Typedef

Static Public Summary
public	AngleRepresentationParameters: Object
public	BallAndStickRepresentationParameters: Object Ball And Stick representation parameter object.
public	BufferParameters: Object Buffer parameter object.
public	ColormakerParameters: Object Colormaker parameter object.
public	ComponentParameters: Object Component parameter object.
public	ComponentSignals: Object
public	DihedralRepresentationParameters: Object
public	DistanceRepresentationParameters: Object Distance representation parameter object.
public	DotRepresentationParameters: Object Dot representation parameter object.
public	ImageParameters: Object Image parameter object.
public	LabelRepresentationParameters: Object Label representation parameter object.
public	LoaderParameters: Object Loader parameter object.
public	MeasurementRepresentationParameters: Object Measurement representation parameter object.
public	MolecularSurfaceParameters: Object Molecular surface parameter object.
public	MouseSignals: Object
public	OrientationMatrix: Matrix4 Orientation matrix, a 4x4 transformation matrix with rotation part used for scene rotation, scale part for scene camera distance and position part for scene translation
public	PickingData: Object Picking data object.
public	RepresentationComponentSignals: Object Extends ComponentSignals
public	RepresentationParameters: Object Representation parameter object.
public	SliceRepresentationParameters: Object Slice representation parameter object.
public	StageParameters: Object Stage parameter object.
public	StageSignals: Object
public	StructureComponentSignals: Object Extends ComponentSignals
public	StructureExtraData: Object Structure extra data.
public	StructureHeader: Object Structure header object.
public	StructureRepresentationParameters: Object Structure representation parameter object.
public	SurfaceRepresentationParameters: Object Surface representation parameter object.
public	TextBufferParameters: Object Text buffer parameter object.
public	TrajectoryComponentParameters: Object Trajectory component parameter object.
public	TrajectoryComponentSignals: Object Extends ComponentSignals
public	TrajectoryParameters: Object Trajectory parameter object.
public	TrajectoryPlayerParameters: Object Trajectory player parameter object.
public	TrajectoryRepresentationParameters: Object Trajectory representation parameter object.
public	TrajectorySignals: Object
public	TriggerString: String Strings to describe mouse events (including optional keyboard modifiers).

Static Public

public AngleRepresentationParameters: Object source

Properties:

Name	Type	Attribute	Description
atomTriple	String		list of triplets of selection strings or atom indices
vectorVisible	Boolean		Indicate the 3 points for each angle by drawing lines 1-2-3
arcVisible	Boolean		Show the arc outline for each angle
lineOpacity	Number		opacity for the line part of the representation
linewidth	Number		width for line part of representation
sectorVisible	Boolean		Show the filled arc for each angle

public BallAndStickRepresentationParameters: Object source

Ball And Stick representation parameter object. Extends RepresentationParameters and StructureRepresentationParameters.

Properties:

Name	Type	Attribute	Description
sphereDetail	Integer		sphere quality (icosahedron subdivisions)
radialSegments	Integer		cylinder quality (number of segments)
openEnded	Boolean		capped or not
disableImpostor	Boolean		disable use of raycasted impostors for rendering
aspectRatio	Float		size difference between atom and bond radii
lineOnly	Boolean		render only bonds, and only as lines
linewidth	Integer		width of lines
cylinderOnly	Boolean		render only bonds (no atoms)
multipleBond	String		one off "off", "symmetric", "offset"
bondSpacing	Float		spacing for multiple bond rendering
bondScale	Float		scale/radius for multiple bond rendering

public BufferParameters: Object source

Buffer parameter object.

Properties:

Name	Type	Attribute	Description
opaqueBack	Boolean		render back-side opaque
dullInterior	Boolean		render back-side with dull lighting
side	String		which triangle sides to render, "front" front-side, "back" back-side, "double" front- and back-side
opacity	Float		translucency: 1 is fully opaque, 0 is fully transparent
depthWrite	Boolean		depth write
clipNear	Integer		position of camera near/front clipping plane in percent of scene bounding box
flatShaded	Boolean		render flat shaded
wireframe	Boolean		render as wireframe
roughness	Float		how rough the material is, between 0 and 1
metalness	Float		how metallic the material is, between 0 and 1
diffuse	Color		diffuse color for lighting
forceTransparent	Boolean		force the material to allow transparency
matrix	Matrix4		additional transformation matrix
disablePicking	Boolean		disable picking

public ColormakerParameters: Object source

Colormaker parameter object.

Properties:

Name	Type	Attribute	Description
scale	String \| Array	optional	color scale, either a string for a predefined scale or an array of colors to be used as the scale
mode	String	optional	color mode, one of rgb, hsv, hsl, hsi, lab, hcl
colorDomain	Integer[]	optional	scale value range
colorDomain.0	Integer		min value
colorDomain.1	Integer		max value
value	Color \| String \| Integer	optional	color value
structure	Structure	optional	structure object
volume	Volume	optional	volume object
surface	Surface	optional	surface object

public ComponentParameters: Object source

Component parameter object.

Properties:

Name	Type	Attribute	Description
name	String		component name
visible	Boolean		component visibility

public ComponentSignals: Object source

Properties:

Name	Type	Attribute	Description
representationAdded	Signal<RepresentationComponent>		when a representation is added
representationRemoved	Signal<RepresentationComponent>		when a representation is removed
matrixChanged	Signal<Matrix4>		on matrix change
visibilityChanged	Signal<Boolean>		on visibility change
statusChanged	Signal<String>		on status change
nameChanged	Signal<String>		on name change
disposed	Signal		on dispose

Example:

component.signals.representationAdded.add(function (representationComponent) { ... });

public DihedralRepresentationParameters: Object source

Properties:

Name	Type	Attribute	Description
atomQuad	String		list of quadruplets of selection strings or atom indices
lineOpacity	Number		Opacity for the line part of the representation
lineVisible	Boolean		Display the line part of the representation
linewidth	Number		width for line part of representation
planeVisible	Boolean		Display the two planes corresponding to dihedral
sectorVisible	Boolean		Display the filled arc for each angle

public DistanceRepresentationParameters: Object source

Distance representation parameter object.

Properties:

Name	Type	Attribute	Description
labelUnit	String		distance unit (e.g. "angstrom" or "nm"). If set, a distance symbol is appended to the label (i.e. 'nm' or '\u00C5'). In case of 'nm', the distance value is computed in nanometers instead of Angstroms.
atomPair	Array[]		list of pairs of selection strings (see Selection) or pairs of atom indices. Using atom indices is much more when the representation is updated often, e.g. by changing the selection or the atom positions, as their are no selection strings to be evaluated.
radialSegments	Integer		cylinder quality (number of segments)
disableImpostor	Boolean		disable use of raycasted impostors for rendering

public DotRepresentationParameters: Object source

Dot representation parameter object. Extends RepresentationParameters

Properties:

Name	Type	Attribute	Description
thresholdType	String		Meaning of the threshold values. Either value for the literal value or sigma as a factor of the sigma of the data. For volume data only.
thresholdMin	Number		Minimum value to be displayed. For volume data only.
thresholdMax	Number		Maximum value to be displayed. For volume data only.
thresholdOut	Number		Show only values falling outside of the treshold minumum and maximum. For volume data only.

public ImageParameters: Object source

Image parameter object.

Properties:

Name	Type	Attribute	Description
trim	Boolean		trim the image
factor	Integer		scaling factor to apply to the viewer canvas
antialias	Boolean		antialias the image
transparent	Boolean		transparent image background

public LabelRepresentationParameters: Object source

Label representation parameter object. Extends RepresentationParameters and StructureRepresentationParameters.

Properties:

Name	Type	Attribute	Description
clipNear	Integer		position of camera near/front clipping plane in percent of scene bounding box
opacity	Float		translucency: 1 is fully opaque, 0 is fully transparent
labelType	String		type of the label, one of: "atomname", "atomindex", "occupancy", "bfactor", "serial", "element", "atom", "resname", "resno", "res", "text", "qualified". When set to "text", the `labelText` list is used.
labelText	String[]		list of label strings, must set `labelType` to "text" to take effect
fontFamily	String		font family, one of: "sans-serif", "monospace", "serif"
fontStyle	String		font style, "normal" or "italic"
fontWeight	String		font weight, "normal" or "bold"
sdf	Boolean		use "signed distance field"-based rendering for sharper edges
xOffset	Float		offset in x-direction
yOffset	Float		offset in y-direction
zOffset	Float		offset in z-direction (i.e. in camera direction)
attachment	String		attachment of the label, one of: "bottom-left", "bottom-center", "bottom-right", "middle-left", "middle-center", "middle-right", "top-left", "top-center", "top-right"
showBorder	Boolean		show border/outline
borderColor	Color		color of the border/outline
borderWidth	Float		width of the border/outline
showBackground	Boolean		show background rectangle
backgroundColor	Color		color of the background
backgroundMargin	Float		width of the background
backgroundOpacity	Float		opacity of the background

public LoaderParameters: Object source

Loader parameter object.

Properties:

Name	Type	Attribute	Description
ext	String		file extension, determines file type
compressed	Boolean		flag data as compressed
binary	Boolean		flag data as binary
name	String		set data name

public MeasurementRepresentationParameters: Object source

Measurement representation parameter object.

Properties:

Name	Type	Attribute	Description
labelSize	Float		size of the distance label
labelColor	Color		color of the distance label
labelVisible	Boolean		visibility of the distance label
labelZOffset	Float		offset in z-direction (i.e. in camera direction)

public MolecularSurfaceParameters: Object source

Molecular surface parameter object.

Properties:

Name	Type	Attribute	Description
type	String		"av" or "edt"
probeRadius	Number		probe radius
scaleFactor	Number		higher for better quality
smooth	Integer		number of smoothing cycles to apply
name	String		name for created surface

public MouseSignals: Object source

Properties:

Name	Type	Attribute	Description
moved	Signal<Integer, Integer>		on move: deltaX, deltaY
scrolled	Signal<Number>		on scroll: delta
dragged	Signal<Integer, Integer>		on drag: deltaX, deltaY
dropped	Signal		on drop
clicked	Signal		on click
hovered	Signal		on hover

Example:

mouseObserver.signals.scrolled.add( function( delta ){ ... } );

public OrientationMatrix: Matrix4 source

Orientation matrix, a 4x4 transformation matrix with rotation part used for scene rotation, scale part for scene camera distance and position part for scene translation

public PickingData: Object source

Picking data object.

Properties:

Name	Type	Attribute	Description
pid	Number	optional	picking id
instance	Object	optional	instance data
instance.id	Integer		instance id
instance.name	String \| Integer		instance name
instance.matrix	Matrix4		transformation matrix of the instance
picker	Picker	optional	picker object

public RepresentationComponentSignals: Object source

Extends ComponentSignals

Properties:

Name	Type	Attribute	Description
parametersChanged	Signal<String>		on parameters change

public RepresentationParameters: Object source

Representation parameter object.

Properties:

Name	Type	Attribute	Description
lazy	Boolean	optional	only build & update the representation when visible otherwise defer changes until set visible again
clipNear	Integer	optional	position of camera near/front clipping plane in percent of scene bounding box
clipRadius	Integer	optional	radius of clipping sphere
clipCenter	Vector3	optional	position of for spherical clipping
flatShaded	Boolean	optional	render flat shaded
opacity	Float	optional	translucency: 1 is fully opaque, 0 is fully transparent
depthWrite	Boolean	optional	depth write
side	String	optional	which triangle sides to render, "front" front-side, "back" back-side, "double" front- and back-side
wireframe	Boolean	optional	render as wireframe
colorScheme	String	optional	color scheme
colorScale	String	optional	color scale, either a string for a predefined scale or an array of colors to be used as the scale
colorReverse	Boolean	optional	reverse color scale
colorValue	Color	optional	color value
colorDomain	Integer[]	optional	scale value range
colorDomain.0	Integer		min value
colorDomain.1	Integer		max value
colorMode	String	optional	color mode, one of rgb, hsv, hsl, hsi, lab, hcl
roughness	Float	optional	how rough the material is, between 0 and 1
metalness	Float	optional	how metallic the material is, between 0 and 1
diffuse	Color	optional	diffuse color for lighting
disablePicking	Boolean	optional	disable picking

public SliceRepresentationParameters: Object source

Slice representation parameter object. Extends RepresentationParameters

Properties:

Name	Type	Attribute	Description
filter	String		filter applied to map the volume data on the slice, one of "nearest", "linear", "cubic-bspline", "cubic-catmulrom", "cubic-mitchell".
positionType	String		Meaning of the position value. Either "persent" od "coordinate".
position	Number		position of the slice.
dimension	String		one of "x", "y" or "z"
thresholdType	String		Meaning of the threshold values. Either value for the literal value or sigma as a factor of the sigma of the data. For volume data only.
thresholdMin	Number		Minimum value to be displayed. For volume data only.
thresholdMax	Number		Maximum value to be displayed. For volume data only.
normalize	Boolean		Flag indicating wheather to normalize the data in a slice when coloring.

public StageParameters: Object source

Stage parameter object.

Properties:

Name	Type	Attribute	Description
backgroundColor	Color		background color
sampleLevel	Integer		sampling level for antialiasing, between -1 and 5; -1: no sampling, 0: only sampling when not moving
workerDefault	Boolean		default value for useWorker parameter of representations
rotateSpeed	Float		camera-controls rotation speed, between 0 and 10
zoomSpeed	Float		camera-controls zoom speed, between 0 and 10
panSpeed	Float		camera-controls pan speed, between 0 and 10
clipNear	Integer		position of camera near/front clipping plane in percent of scene bounding box
clipFar	Integer		position of camera far/back clipping plane in percent of scene bounding box
clipDist	Float		camera clipping distance in Angstrom
fogNear	Integer		position of the start of the fog effect in percent of scene bounding box
fogFar	Integer		position where the fog is in full effect in percent of scene bounding box
cameraType	String		type of camera, either 'persepective' or 'orthographic'
cameraFov	Float		camera field of view in degree, between 15 and 120
lightColor	Color		point light color
lightIntensity	Float		point light intensity
ambientColor	Color		ambient light color
ambientIntensity	Float		ambient light intensity
hoverTimeout	Integer		timeout for hovering

public StageSignals: Object source

Properties:

Name	Type	Attribute	Description
parametersChanged	Signal<StageParameters>		on parameters change
fullscreenChanged	Signal<Boolean>		on fullscreen change
componentAdded	Signal<Component>		when a component is added
componentRemoved	Signal<Component>		when a component is removed
clicked	Signal<PickingProxy\|undefined>		on click
hovered	Signal<PickingProxy\|undefined>		on hover

Example:

stage.signals.componentAdded.add( function( component ){ ... } );

public StructureComponentSignals: Object source

Extends ComponentSignals

Properties:

Name	Type	Attribute	Description
trajectoryAdded	Signal<RepresentationComponent>		when a trajectory is added
trajectoryRemoved	Signal<RepresentationComponent>		when a trajectory is removed
defaultAssemblyChanged	Signal<String>		on default assembly change

Example:

component.signals.representationAdded.add( function( representationComponent ){ ... } );

public StructureExtraData: Object source

Structure extra data.

Properties:

Name	Type	Attribute	Description
cif	Object	optional	dictionary from cif parser
sdf	Object[]	optional	associated data items from sdf parser, one per compound

public StructureHeader: Object source

Structure header object.

Properties:

Name	Type	Attribute	Description
releaseDate	String	optional	release data, YYYY-MM-DD
depositionDate	String	optional	deposition data, YYYY-MM-DD
resolution	Float	optional	experimental resolution
rFree	Float	optional	r-free value
rWork	Float	optional	r-work value
experimentalMethods	String[]	optional	experimental methods

public StructureRepresentationParameters: Object source

Structure representation parameter object.

Properties:

Name	Type	Attribute	Description
radiusType	String		A list of possible sources of the radius used for rendering the representation. The radius can be based on the vdW radius, the covalent radius or the B-factor value of the corresponding atom. Additionally the radius can be based on the secondary structure. Alternatively, when set to size, the value from the radius parameter is used for all atoms.
radius	Float		A number providing a fixed radius used for rendering the representation.
scale	Float		A number that scales the value defined by the radius or the radiusType parameter.
assembly	String		name of an assembly object. Included are the asymmetric unit (AU) corresponding to the coordinates given in the structure file, biological assemblies from PDB, mmCIF or MMTF files (BU1, BU2, ...), a filled (crystallographic) unitcell of a given space group (UNITCELL), a supercell consisting of a center unitcell and its 26 direct neighbors (SUPERCELL). Set to default to use the default asemmbly of the structure object.

public SurfaceRepresentationParameters: Object source

Surface representation parameter object. Extends RepresentationParameters

Properties:

Name	Type	Attribute	Description
isolevelType	String		Meaning of the isolevel value. Either value for the literal value or sigma as a factor of the sigma of the data. For volume data only.
isolevel	Float		The value at which to create the isosurface. For volume data only.
smooth	Integer		How many iterations of laplacian smoothing after surface triangulation. For volume data only.
background	Boolean		Render the surface in the background, unlit.
opaqueBack	Boolean		Render the back-faces (where normals point away from the camera) of the surface opaque, ignoring the transparency parameter.
boxSize	Integer		Size of the box to triangulate volume data in. Set to zero to triangulate the whole volume. For volume data only.
useWorker	Boolean		Weather or not to triangulate the volume asynchronously in a Web Worker. For volume data only.
wrap	Boolean		Wrap volume data around the edges; use in conjuction with boxSize but not larger than the volume dimension. For volume data only.

public TextBufferParameters: Object source

Text buffer parameter object.

Properties:

Name	Type	Attribute	Description
opacity	Float		translucency: 1 is fully opaque, 0 is fully transparent
clipNear	Integer		position of camera near/front clipping plane in percent of scene bounding box
labelType	String		type of the label, one of: "atomname", "atomindex", "occupancy", "bfactor", "serial", "element", "atom", "resname", "resno", "res", "text", "qualified". When set to "text", the `labelText` list is used.
labelText	String[]		list of label strings, must set `labelType` to "text" to take effect
fontFamily	String		font family, one of: "sans-serif", "monospace", "serif"
fontStyle	String		font style, "normal" or "italic"
fontWeight	String		font weight, "normal" or "bold"
sdf	Boolean		use "signed distance field"-based rendering for sharper edges
xOffset	Float		offset in x-direction
yOffset	Float		offset in y-direction
zOffset	Float		offset in z-direction (i.e. in camera direction)
attachment	String		attachment of the label, one of: "bottom-left", "bottom-center", "bottom-right", "middle-left", "middle-center", "middle-right", "top-left", "top-center", "top-right"
showBorder	Boolean		show border/outline
borderColor	Color		color of the border/outline
borderWidth	Float		width of the border/outline
showBackground	Boolean		show background rectangle
backgroundColor	Color		color of the background
backgroundMargin	Float		width of the background
backgroundOpacity	Float		opacity of the background

public TrajectoryComponentParameters: Object source

Trajectory component parameter object.

Properties:

Name	Type	Attribute	Description
name	String		component name
initialFrame	Integer		initial frame the trajectory is set to
defaultStep	Integer		default step size to be used by trajectory players
defaultTimeout	Integer		default timeout to be used by trajectory players
defaultInterpolateType	String		one of "" (empty string), "linear" or "spline"
defaultInterpolateStep	Integer		window size used for interpolation
defaultMode	String		either "loop" or "once"
defaultDirection	String		either "forward" or "backward"

public TrajectoryComponentSignals: Object source

Extends ComponentSignals

Properties:

Name	Type	Attribute	Description
frameChanged	Signal<RepresentationComponent>		on frame change
playerChanged	Signal<RepresentationComponent>		on player change
countChanged	Signal<Integer>		when frame count is available
parametersChanged	Signal<TrajectoryComponentParameters>		on parameters change

Example:

component.signals.representationAdded.add( function( representationComponent ){ ... } );

public TrajectoryParameters: Object source

Trajectory parameter object.

Properties:

Name	Type	Attribute	Description
deltaTime	Number		timestep between frames in picoseconds
timeOffset	Number		starting time of frames in picoseconds
sele	String		to restrict atoms used for superposition
centerPbc	Boolean		center on initial frame
removePeriodicity	Boolean		move atoms into the origin box
remo	Boolean		try fixing periodic boundary discontinuities
superpose	Boolean		superpose on initial frame

public TrajectoryPlayerParameters: Object source

Trajectory player parameter object.

Properties:

Name	Type	Attribute	Description
step	Integer		how many frames to skip when playing
timeout	Integer		how many milliseconds to wait between playing frames
start	Integer		first frame to play
end	Integer		last frame to play
interpolateType	String		one of "" (empty string), "linear" or "spline"
interpolateStep	Integer		window size used for interpolation
mode	String		either "loop" or "once"
direction	String		either "forward", "backward" or "bounce"

public TrajectoryRepresentationParameters: Object source

Trajectory representation parameter object.

Properties:

Name	Type	Attribute	Description
drawLine	Boolean		draw lines
drawCylinder	Boolean		draw cylinders
drawPoint	Boolean		draw points
drawSphere	Boolean		draw sphere
linewidth	Integer		line width
pointSize	Integer		point size
sizeAttenuation	Boolean		size attenuation
sort	Boolean		sort flag for points

public TrajectorySignals: Object source

Properties:

Name	Type	Attribute	Description
countChanged	Signal<Integer>		when the frame count is changed
frameChanged	Signal<Integer>		when the set frame is changed
playerChanged	Signal<TrajectoryPlayer>		when the player is changed

Example:

trajectory.signals.frameChanged.add( function(i){ ... } );

public TriggerString: String source

Strings to describe mouse events (including optional keyboard modifiers). Must contain an event type: "scroll", "drag", "click", "doubleClick", "hover", "clickPick" or "hoverPick". Optionally contain one or more (seperated by plus signs) keyboard modifiers: "alt", "ctrl", "meta" or "shift". Can contain the mouse button performing the event: "left", "middle" or "right". The type, key and button parts must be seperated by dashes.

Example:

// triggered on scroll event (no key or button)
"scroll"

// triggered on scroll event while shift key is pressed
"scroll-shift"

// triggered on drag event with left mouse button
"drag-left"

// triggered on drag event with right mouse button
// while ctrl and shift keys are pressed
"drag-right-ctrl+shift"