BALL::VIEW Namespace Reference


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	QColorTable
class	ColoringSettingsDialog
class	CompositeProperties
class	ContourSurfaceDialog
class	DisplayProperties
class	DockDialog
class	DockProgressDialog
class	DockResultDialog
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	ComboBoxDelegate
class	HotkeyTable
class	PythonSettings
class	RaytraceableContourSurfaceDialog
class	RunGAMESSDialog
class	ServerPreferences
class	SetCamera
class	SetClippingPlane
class	ShortcutDialog
class	SnapshotVisualisationDialog
class	StageSettings
class	StereoSettingsDialog
class	ButtonEvent
class	DeviceEvent
class	FakeDriver
class	HeadTrackingEvent
class	InputDeviceDriver
class	InputPlugin
class	MotionTrackingEvent
class	TransformationEvent6D
class	ClippingPlane
class	LogEvent
	Event class used for thread safe output to logview. More...
class	CompositeManager
class	ConnectionObject
class	GeometricObject
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	LightSource
class	Camera
class	Stage
class	MessageEvent
class	BALLThread
class	FetchHTMLThread
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	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	DatasetControl
class	DockingController
class	DockWidget
class	EditableScene
class	EditFunctions
class	FileObserver
class	TreeWidget
class	GenericControl
class	GeometricControl
class	MyTextBrowser
class	HelpViewer
class	DragLogView
class	LogView
class	MolecularControl
class	MolecularStructure
class	PythonHighlighter
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	DemoTutorialDialog
Typedefs
typedef TRegularData3D< Vector3 >	VectorGrid
typedef QFlags< InputDeviceButton >	InputDeviceButtons
typedef List< GeometricObject * >	GeometricObjectList
typedef 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 }
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.
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
BALL_VIEW_EXPORT MainControl *	getMainControl ()
BALL_VIEW_EXPORT String	createTemporaryFilename ()
	Create a temporary filename in the users home dir.
BALL_VIEW_EXPORT Vector3	getNormal (const Vector3 &v)
BALL_VIEW_EXPORT void	logString (const String &data)
	thread safe output to logview
BALL_VIEW_EXPORT void	processDropEvent (QDropEvent *e)
BALL_VIEW_EXPORT Camera	focusCamera (Composite *composite)
BALL_VIEW_EXPORT Camera	focusCamera (const 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

Typedef Documentation

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

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

typedef List<GeometricObject*> BALL::VIEW::GeometricObjectList

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

typedef List<Representation*> BALL::VIEW::RepresentationList

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

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

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

enum BALL::VIEW::DrawingMode

Enumeration for Drawing Modes.

Enumerator:

DRAWING_MODE_DOTS
DRAWING_MODE_WIREFRAME
DRAWING_MODE_SOLID
DRAWING_MODE_TOON

enum BALL::VIEW::DrawingPrecision

Enumeration for Drawing Precisions.

Enumerator:

DRAWING_PRECISION_INVALID
DRAWING_PRECISION_LOW
DRAWING_PRECISION_MEDIUM
DRAWING_PRECISION_HIGH
DRAWING_PRECISION_ULTRA

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.

enum BALL::VIEW::InputDeviceButton

Enumerator:

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

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

enum BALL::VIEW::TutorialSteps

Enumerator:

TUTORIAL_PEPTIDE
TUTORIAL_ROTATE
TUTORIAL_HIERARCHY
TUTORIAL_MDS
TUTORIAL_TRAJECTORY
TUTORIAL_ES
TUTORIAL_SES
TUTORIAL_SES_COLORING
TUTORIAL_CS

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 ( const List< Vector3 > & points )

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

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

Focus the camera on a Composite 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]`

References BALL::VIEW::FrameBufferFormat::getHeight(), BALL::VIEW::FrameBufferFormat::getPitch(), BALL::VIEW::FrameBufferFormat::getPixelFormat(), and BALL::VIEW::FrameBufferFormat::getWidth().

std::ostream& BALL::VIEW::operator<<	(	std::ostream &	o,
		const PixelFormat &	f
	)			`[inline]`

References BALL::VIEW::PixelFormat::print().

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.

BALL::VIEW Namespace Reference

Classes

Typedefs

Enumerations

Functions

Variables

Enumerations for Representations and Renderer

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation