Classes
class	ColorExtension2

class	MultiColorExtension

class	ColorHSV

class	ColorMap

class	ColorRGBA

class	ColorUnit

class	ColorUnitHue

class	Dataset

class	DatasetController

class	RaytraceableGrid

class	RegularData3DController

class	TrajectoryController

class	DockResultController

class	VectorGridController

class	RaytraceableGridController

class	Vertex

class	Vertex2

class	AmberConfigurationDialog

class	AssignBondOrderConfigurationDialog

class	AssignBondOrderResultsDialog

class	AtomOverview

class	BondProperties

class	CharmmConfigurationDialog

class	ClippingDialog

class	ColoringSettingsDialog

class	CompositeProperties

class	ContourSurfaceDialog

class	DisplayProperties

class	DockDialog

class	DockProgressDialog

class	DockResultDialog

class	DownloadElectronDensity

class	DownloadPDBFile

class	EditOperationDialog

class	EditSettings

class	EditSingleShortcut

class	ExportGeometryDialog

class	FDPBDialog

class	FieldLinesDialog

class	GeometricFitDialog

class	GridVisualizationDialog

class	LabelDialog

class	LightSettings

class	MainControlPreferences

class	MaterialSettings

class	MinimizationDialog

class	MMFF94ConfigurationDialog

class	ModelSettingsDialog

class	ModifyRepresentationDialog

class	MolecularDynamicsDialog

class	MolecularFileDialog

class	NetworkPreferences

class	OpenBruker1DFile

class	OpenBruker2DFile

class	OpenSavePreferences

class	ParsedFunctionDialog

class	PeptideDialog

class	PluginModel

class	PluginDialog

class	Preferences

class	PTEDialog

class	PubChemDialog

class	PythonSettings

class	RaytraceableContourSurfaceDialog

class	RunGAMESSDialog

class	ServerPreferences

class	SetCamera

class	SetClippingPlane

class	ShortcutDialog

class	SnapshotVisualisationDialog

class	StageSettings

class	StereoSettingsDialog

class	UndoManagerDialog

class	ButtonEvent

class	DeviceEvent

class	FakeDriver

class	HeadTrackingEvent

class	InputDeviceDriver

class	InputPlugin

class	MotionTrackingEvent

class	NotificationEvent

class	TransformationEvent6D

class	ClippingPlane

class	LogEvent
	Event class used for thread safe output to logview. More...

class	CompositeManager

class	ConnectionObject

class	GeometricObject

class	IconLoader

class	MainControl

class	Message

class	DatasetMessage

class	CompositeMessage

class	SceneMessage

class	GenericSelectionMessage

class	ControlSelectionMessage

class	NewSelectionMessage

class	GeometricObjectSelectionMessage

class	RepresentationMessage
	Base class for all messages concerning a Representation. More...

class	MolecularTaskMessage

class	ShowDisplayPropertiesMessage

class	CreateRepresentationMessage

class	DeselectControlsMessage

class	TransformationMessage

class	FinishedSimulationMessage

class	SyncClippingPlanesMessage

class	ShowHelpMessage

class	RegisterHelpSystemMessage

class	DockingFinishedMessage
	Message to notify docking has finished. More...

class	ModelInformation

class	ModularWidget

class	PreferencesEntry

class	Representation

class	RepresentationManager

class	ServerWidget

class	ShortcutRegistry

class	SnapshotManagerInterface

class	LightSource

class	Camera

class	Stage

class	MessageEvent

class	BALLThread

class	CalculateFDPBThread

class	UpdateRepresentationThread

class	SimulationThread

class	EnergyMinimizerThread
	Thread for EnergyMinimization. More...

class	MDSimulationThread
	Thread for MDSimulation. More...

class	DockingThread
	Thread for Docking. More...

class	AtomBondModelBaseProcessor

class	AddBackboneModel

class	AddBallAndStickModel

class	AddCartoonModel

class	ColorByGridProcessor

class	ColorProcessor

class	InterpolateColorProcessor

class	FieldLineCreator

class	ForceModel

class	HBondModelProcessor

class	LabelModel

class	AddLineModel

class	ModelProcessor

class	ElementColorProcessor

class	ResidueNumberColorProcessor

class	PositionColorProcessor

class	ChainColorProcessor

class	MoleculeColorProcessor

class	ResidueNameColorProcessor

class	AtomChargeColorProcessor

class	AtomDistanceColorProcessor

class	CustomColorProcessor

class	TemperatureFactorColorProcessor

class	OccupancyColorProcessor

class	ForceColorProcessor

class	SecondaryStructureColorProcessor

class	ResidueTypeColorProcessor

class	AddSurfaceModel

class	AddVanDerWaalsModel

class	InputDevPluginHandler

class	VIEWPlugin

class	Box

class	Disc

class	GridVisualisation

class	Label

class	Line

class	Mesh

class	MultiLine

class	Point

class	QuadMesh

class	SimpleBox

class	Sphere

class	Tube

class	TwoColoredLine

class	TwoColoredTube

class	BufferedRenderer

class	GLDisplayList

class	GLOffscreenTarget

class	GLRenderer

class	GLRenderWindow

struct	ChannelFormat

class	PixelFormat

class	POVRenderer

class	Renderer

class	RenderSetup

struct	Resolution

class	FrameBufferFormat

class	FrameBuffer

class	RenderTarget

class	RenderWindow

class	STLRenderer

class	TilingRenderer

class	MeshBuffer

class	VRMLRenderer

class	CanvasWidget

class	ColorButton

class	ColorTable

class	DatasetControl

class	DockingController

class	DockWidget

class	EditableScene

class	EditFunctions

class	FileObserver

class	TreeWidget

class	GenericControl

class	GeometricControl

class	GridColorWidget

class	MyTextBrowser

class	HelpViewer

class	ComboBoxDelegate

class	HotkeyTable

class	DragLogView

class	LogView

class	MolecularControl

class	MolecularStructure

class	PropEditorWidget

class	BoolEditorWidget

class	IntEditorWidget

class	UIntEditorWidget

class	FloatEditorWidget

class	DoubleEditorWidget

class	StringEditorWidget

class	PropDeleteWidget

class	PDBInfoEditorWidget

class	PropertyEditor

class	PythonHighlighter

class	PythonValidator

class	RunPythonThread

struct	Hotkey

class	PyWidget

class	RegularData1DWidget

class	DockableRegularData1DWidget

class	RegularData2DWidget

class	DockableRegularData2DWidget

class	Scene

class	AnimationThread

class	SDWidget

class	ShortcutTableView

class	ShortcutTableModel

class	TestFramework

class	TextEditorWidget

class	DemoTutorialDialog

Typedefs
typedef TRegularData3D< Vector3 >	VectorGrid

typedef QFlags< InputDeviceButton >	InputDeviceButtons

typedef std::list < GeometricObject * >	GeometricObjectList

typedef std::list < Representation * >	RepresentationList

typedef std::vector < FrameBufferFormat >	BufferFormatList

typedef boost::shared_ptr < FrameBuffer >	FrameBufferPtr

typedef RenderWindow< float >	t_RenderWindow

Enumerations
enum	InputDeviceButton { BUTTON1 = 1 << 0, BUTTON2 = 1 << 1, BUTTON3 = 1 << 2, BUTTON4 = 1 << 3, BUTTON5 = 1 << 4, BUTTON6 = 1 << 5, BUTTON7 = 1 << 6, BUTTON8 = 1 << 7, BUTTON9 = 1 << 8, BUTTON10 = 1 << 9, BUTTON11 = 1 << 10, BUTTON12 = 1 << 11 }

enum	TutorialSteps { TUTORIAL_PEPTIDE = 1, TUTORIAL_ROTATE, TUTORIAL_HIERARCHY, TUTORIAL_MDS, TUTORIAL_TRAJECTORY, TUTORIAL_ES, TUTORIAL_SES, TUTORIAL_SES_COLORING, TUTORIAL_CS }

General enumerations, methods and typedefs
These predefined types are used in VIEW for portability and comprehensibility.
enum	EventsIDs { MESSAGE_EVENT = 60000, LOG_EVENT, TRANSFORMATION_EVENT_6D, HEADTRACKING_EVENT, MOTIONTRACKING_EVENT, BUTTON_PRESS_EVENT, BUTTON_RELEASE_EVENT, NOTIFICATION_EVENT }

Functions
std::ostream &	operator<< (std::ostream &o, const PixelFormat &f)

std::ostream &	operator<< (std::ostream &o, const FrameBufferFormat &f)

Variables
ColorRGBA	BALL_SELECTED_COLOR

PreciseTime	BALL_SELECTED_COLOR_CHANGE_TIME

Enumerations for Representations and Renderer
Enums and methods to describe the models and drawing methods.
enum	DrawingMode { DRAWING_MODE_DOTS = 0, DRAWING_MODE_WIREFRAME, DRAWING_MODE_SOLID, DRAWING_MODE_TOON }
	Enumeration for Drawing Modes. More...

enum	DrawingPrecision { DRAWING_PRECISION_INVALID = -1, DRAWING_PRECISION_LOW = 0, DRAWING_PRECISION_MEDIUM, DRAWING_PRECISION_HIGH, DRAWING_PRECISION_ULTRA }
	Enumeration for Drawing Precisions. More...

enum	ModelType { MODEL_LINES = 0, MODEL_STICK, MODEL_BALL_AND_STICK, MODEL_VDW, MODEL_SE_SURFACE, MODEL_SA_SURFACE, MODEL_BACKBONE, MODEL_CARTOON, MODEL_RIBBON, MODEL_HBONDS, MODEL_FORCES, MODEL_LABEL = 100, MODEL_CONTOUR_SURFACE, MODEL_GRID_SLICE, MODEL_GRID_VOLUME, MODEL_FIELD_LINES, MODEL_INFORMATIONS, MODEL_COORDINATE_SYSTEM, MODEL_UNKNOWN = 200 }

enum	ColoringMethod { COLORING_ELEMENT = 0, COLORING_RESIDUE_INDEX, COLORING_RESIDUE_NAME, COLORING_SECONDARY_STRUCTURE, COLORING_ATOM_CHARGE, COLORING_DISTANCE, COLORING_TEMPERATURE_FACTOR, COLORING_OCCUPANCY, COLORING_FORCES, COLORING_RESIDUE_TYPE, COLORING_CHAIN, COLORING_MOLECULE, COLORING_CUSTOM, COLORING_UNKNOWN = 200 }

BALL_VIEW_EXPORT float	SurfaceDrawingPrecisions [4]
	Mapping from the enum to the float values of Surfaces. More...

BALL_VIEW_EXPORT Composite	composite_to_be_ignored_for_colorprocessors_

float	icosaeder_vertices [12][3]

Position	icosaeder_indices [20][3]

BALL_VIEW_EXPORT String	vector3ToString (const Vector3 &v)

BALL_VIEW_EXPORT bool	stringToVector3 (const String &data, Vector3 &v)

BALL_VIEW_EXPORT String	createFloatString (float value, Size precision)
	create a string from a float and cut after a given number of digits after the dot More...

BALL_VIEW_EXPORT MainControl *	getMainControl ()

BALL_VIEW_EXPORT String	createTemporaryFilename ()
	Create a temporary filename in the users home dir. More...

BALL_VIEW_EXPORT Vector3	getNormal (const Vector3 &v)

BALL_VIEW_EXPORT void	logString (const String &data)
	thread safe output to logview More...

BALL_VIEW_EXPORT void	processDropEvent (QDropEvent *e)

BALL_VIEW_EXPORT Camera	focusCamera (Composite *composite)

BALL_VIEW_EXPORT Camera	focusCamera (const std::list< Vector3 > &points)

BALL_VIEW_EXPORT String	ascii (const QString &str)

BALL_VIEW_EXPORT ColorRGBA	getColor (const QLabel *label)

BALL_VIEW_EXPORT void	setColor (const QLabel *label, const ColorRGBA &color)

BALL_VIEW_EXPORT QColor	chooseColor (QLabel *label)

BALL_VIEW_EXPORT void	setTextColor (QLabel *label, const ColorRGBA &color)

BALL_VIEW_EXPORT void	cubicInterpolation (const Vector3 &a, const Vector3 &b, const Vector3 &tangent_a, const Vector3 &tangent_b, std::vector< Vector3 > &interpolated_values)

BALL_VIEW_EXPORT void	subdivideTriangle (vector< Vector3 > &results, Vector3 &v1, Vector3 &v2, Vector3 &v3, Size precision)

BALL_VIEW_EXPORT vector< Vector3 >	createSphere (Size precision)

BALL_VIEW_EXPORT void	calculateHistogramEqualization (const vector< float > &values, vector< float > &normalized_values, bool use_absolute_values=false)

BALL_VIEW_EXPORT void	calculateRandomPoints (const RegularData3D &grid, Size nr_points, vector< Vector3 > &resulting_points)
	calcualte a random set of points, dependening of the field strength of a grid More...

Typedef Documentation

typedef std::vector<FrameBufferFormat> BALL::VIEW::BufferFormatList

Definition at line 171 of file renderTarget.h.

typedef boost::shared_ptr<FrameBuffer> BALL::VIEW::FrameBufferPtr

Definition at line 222 of file renderTarget.h.

typedef std::list<GeometricObject*> BALL::VIEW::GeometricObjectList

Definition at line 185 of file geometricObject.h.

typedef QFlags<InputDeviceButton> BALL::VIEW::InputDeviceButtons

Definition at line 28 of file buttonEvent.h.

typedef std::list<Representation*> BALL::VIEW::RepresentationList

Definition at line 342 of file representation.h.

typedef RenderWindow<float> BALL::VIEW::t_RenderWindow

Definition at line 104 of file renderWindow.h.

typedef TRegularData3D<Vector3> BALL::VIEW::VectorGrid

Definition at line 251 of file standardDatasets.h.

Enumeration Type Documentation

enum BALL::VIEW::ColoringMethod

Enumeration for Coloring Methods. Add new coloring methods before COLORING_CUSTOM.

Enumerator
COLORING_ELEMENT
COLORING_RESIDUE_INDEX
COLORING_RESIDUE_NAME
COLORING_SECONDARY_STRUCTURE
COLORING_ATOM_CHARGE
COLORING_DISTANCE
COLORING_TEMPERATURE_FACTOR
COLORING_OCCUPANCY
COLORING_FORCES
COLORING_RESIDUE_TYPE
COLORING_CHAIN
COLORING_MOLECULE
COLORING_CUSTOM
COLORING_UNKNOWN

Definition at line 230 of file VIEW/KERNEL/common.h.

enum BALL::VIEW::DrawingMode

Enumeration for Drawing Modes.

Enumerator
DRAWING_MODE_DOTS
DRAWING_MODE_WIREFRAME
DRAWING_MODE_SOLID
DRAWING_MODE_TOON

Definition at line 106 of file VIEW/KERNEL/common.h.

enum BALL::VIEW::DrawingPrecision

Enumeration for Drawing Precisions.

Enumerator
DRAWING_PRECISION_INVALID
DRAWING_PRECISION_LOW
DRAWING_PRECISION_MEDIUM
DRAWING_PRECISION_HIGH
DRAWING_PRECISION_ULTRA

Definition at line 125 of file VIEW/KERNEL/common.h.

enum BALL::VIEW::EventsIDs

Enumeration of Events These events are used to communicate between different threads. Have a look at QWidget::customEvent(QEvent*) to learn about QT and its events concept. This enum is used to give every type of derived QEvent its individual type id.

Enumerator
MESSAGE_EVENT	An event with a contained VIEW message.
LOG_EVENT	Event to print output from a Thread.
TRANSFORMATION_EVENT_6D	Event that encodes a 6 dimensional transformation.
HEADTRACKING_EVENT	Event that encodes a head tracker position change.
MOTIONTRACKING_EVENT	Event that encodes a motion tracker position change.
BUTTON_PRESS_EVENT	Event for button press events of custom input devices.
BUTTON_RELEASE_EVENT	Event for button press events of custom input devices.
NOTIFICATION_EVENT	Event for passing BALL Messages accross threads.

Definition at line 71 of file VIEW/KERNEL/common.h.

enum BALL::VIEW::InputDeviceButton

Enumerator
BUTTON1
BUTTON2
BUTTON3
BUTTON4
BUTTON5
BUTTON6
BUTTON7
BUTTON8
BUTTON9
BUTTON10
BUTTON11
BUTTON12

Definition at line 13 of file buttonEvent.h.

enum BALL::VIEW::ModelType

This properties define the available models. Add new model entries directly before MODEL_LABEL if you want them to show up in the DisplayProperties dialog! You may have to modify the following methods, if you add a new ModelType:

See Also: getModelName(ModelType type); getColoringName(ColoringMethod type); isSurfaceModel(ModelType type); modelMuteableByDisplayProperties(ModelType type); modelMustBeRebuild(ModelType type)

Enumerator
MODEL_LINES	defines the property for the model: Lines
MODEL_STICK	defines the property for the model: Stick
MODEL_BALL_AND_STICK	defines the property for the model: Ball and Stick
MODEL_VDW	defines the property for the model: Van der Waals
MODEL_SE_SURFACE	defines the property for the model: solvent-excluded surface
MODEL_SA_SURFACE	defines the property for the model: solvent-accessible surface
MODEL_BACKBONE	defines the property for the model: Backbone
MODEL_CARTOON	defines the property for the model: Cartoon
MODEL_RIBBON	defines the property for the model: Ribbon
MODEL_HBONDS	defines the property for the model: H-Bonds
MODEL_FORCES
MODEL_LABEL	defines the property for the model: Label
MODEL_CONTOUR_SURFACE	defines the property for the model: contour surface
MODEL_GRID_SLICE
MODEL_GRID_VOLUME
MODEL_FIELD_LINES
MODEL_INFORMATIONS
MODEL_COORDINATE_SYSTEM
MODEL_UNKNOWN	unkown property

Definition at line 162 of file VIEW/KERNEL/common.h.

enum BALL::VIEW::TutorialSteps

Enumerator
TUTORIAL_PEPTIDE
TUTORIAL_ROTATE
TUTORIAL_HIERARCHY
TUTORIAL_MDS
TUTORIAL_TRAJECTORY
TUTORIAL_ES
TUTORIAL_SES
TUTORIAL_SES_COLORING
TUTORIAL_CS

Definition at line 40 of file demoTutorialDialog.C.

Function Documentation

BALL_VIEW_EXPORT String BALL::VIEW::ascii ( const QString & str )

BALL_VIEW_EXPORT void BALL::VIEW::calculateHistogramEqualization	(	const vector< float > &	values,
		vector< float > &	normalized_values,
		bool	use_absolute_values = `false`
	)

BALL_VIEW_EXPORT void BALL::VIEW::calculateRandomPoints	(	const RegularData3D &	grid,
		Size	nr_points,
		vector< Vector3 > &	resulting_points
	)

calcualte a random set of points, dependening of the field strength of a grid

BALL_VIEW_EXPORT QColor BALL::VIEW::chooseColor ( QLabel * label )

BALL_VIEW_EXPORT String BALL::VIEW::createFloatString	(	float	value,
		Size	precision
	)

create a string from a float and cut after a given number of digits after the dot

BALL_VIEW_EXPORT vector<Vector3> BALL::VIEW::createSphere ( Size precision )

BALL_VIEW_EXPORT String BALL::VIEW::createTemporaryFilename ( )

Create a temporary filename in the users home dir.

BALL_VIEW_EXPORT void BALL::VIEW::cubicInterpolation	(	const Vector3 &	a,
		const Vector3 &	b,
		const Vector3 &	tangent_a,
		const Vector3 &	tangent_b,
		std::vector< Vector3 > &	interpolated_values
	)

Uses the de-Casteljou algorithm to evalute a cubic Hermite interpolation polynomial at interpolated_values.size() equidistant values.

BALL_VIEW_EXPORT Camera BALL::VIEW::focusCamera ( Composite * composite )

Focus the camera on a Composite Sends a SceneMessage.

BALL_VIEW_EXPORT Camera BALL::VIEW::focusCamera ( const std::list< Vector3 > & points )

Focus the camera on a list of points, e.g. atoms or geometric objects. Sends a SceneMessage.

BALL_VIEW_EXPORT ColorRGBA BALL::VIEW::getColor ( const QLabel * label )

BALL_VIEW_EXPORT MainControl* BALL::VIEW::getMainControl ( )

Get MainControl This method is only to be used for code, which is not part of a ModularWidget. On Windows, it uses the following cast:\ MainControl* mc = dynamic_cast<MainControl*>(qApp->mainWidget());\ On all other platforms, it uses MainControl::getInstance(0);

BALL_VIEW_EXPORT Vector3 BALL::VIEW::getNormal ( const Vector3 & v )

BALL_VIEW_EXPORT void BALL::VIEW::logString ( const String & data )

thread safe output to logview

std::ostream& BALL::VIEW::operator<<	(	std::ostream &	o,
		const FrameBufferFormat &	f
	)

inline

Definition at line 164 of file renderTarget.h.

std::ostream& BALL::VIEW::operator<<	(	std::ostream &	o,
		const PixelFormat &	f
	)

inline

Definition at line 209 of file pixelFormat.h.

BALL_VIEW_EXPORT void BALL::VIEW::processDropEvent ( QDropEvent * e )

BALL_VIEW_EXPORT void BALL::VIEW::setColor	(	const QLabel *	label,
		const ColorRGBA &	color
	)

BALL_VIEW_EXPORT void BALL::VIEW::setTextColor	(	QLabel *	label,
		const ColorRGBA &	color
	)

BALL_VIEW_EXPORT bool BALL::VIEW::stringToVector3	(	const String &	data,
		Vector3 &	v
	)

BALL_VIEW_EXPORT void BALL::VIEW::subdivideTriangle	(	vector< Vector3 > &	results,
		Vector3 &	v1,
		Vector3 &	v2,
		Vector3 &	v3,
		Size	precision
	)

BALL_VIEW_EXPORT String BALL::VIEW::vector3ToString ( const Vector3 & v )

Variable Documentation

ColorRGBA BALL::VIEW::BALL_SELECTED_COLOR

Static instance for the color of selected geometric objects

PreciseTime BALL::VIEW::BALL_SELECTED_COLOR_CHANGE_TIME

BALL_VIEW_EXPORT Composite BALL::VIEW::composite_to_be_ignored_for_colorprocessors_

A special Composite, which is ignored by all ColoringProcessors, the GeometricObjects, which have this Composite set, will be colored by the default color.

Position BALL::VIEW::icosaeder_indices[20][3]

float BALL::VIEW::icosaeder_vertices[12][3]

Code to refine a icosaeder:

BALL_VIEW_EXPORT float BALL::VIEW::SurfaceDrawingPrecisions[4]

Mapping from the enum to the float values of Surfaces.

Classes

Typedefs

Enumerations

Functions

Variables

Enumerations for Representations and Renderer

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation