#include <BALL/VIEW/WIDGETS/molecularStructure.h>

Inheritance diagram for BALL::VIEW::MolecularStructure:

Public Types
enum	{ AMBER_FF = 0, CHARMM_FF, MMFF94_FF }

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

Public Member Functions
Constructors
	MolecularStructure (QWidget parent=0, const char name=0)

	MolecularStructure (const MolecularStructure &m)
	only needed for Python Interface, dont call it! More...

Destructors
virtual	~MolecularStructure ()

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 ()

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)

virtual bool	canHandle (const String &) const

virtual bool	openFile (const String &)

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

Accessors: inspectors and mutators
virtual void	onNotify (Message *message)

virtual void	checkMenu (MainControl &main_control)

virtual void	initializeWidget (MainControl &main_control)

ForceField &	getForceField ()

Position	getForceFieldID ()

AmberFF &	getAmberFF ()

CharmmFF &	getCharmmFF ()

MMFF94 &	getMMFF94 ()

AmberConfigurationDialog &	getAmberConfigurationDialog ()
	Get an instance of an dialog to setup the AMBER forcefield. More...

CharmmConfigurationDialog &	getCharmmConfigurationDialog ()
	Get an instance of an dialog to setup the CHARMM forcefield. More...

MMFF94ConfigurationDialog &	getMMFF94ConfigurationDialog ()

virtual void	fetchPreferences (INIFile &inifile)

virtual void	writePreferences (INIFile &inifile)

MolecularDynamicsDialog &	getMDSimulationDialog ()

MinimizationDialog &	getMinimizationDialog ()

FDPBDialog *	getFDPBDialog ()

AssignBondOrderConfigurationDialog &	getBondOrderDialog ()

const AssignBondOrderConfigurationDialog &	getBondOrderDialog () const

AssignBondOrderResultsDialog &	getBondOrderResultsDialog ()

const AssignBondOrderResultsDialog &	getBondOrderResultsDialog () const

void	centerCamera (Composite *composite=0)

void	buildBonds ()

void	buildEndcaps ()

void	runBondOrderAssignment (bool show_dialog=true)

void	showBondOrderAssignmentResults (AssignBondOrderProcessor &bop)

void	addHydrogens ()

virtual bool	checkResidue ()

virtual void	createGridFromDistance ()
	Create a RegularData3D instance with the distance from the geometric center. More...

virtual void	createGridFromCameraDistance ()

virtual void	calculateSecondaryStructure ()
	Calculate the secondary structure for a protein. More...

virtual void	mapProteins ()
	Map two Proteins and apply the resulting transformation matrix. More...

virtual void	calculateRMSD ()
	Calculate the RMSD between two Molecules. More...

void	buildPeptide ()
	Build a Peptide from a amino acid sequence. More...

bool	generateCrystal (bool show=true)
	Build a crystal packing for a loaded system. More...

void	calculateHBonds ()
	Calculate the H-Bonds for a Protein. More...

void	calculateRamachandranPlot ()
	Calculate a Ramachandran Plot. More...

void	calculateForceFieldEnergy ()
	Calculate the energy for the currently selected force field. More...

void	runMinimization (bool show_dialog_=true)
	Run a energy minization with the currently selected force field. More...

void	MDSimulation (bool show_dialog_=true)
	Perfomr a molecular dynamics simulation with the currently selected force field. More...

void	showAmberForceFieldOptions ()
	Show the dialog to setup the AMBER force field. More...

void	showCharmmForceFieldOptions ()
	Show the dialog to setup the CHARMM force field. More...

void	showMMFF94ForceFieldOptions ()

void	chooseAmberFF ()
	Slot for a menu entry to select the AMBER force field. More...

void	chooseCharmmFF ()
	Slot for a menu entry to select the CHARMM force field. More...

void	chooseMMFF94 ()
	Slot for a menu entry to select the MMFF94 force field. More...

void	chooseForceField (Position nr)

void	setupForceField ()
	Show a dialog to setup the currently selected force field. More...

bool	calculateFDPB (bool show=true)

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

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

void	notify_ (Message *message)

void	notify_ (Message &message)

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)

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

bool	show_window_enty_

bool	default_visible_

QList< QAction * >	main_toolbar_actions_

Detailed Description

MolecularStructure provides means to modify molecular structures and do several calculations. To do so, it contains the MMFF94, AMBER and CHARMM forcefields and dialogs to do the setup. The widget itself is invisible, but it has several menu entries, e.g.:

checkResidue
centerCamera
buildBonds
assignBondOrders
addHydrogens
createGridFromDistance
calculateSecondaryStructure This class is also necessary to add certain properties to new Composite objects, which were opened with the MolecularFileDialog. So it reacts to Messages itself and converts some to other Message objects. Further it converts the geometric selection sent by Scene to a molecular selection whose objects can be given a new graphical representation by the DisplayProperties dialog. See onNotify for information concerning the conversion mechanism.

Definition at line 90 of file molecularStructure.h.

Member Enumeration Documentation

anonymous enum

Enumerator
AMBER_FF
CHARMM_FF
MMFF94_FF

Definition at line 101 of file molecularStructure.h.

Constructor & Destructor Documentation

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

Default Constructor. Calls registerWidget.

See also: ModularWidget

BALL::VIEW::MolecularStructure::MolecularStructure ( const MolecularStructure & m )

only needed for Python Interface, dont call it!

virtual BALL::VIEW::MolecularStructure::~MolecularStructure ( )

virtual

Destructor.

Member Function Documentation

void BALL::VIEW::MolecularStructure::addHydrogens ( )

slot

Adds hydrogens. If selected molecular objects are available hydrogens will be created for each object in the selection list using the add_hydrogens processor of the FragmentDB. A CompositeMessage will be sent for each object in the selection list. The number of hydrogens created will be written into the Log object.

void BALL::VIEW::MolecularStructure::buildBonds ( )

slot

Creates bonds. If selected molecular objects are available Bond objects will be created for each object in the selection list using the build_bonds processor of the FragmentDB. A CompositeMessage will be sent for each object in the selection list. The number of bonds created will be written into the Log object.

void BALL::VIEW::MolecularStructure::buildEndcaps ( )

slot

Adds neutral end caps to a protein chain. This function runs our PeptideCapProcessor to replace the terminals by neutral end caps.

void BALL::VIEW::MolecularStructure::buildPeptide ( )

slot

Build a Peptide from a amino acid sequence.

bool BALL::VIEW::MolecularStructure::calculateFDPB ( bool show = true )

slot

void BALL::VIEW::MolecularStructure::calculateForceFieldEnergy ( )

slot

Calculate the energy for the currently selected force field.

void BALL::VIEW::MolecularStructure::calculateHBonds ( )

slot

Calculate the H-Bonds for a Protein.

void BALL::VIEW::MolecularStructure::calculateRamachandranPlot ( )

slot

Calculate a Ramachandran Plot.

virtual void BALL::VIEW::MolecularStructure::calculateRMSD ( )

virtualslot

Calculate the RMSD between two Molecules.

virtual void BALL::VIEW::MolecularStructure::calculateSecondaryStructure ( )

virtualslot

Calculate the secondary structure for a protein.

void BALL::VIEW::MolecularStructure::centerCamera ( Composite * composite = 0 )

slot

Centers the camera of Scene to the geometric center of the molecular objects in the selection list. A SceneMessage will be sent to inform the Scene.

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

virtual

Check the menu entries. The menus Select, Deselect, Add Hydrogens and Build Bonds will be enabled if the selection of molecular objects is not empty. The menu Focus camera will be enabled only if only one molecular object is in the selection list.

Reimplemented from BALL::VIEW::ModularWidget.

virtual bool BALL::VIEW::MolecularStructure::checkResidue ( )

virtualslot

Check the residues

void BALL::VIEW::MolecularStructure::chooseAmberFF ( )

slot

Slot for a menu entry to select the AMBER force field.

void BALL::VIEW::MolecularStructure::chooseCharmmFF ( )

slot

Slot for a menu entry to select the CHARMM force field.

void BALL::VIEW::MolecularStructure::chooseForceField ( Position nr )

slot

void BALL::VIEW::MolecularStructure::chooseMMFF94 ( )

slot

Slot for a menu entry to select the MMFF94 force field.

virtual void BALL::VIEW::MolecularStructure::createGridFromCameraDistance ( )

virtualslot

virtual void BALL::VIEW::MolecularStructure::createGridFromDistance ( )

virtualslot

Create a RegularData3D instance with the distance from the geometric center.

virtual void BALL::VIEW::MolecularStructure::fetchPreferences ( INIFile & inifile )

virtual

Fetch the widgets preferences from the INIfile.

Parameters

inifile the INIFile that contains the required values

Reimplemented from BALL::VIEW::ModularWidget.

bool BALL::VIEW::MolecularStructure::generateCrystal ( bool show = true )

slot

Build a crystal packing for a loaded system.

AmberConfigurationDialog& BALL::VIEW::MolecularStructure::getAmberConfigurationDialog ( )

Get an instance of an dialog to setup the AMBER forcefield.

AmberFF& BALL::VIEW::MolecularStructure::getAmberFF ( )

Get the instance of the AMBER forcefield. The forcefield will be created, when this function is called the first time.

AssignBondOrderConfigurationDialog& BALL::VIEW::MolecularStructure::getBondOrderDialog ( )

inline

Definition at line 220 of file molecularStructure.h.

const AssignBondOrderConfigurationDialog& BALL::VIEW::MolecularStructure::getBondOrderDialog ( ) const

inline

Definition at line 223 of file molecularStructure.h.

AssignBondOrderResultsDialog& BALL::VIEW::MolecularStructure::getBondOrderResultsDialog ( )

inline

Definition at line 226 of file molecularStructure.h.

const AssignBondOrderResultsDialog& BALL::VIEW::MolecularStructure::getBondOrderResultsDialog ( ) const

inline

Definition at line 229 of file molecularStructure.h.

CharmmConfigurationDialog& BALL::VIEW::MolecularStructure::getCharmmConfigurationDialog ( )

Get an instance of an dialog to setup the CHARMM forcefield.

CharmmFF& BALL::VIEW::MolecularStructure::getCharmmFF ( )

Get the instance of the CHARMM forcefield. The forcefield will be created, when this function is called the first time.

FDPBDialog* BALL::VIEW::MolecularStructure::getFDPBDialog ( )

inline

Definition at line 217 of file molecularStructure.h.

ForceField& BALL::VIEW::MolecularStructure::getForceField ( )

Get the currently selected force field instance. This returns either a reference to the amber_ff_ member or to the charmm_ff_ member, depending on the value of use_amber_.

Position BALL::VIEW::MolecularStructure::getForceFieldID ( )

Get the force_field_id of the currently selected ForceField

MolecularDynamicsDialog& BALL::VIEW::MolecularStructure::getMDSimulationDialog ( )

inline

Definition at line 211 of file molecularStructure.h.

MinimizationDialog& BALL::VIEW::MolecularStructure::getMinimizationDialog ( )

inline

Definition at line 214 of file molecularStructure.h.

MMFF94& BALL::VIEW::MolecularStructure::getMMFF94 ( )

MMFF94ConfigurationDialog& BALL::VIEW::MolecularStructure::getMMFF94ConfigurationDialog ( )

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

virtual

Initialize the popup menus for this Widget. This method is called automatically immediately before the main application is started by MainControl::show().

Parameters

main_control the MainControl object to be initialized

See also: finalizeWidget

Reimplemented from BALL::VIEW::ModularWidget.

virtual void BALL::VIEW::MolecularStructure::mapProteins ( )

virtualslot

Map two Proteins and apply the resulting transformation matrix.

void BALL::VIEW::MolecularStructure::MDSimulation ( bool show_dialog_ = true )

slot

Perfomr a molecular dynamics simulation with the currently selected force field.

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

virtual

Handles messages sent by other registered ConnectionObject objects. Converts CompositeMessage if the retrieved Composite object is kind of AtomContainer and applies molecular properties to it (like normalize_names and build_bonds).

Parameters

message the pointer to the message that should be processed

See also: CompositeMessage; GeometricObjectSelectionMessage; MolecularTaskMessage

Reimplemented from BALL::VIEW::ConnectionObject.

void BALL::VIEW::MolecularStructure::runBondOrderAssignment ( bool show_dialog = true )

slot

Assigns bond orders. If a single selected molecular object is available Bond Orders will be set for each bond object of the selected AtomContainer using the assign_bond_order processor. A CompositeMessage will be sent for the object in the selection list. The number of bond orders changed will be written into the Log object.

void BALL::VIEW::MolecularStructure::runMinimization ( bool show_dialog_ = true )

slot

Run a energy minization with the currently selected force field.

void BALL::VIEW::MolecularStructure::setupForceField ( )

slot

Show a dialog to setup the currently selected force field.

void BALL::VIEW::MolecularStructure::showAmberForceFieldOptions ( )

slot

Show the dialog to setup the AMBER force field.

void BALL::VIEW::MolecularStructure::showBondOrderAssignmentResults ( AssignBondOrderProcessor & bop )

slot

Shows the results of the given BondOrderAssigner. All bond order assignment sets found by the given BondOrderAssigner will be presented as structural sketch, additional scoring information is provided by click on the entry. A single assignment can either be applied to the selected AtomContainer, or a copy of the original system with the bond order assignment of the current result is added to the Structure list.

void BALL::VIEW::MolecularStructure::showCharmmForceFieldOptions ( )

slot

Show the dialog to setup the CHARMM force field.

void BALL::VIEW::MolecularStructure::showMMFF94ForceFieldOptions ( )

slot

virtual void BALL::VIEW::MolecularStructure::writePreferences ( INIFile & inifile )

virtual

Writes the widgets preferences to the INIFile.

Parameters

inifile the INIFile that contains the needed values

Reimplemented from BALL::VIEW::ModularWidget.

Public Types

Public Member Functions

Accessors: inspectors and mutators

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation