VIEW::MolecularStructure Class Reference
[Modular Widgets]

MolecularStructure provides means to modify molecular structures and do several calculations. More...

#include <molecularStructure.h>

Inheritance diagram for VIEW::MolecularStructure:

List of all members.

Accessors: inspectors and mutators
virtual void	onNotify (Message *message) throw ()
	Handles messages sent by other registered ConnectionObject objects.
virtual void	checkMenu (MainControl &main_control) throw ()
	Check the menu entries.
virtual void	initializeWidget (MainControl &main_control)
	Initialize the popup menus for this Widget.
ForceField &	getForceField () throw ()
	Get the currently selected force field instance.
AmberFF &	getAmberFF () throw ()
	Get the instance of the AMBER forcefield.
CharmmFF &	getCharmmFF () throw ()
	Get the instance of the CHARMM forcefield.
MMFF94 &	getMMFF94 () throw ()
AmberConfigurationDialog &	getAmberConfigurationDialog () throw ()
	Get an instance of an dialog to setup the AMBER forcefield.
CharmmConfigurationDialog &	getCharmmConfigurationDialog () throw ()
	Get an instance of an dialog to setup the CHARMM forcefield.
MMFF94ConfigurationDialog &	getMMFF94ConfigurationDialog () throw ()
virtual void	fetchPreferences (INIFile &inifile) throw ()
	Fetch the widgets preferences from the INIfile.
virtual void	writePreferences (INIFile &inifile) throw ()
	Writes the widgets preferences to the INIFile.
MolecularDynamicsDialog &	getMDSimulationDialog ()
MinimizationDialog &	getMinimizationDialog ()
FDPBDialog *	getFDPBDialog ()
void	centerCamera (Composite *composite=0)
	Centers the camera of Scene to the geometric center of the molecular objects in the selection list.
void	buildBonds ()
	Creates bonds.
void	addHydrogens ()
	Adds hydrogens.
virtual bool	checkResidue ()
	Check the residues.
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)
Public Types
enum	{ AMBER_FF = 0, CHARMM_FF, MMFF94_FF }
Public Member Functions
Constructors
	MolecularStructure (QWidget *parent=0, const char *name=0) throw ()
	Default Constructor.
	MolecularStructure (const MolecularStructure &m)
	only needed for Python Interface, dont call it!
Destructors
virtual	~MolecularStructure () throw ()
	Destructor.

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Detailed Description

MolecularStructure provides means to modify molecular structures and do several calculations.

To do so, it contains the 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
• 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.

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Constructor & Destructor Documentation

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

Default Constructor. Calls registerWidget. See also: ModularWidget

virtual VIEW::MolecularStructure::~MolecularStructure (   )  throw () [virtual]

Destructor.

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Member Function Documentation

void 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 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 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 VIEW::MolecularStructure::checkMenu (  MainControl &  main_control  )  throw () [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 VIEW::ModularWidget.

virtual void VIEW::MolecularStructure::fetchPreferences (  INIFile &  inifile  )  throw () [virtual]

Fetch the widgets preferences from the INIfile. Parameters: inifile  the INIFile that contains the required values Reimplemented from VIEW::ModularWidget.

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

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

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

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

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

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_.

virtual void 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 VIEW::ModularWidget.

virtual void VIEW::MolecularStructure::onNotify (  Message *  message  )  throw () [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 VIEW::ConnectionObject.

virtual void VIEW::MolecularStructure::writePreferences (  INIFile &  inifile  )  throw () [virtual]

Writes the widgets preferences to the INIFile. Parameters: inifile  the INIFile that contains the needed values Reimplemented from VIEW::ModularWidget.