name can be stored for a given convention.

void gcu::Molecule::UpdateCycles ( Bond * pBond )

Parameters

pBond a bond in the molecule.

Updates the cycles list after a change, starting the exploration from pBond.

void gcu::Molecule::UpdateCycles ( )

Updates the cycles list after a change.

Member Data Documentation

std::list<Atom*> gcu::Molecule::m_Atoms

protected

The atoms in the molecule.

Definition at line 224 of file gcu/molecule.h.

Referenced by GetAtomsNumber().

std::list<Bond*> gcu::Molecule::m_Bonds

protected

The bonds in the molecule.

Definition at line 228 of file gcu/molecule.h.

std::list<Chain*> gcu::Molecule::m_Chains

protected

The non cyclic chains contained in the molecules (not used at the moment).

Definition at line 220 of file gcu/molecule.h.

std::list<Cycle*> gcu::Molecule::m_Cycles

protected

The cycles contained in the molecules.

Definition at line 216 of file gcu/molecule.h.

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

gcu/molecule.h

Public Member Functions

Static Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation