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Classes

Interfaces

Type aliases

Events

Variables

Functions

Object literals

Type aliases

ArrowBufferParameters

ArrowBufferParameters: object & object

Private Attributes

Attributes: object
file

Parse Xml

author

Alexander Rose alexander.rose@weirdbyte.de

Type declaration

  • [k: string]: any

BooleanParam

  • BooleanParam(): object

BufferMaterials

BufferMaterials: "material" | "wireframeMaterial" | "pickingMaterial"

BufferParameters

BufferParameters: object

Type declaration

  • background: boolean
  • clipCenter: Vector3
  • clipNear: number
  • clipRadius: number
  • depthWrite: boolean
  • diffuse: number
  • diffuseInterior: boolean
  • disablePicking: boolean
  • flatShaded: boolean
  • forceTransparent: boolean
  • interiorColor: number
  • interiorDarkening: number
  • matrix: Matrix4
  • metalness: number
  • opacity: number
  • opaqueBack: boolean
  • roughness: number
  • side: "double" | "front" | "back"
  • sortParticles: boolean
  • useInteriorColor: boolean
  • wireframe: boolean

BufferSide

BufferSide: "front" | "back" | "double"

BufferTypes

BufferTypes: "picking" | "background"

CameraType

CameraType: "perspective" | "orthographic" | "stereo"

ChainidDict

ChainidDict: object

Type declaration

  • [k: string]: number

ChainnameDict

ChainnameDict: object

Type declaration

  • [k: string]: number

ColorParam

  • ColorParam(): object

ColormakerScale

ColormakerScale: function

Type declaration

    • (v: number): number

    • Parameters

      • v: number

      Returns number

ComponentParameters

ComponentParameters: object

Type declaration

  • name: string
  • status: string
  • visible: boolean

ConeBufferParameters

ConeBufferParameters: object & object

ContactDataParams

ContactDataParams: object

Type declaration

  • backboneHydrogenBond: boolean
  • cationPi: boolean
  • filterSele: string
  • halogenBond: boolean
  • hydrogenBond: boolean
  • hydrophobic: boolean
  • ionicInteraction: boolean
  • metalCoordination: boolean
  • piStacking: boolean
  • radius: number
  • waterHydrogenBond: boolean
  • weakHydrogenBond: boolean

CylinderBufferParameters

CylinderBufferParameters: object & object & object & object

CylinderGeometryBufferParameters

CylinderGeometryBufferParameters: object & object

CylinderImpostorBufferParameters

CylinderImpostorBufferParameters: object & object

DragCallback

DragCallback: function

Type declaration

    • (stage: Stage, dx: number, dy: number): void

    • Parameters

      • stage: Stage
      • dx: number
      • dy: number

      Returns void

ElementParameters

ElementParameters: object

Type declaration

  • name: string
  • status: string

EllipsoidBufferParameters

EllipsoidBufferParameters: object & object

FilterFn

FilterFn: function

Type declaration

FunctionWithDeps

FunctionWithDeps: object & Function

HyperballStickBufferParameters

HyperballStickBufferParameters: object & object & object & object

HyperballStickImpostorBufferParameters

HyperballStickImpostorBufferParameters: object & object

ImageBufferParameters

ImageBufferParameters: object & object

ImageFilterTypes

ImageFilterTypes: "nearest" | "linear" | "cubic-bspline" | "cubic-catmulrom" | "cubic-mitchell"

ImageParameters

ImageParameters: object

Type declaration

  • antialias: boolean
  • factor: number
  • onProgress: undefined | Function
  • transparent: boolean
  • trim: boolean

IntegerParam

  • IntegerParam(max: number, min: number): object

  • Parameters

    • max: number
    • min: number

    Returns object

    • max: number
    • min: number
    • type: "integer"

KeyActionCallback

KeyActionCallback: function

Type declaration

    • Parameters

      Returns void

KeyActionPreset

KeyActionPreset: [string, KeyActionCallback][]

KeyControlPreset

KeyControlPreset: keyof object

LabelType

LabelType: keyof object

LoaderInput

LoaderInput: File | Blob | string

MappingType

MappingType: "v2" | "v3"

MouseActionCallback

MouseActionCallback: ScrollCallback | DragCallback | PickCallback

MouseActionPreset

MouseActionPreset: [string, MouseActionCallback][]

MouseActionType

MouseActionType: "" | "scroll" | "drag" | "click" | "doubleClick" | "hover" | "clickPick" | "hoverPick"

MouseControlPreset

MouseControlPreset: keyof object

NumberArray

NumberArray: number[] | TypedArray

NumberParam

  • NumberParam(precision: number, max: number, min: number): object

  • Parameters

    • precision: number
    • max: number
    • min: number

    Returns object

    • max: number
    • min: number
    • precision: number
    • type: "number"

ParamType

ParamType: BooleanParam | ColorParam | IntegerParam | NumberParam | RangeParam | SelectParam

Partial

Partial: object

Type declaration

PickCallback

PickCallback: function

Type declaration

PointBufferParameters

PointBufferParameters: object & object

Positions

Positions: object

Type declaration

  • x: ArrayLike<number>
  • y: ArrayLike<number>
  • z: ArrayLike<number>

PrimitiveFields

PrimitiveFields: object

Type declaration

  • [k: string]: string

ProxyEntity

ProxyEntity: AtomProxy | ResidueProxy | ChainProxy | ModelProxy

RadiusType

RadiusType: keyof object

RangeParam

  • RangeParam(step: number, max: number, min: number): object

  • Parameters

    • step: number
    • max: number
    • min: number

    Returns object

    • max: number
    • min: number
    • step: number
    • type: "range"

RenderQualityType

RenderQualityType: "auto" | "low" | "medium" | "high"

RepresentationElementParameters

RepresentationElementParameters: object & object

ScaleParameters

ScaleParameters: object

Type declaration

  • domain: number[]
  • mode: "hcl" | "rgb" | "hsv" | "hsl" | "hsi" | "lab"
  • reverse: boolean
  • scale: string | string[]
  • value: number

ScrollCallback

ScrollCallback: function

Type declaration

    • (stage: Stage, delta: number): void

    • Parameters

      • stage: Stage
      • delta: number

      Returns void

SelectParam

  • SelectParam(...options: string[]): object

  • Parameters

    • Rest ...options: string[]

    Returns object

    • options: object
      • [k: string]: string
    • type: "select"

SelectionOperator

SelectionOperator: "AND" | "OR"

SelectionSchemeData

SelectionSchemeData: [any, string, ColormakerParameters | undefined]

SelectionSignals

SelectionSignals: object

Type declaration

  • stringChanged: Signal

SelectionTest

SelectionTest: false | function

ShaderDefine

ShaderDefine: "NEAR_CLIP" | "RADIUS_CLIP" | "PICKING" | "NOLIGHT" | "FLAT_SHADED" | "OPAQUE_BACK" | "DIFFUSE_INTERIOR" | "USE_INTERIOR_COLOR" | "USE_SIZEATTENUATION" | "USE_MAP" | "ALPHATEST" | "SDF" | "FIXED_SIZE" | "CUBIC_INTERPOLATION" | "BSPLINE_FILTER" | "CATMULROM_FILTER" | "MITCHELL_FILTER"

ShaderDefines

ShaderDefines: object

Type declaration

ShapeParameters

ShapeParameters: object

Type declaration

  • aspectRatio: number
  • dashedCylinder: boolean
  • disableImpostor: boolean
  • labelParams: object
  • lineWidth: number
  • openEnded: boolean
  • pointSize: number
  • radialSegments: number
  • sizeAttenuation: boolean
  • sphereDetail: number
  • useTexture: boolean

ShapeRepresentationType

ShapeRepresentationType: "buffer"

SphereBufferParameters

SphereBufferParameters: object & object & object

SphereGeometryBufferParameters

SphereGeometryBufferParameters: object & object

StageParameters

StageParameters: object

Type declaration

  • ambientColor: string | number
  • ambientIntensity: number
  • backgroundColor: string | number
  • cameraEyeSep: number
  • cameraFov: number
  • cameraType: "perspective" | "orthographic" | "stereo"
  • clipDist: number
  • clipFar: number
  • clipNear: number
  • fogFar: number
  • fogNear: number
  • hoverTimeout: number
  • impostor: boolean
  • lightColor: string | number
  • lightIntensity: number
  • mousePreset: "default" | "pymol" | "coot" | "astexviewer"
  • panSpeed: number
  • quality: "high" | "medium" | "low" | "auto"
  • rotateSpeed: number
  • sampleLevel: number
  • tooltip: boolean
  • workerDefault: boolean
  • zoomSpeed: number

StoreField

StoreField: [string, number, TypedArrayString]

StructureComponentParameters

StructureComponentParameters: object & object

StructureExtraData

StructureExtraData: object

Type declaration

  • Optional cif?: undefined | object
  • Optional sdf?: any[]

StructureHeader

StructureHeader: object

Type declaration

  • Optional depositionDate?: undefined | string
  • Optional experimentalMethods?: string[]
  • Optional rFree?: undefined | number
  • Optional rWork?: undefined | number
  • Optional releaseDate?: undefined | string
  • Optional resolution?: undefined | number

StructureRepresentationType

StructureRepresentationType: "base" | "label" | "axes" | "contact" | "distance" | "surface" | "unitcell" | "angle" | "backbone" | "ball+stick" | "cartoon" | "dihedral" | "helixorient" | "hyperball" | "licorice" | "line" | "ribbon" | "rocket" | "rope" | "spacefill" | "trace" | "tube"

StructureSignals

StructureSignals: object

Type declaration

  • refreshed: Signal

StuctureColormakerParams

StuctureColormakerParams: object & Partial<ColormakerParameters>

SubstitutionMatrix

SubstitutionMatrix: "" | "blosum62" | "blosum62x"

SurfaceRepresentationType

SurfaceRepresentationType: "surface" | "dot"

TestEntityFn

TestEntityFn: function

Type declaration

TextAtlasMap

TextAtlasMap: object

Type declaration

  • h: number
  • w: number
  • x: number
  • y: number

TextAtlasParams

TextAtlasParams: object

Type declaration

  • font: "sans-serif" | "monospace" | "serif"
  • height: number
  • outline: number
  • size: number
  • style: "normal" | "italic"
  • variant: "normal"
  • weight: "normal" | "bold"
  • width: number

TextAttachments

TextAttachments: "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right"

TextBufferParameters

TextBufferParameters: object & object

TextFonts

TextFonts: "sans-serif" | "monospace" | "serif"

TextStyles

TextStyles: "normal" | "italic"

TextVariants

TextVariants: "normal"

TextWeights

TextWeights: "normal" | "bold"

TorusBufferParameters

TorusBufferParameters: object & object

TrajectoryElementParameters

TrajectoryElementParameters: object & object

TrajectoryPlayerDirection

TrajectoryPlayerDirection: "forward" | "backward" | "bounce"

TrajectoryPlayerInterpolateType

TrajectoryPlayerInterpolateType: "" | "linear" | "spline"

TrajectoryPlayerMode

TrajectoryPlayerMode: "loop" | "once"

TrajectoryPlayerParameters

TrajectoryPlayerParameters: object

Type declaration

  • direction: "forward" | "backward" | "bounce"
  • end: number
  • interpolateStep: number
  • interpolateType: "" | "linear" | "spline"
  • mode: "loop" | "once"
  • start: number
  • step: number
  • timeout: number

TubeMeshBufferParameters

TubeMeshBufferParameters: object & object

TypedArray

TypedArray: Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

TypedArrayString

TypedArrayString: "int8" | "int16" | "int32" | "uint8" | "uint16" | "uint32" | "float32"

Uniforms

Uniforms: object

Type declaration

  • [k: string]: Uniform | object

VectorBufferParameters

VectorBufferParameters: object & object

VolumeColormakerParams

VolumeColormakerParams: object & Partial<ColormakerParameters>

VolumeRepresentationType

VolumeRepresentationType: "surface" | "slice" | "dot"

WideLineBufferParameters

WideLineBufferParameters: object & object

Events

CounterSignals

CounterSignals:

{@link Signal}, dispatched when the count changes

example

counter.signals.countChanged.add( function( delta ){ ... } );

type

{Integer}

countChanged

countChanged: Signal

Variables

Const AA3

AA3: string[] = Object.keys(AA1)

Const AcidicResname

AcidicResname: string[] = [ 'ASP', 'GLU' ]

Const AliphaticResname

AliphaticResname: string[] = [ 'ALA', 'GLY', 'ILE', 'LEU', 'VAL' ]

Const AlkaliMetals

AlkaliMetals: number[] = [ 3, 11, 19, 37, 55, 87 ]

Const AlkalineEarthMetals

AlkalineEarthMetals: number[] = [ 4, 12, 20, 38, 56, 88 ]

AllFields

AllFields: string[] = PassThroughFields.concat( EncodedFields )

Const AmideResname

AmideResname: string[] = [ 'ASN', 'GLN' ]

Const AngleMode

AngleMode: 4 = 4

Const Angles

Angles: Map<AtomGeometry, number> = new Map<AtomGeometry, number>([[ AtomGeometry.Linear, degToRad(180) ],[ AtomGeometry.Trigonal, degToRad(120) ],[ AtomGeometry.Tetrahedral, degToRad(109.4721) ],[ AtomGeometry.Octahedral, degToRad(90) ]])

Const AromaticResname

AromaticResname: string[] = [ 'PHE', 'TRP', 'TYR', 'HIS' ]

Const AromaticRingElements

AromaticRingElements: Elements[] = [Elements.B, Elements.C, Elements.N, Elements.O,Elements.SI, Elements.P, Elements.S,Elements.GE, Elements.AS,Elements.SN, Elements.SB,Elements.BI]

Const AromaticRingPlanarityThreshold

AromaticRingPlanarityThreshold: 0.05 = 0.05

Const ArrowBufferDefaultParameters

ArrowBufferDefaultParameters: object & object = Object.assign({aspectRatio: 1.5,radialSegments: 50,openEnded: false,disableImpostor: false}, BufferDefaultParameters)

Const AtomFormat

AtomFormat: "ATOM %5d %-4s %3s %1s%4d %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s" = "ATOM %5d %-4s %3s %1s%4d %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s"

Const AtomLine

AtomLine: "%10.4f%10.4f%10.4f %-3s 0%3i 0 0 0" = "%10.4f%10.4f%10.4f %-3s 0%3i 0 0 0"

Const AtomMode

AtomMode: 2 = 2

Const AtomNameMode

AtomNameMode: 3 = 3

Const AtomOnlyKeywords

AtomOnlyKeywords: kwd[] = [kwd.BACKBONE, kwd.SIDECHAIN, kwd.BONDED, kwd.RING, kwd.AROMATICRING, kwd.METAL]

Const AtomsMode

AtomsMode: 4 = 4

BAD

BAD: number = 30

BAD$1

BAD$1: number = 30

Const Bases

Bases: string[] = RnaBases.concat(DnaBases)

Const BasicResname

BasicResname: string[] = [ 'ARG', 'HIS', 'LYS' ]

Const BondFormat

BondFormat: "%3i%3i%3i 0 0 0" = "%3i%3i%3i 0 0 0"

Const BondMode

BondMode: 3 = 3

Const BondsIncHydrogenMode

BondsIncHydrogenMode: 8 = 8

Const BondsMode

BondsMode: 5 = 5

Const BondsWithoutHydrogenMode

BondsWithoutHydrogenMode: 9 = 9

Const Browser

Browser: false | "Opera" | "Chrome" | "Firefox" | "Mobile Safari" | "Internet Explorer" | "Safari" = getBrowser()

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

Const BufferRegistry

BufferRegistry: Registry = new Registry('buffer')

CHECK

CHECK: number = 27

CODELENS

CODELENS: number = 19

CODES

CODES: number = 0

CODES$1

CODES$1: number = 0

COMMENT

COMMENT: number = 8

COPY

COPY: number = 16

COPY_

COPY_: number = 15

Const CgDnaBackboneType

CgDnaBackboneType: 6 = 6

Const CgProteinBackboneType

CgProteinBackboneType: 4 = 4

Const CgRnaBackboneType

CgRnaBackboneType: 5 = 5

Const ChainKeywords

ChainKeywords: kwd[] = [kwd.POLYMER, kwd.WATER]

Const ChainnameAlphabet

ChainnameAlphabet: "ABCDEFGHIJKLMNOPQRSTUVWXYZ" = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"

Const ChargeMode

ChargeMode: 4 = 4

Const ChargedResname

ChargedResname: string[] = [ 'ARG', 'ASP', 'GLU', 'HIS', 'LYS' ]

Const ChemCompDna

ChemCompDna: string[] = ['DNA OH 3 PRIME TERMINUS', 'DNA OH 5 PRIME TERMINUS', 'DNA LINKING','L-DNA LINKING', 'L-RNA LINKING']

Const ChemCompHetero

ChemCompHetero: string[] = ChemCompNonPolymer.concat(ChemCompOther, ChemCompSaccharide)

Const ChemCompNonPolymer

ChemCompNonPolymer: string[] = ['NON-POLYMER']

Const ChemCompOther

ChemCompOther: string[] = ['OTHER']

Const ChemCompProtein

ChemCompProtein: string[] = ['D-BETA-PEPTIDE, C-GAMMA LINKING', 'D-GAMMA-PEPTIDE, C-DELTA LINKING','D-PEPTIDE COOH CARBOXY TERMINUS', 'D-PEPTIDE NH3 AMINO TERMINUS', 'D-PEPTIDE LINKING','L-BETA-PEPTIDE, C-GAMMA LINKING', 'L-GAMMA-PEPTIDE, C-DELTA LINKING','L-PEPTIDE COOH CARBOXY TERMINUS', 'L-PEPTIDE NH3 AMINO TERMINUS', 'L-PEPTIDE LINKING','PEPTIDE LINKING', 'PEPTIDE-LIKE']

Const ChemCompRna

ChemCompRna: string[] = ['RNA OH 3 PRIME TERMINUS', 'RNA OH 5 PRIME TERMINUS', 'RNA LINKING']

Const ChemCompSaccharide

ChemCompSaccharide: string[] = ['D-SACCHARIDE', 'D-SACCHARIDE 1,4 AND 1,4 LINKING', 'D-SACCHARIDE 1,4 AND 1,6 LINKING','L-SACCHARIDE', 'L-SACCHARIDE 1,4 AND 1,4 LINKING', 'L-SACCHARIDE 1,4 AND 1,6 LINKING','SACCHARIDE']

Const ComponentRegistry

ComponentRegistry: Registry = new Registry('component')

Const ConeBufferDefaultParameters

ConeBufferDefaultParameters: object & object = Object.assign({radialSegments: 60,openEnded: false}, BufferDefaultParameters)

Const CountFormat

CountFormat: "%3i%3i 0 0 0 0 0 0 0 0999 V2000" = "%3i%3i 0 0 0 0 0 0 0 0999 V2000"

Const CyclicResname

CyclicResname: string[] = [ 'HIS', 'PHE', 'PRO', 'TRP', 'TYR' ]

Const CylinderBufferDefaultParameters

CylinderBufferDefaultParameters: object & object & object & object = Object.assign({disableImpostor: false}, CylinderGeometryBufferDefaultParameters, CylinderImpostorBufferDefaultParameters)

Const CylinderGeometryBufferDefaultParameters

CylinderGeometryBufferDefaultParameters: object & object = Object.assign({radialSegments: 1,openEnded: true}, BufferDefaultParameters)

Const CylinderImpostorBufferDefaultParameters

CylinderImpostorBufferDefaultParameters: object & object = Object.assign({openEnded: false}, BufferDefaultParameters)

Const CylinderImpostorBufferParameterTypes

CylinderImpostorBufferParameterTypes: object & object = Object.assign({openEnded: { updateShader: true }}, BufferParameterTypes)

Const DEG2RAD

DEG2RAD: number = Math.PI / 180

DICT

DICT: number = 11

DICTID

DICTID: number = 10

DIST

DIST: number = 23

DISTEXT

DISTEXT: number = 24

DISTS

DISTS: number = 2

DISTS$1

DISTS$1: number = 2

DONE

DONE: number = 29

Const DatasourceRegistry

DatasourceRegistry: Registry = new Registry('datasource')

Let Debug

Debug: boolean = boolean(getQuery('debug'))

Const DecompressorRegistry

DecompressorRegistry: Registry = new Registry('decompressor')

Const DefaultAtomWeight

DefaultAtomWeight: 10.81 = 10.81

Const DefaultAtomicNumber

DefaultAtomicNumber: 0 = 0

Const DefaultCovalentRadius

DefaultCovalentRadius: 1.6 = 1.6

Const DefaultElementColor

DefaultElementColor: 16777215 = 16777215

Const DefaultOuterShellElectronCount

DefaultOuterShellElectronCount: 2 = 2

Const DefaultResidueColor

DefaultResidueColor: 16711935 = 16711935

Const DefaultResidueHydrophobicity

DefaultResidueHydrophobicity: number[] = [ 0.00, 0.00, 0.00 ]

Const DefaultResidueRadius

DefaultResidueRadius: 5 = 5

Const DefaultStructureColor

DefaultStructureColor: 8421504 = 8421504

Const DefaultValence

DefaultValence: -1 = -1

Const DefaultVdwRadius

DefaultVdwRadius: 2 = 2

Const DiatomicNonmetals

DiatomicNonmetals: number[] = [ 1, 7, 8, 9, 17, 35, 53 ]

Const DihedralMode

DihedralMode: 5 = 5

Const DnaBackboneType

DnaBackboneType: 3 = 3

Const DnaBases

DnaBases: string[] = [ 'DA', 'DC', 'DT', 'DG', 'DU' ]

Const DnaType

DnaType: 5 = 5

ENOUGH_DISTS

ENOUGH_DISTS: number = 592

ENOUGH_DISTS$1

ENOUGH_DISTS$1: number = 592

ENOUGH_LENS

ENOUGH_LENS: number = 852

ENOUGH_LENS$1

ENOUGH_LENS$1: number = 852

Private Const EPS

EPS: 1e-7 = 1e-7
file

Math Constants

author

Alexander Rose alexander.rose@weirdbyte.de

Const EPSILON

EPSILON: 1.192092896e-7 = 1.192092896e-7

EXLEN

EXLEN: number = 5

EXTRA

EXTRA: number = 6

Const EllipsoidBufferDefaultParameters

EllipsoidBufferDefaultParameters: object & object = Object.assign({sphereDetail: 2,}, BufferDefaultParameters)

EncodedFields

EncodedFields: string[] = [// required"xCoordList", "yCoordList", "zCoordList","groupIdList", "groupTypeList","chainIdList",// optional"bFactorList", "atomIdList", "altLocList", "occupancyList","secStructList", "insCodeList", "sequenceIndexList","chainNameList","bondAtomList", "bondOrderList"]

Let ExtensionFragDepth

ExtensionFragDepth: boolean = false

Flag indicating support for the EXT_frag_depth WebGL extension

FLAGS

FLAGS: number = 2

Const FLT_MIN

FLT_MIN: 1e-37 = 1e-37

Const FirstIdx

FirstIdx: 9 = 9

HCRC

HCRC: number = 9

HEAD

HEAD: number = 1

Const Halogens

Halogens: number[] = [ 9, 17, 35, 53, 85 ]

Const HetatmFormat

HetatmFormat: "HETATM%5d %-4s %3s %1s%4d %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s" = "HETATM%5d %-4s %3s %1s%4d %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s"

Const HydrophobicResname

HydrophobicResname: string[] = [ 'ALA', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'VAL' ]

Const HyperballStickBufferDefaultParameters

HyperballStickBufferDefaultParameters: object & object & object & object = Object.assign({disableImpostor: false}, CylinderGeometryBufferDefaultParameters, HyperballStickImpostorBufferDefaultParameters)

Const HyperballStickImpostorBufferDefaultParameters

HyperballStickImpostorBufferDefaultParameters: object & object = Object.assign({shrink: 0.14}, BufferDefaultParameters)

Const HyperballStickImpostorBufferParameterTypes

HyperballStickImpostorBufferParameterTypes: object & object = Object.assign({shrink: { uniform: true }}, BufferParameterTypes)

Const ImageBufferDefaultParameters

ImageBufferDefaultParameters: object & object = Object.assign({filter: 'nearest' as ImageFilterTypes,forceTransparent: true}, BufferDefaultParameters)

Const ImageBufferParameterTypes

ImageBufferParameterTypes: object & object = Object.assign({filter: { updateShader: true, uniform: true }}, BufferParameterTypes)

Const ImproperMode

ImproperMode: 6 = 6

Const IonNames

IonNames: string[] = ['118', '119', '1AL', '1CU', '2FK', '2HP', '2OF', '3CO','3MT', '3NI', '3OF', '3P8', '4MO', '4PU', '543', '6MO', 'ACT', 'AG', 'AL','ALF', 'AM', 'ATH', 'AU', 'AU3', 'AUC', 'AZI', 'BA', 'BCT', 'BEF', 'BF4', 'BO4','BR', 'BS3', 'BSY', 'CA', 'CAC', 'CD', 'CD1', 'CD3', 'CD5', 'CE', 'CHT', 'CL','CO', 'CO3', 'CO5', 'CON', 'CR', 'CS', 'CSB', 'CU', 'CU1', 'CU3', 'CUA', 'CUZ','CYN', 'DME', 'DMI', 'DSC', 'DTI', 'DY', 'E4N', 'EDR', 'EMC', 'ER3', 'EU','EU3', 'F', 'FE', 'FE2', 'FPO', 'GA', 'GD3', 'GEP', 'HAI', 'HG', 'HGC', 'IN','IOD', 'IR', 'IR3', 'IRI', 'IUM', 'K', 'KO4', 'LA', 'LCO', 'LCP', 'LI', 'LU','MAC', 'MG', 'MH2', 'MH3', 'MLI', 'MLT', 'MMC', 'MN', 'MN3', 'MN5', 'MN6','MO1', 'MO2', 'MO3', 'MO4', 'MO5', 'MO6', 'MOO', 'MOS', 'MOW', 'MW1', 'MW2','MW3', 'NA', 'NA2', 'NA5', 'NA6', 'NAO', 'NAW', 'NCO', 'NET', 'NH4', 'NI','NI1', 'NI2', 'NI3', 'NO2', 'NO3', 'NRU', 'O4M', 'OAA', 'OC1', 'OC2', 'OC3','OC4', 'OC5', 'OC6', 'OC7', 'OC8', 'OCL', 'OCM', 'OCN', 'OCO', 'OF1', 'OF2','OF3', 'OH', 'OS', 'OS4', 'OXL', 'PB', 'PBM', 'PD', 'PDV', 'PER', 'PI', 'PO3','PO4', 'PR', 'PT', 'PT4', 'PTN', 'RB', 'RH3', 'RHD', 'RU', 'SB', 'SCN', 'SE4','SEK', 'SM', 'SMO', 'SO3', 'SO4', 'SR', 'T1A', 'TB', 'TBA', 'TCN', 'TEA', 'TH','THE', 'TL', 'TMA', 'TRA', 'UNX', 'V', 'VN3', 'VO4', 'W', 'WO5', 'Y1', 'YB','YB2', 'YH', 'YT3', 'ZCM', 'ZN', 'ZN2', 'ZN3', 'ZNO', 'ZO3',// additional ion names'OHX']

Const IonType

IonType: 2 = 2

Const IonicTypeMetals

IonicTypeMetals: Elements[] = [Elements.LI, Elements.NA, Elements.K, Elements.RB, Elements.CS,Elements.MG, Elements.CA, Elements.SR, Elements.BA, Elements.AL,Elements.GA, Elements.IN, Elements.TL, Elements.SC, Elements.SN,Elements.PB, Elements.BI, Elements.SB, Elements.HG]

Const JitterVectors

JitterVectors: number[][][] = [[[ 0, 0 ]],[[ 4, 4 ], [ -4, -4 ]],[[ -2, -6 ], [ 6, -2 ], [ -6, 2 ], [ 2, 6 ]],[[ 1, -3 ], [ -1, 3 ], [ 5, 1 ], [ -3, -5 ],[ -5, 5 ], [ -7, -1 ], [ 3, 7 ], [ 7, -7 ]],[[ 1, 1 ], [ -1, -3 ], [ -3, 2 ], [ 4, -1 ],[ -5, -2 ], [ 2, 5 ], [ 5, 3 ], [ 3, -5 ],[ -2, 6 ], [ 0, -7 ], [ -4, -6 ], [ -6, 4 ],[ -8, 0 ], [ 7, -4 ], [ 6, 7 ], [ -7, -8 ]],[[ -4, -7 ], [ -7, -5 ], [ -3, -5 ], [ -5, -4 ],[ -1, -4 ], [ -2, -2 ], [ -6, -1 ], [ -4, 0 ],[ -7, 1 ], [ -1, 2 ], [ -6, 3 ], [ -3, 3 ],[ -7, 6 ], [ -3, 6 ], [ -5, 7 ], [ -1, 7 ],[ 5, -7 ], [ 1, -6 ], [ 6, -5 ], [ 4, -4 ],[ 2, -3 ], [ 7, -2 ], [ 1, -1 ], [ 4, -1 ],[ 2, 1 ], [ 6, 2 ], [ 0, 4 ], [ 4, 4 ],[ 2, 5 ], [ 7, 5 ], [ 5, 6 ], [ 3, 7 ]]]

LEN

LEN: number = 21

LENEXT

LENEXT: number = 22

LENGTH

LENGTH: number = 28

LENLENS

LENLENS: number = 18

LENS

LENS: number = 1

LENS$1

LENS$1: number = 1

LEN_

LEN_: number = 20

LIT

LIT: number = 26

Private Const LeftMouseButton

LeftMouseButton: 1 = 1
file

Constants

author

Alexander Rose alexander.rose@weirdbyte.de

Let ListingDatasource

ListingDatasource: any

MATCH

MATCH: number = 25

MAXBITS

MAXBITS: number = 15

MEM

MEM: number = 31

Const MacrolideEntity

MacrolideEntity: 3 = 3

Const MagicInts

MagicInts: Uint32Array = new Uint32Array([0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 10, 12, 16, 20, 25, 32, 40, 50, 64,80, 101, 128, 161, 203, 256, 322, 406, 512, 645, 812, 1024, 1290,1625, 2048, 2580, 3250, 4096, 5060, 6501, 8192, 10321, 13003,16384, 20642, 26007, 32768, 41285, 52015, 65536, 82570, 104031,131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561,832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021,4194304, 5284491, 6658042, 8388607, 10568983, 13316085, 16777216])

Const MassMode

MassMode: 5 = 5

Const Metalloids

Metalloids: number[] = [ 5, 14, 32, 33, 51, 52, 85 ]

Const MiddleMouseButton

MiddleMouseButton: 2 = 2

Const Mobile

Mobile: boolean = typeof window !== 'undefined' ? typeof window.orientation !== 'undefined' : false

Flag indicating a mobile browser

Const MoleculesMode

MoleculesMode: 2 = 2

Const MoleculetypeMode

MoleculetypeMode: 3 = 3

NAME

NAME: number = 7

Const NC_ATTRIBUTE

NC_ATTRIBUTE: 12 = 12

Const NC_DIMENSION

NC_DIMENSION: 10 = 10

Const NC_VARIABLE

NC_VARIABLE: 11 = 11

Const NegativelyCharged

NegativelyCharged: string[] = [ 'GLU', 'ASP' ]

Const NobleGases

NobleGases: number[] = [ 2, 10, 18, 36, 54, 86 ]

Const NonPolymerEntity

NonPolymerEntity: 2 = 2

Const NonpolarResname

NonpolarResname: string[] = [ 'ALA', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'VAL' ]

Const NucleicBackboneAtoms

NucleicBackboneAtoms: string[] = ['P', 'OP1', 'OP2',"O2'", "O3'", "O4'", "O5'", "C1'", "C2'", "C3'", "C4'", "C5'",'O2*', 'O3*', 'O4*', 'O5*', 'C1*', 'C2*', 'C3*', 'C4*', 'C5*']

Const NucleophilicResname

NucleophilicResname: string[] = [ 'CYS', 'SER', 'THR' ]

OS

OS: number = 4

Const OptimalAcceptorAngle

OptimalAcceptorAngle: number = degToRad(120)

Const OptimalHalogenAngle

OptimalHalogenAngle: number = degToRad(180)

Private PassThroughFields

PassThroughFields: string[] = ["mmtfVersion", "mmtfProducer","unitCell", "spaceGroup", "structureId", "title","depositionDate", "releaseDate","experimentalMethods", "resolution", "rFree", "rWork","bioAssemblyList", "ncsOperatorList", "entityList", "groupList","numBonds", "numAtoms", "numGroups", "numChains", "numModels","groupsPerChain", "chainsPerModel",]
file

mmtf-constants

author

Alexander Rose alexander.rose@weirdbyte.de

Const PickerRegistry

PickerRegistry: Registry = new Registry('picker')

Const PointBufferDefaultParameters

PointBufferDefaultParameters: object & object = Object.assign({pointSize: 1,sizeAttenuation: true,sortParticles: false,alphaTest: 0.5,useTexture: false,forceTransparent: false,edgeBleach: 0.0}, BufferDefaultParameters)

Const PointBufferParameterTypes

PointBufferParameterTypes: object & object = Object.assign({pointSize: { uniform: 'size' },sizeAttenuation: { updateShader: true },sortParticles: {},alphaTest: { updateShader: true },useTexture: { updateShader: true },forceTransparent: {},edgeBleach: { uniform: true }}, BufferParameterTypes)

Const PointersMode

PointersMode: 2 = 2

Const PolarElements

PolarElements: Elements[] = [Elements.N, Elements.O, Elements.S,Elements.F, Elements.CL, Elements.BR, Elements.I]

Const PolarResname

PolarResname: string[] = [ 'ASN', 'ARG', 'ASP', 'CYS', 'GLY', 'GLN', 'GLU', 'HIS', 'LYS', 'SER', 'THR', 'TYR' ]

Const PolyatomicNonmetals

PolyatomicNonmetals: number[] = [ 6, 15, 16, 34, ]

Const PolymerEntity

PolymerEntity: 1 = 1

Const PositvelyCharged

PositvelyCharged: string[] = [ 'ARG', 'HIS', 'LYS' ]

Const PostTransitionMetals

PostTransitionMetals: number[] = [ 13, 30, 31, 48, 49, 50, 80, 81, 82, 83, 84, 85, 112 ]

Const Primitives

Primitives: (PointPrimitive | WidelinePrimitive)[] = [ArrowPrimitive, BoxPrimitive, ConePrimitive, CylinderPrimitive,EllipsoidPrimitive, OctahedronPrimitive, SpherePrimitive, TetrahedronPrimitive,TextPrimitive, TorusPrimitive, PointPrimitive, WidelinePrimitive]

Const ProteinBackboneAtoms

ProteinBackboneAtoms: string[] = ['CA', 'C', 'N', 'O','O1', 'O2', 'OC1', 'OC2', 'OX1', 'OXT','H', 'H1', 'H2', 'H3', 'HA', 'HN','BB']

Const ProteinBackboneType

ProteinBackboneType: 1 = 1

Const ProteinType

ProteinType: 3 = 3

Const PurinBases

PurinBases: string[] = [ 'A', 'G', 'DA', 'DG' ]

Const RAD2DEG

RAD2DEG: number = 180 / Math.PI

Const RadiiMode

RadiiMode: 10 = 10

Const RepresentationElementDefaultParameters

RepresentationElementDefaultParameters: object & object = Object.assign({visible: true}, ElementDefaultParameters)

Const RepresentationRegistry

RepresentationRegistry: Registry = new Registry('representatation')

Const ResidueLabelMode

ResidueLabelMode: 6 = 6

Const ResiduePointerMode

ResiduePointerMode: 7 = 7

Const ResidueTypeAtoms

ResidueTypeAtoms: object

Type declaration

  • [k: number]: object
    • [k: string]: string | string[]

Const RightMouseButton

RightMouseButton: 3 = 3

Const RingFinderMaxDepth

RingFinderMaxDepth: 4 = 4

Const RnaBackboneType

RnaBackboneType: 2 = 2

Const RnaBases

RnaBases: string[] = [ 'A', 'C', 'T', 'G', 'U' ]

Const RnaType

RnaType: 4 = 4

STORED

STORED: number = 14

STR_APPLY_OK

STR_APPLY_OK: boolean = true

STR_APPLY_UIA_OK

STR_APPLY_UIA_OK: boolean = true

SYNC

SYNC: number = 32

Const SaccharideNames

SaccharideNames: string[] = ['045', '0AT', '0BD', '0MK', '0NZ', '0TS', '0V4', '0XY', '0YT', '10M','147', '149', '14T', '15L', '16G', '18T', '18Y', '1AR', '1BW', '1GL', '1GN','1JB', '1LL', '1NA', '1S3', '26M', '26Q', '26R', '26V', '26W', '26Y', '27C','289', '291', '293', '2DG', '2F8', '2FG', '2FL', '2FP', '2GL', '2M4', '2M5','32O', '34V', '3CM', '3DO', '3DY', '3FM', '3LR', '3MF', '3MG', '3SA', '3ZW','46D', '46M', '46Z', '48Z', '4CQ', '4GC', '4NN', '50A', '5DI', '5GF', '5MM','5RP', '5SA', '5SP', '64K', '6PG', '6SA', '7JZ', '7SA', 'A1Q', 'A2G', 'AAB','AAL', 'AAO', 'ABC', 'ABD', 'ABE', 'ABF', 'ABL', 'ACG', 'ACI', 'ACR', 'ACX','ADA', 'ADG', 'ADR', 'AF1', 'AFD', 'AFL', 'AFO', 'AFP', 'AFR', 'AGC', 'AGH','AGL', 'AHR', 'AIG', 'ALL', 'ALX', 'AMU', 'AOG', 'AOS', 'ARA', 'ARB', 'ARE','ARI', 'ASG', 'ASO', 'AXP', 'AXR', 'B0D', 'B16', 'B2G', 'B4G', 'B6D', 'B8D','B9D', 'BBK', 'BCD', 'BDG', 'BDP', 'BDR', 'BEM', 'BFP', 'BGC', 'BGL', 'BGP','BGS', 'BHG', 'BMA', 'BMX', 'BNG', 'BNX', 'BOG', 'BRI', 'BXF', 'BXP', 'BXX','BXY', 'C3X', 'C4X', 'C5X', 'CAP', 'CBI', 'CBK', 'CBS', 'CDR', 'CEG', 'CGF','CHO', 'CR1', 'CR6', 'CRA', 'CT3', 'CTO', 'CTR', 'CTT', 'D6G', 'DAF', 'DAG','DDA', 'DDB', 'DDL', 'DEL', 'DFR', 'DFX', 'DG0', 'DGC', 'DGD', 'DGM', 'DGS','DIG', 'DLF', 'DLG', 'DMU', 'DNO', 'DOM', 'DP5', 'DQQ', 'DQR', 'DR2', 'DR3','DR4', 'DRI', 'DSR', 'DT6', 'DVC', 'E4P', 'E5G', 'EAG', 'EBG', 'EBQ', 'EGA','EJT', 'EPG', 'ERE', 'ERI', 'F1P', 'F1X', 'F6P', 'FBP', 'FCA', 'FCB', 'FCT','FDP', 'FDQ', 'FFC', 'FIX', 'FMO', 'FRU', 'FSI', 'FU4', 'FUB', 'FUC', 'FUD','FUL', 'FXP', 'G16', 'G1P', 'G2F', 'G3I', 'G4D', 'G4S', 'G6D', 'G6P', 'G6S','GAC', 'GAD', 'GAL', 'GC1', 'GC4', 'GCD', 'GCN', 'GCO', 'GCS', 'GCT', 'GCU','GCV', 'GCW', 'GCX', 'GE1', 'GFG', 'GFP', 'GIV', 'GL0', 'GL2', 'GL5', 'GL6','GL7', 'GL9', 'GLA', 'GLB', 'GLC', 'GLD', 'GLF', 'GLG', 'GLO', 'GLP', 'GLS','GLT', 'GLW', 'GMH', 'GN1', 'GNX', 'GP1', 'GP4', 'GPH', 'GPM', 'GQ1', 'GQ2','GQ4', 'GS1', 'GS4', 'GSA', 'GSD', 'GTE', 'GTH', 'GTK', 'GTR', 'GTZ', 'GU0','GU1', 'GU2', 'GU3', 'GU4', 'GU5', 'GU6', 'GU8', 'GU9', 'GUF', 'GUP', 'GUZ','GYP', 'GYV', 'H2P', 'HDL', 'HMS', 'HS2', 'HSD', 'HSG', 'HSH', 'HSJ', 'HSQ','HSR', 'HSU', 'HSX', 'HSY', 'HSZ', 'IAB', 'IDG', 'IDR', 'IDS', 'IDT', 'IDU','IDX', 'IDY', 'IMK', 'IN1', 'IPT', 'ISL', 'KBG', 'KD2', 'KDA', 'KDM', 'KDO','KFN', 'KO1', 'KO2', 'KTU', 'L6S', 'LAG', 'LAI', 'LAK', 'LAO', 'LAT', 'LB2','LBT', 'LCN', 'LDY', 'LGC', 'LGU', 'LM2', 'LMT', 'LMU', 'LOG', 'LOX', 'LPK','LSM', 'LTM', 'LVZ', 'LXB', 'LXZ', 'M1F', 'M3M', 'M6P', 'M8C', 'MA1', 'MA2','MA3', 'MAB', 'MAG', 'MAL', 'MAN', 'MAT', 'MAV', 'MAW', 'MBG', 'MCU', 'MDA','MDM', 'MDP', 'MFA', 'MFB', 'MFU', 'MG5', 'MGA', 'MGL', 'MLB', 'MMA', 'MMN','MN0', 'MRP', 'MTT', 'MUG', 'MVP', 'MXY', 'N1L', 'N9S', 'NAA', 'NAG', 'NBG','NDG', 'NED', 'NG1', 'NG6', 'NGA', 'NGB', 'NGC', 'NGE', 'NGF', 'NGL', 'NGS','NGY', 'NHF', 'NM6', 'NM9', 'NTF', 'NTO', 'NTP', 'NXD', 'NYT', 'OPG', 'OPM','ORP', 'OX2', 'P3M', 'P53', 'P6P', 'PA5', 'PNA', 'PNG', 'PNW', 'PRP', 'PSJ','PSV', 'PTQ', 'QDK', 'QPS', 'QV4', 'R1P', 'R1X', 'R2B', 'R5P', 'RAA', 'RAE','RAF', 'RAM', 'RAO', 'RAT', 'RB5', 'RBL', 'RCD', 'RDP', 'REL', 'RER', 'RF5','RG1', 'RGG', 'RHA', 'RIB', 'RIP', 'RNS', 'RNT', 'ROB', 'ROR', 'RPA', 'RST','RUB', 'RUU', 'RZM', 'S6P', 'S7P', 'SA0', 'SCR', 'SDD', 'SF6', 'SF9', 'SG4','SG5', 'SG6', 'SG7', 'SGA', 'SGC', 'SGD', 'SGN', 'SGS', 'SHB', 'SHG', 'SI3','SIO', 'SOE', 'SOL', 'SSG', 'SUC', 'SUP', 'SUS', 'T6P', 'T6T', 'TAG', 'TCB','TDG', 'TGK', 'TGY', 'TH1', 'TIA', 'TM5', 'TM6', 'TM9', 'TMR', 'TMX', 'TOA','TOC', 'TRE', 'TYV', 'UCD', 'UDC', 'VG1', 'X0X', 'X1X', 'X2F', 'X4S', 'X5S','X6X', 'XBP', 'XDN', 'XDP', 'XIF', 'XIM', 'XLF', 'XLS', 'XMM', 'XUL', 'XXR','XYP', 'XYS', 'YO5', 'Z3Q', 'Z6J', 'Z9M', 'ZDC', 'ZDM']

Const SaccharideType

SaccharideType: 6 = 6

Const ScriptExtensions

ScriptExtensions: string[] = [ 'ngl', 'js' ]

List of file extensions to be recognized as scripts

Const SecStrucHelix

SecStrucHelix: string[] = [ 'h', 'g', 'i' ]

Const SecStrucSheet

SecStrucSheet: string[] = [ 'e', 'b' ]

Const SecStrucTurn

SecStrucTurn: string[] = [ 's', 't', 'l', '' ]

Const SelectAllKeyword

SelectAllKeyword: string[] = [ '*', '', 'ALL' ]

Const SelectNoneKeyword

SelectNoneKeyword: string[] = [ 'NONE' ]

Const ShaderRegistry

ShaderRegistry: Registry = new Registry('shader')

Const SmallResname

SmallResname: string[] = [ 'ALA', 'GLY', 'SER' ]

Const SphereBufferDefaultParameters

SphereBufferDefaultParameters: object & object & object = Object.assign({disableImpostor: false}, SphereGeometryBufferDefaultParameters)

Const SphereGeometryBufferDefaultParameters

SphereGeometryBufferDefaultParameters: object & object = Object.assign({sphereDetail: 1}, BufferDefaultParameters)

Const StructureComponentDefaultParameters

StructureComponentDefaultParameters: object & object = Object.assign({sele: '',defaultAssembly: ''}, ComponentDefaultParameters)

Const SubstitutionMatrices

SubstitutionMatrices: object = (function () {return {blosum62: prepareMatrix(aminoacids, blosum62),blosum62x: prepareMatrix(aminoacidsX, blosum62x)}}())

Type declaration

  • blosum62: object
    • [k: string]: object
      • [k: string]: number
  • blosum62x: object
    • [k: string]: object
      • [k: string]: number

Let SupportsPassiveEventHandler

SupportsPassiveEventHandler: boolean = false

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

Let SupportsReadPixelsFloat

SupportsReadPixelsFloat: boolean = false

Const SystemMode

SystemMode: 1 = 1

TABLE

TABLE: number = 17

TIME

TIME: number = 3

TYPE

TYPE: number = 12

TYPE$1

TYPE$1: number = 12

TYPEDO

TYPEDO: number = 13

Const TextAtlasCache

TextAtlasCache: object

Type declaration

Const TextBufferDefaultParameters

TextBufferDefaultParameters: object & object = Object.assign({fontFamily: 'sans-serif' as TextFonts,fontStyle: 'normal' as TextStyles,fontWeight: 'bold' as TextWeights,fontSize: 36,xOffset: 0.0,yOffset: 0.0,zOffset: 0.5,attachment: 'bottom-left' as TextAttachments,showBorder: false,borderColor: 'lightgrey' as number|string,borderWidth: 0.15,showBackground: false,backgroundColor: 'lightgrey' as number|string,backgroundMargin: 0.5,backgroundOpacity: 1.0,forceTransparent: true,fixedSize: false}, BufferDefaultParameters)

Const TextBufferParameterTypes

TextBufferParameterTypes: object & object = Object.assign({fontFamily: { uniform: true },fontStyle: { uniform: true },fontWeight: { uniform: true },fontSize: { uniform: true },xOffset: { uniform: true },yOffset: { uniform: true },zOffset: { uniform: true },showBorder: { uniform: true },borderColor: { uniform: true },borderWidth: { uniform: true },backgroundColor: { uniform: true },backgroundOpacity: { uniform: true },fixedSize: { updateShader: true }}, BufferParameterTypes)

Const TextureTestFragShader

TextureTestFragShader: "precision mediump float;uniform vec4 u_color;uniform sampler2D u_texture;void main() {gl_FragColor = texture2D(u_texture, vec2(0.5, 0.5)) * u_color;}" = `precision mediump float;uniform vec4 u_color;uniform sampler2D u_texture;void main() {gl_FragColor = texture2D(u_texture, vec2(0.5, 0.5)) * u_color;}`

Const TextureTestTexCoords

TextureTestTexCoords: Float32Array = new Float32Array([-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0])

Const TextureTestVertShader

TextureTestVertShader: "attribute vec4 a_position;void main() {gl_Position = a_position;}" = `attribute vec4 a_position;void main() {gl_Position = a_position;}`

Const TitleMode

TitleMode: 1 = 1

Const TorusBufferDefaultParameters

TorusBufferDefaultParameters: object & object = Object.assign({radiusRatio: 0.2,radialSegments: 16,tubularSegments: 32}, BufferDefaultParameters)

Let TrajectoryDatasource

TrajectoryDatasource: any

Const TrajectoryElementDefaultParameters

TrajectoryElementDefaultParameters: object & object = Object.assign({defaultStep: 1,defaultTimeout: 50,defaultInterpolateType: '' as TrajectoryPlayerInterpolateType,defaultInterpolateStep: 5,defaultMode: 'loop' as TrajectoryPlayerMode,defaultDirection: 'forward' as TrajectoryPlayerDirection,initialFrame: 0}, ElementDefaultParameters)

Trajectory component parameter object.

typedef

{Object} TrajectoryComponentParameters - component parameters

property

{String} name - component name

property

{Integer} initialFrame - initial frame the trajectory is set to

property

{Integer} defaultStep - default step size to be used by trajectory players

property

{Integer} defaultTimeout - default timeout to be used by trajectory players

property

{String} defaultInterpolateType - one of "" (empty string), "linear" or "spline"

property

{Integer} defaultInterpolateStep - window size used for interpolation

property

{String} defaultMode - either "loop" or "once"

property

{String} defaultDirection - either "forward" or "backward"

Const TubeMeshBufferDefaultParameters

TubeMeshBufferDefaultParameters: object & object = Object.assign({radialSegments: 4,capped: false,aspectRatio: 1.0}, BufferDefaultParameters)

Const TwoPI

TwoPI: number = 2 * Math.PI

Const UnknownBackboneType

UnknownBackboneType: 0 = 0

Private Const UnknownEntity

UnknownEntity: 0 = 0
file

Structure Constants

author

Alexander Rose alexander.rose@weirdbyte.de

Const UnknownType

UnknownType: 0 = 0

Const VectorBufferDefaultParameters

VectorBufferDefaultParameters: object & object = Object.assign({scale: 1,color: 'grey'}, BufferDefaultParameters)

Const Version

Version: string = (data as any).version as string

Version name

type

{String}

Const WaterEntity

WaterEntity: 4 = 4

Const WaterNames

WaterNames: string[] = ['SOL', 'WAT', 'HOH', 'H2O', 'W', 'DOD', 'D3O', 'TIP3', 'TIP4', 'SPC']

Const WaterType

WaterType: 1 = 1

Const WebglErrorMessage

WebglErrorMessage: "<div style="display:flex;align-items:center;justify-content:center;height:100%;"><p style="padding:15px;text-align:center;">Your browser/graphics card does not seem to support <a target="_blank" href="https://en.wikipedia.org/wiki/WebGL">WebGL</a>.<br/><br/>Find out how to get it <a target="_blank" href="http://get.webgl.org/">here</a>.</p></div>" = "<div style="display:flex;align-items:center;justify-content:center;height:100%;"><p style="padding:15px;text-align:center;">Your browser/graphics card does not seem to support <a target="_blank" href="https://en.wikipedia.org/wiki/WebGL">WebGL</a>.<br/><br/>Find out how to get it <a target="_blank" href="http://get.webgl.org/">here</a>.</p></div>"

Const WideLineBufferDefaultParameters

WideLineBufferDefaultParameters: object & object = Object.assign({linewidth: 2}, BufferDefaultParameters)

Const WideLineBufferParameterTypes

WideLineBufferParameterTypes: object & object = Object.assign({linewidth: { uniform: true }}, BufferParameterTypes)

Const X

X: Elements[] = [ Elements.N, Elements.O, Elements.S ]

Const Y

Y: Elements[] = [ Elements.C, Elements.N, Elements.P, Elements.S ]

Const ZERO

ZERO: 0 = 0

Z_BLOCK

Z_BLOCK: number = 5

Z_BUF_ERROR

Z_BUF_ERROR: number = -5

Z_BUF_ERROR$1

Z_BUF_ERROR$1: number = -5

Z_DATA_ERROR

Z_DATA_ERROR: number = -3

Z_DEFLATED

Z_DEFLATED: number = 8

Z_FINISH

Z_FINISH: number = 4

Z_FINISH$1

Z_FINISH$1: number = 4

Z_MEM_ERROR

Z_MEM_ERROR: number = -4

Z_NEED_DICT

Z_NEED_DICT: number = 2

Z_NEED_DICT$1

Z_NEED_DICT$1: number = 2

Z_NO_FLUSH

Z_NO_FLUSH: number = 0

Z_OK

Z_OK: number = 0

Z_OK$1

Z_OK$1: number = 0

Z_STREAM_END

Z_STREAM_END: number = 1

Z_STREAM_END$1

Z_STREAM_END$1: number = 1

Z_STREAM_ERROR

Z_STREAM_ERROR: number = -2

Z_SYNC_FLUSH

Z_SYNC_FLUSH: number = 2

Z_TREES

Z_TREES: number = 6

Const _m

_m: Matrix4 = new Matrix4()

Const _tmpBytes

_tmpBytes: Uint8Array = new Uint8Array(32)

Const _tmpIntBytes

_tmpIntBytes: Int32Array = new Int32Array(32)

_utf8len

_utf8len: Uint8Array = new Uint8Array(256)

Const _v

_v: Vector3 = new Vector3()

Const amberChargeUnitFactor

amberChargeUnitFactor: 18.2223 = 18.2223

Const aminoacids

aminoacids: "ARNDCQEGHILKMFPSTWYVBZ?" = "ARNDCQEGHILKMFPSTWYVBZ?"

Const aminoacidsX

aminoacidsX: "ACDEFGHIKLMNPQRSTVWY" = "ACDEFGHIKLMNPQRSTVWY"

Const Private baseUrl

baseUrl: string = "//mmtf.rcsb.org/v1.0/"

Version name

type

{String}

Const blosum62

blosum62: number[][] = [// A R N D C Q E G H I L K M F P S T W Y V B Z X[4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0], // A[-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1], // R[-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1], // N[-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1], // D[0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2], // C[-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1], // Q[-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1], // E[0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1], // G[-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1], // H[-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1], // I[-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1], // L[-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1], // K[-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1], // M[-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1], // F[-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2], // P[1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0], // S[0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0], // T[-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2], // W[-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1], // Y[0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1], // V[-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1], // B[-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1], // Z[0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1] // X]

Const blosum62x

blosum62x: number[][] = [[4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, -2], // A[0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -2], // C[-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -3], // D[-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -2], // E[-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, 3], // F[0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -3], // G[-2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, 2], // H[-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1], // I[-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -2], // K[-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1], // L[-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1], // M[-2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -2], // N[-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -3], // P[-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1], // Q[-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -2], // R[1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, -2], // S[0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, -2], // T[0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1], // V[-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, 2], // W[-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, 7] // Y]

Const bohrToAngstromFactor

bohrToAngstromFactor: 0.529177210859 = 0.529177210859

Const calculateSecondaryStructure

calculateSecondaryStructure: calculateSecondaryStructure = (function () {// Implementation for proteins based on "pv"//// assigns secondary structure information based on a simple and very fast// algorithm published by Zhang and Skolnick in their TM-align paper.// Reference://// TM-align: a protein structure alignment algorithm based on the Tm-score// (2005) NAR, 33(7) 2302-2309const zhangSkolnickSS = function (polymer: Polymer, i: number, distances: number[], delta: number) {const structure = polymer.structureconst offset = polymer.residueIndexStartconst rp1 = structure.getResidueProxy()const rp2 = structure.getResidueProxy()const ap1 = structure.getAtomProxy()const ap2 = structure.getAtomProxy()for (let j = Math.max(0, i - 2); j <= i; ++j) {for (let k = 2; k < 5; ++k) {if (j + k >= polymer.residueCount) {continue}rp1.index = offset + jrp2.index = offset + j + kap1.index = rp1.traceAtomIndexap2.index = rp2.traceAtomIndexconst d = ap1.distanceTo(ap2)if (Math.abs(d - distances[ k - 2 ]) > delta) {return false}}}return true}const isHelical = function (polymer: Polymer, i: number) {const helixDistances = [ 5.45, 5.18, 6.37 ]const helixDelta = 2.1return zhangSkolnickSS(polymer, i, helixDistances, helixDelta)}const isSheet = function (polymer: Polymer, i: number) {const sheetDistances = [ 6.1, 10.4, 13.0 ]const sheetDelta = 1.42return zhangSkolnickSS(polymer, i, sheetDistances, sheetDelta)}const proteinPolymer = function (p: Polymer) {const residueStore = p.residueStoreconst offset = p.residueIndexStartfor (let i = 0, il = p.residueCount; i < il; ++i) {let sstruc = 'c'if (isHelical(p, i)) {sstruc = 'h'} else if (isSheet(p, i)) {sstruc = 's'}residueStore.sstruc[ offset + i ] = sstruc.charCodeAt(0)}}const cgPolymer = function (p: Polymer) {const localAngle = 20const centerDist = 2.0const residueStore = p.residueStoreconst offset = p.residueIndexStartconst helixbundle = new Helixbundle(p)const pos = helixbundle.positionconst c1 = new Vector3()const c2 = new Vector3()for (let i = 0, il = p.residueCount; i < il; ++i) {c1.fromArray(pos.center as any, i * 3) // TODOc2.fromArray(pos.center as any, i * 3 + 3) // TODOconst d = c1.distanceTo(c2)if (d < centerDist && d > 1.0 && pos.bending[ i ] < localAngle) {residueStore.sstruc[ offset + i ] = 'h'.charCodeAt(0)residueStore.sstruc[ offset + i + 1 ] = 'h'.charCodeAt(0)}}}return function calculateSecondaryStructure (structure: Structure) {if (Debug) Log.time('calculateSecondaryStructure')structure.eachPolymer(function (p) {// assign secondary structureif (p.residueCount < 4) returnif (p.isCg()) {cgPolymer(p)} else if (p.isProtein()) {proteinPolymer(p)} else {return}// set lone secondary structure assignments to "c"let prevSstruc: stringlet sstrucCount = 0p.eachResidue(function (r: ResidueProxy) {if (r.sstruc === prevSstruc) {sstrucCount += 1} else {if (sstrucCount === 1) {r.index -= 1r.sstruc = 'c'}sstrucCount = 1prevSstruc = r.sstruc}})})if (Debug) Log.timeEnd('calculateSecondaryStructure')}}())

Const charArray

charArray: string[] = []

Const charmmTimeUnitFactor

charmmTimeUnitFactor: 20.45482949774598 = 20.45482949774598

Const chars

chars: string[] = '0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz'.split('')

crcTable

crcTable: number[] = makeTable()

Const dAminoAcids

dAminoAcids: string[] = ['DAL', // D-ALANINE'DAR', // D-ARGININE'DSG', // D-ASPARAGINE'DAS', // D-ASPARTIC ACID'DCY', // D-CYSTEINE'DGL', // D-GLUTAMIC ACID'DGN', // D-GLUTAMINE'DHI', // D-HISTIDINE'DIL', // D-ISOLEUCINE'DLE', // D-LEUCINE'DLY', // D-LYSINE'MED', // D-METHIONINE'DPN', // D-PHENYLALANINE'DPR', // D-PROLINE'DSN', // D-SERINE'DTH', // D-THREONINE'DTR', // D-TRYPTOPHAN'DTY', // D-TYROSINE'DVA', // D-VALINE'DNE' // D-NORLEUCINE// ??? // D-SELENOCYSTEINE]

dbase

dbase: number[] = [ /* Distance codes 0..29 base */1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,8193, 12289, 16385, 24577, 0, 0]

Const defaultByteLength

defaultByteLength: number = 1024 * 8

dext

dext: number[] = [ /* Distance codes 0..29 extra */16, 16, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22,23, 23, 24, 24, 25, 25, 26, 26, 27, 27,28, 28, 29, 29, 64, 64]

distfix

distfix: any

Const elm1

elm1: string[] = [ 'H', 'C', 'O', 'N', 'S', 'P' ]

Const elm2

elm2: string[] = [ 'NA', 'CL', 'FE' ]

Const entityKeyList

entityKeyList: string[] = ['MOL_ID', 'MOLECULE', 'CHAIN', 'FRAGMENT', 'SYNONYM','EC', 'ENGINEERED', 'MUTATION', 'OTHER_DETAILS']

Const eye

eye: Vector3 = new Vector3(0, 0, 0)

fetchReducedUrl

fetchReducedUrl: string = baseUrl + "reduced/"

URL of the RCSB webservice to obtain reduced MMTF files

static
type

{String}

fetchUrl

fetchUrl: string = baseUrl + "full/"

URL of the RCSB webservice to obtain MMTF files

static
type

{String}

Const halBondElements

halBondElements: number[] = [17, 35, 53, 85]

lbase

lbase: number[] = [ /* Length codes 257..285 base */3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0]

lenfix

lenfix: any

lext

lext: number[] = [ /* Length codes 257..285 extra */16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 18,19, 19, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 16, 72, 78]

Const mapping

mapping: Float32Array = new Float32Array([-1.0, -1.0, -1.0,1.0, -1.0, -1.0,1.0, -1.0, 1.0,-1.0, -1.0, 1.0,-1.0, 1.0, -1.0,1.0, 1.0, -1.0,1.0, 1.0, 1.0,-1.0, 1.0, 1.0])

Const mappingIndices

mappingIndices: Uint16Array = new Uint16Array([0, 1, 2,0, 2, 3,1, 5, 6,1, 6, 2,4, 6, 5,4, 7, 6,0, 7, 4,0, 3, 7,0, 5, 1,0, 4, 5,3, 2, 6,3, 6, 7])

Const matrix

matrix: Matrix4 = new Matrix4()

Const maxRadius

maxRadius: 12 = 12

Const maxRadius2

maxRadius2: number = maxRadius * maxRadius

Const mmtfBaseUrl

mmtfBaseUrl: "//mmtf.rcsb.org/v1.0/" = "//mmtf.rcsb.org/v1.0/"

Const mmtfFullUrl

mmtfFullUrl: string = mmtfBaseUrl + 'full/'

Const mmtfReducedUrl

mmtfReducedUrl: string = mmtfBaseUrl + 'reduced/'

Const modelViewProjectionMatrix

modelViewProjectionMatrix: Matrix4 = new Matrix4()

Const nHBondDistance

nHBondDistance: 1.04 = 1.04

Const nHCharge

nHCharge: 0.25 = 0.25

Const negateVector

negateVector: Vector3 = new Vector3(-1, -1, -1)

Const normalMatrix

normalMatrix: Matrix3 = new Matrix3()

Const passive

passive: false | object = SupportsPassiveEventHandler ? { passive: true } : false

Const pixelBufferFloat

pixelBufferFloat: Float32Array = new Float32Array(4)

Const pixelBufferUint

pixelBufferUint: Uint8Array = new Uint8Array(4)

Const pointArray

pointArray: Float32Array = new Float32Array(3)

Const projectionMatrixInverse

projectionMatrixInverse: Matrix4 = new Matrix4()

Const projectionMatrixTranspose

projectionMatrixTranspose: Matrix4 = new Matrix4()

Const quadIndices

quadIndices: Uint16Array = new Uint16Array([0, 1, 2,1, 3, 2])

Const quadUvs

quadUvs: Float32Array = new Float32Array([0, 1,0, 0,1, 1,1, 0])

Const reAttr

reAttr: RegExp = /([\w:-]+)\s*=\s*("[^"]*"|'[^']*'|\w+)\s*/

Const reCollapseEqual

reCollapseEqual: RegExp = /\s*=\s*/g

Const reContent

reContent: RegExp = /^([^<]*)/

Const reCurlyWhitespace

reCurlyWhitespace: RegExp = /[^{}\s]*{[^{}]+}|[^{}\s]+/g

Const reDoubleQuote

reDoubleQuote: RegExp = /"/g

Const reField

reField: RegExp = /\[ (.+) \]/

Const reInclude

reInclude: RegExp = /^(?!\/\/)\s*#include\s+(\S+)/gmi

Const reInteger

reInteger: RegExp = /^[1-9]$/

Const reItem

reItem: RegExp = /> <(.+)>/

Const reProtocol

reProtocol: RegExp = /^((http|https|ftp):)*\/\//

Const reQuotedWhitespace

reQuotedWhitespace: RegExp = /'((?:(?!'\s).)*)'|"((?:(?!"\s).)*)"|(\S+)/g

Const reScientificNotation

reScientificNotation: RegExp = /-?\d+(?:\.\d*)?(?:[eE][+-]?\d+)?/g

Const reStrip

reStrip: RegExp = /^['"]|['"]$/g

Const reTag

reTag: RegExp = /^<([\w-:.]+)\s*/

Const reTitle

reTitle: RegExp = /(^\*|REMARK)*/

Const reTrimCurly

reTrimCurly: RegExp = /^{+|}+$/g

Const reTrimQuotes

reTrimQuotes: RegExp = /^['"]+|['"]+$/g

Const reWhitespace

reWhitespace: RegExp = /\s+/

Const reWhitespaceComma

reWhitespaceComma: RegExp = /[\s,]+/

Const resolution

resolution: Vector2 = new Vector2()

Const scale

scale: Vector3 = new Vector3()

Const shaderCache

shaderCache: object

Type declaration

  • [k: string]: string

Const suffixUrl

suffixUrl: "/SDF?record_type=3d" = "/SDF?record_type=3d"

Const swap

  • swap(A: NumberArray, i0: number, i1: number, t: number): void

Const target

target: Vector3 = new Vector3()

Const temp

temp: Float32Array = new Float32Array(4)

Const tmpAlignMatrix

tmpAlignMatrix: Matrix4 = new Matrix4()

Const tmpAtomVector

tmpAtomVector: Vector3 = new Vector3()

Const tmpBox

tmpBox: Box3 = new Box3()

Const tmpCanvasVector

tmpCanvasVector: Vector3 = new Vector3()

Const tmpColor

tmpColor: Color = new Color()

Const tmpMatrix

tmpMatrix: Matrix4 = new Matrix4()

Const tmpP

tmpP: Vector3 = new Vector3()

Const tmpPanMatrix

tmpPanMatrix: Matrix4 = new Matrix4()

Const tmpPanVector

tmpPanVector: Vector3 = new Vector3()

Const tmpQ

tmpQ: Quaternion = new Quaternion()

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

typedef

{Matrix4} OrientationMatrix - orientation matrix

Const tmpRotateMatrix

tmpRotateMatrix: Matrix4 = new Matrix4()

Const tmpRotateQuaternion

tmpRotateQuaternion: Quaternion = new Quaternion()

Const tmpRotateVector

tmpRotateVector: Vector3 = new Vector3()

Const tmpRotateXMatrix

tmpRotateXMatrix: Matrix4 = new Matrix4()

Const tmpRotateYMatrix

tmpRotateYMatrix: Matrix4 = new Matrix4()

Const tmpRotateZMatrix

tmpRotateZMatrix: Matrix4 = new Matrix4()

Const tmpS

tmpS: Vector3 = new Vector3()

Const tmpScaleVector

tmpScaleVector: Vector3 = new Vector3()

Const tmpVec

tmpVec: Vector3 = new Vector3()

Const tmpZoomVector

tmpZoomVector: Vector3 = new Vector3()

toString

toString: toString = Object.prototype.toString

Const up

up: Vector3 = new Vector3()

Const uuid

uuid: any[] = new Array(36)

Const vMeshNormal

vMeshNormal: Vector3 = new Vector3()

Const vTangent

vTangent: Vector3 = new Vector3()

version

version: string = "v1.1.0dev"

Version name

static
type

{String}

Const vertex

vertex: Vector3 = new Vector3()

virgin

virgin: boolean = true

Functions

AVHash

  • AVHash(atomsX: Float32Array, atomsY: Float32Array, atomsZ: Float32Array, atomsR: Float32Array, min: Float32Array, max: Float32Array, maxDistance: any): void

  • Modifed from SpatialHash

    Main differences are:

    • Optimized grid size to ensure we only ever need to look +/-1 cell
    • Aware of atomic radii and will only output atoms within rAtom + rExtra (see withinRadii method)

    (Uses rounding rather than bitshifting as consequence of arbitrary grid size)

    class

    Parameters

    • atomsX: Float32Array

      x coordinates

    • atomsY: Float32Array

      y coordinates

    • atomsZ: Float32Array

      z coordinates

    • atomsR: Float32Array

      atom radii

    • min: Float32Array

      xyz min coordinates

    • max: Float32Array

      xyz max coordinates

    • maxDistance: any

      max distance

    Returns void

AVSurface

  • AVSurface(coordList: any, radiusList: any, indexList: any): void

EDTSurface

  • EDTSurface(coordList: any, radiusList: any, indexList: any): void

GZheader

  • GZheader(): void

Private Grid

  • Grid(length: any, width: any, height: any, DataCtor: any, elemSize: any): void

Inflate

  • Inflate(options: any): undefined | Inflate

  • new Inflate(options)

    • options (Object): zlib inflate options.

    Creates new inflator instance with specified params. Throws exception on bad params. Supported options:

    • windowBits
    • dictionary

    http://zlib.net/manual.html#Advanced for more information on these.

    Additional options, for internal needs:

    • chunkSize - size of generated data chunks (16K by default)
    • raw (Boolean) - do raw inflate
    • to (String) - if equal to 'string', then result will be converted from utf8 to utf16 (javascript) string. When string output requested, chunk length can differ from chunkSize, depending on content.

    By default, when no options set, autodetect deflate/gzip data format via wrapper header.

    Example:
    var pako = require('pako')
  , chunk1 = Uint8Array([1,2,3,4,5,6,7,8,9])
  , chunk2 = Uint8Array([10,11,12,13,14,15,16,17,18,19]);

var inflate = new pako.Inflate({ level: 3});

inflate.push(chunk1, false);
inflate.push(chunk2, true);  // true -> last chunk

if (inflate.err) { throw new Error(inflate.err); }

console.log(inflate.result);

    Parameters

    • options: any

    Returns undefined | Inflate

InflateState

  • InflateState(): void

Interpolator

  • Interpolator(m: any, tension: any): void

JacobiSVDImpl

MarchingCubes

  • MarchingCubes(field: any, nx: any, ny: any, nz: any, atomindex: any): void

Private OBJLoader

  • OBJLoader(): void

Private PLYLoader

  • PLYLoader(): void

  • PLYLoader

    class
    author

    Wei Meng / http://about.me/menway

    description

    A THREE loader for PLY ASCII files (known as the Polygon File Format or the Stanford Triangle Format).

    Limitations: ASCII decoding assumes file is UTF-8.

    example

    var loader = new THREE.PLYLoader(); loader.load('./models/ply/ascii/dolphins.ply', function (geometry) { scene.add( new THREE.Mesh( geometry ) ); } );

    // If the PLY file uses non standard property names, they can be mapped while // loading. For example, the following maps the properties // “diffuse_(red|green|blue)” in the file to standard color names.

    loader.setPropertyNameMapping( { diffuse_red: 'red', diffuse_green: 'green', diffuse_blue: 'blue' } );

    Returns void

Spline

  • Spline(polymer: any, params: any): void

VolumeSurface

  • VolumeSurface(data: any, nx: any, ny: any, nz: any, atomindex: any): void

ZStream

  • ZStream(): void

_buf2binstring

  • _buf2binstring(buf: any, len: any): any

_ensureClassFromArg

  • _ensureClassFromArg(arg: any, constructor: object): any

  • Parameters

    • arg: any
    • constructor: object
      • constructor: function
        • new __type(arg: any): any

    Returns any

_ensureClassFromArray

  • _ensureClassFromArray(array: any, constructor: object): any

  • Parameters

    • array: any
    • constructor: object
      • constructor: function
        • new __type(): any

    Returns any

Private _fetch

  • _fetch(pdbid: string, baseUrl: string, onLoad: any, onError: Function): undefined

  • helper method to fetch binary files from an URL

    Parameters

    • pdbid: string

      PDB ID to fetch

    • baseUrl: string

      URL to fetch from

    • onLoad: any

      callback( mmtfData )

    • onError: Function

      callback( error )

    Returns undefined

_trimCanvas

  • _trimCanvas(canvas: HTMLCanvasElement, r: number, g: number, b: number, a: number): HTMLCanvasElement

  • Parameters

    • canvas: HTMLCanvasElement
    • r: number
    • g: number
    • b: number
    • a: number

    Returns HTMLCanvasElement

addAromaticRings

addAtom

addChargedContacts

addCols

  • addCols(A: Matrix, col: number[]): void

addElement

  • addElement(elm: any, array: any[]): void

addFeature

addHalogenAcceptors

addHalogenBonds

addHalogenDonors

addHydrogenAcceptors

addHydrogenBonds

addHydrogenDonors

addHydrophobic

addHydrophobicContacts

addMetalBinding

addMetalComplexation

addMetals

addNegativeCharges

addPositiveCharges

addRing

addRows

  • addRows(A: Matrix, row: number[]): void

addWeakHydrogenDonors

adler32

  • adler32(adler: any, buf: any, len: any, pos: any): number

almostIdentity

  • almostIdentity(value: number, start: number, stop: number): number

applyMatrix3toVector3array

  • applyMatrix3toVector3array(m: Float32Array, a: Float32Array): void

applyMatrix4toVector3array

  • applyMatrix4toVector3array(m: Float32Array, a: Float32Array): void

arrayMax

arrayMean

  • arrayMean(array: NumberArray, stride?: number, offset?: number): number

arrayMean3

arrayMin

arrayRms

arraySet

  • arraySet(dest: any, src: any, src_offs: any, len: any, dest_offs: any): void

arraySorted

arraySortedCmp

  • arraySortedCmp<T>(array: T[], cmp: function): boolean

  • Type parameters

    • T

    Parameters

    • array: T[]
    • cmp: function
        • (a: T, b: T): number

        • Parameters

          • a: T
          • b: T

          Returns number

    Returns boolean

arraySum

  • arraySum(array: NumberArray, stride?: number, offset?: number): number

assign

  • assign(obj: any): any

assignGeometry

assignResidueTypeBonds

  • assignResidueTypeBonds(structure: Structure): void

assignSecondaryStructure

atomTestFn

atomTriplePositions

  • atomTriplePositions(sview: any, atomTriple: any): Float32Array

attributesList

  • attributesList(buffer: IOBuffer): any[]

  • List of attributes

    ignore

    Parameters

    • buffer: IOBuffer

      Buffer for the file data

    Returns any[]

    • List of attributes with:
      • name: String with the name of the attribute
      • type: String with the type of the attribute
      • value: A number or string with the value of the attribute

autoLoad

  • Load a file

    example

    // load from URL NGL.autoLoad( "http://files.rcsb.org/download/5IOS.cif" );

    example

    // load binary data in CCP4 format via a Blob var binaryBlob = new Blob( [ ccp4Data ], { type: 'application/octet-binary'} ); NGL.autoLoad( binaryBlob, { ext: "ccp4" } );

    example

    // load string data in PDB format via a Blob var stringBlob = new Blob( [ pdbData ], { type: 'text/plain'} ); NGL.autoLoad( stringBlob, { ext: "pdb" } );

    example

    // load a File object NGL.autoLoad( file );

    Parameters

    Returns any

    Promise resolves to the loaded data

backboneNHPosition

  • backboneNHPosition(ap: AtomProxy, position?: Vector3): undefined | Vector3

  • Populates position vector with location of implicit or explicit H Returns position or undefined if not able to locate H

    Parameters

    • ap: AtomProxy

      the nitrogen atom

    • Default value position: Vector3 = new Vector3()

    Returns undefined | Vector3

    the hydrogen atom position

binarySearchForLeftRange

  • binarySearchForLeftRange(array: number[], leftRange: number): number

  • Parameters

    • array: number[]
    • leftRange: number

    Returns number

binarySearchForRightRange

  • binarySearchForRightRange(array: number[], rightRange: number): number

  • Parameters

    • array: number[]
    • rightRange: number

    Returns number

binarySearchIndexOf

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

    function
    example

    var array = [ 1, 2, 3, 4, 5, 6 ]; var element = 4; binarySearchIndexOf( array, element ); // returns 3

    Type parameters

    • T

    Parameters

    • array: T[]

      sorted array

    • element: T

      element to search for in the array

    • Default value compareFunction: lexicographicCompare = lexicographicCompare

    Returns number

    the index of the element or -1 if not in the array

binstring2buf

  • binstring2buf(str: any): Uint8Array

boolean

  • boolean(value: any): boolean

buf2string

  • buf2string(buf: any, max: any): any

buildStoreLike

  • buildStoreLike(positions: Vector3[]): object

  • Takes an array of Vector3 objects and converts to an object that looks like an AtomStore

    Parameters

    • positions: Vector3[]

      array of positions

    Returns object

    AtomStore-like object

    • count: number
    • x: Float32Array
    • y: Float32Array
    • z: Float32Array

buildUnitcellAssembly

  • buildUnitcellAssembly(structure: Structure): void

calcAngles

  • Calculate the angles x-1-2 for all x where x is a heavy atom bonded to ap1.

    Parameters

    Returns number[]

    Angles in radians

calcArcPoint

  • calcArcPoint(out: any, center: any, v1: any, v2: any, angle: any): void

calcPlaneAngle

  • Find two neighbours of ap1 to define a plane (if possible) and measure angle out of plane to ap2

    Parameters

    Returns number | undefined

    Angle from plane to second atom

calculateAtomBondMap

  • calculateAtomBondMap(structure: Structure): number[][]

calculateBonds

calculateBondsBetween

  • calculateBondsBetween(structure: Structure, onlyAddBackbone?: boolean, useExistingBonds?: boolean): void

calculateBondsWithin

  • calculateBondsWithin(structure: Structure, onlyAddRung?: boolean): void

calculateCenterArray

  • calculateCenterArray(array1: NumberArray, array2: NumberArray, center?: NumberArray, offset?: number): number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

  • Parameters

    Returns number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

calculateChainnames

  • calculateChainnames(structure: Structure, useExistingBonds?: boolean): void

calculateContacts

  • Parameters

    • structure: Structure
    • Default value params: object = ContactDefaultParams
      • lineOfSightDistFactor: number
      • masterModelIndex: number
      • maxCationPiDist: number
      • maxCationPiOffset: number
      • maxHalogenBondAngle: number
      • maxHalogenBondDist: number
      • maxHbondAccAngle: number
      • maxHbondAccPlaneAngle: number
      • maxHbondDist: number
      • maxHbondDonAngle: number
      • maxHbondDonPlaneAngle: number
      • maxHbondSulfurDist: number
      • maxHydrophobicDist: number
      • maxIonicDist: number
      • maxMetalDist: number
      • maxPiStackingAngle: number
      • maxPiStackingDist: number
      • maxPiStackingOffset: number
      • refineSaltBridges: boolean

    Returns FrozenContacts

calculateDirectionArray

calculateFeatures

calculateHydrogensCharge

calculateMeanArray

calculateMeanVector3

calculateMinArray

calculateResidueBonds

centerArray3

  • centerArray3(array: NumberArray, center?: Vector3): Vector3

centerPbc

  • centerPbc(coords: NumberArray, mean: number[], box: ArrayLike<number>): void

chainTestFn

chargeForAtom

cifDefaults

  • cifDefaults(value: any, defaultValue: any): any

circularMean

  • circularMean(array: NumberArray, max: number, stride?: number, offset?: number, indices?: NumberArray): number

circularMean3

clamp

  • clamp(value: number, min: number, max: number): number

closer

  • closer(x: Vector3, a: Vector3, b: Vector3): boolean

computeBoundingBox

  • computeBoundingBox(array: NumberArray): Float32Array[]

computeVertexNormals

  • computeVertexNormals(position: any, index: any, normal: any): any

concatStructures

contactColor

contactTypeName

  • contactTypeName(type: ContactType): "hydrogen bond" | "hydrophobic contact" | "halogen bond" | "ionic interaction" | "metal coordination" | "cation-pi interaction" | "pi-pi stacking" | "weak hydrogen bond" | "unknown contact"

  • Parameters

    Returns "hydrogen bond" | "hydrophobic contact" | "halogen bond" | "ionic interaction" | "metal coordination" | "cation-pi interaction" | "pi-pi stacking" | "weak hydrogen bond" | "unknown contact"

convertKinTriangleArrays

  • convertKinTriangleArrays(ribbonObject: any): object

  • Parameters

    • ribbonObject: any

    Returns object

    • colorArray: any[]
    • labelArray: any[]
    • masterArray: any
    • name: any
    • positionArray: any[]

copyArray

  • copyArray<T>(src: T, dst: T, srcOffset: number, dstOffset: number, length: number): void

copyWithin

  • copyWithin(array: NumberArray | any[], srcOffset: number, dstOffset: number, length: number): void

countSetBits

  • countSetBits(i: number): number

crc32

  • crc32(crc: any, buf: any, len: any, pos: any): number

createAdjacencyList

createBoundingBox

  • createBoundingBox(positions: Positions): Box3

createContacts

createData

createFeatureState

createFeatures

createFrozenContacts

createParams

  • createParams<T>(params: object, defaultParams: T): T

  • Type parameters

    • T

    Parameters

    • params: object
    • defaultParams: T

    Returns T

Private createProgram

  • createProgram(gl: WebGLRenderingContext, shaders: WebGLShader[], attribs?: string[], locations?: number[]): null | WebGLProgram

createRingBuffer

  • createRingBuffer<T>(length: number): RingBuffer<T>

createSimpleDict

createSimpleSet

dataURItoImage

  • dataURItoImage(dataURI: string): HTMLImageElement

  • Parameters

    • dataURI: string

    Returns HTMLImageElement

decode

  • decode(binOrDict: any, params: object): object

  • Decode MMTF fields

    static
    example

    // bin is Uint8Array containing the mmtf msgpack var mmtfData = MMTF.decode( bin ); console.log( mmtfData.numAtoms );

    Parameters

    • binOrDict: any

      binary MessagePack or encoded MMTF data

    • params: object

    Returns object

    mmtfData

decodeBits

  • decodeBits(buf: any, cbuf: any, numOfBits: any, buf2: any): number

decodeBytes

  • decodeBytes(bytes: any): any[]

decodeDelta

  • decodeDelta(array: any, output: any): any

  • perform delta decoding of the input array by iterativly adding the ith element's value to the i+1th example: dataArray: [ 0, 2, 1, 2, 1, 1, -4, -2, 9 ] return: [ 0, 2, 3, 5, 6, 7, 3, 1, 10 ]

    static

    Parameters

    • array: any
    • output: any

    Returns any

    decoded array

decodeDeltaRun

  • decodeDeltaRun(array: any, output: any): any

decodeFloat32

  • decodeFloat32(bytes: any, output: any): any

decodeInt16

  • decodeInt16(bytes: any, output: any): Int16Array

  • get an Int16Array copy of the the input array data

    static

    Parameters

    • bytes: any
    • output: any

    Returns Int16Array

    copy of the input array data

decodeInt32

  • decodeInt32(bytes: any, output: any): Int32Array

  • get an Int32Array copy of the the input array data

    static

    Parameters

    • bytes: any
    • output: any

    Returns Int32Array

    copy of the input array data

decodeInteger

  • decodeInteger(intArray: any, divisor: number, output: any): Float32Array

  • decode integers into floats using given divisor example: intArray: [ 12, 34, 543, 687, 2, 0, 4689 ] divisor: 100 return: [ 0.12, 0.34, 5.43, 6.87, 0.02, 0.00, 46.89 ]

    static

    Parameters

    • intArray: any

      input array containing integers

    • divisor: number

      number to devide the integers to obtain floats

    • output: any

    Returns Float32Array

    decoded array

decodeIntegerDelta

  • decodeIntegerDelta(intArray: any, divisor: any, output: any): Float32Array

  • Parameters

    • intArray: any
    • divisor: any
    • output: any

    Returns Float32Array

decodeIntegerDeltaPacking

  • decodeIntegerDeltaPacking(int16or8: any, divisor: any, output: any): Float32Array

  • Parameters

    • int16or8: any
    • divisor: any
    • output: any

    Returns Float32Array

decodeIntegerPacking

  • decodeIntegerPacking(int16or8: any, divisor: any, output: any): Float32Array

  • Parameters

    • int16or8: any
    • divisor: any
    • output: any

    Returns Float32Array

decodeIntegerRun

  • decodeIntegerRun(intArray: any, divisor: any, output: any): Float32Array

  • perform run-length decoding followed (@see decodeRunLength) by decoding integers into floats using given divisor (@see decodeIntegerToFloat) example: array: [ 320, 3, 100, 2 ] divisor: 100 return: [ 3.20, 3.20, 3.20, 1.00, 1.00 ]

    static

    Parameters

    • intArray: any
    • divisor: any

      number to devide the integers to obtain floats

    • output: any

    Returns Float32Array

    decoded array

decodeInts

  • decodeInts(buf: any, cbuf: any, numOfInts: any, numOfBits: any, sizes: any, nums: any, buf2: any): void

  • Parameters

    • buf: any
    • cbuf: any
    • numOfInts: any
    • numOfBits: any
    • sizes: any
    • nums: any
    • buf2: any

    Returns void

decodeMmtf

  • decodeMmtf(inputDict: any, params: object): object

  • Decode MMTF fields

    static

    Parameters

    • inputDict: any

      encoded MMTF data

    • params: object

    Returns object

    mmtfData

decodeMsgpack

  • decodeMsgpack(buffer: Uint8Array): any

  • decode binary encoded MessagePack v5 (http://msgpack.org/) data

    static

    Parameters

    • buffer: Uint8Array

      binary encoded MessagePack data

    Returns any

    decoded Messagepack data

decodePacking

  • decodePacking(int16or8: Int8Array | Int16Array, output: Int32Array): Int32Array

  • [decodePacking description]

    Parameters

    • int16or8: Int8Array | Int16Array
    • output: Int32Array

    Returns Int32Array

    [description]

decodeRun

  • decodeRun(array: any, output: any): any

  • perform run-length decoding of input array example: array: [ 0, 2, 3, 5 ] // pairs of values and length of a run return: [ 0, 0, 3, 3, 3, 3, 3 ]

    static

    Parameters

    • array: any

      run-length encoded input array

    • output: any

    Returns any

    decoded array

deepCopy

  • deepCopy(src: any): any

deepEqual

  • deepEqual(a: any, b: any): boolean

defaults

  • defaults(value: any, defaultValue: any): any

  • Parameters

    • value: any
    • defaultValue: any

    Returns any

Private degToRad

  • degToRad(deg: number): number

deltaRun

  • deltaRun(int32: any): Uint8Array

dimensionsList

  • List of dimensions

    ignore

    Parameters

    • buffer: IOBuffer

      Buffer for the file data

    Returns any

    • List of dimensions and record dimension with:
      • name: String with the name of the dimension
      • size: Number with the size of the dimension

distance

  • distance(x0: number, y0: number, x1: number, y1: number): number

doInflate

  • doInflate(input: any, options: any): any

  • inflate(data[, options]) -> Uint8Array|Array|String

    • data (Uint8Array|Array|String): input data to decompress.
    • options (Object): zlib inflate options.

    Decompress data with inflate/ungzip and options. Autodetect format via wrapper header by default. That's why we don't provide separate ungzip method.

    Supported options are:

    • windowBits

    http://zlib.net/manual.html#Advanced for more information.

    Sugar (options):

    • raw (Boolean) - say that we work with raw stream, if you don't wish to specify negative windowBits implicitly.
    • to (String) - if equal to 'string', then result will be converted from utf8 to utf16 (javascript) string. When string output requested, chunk length can differ from chunkSize, depending on content.
    Example:
    var pako = require('pako')
  , input = pako.deflate([1,2,3,4,5,6,7,8,9])
  , output;

try {
  output = pako.inflate(input);
} catch (err)
  console.log(err);
}

    Parameters

    • input: any
    • options: any

    Returns any

download

  • download(data: Blob | string, downloadName?: string): void

  • Parameters

    • data: Blob | string
    • Default value downloadName: string = "download"

    Returns void

edt

edt1d

encode

  • encode(mmtfData: any): Uint8Array

  • Encode MMTF fields

    static

    Parameters

    • mmtfData: any

      mmtf data

    Returns Uint8Array

    encoded MMTF fields

encode$1

  • encode$1(value: any, view: DataView, offset: any): any

  • encode data value (recursively) into binary encoded MessagePack v5 (http://msgpack.org/)

    Parameters

    • value: any
    • view: DataView
    • offset: any

    Returns any

    number of bytes written into view

encodeBytes

  • encodeBytes(type: any, size: any, param: any, bytes: any): Uint8Array

  • Parameters

    • type: any
    • size: any
    • param: any
    • bytes: any

    Returns Uint8Array

encodeDelta

  • encodeDelta(array: any, output: any): any

encodeDeltaRun

  • encodeDeltaRun(array: any): Int32Array

encodeInt16

  • encodeInt16(array: any, output: any): ArrayBuffer

  • make big endian buffer of an int16 array

    static

    Parameters

    • array: any

      array of int16 values

    • output: any

    Returns ArrayBuffer

    big endian buffer

encodeInt32

  • encodeInt32(array: any, output: any): ArrayBuffer

  • make big endian buffer of an int32 array

    static

    Parameters

    • array: any

      array of int32 values

    • output: any

    Returns ArrayBuffer

    big endian buffer

encodeInteger

  • encodeInteger(floatArray: any, factor: any, output: any): any

  • Parameters

    • floatArray: any
    • factor: any
    • output: any

    Returns any

encodeIntegerDelta

  • encodeIntegerDelta(floatArray: any, factor: any, output: any): any

  • Parameters

    • floatArray: any
    • factor: any
    • output: any

    Returns any

encodeIntegerDeltaPacking

  • encodeIntegerDeltaPacking(floatArray: any, factor: any, useInt8: any): Int8Array | Int16Array

  • Parameters

    • floatArray: any
    • factor: any
    • useInt8: any

    Returns Int8Array | Int16Array

encodeIntegerRun

  • encodeIntegerRun(floatArray: any, factor: any): Int32Array

encodeMmtf

  • encodeMmtf(inputDict: any): object

encodeMsgpack

  • encodeMsgpack(value: any): Uint8Array

encodePacking

  • encodePacking(intArray: any, useInt8: boolean): Int8Array | Int16Array

  • integer packing using recursive indexing

    Parameters

    • intArray: any
    • useInt8: boolean

    Returns Int8Array | Int16Array

    [description]

encodeRun

  • encodeRun(array: any): Int32Array

encodedSize

  • encodedSize(value: any): number

ensureArray

  • ensureArray(value: any): any[]

ensureBuffer

  • ensureBuffer(a: any): any

ensureFloat32Array

  • ensureFloat32Array(a?: number[] | Float32Array): any

  • Parameters

    • Optional a: number[] | Float32Array

    Returns any

ensureMatrix4

  • ensureMatrix4(m?: number[] | Matrix4): any

  • Parameters

    • Optional m: number[] | Matrix4

    Returns any

ensureQuaternion

  • ensureQuaternion(q?: number[] | Quaternion): any

  • Parameters

    • Optional q: number[] | Quaternion

    Returns any

ensureVector2

  • ensureVector2(v?: number[] | Vector2): any

  • Parameters

    • Optional v: number[] | Vector2

    Returns any

ensureVector3

  • ensureVector3(v?: number[] | Vector3): any

  • Parameters

    • Optional v: number[] | Vector3

    Returns any

entityTypeFromString

  • entityTypeFromString(string: string): 1 | 0 | 4 | 2 | 3

euclideanDist

  • euclideanDist(a: number[], b: number[]): number

euclideanDistSq

  • euclideanDistSq(a: number[], b: number[]): number

explicitValence

fetch

  • fetch(pdbid: string, onLoad: any, onError: Function): undefined

  • Fetch MMTF file from RCSB webservice which contains

    static
    example

    MMTF.fetch( "3PQR", // onLoad callback function( mmtfData ){ console.log( mmtfData ) }, // onError callback function( error ){ console.error( error ) } );

    Parameters

    • pdbid: string

      PDB ID to fetch

    • onLoad: any

      callback( mmtfData )

    • onError: Function

      callback( error )

    Returns undefined

fetchReduced

  • fetchReduced(pdbid: string, onLoad: any, onError: Function): undefined

  • Fetch reduced MMTF file from RCSB webservice which contains protein C-alpha, nucleotide phosphate and ligand atoms

    static
    example

    MMTF.fetchReduced( "3PQR", // onLoad callback function( mmtfData ){ console.log( mmtfData ) }, // onError callback function( error ){ console.error( error ) } );

    Parameters

    • pdbid: string

      PDB ID to fetch

    • onLoad: any

      callback( mmtfData )

    • onError: Function

      callback( error )

    Returns undefined

filter

findRings

fixedtables

  • fixedtables(state: any): void

flatten

  • flatten(array: any[], ret: any[]): any[]

  • Parameters

    • array: any[]
    • ret: any[]

    Returns any[]

flattenChunks

  • flattenChunks(chunks: any): Uint8Array

Private fromCharCode

  • fromCharCode(charCodeArray: any[]): string

  • Converts an array of ASCII codes trimming '\0' bytes

    Parameters

    • charCodeArray: any[]

      array of ASCII char codes

    Returns string

    '\0' trimmed string

generateUUID

  • generateUUID(): string

getAbsolutePath

  • getAbsolutePath(relativePath: string): string

getAllowedContours

  • getAllowedContours(): number[][]

getAngleData

  • getAngleData(position: any, params: any): object

  • Converts triple positions into data required to build various buffers.

    Parameters

    • position: any
    • params: any

    Returns object

    • arcPosition1: Float32Array
    • arcPosition2: Float32Array
    • labelPosition: Float32Array
    • labelText: any[]
    • sectorPosition: Float32Array
    • vectorPosition1: Float32Array
    • vectorPosition2: Float32Array

getAtomSele

getBondOrder

  • getBondOrder(valueOrder: any): 1 | 0 | 4 | 2 | 3

getBondOrderFromTable

  • getBondOrderFromTable(resname: string, atomname1: string, atomname2: string): number

getBrowser

  • getBrowser(): false | "Opera" | "Chrome" | "Firefox" | "Mobile Safari" | "Internet Explorer" | "Safari"

  • Returns false | "Opera" | "Chrome" | "Firefox" | "Mobile Safari" | "Internet Explorer" | "Safari"

getChainname

  • getChainname(index: number): string

getCharCount

getContactData

getData

  • getData(data: BufferData, geo: BufferGeometry): object

  • Parameters

    Returns object

    • color: Float32Array
    • index: undefined | Uint16Array | Uint32Array
    • normal: Float32Array
    • picking: undefined | Picker
    • position: Float32Array
    • primitiveId: Float32Array

getDataInfo

  • Parameters

    Returns object

    • base: string
    • compressed: string | true | false
    • dir: string
    • ext: string
    • name: string
    • path: string
    • protocol: string
    • query: string
    • src: string | Blob | File

getDataView

  • getDataView(typedArray: any): any

getDefines

getDihedralData

  • getDihedralData(position: any, params: any): any

getEdgeTable

  • getEdgeTable(): Uint32Array

getErrorDescription

  • getErrorDescription(gl: WebGLRenderingContext, error: number): "no error" | "invalid enum" | "invalid value" | "invalid operation" | "invalid framebuffer operation" | "out of memory" | "context lost" | "unknown error"

  • Parameters

    • gl: WebGLRenderingContext
    • error: number

    Returns "no error" | "invalid enum" | "invalid value" | "invalid operation" | "invalid framebuffer operation" | "out of memory" | "context lost" | "unknown error"

getExtension

  • getExtension(gl: WebGLRenderingContext, name: string): any

getFileInfo

  • Parameters

    Returns object

    • base: string
    • compressed: string | true | false
    • dir: string
    • ext: string
    • name: string
    • path: string
    • protocol: string
    • query: string
    • src: string | Blob | File

getFixedCountDashData

  • getFixedCountDashData<T>(data: T, segmentCount?: number): T

getFixedLengthDashData

  • getFixedLengthDashData<T>(data: T, segmentLength?: number): T

getFixedLengthWrappedDashData

  • getFixedLengthWrappedDashData<T>(data: T, segmentLength?: number): T

getFloat32View

  • getFloat32View(typedArray: any): any

getGeo

getHash

  • getHash(resname: string, atomTypeIdList: number[], hetero: boolean, chemCompType?: string): string

  • Parameters

    • resname: string
    • atomTypeIdList: number[]
    • hetero: boolean
    • Default value chemCompType: string = ""

    Returns string

getHydrogenBondType

getInt32View

  • getInt32View(typedArray: any): Int32Array

  • get an Int32Array view on the input array memory

    static

    Parameters

    • typedArray: any

    Returns Int32Array

    new view on the input array memory

getInt8View

  • getInt8View(typedArray: any): Int8Array

  • get an Int8Array view on the input array memory

    static

    Parameters

    • typedArray: any

    Returns Int8Array

    new view on the input array memory

getLoneAtomSet

  • getLoneAtomSet(structure: any): any

  • Determine which atoms in a Structure[View] form no bonds to any other atoms in that Structure.

    This differs from setting the selection to "nonbonded" as it finds atoms that have no bonds within the current selection.

    Parameters

    • structure: any

      The Structure or StructureView object

    Returns any

    AtomSet of lone atoms

getModresId

  • getModresId(resno: any, chainname: any, inscode: any): string

getMouseButtons

  • getMouseButtons(event: MouseEvent): number

getNamedItem

  • getNamedItem(a: NamedNodeMap, name: string): string

getProblemCount

  • getProblemCount(clashDict: object, g: Element, ga: NamedNodeMap): number

  • Parameters

    • clashDict: object
      • [k: string]: object
        • [k: string]: string
    • g: Element
    • ga: NamedNodeMap

    Returns number

getProtocol

  • getProtocol(): string

getQuery

  • getQuery(id: string): undefined | string

  • Parameters

    • id: string

    Returns undefined | string

getRadiusDict

  • getRadiusDict(radiusList: any): object

getSele

  • getSele(a: NamedNodeMap, atomname?: undefined | string, useAltcode?: boolean): string

  • Parameters

    • a: NamedNodeMap
    • Optional atomname: undefined | string
    • Default value useAltcode: boolean = false

    Returns string

getShader

getSize

getSurfaceGrid

  • getSurfaceGrid(min: any, max: any, maxRadius: any, scaleFactor: any, extraMargin: any): object

  • Parameters

    • min: any
    • max: any
    • maxRadius: any
    • scaleFactor: any
    • extraMargin: any

    Returns object

    • dim: Float32Array
    • matrix: Float32Array
    • scaleFactor: any
    • tran: Float32Array

getSymmetryOperations

  • getSymmetryOperations(spacegroup: string): object

getTextAtlas

getThreeSide

getTouchDistance

  • getTouchDistance(event: TouchEvent): number
  • example

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

    typedef

    {Object} MouseSignals

    property

    {Signal<Integer, Integer>} moved - on move: deltaX, deltaY

    property

    {Signal} scrolled - on scroll: delta

    property

    {Signal<Integer, Integer>} dragged - on drag: deltaX, deltaY

    property

    {Signal} dropped - on drop

    property

    {Signal} clicked - on click

    property

    {Signal} hovered - on hover

    Parameters

    • event: TouchEvent

    Returns number

getTriTable

  • getTriTable(): Int32Array

getTypedArray

  • getTypedArray(arrayType: TypedArrayString, arraySize: number): Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array

  • Parameters

    Returns Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array

getUint8View

  • getUint8View(typedArray: any): Uint8Array

  • get an Uint8Array view on the input array memory

    static

    Parameters

    • typedArray: any

    Returns Uint8Array

    new view on the input array memory

getUintArray

  • getUintArray(sizeOrArray: any, maxUint: number): Uint16Array | Uint32Array

  • Parameters

    • sizeOrArray: any
    • maxUint: number

    Returns Uint16Array | Uint32Array

getView

  • getView(ctor: any, typedArray: any, elemSize: any): any

  • mmtf utils module.

    module

    MmtfUtils

    Parameters

    • ctor: any
    • typedArray: any
    • elemSize: any

    Returns any

getWorkerDeps

guessElement

  • guessElement(atomName: string): string

gzipDecompress

  • gzipDecompress(data: ArrayBuffer | Uint8Array): any

hammingWeight

  • hammingWeight(v: number): number

  • Compute the Hamming weight of a 32-bit unsigned integer

    Parameters

    • v: number

      a 32-bit unsigned integer

    Returns number

    the Hamming weight

hasAromaticNeighbour

  • hasAromaticNeighbour(a: AtomProxy): boolean

hasAttrValue

  • hasAttrValue(attr: Attr | null, value: string): boolean

hasPolarNeighbour

hasValue

  • hasValue(d: any): boolean

header

  • header(buffer: IOBuffer, version: number): any

  • Read the header of the file

    ignore

    Parameters

    • buffer: IOBuffer

      Buffer for the file data

    • version: number

      Version of the file

    Returns any

    • Object with the fields:
      • recordDimension: Number with the length of record dimension
      • dimensions: List of dimensions
      • globalAttributes: List of global attributes
      • variables: List of variables

hsvToRgb

  • hsvToRgb(h: any, s: any, v: any): any[]

hypot

  • hypot(a: number, b: number): number

inAromaticRingWithElectronNegativeElement

  • inAromaticRingWithElectronNegativeElement(a: AtomProxy): boolean

inflate

  • inflate(strm: any, flush: any): number

inflateEnd

  • inflateEnd(strm: any): number

inflateGetHeader

  • inflateGetHeader(strm: any, head: any): number