The Gnome Chemistry Utils  0.14.15
Public Types | Public Member Functions | List of all members
gcp::Fragment Class Reference

Atoms groups. More...

#include <gcp/fragment.h>

Inheritance diagram for gcp::Fragment:
gcp::TextObject gcu::Object gccv::TextClient gccv::ItemClient

Public Types

enum  Validity { Invalid, Valid, Valid2D, Valid3D }
 The validity state of a Fragment as it is currently evaluated by the framework. The 0.12.x version don't do anything useful with it and all Fragment instances are invalid. More...
 
enum  FragmentMode {
  AutoMode, NormalMode, SubscriptMode, SuperscriptMode,
  ChargeMode, StoichiometryMode
}
 Edition mode. More...
 

Public Member Functions

 Fragment ()
 
 Fragment (double x, double y)
 
virtual ~Fragment ()
 
void AddItem ()
 
void UpdateItem ()
 
void SetSelected (int state)
 
xmlNodePtr Save (xmlDocPtr xml) const
 
xmlNodePtr SaveSelection (xmlDocPtr xml) const
 
bool Load (xmlNodePtr node)
 
bool OnChanged (bool save)
 
void AnalContent ()
 
void AnalContent (unsigned start, unsigned &end)
 
ObjectGetAtomAt (double x, double y, double z=0.)
 
void Move (double x, double y, double z=0)
 
void Transform2D (gcu::Matrix2D &m, double x, double y)
 
void OnChangeAtom ()
 
AtomGetAtom ()
 
int GetElementAtPos (unsigned start, unsigned &end)
 
gccv::Anchor GetChargePosition (FragmentAtom *pAtom, unsigned char &Pos, double Angle, double &x, double &y)
 
int GetAvailablePosition (double &x, double &y)
 
bool GetPosition (double angle, double &x, double &y)
 
bool Validate ()
 
double GetYAlign ()
 
bool SetProperty (unsigned property, char const *value)
 
std::string GetProperty (unsigned property) const
 
bool Analyze ()
 
bool Update ()
 
gccv::ItemGetChargeItem ()
 
std::string Name ()
 
bool GetCoords (double *x, double *y, double *z=NULL) const
 
Validity GetValid (void) const
 
void SetMode (FragmentMode val)
 
FragmentMode GetMode (void) const
 
FragmentModeGetRefMode (void)
 
- Public Member Functions inherited from gcp::TextObject
 TextObject (gcu::TypeId Type)
 
 TextObject (double x, double y, gcu::TypeId Type)
 
virtual ~TextObject ()
 
void GetSize (double &x, double &y)
 
xmlNodePtr SaveSelected ()
 
void LoadSelected (xmlNodePtr node)
 
bool SaveNode (xmlDocPtr xml, xmlNodePtr node) const
 
bool Load (xmlNodePtr node)
 
void Move (double x, double y, double z=0)
 
bool IsLocked ()
 
void GetSelectionBounds (unsigned &start, unsigned &end)
 
std::string GetBuffer ()
 
void SelectionChanged (unsigned start, unsigned end)
 
void TextChanged (unsigned pos)
 
gccv::TextTagList GetTagList (void)
 
void SetEditor (TextEditor *val)
 
TextEditorGetEditor (void) const
 
TextEditor *& GetRefEditor (void)
 
gccv::TextGetTextItem (void)
 
- 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)
 
ObjectGetMolecule () const
 
ObjectGetReaction () const
 
ObjectGetGroup () const
 
DocumentGetDocument () const
 
ApplicationGetApplication () 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 char *Id) const
 
ObjectGetParent () const
 
void SetParent (Object *Parent)
 
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)
 
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 ()
 
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 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
 
- Public Member Functions inherited from gccv::TextClient
 TextClient ()
 
virtual ~TextClient ()
 
virtual void InterlineChanged (G_GNUC_UNUSED double interline)
 
virtual void JustificationChanged (G_GNUC_UNUSED GtkJustification justification)
 
- Public Member Functions inherited from gccv::ItemClient
 ItemClient ()
 
virtual ~ItemClient ()
 
ItemGetItem (void)
 

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 ObjectCreateObject (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 DialogBuildPropertiesDialog ()
 
- Protected Attributes inherited from gcp::TextObject
double m_x
 
double m_y
 
double m_length
 
double m_height
 
int m_ascent
 
int m_InsertOffset
 
std::string m_buf
 
bool m_bLoading
 
unsigned m_StartSel
 
unsigned m_EndSel
 
bool m_RealSave
 
gccv::TextTagList m_TagList
 
gccv::Textm_TextItem
 
- Protected Attributes inherited from gccv::ItemClient
Itemm_Item
 

Detailed Description

Atoms groups.

Represents atoms groups displayed as a string. Currntly, the string is not fully parsed, so that some non sense strings might be accepted. Anyway, this will not always be the case in the future.

Definition at line 109 of file fragment.h.

Member Enumeration Documentation

§ FragmentMode

Edition mode.

Current edition mode for the fragment. Used to know how inserted symbolds need to be interpreted.

Enumerator
AutoMode 

Automatic mode, try to guess what each new symbol represent.

NormalMode 

New characters are aligned on the base line.

SubscriptMode 

New characters are subscripts, but are not related to stoichiometry.

SuperscriptMode 

New characters are superscripts, but are not related to charge.

ChargeMode 

New characters are interpreted as charge and superscript.

StoichiometryMode 

New characters are interpreted as stoichiometry and subscript.

Definition at line 351 of file fragment.h.

§ Validity

The validity state of a Fragment as it is currently evaluated by the framework. The 0.12.x version don't do anything useful with it and all Fragment instances are invalid.

Enumerator
Invalid 

Invalid Fragment or validity not checked.

Valid 

Valid Fragment, all symbols in the string can be interpreted.

Valid2D 

Valid Fragment, with a known and reasonable 2D structure.

Valid3D 

Valid Fragment, with a known and reasonable 3D structure.

Definition at line 326 of file fragment.h.

Constructor & Destructor Documentation

§ Fragment() [1/2]

gcp::Fragment::Fragment ( )

The default constructor.

§ Fragment() [2/2]

gcp::Fragment::Fragment ( double  x,
double  y 
)
Parameters
xthe x position of the new fragment.
ythe y position of the new fragment.

Constructs a new fragment and position it. x and y are the position of the main atom or residue in the fragment.

§ ~Fragment()

virtual gcp::Fragment::~Fragment ( )
virtual

The destructor.

Member Function Documentation

§ AddItem()

void gcp::Fragment::AddItem ( )
virtual

Used to add a representation of the fragment in the view.

Reimplemented from gccv::ItemClient.

§ AnalContent() [1/2]

void gcp::Fragment::AnalContent ( )

Analyses the whole contents.

§ AnalContent() [2/2]

void gcp::Fragment::AnalContent ( unsigned  start,
unsigned &  end 
)
Parameters
startthe start fo the substring to parse, in bytes.
endthe end fo the substring to parse, in bytes.

Analyses a substring.

§ Analyze()

bool gcp::Fragment::Analyze ( )

Analyses the text in the fragment. This calls gcp::Fragment::AnalContent() and updates the attribute list.

§ GetAtom()

Atom* gcp::Fragment::GetAtom ( )
inline
Returns
the main atom, which might have a bond.

Definition at line 217 of file fragment.h.

§ GetAtomAt()

Object* gcp::Fragment::GetAtomAt ( double  x,
double  y,
double  z = 0. 
)
virtual
Parameters
xthe x coordinate
ythe y coordinate
zthe z coordinate (unused)
Returns
a pointer to the Atom correpoding to the symbol at or near the position defined by the coordinates passed as parameters, if any.

Reimplemented from gcu::Object.

§ GetAvailablePosition()

int gcp::Fragment::GetAvailablePosition ( double &  x,
double &  y 
)
Parameters
xthe x position.
ythe y position.

This method finds an available position for drawing a charge sign or electrons and returns it as a symbolic value (see POSITION_E, POSITION_N,...). The x and y are updated so that they give the absolute position.

Returns
an available position.

§ GetChargeItem()

gccv::Item* gcp::Fragment::GetChargeItem ( )
Returns
the gccv::Item used to represent the formal charge of the main atom.

§ GetChargePosition()

gccv::Anchor gcp::Fragment::GetChargePosition ( FragmentAtom pAtom,
unsigned char &  Pos,
double  Angle,
double &  x,
double &  y 
)
Parameters
pAtomthe main atom which will get the local charge.
Posthe approximate position of the charge.
Anglethe angle from horizontal left.
xthe x position of the charge symbol.
ythe y position of the charge symbol.

If pAtom is not the main atom of the fragment, 0 is returned and Pos is not updated. On input Pos can be one of POSITION_E, POSITION_N,... or 0xff, in which case, it will be given a default value. x and y are set to the position where the charge sign should be displayed usding the alignment code returned by this method.

Returns
the anchor for the charge symbol. On error, gccv::AnchorCenter is used as the returned value.

§ GetCoords()

bool gcp::Fragment::GetCoords ( double *  x,
double *  y,
double *  z = NULL 
) const
virtual
Parameters
xa pointer to the double value which will receive the x coordinate of the Fragment.
ya pointer to the double value which will receive the y coordinate of the Fragment.
za pointer to the double value which will receive the z coordinate of the Fragment or NULL for 2D representations.

Retrieves the coordinates of this Arrow.

Returns
true if successful and false if an error occurs (if x or y is NULL).

Reimplemented from gcu::Object.

§ GetElementAtPos()

int gcp::Fragment::GetElementAtPos ( unsigned  start,
unsigned &  end 
)
Parameters
startthe start position of the atomic symbol.
endthe end position of the atomic symbol.
Returns
the atomic number corresponding to the symbol starting at start, if any, or 0. end is updated accordingly.

§ GetMode()

gcp::Fragment::GetMode ( void  ) const
inline
Returns
the current edition mode for the Fragment instance.

Definition at line 403 of file fragment.h.

§ GetPosition()

bool gcp::Fragment::GetPosition ( double  angle,
double &  x,
double &  y 
)
Parameters
anglethe angle at which a charge sign should be displayed.
xthe x position.
ythe y position.
Returns
false and do not update the coordinates.

§ GetProperty()

std::string gcp::Fragment::GetProperty ( unsigned  property) const
virtual
Parameters
propertythe property id as defined in objprops.h

Used when saving to get properties from fragments.

Reimplemented from gcp::TextObject.

§ GetRefMode()

gcp::Fragment::GetRefMode ( void  )
inline
Returns
the current edition mode for the Fragment instance as a reference.

Definition at line 403 of file fragment.h.

§ GetValid()

gcp::Fragment::GetValid ( void  ) const
inline
Returns
the current Fragment::Validity for the Fragment instance.

Definition at line 391 of file fragment.h.

§ GetYAlign()

double gcp::Fragment::GetYAlign ( )
virtual
Returns
the y coordinate at half height of a carbon atom symbol if any was present.

Reimplemented from gcu::Object.

§ Load()

bool gcp::Fragment::Load ( xmlNodePtr  node)
virtual
Parameters
nodea pointer to the xmlNode containing the serialized fragment.

Used to load a fragment in memory. The Fragment must already exist.

Returns
true on succes, false otherwise.

Reimplemented from gcu::Object.

§ Move()

void gcp::Fragment::Move ( double  x,
double  y,
double  z = 0 
)
virtual
Parameters
xthe x component of the transation vector.
ythe y component of the transation vector.
zthe z component of the transation vector.

Moves the fragment.

Reimplemented from gcu::Object.

§ Name()

std::string gcp::Fragment::Name ( )
virtual
Returns
the localized object generic name.

Reimplemented from gcu::Object.

§ OnChangeAtom()

void gcp::Fragment::OnChangeAtom ( )

Called by the framework when the user changes the nature of an atom using the element tool.

§ OnChanged()

bool gcp::Fragment::OnChanged ( bool  save)
virtual
Parameters
savewhether the text should be saved for undo/redo operations.

Called after any change in the text.

Implements gcp::TextObject.

§ Save()

xmlNodePtr gcp::Fragment::Save ( xmlDocPtr  xml) const
virtual
Parameters
xmlthe xmlDoc used to save the document.

Used to save the fragment to the xmlDoc.

Returns
the xmlNode containing the serialized fragment.

Reimplemented from gcu::Object.

§ SaveSelection()

xmlNodePtr gcp::Fragment::SaveSelection ( xmlDocPtr  xml) const
Parameters
xmlthe xmlDoc used for clipboard operations.

Saves the currently selected text inside the fragment. This method is used by the framework when editing the fragment.

Returns
the xmlNode containing the serialized selection.

§ SetMode()

gcp::Fragment::SetMode ( FragmentMode  mode)
inline
Parameters
modethe nexw edition mode.

Sets the current edition mode for the Fragment instance.

Definition at line 403 of file fragment.h.

§ SetProperty()

bool gcp::Fragment::SetProperty ( unsigned  property,
char const *  value 
)
virtual
Parameters
propertythe property id as defined in objprops.h
valuethe property value as a string

Used when loading to set properties for the fragment. This method supports GCU_PROP_POS2D, GCU_PROP_TEXT_TEXT, GCU_PROP_FRAGMENT_ATOM_START, and GCU_PROP_FRAGMENT_ATOM_ID.

Returns
true if the property could be set, or if the property is not relevant, false otherwise.

Reimplemented from gcu::Object.

§ SetSelected()

void gcp::Fragment::SetSelected ( int  state)
virtual
Parameters
statethe selection state of the fragment.

Used to set the selection state of the fragment inside the widget. The values of state might be gcp::SelStateUnselected, gcp::SelStateSelected, gcp::SelStateUpdating, or gcp::SelStateErasing.

Reimplemented from gccv::ItemClient.

§ Transform2D()

void gcp::Fragment::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.

Moves and/or transform an object.

Reimplemented from gcu::Object.

§ Update()

bool gcp::Fragment::Update ( )

Changes the order of the symbols if necessary when a bond is at an extremity of the fragment.

Returns
true, if the order has been reversed.

§ UpdateItem()

void gcp::Fragment::UpdateItem ( )
virtual

Used to update a representation of the fragment in the view.

Reimplemented from gccv::ItemClient.

§ Validate()

bool gcp::Fragment::Validate ( )

Validates the contents of the fragment text, and display error messages when necessary.


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