BALL 1.5.0
Public Types | List of all members
BALL::VIEW::MolecularStructure Class Reference

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

Inheritance diagram for BALL::VIEW::MolecularStructure:
QWidget BALL::VIEW::ModularWidget BALL::Embeddable BALL::VIEW::ConnectionObject

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
 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)
 
BALL_DEPRECATED void setMenuHelp (QAction *, const String &)
 
virtual BALL_DEPRECATED void registerForHelpSystem (const QObject *, const String &)
 
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...
 
MainControlgetMainControl () 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...
 
FragmentDBgetFragmentDB () const
 
virtual void dump (std::ostream &s=std::cout, Size depth=0) const
 
void setWorkingDirFromFilename_ (String filename)
 
virtual BALL_DEPRECATED void showHelp (const String &)
 
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 StringgetIdentifier () 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)
 
ConnectionObjectgetParent () const
 
ConnectionObjectgetRoot ()
 
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)
 
ForceFieldgetForceField ()
 
Position getForceFieldID ()
 
AmberFFgetAmberFF ()
 
CharmmFFgetCharmmFF ()
 
MMFF94getMMFF94 ()
 
AmberConfigurationDialoggetAmberConfigurationDialog ()
 Get an instance of an dialog to setup the AMBER forcefield. More...
 
CharmmConfigurationDialoggetCharmmConfigurationDialog ()
 Get an instance of an dialog to setup the CHARMM forcefield. More...
 
MMFF94ConfigurationDialoggetMMFF94ConfigurationDialog ()
 
virtual void fetchPreferences (INIFile &inifile)
 
virtual void writePreferences (INIFile &inifile)
 
MolecularDynamicsDialoggetMDSimulationDialog ()
 
MinimizationDialoggetMinimizationDialog ()
 
FDPBDialoggetFDPBDialog ()
 
AssignBondOrderConfigurationDialoggetBondOrderDialog ()
 
const AssignBondOrderConfigurationDialoggetBondOrderDialog () const
 
AssignBondOrderResultsDialoggetBondOrderResultsDialog ()
 
const AssignBondOrderResultsDialoggetBondOrderResultsDialog () 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)
 
- Protected Member Functions inherited from BALL::VIEW::ConnectionObject
void notify_ (Message *message)
 
void notify_ (Message &message)
 
void onNotify_ (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 EmbeddablegetInstance_ (const std::type_info &type, Position index)
 
static EmbeddablegetInstance_ (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.:

Definition at line 90 of file molecularStructure.h.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum
Enumerator
AMBER_FF 
CHARMM_FF 
MMFF94_FF 

Definition at line 101 of file molecularStructure.h.

Constructor & Destructor Documentation

◆ MolecularStructure() [1/2]

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

Default Constructor. Calls registerWidget.

See also
ModularWidget

◆ MolecularStructure() [2/2]

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

only needed for Python Interface, dont call it!

◆ ~MolecularStructure()

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

Destructor.

Member Function Documentation

◆ addHydrogens

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.

◆ buildBonds

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.

◆ buildEndcaps

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.

◆ buildPeptide

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

Build a Peptide from a amino acid sequence.

◆ calculateFDPB

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

◆ calculateForceFieldEnergy

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

Calculate the energy for the currently selected force field.

◆ calculateHBonds

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

Calculate the H-Bonds for a Protein.

◆ calculateRamachandranPlot

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

Calculate a Ramachandran Plot.

◆ calculateRMSD

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

Calculate the RMSD between two Molecules.

◆ calculateSecondaryStructure

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

Calculate the secondary structure for a protein.

◆ centerCamera

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.

◆ checkMenu()

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.

◆ checkResidue

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

Check the residues

◆ chooseAmberFF

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

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

◆ chooseCharmmFF

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

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

◆ chooseForceField

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

◆ chooseMMFF94

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

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

◆ createGridFromCameraDistance

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

◆ createGridFromDistance

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

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

◆ fetchPreferences()

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

Fetch the widgets preferences from the INIfile.

Parameters
inifilethe INIFile that contains the required values

Reimplemented from BALL::VIEW::ModularWidget.

◆ generateCrystal

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

Build a crystal packing for a loaded system.

◆ getAmberConfigurationDialog()

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

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

◆ getAmberFF()

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.

◆ getBondOrderDialog() [1/2]

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

Definition at line 220 of file molecularStructure.h.

◆ getBondOrderDialog() [2/2]

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

Definition at line 223 of file molecularStructure.h.

◆ getBondOrderResultsDialog() [1/2]

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

Definition at line 226 of file molecularStructure.h.

◆ getBondOrderResultsDialog() [2/2]

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

Definition at line 229 of file molecularStructure.h.

◆ getCharmmConfigurationDialog()

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

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

◆ getCharmmFF()

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.

◆ getFDPBDialog()

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

Definition at line 217 of file molecularStructure.h.

◆ getForceField()

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_.

◆ getForceFieldID()

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

Get the force_field_id of the currently selected ForceField

◆ getMDSimulationDialog()

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

Definition at line 211 of file molecularStructure.h.

◆ getMinimizationDialog()

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

Definition at line 214 of file molecularStructure.h.

◆ getMMFF94()

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

◆ getMMFF94ConfigurationDialog()

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

◆ initializeWidget()

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_controlthe MainControl object to be initialized
See also
finalizeWidget

Reimplemented from BALL::VIEW::ModularWidget.

◆ mapProteins

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

Map two Proteins and apply the resulting transformation matrix.

◆ MDSimulation

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

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

◆ onNotify()

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
messagethe pointer to the message that should be processed
See also
CompositeMessage
GeometricObjectSelectionMessage
MolecularTaskMessage

Reimplemented from BALL::VIEW::ConnectionObject.

◆ runBondOrderAssignment

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.

◆ runMinimization

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

Run a energy minization with the currently selected force field.

◆ setupForceField

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

Show a dialog to setup the currently selected force field.

◆ showAmberForceFieldOptions

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

Show the dialog to setup the AMBER force field.

◆ showBondOrderAssignmentResults

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.

◆ showCharmmForceFieldOptions

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

Show the dialog to setup the CHARMM force field.

◆ showMMFF94ForceFieldOptions

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

◆ writePreferences()

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

Writes the widgets preferences to the INIFile.

Parameters
inifilethe INIFile that contains the needed values

Reimplemented from BALL::VIEW::ModularWidget.