gcp::Molecule Class Reference

GChemPaint molecule class. More...

#include <gcp/molecule.h>

Inheritance diagram for gcp::Molecule:

gcu::Molecule gcu::Object

List of all members.

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 (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


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:
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 gcu::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::AddFragment ( Fragment pFragment  ) 

Parameters:
pFragment an atoms group.
Adds a fragment to the molecule.

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

Parameters:
UIManager the GtkUIManager 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::BuildInChI (  ) 

Builds the InChI for the molecule.

void gcp::Molecule::BuildOBMol ( OpenBabel::OBMol &  Mol  ) 

Parameters:
Mol the 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:
Mol the 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:
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.

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:
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.

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:
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::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_start the first part of the URI to open.
uri_end the 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:
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:

Generated on Fri Sep 24 15:58:44 2010 for The Gnome Chemistry Utils by  doxygen 1.5.9