The Gnome Chemistry Utils  0.12.13
Public Member Functions | List of all members
gcp::Molecule Class Reference

GChemPaint molecule class. More...

#include <gcp/molecule.h>

Inheritance diagram for gcp::Molecule:
gcu::Molecule gcu::Object

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)
ObjectGetAtomAt (double x, double y, double z=0.)
double GetYAlign ()
bool BuildContextualMenu (GtkUIManager *UIManager, gcu::Object *object, double x, double y)
bool OnSignal (gcu::SignalId Signal, gcu::Object *Child)
void ExportToGhemical ()
void SelectAlignmentItem (gcu::Object *child)
std::string GetAlignmentId ()
void BuildOBMol (OpenBabel::OBMol &Mol)
void BuildOBMol2D (OpenBabel::OBMol &Mol)
void ShowInChI ()
void BuildInChI ()
void BuildSMILES ()
void ShowWebBase (char const *uri_start, char const *uri_end)
void OpenCalc ()
void CheckCrossings (Bond *pBond)
char const * GetInChI ()
std::string GetRawFormula () const
void OnLoaded ()
unsigned GetAtomsNumber () const
- Public Member Functions inherited from gcu::Molecule
 Molecule (Atom *pAtom)
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 ()
- Public Member Functions inherited from gcu::Object
 Object (TypeId Id=OtherType)
virtual ~Object ()
TypeId GetType () const
void SetId (gchar const *Id)
gchar const * GetId () const
ObjectGetMolecule () const
ObjectGetReaction () const
ObjectGetGroup () const
DocumentGetDocument () const
ObjectGetParentOfType (TypeId Id) const
ObjectGetChild (const gchar *Id) const
ObjectGetFirstChild (std::map< std::string, Object * >::iterator &i)
ObjectGetNextChild (std::map< std::string, Object * >::iterator &i)
ObjectGetDescendant (const gchar *Id) const
ObjectGetParent () const
void SetParent (Object *Parent)
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::list< Object * > &Children) throw (std::invalid_argument)
void EmitSignal (SignalId Signal)
void Lock (bool state=true)
bool IsLocked ()
ObjectGetFirstLink (std::set< Object * >::iterator &i)
ObjectGetNextLink (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
void ShowPropertiesDialog ()
bool GetDirty (void) const

Additional Inherited Members

- Static Public Member Functions inherited from gcu::Molecule
static MoleculeMoleculeFromFormula (Document *Doc, Formula const &formula, bool add_pseudo=true)
- Protected Member Functions inherited from gcu::Object
virtual DialogBuildPropertiesDialog ()
- 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 41 of file gcp/molecule.h.

Constructor & Destructor Documentation

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

The default constructor. Builds a new empty molecule.

Reimplemented from gcu::Molecule.

gcp::Molecule::Molecule ( Atom pAtom)
Parameters
pAtoman 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 gcu::Molecule.

Member Function Documentation

void gcp::Molecule::AddAtom ( gcu::Atom pAtom)
virtual
Parameters
pAtoman atom.

Adds an atom to the molecule.

Reimplemented from gcu::Molecule.

void gcp::Molecule::AddBond ( gcu::Bond pBond)
virtual
Parameters
pBonda bond.

Adds a bond to the molecule.

Reimplemented from gcu::Molecule.

void gcp::Molecule::AddChild ( gcu::Object object)
virtual
Parameters
objectthe object to add to the molecule.

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

Reimplemented from gcu::Molecule.

void gcp::Molecule::AddFragment ( Fragment pFragment)
Parameters
pFragmentan atoms group.

Adds a fragment to the molecule.

bool gcp::Molecule::BuildContextualMenu ( GtkUIManager *  UIManager,
gcu::Object object,
double  x,
double  y 
)
virtual
Parameters
UIManagerthe GtkUIManager to populate.
objectthe Object on which occured the mouse click.
xx coordinate of the mouse click.
yy 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::BuildInChI ( )

Builds the InChI for the molecule.

void gcp::Molecule::BuildOBMol ( OpenBabel::OBMol &  Mol)
Parameters
Molthe OpenBabel molecule used for export.

Builds an OpenBabel molecule from this instance. The new molecule is built trying to guess appropriate z coordinates so that stereochemistry is preserved.

void gcp::Molecule::BuildOBMol2D ( OpenBabel::OBMol &  Mol)
Parameters
Molthe OpenBabel molecule used for export.

Builds a 2D OpenBabel molecule from this instance.

void gcp::Molecule::BuildSMILES ( )

Builds the SMILES representation for the molecule and opens a new StringDlg instance displaying it.

void gcp::Molecule::CheckCrossings ( Bond pBond)
Parameters
pBonda 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.

void gcp::Molecule::ExportToGhemical ( )

Opens a Ghemical window with a copy of the molecule trying to preserve the stereochemistry as far as possible.

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
xthe x coordinate
ythe y coordinate
zthe 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.

char const* gcp::Molecule::GetInChI ( )
Returns
the InChI. The returned string should not be freed (it's a const char*). Molecules with fragments are not currently supported.
std::string gcp::Molecule::GetRawFormula ( ) const
Returns
the raw formula as a string. Molecules with fragments are not currently supported.
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
nodea 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
pMoleculea molecule.
RemoveDuplicateswhether 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
Signalthe appropriate SignalId
Childthe 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
pObjectan 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
xmlthe 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
childthe 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::ShowInChI ( )

Builds the InChI for the molecule if necessary and opens a new StringDlg instance displaying it.

void gcp::Molecule::ShowWebBase ( char const *  uri_start,
char const *  uri_end 
)
Parameters
uri_startthe first part of the URI to open.
uri_endthe last part of the URI to open.

Opens a web browser with an URI constructed from both arguments and the InChI for the molecule ntercalated between uri_start and uri_end.

void gcp::Molecule::Transform2D ( gcu::Matrix2D m,
double  x,
double  y 
)
virtual
Parameters
mthe Matrix2D of the transformation.
xthe x component of the center of the transformation.
ythe 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: