BALL::VIEW::MolecularStructure Class Reference
[Modular Widgets]

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

Inheritance diagram for BALL::VIEW::MolecularStructure:

Public Types
enum	{ AMBER_FF = 0, CHARMM_FF, MMFF94_FF }
Public Member Functions
Constructors

	MolecularStructure (QWidget parent=0, const char name=0)
	MolecularStructure (const MolecularStructure &m)
	only needed for Python Interface, dont call it!
Destructors

virtual	~MolecularStructure ()
Private Member Functions
virtual void	addComposite_ (Composite &composite, const String &name)
void	applyForceFieldSettings_ ()
void	selectUnassignedForceFieldAtoms_ ()
bool	setupForceField_ (System *system, bool disable_selection=false)
Private Attributes
QAction *	center_camera_id_
QAction *	build_bonds_id_
QAction *	build_endcaps_id_
QAction *	assign_bond_orders_id_
QAction *	add_hydrogens_id_
QAction *	check_structure_id_
QAction *	create_distance_grid_id_
QAction *	create_distance_grid_id2_
QAction *	calculate_ss_id_
QAction *	map_proteins_id_
QAction *	calculate_RMSD_id_
QAction *	assign_charges_id_
QAction *	energy_id_
QAction *	minimization_id_
QAction *	mdsimulation_id_
QAction *	build_peptide_id_
QAction *	calculate_hbonds_id_
QAction *	amber_ff_id_
QAction *	charmm_ff_id_
QAction *	mmff94_id_
QAction *	setup_ff_
QAction *	calculate_ramachandran_
QAction *	menu_FPDB_
AmberFF	amber_
CharmmFF	charmm_
MMFF94	mmff_
AmberConfigurationDialog	amber_dialog_
CharmmConfigurationDialog	charmm_dialog_
MMFF94ConfigurationDialog	mmff94_dialog_
MinimizationDialog	minimization_dialog_
MolecularDynamicsDialog	md_dialog_
FDPBDialog *	fdpb_dialog_
AssignBondOrderConfigurationDialog	bond_order_dialog_
AssignBondOrderResultsDialog	bond_order_results_dialog_
Position	force_field_id_
Accessors: inspectors and mutators

virtual void	onNotify (Message *message)
virtual void	checkMenu (MainControl &main_control)
virtual void	initializeWidget (MainControl &main_control)
ForceField &	getForceField ()
AmberFF &	getAmberFF ()
CharmmFF &	getCharmmFF ()
MMFF94 &	getMMFF94 ()
AmberConfigurationDialog &	getAmberConfigurationDialog ()
	Get an instance of an dialog to setup the AMBER forcefield.
CharmmConfigurationDialog &	getCharmmConfigurationDialog ()
	Get an instance of an dialog to setup the CHARMM forcefield.
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.
virtual void	createGridFromCameraDistance ()
virtual void	calculateSecondaryStructure ()
	Calculate the secondary structure for a protein.
virtual void	mapProteins ()
	Map two Proteins and apply the resulting transformation matrix.
virtual void	calculateRMSD ()
	Calculate the RMSD between two Molecules.
void	buildPeptide ()
	Build a Peptide from a amino acid sequence.
void	calculateHBonds ()
	Calculate the H-Bonds for a Protein.
void	calculateRamachandranPlot ()
	Calculate a Ramachandran Plot.
void	calculateForceFieldEnergy ()
	Calculate the energy for the currently selected force field.
void	runMinimization (bool show_dialog_=true)
	Run a energy minization with the currently selected force field.
void	MDSimulation (bool show_dialog_=true)
	Perfomr a molecular dynamics simulation with the currently selected force field.
void	showAmberForceFieldOptions ()
	Show the dialog to setup the AMBER force field.
void	showCharmmForceFieldOptions ()
	Show the dialog to setup the CHARMM force field.
void	showMMFF94ForceFieldOptions ()
void	chooseAmberFF ()
	Slot for a menu entry to select the AMBER force field.
void	chooseCharmmFF ()
	Slot for a menu entry to select the CHARMM force field.
void	chooseMMFF94 ()
	Slot for a menu entry to select the MMFF94 force field.
void	chooseForceField (Position nr)
void	setupForceField ()
	Show a dialog to setup the currently selected force field.
bool	calculateFDPB (bool show=true)

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 86 of file molecularStructure.h.

Member Enumeration Documentation

anonymous enum

Enumerator:

AMBER_FF
CHARMM_FF
MMFF94_FF

Definition at line 97 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

virtual void BALL::VIEW::MolecularStructure::addComposite_	(	Composite &	composite,
		const String &	name
	)			`[private, virtual]`

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::applyForceFieldSettings_ ( ) [private]

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 ( ) [virtual, slot]

Calculate the RMSD between two Molecules.

virtual void BALL::VIEW::MolecularStructure::calculateSecondaryStructure ( ) [virtual, slot]

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 ( ) [virtual, slot]

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 ( ) [virtual, slot]

virtual void BALL::VIEW::MolecularStructure::createGridFromDistance ( ) [virtual, slot]

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.

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.

const AssignBondOrderConfigurationDialog& BALL::VIEW::MolecularStructure::getBondOrderDialog ( ) const [inline]

Definition at line 215 of file molecularStructure.h.

AssignBondOrderConfigurationDialog& BALL::VIEW::MolecularStructure::getBondOrderDialog ( ) [inline]

Definition at line 212 of file molecularStructure.h.

const AssignBondOrderResultsDialog& BALL::VIEW::MolecularStructure::getBondOrderResultsDialog ( ) const [inline]

Definition at line 221 of file molecularStructure.h.

AssignBondOrderResultsDialog& BALL::VIEW::MolecularStructure::getBondOrderResultsDialog ( ) [inline]

Definition at line 218 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 209 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_.

MolecularDynamicsDialog& BALL::VIEW::MolecularStructure::getMDSimulationDialog ( ) [inline]

Definition at line 203 of file molecularStructure.h.

MinimizationDialog& BALL::VIEW::MolecularStructure::getMinimizationDialog ( ) [inline]

Definition at line 206 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 ( ) [virtual, slot]

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::selectUnassignedForceFieldAtoms_ ( ) [private]

void BALL::VIEW::MolecularStructure::setupForceField ( ) [slot]

Show a dialog to setup the currently selected force field.

bool BALL::VIEW::MolecularStructure::setupForceField_	(	System *	system,
		bool	disable_selection = `false`
	)			`[private]`

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.