#include <BALL/VIEW/DIALOGS/molecularFileDialog.h>

Inheritance diagram for BALL::VIEW::MolecularFileDialog:

Public Slots
virtual void	readFiles ()

virtual bool	writeFile ()

Public Member Functions
	MolecularFileDialog (QWidget parent=0, const char name="MolecularFileDialog")

virtual	~MolecularFileDialog ()
	Destructor. More...

virtual void	initializeWidget (MainControl &main_control)

virtual bool	canHandle (const String &fileformat) const

virtual bool	openFile (const String &filename)

virtual System *	openMolecularFile (const String &file)

virtual System *	openMolecularFile (const String &filename, const String &filetype, const String &system_name)

System *	openPDBFile ()

System *	openHINFile ()

System *	openMOLFile ()

System *	openMOL2File ()

System *	openSDFile ()

System *	openACFile ()

System *	openXYZFile ()

System *	readPDBFile (String filename, String system_name)

System *	readHINFile (String filename, String system_name)

System *	readMOLFile (String filename, String system_name)

System *	readMOL2File (String filename, String system_name)

System *	readSDFile (String filename, String system_name)

System *	readACFile (String filename, String system_name)

System *	readXYZFile (String filename, String system_name)

bool	writePDBFile (String filename, const System &system)

bool	writeHINFile (String filename, const System &system)

bool	writeMOLFile (String filename, const System &system)

bool	writeMOL2File (String filename, const System &system)

bool	writeSDFile (String filename, const System &system)

bool	writeACFile (String filename, const System &system)

bool	writeXYZFile (String filename, const System &system)

virtual void	checkMenu (MainControl &main_control)
	Overloaded from ModularWidget. More...

virtual String	getSupportedFileFormats () const

virtual String	getSupportedFileFormatsList () const

void	setReadPDBModels (bool read)

Public Member Functions inherited from BALL::VIEW::ModularWidget
void	setWorkingDirFromFilename_ (String filename)

virtual void	showHelp (const String &url)

	ModularWidget (const char *name="<ModularWidget>")

	ModularWidget (const ModularWidget &widget)

virtual	~ModularWidget ()

virtual void	destroy ()

virtual void	clear ()

QAction *	insertMenuEntry (Position parent_id, const QString &name, const QObject receiver=0, const char slot=0, const String &description="", QKeySequence accel=QKeySequence(), const QString &menu_hint=QString(""), UIOperationMode::OperationMode minimal_mode=UIOperationMode::MODE_ALL)

void	setMenuHelp (QAction *action, const String &url)

virtual void	registerForHelpSystem (const QObject *object, const String &url)

virtual void	addToolBarEntries (QToolBar *main_tb)

void	setIcon (QAction *action, const String &filename, bool add_to_main_toolbar=true)

virtual void	initializePreferencesTab (Preferences &preferences)

virtual void	finalizePreferencesTab (Preferences &preferences)

virtual void	applyPreferences ()

virtual void	fetchPreferences (INIFile &inifile)

virtual void	writePreferences (INIFile &inifile)

bool	lockComposites ()

bool	unlockComposites ()
	Unlock the Composites. More...

MainControl *	getMainControl () const

virtual void	setStatusbarText (const String &text, bool important=false)

virtual void	setStatusbarText (const QString &text, bool important=false)

String	getWorkingDir ()
	Implemented for convenience. More...

void	setWorkingDir (const String &dir)
	Implemented for convenience. More...

FragmentDB &	getFragmentDB () const

virtual void	dump (std::ostream &s=std::cout, Size depth=0) const

virtual void	finalizeWidget (MainControl &main_control)

Public Member Functions inherited from BALL::Embeddable
	Embeddable (const String &identifier="<Embeddable>")

	Embeddable (const Embeddable &embeddable)

virtual	~Embeddable ()

void	setIdentifier (const String &identifier)

const String &	getIdentifier () const

void	unregisterThis ()

virtual void	registerThis ()

Public Member Functions inherited from BALL::VIEW::ConnectionObject
	ConnectionObject ()

virtual	~ConnectionObject ()

void	registerConnectionObject (ConnectionObject &object)

void	unregisterConnectionObject (ConnectionObject &object)

bool	isConnectionObjectRegistered (const ConnectionObject &object)

ConnectionObject *	getParent () const

ConnectionObject *	getRoot ()

virtual bool	isValid () const

Protected Types
enum	FileFormats { PDB_FILE = 0, HIN_FILE, MOL_FILE, MOL2_FILE, SD_FILE, XYZ_FILE }

Protected Member Functions
virtual void	onNotify (Message *message)

	MolecularFileDialog (const MolecularFileDialog &mfd)

virtual bool	finish_ (const String &filename, const String &system_name, System *system)

System *	openFile_ (String type)

Protected Member Functions inherited from BALL::VIEW::ConnectionObject
void	onNotify_ (Message *message)

void	notify_ (Message *message)

void	notify_ (Message &message)

Protected Attributes
QAction *	save_id_

QAction *	open_id_

String	file_format_

bool	read_all_pdb_models_

Protected Attributes inherited from BALL::VIEW::ModularWidget
QAction *	window_menu_entry_

bool	show_window_enty_

bool	default_visible_

QList< QAction * >	main_toolbar_actions_

Additional Inherited Members
Public Types inherited from BALL::Embeddable
typedef std::vector< Embeddable * >	EmbeddableVector

Static Public Member Functions inherited from BALL::VIEW::ModularWidget
static void	registerWidget (ModularWidget *mwidget) throw (Exception::NullPointer)

Static Protected Member Functions inherited from BALL::Embeddable
static void	registerInstance_ (const std::type_info &type, const Embeddable *instance)

static void	unregisterInstance_ (const Embeddable *instance)

static Size	countInstances_ (const std::type_info &type)

static Embeddable *	getInstance_ (const std::type_info &type, Position index)

static Embeddable *	getInstance_ (const std::type_info &type, const String &identifier)

Detailed Description

Dialog for opening molecular data files. This class is used to read or write Molecular files in one of several file formats. Currently supported file formats are:

: HIN, MOL, MOL2, PDB, SD, XYZ

: Upon reading a file, the information will be stored in a System. This class can also take a System and write it in one of the supported file formats. This class is derived from ModularWidget.

See also: HINFile; MOLFile; MOL2File; PDBFile; SDFile; XYZFile

Definition at line 45 of file molecularFileDialog.h.

Member Enumeration Documentation

enum BALL::VIEW::MolecularFileDialog::FileFormats

protected

Enumerator
PDB_FILE
HIN_FILE
MOL_FILE
MOL2_FILE
SD_FILE
XYZ_FILE

Definition at line 215 of file molecularFileDialog.h.

Constructor & Destructor Documentation

BALL::VIEW::MolecularFileDialog::MolecularFileDialog	(	QWidget *	parent = `0`,
		const char *	name = `"MolecularFileDialog"`
	)

Default Constructor. Calls ModularWidget::registerWidget()

virtual BALL::VIEW::MolecularFileDialog::~MolecularFileDialog ( )

virtual

Destructor.

BALL::VIEW::MolecularFileDialog::MolecularFileDialog ( const MolecularFileDialog & mfd )

protected

Member Function Documentation

virtual bool BALL::VIEW::MolecularFileDialog::canHandle ( const String & fileformat ) const

virtual

Test if this ModularWidget can handle a given file format. (Overloaded from ModularWidget)

Parameters

fileform short string with the file extension (e.g. PDB)

See also: openFile

Reimplemented from BALL::VIEW::ModularWidget.

virtual void BALL::VIEW::MolecularFileDialog::checkMenu ( MainControl & main_control )

virtual

Overloaded from ModularWidget.

Reimplemented from BALL::VIEW::ModularWidget.

virtual bool BALL::VIEW::MolecularFileDialog::finish_	(	const String &	filename,
		const String &	system_name,
		System *	system
	)

protectedvirtual

virtual String BALL::VIEW::MolecularFileDialog::getSupportedFileFormats ( ) const

virtual

virtual String BALL::VIEW::MolecularFileDialog::getSupportedFileFormatsList ( ) const

virtual

virtual void BALL::VIEW::MolecularFileDialog::initializeWidget ( MainControl & main_control )

virtual

Initializes the menu entries in File. This method is called automatically immediately before the main application is started. This method will be called MainControl::show().

Parameters

main_control the MainControl object to be initialized

See also: finalizeWidget

Reimplemented from BALL::VIEW::ModularWidget.

virtual void BALL::VIEW::MolecularFileDialog::onNotify ( Message * message )

protectedvirtual

Message handling method. This method handles messages sent to this connectionObject. If a certain message should be processed for this connectionObject this method must be overridden. With the help of the RTTI methods one can easily determine if an incoming message is relevant for this connectionObject. See Message for further information concerning messages.

Parameters

message a pointer to a message. Do not delete the message in this method.

Reimplemented from BALL::VIEW::ConnectionObject.

System* BALL::VIEW::MolecularFileDialog::openACFile ( )

virtual bool BALL::VIEW::MolecularFileDialog::openFile ( const String & filename )

virtual

Tell this ModularWidget to open a given file. (Overloaded from ModularWidget)

See also: canHandle

Reimplemented from BALL::VIEW::ModularWidget.

System* BALL::VIEW::MolecularFileDialog::openFile_ ( String type )

protected

System* BALL::VIEW::MolecularFileDialog::openHINFile ( )

System* BALL::VIEW::MolecularFileDialog::openMOL2File ( )

virtual System* BALL::VIEW::MolecularFileDialog::openMolecularFile ( const String & file )

virtual

Open a given molecular file. The file type is identified by the filename extension. This method can be used to load molecular files, which were given as command line arguments.

virtual System* BALL::VIEW::MolecularFileDialog::openMolecularFile	(	const String &	filename,
		const String &	filetype,
		const String &	system_name
	)

virtual

Wrapper for the read methods. The filetype String is used to indentify the file type (HIN, PDP, MOL, MOL2). It is possible to give the system a designated name, otherwise it is named by the file.

System* BALL::VIEW::MolecularFileDialog::openMOLFile ( )

System* BALL::VIEW::MolecularFileDialog::openPDBFile ( )

System* BALL::VIEW::MolecularFileDialog::openSDFile ( )

System* BALL::VIEW::MolecularFileDialog::openXYZFile ( )

System* BALL::VIEW::MolecularFileDialog::readACFile	(	String	filename,
		String	system_name
	)

Read an AC file

virtual void BALL::VIEW::MolecularFileDialog::readFiles ( )

virtualslot

Open a molecular file. This method tries to open and read a molecular file, selected from a QFileDialog, and, if susccesfull, converts is into a System. Then it sends a CompositeMessage containing the System to the other ConnectionObject instances.

See also: CompositeMessage; ConnectionObject

System* BALL::VIEW::MolecularFileDialog::readHINFile	(	String	filename,
		String	system_name
	)

Read a HIN file

System* BALL::VIEW::MolecularFileDialog::readMOL2File	(	String	filename,
		String	system_name
	)

Read a MOL2 file

System* BALL::VIEW::MolecularFileDialog::readMOLFile	(	String	filename,
		String	system_name
	)

Read a MOL file

System* BALL::VIEW::MolecularFileDialog::readPDBFile	(	String	filename,
		String	system_name
	)

Read a PDB file

System* BALL::VIEW::MolecularFileDialog::readSDFile	(	String	filename,
		String	system_name
	)

Read a SD file

System* BALL::VIEW::MolecularFileDialog::readXYZFile	(	String	filename,
		String	system_name
	)

Read a XYZ file

void BALL::VIEW::MolecularFileDialog::setReadPDBModels ( bool read )

inline

Definition at line 184 of file molecularFileDialog.h.

bool BALL::VIEW::MolecularFileDialog::writeACFile	(	String	filename,
		const System &	system
	)

Write an AC file

virtual bool BALL::VIEW::MolecularFileDialog::writeFile ( )

virtualslot

Write a molecular file. This method takes a System and saves it into a molecular file, selected from a QFileDialog.

bool BALL::VIEW::MolecularFileDialog::writeHINFile	(	String	filename,
		const System &	system
	)

Write a HIN file

bool BALL::VIEW::MolecularFileDialog::writeMOL2File	(	String	filename,
		const System &	system
	)

Write a MOL2 file

bool BALL::VIEW::MolecularFileDialog::writeMOLFile	(	String	filename,
		const System &	system
	)

Write a MOL file

bool BALL::VIEW::MolecularFileDialog::writePDBFile	(	String	filename,
		const System &	system
	)

Write a PDB file

bool BALL::VIEW::MolecularFileDialog::writeSDFile	(	String	filename,
		const System &	system
	)

Write a SD file

bool BALL::VIEW::MolecularFileDialog::writeXYZFile	(	String	filename,
		const System &	system
	)

Write a XYZ file

Member Data Documentation

String BALL::VIEW::MolecularFileDialog::file_format_

protected

Definition at line 226 of file molecularFileDialog.h.

QAction * BALL::VIEW::MolecularFileDialog::open_id_

protected

Definition at line 225 of file molecularFileDialog.h.

bool BALL::VIEW::MolecularFileDialog::read_all_pdb_models_

protected

Definition at line 227 of file molecularFileDialog.h.

QAction* BALL::VIEW::MolecularFileDialog::save_id_

protected

Definition at line 225 of file molecularFileDialog.h.

Public Slots

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation