NGL@1.0.0-beta.7 Home Manual Reference Source Gallery

References

summary
public

C Script

Script class

public

F setDebug()

public
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public

F binarySearchIndexOf(array: Array, element: Anything, compareFunction: Function): Number

Does a binary search to get the index of an element in the input array

public

F boolean()

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F deepCopy()

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F defaults()

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F download()

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F flatten()

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F getQuery()

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F open()

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F pick()

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F submit()

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F throttle()

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V Browser: String | false

The browser name: "Opera", "Chrome", "Firefox", "Mobile Safari", "Internet Explorer", "Safari" or false.

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V Debug

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Flag indicating support for the EXT_frag_depth WebGL extension

public

V Log

public

Flag indicating a mobile browser

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List of file extensions to be recognized as scripts

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Flag indicating support for the 'passive' option for event handler

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Version name

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E Box3

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E Char

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E Color

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E Euler

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E Float

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E Plane

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E Signal

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align

summary
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Perform structural superposition of two structures, optionally guided by a sequence alignment

animation

summary
public

Animation list.

public

Move animation.

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Rock animation.

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Rotate animation.

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Spin animation.

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Timeout animation.

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Value animation.

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Zoom animation.

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Animation.

buffer

summary
public

Arrow buffer.

public

Box buffer.

public

Cone buffer.

public

Cone geometry buffer.

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Contour buffer.

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Cylinder buffer.

public

Cylinder geometry buffer.

public

Cylinder impostor buffer.

public

A double-sided mesh buffer.

public

Ellipsoid buffer.

public

Ellipsoid geometry buffer.

public

Hyperball stick buffer.

public

Hyperball stick impostor buffer.

public

Image buffer.

public

Line buffer.

public

Mesh buffer.

public

Octahedron buffer.

public

Point buffer.

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Ribbon buffer.

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Sphere buffer.

public

Sphere geometry buffer.

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Sphere impostor buffer.

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Surface buffer.

public

Tetrahedron buffer.

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Text buffer.

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Torus geometry buffer.

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Trace buffer.

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Tube mesh buffer.

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Vector buffer.

public

Wide Line buffer.

public

I Buffer

Buffer class.

public

Geometry buffer.

public

Mapped buffer.

public

Mapped Aligned box buffer.

public

Mapped Box buffer.

public

Mapped Quad buffer.

public

Buffer parameter object.

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Text buffer parameter object.

color

summary
public

Color by atom index.

public

Color by b-factor.

public

Color by chain id

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Color by chain index

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Color by chain name

public

Class for registering Colormakers.

public

Color by validation density fit

public

Color a surface by electrostatic charge.

public

Color by element

public

Color by entiry index

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Color by entity type

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Color by validation gometry quality

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Color by hydrophobicity

public

Color by model index

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Color by molecule type

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Color by occupancy

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Color by partial charge.

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Class by random color

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Color by residue index

public

Color by residue name

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Color based on Selection

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Color by secondary structure

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Color by uniform color

public

Color by volume value

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Color by volume position

public

Class for making colors.

public

Colormaker parameter object.

component

summary
public

Annotation HTML element floating on top of a position rendered in 3d

private
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Component wrapping a Representation object

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Component wrapping a Script object

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Component wrapping a Shape object

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Component wrapping a Structure object

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Component wrapping a Surface object

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Component wrapping a Trajectory object

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Component wrapping a Volume object

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Base class for components

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Component parameter object.

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Trajectory component parameter object.

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controls

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Animation controls

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Component controls

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Key actions provided as static methods

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Mouse controls

public

Mouse actions provided as static methods

public

Mouse controls

public

Picking controls

public

Picking proxy class.

public

Trackball controls

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Viewer controls

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Strings to describe mouse events (including optional keyboard modifiers).

public

Picking data object.

public

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

datasource

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Datasource base class

geometry

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Arrow geometry primitive

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Box geometry primitive

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Cone geometry primitive

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Cylinder geometry primitive

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Ellipsoid geometry primitive

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Octahedron geometry primitive

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Sphere geometry primitive

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Tetrahedron geometry primitive

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Text geometry primitive

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Torus geometry primitive

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C Shape

Class for building custom shapes.

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F Grid()

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F Kdtree()

private
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F Spline()

loader

summary
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C Loader

Loader base class

public

Parser loader class

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Plugin loader class

public

Script loader class

public

F autoLoad(file: String | File | Blob, params: LoaderParameters): Promise

Load a file

public
public

Loader parameter object.

math

summary
public

Principal axes

public

F arrayMax()

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F arrayMean()

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F arrayMin()

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F arrayRms()

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F arraySum()

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F copyArray()

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F quicksortIP(arr: TypedArray, eleSize: Integer, orderElement: Integer, begin: Integer, end: Integer): TypedArray

quicksortIP

public
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F clamp()

public
private

F degToRad()

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F lerp()

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F normalize()

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F pclamp()

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F radToDeg()

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F saturate()

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F spline()

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F Matrix()

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F addCols()

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F addRows()

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F invert3x3()

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F m3new()

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F m4new()

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F meanCols()

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F meanRows()

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F multiply()

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F subCols()

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F subRows()

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F svd()

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F transpose()

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F v3add()

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F v3angle()

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F v3ceil()

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F v3cross()

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F v3divide()

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F v3dot()

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F v3floor()

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F v3forEach()

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F v3length()

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F v3negate()

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F v3new()

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F v3round()

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F v3sub()

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F v3toArray()

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private

V EPS

public
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V TwoPI

parser

summary
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CSV parser

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C Parser

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proxy

summary
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Atom proxy

public

Bond proxy

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Chain proxy

public

Model proxy

public

Polymer

public

Residue proxy

representation

summary
public

Angle representation object

public

Axes representation.

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Backbone representation.

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Ball And Stick representation.

public

Base representation.

public

Representation for showing buffer objects.

public

Cartoon representation.

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Contact representation.

public

Dihedral representation object

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Distance representation

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Dot representation

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Helixorient Representation

public

Hyperball Representation

public

Label representation

public

Licorice representation object (BallAndStickRepresentation with aspectRatio fixed at 1.0)

public

Line representation

public

Molecular Surface Representation

public

Point Representation

public

Ribbon Representation

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Rocket Representation

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Rope Representation

public

Slice representation

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Spacefill Representation

public

Surface representation

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Trace Representation

public

Trajectory representation

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Tube Representation

public

Unitcell Representation

public

Validation representation

public

I Representation(object: Object, viewer: Viewer, params: RepresentationParameters)

Representation object

public

Structure representation

public
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MeasurementRepresentations take atom[Pair|Triple|Quad] parameters.

public
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Ball And Stick representation parameter object.

public
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Distance representation parameter object.

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Dot representation parameter object.

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Label representation parameter object.

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Measurement representation parameter object.

public

Representation parameter object.

public

Slice representation parameter object.

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Structure representation parameter object.

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Surface representation parameter object.

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Trajectory representation parameter object.

selection

summary
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Selection

public

F parseSele()

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V kwd

shader

summary
public

F getShader()

stage

summary
private
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private
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Mouse observer

private
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C Stage

Stage class, central for creating molecular scenes with NGL.

public
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Stage parameter object.

public

store

summary
public
public

Atom store

public

Atom type

public
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Bond store

public

Chain store

public

Model store

public
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Residue store

public

Residue type

public

I Store

Store base class

streamer

summary
public
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structure

summary
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C Entity

Entity of a Structure

public

View on the structure, restricted to the selection

public

Structure

public
private
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Assigns ResidueType bonds.

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V AA1

public

V AA3

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Structure extra data.

public

Structure header object.

surface

summary
public
public

Create Molecular surfaces

public

Surface

public
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C Volume

Volume

public

F AVHash(atomsX: Float32Array, atomsY: Float32Array, atomsZ: Float32Array, atomsR: Float32Array, min: Float32Array, max: Float32Array, maxDistance: Float)

Modifed from SpatialHash

public

F AVSurface()

public
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Molecular surface parameter object.

symmetry

summary
public

Assembly of transformed parts of a Structure

public

Unitcell class

public
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private

trajectory

summary
public

Frames trajectory class.

private

C Frames

public

Remote trajectory class.

public

Structure trajectory class.

public

Trajectory player for animating coordinate frames

public

Base class for trajectories, tying structures and coordinates together

public
public

Trajectory player parameter object.

public

Trajectory parameter object.

public

utils

summary
public

Bit array

public

Counter class for keeping track of counts

public

Class for writing and reading binary data

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I Picker

Picker class

public

Shape picker class

public

F BinaryHeap(scoreFunction: Function)

Binary heap implementation

public

F Kdtree(points: Float32Array, metric: Function)

Kdtree

public
public

F parseXml()

private

F Queue()

public

viewer

summary
public
public

F Stats()

private
public

F makeImage(viewer: Viewer, params: ImageParameters): Promise

Make image from what is shown in a viewer canvas

public
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F Viewer(idOrElement: String | Element)

Viewer class

public
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Image parameter object.

worker

summary
public
public
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public

F Worker()

writer

summary
public

Create a PDB file from a Structure object

public
public

Create an STL File from a surface Object (e.g.

public

I Writer

Base class for writers