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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

inflateInit2

  • inflateInit2(strm: any, windowBits: any): number

inflateReset

  • inflateReset(strm: any): number

inflateReset2

  • inflateReset2(strm: any, windowBits: any): number

inflateResetKeep

  • inflateResetKeep(strm: any): number

inflateSetDictionary

  • inflateSetDictionary(strm: any, dictionary: any): number

inflate_fast

  • inflate_fast(strm: any, start: any): void

inflate_table

  • inflate_table(type: any, lens: any, lens_index: any, codes: any, table: any, table_index: any, work: any, opts: any): 1 | -1 | 0

  • Parameters

    • type: any
    • lens: any
    • lens_index: any
    • codes: any
    • table: any
    • table_index: any
    • work: any
    • opts: any

    Returns 1 | -1 | 0

integerDeltaPacking16

  • integerDeltaPacking16(float32: any, factor: any): Uint8Array

integerRun

  • integerRun(float32: any, factor: any): Uint8Array

interpolateLerp

interpolateSpline

invalidAtomContact

  • invalidAtomContact(ap1: AtomProxy, ap2: AtomProxy, masterIdx: number): true | false | ""

invert3x3

isAcetamidine

isAmide

isBackboneHydrogenBond

isCarbonyl

isCarboxylate

isCationPi

isConjugated

  • Are we involved in some kind of pi system. Either explicitly forming double bond or N, O next to a double bond, except:

    N,O with degree 4 cannot be conjugated. N,O adjacent to P=O or S=O do not qualify (keeps sulfonamide N sp3 geom)

    Parameters

    Returns boolean

isGuanidine

isHalocarbon

isHalogenBond

isHistidineNitrogen

  • isHistidineNitrogen(ap: AtomProxy): boolean

isHydrogenBond

isHydrogenBondType

  • isHydrogenBondType(type: number): boolean

isHydrophobicContact

isImide

isIonicInteraction

isMasterContact

isMetalComplex

isPhosphate

isPiStacking

isPointOnSegment

  • isPointOnSegment(p: Vector3, l1: Vector3, l2: Vector3): boolean

isPolar

isQuaternaryAmine

isRingAromatic

isSulfate

isSulfonicAcid

isSulfonium

isTertiaryAmine

  • isTertiaryAmine(a: AtomProxy, idealValence: number): boolean

isWaterHydrogenBond

isWeakHydrogenBond

laplacianSmooth

  • laplacianSmooth(verts: any, faces: any, numiter: any, inflate: any): void

lerp

  • lerp(start: number, stop: number, alpha: number): number

lexicographicCompare

  • lexicographicCompare<T>(elm1: T, elm2: T): 1 | -1 | 0

  • Type parameters

    • T

    Parameters

    • elm1: T
    • elm2: T

    Returns 1 | -1 | 0

lineLineIntersect

  • lineLineIntersect(p1: Vector3, p2: Vector3, p3: Vector3, p4: Vector3): null | Vector3[]

loadShader

  • loadShader(gl: WebGLRenderingContext, shaderSource: string, shaderType: number): null | WebGLShader

  • Parameters

    • gl: WebGLRenderingContext
    • shaderSource: string
    • shaderType: number

    Returns null | WebGLShader

logReprUnknown

  • logReprUnknown(type: string): void

m3makeNormal

  • m3makeNormal(out: Float32Array, m4: Float32Array): void

m3new

  • m3new(): Float32Array

m4identity

  • m4identity(out: Float32Array): void

m4makeRotationY

  • m4makeRotationY(out: Float32Array, theta: number): void

m4makeScale

  • m4makeScale(out: Float32Array, x: number, y: number, z: number): void

m4makeTranslation

  • m4makeTranslation(out: Float32Array, x: number, y: number, z: number): void

m4multiply

  • m4multiply(out: Float32Array, a: Float32Array, b: Float32Array): void

m4new

  • m4new(): Float32Array

m4set

  • m4set(out: Float32Array, n11: number, n12: number, n13: number, n14: number, n21: number, n22: number, n23: number, n24: number, n31: number, n32: number, n33: number, n34: number, n41: number, n42: number, n43: number, n44: number): void

  • Parameters

    • out: Float32Array
    • n11: number
    • n12: number
    • n13: number
    • n14: number
    • n21: number
    • n22: number
    • n23: number
    • n24: number
    • n31: number
    • n32: number
    • n33: number
    • n34: number
    • n41: number
    • n42: number
    • n43: number
    • n44: number

    Returns void

makeAtomTest

  • makeAtomTest(selection: SelectionRule, atomOnly?: boolean): false | function

makeChainTest

  • makeChainTest(selection: SelectionRule, chainOnly?: boolean): false | function

makeImage

makeModelTest

  • makeModelTest(selection: SelectionRule, modelOnly?: boolean): false | function

makePointTexture

makeRepresentation

  • makeRepresentation(type: string, object: any, viewer: Viewer, params: any): any

makeResidueTest

  • makeResidueTest(selection: SelectionRule, residueOnly?: boolean): false | function

makeTable

  • makeTable(): number[]

makeTest

makeTrajectory

makeWorkerBlob

  • makeWorkerBlob(func: Function, deps: Function[]): Blob

makeWorkerString

  • makeWorkerString(vars: any): string

mat3x3determinant

  • mat3x3determinant(M: Matrix): number

matchName

  • matchName(name: string | RegExp, object: object): boolean

  • Parameters

    • name: string | RegExp
    • object: object
      • name: string

    Returns boolean

meanCols

meanRows

modelTestFn

multiply

multiply3x3

multiplyABt

multiplyAtB

nonRecord

  • nonRecord(buffer: IOBuffer, variable: any): any[]

  • Read data for the given non-record variable

    ignore

    Parameters

    • buffer: IOBuffer

      Buffer for the file data

    • variable: any

      Variable metadata

    Returns any[]

    • Data of the element

normalize

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

normalizeVector3array

  • normalizeVector3array(a: Float32Array): void

notNetcdf

  • notNetcdf(statement: boolean, reason: string): void

  • Throws a non-valid NetCDF exception if the statement it's true

    ignore

    Parameters

    • statement: boolean

      Throws if true

    • reason: string

      Reason to throw

    Returns void

num2bytes

  • num2bytes(type: number): number

  • Parse a number type identifier to his size in bytes

    ignore

    Parameters

    • type: number

      integer that represents the type

    Returns number

    -size of the type

num2str

  • num2str(type: number): string

  • Parse a number into their respective type

    ignore

    Parameters

    • type: number

      integer that represents the type

    Returns string

    • parsed value of the type

onBeforeRender

  • onBeforeRender(this: Object3D, renderer: WebGLRenderer, scene: Scene, camera: PerspectiveCamera | OrthographicCamera, geometry: Geometry, material: ShaderMaterial): void

  • Parameters

    • this: Object3D
    • renderer: WebGLRenderer
    • scene: Scene
    • camera: PerspectiveCamera | OrthographicCamera
    • geometry: Geometry
    • material: ShaderMaterial

    Returns void

onmessage

open

  • open(callback: Function, extensionList?: string[]): void

  • Parameters

    • callback: Function
    • Default value extensionList: string[] = ['*']

    Returns void

openUrl

  • openUrl(url: string): void

padding

parseChemComp

  • parseChemComp(cif: any, structure: any, structureBuilder: any): void

parseCore

  • parseCore(cif: any, structure: any, structureBuilder: any): void

parseFlag

  • parseFlag(line: any): any

parseGroup

  • parseGroup(line: any): any[]

parseIntSubstr

  • parseIntSubstr(line: any, start: any, length: any): number

parseListDef

  • parseListDef(line: any): object

  • Parameters

    • line: any

    Returns object

    • listColor: any
    • listMasters: any[]
    • listName: any
    • listWidth: undefined | number

parseListElm

  • parseListElm(line: any): object

  • Parameters

    • line: any

    Returns object

    • color: any
    • label: any
    • position: number[]
    • radius: undefined | number
    • width: undefined | number

parseNestedAtoms

  • parseNestedAtoms(sview: any, atoms: any[]): Float32Array

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

    Parses nested array of either integer atom indices or selection expressions into a flat array of coordinates.

    Parameters

    • sview: any

      The structure to which the atoms refer

    • atoms: any[]

      Nested array of atom pairs|triples|quads as Integer indices or selection expressions

    Returns Float32Array

    Flattened array of position coordinates

parseNumberLine

  • parseNumberLine(line: any): any

parseSele

parseStr

  • parseStr(line: any): any

parseXml

  • parseXml(xml: string): object

passInt32

  • passInt32(int32: any): Uint8Array

passInt8

  • passInt8(int8: any): Uint8Array

passString

  • passString(stringBytes: any, length: any): Uint8Array

pclamp

  • pclamp(value: number): number

performDecoding

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

  • [performDecoding description]

    Parameters

    • type: any
    • bytes: any
    • size: any
    • param: Uint8Array

    Returns any

    [description]

pick

  • pick(object: object): any

  • Parameters

    • object: object
      • [index: string]: any

    Returns any

prepareMatrix

  • prepareMatrix(cellNames: string, mat: number[][]): object

  • Parameters

    • cellNames: string
    • mat: number[][]

    Returns object

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

processConnections

  • processConnections(cif: any, structure: any, asymIdDict: any): void

processEntities

  • processEntities(cif: any, structure: any, chainIndexDict: any): void

processSecondaryStructure

  • processSecondaryStructure(cif: any, structure: any, asymIdDict: any): false | object

processSymmetry

  • processSymmetry(cif: any, structure: any, asymIdDict: any): void

projectPointOnVector

  • projectPointOnVector(point: Vector3, vector: Vector3, origin?: Vector3): Vector3

quickselectCmp

  • quickselectCmp<T>(arr: T[], n: number, cmp?: undefined | function, left?: number, right?: undefined | number): T

  • Type parameters

    • T

    Parameters

    • arr: T[]
    • n: number
    • Optional cmp: undefined | function
    • Default value left: number = 0
    • Optional right: undefined | number

    Returns T

quicksortCmp

  • quicksortCmp<T>(arr: T[], cmp?: undefined | function, begin?: number, end?: undefined | number): T[]

  • Type parameters

    • T

    Parameters

    • arr: T[]
    • Optional cmp: undefined | function
    • Default value begin: number = 0
    • Optional end: undefined | number

    Returns T[]

quicksortIP

  • quicksortIP(arr: NumberArray, eleSize: number, orderElement: number, begin?: number, end?: undefined | number): number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

  • quicksortIP

    function
    author

    Roman Bolzern roman.bolzern@fhnw.ch, 2013

    author

    I4DS http://www.fhnw.ch/i4ds, 2013

    license

    MIT License http://www.opensource.org/licenses/mit-license.php

    description

    In-place quicksort for typed arrays (e.g. for Float32Array) provides fast sorting useful e.g. for a custom shader and/or BufferGeometry Complexity: http://bigocheatsheet.com/ see Quicksort

    example

    points: [x, y, z, x, y, z, x, y, z, ...] eleSize: 3 //because of (x, y, z) orderElement: 0 //order according to x

    Parameters

    • arr: NumberArray

      array to be sorted

    • eleSize: number

      element size

    • orderElement: number

      index of element used for sorting, < eleSize

    • Default value begin: number = 0
    • Optional end: undefined | number

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

    the input array

radToDeg

  • radToDeg(rad: number): number

randomColor

  • randomColor(): number

randomColorArray

  • randomColorArray(n: number): Float32Array

rangeInSortedArray

  • rangeInSortedArray(array: number[], min: number, max: number): number

  • Parameters

    • array: number[]
    • min: number
    • max: number

    Returns number

readName

readNumber

  • readNumber(size: number, bufferReader: Function): number | number[]

  • Auxiliary function to read numeric data

    ignore

    Parameters

    • size: number

      Size of the element to read

    • bufferReader: Function

      Function to read next value

    Returns number | number[]

readType

  • readType(buffer: IOBuffer, type: number, size: number): string | number | number[]

  • Given a type and a size reads the next element

    ignore

    Parameters

    • buffer: IOBuffer

      Buffer for the file data

    • type: number

      Type of the data to read

    • size: number

      Size of the element to read

    Returns string | number | number[]

record

  • record(buffer: IOBuffer, variable: any, recordDimension: any): any[]

  • Read data for the given record variable

    ignore

    Parameters

    • buffer: IOBuffer

      Buffer for the file data

    • variable: any

      Variable metadata

    • recordDimension: any

      Record dimension metadata

    Returns any[]

    • Data of the element

refineHydrophobicContacts

refineLineOfSight

refineMetalCoordination

refinePiStacking

refineSaltBridges

refineWeakHydrogenBonds

removePbc

  • removePbc(x: NumberArray, box: ArrayLike<number>): undefined | number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

  • Parameters

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

removePeriodicity

  • removePeriodicity(x: NumberArray, box: ArrayLike<number>, mean: number[]): undefined | number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

  • Parameters

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

reorderAtoms

replicateArray3Entries

  • replicateArray3Entries(array: NumberArray, m: number): Float32Array

replicateArrayEntries

  • replicateArrayEntries(array: NumberArray, m: number): Float32Array

residueTestFn

runChar

  • runChar(charBytes: any): Uint8Array

saturate

  • saturate(value: number): number

selectionFromChains

  • selectionFromChains(chainList: string[]): Selection

serialArray

  • serialArray(n: number): Float32Array

serialBlockArray

  • serialBlockArray(n: number, b: number, offset?: number, optionalTarget?: NumberArray): number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

  • Parameters

    • n: number
    • b: number
    • Default value offset: number = 0
    • Optional optionalTarget: NumberArray

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

setBitDict

  • setBitDict(dict: object, key: string, bit: number): void

setDebug

  • setDebug(value: boolean): void

setExtensionFragDepth

  • setExtensionFragDepth(value: boolean): void

setListingDatasource

  • setListingDatasource(value: boolean): void

setMeasurementDefaultParams

  • setMeasurementDefaultParams(params?: object): void

  • Parameters

    • Default value params: object = {}

    Returns void

setObjectMatrix

  • setObjectMatrix(object: Object3D, matrix: Matrix4): void

setSupportsReadPixelsFloat

  • setSupportsReadPixelsFloat(value: boolean): void

setTrajectoryDatasource

  • setTrajectoryDatasource(value: boolean): void

setVisibilityFalse

  • setVisibilityFalse(m: Object3D): void

setVisibilityTrue

  • setVisibilityTrue(m: Object3D): void

shrinkBuf

  • shrinkBuf(buf: any, size: any): any

sizeOfInt

  • sizeOfInt(size: any): number

sizeOfInts

  • sizeOfInts(numOfInts: any, sizes: any): number

smootherstep

  • smootherstep(min: number, max: number, x: number): number

smootheststep

  • smootheststep(min: number, max: number, x: number): number

smoothstep

  • smoothstep(min: number, max: number, x: number): number

sortProjectedPosition

  • sortProjectedPosition(scene: Scene, camera: Camera): void

spatialLookup

spline

  • spline(p0: number, p1: number, p2: number, p3: number, t: number, tension: number): number

  • Parameters

    • p0: number
    • p1: number
    • p2: number
    • p3: number
    • t: number
    • tension: number

    Returns number

str2num

  • str2num(type: string): number

  • Reverse search of num2str

    ignore

    Parameters

    • type: string

      string that represents the type

    Returns number

    • parsed value of the type

string2buf

  • string2buf(str: any): Uint8Array

strip

  • strip(val: string): string

subCols

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

subRows

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

submit

  • submit(url: string, data: FormData, callback: Function, onerror: Function): void

  • Parameters

    • url: string
    • data: FormData
    • callback: Function
    • onerror: Function

    Returns void

superpose

  • superpose(s1: Structure, s2: Structure, align?: boolean, sele1?: string, sele2?: string): void

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

    Parameters

    • s1: Structure

      structure 1 which is superposed onto structure 2

    • s2: Structure

      structure 2 onto which structure 1 is superposed

    • Default value align: boolean = false
    • Default value sele1: string = ""
    • Default value sele2: string = ""

    Returns void

svd

testTextureSupport

  • testTextureSupport(type: number): boolean

throttle

  • throttle(func: Function, wait: number, options: object): throttle

  • Parameters

    • func: Function
    • wait: number
    • options: object
      • Optional leading?: undefined | true | false
      • Optional trailing?: undefined | true | false

    Returns throttle

toLowerCaseString

  • toLowerCaseString(value: string): any

transpose

traverseMmtf

  • traverseMmtf(mmtfData: any, eventCallbacks: any, params: object): void

  • Traverse the MMTF structure data.

    static

    Parameters

    • mmtfData: any

      decoded mmtf data

    • eventCallbacks: any
    • params: object

    Returns void

triggerFromString

  • triggerFromString(str: string): Object

trimNull

  • trimNull(value: string): string

trimQuotes

  • trimQuotes(str: any): any

uint8ToLines

  • uint8ToLines(u8a: Uint8Array, chunkSize?: number, newline?: string): string[]

  • Parameters

    • u8a: Uint8Array
    • Default value chunkSize: number = 1024 * 1024 * 10
    • Default value newline: string = ""

    Returns string[]

uint8ToString

  • uint8ToString(u8a: Uint8Array): any

uniformArray

  • uniformArray(n: number, a: number, optionalTarget?: NumberArray): number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

  • Parameters

    • n: number
    • a: number
    • Optional optionalTarget: NumberArray

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

uniformArray3

  • uniformArray3(n: number, a: number, b: number, c: number, optionalTarget?: NumberArray): number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

  • Parameters

    • n: number
    • a: number
    • b: number
    • c: number
    • Optional optionalTarget: NumberArray

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

uniqueArray

  • uniqueArray(array: any[]): any[]

updateCameraUniforms

  • updateCameraUniforms(group: Object3D, camera: Camera): void

updateMaterialUniforms

  • updateMaterialUniforms(group: Object3D, camera: Camera, renderer: WebGLRenderer, cDist: number, bRadius: number): void

  • Parameters

    • group: Object3D
    • camera: Camera
    • renderer: WebGLRenderer
    • cDist: number
    • bRadius: number

    Returns void

updateParams

  • updateParams<T>(params: T, newParams: object): T

  • Type parameters

    • T

    Parameters

    • params: T
    • newParams: object

    Returns T

updatewindow

  • updatewindow(strm: any, src: any, end: any, copy: any): number

utf8ByteCount

  • utf8ByteCount(string: any): number

Private utf8Write

  • utf8Write(view: any, offset: any, string: any): void

utf8border

  • utf8border(buf: any, max: any): any

v3add

  • v3add(out: Float32Array, a: Float32Array, b: Float32Array): void

v3addScalar

  • v3addScalar(out: Float32Array, a: Float32Array, s: number): void

v3angle

  • v3angle(a: Float32Array, b: Float32Array): number

v3ceil

  • v3ceil(out: Float32Array, a: Float32Array): void

v3cross

  • v3cross(out: Float32Array, a: Float32Array, b: Float32Array): void

v3divide

  • v3divide(out: Float32Array, a: Float32Array, b: Float32Array): void

v3divideScalar

  • v3divideScalar(out: Float32Array, a: Float32Array, s: number): void

v3dot

  • v3dot(a: Float32Array, b: Float32Array): number

v3floor

  • v3floor(out: Float32Array, a: Float32Array): void

v3forEach

  • v3forEach(array: Float32Array, fn: function, b: Float32Array): void

  • Parameters

    • array: Float32Array
    • fn: function
        • (i: Float32Array, j: Float32Array, k: Float32Array): void

        • Parameters

          • i: Float32Array
          • j: Float32Array
          • k: Float32Array

          Returns void

    • b: Float32Array

    Returns void

v3fromArray

  • v3fromArray(out: Float32Array, array: Float32Array, offset?: number): void

v3length

  • v3length(a: Float32Array): number

v3multiply

  • v3multiply(out: Float32Array, a: Float32Array, b: Float32Array): void

v3multiplyScalar

  • v3multiplyScalar(out: Float32Array, a: Float32Array, s: number): void

v3negate

  • v3negate(out: Float32Array, a: Float32Array): void

v3new

v3normalize

  • v3normalize(out: Float32Array, a: Float32Array): void

v3round

  • v3round(out: Float32Array, a: Float32Array): void

v3sub

  • v3sub(out: Float32Array, a: Float32Array, b: Float32Array): void

v3subScalar

  • v3subScalar(out: Float32Array, a: Float32Array, s: number): void

v3toArray

  • v3toArray(input: Float32Array, array: Float32Array, offset?: number): void

valenceModel

validatePositions

  • validatePositions(position: Float32Array): Float32Array

  • Ensure mid point does not coincide with first or second

    Parameters

    • position: Float32Array

      9*nAngle array of coordinates

    Returns Float32Array

    Filtered position array, may be shorter

variablesList

  • variablesList(buffer: IOBuffer, recordId: number, version: number): any

  • List of variables

    ignore

    Parameters

    • buffer: IOBuffer

      Buffer for the file data

    • recordId: number

      Id if the record dimension

    • version: number

      Version of the file

    Returns any

    • Number of recordStep and list of variables with:
      • name: String with the name of the variable
      • dimensions: Array with the dimension IDs of the variable
      • attributes: Array with the attributes of the variable
      • type: String with the type of the variable
      • size: Number with the size of the variable
      • offset: Number with the offset where of the variable begins
      • record: True if is a record variable, false otherwise

zswap32

  • zswap32(q: any): number

Object literals

Const AA1

AA1: object

ALA

ALA: string = "A"

ARG

ARG: string = "R"

ASN

ASN: string = "N"

ASP

ASP: string = "D"

CYS

CYS: string = "C"

GLN

GLN: string = "Q"

GLU

GLU: string = "E"

GLY

GLY: string = "G"

HIS

HIS: string = "H"

ILE

ILE: string = "I"

LEU

LEU: string = "L"

LYS

LYS: string = "K"

MET

MET: string = "M"

PHE

PHE: string = "F"

PRO

PRO: string = "P"

PYL

PYL: string = "O"

SEC

SEC: string = "U"

SER

SER: string = "S"

THR

THR: string = "T"

TRP

TRP: string = "W"

TYR

TYR: string = "Y"

VAL

VAL: string = "V"

Const AtomWeights

AtomWeights: object

1

1: number = 1.008

10

10: number = 20.18

100

100: number = 257.095

101

101: number = 258.098

102

102: number = 259.101

103

103: number = 262.11

104

104: number = 267.122

105

105: number = 270.131

106

106: number = 271.134

107

107: number = 270.133

108

108: number = 270.134

109

109: number = 278.156

11

11: number = 22.99

110

110: number = 281.165

111

111: number = 281.166

112

112: number = 285.177

113

113: number = 286.182

114

114: number = 289.19

115

115: number = 289.194

116

116: number = 293.204

117

117: number = 293.208

118

118: number = 294.214

12

12: number = 24.305

13

13: number = 26.982

14

14: number = 28.085

15

15: number = 30.974

16

16: number = 32.06

17

17: number = 35.45

18

18: number = 39.948

19

19: number = 39.098

2

2: number = 4.0026

20

20: number = 40.078

21

21: number = 44.956

22

22: number = 47.867

23

23: number = 50.942

24

24: number = 51.996

25

25: number = 54.938

26

26: number = 55.845

27

27: number = 58.933

28

28: number = 58.693

29

29: number = 63.546

3

3: number = 6.94

30

30: number = 65.38

31

31: number = 69.723

32

32: number = 72.63

33

33: number = 74.922

34

34: number = 78.971

35

35: number = 79.904

36

36: number = 83.798

37

37: number = 85.468

38

38: number = 87.62

39

39: number = 88.906

4

4: number = 9.0122

40

40: number = 91.224

41

41: number = 92.906

42

42: number = 95.95

43

43: number = 96.906

44

44: number = 101.07

45

45: number = 102.91

46

46: number = 106.42

47

47: number = 107.87

48

48: number = 112.41

49

49: number = 114.82

5

5: number = 10.81

50

50: number = 118.71

51

51: number = 121.76

52

52: number = 127.6

53

53: number = 127.6

54

54: number = 131.29

55

55: number = 132.91

56

56: number = 137.33

57

57: number = 138.91

58

58: number = 140.12

59

59: number = 140.91

6

6: number = 10.81

60

60: number = 144.24

61

61: number = 144.912

62

62: number = 150.36

63

63: number = 151.96

64

64: number = 157.25

65

65: number = 158.93

66

66: number = 162.5

67

67: number = 164.93

68

68: number = 167.26

69

69: number = 168.93

7

7: number = 14.007

70

70: number = 173.05

71

71: number = 174.97

72

72: number = 178.49

73

73: number = 180.95

74

74: number = 183.84

75

75: number = 186.21

76

76: number = 190.23

77

77: number = 192.22

78

78: number = 195.08

79

79: number = 196.97

8

8: number = 15.999

80

80: number = 200.59

81

81: number = 204.38

82

82: number = 207.2

83

83: number = 208.98

84

84: number = 1.97

85

85: number = 2.02

86

86: number = 2.2

87

87: number = 3.48

88

88: number = 2.83

89

89: number = 2

9

9: number = 18.998

90

90: number = 232.04

91

91: number = 231.04

92

92: number = 238.03

93

93: number = 237.048

94

94: number = 244.064

95

95: number = 243.061

96

96: number = 247.07

97

97: number = 247.07

98

98: number = 251.079

99

99: number = 252.083

Const AtomicNumbers

AtomicNumbers: object

AC

AC: number = 89

AG

AG: number = 47

AL

AL: number = 13

AM

AM: number = 95

AR

AR: number = 18

AS

AS: number = 33

AT

AT: number = 85

AU

AU: number = 79

B

B: number = 5

BA

BA: number = 56

BE

BE: number = 4

BH

BH: number = 107

BI

BI: number = 83

BK

BK: number = 97

BR

BR: number = 35

C

C: number = 6

CA

CA: number = 20

CD

CD: number = 48

CE

CE: number = 58

CF

CF: number = 98

CL

CL: number = 17

CM

CM: number = 96

CN

CN: number = 112

CO

CO: number = 27

CR

CR: number = 24

CS

CS: number = 55

CU

CU: number = 29

D

D: number = 1

DB

DB: number = 105

DS

DS: number = 110

DY

DY: number = 66

ER

ER: number = 68

ES

ES: number = 99

EU

EU: number = 63

F

F: number = 9

FE

FE: number = 26

FL

FL: number = 114

FM

FM: number = 100

FR

FR: number = 87

GA

GA: number = 31

GD

GD: number = 64

GE

GE: number = 32

H

H: number = 1

HE

HE: number = 2

HF

HF: number = 72

HG

HG: number = 80

HO

HO: number = 67

HS

HS: number = 108

I

I: number = 53

IN

IN: number = 49

IR

IR: number = 77

K

K: number = 19

KR

KR: number = 36

LA

LA: number = 57

LI

LI: number = 3

LR

LR: number = 103

LU

LU: number = 71

LV

LV: number = 116

MC

MC: number = 115

MD

MD: number = 101

MG

MG: number = 12

MN

MN: number = 25

MO

MO: number = 42

MT

MT: number = 109

N

N: number = 7

NA

NA: number = 11

NB

NB: number = 41

ND

ND: number = 60

NE

NE: number = 10

NH

NH: number = 113

NI

NI: number = 28

NO

NO: number = 102

NP

NP: number = 93

O

O: number = 8

OG

OG: number = 118

OS

OS: number = 76

P

P: number = 15

PA

PA: number = 91

PB

PB: number = 82

PD

PD: number = 46

PM

PM: number = 61

PO

PO: number = 84

PR

PR: number = 59

PT

PT: number = 78

PU

PU: number = 94

RA

RA: number = 88

RB

RB: number = 37

RE

RE: number = 75

RF

RF: number = 104

RG

RG: number = 111

RH

RH: number = 45

RN

RN: number = 86

RU

RU: number = 44

S

S: number = 16

SB

SB: number = 51

SC

SC: number = 21

SE

SE: number = 34

SG

SG: number = 106

SI

SI: number = 14

SM

SM: number = 62

SN

SN: number = 50

SR

SR: number = 38

T

T: number = 1

TA

TA: number = 73

TB

TB: number = 65

TC

TC: number = 43

TE

TE: number = 52

TH

TH: number = 90

TI

TI: number = 22

TL

TL: number = 81

TM

TM: number = 69

TS

TS: number = 117

U

U: number = 92

V

V: number = 23

W

W: number = 74

XE

XE: number = 54

Y

Y: number = 39

YB

YB: number = 70

ZN

ZN: number = 30

ZR

ZR: number = 40

Const BondOrderTable

BondOrderTable: object

ARG|CZ|NH2

ARG|CZ|NH2: number = 2

ASN|CG|OD1

ASN|CG|OD1: number = 2

ASP|CG|OD1

ASP|CG|OD1: number = 2

A|C2|N3

A|C2|N3: number = 2

A|C4|C5

A|C4|C5: number = 2

A|C6|N1

A|C6|N1: number = 2

A|C8|N7

A|C8|N7: number = 2

C|C2|O2

C|C2|O2: number = 2

C|C4|N3

C|C4|N3: number = 2

C|C5|C6

C|C5|C6: number = 2

DA|C2|N3

DA|C2|N3: number = 2

DA|C4|C5

DA|C4|C5: number = 2

DA|C6|N1

DA|C6|N1: number = 2

DA|C8|N7

DA|C8|N7: number = 2

DC|C2|O2

DC|C2|O2: number = 2

DC|C4|N3

DC|C4|N3: number = 2

DC|C5|C6

DC|C5|C6: number = 2

DG|C2|N3

DG|C2|N3: number = 2

DG|C4|C5

DG|C4|C5: number = 2

DG|C6|O6

DG|C6|O6: number = 2

DG|C8|N7

DG|C8|N7: number = 2

DT|C2|O2

DT|C2|O2: number = 2

DT|C4|O4

DT|C4|O4: number = 2

DT|C5|C6

DT|C5|C6: number = 2

GLN|CD|OE1

GLN|CD|OE1: number = 2

GLU|CD|OE1

GLU|CD|OE1: number = 2

G|C2|N3

G|C2|N3: number = 2

G|C4|C5

G|C4|C5: number = 2

G|C6|O6

G|C6|O6: number = 2

G|C8|N7

G|C8|N7: number = 2

HIS|CD2|CG

HIS|CD2|CG: number = 2

HIS|CE1|ND1

HIS|CE1|ND1: number = 2

PHE|CD1|CG

PHE|CD1|CG: number = 2

PHE|CD2|CE2

PHE|CD2|CE2: number = 2

PHE|CE1|CZ

PHE|CE1|CZ: number = 2

TRP|CD1|CG

TRP|CD1|CG: number = 2

TRP|CD2|CE2

TRP|CD2|CE2: number = 2

TRP|CE3|CZ3

TRP|CE3|CZ3: number = 2

TRP|CH2|CZ2

TRP|CH2|CZ2: number = 2

TYR|CD1|CG

TYR|CD1|CG: number = 2

TYR|CD2|CE2

TYR|CD2|CE2: number = 2

TYR|CE1|CZ

TYR|CE1|CZ: number = 2

U|C2|O2

U|C2|O2: number = 2

U|C4|O4

U|C4|O4: number = 2

U|C5|C6

U|C5|C6: number = 2

Const BufferDefaultParameters

BufferDefaultParameters: object

background

background: boolean = false

clipCenter

clipCenter: Vector3 = new Vector3()

clipNear

clipNear: number = 0

clipRadius

clipRadius: number = 0

depthWrite

depthWrite: boolean = true

diffuse

diffuse: number = 16777215

diffuseInterior

diffuseInterior: boolean = false

disablePicking

disablePicking: boolean = false

flatShaded

flatShaded: boolean = false

forceTransparent

forceTransparent: boolean = false

interiorColor

interiorColor: number = 14540253

interiorDarkening

interiorDarkening: number = 0

matrix

matrix: Matrix4 = new Matrix4()

metalness

metalness: number = 0

opacity

opacity: number = 1

opaqueBack

opaqueBack: boolean = false

roughness

roughness: number = 0.4

side

side: "double" | "front" | "back" = 'double' as BufferSide

sortParticles

sortParticles: boolean = false

useInteriorColor

useInteriorColor: boolean = false

wireframe

wireframe: boolean = false

Const BufferParameterTypes

BufferParameterTypes: object

matrix

matrix: object

Type declaration

background

background: object

updateShader

updateShader: boolean = true

clipCenter

clipCenter: object

uniform

uniform: boolean = true

clipNear

clipNear: object

property

property: boolean = true

updateShader

updateShader: boolean = true

clipRadius

clipRadius: object

uniform

uniform: boolean = true

updateShader

updateShader: boolean = true

depthWrite

depthWrite: object

property

property: boolean = true

diffuse

diffuse: object

uniform

uniform: boolean = true

diffuseInterior

diffuseInterior: object

updateShader

updateShader: boolean = true

flatShaded

flatShaded: object

updateShader

updateShader: boolean = true

interiorColor

interiorColor: object

uniform

uniform: boolean = true

interiorDarkening

interiorDarkening: object

uniform

uniform: boolean = true

metalness

metalness: object

uniform

uniform: boolean = true

opacity

opacity: object

uniform

uniform: boolean = true

opaqueBack

opaqueBack: object

updateShader

updateShader: boolean = true

roughness

roughness: object

uniform

uniform: boolean = true

side

side: object

property

property: boolean = true

updateShader

updateShader: boolean = true

useInteriorColor

useInteriorColor: object

updateShader

updateShader: boolean = true

wireframe

wireframe: object

updateVisibility

updateVisibility: boolean = true

Const ColorDict

ColorDict: object

blue

blue: any[] = hsvToRgb(240, 70, 100)

bluetint

bluetint: any[] = hsvToRgb(220, 40, 100)

brown

brown: any[] = hsvToRgb(20, 45, 75)

cyan

cyan: any[] = hsvToRgb(180, 100, 85)

deadblack

deadblack: number[] = [ 0, 0, 0 ]

deadwhite

deadwhite: number[] = [ 1, 1, 1 ]

gold

gold: any[] = hsvToRgb(40, 100, 100)

gray

gray: any[] = hsvToRgb(0, 0, 50)

green

green: any[] = hsvToRgb(120, 80, 100)

greentint

greentint: any[] = hsvToRgb(135, 40, 100)

hotpink

hotpink: any[] = hsvToRgb(335, 100, 100)

invisible

invisible: number[] = [ 0, 0, 0 ]

lilac

lilac: any[] = hsvToRgb(275, 55, 100)

lilactint

lilactint: any[] = hsvToRgb(275, 35, 100)

lime

lime: any[] = hsvToRgb(80, 100, 100)

magenta

magenta: any[] = hsvToRgb(300, 95, 100)

orange

orange: any[] = hsvToRgb(20, 100, 100)

peach

peach: any[] = hsvToRgb(25, 75, 100)

peachtint

peachtint: any[] = hsvToRgb(25, 50, 100)

pink

pink: any[] = hsvToRgb(350, 55, 100)

pinktint

pinktint: any[] = hsvToRgb(340, 30, 100)

purple

purple: any[] = hsvToRgb(275, 75, 100)

red

red: any[] = hsvToRgb(0, 100, 100)

sea

sea: any[] = hsvToRgb(150, 100, 100)

sky

sky: any[] = hsvToRgb(210, 75, 95)

white

white: any[] = hsvToRgb(0, 0, 100)

yellow

yellow: any[] = hsvToRgb(60, 100, 100)

yellowtint

yellowtint: any[] = hsvToRgb(60, 50, 100)

Const ColormakerModes

ColormakerModes: object
: string = ""

hcl

hcl: string = "Hue Chroma Lightness"

hsi

hsi: string = "Hue Saturation Intensity"

hsl

hsl: string = "Hue Saturation Lightness"

hsv

hsv: string = "Hue Saturation Value"

lab

lab: string = "CIE L*a*b*"

rgb

rgb: string = "Red Green Blue"

Const ColormakerScales

ColormakerScales: object
: string = ""

Accent

Accent: string = "[Q] Accent"

Blues

Blues: string = "[S] Blues"

BrBG

BrBG: string = "[D] Brown-Bluegreen"

BuGn

BuGn: string = "[S] Blue-Green"

BuPu

BuPu: string = "[S] Blue-Purple"

Dark2

Dark2: string = "[Q] Dark2"

GnBu

GnBu: string = "[S] Green-Blue"

Greens

Greens: string = "[S] Greens"

Greys

Greys: string = "[S] Greys"

OrRd

OrRd: string = "[S] Orange-Red"

Oranges

Oranges: string = "[S] Oranges"

PRGn

PRGn: string = "[D] Purplered-Green"

Paired

Paired: string = "[Q] Paired"

Pastel1

Pastel1: string = "[Q] Pastel1"

Pastel2

Pastel2: string = "[Q] Pastel2"

PiYG

PiYG: string = "[D] Pink-Yellowgreen"

PuBu

PuBu: string = "[S] Purple-Blue"

PuBuGn

PuBuGn: string = "[S] Purple-Blue-Green"

PuOr

PuOr: string = "[D] Purple-Orange"

PuRd

PuRd: string = "[S] Purple-Red"

Purples

Purples: string = "[S] Purples"

RdBu

RdBu: string = "[D] Red-Blue"

RdGy

RdGy: string = "[D] Red-Grey"

RdPu

RdPu: string = "[S] Red-Purple"

RdYlBu

RdYlBu: string = "[D] Red-Yellow-Blue"

RdYlGn

RdYlGn: string = "[D] Red-Yellow-Green"

Reds

Reds: string = "[S] Reds"

Set1

Set1: string = "[Q] Set1"

Set2

Set2: string = "[Q] Set2"

Set3

Set3: string = "[Q] Set3"

Spectral

Spectral: string = "[D] Spectral"

Viridis

Viridis: string = "[D] Viridis"

YlGn

YlGn: string = "[S] Yellow-Green"

YlGnBu

YlGnBu: string = "[S] Yellow-Green-Blue"

YlOrBr

YlOrBr: string = "[S] Yellow-Orange-Brown"

YlOrRd

YlOrRd: string = "[S] Yellow-Orange-Red"

rainbow

rainbow: string = "[?] Rainbow"

rwb

rwb: string = "[?] Red-White-Blue"

Const ComponentDefaultParameters

ComponentDefaultParameters: object

name

name: string = ""

status

status: string = ""

visible

visible: boolean = true

Const ContactDataDefaultParams

ContactDataDefaultParams: object

backboneHydrogenBond

backboneHydrogenBond: boolean = true

cationPi

cationPi: boolean = true

filterSele

filterSele: string = ""

halogenBond

halogenBond: boolean = true

hydrogenBond

hydrogenBond: boolean = true

hydrophobic

hydrophobic: boolean = true

ionicInteraction

ionicInteraction: boolean = true

metalCoordination

metalCoordination: boolean = true

piStacking

piStacking: boolean = true

radius

radius: number = 1

waterHydrogenBond

waterHydrogenBond: boolean = true

weakHydrogenBond

weakHydrogenBond: boolean = true

Const ContactDefaultParams

ContactDefaultParams: object

lineOfSightDistFactor

lineOfSightDistFactor: number = 1

masterModelIndex

masterModelIndex: number = -1

maxCationPiDist

maxCationPiDist: number = 6

maxCationPiOffset

maxCationPiOffset: number = 2

maxHalogenBondAngle

maxHalogenBondAngle: number = 30

maxHalogenBondDist

maxHalogenBondDist: number = 4

maxHbondAccAngle

maxHbondAccAngle: number = 45

maxHbondAccPlaneAngle

maxHbondAccPlaneAngle: number = 90

maxHbondDist

maxHbondDist: number = 3.5

maxHbondDonAngle

maxHbondDonAngle: number = 45

maxHbondDonPlaneAngle

maxHbondDonPlaneAngle: number = 30

maxHbondSulfurDist

maxHbondSulfurDist: number = 4.1

maxHydrophobicDist

maxHydrophobicDist: number = 4

maxIonicDist

maxIonicDist: number = 5

maxMetalDist

maxMetalDist: number = 3

maxPiStackingAngle

maxPiStackingAngle: number = 30

maxPiStackingDist

maxPiStackingDist: number = 5.5

maxPiStackingOffset

maxPiStackingOffset: number = 2

refineSaltBridges

refineSaltBridges: boolean = true

Const CovalentRadii

CovalentRadii: object

1

1: number = 0.31

10

10: number = 0.58

100

100: number = 1.6

101

101: number = 1.6

102

102: number = 1.6

103

103: number = 1.6

104

104: number = 1.6

105

105: number = 1.6

106

106: number = 1.6

107

107: number = 1.6

108

108: number = 1.6

109

109: number = 1.6

11

11: number = 1.66

110

110: number = 1.6

111

111: number = 1.6

112

112: number = 1.6

113

113: number = 1.6

114

114: number = 1.6

115

115: number = 1.6

116

116: number = 1.6

117

117: number = 1.6

118

118: number = 1.6

12

12: number = 1.41

13

13: number = 1.21

14

14: number = 1.11

15

15: number = 1.07

16

16: number = 1.05

17

17: number = 1.02

18

18: number = 1.06

19

19: number = 2.03

2

2: number = 0.28

20

20: number = 1.76

21

21: number = 1.7

22

22: number = 1.6

23

23: number = 1.53

24

24: number = 1.39

25

25: number = 1.39

26

26: number = 1.32

27

27: number = 1.26

28

28: number = 1.24

29

29: number = 1.32

3

3: number = 1.28

30

30: number = 1.22

31

31: number = 1.22

32

32: number = 1.2

33

33: number = 1.19

34

34: number = 1.2

35

35: number = 1.2

36

36: number = 1.16

37

37: number = 2.2

38

38: number = 1.95

39

39: number = 1.9

4

4: number = 0.96

40

40: number = 1.75

41

41: number = 1.64

42

42: number = 1.54

43

43: number = 1.47

44

44: number = 1.46

45

45: number = 1.42

46

46: number = 1.39

47

47: number = 1.45

48

48: number = 1.44

49

49: number = 1.42

5

5: number = 0.84

50

50: number = 1.39

51

51: number = 1.39

52

52: number = 1.38

53

53: number = 1.39

54

54: number = 1.4

55

55: number = 2.44

56

56: number = 2.15

57

57: number = 2.07

58

58: number = 2.04

59

59: number = 2.03

6

6: number = 0.76

60

60: number = 2.01

61

61: number = 1.99

62

62: number = 1.98

63

63: number = 1.98

64

64: number = 1.96

65

65: number = 1.94

66

66: number = 1.92

67

67: number = 1.92

68

68: number = 1.89

69

69: number = 1.9

7

7: number = 0.71

70

70: number = 1.87

71

71: number = 1.87

72

72: number = 1.75

73

73: number = 1.7

74

74: number = 1.62

75

75: number = 1.51

76

76: number = 1.44

77

77: number = 1.41

78

78: number = 1.36

79

79: number = 1.36

8

8: number = 0.66

80

80: number = 1.32

81

81: number = 1.45

82

82: number = 1.46

83

83: number = 1.48

84

84: number = 1.4

85

85: number = 1.5

86

86: number = 1.5

87

87: number = 2.6

88

88: number = 2.21

89

89: number = 2.15

9

9: number = 0.57

90

90: number = 2.06

91

91: number = 2

92

92: number = 1.96

93

93: number = 1.9

94

94: number = 1.87

95

95: number = 1.8

96

96: number = 1.69

97

97: number = 1.6

98

98: number = 1.6

99

99: number = 1.6

Const DefaultBoxParams

DefaultBoxParams: object

a

a: number = 1

alpha

alpha: number = 90

b

b: number = 1

beta

beta: number = 90

c

c: number = 1

gamma

gamma: number = 90

spacegroup

spacegroup: string = "P 1"

Const ElementColors

ElementColors: object

AC

AC: number = 7384058

AG

AG: number = 12632256

AL

AL: number = 12560038

AM

AM: number = 5528818

AR

AR: number = 8442339

AS

AS: number = 12419299

AT

AT: number = 7688005

AU

AU: number = 16765219

B

B: number = 16758197

BA

BA: number = 51456

BE

BE: number = 12779264

BH

BH: number = 14680120

BI

BI: number = 10375093

BK

BK: number = 9064419

BR

BR: number = 10889513

C

C: number = 9474192

CA

CA: number = 4062976

CD

CD: number = 16767375

CE

CE: number = 16777159

CF

CF: number = 10565332

CL

CL: number = 2093087

CM

CM: number = 7888099

CN

CN: number = 16777215

CO

CO: number = 15765664

CR

CR: number = 9083335

CS

CS: number = 5707663

CU

CU: number = 13140019

D

D: number = 16777152

DB

DB: number = 13697103

DS

DS: number = 16777215

DY

DY: number = 2097095

ER

ER: number = 58997

ES

ES: number = 11739092

EU

EU: number = 6422471

F

F: number = 9494608

FE

FE: number = 14706227

FL

FL: number = 16777215

FM

FM: number = 11739066

FR

FR: number = 4325478

GA

GA: number = 12750735

GD

GD: number = 4587463

GE

GE: number = 6721423

H

H: number = 16777215

HE

HE: number = 14286847

HF

HF: number = 5096191

HG

HG: number = 12105936

HO

HO: number = 65436

HS

HS: number = 15073326

I

I: number = 9699476

IN

IN: number = 10909043

IR

IR: number = 1528967

K

K: number = 9388244

KR

KR: number = 6076625

LA

LA: number = 7394559

LI

LI: number = 13402367

LR

LR: number = 13041766

LU

LU: number = 43812

LV

LV: number = 16777215

MD

MD: number = 11734438

MG

MG: number = 9109248

MN

MN: number = 10255047

MO

MO: number = 5551541

MT

MT: number = 15400998

N

N: number = 3166456

NA

NA: number = 11230450

NB

NB: number = 7586505

ND

ND: number = 13107143

NE

NE: number = 11789301

NI

NI: number = 5296208

NO

NO: number = 12389767

NP

NP: number = 33023

O

O: number = 16715021

OS

OS: number = 2516630

P

P: number = 16744448

PA

PA: number = 41471

PB

PB: number = 5724513

PD

PD: number = 27013

PM

PM: number = 10747847

PO

PO: number = 11230208

PR

PR: number = 14286791

PT

PT: number = 13684960

PU

PU: number = 27647

RA

RA: number = 32000

RB

RB: number = 7351984

RE

RE: number = 2522539

RF

RF: number = 13369433

RG

RG: number = 16777215

RH

RH: number = 687500

RN

RN: number = 4358806

RU

RU: number = 2396047

S

S: number = 16777008

SB

SB: number = 10380213

SC

SC: number = 15132390

SE

SE: number = 16752896

SG

SG: number = 14221381

SI

SI: number = 15780000

SM

SM: number = 9437127

SN

SN: number = 6717568

SR

SR: number = 65280

T

T: number = 16777120

TA

TA: number = 5089023

TB

TB: number = 3211207

TC

TC: number = 3907230

TE

TE: number = 13924864

TH

TH: number = 47871

TI

TI: number = 12567239

TL

TL: number = 10900557

TM

TM: number = 54354

U

U: number = 36863

UUH

UUH: number = 16777215

UUP

UUP: number = 16777215

UUT

UUT: number = 16777215

V

V: number = 10921643

W

W: number = 2200790

XE

XE: number = 9699476

Y

Y: number = 9764863

YB

YB: number = 48952

ZN

ZN: number = 8224944

ZR

ZR: number = 9756896

Const ElementDefaultParameters

ElementDefaultParameters: object

name

name: string = "some element"

status

status: string = ""

Const EncodedSymOp

EncodedSymOp: object

A 1 2 1

A 1 2 1: string = " !#$!& )+$)-"

A b a 2

A b a 2: string = " !#$%#(,#*)# )+$,+(%+*!+"

A b m 2

A b m 2: string = " !#$%# ,#$)# )+$,+ %+$!+"

A m a 2

A m a 2: string = " !#$%#(%#*!# )+$,+(,+*)+"

A m m 2

A m m 2: string = " !#$%# %#$!# )+$,+ ,+$)+"

B 1 1 2

B 1 1 2: string = " !#$%#(g+*%+"

B 1 1 2/b

B 1 1 2/b: string = " !#$,#$%& )&(!+*,+*%-()-"

B 1 1 2/m

B 1 1 2/m: string = " !# !&$%#$%&(!+(!-*%+*%-"

B 1 1 b

B 1 1 b: string = " !# )&(!+()-"

B 1 1 m

B 1 1 m: string = " !# !&(!+(!-"

C 1 2 1

C 1 2 1: string = " !#$!&()#*)&"

C 1 2/c 1

C 1 2/c 1: string = " !#$!-$%& %+()#*)-*,&(,+"

C 1 2/m 1

C 1 2/m 1: string = " !# %#$!&$%&()#(,#*)&*,&"

C 1 21 1

C 1 21 1: string = " !#$)&()#*!&"

C 1 c 1

C 1 c 1: string = " !# %+()#(,+"

C 1 m 1

C 1 m 1: string = " !# %#()#(,#"

C 2 2 2

C 2 2 2: string = " !#$%#$!& %&()#*,#*)&(,&"

C 2 2 21

C 2 2 21: string = " !#$%+$!- %&()#*,+*)-(,&"

C 2 2 21a)

C 2 2 21a): string = " !#*%+(,&$)-()#$,+ %&*!-"

C 2 2 2a

C 2 2 2a: string = " !#*,#.%&$'&()#$%# ,&*!&"

C 2/c 2/c 2/a

C 2/c 2/c 2/a: string = " !#*,#$!&(,&$,-(!- ,+*!+()#$%#*)& %&*%- )-(%+$)+"

C 2/c 2/c 2/m

C 2/c 2/c 2/m: string = " !#$%#$!- %-$%& !& %+$!+()#*,#*)-(,-*,&()&(,+*)+"

C 2/m 2/c 21/a

C 2/m 2/c 21/a: string = " !#$,+$)- %&$%& )- ,+$!#()#*%+*!-(,&*,&(!-(%+*)#"

C 2/m 2/c 21/m

C 2/m 2/c 21/m: string = " !#$%+$!- %&$%& !- %+$!#()#*,+*)-(,&*,&()-(,+*)#"

C 2/m 2/m 2/a

C 2/m 2/m 2/a: string = " !#$,#$)& %&$%& )& ,#$!#()#*%#*!&(,&*,&(!&(%#*)#"

C 2/m 2/m 2/m

C 2/m 2/m 2/m: string = " !#$%#$!& %&$%& !& %#$!#()#*,#*)&(,&*,&()&(,#*)#"

C c c 2

C c c 2: string = " !#$%# %+$!+()#*,#(,+*)+"

C m c 21

C m c 21: string = " !#$%+ %+$!#()#*,+(,+*)#"

C m m 2

C m m 2: string = " !#$%# %#$!#()#*,#(,#*)#"

F -4 3 c

F -4 3 c: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& )(+,*+)*-,(-(+)*+,*-)(-,+)(+,*-)*-,( )+$,+$)- ,-#()#*,&*)&(,!+(%+*!-*%-() #,$#)$&, &(#!*#%*&!(&%+! +%$-!$-% (!+*%+*!-(%-+ )+$,-$)- ,)#(,#*)&*,&(!(#%*#!*&%(& +!$+%$-! -%#) #,$&)$&, ()#*,#*)&(,&+(!+*%-*!-(%)+ ,+$)-$,- ! +%$+!$-% - #)$#,$&) &,#!(#%*&!*&%("

F -4 3 m

F -4 3 m: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! #%$#!$&% & #!$#%$&! &%#! #%$&!$&% )+$,+$)- ,-#()#*,&*)&(,!+(%+*!-*%-(!(+%*+!*-%(- +)$+,$-) -,#)(#,*&)*&,((!+*%+*!-(%-+ )+$,-$)- ,)#(,#*)&*,&() +,$+)$-, -(#)*#,*&)(&,+!(+%*-!*-%(()#*,#*)&(,&+(!+*%-*!-(%)+ ,+$)-$,- )(#,*#)*&,(&(+!*+%*-!(-%+) +,$-)$-, "

F 2 2 2

F 2 2 2: string = " !#$%#$!& %& )+$,+$)- ,-(!+*%+*!-(%-()#*,#*)&(,&"

F 2 2 2a

F 2 2 2a: string = " !#*,#.%&$'& '/*%/.12$!2.!/$,/ %20'2.'#$%# 1&0!&"

F 2 3

F 2 3: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& )+$,+$)- ,-#()#*,&*)&(,!+(%+*!-*%-((!+*%+*!-(%-+ )+$,-$)- ,)#(,#*)&*,&(()#*,#*)&(,&+(!+*%-*!-(%)+ ,+$)-$,- "

F 2/d -3

F 2/d -3: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& 64=37=345675=64=375345674=67=3453756 )+$,+$)- ,-#()#*,&*)&(,!+(%+*!-*%-(68>3:>3896:9=<8=;:5;85<:4><7>;49;79<(!+*%+*!-(%-+ )+$,-$)- ,)#(,#*)&*,&(<4>;7>;49<79>68>3:93896:8=<:=;85;:5<()#*,#*)&(,&+(!+*%-*!-(%)+ ,+$)-$,- <8=;:=;8f<:f><4>;79;49<78>6:>3893:96"

F 2/d 2/d 2/d

F 2/d 2/d 2/d: string = " !#$%#$!& %&64=37=345675 )+$,+$)- ,-68>3:>3896:9(!+*%+*!-(%-<4>;7>;49<79()#*,#*)&(,&<8=;:=;85<:5"

F 2/m -3

F 2/m -3: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& $%& !& %#$!#&$%& !# %#$!%&$!& %# !#$ )+$,+$)- ,-#()#*,&*)&(,!+(%+*!-*%-($,- )- ,+$)+&*,&()#(,#*)%-*!-(%+(!+*(!+*%+*!-(%-+ )+$,-$)- ,)#(,#*)&*,&(*%-(!-(%+*!+-$,- )+ ,+$),&*)&(,#()#*()#*,#*)&(,&+(!+*%-*!-(%)+ ,+$)-$,- *,&()&(,#*)#-*%-(!+(%+*!,-$)- ,+ )+$"

F 2/m 2/m 2/m

F 2/m 2/m 2/m: string = " !#$%#$!& %&$%& !& %#$!# )+$,+$)- ,-$,- )- ,+$)+(!+*%+*!-(%-*%-(!-(%+*!+()#*,#*)&(,&*,&()&(,#*)#"

F 4 3 2

F 4 3 2: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! &%$&!$#% # #%$#!$&% &!#!$#% &! &%$ )+$,+$)- ,-#()#*,&*)&(,!+(%+*!-*%-(!(-%*-!*+%(+ +,$+)$-, -)#)*#,(&)(&,*(!+*%+*!-(%-+ )+$,-$)- ,)#(,#*)&*,&() -,$-)$+, +(#,*#)*&,(&)+!*+%(-!(-%*()#*,#*)&(,&+(!+*%-*!-(%)+ ,+$)-$,- )(&,*&)*#,(#(+%*+!*-%(-!+)$+, -) -,$"

F 4/m -3 2/c

F 4/m -3 2/c: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& )(-,*-)*+,(+(+,*+)*-,(-)+)*+,(-)(-,*$%& !& %#$!#&$%& !# %#$!%&$!& %# !#$,*+)(+,(-)*-*-)(-,(+)*+,-,(-)*+,*+)( )+$,+$)- ,-#()#*,&*)&(,!+(%+*!-*%-() &,$&)$#, #(#%*#!*&%(&!+!$+% -! -%$$,- )- ,+$)+&*,&()#(,#*)%-*!-(%+(!+*,$#) #, &)$&*&!(&%(#!*#%-% -!$+%$+! (!+*%+*!-(%-+ )+$,-$)- ,)#(,#*)&*,&(!(&%*&!*#%(# +%$+!$-% -!#)$#, &) &,$*%-(!-(%+*!+-$,- )+ ,+$),&*)&(,#()#*%*#!(#%(&!*&$-! -% +!$+%&, &)$#,$#) ()#*,#*)&(,&+(!+*%-*!-(%)+ ,+$)-$,- ! -%$-!$+% + #,$#)$&, &)#!*#%(&!(&%**,&()&(,#*)#-*%-(!+(%+*!,-$)- ,+ )+$%$+! +% -!$-$&) &, #)$#,&%(&!*#%*#!("

F 4/m -3 2/m

F 4/m -3 2/m: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! &%$&!$#% # #%$#!$&% &!#!$#% &! &%$$%& !& %#$!#&$%& !# %#$!%&$!& %# !#$%$#! #% &!$&$&! &% #!$#%&% &!$#%$#! )+$,+$)- ,-#()#*,&*)&(,!+(%+*!-*%-(!(-%*-!*+%(+ +,$+)$-, -)#)*#,(&)(&,*$,- )- ,+$)+&*,&()#(,#*)%-*!-(%+(!+*%*+!(+%(-!*-$-) -, +)$+,&,(&)*#,*#)((!+*%+*!-(%-+ )+$,-$)- ,)#(,#*)&*,&() -,$-)$+, +(#,*#)*&,(&)+!*+%(-!(-%**%-(!-(%+*!+-$,- )+ ,+$),&*)&(,#()#*,$+) +, -)$-*&)(&,(#)*#,-%(-!*+%*+!(()#*,#*)&(,&+(!+*%-*!-(%)+ ,+$)-$,- )(&,*&)*#,(#(+%*+!*-%(-!+)$+, -) -,$*,&()&(,#*)#-*%-(!+(%+*!,-$)- ,+ )+$,*#)(#,(&)*&*-!(-%(+!*+%-, -)$+,$+) "

F 41 3 2

F 41 3 2: string = " !#$,+*)&(%-# !+$,&*)-(%!# ,+$)&*%-(:3>46=7<98;5;58<976=43>:97<58;>:3=46 )+$%#*!-(,&#()+*%&$!- ,!+(,#*)-$%& :;=4<>765839;94<5:6>83=79:6543>7;=8<(!+*,#$)- %&+ )#$%-*!&(,)#(%+*!&$,- 73=86>:<54;935469:<=8;>7576983=:;>4<()#*%+$!& ,-+(!#*,-$)& %)+ %#$!-*,&(7;>8<=:69435398657<>4;=:5:<94;=73>86"

F 41/d -3 2/c

F 41/d -3 2/c: string = 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

F 41/d -3 2/m

F 41/d -3 2/m: string = 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

F d d 2

F d d 2: string = " !#$%#345675 )+$,+3896:9(!+*%+;49<79()#*,#;85<:5"

F m m 2

F m m 2: string = " !#$%# %#$!# )+$,+ ,+$)+(!+*%+(%+*!+()#*,#(,#*)#"

H -3

H -3: string = " !#%?#@$#$%&!@&? &OPQRSQTUQVWXYZX[]X]Y^W[^ZV^UR_PT_SO_"

H -3 2/c

H -3 2/c: string = " !#%?#@$#! -?%-$@-$%&!@&? &%$+@!+ ?+OPQRSQTUQY]b[WbVZbVWXYZX[]XRU`TP`OS`]Y^W[^ZV^POcSRcUTcUR_PT_SO_WVaZYa][a"

H -3 2/m

H -3 2/m: string = " !#%?#@$#! &?%&$@&$%&!@&? &%$#@!# ?#OPQRSQTUQY]X[WXVZXVWXYZX[]XRUQTPQOSQ]Y^W[^ZV^PO_SR_UT_UR_PT_SO_WV^ZY^][^"

H 3

H 3: string = " !#%?#@$#CDAEFAGHAIJBKLBMNB"

H 3 2

H 3 2: string = " !#%?#@$#! &?%&$@&OPQRSQTUQY]X[WXVZX]Y^W[^ZV^PO_SR_UT_"

H 3 c

H 3 c: string = " !#%?#@$#%$+@!+ ?+OPQRSQTUQRU`TP`OS`]Y^W[^ZV^WVaZYa][a"

H 3 m

H 3 m: string = " !#%?#@$#%$#@!# ?#OPQRSQTUQRUQTPQOSQ]Y^W[^ZV^WV^ZY^][^"

I -4

I -4: string = " !#$%#!$&% &()+*,+)*-,(-"

I -4 2 d

I -4 2 d: string = " !#$%#% &!$&*!>(%>,$9) 9()+*,+,(-)*-$)= ,=%*5!(5"

I -4 2 m

I -4 2 m: string = " !#$%#% &!$&$!& %&%$#! #()+*,+,(-)*-*)-(,-,*+)(+"

I -4 3 d

I -4 3 d: string = " !#*%+$)-(,&# !+*%-$)&(,!# %+*)-$,&(7354<9:6>8;=357<946>:;=857394<>:6=8;()+$,#*!& %-+()#$,&*!- %)+(,#$!&*%- :;98657<=43>;9:658<=73>49:;586=7<>43"

I -4 3 m

I -4 3 m: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! #%$#!$&% & #!$#%$&! &%#! #%$&!$&% ()+*,+*)-(,-+()+*,-*)-(,)+(,+*)-*,-()(+,*+)*-,(-(+)*+,*-)(-,+)(+,*-)*-,("

I -4 c 2

I -4 c 2: string = " !#$%#% &!$& %+$!+! -%$-()+*,+,(-)*-(,#*)#)(&,*&"

I -4 m 2

I -4 m 2: string = " !#$%#% &!$& %#$!#! &%$&()+*,+,(-)*-(,+*)+)(-,*-"

I 1 2 1

I 1 2 1: string = " !#$!&.'/0'2"

I 1 21 1

I 1 21 1: string = " !#$)&.'/0!-"

I 2 2 2

I 2 2 2: string = " !#$%# %&$!&.'/01/.120'2"

I 2 2 2a

I 2 2 2a: string = " !#*,#.%&$'&()+$%+*!- ,-"

I 2 3

I 2 3: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ()+*,+*)-(,-+()+*,-*)-(,)+(,+*)-*,-("

I 2 3a

I 2 3a: string = " !#*,#.%&$'&!# ,- '&$%/$# !-*!/$%&.%()+$%+ ,-*!-)+(%&(!-*,#*+()&$)#*,- ,"

I 2/b 2/a 2/m

I 2/b 2/a 2/m: string = " !#$%#*)&(,&$%& !&(,#*)#()+*,+$!- %-*,-()- %+$!+"

I 2/m -3

I 2/m -3: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& $%& !& %#$!#&$%& !# %#$!%&$!& %# !#$()+*,+*)-(,-+()+*,-*)-(,)+(,+*)-*,-(*,-()-(,+*)+-*,-()+(,+*),-*)-(,+()+*"

I 2/m 2/m 2/m

I 2/m 2/m 2/m: string = " !#$%#$!& %&$%& !& %#$!#()+*,+*)-(,-*,-()-(,+*)+"

I 21 21 21

I 21 21 21: string = " !#*%+$)-(,&()+$,#*!& %-"

I 21 3

I 21 3: string = " !#*%+$)-(,&# !+*%-$)&(,!# %+*)-$,&(()+$,#*!& %-+()#$,&*!- %)+(,#$!&*%- "

I 21/a -3

I 21/a -3: string = " !#*%+$)-(,&# !+*%-$)&(,!# %+*)-$,&($%&(!- ,+*)#&$%-(!+ ,#*)%&$!-(,+ )#*()+$,#*g& %-+()#$,&*!- %)+(,#$!&*%- *,- )&(%#$!+-*,& )#(%+$!,-*)& %#(!+$"

I 21/b 21/c 21/a

I 21/b 21/c 21/a: string = " !#*%+$)-(,&$%&(!- ,+*)#()+$,#*!& %-*,- )&(%#$!+"

I 21/m 21/m 21/a

I 21/m 21/m 21/a: string = " !#$,#$)& %&$%& )& ,#$!#()+*%+*!-(,-*,-(!-(%+*)+"

I 4

I 4: string = " !#$%#% #!$#()+*,+,(+)*+"

I 4 2 2

I 4 2 2: string = " !#$%#% #!$#$!& %&! &%$&()+*,+,(+)*+*)-(,-)(-,*-"

I 4 3 2

I 4 3 2: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! &%$&!$#% # #%$#!$&% &!#!$#% &! &%$()+*,+*)-(,-+()+*,-*)-(,)+(,+*)-*,-()(-,*-)*+,(+(+,*+)*-,(-)+)*+,(-)(-,*"

I 4 c m

I 4 c m: string = " !#$%#% #!$# %+$!+%$+! +()+*,+,(+)*+(,#*)#,*#)(#"

I 4 m m

I 4 m m: string = " !#$%#% #!$# %#$!#%$#! #()+*,+,(+)*+(,+*)+,*+)(+"

I 4/m

I 4/m: string = " !#$%#% #!$#$%& !&!$&% &()+*,+,(+)*+*,-()-)*-,(-"

I 4/m -3 2/m

I 4/m -3 2/m: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! &%$&!$#% # #%$#!$&% &!#!$#% &! &%$$%& !& %#$!#&$%& !# %#$!%&$!& %# !#$%$#! #% &!$&$&! &% #!$#%&% &!$#%$#! ()+*,+*)-(,-+()+*,-*)-(,)+(,+*)-*,-()(-,*-)*+,(+(+,*+)*-,(-)+)*+,(-)(-,**,-()-(,+*)+-*,-()+(,+*),-*)-(,+()+*,*+)(+,(-)*-*-)(-,(+)*+,-,(-)*+,*+)("

I 4/m 2/c 2/m

I 4/m 2/c 2/m: string = " !#$%#% #!$#$!- %-! -%$-$%& !&!$&% & %+$!+%$+! +()+*,+,(+)*+*)&(,&)(&,*&*,-()-)*-,(-(,#*)#,*#)(#"

I 4/m 2/m 2/m

I 4/m 2/m 2/m: string = " !#$%#% #!$#$!& %&! &%$&$%& !&!$&% & %#$!#%$#! #()+*,+,(+)*+*)-(,-)(-,*-*,-()-)*-,(-(,+*)+,*+)(+"

I 41

I 41: string = " !#*,+%(5)$9()+$%#, 9!*5"

I 41 2 2

I 41 2 2: string = " !#*,+%(5)$9*!> ,=)(-%$&()+$%#, 9!*5$)=(%>! &,*-"

I 41 3 2

I 41 3 2: string = " !#*%+$)-(,&# !+*%-$)&(,!# %+*)-$,&(:3=8<>7694;5;54697<>83=:97654;=:3>8<()+$,#*!& %-+()#$,&*!- %)+(,#$!&*%- 7;>46=:<5839398<5:6=4;>75:<983>7;=46"

I 41 c d

I 41 c d: string = " !#*,+%(5)$9 %+*)#%*9) 5()+$%#, 9!*5(,#$!+,$5!(9"

I 41 m d

I 41 m d: string = " !#*,+%(5)$9 %#*)+%*5) 9()+$%#, 9!*5(,+$!#,$9!(5"

I 41/a

I 41/a: string = " !#*,+%(5)$9$,=(!>!$&,(-()+$%#, 9!*5*%> )=)*-% &"

I 41/a -3 2/d

I 41/a -3 2/d: string = " !#*%+$)-(,&# !+*%-$)&(,!# %+*)-$,&(:3=8<>7694;5;54697<>83=:97654;=:3>8<$%&(!- ,+*)#&$%-(!+ ,#*)%&$!-(,+ )#*4<97358;=:6>6>:;=8357<94=8;>:694<573()+$,#*!& %-+()#$,&*!- %)+(,#$!&*%- 7;>46=:<5839398<5:6=4;>75:<983>7;=46*,- )&(%#$!+-*,& )#(%+$!,-*)& %#(!+$865:;943>7<=<=73>4;9:658>43=7<5869:;"

I 41/a 2/c 2/d

I 41/a 2/c 2/d: string = " !#*,+%(5)$9*!= ,>)(&%$-$,=(!>!$&,(-(,#$!+,$5!(9()+$%#, 9!*5$)>(%=! -,*&*%> )=)*-% & %+*)#%*9) 5"

I 41/a 2/m 2/d

I 41/a 2/m 2/d: string = " !#*,+%(5)$9*!> ,=)(-%$&$,=(!>!$&,(-(,+$!#,$9!(5()+$%#, 9!*5$)=(%>! &,*-*%> )=)*-% & %#*)+%*5) 9"

I b a 2

I b a 2: string = " !#$%#(,#*)#()+*,+ %+$!+"

I m a 2

I m a 2: string = " !#$%#(%#*!#()+*,+ ,+$)+"

I m m 2

I m m 2: string = " !#$%# %#$!#()+*,+(,+*)+"

P -1

P -1: string = " !#$%&"

P -3

P -3: string = " !#%?#@$#$%&!@&? &"

P -3 1 2/c

P -3 1 2/c: string = " !#%?#@$#%$-@!- ?-$%&!@&? &! +?%+$@+"

P -3 1 2/m

P -3 1 2/m: string = " !#%?#@$#%$&@!& ?&$%&!@&? &! #?%#$@#"

P -3 2/c 1

P -3 2/c 1: string = " !#%?#@$#! -?%-$@-$%&!@&? &%$+@!+ ?+"

P -3 2/m 1

P -3 2/m 1: string = " !#%?#@$#! &?%&$@&$%&!@&? &%$#@!# ?#"

P -4

P -4: string = " !#$%#!$&% &"

P -4 2 c

P -4 2 c: string = " !#$%#% &!$&$!- %-%$+! +"

P -4 2 m

P -4 2 m: string = " !#$%#% &!$&$!& %&%$#! #"

P -4 21 c

P -4 21 c: string = " !#$%#% &!$&*)-(,-,*+)(+"

P -4 21 m

P -4 21 m: string = " !#$%#% &!$&*)&(,&,*#)(#"

P -4 3 m

P -4 3 m: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! #%$#!$&% & #!$#%$&! &%#! #%$&!$&% "

P -4 3 n

P -4 3 n: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& )(+,*+)*-,(-(+)*+,*-)(-,+)(+,*-)*-,("

P -4 b 2

P -4 b 2: string = " !#$%#% &!$&(,#*)#)(&,*&"

P -4 c 2

P -4 c 2: string = " !#$%#% &!$& %+$!+! -%$-"

P -4 m 2

P -4 m 2: string = " !#$%#!$&% & %#$!#! &%$&"

P -4 n 2

P -4 n 2: string = " !#$%#% &!$&(,+*)+)(-,*-"

P -6

P -6: string = " !#%?#@$# !&%?&@$&"

P -6 2 c

P -6 2 c: string = " !#%?#@$# !-%?-@$-! &?%&$@&! +?%+$@+"

P -6 2 m

P -6 2 m: string = " !#%?#@$# !&%?&@$&! &?%&$@&! #?%#$@#"

P -6 c 2

P -6 c 2: string = " !#%?#@$# !-%?-@$-%$+@!+ ?+%$&@!& ?&"

P -6 m 2

P -6 m 2: string = " !#%?#@$# !&%?&@$&%$#@!# ?#%$&@!& ?&"

P 1

P 1: string = " !#"

P 1 1 2

P 1 1 2: string = " !#$%#"

P 1 1 2/b

P 1 1 2/b: string = " !#$,#$%& )&"

P 1 1 2/m

P 1 1 2/m: string = " !# !&$%#$%&"

P 1 1 21

P 1 1 21: string = " !#$%+"

P 1 1 21/b

P 1 1 21/b: string = " !#$%&$,+ )-"

P 1 1 21/m

P 1 1 21/m: string = " !#$%+$%& !-"

P 1 1 b

P 1 1 b: string = " !# )&"

P 1 1 m

P 1 1 m: string = " !# !&"

P 1 2 1

P 1 2 1: string = " !#$!&"

P 1 2/c 1

P 1 2/c 1: string = " !#$!-$%& %+"

P 1 2/m 1

P 1 2/m 1: string = " !# %#$!&$%&"

P 1 21 1

P 1 21 1: string = " !#$'&"

P 1 21/c 1

P 1 21/c 1: string = " !#$%&$)- ,+"

P 1 21/m 1

P 1 21/m 1: string = " !#$)&$%& ,#"

P 1 c 1

P 1 c 1: string = " !# %+"

P 1 m 1

P 1 m 1: string = " !# %#"

P 2 2 2

P 2 2 2: string = " !#$%#$!& %&"

P 2 2 21

P 2 2 21: string = " !#$%+$!- %&"

P 2 21 2

P 2 21 2: string = " !# ,&$)&$%#"

P 2 21 21

P 2 21 21: string = " !# %&$)-$,+"

P 2 3

P 2 3: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& "

P 2/b 2/a 2/n

P 2/b 2/a 2/n: string = " !#$%#$!& %&*,&()&(,#*)#"

P 2/b 21/c 21/m

P 2/b 21/c 21/m: string = " !#$%+$)- ,&$%& !- ,+$)#"

P 2/c 2/c 2/m

P 2/c 2/c 2/m: string = " !#$%#$!- %-$%& !& %+$!+"

P 2/m -3

P 2/m -3: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& $%& !& %#$!#&$%& !# %#$!%&$!& %# !#$"

P 2/m 2/m 2/m

P 2/m 2/m 2/m: string = " !#$%#$!& %&$%& !& %#$!#"

P 2/m 2/n 21/a

P 2/m 2/n 21/a: string = " !#*%+*!- %&$%&(!-(%+$!#"

P 2/n -3

P 2/n -3: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& *,-()-(,+*)+-*,-()+(,+*),-*)-(,+()+*"

P 2/n 2/n 2/n

P 2/n 2/n 2/n: string = " !#$%#$!& %&*,-()-(,+*)+"

P 2/n 21/n 2/a

P 2/n 21/n 2/a: string = " !#*%#*)- ,-$%&(!&(,+$)+"

P 21 2 2

P 21 2 2: string = " !#$!&(%&*%#"

P 21 2 21

P 21 2 21: string = " !#$!&(%-*%+"

P 21 21 2

P 21 21 2: string = " !#$%#*)&(,&"

P 21 21 2 (a)

P 21 21 2 (a): string = " !#*,#.%&$'&"

P 21 21 21

P 21 21 21: string = " !#*%+$)-(,&"

P 21 3

P 21 3: string = " !#*%+$)-(,&# !+*%-$)&(,!# %+*)-$,&("

P 21/a -3

P 21/a -3: string = " !#*%+$)-(,&# !+*%-$)&(,!# %+*)-$,&($%&(!- ,+*)#&$%-(!+ ,#*)%&$!-(,+ )#*"

P 21/b 2/c 21/n

P 21/b 2/c 21/n: string = " !#*,+$!-(,&$%&()- %+*)#"

P 21/b 21/a 2/m

P 21/b 21/a 2/m: string = " !#$%#*)&(,&$%& !&(,#*)#"

P 21/b 21/c 21/a

P 21/b 21/c 21/a: string = " !#*%+$)-(,&$%&(!- ,+*)#"

P 21/c 2/c 2/a

P 21/c 2/c 2/a: string = " !#*%#$!-(%-$%&(!& %+*!+"

P 21/c 21/c 2/n

P 21/c 21/c 2/n: string = " !#*,#$)-(%-$%&()& ,+*!+"

P 21/m 2/m 2/a

P 21/m 2/m 2/a: string = " !#*%#$!&(%&$%&(!& %#*!#"

P 21/m 21/m 2/n

P 21/m 21/m 2/n: string = " !#$%#*'&.,&*,&.'& %#$!#"

P 21/m 21/m 2/n a

P 21/m 21/m 2/n a: string = " !#*,#$)&(%&$%&.'& ,#*!#"

P 21/n 21/m 21/a

P 21/n 21/m 21/a: string = " !#0%/$'&.12$%&.!2 1#0'/"

P 21/n 21/n 2/m

P 21/n 21/n 2/m: string = " !#$%#*)-(,-$%& !&(,+*)+"

P 3

P 3: string = " !#%?#@$#"

P 3 1 2

P 3 1 2: string = " !#%?#@$#%$&@!& ?&"

P 3 1 c

P 3 1 c: string = " !#%?#@$#! +?%+$@+"

P 3 1 m

P 3 1 m: string = " !#%?#@$#! #?%#$@#"

P 3 2 1

P 3 2 1: string = " !#%?#@$#! &?%&$@&"

P 3 c 1

P 3 c 1: string = " !#%?#@$#%$+@!+ ?+"

P 3 m 1

P 3 m 1: string = " !#%?#@$#%$#@!# ?#"

P 31

P 31: string = " !#%?A@$B"

P 31 1 2

P 31 1 2: string = " !#%?Q@$^%$_@!X ?&"

P 31 2 1

P 31 2 1: string = " !#%?A@$B! &?%_$@X"

P 32

P 32: string = " !#%?B@$A"

P 32 1 2

P 32 1 2: string = " !#%?^@$Q%$X@!_ ?&"

P 32 2 1

P 32 2 1: string = " !#%?B@$A! &?%X$@_"

P 4

P 4: string = " !#$%#% #!$#"

P 4 2 2

P 4 2 2: string = " !#$%#% #!$#$!& %&! &%$&"

P 4 21 2

P 4 21 2: string = " !#$%#,(#)*#*)&(,&! &%$&"

P 4 3 2

P 4 3 2: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! &%$&!$#% # #%$#!$&% &!#!$#% &! &%$"

P 4 b m

P 4 b m: string = " !#$%#% #!$#(,#*)#,*#)(#"

P 4 c c

P 4 c c: string = " !#$%#% #!$# %+$!+%$+! +"

P 4 m m

P 4 m m: string = " !#$%#% #!$# %#$!#%$#! #"

P 4 n c

P 4 n c: string = " !#$%#% #!$#(,+*)+,*+)(+"

P 4/m

P 4/m: string = " !#$%#% #!$#$%& !&!$&% &"

P 4/m -3 2/m

P 4/m -3 2/m: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! &%$&!$#% # #%$#!$&% &!#!$#% &! &%$$%& !& %#$!#&$%& !# %#$!%&$!& %# !#$%$#! #% &!$&$&! &% #!$#%&% &!$#%$#! "

P 4/m 2/c 2/c

P 4/m 2/c 2/c: string = " !#$%#% #!$#$!- %-! -%$-$%& !&!$&% & %+$!+%$+! +"

P 4/m 2/m 2/m

P 4/m 2/m 2/m: string = " !#$%#% #!$#$!& %&! &%$&$%& !&!$&% & %#$!#%$#! #"

P 4/m 21/b 2/m

P 4/m 21/b 2/m: string = " !#$%#% #!$#*)&(,&)(&,*&$%& !&!$&% &(,#*)#,*#)(#"

P 4/m 21/n 2/c

P 4/m 21/n 2/c: string = " !#$%#% #!$#*)-(,-)(-,*-$%& !&!$&% &(,+*)+,*+)(+"

P 4/n

P 4/n: string = " !#$%#,(#)*#*,&()&!$&% &"

P 4/n -3 2/n

P 4/n -3 2/n: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& ! &%$&!$#% # #%$#!$&% &!#!$#% &! &%$*,-()-(,+*)+-*,-()+(,+*),-*)-(,+()+*,*+)(+,(-)*-*-)(-,(+)*+,-,(-)*+,*+)("

P 4/n 2/b 2/m

P 4/n 2/b 2/m: string = " !#$%#% #!$#$!& %&! &%$&*,&()&)*&,(&(,#*)#,*#)(#"

P 4/n 2/c 2/c

P 4/n 2/c 2/c: string = " !#$%#,(#)*#*)-(,-! -%$-*,&()&!$&% & %+$!+,*+)(+"

P 4/n 2/n 2/c

P 4/n 2/n 2/c: string = " !#$%#% #!$#$!& %&! &%$&*,-()-)*-,(-(,+*)+,*+)(+"

P 4/n 21/m 2/m

P 4/n 21/m 2/m: string = " !#$%#,(#)*#*)&(,&! &%$&*,&()&!$&% & %#$!#,*#)(#"

P 41

P 41: string = " !#$%+% 5!$9"

P 41 2 2

P 41 2 2: string = " !#$%+% 5!$9$!& %-! >%$="

P 41 21 2

P 41 21 2: string = " !#$%+,(5)*9*)=(,>! &%$-"

P 41 3 2

P 41 3 2: string = " !#*%+$)-(,&# !+*%-$)&(,!# %+*)-$,&(:3=8<>7694;5;54697<>83=:97654;=:3>8<"

P 42

P 42: string = " !#$%#% +!$+"

P 42 2 2

P 42 2 2: string = " !#$%#% +!$+$!& %&! -%$-"

P 42 21 2

P 42 21 2: string = " !#$%#,(+)*+*)-(,-! &%$&"

P 42 21 2a

P 42 21 2a: string = " !#*,#%.+'$+$'&.%&! -,*-"

P 42 3 2

P 42 3 2: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& )(-,*-)*+,(+(+,*+)*-,(-)+)*+,(-)(-,*"

P 42 b c

P 42 b c: string = " !#$%#% +!$+(,#*)#,*+)(+"

P 42 c m

P 42 c m: string = " !#$%#% +!$+ %+$!+%$#! #"

P 42 m c

P 42 m c: string = " !#$%#% +!$+ %#$!#%$+! +"

P 42 n m

P 42 n m: string = " !#$%#,(+)*+(,+*)+%$#! #"

P 42/m

P 42/m: string = " !#$%#% +!$+$%& !&!$-% -"

P 42/m -3 2/n

P 42/m -3 2/n: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& )(-,*-)*+,(+(+,*+)*-,(-)+)*+,(-)(-,*$%& !& %#$!#&$%& !# %#$!%&$!& %# !#$,*+)(+,(-)*-*-)(-,(+)*+,-,(-)*+,*+)("

P 42/m 2/c 2/m

P 42/m 2/c 2/m: string = " !#$%#% +!$+$!- %-! &%$&$%& !&!$-% - %+$!+%$#! #"

P 42/m 2/m 2/c

P 42/m 2/m 2/c: string = " !#$%#% +!$+$!& %&! -%$-$%& !&!$-% - %#$!#%$+! +"

P 42/m 21/b 2/c

P 42/m 21/b 2/c: string = " !#$%#% +!$+*)&(,&)(-,*-$%& !&!$-% -(,#*)#,*+)(+"

P 42/m 21/n 2/m

P 42/m 21/n 2/m: string = " !#$%#,./'*/*'-.,-! &%$&$%& !&'*-,.-.,/*'/%$#! #"

P 42/n

P 42/n: string = " !#$%#,(+)*+*,-()-!$&% &"

P 42/n -3 2/m

P 42/n -3 2/m: string = " !#$%#$!& %&# !#$%&$!& %!# %#$!&$%& )(-,*-)*+,(+(+,*+)*-,(-)+)*+,(-)(-,**,-()-(,+*)+-*,-()+(,+*),-*)-(,+()+*%$#! #% &!$&$&! &% #!$#%&% &!$#%$#! "

P 42/n 2/b 2/c

P 42/n 2/b 2/c: string = " !#$%#,(+)*+$!- %-)(&,*&*,-()-!$&% &(,#*)#%$+! +"

P 42/n 2/n 2/m

P 42/n 2/n 2/m: string = " !#$%#,(+)*+$!& %&)(-,*-*,-()-!$&% &(,+*)+%$#! #"

P 42/n 21/c 2/m

P 42/n 21/c 2/m: string = " !#$%#,(+)*+*)&(,&! -%$-*,-()-!$&% & %+$!+,*#)(#"

P 42/n 21/m 2/c

P 42/n 21/m 2/c: string = " !#$%#,(+)*+*)-(,-! &%$&*,-()-!$&% & %#$!#,*+)(+"

P 43

P 43: string = " !#$%+% 9!$5"

P 43 2 2

P 43 2 2: string = " !#$%+% 9!$5$!& %-! =%$>"

P 43 21 2

P 43 21 2: string = " !#$%+,(9)*5*)>(,=! &%$-"

P 43 3 2

P 43 3 2: string = " !#*%+$)-(,&# !+*%-$)&(,!# %+*)-$,&(7;>46=:<5839398<5:6=4;>75:<983>7;=46"

P 6

P 6: string = " !#%?#@$#$%#!@#? #"

P 6 2 2

P 6 2 2: string = " !#%?#@$#$%#!@#? #! &?%&$@&%$&@!& ?&"

P 6 c c

P 6 c c: string = " !#%?#@$#$%#!@#? #%$+@!+ ?+! +?%+$@+"

P 6 m m

P 6 m m: string = " !#%?#@$#$%#!@#? #%$#@!# ?#! #?%#$@#"

P 6/m

P 6/m: string = " !#%?#@$#$%#!@#? #$%&!@&? & !&%?&@$&"

P 6/m 2/c 2/c

P 6/m 2/c 2/c: string = " !#%?#@$#$%#!@#? #! -?%-$@-%$-@!- ?-$%&!@&? & !&@$&%?&%$+@!+ ?+! +?%+$@+"

P 6/m 2/m 2/m

P 6/m 2/m 2/m: string = " !#%?#@$#$%#!@#? #! &?%&$@&%$&@!& ?&$%&!@&? & !&@$&%?&%$#@!# ?#! #?%#$@#"

P 61

P 61: string = " !#%?A@$B$%/!@d? e"

P 61 2 2

P 61 2 2: string = " !#%?Q@$^$%+!@`? a! X?%&$@_%$b@!- ?c"

P 62

P 62: string = " !#%?^@$Q$%#!@^? Q"

P 62 2 2

P 62 2 2: string = " !#%?^@$Q$%#!@^? Q! _?%&$@X%$_@!& ?X"

P 63

P 63: string = " !#%?#@$#$%+!@+? +"

P 63 2 2

P 63 2 2: string = " !#%?#@$#$%+!@+? +! &?%&$@&%$-@!- ?-"

P 63 c m

P 63 c m: string = " !#%?#@$#$%+!@+? +%$+@!+ ?+! #?%#$@#"

P 63 m c

P 63 m c: string = " !#%?#@$#$%+!@+? +%$#@!# ?#! +?%+$@+"

P 63/m

P 63/m: string = " !#%?#@$#$%+!@+? +$%&!@&? & !-%?-@$-"

P 63/m 2/c 2/m

P 63/m 2/c 2/m: string = " !#%?#@$#$%+!@+? +! -?%-$@-%$&@!& ?&$%&!@&? & !-@$-%?-%$+@!+ ?+! #?%#$@#"

P 63/m 2/m 2/c

P 63/m 2/m 2/c: string = " !#%?#@$#$%+!@+? +! &?%&$@&%$-@!- ?-$%&!@&? & !-@$-%?-%$#@!# ?#! +?%+$@+"

P 64

P 64: string = " !#%?Q@$^$%#!@Q? ^"

P 64 2 2

P 64 2 2: string = " !#%?Q@$^$%#!@Q? ^! X?%&$@_%$X@!& ?_"

P 65

P 65: string = " !#%?B@$A$%/!@e? d"

P 65 2 2

P 65 2 2: string = " !#%?^@$Q$%+!@a? `! _?%&$@X%$c@!- ?b"

P b a 2

P b a 2: string = " !#$%#(,#*)#"

P c a 21

P c a 21: string = " !#$%+(%#*!+"

P c c 2

P c c 2: string = " !#$%# %+$!+"

P m a 2

P m a 2: string = " !#$%#(%#*!#"

P m c 21

P m c 21: string = " !#$%+ %+$!#"

P m m 2

P m m 2: string = " !#$%# %#$!#"

P m n 21

P m n 21: string = " !#*%+(%+$!#"

P n a 21

P n a 21: string = " !#$%+(,#*)+"

P n c 2

P n c 2: string = " !#$%# ,+$)+"

P n n 2

P n n 2: string = " !#$%#(,+*)+"

R -3

R -3: string = " !## !!# $%&&$%%&$"

R -3 2/c

R -3 2/c: string = " !## !!# 102021210$%&&$%%&$'././'/'."

R -3 2/m

R -3 2/m: string = " !## !!# %$&$&%&%$$%&&$%%&$! # #!#! "

R 3

R 3: string = " !## !!# "

R 3 2

R 3 2: string = " !## !!# %$&$&%&%$"

R 3 c

R 3 c: string = " !## !!# '././'/'."

R 3 m

R 3 m: string = " !## !!# ! # #!#! "

Const EntityTypeString

EntityTypeString: keyof object

macrolide

macrolide: number = MacrolideEntity

non-polymer

non-polymer: number = NonPolymerEntity

polymer

polymer: number = PolymerEntity

water

water: number = WaterEntity

Const HelixTypes

HelixTypes: object
: string = "h"

1

1: string = "h"

10

10: string = "h"

2

2: string = "h"

3

3: string = "i"

4

4: string = "h"

5

5: string = "g"

6

6: string = "h"

7

7: string = "h"

8

8: string = "h"

9

9: string = "h"

Const ImageDefaultParameters

ImageDefaultParameters: object

Image parameter object.

typedef

{Object} ImageParameters - image generation parameters

property

{Boolean} trim - trim the image

property

{Integer} factor - scaling factor to apply to the viewer canvas

property

{Boolean} antialias - antialias the image

property

{Boolean} transparent - transparent image background

antialias

antialias: boolean = false

factor

factor: number = 1

onProgress

onProgress: undefined | Function = undefined as Function|undefined

transparent

transparent: boolean = false

trim

trim: boolean = false

Const KeyActionPresets

KeyActionPresets: object

default

default: Object[] = [[ 'i', KeyActions.toggleSpin ],[ 'k', KeyActions.toggleRock ],[ 'p', KeyActions.toggleAnimations ],[ 'a', KeyActions.toggleAntialiasing ],[ 'r', KeyActions.autoView ]] as KeyActionPreset

Const LabelFactoryTypes

LabelFactoryTypes: object
: string = ""

atom

atom: string = "atom name + index"

atomindex

atomindex: string = "atom index"

atomname

atomname: string = "atom name"

bfactor

bfactor: string = "b-factor"

element

element: string = "element"

format

format: string = "format"

occupancy

occupancy: string = "occupancy"

qualified

qualified: string = "qualified name"

res

res: string = "one letter code + no"

residue

residue: string = "[residue name] + no + inscode"

resname

resname: string = "residue name"

resno

resno: string = "residue no"

serial

serial: string = "serial"

text

text: string = "text"

Const Log

Log: object

error

error: any = Function.prototype.bind.call(console.error, console)

info

info: any = Function.prototype.bind.call(console.info, console)

log

log: any = Function.prototype.bind.call(console.log, console)

time

time: any = Function.prototype.bind.call(console.time, console)

timeEnd

timeEnd: any = Function.prototype.bind.call(console.timeEnd, console)

warn

warn: any = Function.prototype.bind.call(console.warn, console)

Let MeasurementDefaultParams

MeasurementDefaultParams: object

arcVisible

arcVisible: boolean = true

color

color: string = "green"

labelAttachment

labelAttachment: string = "bottom-center"

labelBorder

labelBorder: boolean = true

labelBorderColor

labelBorderColor: string = "lightgrey"

labelBorderWidth

labelBorderWidth: number = 0.25

labelColor

labelColor: string = "grey"

labelSize

labelSize: number = 0.7

labelUnit

labelUnit: string = "angstrom"

labelYOffset

labelYOffset: number = 0.1

labelZOffset

labelZOffset: number = 0.5

lineOpacity

lineOpacity: number = 0.8

linewidth

linewidth: number = 5

opacity

opacity: number = 0.6

planeVisible

planeVisible: boolean = false

Const MouseActionPresets

MouseActionPresets: object

astexviewer

astexviewer: Object[] = [[ 'drag-left', MouseActions.rotateDrag ],[ 'drag-ctrl-left', MouseActions.panDrag ],[ 'drag-shift-left', MouseActions.zoomDrag ],[ 'scroll', MouseActions.focusScroll ],[ 'clickPick-middle', MouseActions.movePick ],[ 'hoverPick', MouseActions.tooltipPick ]] as MouseActionPreset

coot

coot: Object[] = [[ 'scroll', MouseActions.isolevelScroll ],[ 'drag-left', MouseActions.rotateDrag ],[ 'drag-middle', MouseActions.panDrag ],[ 'drag-ctrl-left', MouseActions.panDrag ],[ 'drag-right', MouseActions.zoomFocusDrag ],[ 'drag-ctrl-right', MouseActions.focusScroll ],[ 'clickPick-middle', MouseActions.movePick ],[ 'hoverPick', MouseActions.tooltipPick ]] as MouseActionPreset

default

default: Object[] = [[ 'scroll', MouseActions.zoomScroll ],[ 'scroll-shift', MouseActions.focusScroll ],[ 'scroll-ctrl', MouseActions.isolevelScroll ],[ 'scroll-shift-ctrl', MouseActions.zoomFocusScroll ],[ 'drag-left', MouseActions.rotateDrag ],[ 'drag-right', MouseActions.panDrag ],[ 'drag-ctrl-left', MouseActions.panDrag ],[ 'drag-ctrl-right', MouseActions.zRotateDrag ],[ 'drag-shift-left', MouseActions.zoomDrag ],[ 'drag-middle', MouseActions.zoomFocusDrag ],[ 'drag-ctrl-shift-right', MouseActions.panComponentDrag ],[ 'drag-ctrl-shift-left', MouseActions.rotateComponentDrag ],[ 'clickPick-right', MouseActions.measurePick ],[ 'clickPick-ctrl-left', MouseActions.measurePick ],[ 'clickPick-middle', MouseActions.movePick ],[ 'clickPick-left', MouseActions.movePick ],[ 'hoverPick', MouseActions.tooltipPick ]] as MouseActionPreset

pymol

pymol: Object[] = [[ 'drag-left', MouseActions.rotateDrag ],[ 'drag-middle', MouseActions.panDrag ],[ 'drag-right', MouseActions.zoomDrag ],[ 'drag-shift-right', MouseActions.focusScroll ],[ 'clickPick-ctrl+shift-middle', MouseActions.movePick ],[ 'hoverPick', MouseActions.tooltipPick ]] as MouseActionPreset

Const OuterShellElectronCounts

OuterShellElectronCounts: object

1

1: number = 1

10

10: number = 8

100

100: number = 12

101

101: number = 13

102

102: number = 14

103

103: number = 15

104

104: number = 2

105

105: number = 2

106

106: number = 2

107

107: number = 2

108

108: number = 2

109

109: number = 2

11

11: number = 1

110

110: number = 2

111

111: number = 2

112

112: number = 2

113

113: number = 3

114

114: number = 4

115

115: number = 5

116

116: number = 6

117

117: number = 7

118

118: number = 8

12

12: number = 2

13

13: number = 3

14

14: number = 4

15

15: number = 5

16

16: number = 6

17

17: number = 7

18

18: number = 8

19

19: number = 1

2

2: number = 2

20

20: number = 2

21

21: number = 3

22

22: number = 4

23

23: number = 5

24

24: number = 6

25

25: number = 7

26

26: number = 8

27

27: number = 9

28

28: number = 10

29

29: number = 11

3

3: number = 1

30

30: number = 2

31

31: number = 3

32

32: number = 4

33

33: number = 5

34

34: number = 6

35

35: number = 7

36

36: number = 8

37

37: number = 1

38

38: number = 2

39

39: number = 3

4

4: number = 2

40

40: number = 4

41

41: number = 5

42

42: number = 6

43

43: number = 7

44

44: number = 8

45

45: number = 9

46

46: number = 10

47

47: number = 11

48

48: number = 2

49

49: number = 3

5

5: number = 3

50

50: number = 4

51

51: number = 5

52

52: number = 6

53

53: number = 7

54

54: number = 8

55

55: number = 1

56

56: number = 2

57

57: number = 3

58

58: number = 4

59

59: number = 3

6

6: number = 4

60

60: number = 4

61

61: number = 5

62

62: number = 6

63

63: number = 7

64

64: number = 8

65

65: number = 9

66

66: number = 10

67

67: number = 11

68

68: number = 12

69

69: number = 13

7

7: number = 5

70

70: number = 14

71

71: number = 15

72

72: number = 4

73

73: number = 5

74

74: number = 6

75

75: number = 7

76

76: number = 8

77

77: number = 9

78

78: number = 10

79

79: number = 11

8

8: number = 6

80

80: number = 2

81

81: number = 3

82

82: number = 4

83

83: number = 5

84

84: number = 6

85

85: number = 7

86

86: number = 8

87

87: number = 1

88

88: number = 2

89

89: number = 3

9

9: number = 7

90

90: number = 4

91

91: number = 3

92

92: number = 4

93

93: number = 5

94

94: number = 6

95

95: number = 7

96

96: number = 8

97

97: number = 9

98

98: number = 10

99

99: number = 11

Const RadiusFactoryTypes

RadiusFactoryTypes: object
: string = ""

bfactor

bfactor: string = "by bfactor"

covalent

covalent: string = "by covalent radius"

data

data: string = "data"

size

size: string = "size"

sstruc

sstruc: string = "by secondary structure"

vdw

vdw: string = "by vdW radius"

Const ResidueColors

ResidueColors: object

A

A: number = 14423100

ALA

ALA: number = 9240460

ARG

ARG: number = 124

ASH

ASH: number = 16711935

ASN

ASN: number = 16743536

ASP

ASP: number = 10485826

ASX

ASX: number = 16711935

C

C: number = 16766720

CYS

CYS: number = 16777072

D

D: number = 35723

DA

DA: number = 14423100

DC

DC: number = 16766720

DD

DD: number = 35723

DG

DG: number = 3329330

DI

DI: number = 10145074

DT

DT: number = 4286945

DU

DU: number = 4251856

DX

DX: number = 8190976

G

G: number = 3329330

GLH

GLH: number = 16711935

GLN

GLN: number = 16731212

GLU

GLU: number = 6684672

GLX

GLX: number = 16711935

GLY

GLY: number = 16777215

HIS

HIS: number = 7368959

I

I: number = 10145074

ILE

ILE: number = 19456

LEU

LEU: number = 4546117

LYS

LYS: number = 4671416

MET

MET: number = 12099650

PHE

PHE: number = 5459026

PRO

PRO: number = 5395026

SER

SER: number = 16740418

T

T: number = 4286945

THR

THR: number = 12078080

TRP

TRP: number = 5195264

TYR

TYR: number = 9203788

U

U: number = 4251856

VAL

VAL: number = 16747775

X

X: number = 8190976

Const ResidueHydrophobicity

ResidueHydrophobicity: object

ALA

ALA: Object = [ 0.17, 0.50, 0.33 ]

ARG

ARG: Object = [ 0.81, 1.81, 1.00 ]

ASH

ASH: Object = [ -0.07, 0.43, 0.50 ]

ASN

ASN: Object = [ 0.42, 0.85, 0.43 ]

ASP

ASP: Object = [ 1.23, 3.64, 2.41 ]

CYS

CYS: Object = [ -0.24, -0.02, 0.22 ]

GLH

GLH: Object = [ -0.01, 0.11, 0.12 ]

GLN

GLN: Object = [ 0.58, 0.77, 0.19 ]

GLU

GLU: Object = [ 2.02, 3.63, 1.61 ]

GLY

GLY: Object = [ 0.01, 1.15, 1.14 ]

HIS

HIS: Object = [ 0.17, 0.11, -0.06 ]

ILE

ILE: Object = [ -0.31, -1.12, -0.81 ]

LEU

LEU: Object = [ -0.56, -1.25, -0.69 ]

LYS

LYS: Object = [ 0.99, 2.80, 1.81 ]

MET

MET: Object = [ -0.23, -0.67, -0.44 ]

PHE

PHE: Object = [ -1.13, -1.71, -0.58 ]

PRO

PRO: Object = [ 0.45, 0.14, -0.31 ]

SER

SER: Object = [ 0.13, 0.46, 0.33 ]

THR

THR: Object = [ 0.14, 0.25, 0.11 ]

TRP

TRP: Object = [ -1.85, -2.09, -0.24 ]

TYR

TYR: Object = [ -0.94, -0.71, 0.23 ]

VAL

VAL: Object = [ 0.07, -0.46, -0.53 ]

Const ResidueRadii

ResidueRadii: object

004

004: number = 4.33

01W

01W: number = 8.55

02K

02K: number = 2.94

02V

02V: number = 4.83

02Y

02Y: number = 4.77

03E

03E: number = 3.38

03Y

03Y: number = 2.6

07O

07O: number = 8.05

0A0

0A0: number = 3.45

0A1

0A1: number = 7.1

0A8

0A8: number = 8.1

0A9

0A9: number = 5.17

0AF

0AF: number = 6.72

0AH

0AH: number = 5.78

0AK

0AK: number = 6.11

0AR

0AR: number = 8.46

0BN

0BN: number = 7

0CS

0CS: number = 4.07

0FL

0FL: number = 2.76

0LF

0LF: number = 9.96

0QL

0QL: number = 5.72

0TD

0TD: number = 3.62

0WZ

0WZ: number = 7.61

11Q

11Q: number = 4.85

11W

11W: number = 14.39

143

143: number = 8.22

175

175: number = 5.64

192

192: number = 2.44

193

193: number = 7.38

19W

19W: number = 3.94

1AC

1AC: number = 2.42

1C3

1C3: number = 7.43

1E3

1E3: number = 8.71

1MH

1MH: number = 5.04

1OP

1OP: number = 11.55

1PA

1PA: number = 8.07

1TQ

1TQ: number = 8.58

1TY

1TY: number = 8.84

1U8

1U8: number = 3.62

1VR

1VR: number = 3.89

1X6

1X6: number = 6.84

200

200: number = 6.89

22G

22G: number = 8.8

23F

23F: number = 5.27

23P

23P: number = 5.42

23S

23S: number = 6.09

26B

26B: number = 8.39

28X

28X: number = 7.84

2AG

2AG: number = 3.7

2AS

2AS: number = 3.57

2CO

2CO: number = 4.45

2FM

2FM: number = 5.54

2HF

2HF: number = 5.52

2JC

2JC: number = 2.97

2JF

2JF: number = 9.13

2JG

2JG: number = 5.67

2JH

2JH: number = 4.56

2ML

2ML: number = 3.86

2MR

2MR: number = 7.35

2MT

2MT: number = 3.67

2OR

2OR: number = 6.91

2P0

2P0: number = 8.52

2QY

2QY: number = 6.58

2QZ

2QZ: number = 2.52

2R1

2R1: number = 3.78

2R3

2R3: number = 6.94

2RX

2RX: number = 4.91

2TY

2TY: number = 8.65

2VA

2VA: number = 9.82

2XA

2XA: number = 8.25

2ZC

2ZC: number = 4.29

30V

30V: number = 8.53

31Q

31Q: number = 10.46

32L

32L: number = 6.75

32S

32S: number = 5.68

32T

32T: number = 5.72

3A5

3A5: number = 5.37

3AH

3AH: number = 9.11

3AR

3AR: number = 7.86

3CF

3CF: number = 6.47

3EG

3EG: number = 3.66

3FG

3FG: number = 4.96

3GL

3GL: number = 4.84

3PX

3PX: number = 4.7

3TY

3TY: number = 8.42

3YM

3YM: number = 6.52

4AW

4AW: number = 6.22

4BF

4BF: number = 6.92

4CF

4CF: number = 7.72

4CY

4CY: number = 4.6

4DB

4DB: number = 9.73

4DP

4DP: number = 9.28

4FB

4FB: number = 3.08

4FW

4FW: number = 6.1

4HL

4HL: number = 8.79

4HT

4HT: number = 6.03

4IK

4IK: number = 11.81

4IN

4IN: number = 6.31

4PH

4PH: number = 6.79

56A

56A: number = 13.01

5CS

5CS: number = 8.34

5CW

5CW: number = 7.21

5OH

5OH: number = 4.7

5PG

5PG: number = 5.69

6CL

6CL: number = 6.47

6CW

6CW: number = 7.56

6FL

6FL: number = 4.85

6HN

6HN: number = 7.34

7JA

7JA: number = 9.46

7MN

7MN: number = 7.34

8SP

8SP: number = 14.26

9AT

9AT: number = 2.47

9DN

9DN: number = 9.31

9DS

9DS: number = 9.29

9NE

9NE: number = 9.77

9NF

9NF: number = 8.93

9NR

9NR: number = 9.33

9NV

9NV: number = 8.99

A5N

A5N: number = 5.21

A8E

A8E: number = 3.76

AA4

AA4: number = 4.47

AAR

AAR: number = 6.39

ABA

ABA: number = 2.55

AC5

AC5: number = 2.44

AEI

AEI: number = 6.34

AGM

AGM: number = 6.57

AGQ

AGQ: number = 7.79

AGT

AGT: number = 9.04

AHB

AHB: number = 3.47

AHH

AHH: number = 5.06

AHP

AHP: number = 5.26

AIB

AIB: number = 2.4

ALA

ALA: number = 2.38

ALC

ALC: number = 5.26

ALN

ALN: number = 6.16

ALO

ALO: number = 2.57

ALT

ALT: number = 2.72

ALY

ALY: number = 7.38

APK

APK: number = 8.79

AR4

AR4: number = 8.42

ARG

ARG: number = 6.33

ARM

ARM: number = 6.86

ARO

ARO: number = 7.35

ARV

ARV: number = 7.59

AS9

AS9: number = 4.1

ASA

ASA: number = 3.64

ASB

ASB: number = 5.59

ASL

ASL: number = 5.36

ASN

ASN: number = 3.54

ASP

ASP: number = 3.55

ASX

ASX: number = 3.54

AYA

AYA: number = 3.65

AZH

AZH: number = 5.36

AZK

AZK: number = 6.03

AZS

AZS: number = 5.61

AZY

AZY: number = 7.37

B27

B27: number = 2.78

B3A

B3A: number = 2.48

B3E

B3E: number = 5.4

B3K

B3K: number = 5.89

B3L

B3L: number = 4.96

B3M

B3M: number = 5.07

B3Q

B3Q: number = 4.48

B3T

B3T: number = 3.34

B3U

B3U: number = 6.06

B3X

B3X: number = 4.38

B3Y

B3Y: number = 7.45

BB6

BB6: number = 2.62

BB7

BB7: number = 4.56

BB8

BB8: number = 5.14

BB9

BB9: number = 2.56

BBC

BBC: number = 6.42

BCS

BCS: number = 8.03

BCX

BCX: number = 2.99

BFD

BFD: number = 5.33

BG1

BG1: number = 8.02

BH2

BH2: number = 3.51

BHD

BHD: number = 3.48

BIF

BIF: number = 9.63

BIL

BIL: number = 4.7

BL2

BL2: number = 5.82

BMT

BMT: number = 6.37

BPE

BPE: number = 7.24

BTK

BTK: number = 8.59

BTR

BTR: number = 7.98

BUC

BUC: number = 5.8

C1X

C1X: number = 11.63

C3Y

C3Y: number = 5.24

C4R

C4R: number = 5.63

C5C

C5C: number = 5.35

C6C

C6C: number = 6.42

CAB

CAB: number = 4.19

CAF

CAF: number = 5.46

CAS

CAS: number = 5.35

CCS

CCS: number = 4.58

CDE

CDE: number = 2.51

CDV

CDV: number = 3.72

CGA

CGA: number = 7.91

CGU

CGU: number = 4.71

CHG

CHG: number = 4.2

CHP

CHP: number = 5.75

CLG

CLG: number = 13.62

CLH

CLH: number = 7.13

CME

CME: number = 5.86

CMH

CMH: number = 5.3

CML

CML: number = 6.16

CMT

CMT: number = 3.54

CPC

CPC: number = 2.65

CS1

CS1: number = 7.23

CS3

CS3: number = 8.24

CS4

CS4: number = 11.21

CSA

CSA: number = 5.7

CSB

CSB: number = 3.51

CSD

CSD: number = 3.95

CSJ

CSJ: number = 7.51

CSK

CSK: number = 3.91

CSO

CSO: number = 3.53

CSP

CSP: number = 5.26

CSR

CSR: number = 5.42

CSS

CSS: number = 3.61

CSU

CSU: number = 4.89

CSW

CSW: number = 3.68

CSX

CSX: number = 3.47

CSZ

CSZ: number = 3.6

CTE

CTE: number = 7.27

CTH

CTH: number = 3.45

CXM

CXM: number = 4.69

CY0

CY0: number = 11.98

CY1

CY1: number = 6.59

CY3

CY3: number = 2.79

CY4

CY4: number = 4.57

CYD

CYD: number = 8.55

CYF

CYF: number = 13.54

CYG

CYG: number = 8.03

CYJ

CYJ: number = 11.64

CYQ

CYQ: number = 5.67

CYR

CYR: number = 10.33

CYS

CYS: number = 2.78

CYW

CYW: number = 4.65

CZ2

CZ2: number = 5.16

CZZ

CZZ: number = 5.14

D4P

D4P: number = 5.66

DA2

DA2: number = 7.79

DAB

DAB: number = 3.48

DAH

DAH: number = 6.47

DAM

DAM: number = 2.49

DBU

DBU: number = 2.49

DBY

DBY: number = 6.46

DBZ

DBZ: number = 7.08

DDE

DDE: number = 6.86

DDZ

DDZ: number = 2.52

DFI

DFI: number = 3.93

DFO

DFO: number = 3.94

DHA

DHA: number = 2.32

DHL

DHL: number = 2.69

DIR

DIR: number = 5.8

DLS

DLS: number = 6.84

DM0

DM0: number = 6.99

DMH

DMH: number = 4.92

DMK

DMK: number = 3.52

DMT

DMT: number = 6.67

DNP

DNP: number = 2.45

DNS

DNS: number = 8.79

DNW

DNW: number = 7.97

DO2

DO2: number = 4.44

DOA

DOA: number = 12.33

DON

DON: number = 6.72

DPL

DPL: number = 3.58

DPP

DPP: number = 2.51

DPQ

DPQ: number = 6.54

DYS

DYS: number = 7.87

ECC

ECC: number = 4.79

ECX

ECX: number = 5.51

EFC

EFC: number = 5.28

ELY

ELY: number = 7.42

EME

EME: number = 4.69

ESB

ESB: number = 6.69

ESC

ESC: number = 5.65

ETA

ETA: number = 2.4

EXY

EXY: number = 7.37

F2F

F2F: number = 6.25

F2Y

F2Y: number = 6.2

FAK

FAK: number = 9.8

FC0

FC0: number = 5.18

FCL

FCL: number = 6.25

FDL

FDL: number = 9.49

FGL

FGL: number = 2.56

FGP

FGP: number = 4.34

FH7

FH7: number = 6.99

FHL

FHL: number = 9.75

FHO

FHO: number = 6.75

FLA

FLA: number = 2.4

FLE

FLE: number = 6.17

FLT

FLT: number = 9.65

FME

FME: number = 4.52

FOE

FOE: number = 8.17

FP9

FP9: number = 3.03

FPK

FPK: number = 3.08

FPR

FPR: number = 8.85

FRD

FRD: number = 5.05

FT6

FT6: number = 7.5

FTR

FTR: number = 6.08

FTY

FTY: number = 9.07

FVA

FVA: number = 2.9

FZN

FZN: number = 24.42

G8M

G8M: number = 3.57

GAU

GAU: number = 4.67

GEE

GEE: number = 4.76

GFT

GFT: number = 8.18

GHG

GHG: number = 4.83

GL3

GL3: number = 2.72

GLJ

GLJ: number = 3.7

GLN

GLN: number = 4.46

GLU

GLU: number = 4.49

GLX

GLX: number = 4.52

GLY

GLY: number = 2.37

GLZ

GLZ: number = 2.39

GMA

GMA: number = 4.4

GME

GME: number = 4.66

GNC

GNC: number = 4.6

GND

GND: number = 6.67

GPL

GPL: number = 10.77

GSU

GSU: number = 11.81

GVL

GVL: number = 9.6

H14

H14: number = 5.27

H5M

H5M: number = 3.61

HAR

HAR: number = 7.55

HBN

HBN: number = 8.8

HCL

HCL: number = 4.96

HCM

HCM: number = 5.53

HCS

HCS: number = 4.09

HFA

HFA: number = 5.14

HG7

HG7: number = 6.8

HGL

HGL: number = 8.07

HHI

HHI: number = 4.58

HHK

HHK: number = 5.11

HIA

HIA: number = 4.64

HIC

HIC: number = 5.76

HIP

HIP: number = 5.47

HIQ

HIQ: number = 7.98

HIS

HIS: number = 4.52

HL2

HL2: number = 3.75

HLU

HLU: number = 3.99

HLX

HLX: number = 4.98

HMR

HMR: number = 5.09

HNC

HNC: number = 10.41

HOX

HOX: number = 6.61

HPE

HPE: number = 6.63

HQA

HQA: number = 7.25

HR7

HR7: number = 6.98

HRG

HRG: number = 7.36

HRP

HRP: number = 5.46

HS8

HS8: number = 7.4

HS9

HS9: number = 4.71

HSL

HSL: number = 2.46

HSO

HSO: number = 4.56

HT7

HT7: number = 6.82

HTI

HTI: number = 7.8

HTR

HTR: number = 6.48

HVA

HVA: number = 2.58

HYP

HYP: number = 2.25

HZP

HZP: number = 3.12

I2M

I2M: number = 3.13

I58

I58: number = 6.73

IAM

IAM: number = 8.88

IAR

IAR: number = 6.77

ICY

ICY: number = 7.76

IEL

IEL: number = 7.07

IGL

IGL: number = 5.52

IIL

IIL: number = 3.81

ILE

ILE: number = 3.65

ILM

ILM: number = 3.84

ILX

ILX: number = 4.99

IML

IML: number = 3.74

IOR

IOR: number = 7.23

IPG

IPG: number = 2.91

IT1

IT1: number = 9.75

IYR

IYR: number = 6.46

IZO

IZO: number = 4.47

JJJ

JJJ: number = 7.5

JJK

JJK: number = 7.43

JJL

JJL: number = 8.3

KBE

KBE: number = 5.64

KCX

KCX: number = 7.28

KGC

KGC: number = 9.88

KOR

KOR: number = 10.1

KPI

KPI: number = 9.79

KPY

KPY: number = 10.17

KST

KST: number = 11.58

KWS

KWS: number = 5.09

KYN

KYN: number = 6.18

KYQ

KYQ: number = 9.75

L3O

L3O: number = 3.89

LA2

LA2: number = 14.07

LAA

LAA: number = 3.23

LAL

LAL: number = 2.41

LBY

LBY: number = 7.75

LCK

LCK: number = 9.81

LDH

LDH: number = 7.06

LE1

LE1: number = 2.72

LED

LED: number = 4.34

LEF

LEF: number = 4.37

LEN

LEN: number = 3.82

LET

LET: number = 11.29

LEU

LEU: number = 3.83

LGY

LGY: number = 11.71

LHC

LHC: number = 7.75

LLO

LLO: number = 10.13

LLP

LLP: number = 10.22

LLY

LLY: number = 8.71

LME

LME: number = 3.99

LMQ

LMQ: number = 4.69

LP6

LP6: number = 8.58

LPD

LPD: number = 2.48

LPG

LPG: number = 2.39

LPL

LPL: number = 7.51

LSO

LSO: number = 10.58

LTA

LTA: number = 6.57

LVG

LVG: number = 3.01

LVN

LVN: number = 2.89

LWY

LWY: number = 4.12

LYF

LYF: number = 12.19

LYH

LYH: number = 5.13

LYN

LYN: number = 4.8

LYO

LYO: number = 4.71

LYR

LYR: number = 18.28

LYS

LYS: number = 5.54

LYX

LYX: number = 13.36

LYZ

LYZ: number = 1.76

M0H

M0H: number = 4.83

M2L

M2L: number = 6.15

M2S

M2S: number = 5.28

M3L

M3L: number = 7.12

M3R

M3R: number = 7.18

MAA

MAA: number = 2.4

MBQ

MBQ: number = 9.55

MCG

MCG: number = 6.46

MCL

MCL: number = 9.73

MCS

MCS: number = 7.56

MD3

MD3: number = 8.41

MD5

MD5: number = 9.33

MD6

MD6: number = 6.44

MDF

MDF: number = 4.95

MDH

MDH: number = 2.58

MDO

MDO: number = 5.03

ME0

ME0: number = 4.52

MEA

MEA: number = 4.95

MEN

MEN: number = 4.33

MEQ

MEQ: number = 5.13

MET

MET: number = 4.49

MF3

MF3: number = 6.37

MGG

MGG: number = 7.34

MGN

MGN: number = 4.84

MH6

MH6: number = 1.72

MHL

MHL: number = 3.92

MHO

MHO: number = 4.89

MHS

MHS: number = 4.51

MHU

MHU: number = 7.51

MHV

MHV: number = 3.6

MHW

MHW: number = 2.74

MIR

MIR: number = 6.54

MIS

MIS: number = 6.32

MK8

MK8: number = 4.76

MKD

MKD: number = 6.42

ML3

ML3: number = 6.26

MLE

MLE: number = 3.87

MLL

MLL: number = 3.76

MLY

MLY: number = 6.88

MLZ

MLZ: number = 6.8

MME

MME: number = 4.99

MMO

MMO: number = 6.53

MNL

MNL: number = 4.9

MOD

MOD: number = 12.62

MP4

MP4: number = 5.86

MP8

MP8: number = 3.75

MPH

MPH: number = 5.29

MPJ

MPJ: number = 5.07

MPQ

MPQ: number = 4.2

MSA

MSA: number = 2.73

MSE

MSE: number = 4.62

MSL

MSL: number = 5.21

MSO

MSO: number = 4.96

MSP

MSP: number = 13.11

MT2

MT2: number = 5.51

MTY

MTY: number = 5.46

MVA

MVA: number = 2.56

MYK

MYK: number = 19.47

MYN

MYN: number = 4.71

N10

N10: number = 8.96

N2C

N2C: number = 3.55

NAL

NAL: number = 7.22

NB8

NB8: number = 11.98

NBQ

NBQ: number = 9.82

NC1

NC1: number = 11.4

NCB

NCB: number = 3.45

NCY

NCY: number = 2.91

NEP

NEP: number = 6.94

NFA

NFA: number = 5.04

NIY

NIY: number = 6.81

NLE

NLE: number = 4.67

NLO

NLO: number = 4.8

NLP

NLP: number = 4.81

NLQ

NLQ: number = 4.65

NLY

NLY: number = 6.37

NMC

NMC: number = 4.23

NMM

NMM: number = 8.25

NNH

NNH: number = 6.86

NOT

NOT: number = 7.15

NPH

NPH: number = 11.66

NPI

NPI: number = 6.9

NRG

NRG: number = 8.35

NVA

NVA: number = 3.76

NYB

NYB: number = 6.07

NYS

NYS: number = 8.1

NZH

NZH: number = 7.66

O12

O12: number = 14.08

OAS

OAS: number = 4.8

OBF

OBF: number = 3.64

OBS

OBS: number = 11.71

OCS

OCS: number = 3.94

OCY

OCY: number = 5

OHI

OHI: number = 5.35

OHS

OHS: number = 6.98

OIC

OIC: number = 4.62

OLD

OLD: number = 10.47

OLZ

OLZ: number = 5.32

OMH

OMH: number = 5.26

OMT

OMT: number = 5.07

OMX

OMX: number = 6.15

OMY

OMY: number = 6.11

ONH

ONH: number = 6.14

ONL

ONL: number = 4.83

ORN

ORN: number = 4.25

ORQ

ORQ: number = 6.04

OSE

OSE: number = 4.49

OTH

OTH: number = 3.6

OTY

OTY: number = 6.51

OXX

OXX: number = 7.05

OYL

OYL: number = 6.42

OZT

OZT: number = 3.4

P2Q

P2Q: number = 9.8

P2Y

P2Y: number = 2.51

P3Q

P3Q: number = 9.54

PAQ

PAQ: number = 8.77

PAT

PAT: number = 6.05

PBF

PBF: number = 9.75

PCA

PCA: number = 3.48

PCS

PCS: number = 5.05

PE1

PE1: number = 8.01

PEC

PEC: number = 6.54

PF5

PF5: number = 6.28

PFF

PFF: number = 6.31

PFX

PFX: number = 11.84

PG1

PG1: number = 10.67

PHA

PHA: number = 5.11

PHD

PHD: number = 5.35

PHE

PHE: number = 5.06

PHI

PHI: number = 7.12

PHL

PHL: number = 5.17

PLJ

PLJ: number = 3.71

PM3

PM3: number = 8.78

POM

POM: number = 3.6

PPN

PPN: number = 7.24

PR3

PR3: number = 5.12

PR4

PR4: number = 4.52

PR7

PR7: number = 4.66

PRJ

PRJ: number = 5.26

PRK

PRK: number = 9.15

PRO

PRO: number = 2.41

PRR

PRR: number = 5.58

PRS

PRS: number = 2.63

PRV

PRV: number = 4.28

PSH

PSH: number = 7.26

PSW

PSW: number = 4.65

PTH

PTH: number = 8.35

PTM

PTM: number = 8.74

PTR

PTR: number = 8.64

PVH

PVH: number = 4.58

PXU

PXU: number = 2.46

PYA

PYA: number = 7.75

PYL

PYL: number = 9.67

PYX

PYX: number = 11.3

QCS

QCS: number = 5.18

QIL

QIL: number = 3.84

QMM

QMM: number = 6.13

QPA

QPA: number = 6.95

QPH

QPH: number = 5.15

R1A

R1A: number = 8.2

R2T

R2T: number = 4.71

R4K

R4K: number = 4.67

RE0

RE0: number = 5.53

RE3

RE3: number = 5.29

RGL

RGL: number = 7.03

RVX

RVX: number = 7.01

S12

S12: number = 18.57

S1H

S1H: number = 19.21

S2C

S2C: number = 7.54

S2P

S2P: number = 4.81

SAC

SAC: number = 3.49

SAH

SAH: number = 11.7

SAR

SAR: number = 2.48

SBL

SBL: number = 8.96

SCH

SCH: number = 4.46

SCS

SCS: number = 5.48

SCY

SCY: number = 4.53

SD4

SD4: number = 4.57

SDP

SDP: number = 6.07

SE7

SE7: number = 4.19

SEB

SEB: number = 8.18

SEC

SEC: number = 2.96

SEE

SEE: number = 4.53

SEL

SEL: number = 2.46

SEN

SEN: number = 6.43

SEP

SEP: number = 4.8

SER

SER: number = 2.41

SET

SET: number = 2.46

SFE

SFE: number = 5.01

SGB

SGB: number = 6.88

SIB

SIB: number = 12.41

SIC

SIC: number = 4.81

SLL

SLL: number = 11.53

SLZ

SLZ: number = 5.69

SMC

SMC: number = 3.39

SME

SME: number = 4.8

SMF

SMF: number = 9

SNC

SNC: number = 3.93

SOC

SOC: number = 4.05

SOY

SOY: number = 10.94

SRZ

SRZ: number = 5.27

SUN

SUN: number = 6.73

SVA

SVA: number = 5.46

SVV

SVV: number = 5.09

SVX

SVX: number = 7.04

SVY

SVY: number = 7.1

SVZ

SVZ: number = 6.6

SXE

SXE: number = 6.65

SYS

SYS: number = 3.01

T0I

T0I: number = 7.34

T11

T11: number = 8.58

TA4

TA4: number = 5.55

TBG

TBG: number = 2.58

TCQ

TCQ: number = 8.56

TEF

TEF: number = 8.63

TH5

TH5: number = 4.65

TH6

TH6: number = 2.85

THC

THC: number = 3.8

THO

THO: number = 2.62

THR

THR: number = 2.5

TIH

TIH: number = 5.02

TIS

TIS: number = 4.81

TLY

TLY: number = 8.78

TMD

TMD: number = 6.76

TNR

TNR: number = 6.88

TOQ

TOQ: number = 7.5

TOX

TOX: number = 6.78

TPL

TPL: number = 5.41

TPO

TPO: number = 4.73

TPQ

TPQ: number = 6.48

TQI

TQI: number = 7.68

TQQ

TQQ: number = 7.76

TQZ

TQZ: number = 6.97

TRF

TRF: number = 6.69

TRN

TRN: number = 5.95

TRO

TRO: number = 5.82

TRP

TRP: number = 6.07

TRQ

TRQ: number = 7.36

TRW

TRW: number = 11.8

TRX

TRX: number = 7.27

TS9

TS9: number = 3.92

TSY

TSY: number = 4.26

TTQ

TTQ: number = 7.71

TTS

TTS: number = 9.41

TXY

TXY: number = 6.44

TY2

TY2: number = 6.49

TY5

TY5: number = 10.6

TY8

TY8: number = 7.22

TYB

TYB: number = 6.46

TYI

TYI: number = 6.49

TYJ

TYJ: number = 6.25

TYN

TYN: number = 9.87

TYO

TYO: number = 7.71

TYQ

TYQ: number = 6.43

TYR

TYR: number = 6.38

TYS

TYS: number = 8.59

TYX

TYX: number = 8.31

TYY

TYY: number = 6.54

U2X

U2X: number = 11.54

U3X

U3X: number = 11.7

UAL

UAL: number = 4.68

UF0

UF0: number = 19.72

UGY

UGY: number = 3.7

UN2

UN2: number = 3.22

UNK

UNK: number = 1.64

UU4

UU4: number = 2.49

UU5

UU5: number = 4.98

VAD

VAD: number = 2.56

VAH

VAH: number = 3.88

VAL

VAL: number = 2.51

VLL

VLL: number = 2.54

VLM

VLM: number = 2.51

VMS

VMS: number = 8.82

VOL

VOL: number = 2.55

VR0

VR0: number = 10.51

WFP

WFP: number = 6.07

WLU

WLU: number = 4.24

WPA

WPA: number = 5.11

WRP

WRP: number = 8.16

WVL

WVL: number = 4.69

X2W

X2W: number = 6.6

XCN

XCN: number = 4.57

XPR

XPR: number = 7.68

XSN

XSN: number = 3.47

XW1

XW1: number = 9.36

XX1

XX1: number = 9.92

XXA

XXA: number = 7.34

YCM

YCM: number = 5.32

YCP

YCP: number = 3.01

YNM

YNM: number = 6.39

YOF

YOF: number = 6.44

YPZ

YPZ: number = 9.38

YYA

YYA: number = 7.3

Z3E

Z3E: number = 7.2

Z70

Z70: number = 7.4

ZBZ

ZBZ: number = 7.79

ZCL

ZCL: number = 6.71

ZYJ

ZYJ: number = 11.4

ZYK

ZYK: number = 11.45

ZZD

ZZD: number = 8.16

ZZJ

ZZJ: number = 2.44

ZZU

ZZU: number = 6.94

Const ScaleDefaultParameters

ScaleDefaultParameters: object

domain

domain: number[] = [ 0, 1 ] as number[]

mode

mode: "hcl" | "rgb" | "hsv" | "hsl" | "hsi" | "lab" = 'hcl' as 'rgb'|'hsv'|'hsl'|'hsi'|'lab'|'hcl'

reverse

reverse: boolean = false

scale

scale: string | string[] = 'uniform' as string|string[]

value

value: number = 16777215

Const ShapeDefaultParameters

ShapeDefaultParameters: object

aspectRatio

aspectRatio: number = 1.5

dashedCylinder

dashedCylinder: boolean = false

disableImpostor

disableImpostor: boolean = false

labelParams

labelParams: object = {} as Partial<TextBufferParameters>

Type declaration

lineWidth

lineWidth: number = 2

openEnded

openEnded: boolean = false

pointSize

pointSize: number = 2

radialSegments

radialSegments: number = 50

sizeAttenuation

sizeAttenuation: boolean = false

sphereDetail

sphereDetail: number = 2

useTexture

useTexture: boolean = true

Const SstrucMap

SstrucMap: object

-1

-1: number = ''.charCodeAt(0)

0

0: number = 'i'.charCodeAt(0)

1

1: number = 's'.charCodeAt(0)

2

2: number = 'h'.charCodeAt(0)

3

3: number = 'e'.charCodeAt(0)

4

4: number = 'g'.charCodeAt(0)

5

5: number = 'b'.charCodeAt(0)

6

6: number = 't'.charCodeAt(0)

7

7: number = 'l'.charCodeAt(0)

Const StageDefaultParameters

StageDefaultParameters: object

ambientColor

ambientColor: string | number = 0xdddddd as string|number

ambientIntensity

ambientIntensity: number = 0.2

backgroundColor

backgroundColor: string | number = 'black' as string|number

cameraEyeSep

cameraEyeSep: number = 0.3

cameraFov

cameraFov: number = 40

cameraType

cameraType: "perspective" | "orthographic" | "stereo" = 'perspective' as 'perspective'|'orthographic'|'stereo'

clipDist

clipDist: number = 10

clipFar

clipFar: number = 100

clipNear

clipNear: number = 0

fogFar

fogFar: number = 100

fogNear

fogNear: number = 50

hoverTimeout

hoverTimeout: number = 0

impostor

impostor: boolean = true

lightColor

lightColor: string | number = 0xdddddd as string|number

lightIntensity

lightIntensity: number = 1

mousePreset

mousePreset: "default" | "pymol" | "coot" | "astexviewer" = 'default' as MouseControlPreset

panSpeed

panSpeed: number = 1

quality

quality: "high" | "medium" | "low" | "auto" = 'medium' as RenderQualityType

rotateSpeed

rotateSpeed: number = 2

sampleLevel

sampleLevel: number = 0

tooltip

tooltip: boolean = true

workerDefault

workerDefault: boolean = true

zoomSpeed

zoomSpeed: number = 1.2

Const StructureColors

StructureColors: object

alphaHelix

alphaHelix: number = 16711808

betaStrand

betaStrand: number = 16762880

betaTurn

betaTurn: number = 6324479

carbohydrate

carbohydrate: number = 10921722

coil

coil: number = 16777215

dna

dna: number = 11403518

piHelix

piHelix: number = 6291584

rna

rna: number = 16580962

threeTenHelix

threeTenHelix: number = 10485888

Private Const SymOpCode

SymOpCode: object
file

Symmetry Constants

author

Alexander Rose alexander.rose@weirdbyte.de

: string = "X"

!

!: string = "Y"

#

#: string = "Z"

$

$: string = "-X"

%

%: string = "-Y"

&

&: string = "-Z"

'

': string = "Y+1/2"

(

(: string = "1/2+X"

)

): string = "1/2+Y"

*

*: string = "1/2-X"

+

+: string = "1/2+Z"

,

,: string = "1/2-Y"

-

-: string = "1/2-Z"

.

.: string = "X+1/2"

/

/: string = "Z+1/2"

0

0: string = "-X+1/2"

1

1: string = "-Y+1/2"

2

2: string = "-Z+1/2"

3

3: string = "1/4+X"

4

4: string = "1/4-Y"

5

5: string = "1/4+Z"

6

6: string = "1/4-X"

7

7: string = "1/4+Y"

8

8: string = "3/4-Y"

9

9: string = "3/4+Z"

:

:: string = "3/4+Y"

;

;: string = "3/4+X"

<

<: string = "3/4-X"

=

=: string = "1/4-Z"

>

>: string = "3/4-Z"

?

?: string = "X-Y"

@

@: string = "Y-X"

A

A: string = "Z+1/3"

B

B: string = "Z+2/3"

C

C: string = "X+2/3"

D

D: string = "Y+1/3"

E

E: string = "-Y+2/3"

F

F: string = "X-Y+1/3"

G

G: string = "Y-X+2/3"

H

H: string = "-X+1/3"

I

I: string = "X+1/3"

J

J: string = "Y+2/3"

K

K: string = "-Y+1/3"

L

L: string = "X-Y+2/3"

M

M: string = "Y-X+1/3"

N

N: string = "-X+2/3"

O

O: string = "2/3+X"

P

P: string = "1/3+Y"

Q

Q: string = "1/3+Z"

R

R: string = "2/3-Y"

S

S: string = "1/3+X-Y"

T

T: string = "2/3+Y-X"

U

U: string = "1/3-X"

V

V: string = "2/3-X"

W

W: string = "1/3-Y"

X

X: string = "1/3-Z"

Y

Y: string = "2/3+Y"

Z

Z: string = "1/3+Y-X"

[

[: string = "2/3+X-Y"

]

]: string = "1/3+X"

^

^: string = "2/3+Z"

_

_: string = "2/3-Z"

`

`: string = "5/6+Z"

a

a: string = "1/6+Z"

b

b: string = "5/6-Z"

c

c: string = "1/6-Z"

d

d: string = "Z+5/6"

e

e: string = "Z+1/6"

f

f: string = "Z+1/4"

g

g: string = "+Y"

Const TextAtlasDefaultParams

TextAtlasDefaultParams: object

font

font: "sans-serif" | "monospace" | "serif" = 'sans-serif' as TextFonts

height

height: number = 1024

outline

outline: number = 3

size

size: number = 36

style

style: "normal" | "italic" = 'normal' as TextStyles

variant

variant: "normal" = 'normal' as TextVariants

weight

weight: "normal" | "bold" = 'normal' as TextWeights

width

width: number = 1024

Const TrajectoryPlayerDefaultParameters

TrajectoryPlayerDefaultParameters: object

direction

direction: "forward" | "backward" | "bounce" = 'forward' as TrajectoryPlayerDirection

end

end: number = 0

interpolateStep

interpolateStep: number = 5

interpolateType

interpolateType: "" | "linear" | "spline" = '' as TrajectoryPlayerInterpolateType

mode

mode: "loop" | "once" = 'loop' as TrajectoryPlayerMode

start

start: number = 0

step

step: number = 1

timeout

timeout: number = 50

Const UIStageParameters

UIStageParameters: object

ambientColor

ambientColor: object = ColorParam()

Type declaration

  • type: "color"

ambientIntensity

ambientIntensity: object = NumberParam(2, 10, 0)

Type declaration

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

backgroundColor

backgroundColor: object = ColorParam()

Type declaration

  • type: "color"

cameraEyeSep

cameraEyeSep: object = NumberParam(3, 1.0, 0.01)

Type declaration

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

cameraFov

cameraFov: object = RangeParam(1, 120, 15)

Type declaration

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

cameraType

cameraType: object = SelectParam('perspective', 'orthographic', 'stereo')

Type declaration

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

clipDist

clipDist: object = IntegerParam(200, 0)

Type declaration

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

clipFar

clipFar: object = RangeParam(1, 100, 0)

Type declaration

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

clipNear

clipNear: object = RangeParam(1, 100, 0)

Type declaration

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

fogFar

fogFar: object = RangeParam(1, 100, 0)

Type declaration

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

fogNear

fogNear: object = RangeParam(1, 100, 0)

Type declaration

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

hoverTimeout

hoverTimeout: object = IntegerParam(10000, -1)

Type declaration

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

impostor

impostor: object = BooleanParam()

Type declaration

  • type: "boolean"

lightColor

lightColor: object = ColorParam()

Type declaration

  • type: "color"

lightIntensity

lightIntensity: object = NumberParam(2, 10, 0)

Type declaration

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

mousePreset

mousePreset: object = SelectParam(...Object.keys(MouseActionPresets))

Type declaration

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

panSpeed

panSpeed: object = NumberParam(1, 10, 0)

Type declaration

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

quality

quality: object = SelectParam('auto', 'low', 'medium', 'high')

Type declaration

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

rotateSpeed

rotateSpeed: object = NumberParam(1, 10, 0)

Type declaration

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

sampleLevel

sampleLevel: object = RangeParam(1, 5, -1)

Type declaration

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

tooltip

tooltip: object = BooleanParam()

Type declaration

  • type: "boolean"

workerDefault

workerDefault: object = BooleanParam()

Type declaration

  • type: "boolean"

zoomSpeed

zoomSpeed: object = NumberParam(1, 10, 0)

Type declaration

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

Const Valences

Valences: object

1

1: number[] = [ 1 ]

10

10: number[] = [ 0 ]

11

11: number[] = [ 1 ]

12

12: number[] = [ 2 ]

13

13: number[] = [ 6 ]

14

14: number[] = [ 6 ]

15

15: number[] = [ 3, 5, 7 ]

16

16: number[] = [ 2, 4, 6 ]

17

17: number[] = [ 1 ]

18

18: number[] = [ 0 ]

19

19: number[] = [ 1 ]

2

2: number[] = [ 0 ]

20

20: number[] = [ 2 ]

3

3: number[] = [ 1 ]

31

31: number[] = [ 3 ]

32

32: number[] = [ 4 ]

33

33: number[] = [ 3, 5 ]

34

34: number[] = [ 2, 4, 6 ]

35

35: number[] = [ 1 ]

36

36: number[] = [ 0 ]

37

37: number[] = [ 1 ]

38

38: number[] = [ 2 ]

4

4: number[] = [ 2 ]

49

49: number[] = [ 3 ]

5

5: number[] = [ 3 ]

50

50: number[] = [ 4 ]

51

51: number[] = [ 3, 5 ]

52

52: number[] = [ 2 ]

53

53: number[] = [ 1, 2, 5 ]

54

54: number[] = [ 0, 2 ]

55

55: number[] = [ 1 ]

56

56: number[] = [ 2 ]

6

6: number[] = [ 4 ]

7

7: number[] = [ 3 ]

8

8: number[] = [ 2 ]

81

81: number[] = [ 3 ]

82

82: number[] = [ 4 ]

83

83: number[] = [ 3 ]

84

84: number[] = [ 2 ]

85

85: number[] = [ 1 ]

86

86: number[] = [ 0 ]

87

87: number[] = [ 1 ]

88

88: number[] = [ 2 ]

9

9: number[] = [ 1 ]

Const VdwRadii

VdwRadii: object

1

1: number = 1.1

10

10: number = 1.54

100

100: number = 2

101

101: number = 2

102

102: number = 2

103

103: number = 2

104

104: number = 2

105

105: number = 2

106

106: number = 2

107

107: number = 2

108

108: number = 2

109

109: number = 2

11

11: number = 2.27

110

110: number = 2

111

111: number = 2

112

112: number = 2

113

113: number = 2

114

114: number = 2

115

115: number = 2

116

116: number = 2

117

117: number = 2

118

118: number = 2

12

12: number = 1.73

13

13: number = 1.84

14

14: number = 2.1

15

15: number = 1.8

16

16: number = 1.8

17

17: number = 1.75

18

18: number = 1.88

19

19: number = 2.75

2

2: number = 1.4

20

20: number = 2.31

21

21: number = 2.3

22

22: number = 2.15

23

23: number = 2.05

24

24: number = 2.05

25

25: number = 2.05

26

26: number = 2.05

27

27: number = 2

28

28: number = 2

29

29: number = 2

3

3: number = 1.81

30

30: number = 2.1

31

31: number = 1.87

32

32: number = 2.11

33

33: number = 1.85

34

34: number = 1.9

35

35: number = 1.83

36

36: number = 2.02

37

37: number = 3.03

38

38: number = 2.49

39

39: number = 2.4

4

4: number = 1.53

40

40: number = 2.3

41

41: number = 2.15

42

42: number = 2.1

43

43: number = 2.05

44

44: number = 2.05

45

45: number = 2

46

46: number = 2.05

47

47: number = 2.1

48

48: number = 2.2

49

49: number = 2.2

5

5: number = 1.92

50

50: number = 1.93

51

51: number = 2.17

52

52: number = 2.06

53

53: number = 1.98

54

54: number = 2.16

55

55: number = 3.43

56

56: number = 2.68

57

57: number = 2.5

58

58: number = 2.48

59

59: number = 2.47

6

6: number = 1.7

60

60: number = 2.45

61

61: number = 2.43

62

62: number = 2.42

63

63: number = 2.4

64

64: number = 2.38

65

65: number = 2.37

66

66: number = 2.35

67

67: number = 2.33

68

68: number = 2.32

69

69: number = 2.3

7

7: number = 1.55

70

70: number = 2.28

71

71: number = 2.27

72

72: number = 2.25

73

73: number = 2.2

74

74: number = 2.1

75

75: number = 2.05

76

76: number = 2

77

77: number = 2

78

78: number = 2.05

79

79: number = 2.1

8

8: number = 1.52

80

80: number = 2.05

81

81: number = 1.96

82

82: number = 2.02

83

83: number = 2.07

84

84: number = 1.97

85

85: number = 2.02

86

86: number = 2.2

87

87: number = 3.48

88

88: number = 2.83

89

89: number = 2

9

9: number = 1.47

90

90: number = 2.4

91

91: number = 2

92

92: number = 2.3

93

93: number = 2

94

94: number = 2

95

95: number = 2

96

96: number = 2

97

97: number = 2

98

98: number = 2

99

99: number = 2

Const bondTypes

bondTypes: object

1

1: number = 1

2

2: number = 2

3

3: number = 3

am

am: number = 1

ar

ar: number = 1

du

du: number = 1

nc

nc: number = 0

un

un: number = 1

Const itemSize

itemSize: object

c

c: number = 3

f

f: number = 1

v2

v2: number = 2

v3

v3: number = 3

messages

messages: object

-1

-1: string = "file error"

-2

-2: string = "stream error"

-3

-3: string = "data error"

-4

-4: string = "insufficient memory"

-5

-5: string = "buffer error"

-6

-6: string = "incompatible version"

0

0: string = ""

1

1: string = "stream end"

2

2: string = "need dictionary"

Const partialCharges

partialCharges: object

ARG

ARG: object

CD

CD: number = 0.1

CZ

CZ: number = 0.5

NE

NE: number = -0.1

ASN

ASN: object

CG

CG: number = 0.55

OD1

OD1: number = -0.55

ASP

ASP: object

CB

CB: number = -0.16

CG

CG: number = 0.36

OD1

OD1: number = -0.6

OD2

OD2: number = -0.6

CYS

CYS: object

CB

CB: number = 0.19

SG

SG: number = -0.19

GLN

GLN: object

CD

CD: number = 0.55

OE1

OE1: number = -0.55

GLU

GLU: object

CD

CD: number = 0.36

CG

CG: number = -0.16

OE1

OE1: number = -0.6

OE2

OE2: number = -0.6

HIS

HIS: object

CB

CB: number = 0.1

CD2

CD2: number = 0.2

CE1

CE1: number = 0.45

CG

CG: number = 0.15

ND1

ND1: number = 0.05

NE2

NE2: number = 0.05

LYS

LYS: object

CE

CE: number = 0.25

NZ

NZ: number = 0.75

MET

MET: object

CE

CE: number = 0.06

CG

CG: number = 0.06

SD

SD: number = -0.12

PTR

PTR: object

C

C: number = 0.55

CA

CA: number = 0.1

CZ

CZ: number = 0.25

N

N: number = -0.35

O

O: number = -0.55

O1P

O1P: number = -0.85

O2P

O2P: number = -0.85

O3P

O3P: number = -0.85

OG1

OG1: number = -1.1

P

P: number = 1.4

SEP

SEP: object

C

C: number = 0.55

CA

CA: number = 0.1

CB

CB: number = 0.25

N

N: number = -0.35

O

O: number = -0.55

O1P

O1P: number = -0.85

O2P

O2P: number = -0.85

O3P

O3P: number = -0.85

OG1

OG1: number = -1.1

P

P: number = 1.4

SER

SER: object

CB

CB: number = 0.25

OG

OG: number = -0.25

THR

THR: object

CB

CB: number = 0.25

OG1

OG1: number = -0.25

TPO

TPO: object

C

C: number = 0.55

CA

CA: number = 0.1

CB

CB: number = 0.25

N

N: number = -0.35

O

O: number = -0.55

O1P

O1P: number = -0.85

O2P

O2P: number = -0.85

O3P

O3P: number = -0.85

OG1

OG1: number = -1.1

P

P: number = 1.4

TRP

TRP: object

CD1

CD1: number = 0.06

CD2

CD2: number = 0.1

CE2

CE2: number = -0.04

CE3

CE3: number = -0.03

CG

CG: number = -0.03

NE1

NE1: number = -0.06

TYR

TYR: object

CZ

CZ: number = 0.25

OH

OH: number = -0.25

backbone

backbone: object

C

C: number = 0.55

CA

CA: number = 0.1

N

N: number = -0.35

O

O: number = -0.55

Const types

types: object

BYTE

BYTE: number = 1

CHAR

CHAR: number = 2

DOUBLE

DOUBLE: number = 6

FLOAT

FLOAT: number = 5

INT

INT: number = 4

SHORT

SHORT: number = 3

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