ngl

Index

Modules

__global

Enumerations

Classes

Interfaces

Type aliases

Events

CounterSignals

Variables

Functions

Object literals

Type aliases

ArrowBufferParameters

ArrowBufferParameters: typeof ArrowBufferDefaultParameters

AtomPair

AtomPair: (string | number)[][]

BooleanParam

BooleanParam: { type: "boolean" }

Type declaration

type: "boolean"

BufferMaterials

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

BufferParameters

BufferParameters: typeof BufferDefaultParameters

BufferSide

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

BufferTypes

BufferTypes: "picking" | "background"

CameraType

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

ChainidDict

ChainidDict: {}

Type declaration

[k: string]: number

ChainnameDict

ChainnameDict: {}

Type declaration

[k: string]: number

ColorDefinition

ColorDefinition: Color | string | number | undefined

ColorMode

ColorMode: "rgb" | "hsv" | "hsl" | "hsi" | "lab" | "hcl"

ColorParam

ColorParam: { type: "color" }

Type declaration

type: "color"

ColormakerScale

ColormakerScale: (v: number) => number

Type declaration

- (v: number): number
- Parameters
  - v: number
  Returns number

ComponentParameters

ComponentParameters: typeof ComponentDefaultParameters

ConeBufferParameters

ConeBufferParameters: typeof ConeBufferDefaultParameters

ContactDataParams

ContactDataParams: typeof ContactDataDefaultParams | { filterSele: string | [string, string] }

ContactLabelParams

ContactLabelParams: typeof ContactLabelDefaultParams

CylinderBufferParameters

CylinderBufferParameters: typeof CylinderBufferDefaultParameters

CylinderGeometryBufferParameters

CylinderGeometryBufferParameters: typeof CylinderGeometryBufferDefaultParameters

CylinderImpostorBufferParameters

CylinderImpostorBufferParameters: typeof CylinderImpostorBufferDefaultParameters

DragCallback

DragCallback: (stage: Stage, dx: number, dy: number) => void

Type declaration

- (stage: Stage, dx: number, dy: number): void
- Parameters
  - stage: Stage
  - dx: number
  - dy: number
  Returns void

ElementParameters

ElementParameters: typeof ElementDefaultParameters

EllipsoidBufferParameters

EllipsoidBufferParameters: typeof EllipsoidBufferDefaultParameters

EntityTypeString

EntityTypeString: keyof typeof EntityTypeString

FilterFn

FilterFn: (s: SelectionRule) => boolean

Type declaration

- (s: SelectionRule): boolean
- Parameters
  - s: SelectionRule
  Returns boolean

FunctionWithDeps

FunctionWithDeps: { __deps?: Function[] } & Function

HyperballStickBufferParameters

HyperballStickBufferParameters: typeof HyperballStickBufferDefaultParameters

HyperballStickImpostorBufferParameters

HyperballStickImpostorBufferParameters: typeof HyperballStickImpostorBufferDefaultParameters

ImageBufferParameters

ImageBufferParameters: typeof ImageBufferDefaultParameters

ImageFilterTypes

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

ImageParameters

ImageParameters: typeof ImageDefaultParameters

IntegerParam

IntegerParam: { max: number; min: number; type: "integer" }

Type declaration

max: number
min: number
type: "integer"

KeyActionCallback

KeyActionCallback: (stage: Stage) => void

Type declaration

- (stage: Stage): void
- Parameters
  - stage: Stage
  Returns void

KeyActionPreset

KeyActionPreset: [string, KeyActionCallback][]

KeyControlPreset

KeyControlPreset: keyof typeof KeyActionPresets

LabelType

LabelType: keyof typeof LabelFactoryTypes

LoaderInput

LoaderInput: File | Blob | string

MappingType

MappingType: "v2" | "v3"

MouseActionCallback

MouseActionCallback: ScrollCallback | DragCallback | PickCallback

MouseActionPreset

MouseActionPreset: [string, MouseActionCallback][]

MouseActionType

MouseControlPreset

MouseControlPreset: keyof typeof MouseActionPresets

NumberArray

NumberArray: number[] | TypedArray

NumberParam

NumberParam: { max: number; min: number; precision: number; type: "number" }

Type declaration

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

ParamType

Partial

Partial<T>: {}

Type parameters

Type declaration

PickCallback

PickCallback: (stage: Stage, pickingProxy: PickingProxy) => void

Type declaration

- (stage: Stage, pickingProxy: PickingProxy): void
- Parameters
  - stage: Stage
  - pickingProxy: PickingProxy
  Returns void

PointBufferParameters

PointBufferParameters: typeof PointBufferDefaultParameters

Positions

Positions: { count?: undefined | number; x: ArrayLike<number>; y: ArrayLike<number>; z: ArrayLike<number> }

Type declaration

Optional count?: undefined | number
x: ArrayLike<number>
y: ArrayLike<number>
z: ArrayLike<number>

PrimitiveFields

PrimitiveFields: {}

Type declaration

[k: string]: string

ProxyEntity

ProxyEntity: AtomProxy | ResidueProxy | ChainProxy | ModelProxy

RadiusType

RadiusType: keyof typeof RadiusFactoryTypes

RangeParam

RangeParam: { max: number; min: number; step: number; type: "range" }

Type declaration

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

RenderQualityType

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

RepresentationElementParameters

RepresentationElementParameters: typeof RepresentationElementDefaultParameters

RequestCallback

RequestCallback: (responseCallback: Function, i?: undefined | number, atomIndices?: number[][]) => void

Type declaration

- (responseCallback: Function, i?: undefined | number, atomIndices?: number[][]): void
- Parameters
  - responseCallback: Function
  - Optional i: undefined | number
  - Optional atomIndices: number[][]
  Returns void

ScaleParameters

ScaleParameters: typeof ScaleDefaultParameters

ScrollCallback

ScrollCallback: (stage: Stage, delta: number) => void

Type declaration

- (stage: Stage, delta: number): void
- Parameters
  - stage: Stage
  - delta: number
  Returns void

SelectParam

SelectParam: { options: {}; type: "select" }

Type declaration

options: {}
- [k: string]: string
type: "select"

SelectionOperator

SelectionOperator: "AND" | "OR"

SelectionSchemeData

SelectionSchemeData: [any, string, ColormakerParameters | undefined]

SelectionSignals

SelectionSignals: { stringChanged: Signal }

Type declaration

stringChanged: Signal

SelectionTest

SelectionTest: false | ((e: ProxyEntity) => boolean | -1)

ShaderDefine

ShaderDefines

ShaderDefines: {}

Type declaration

ShapeParameters

ShapeParameters: typeof ShapeDefaultParameters

ShapeRepresentationType

ShapeRepresentationType: "buffer"

SphereBufferParameters

SphereBufferParameters: typeof SphereBufferDefaultParameters

SphereGeometryBufferParameters

SphereGeometryBufferParameters: typeof SphereGeometryBufferDefaultParameters

StageParameters

StageParameters: typeof StageDefaultParameters

StoreField

StoreField: [string, number, TypedArrayString]

StructureComponentParameters

StructureComponentParameters: typeof StructureComponentDefaultParameters

StructureExtraData

StructureExtraData: { cif?: undefined | object; sdf?: object[] }

Type declaration

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

StructureHeader

StructureHeader: { depositionDate?: undefined | string; experimentalMethods?: string[]; rFree?: undefined | number; rWork?: undefined | number; releaseDate?: undefined | string; resolution?: undefined | number }

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: keyof StructureRepresentationParametersMap

StructureSignals

StructureSignals: { refreshed: Signal }

Type declaration

refreshed: Signal

StuctureColormakerParams

StuctureColormakerParams: { structure: Structure } & Partial<ColormakerParameters>

SubstitutionMatrix

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

SurfaceDataFields

SurfaceDataFields: { color: boolean; index: boolean; normal: boolean; position: boolean; radius: boolean }

Type declaration

color: boolean
index: boolean
normal: boolean
position: boolean
radius: boolean

SurfaceRepresentationType

SurfaceRepresentationType: "surface" | "dot"

TestEntityFn

TestEntityFn: (e: ProxyEntity, s: SelectionRule) => boolean | -1

Type declaration

- (e: ProxyEntity, s: SelectionRule): boolean | -1
- Parameters
  - e: ProxyEntity
  - s: SelectionRule
  Returns boolean | -1

TextAtlasMap

TextAtlasMap: { h: number; w: number; x: number; y: number }

Type declaration

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

TextAtlasParams

TextAtlasParams: typeof TextAtlasDefaultParams

TextAttachments

TextBufferParameters

TextBufferParameters: typeof TextBufferDefaultParameters

TextFonts

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

TextStyles

TextStyles: "normal" | "italic"

TextVariants

TextVariants: "normal"

TextWeights

TextWeights: "normal" | "bold"

TorusBufferParameters

TorusBufferParameters: typeof TorusBufferDefaultParameters

TrajectoryElementParameters

TrajectoryElementParameters: typeof TrajectoryElementDefaultParameters

TrajectoryPlayerDirection

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

TrajectoryPlayerInterpolateType

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

TrajectoryPlayerMode

TrajectoryPlayerMode: "loop" | "once"

TrajectoryPlayerParameters

TrajectoryPlayerParameters: typeof TrajectoryPlayerDefaultParameters

TubeMeshBufferParameters

TubeMeshBufferParameters: typeof TubeMeshBufferDefaultParameters

TypedArray

TypedArrayString

Uniforms

Uniforms: {}

Type declaration

[k: string]: Uniform | { value: any }

VectorBufferParameters

VectorBufferParameters: typeof VectorBufferDefaultParameters

VolumeColormakerParams

VolumeColormakerParams: { volume: Volume } & Partial<ColormakerParameters>

VolumeRepresentationType

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

VolumeSize

VolumeSize: "value" | "abs-value" | "value-min" | "deviation"

WideLineBufferParameters

WideLineBufferParameters: typeof WideLineBufferDefaultParameters

Private XMLNodeAttributes

XMLNodeAttributes: {}

file: Parse Xml
author: Alexander Rose alexander.rose@weirdbyte.de

Type declaration

[k: string]: any

Events

CounterSignals

CounterSignals:

{@link Signal}, dispatched when the count changes

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

countChanged

countChanged: signalsWrapper.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 ]

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: { aspectRatio: number; disableImpostor: false; openEnded: false; radialSegments: number } & { 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 } = 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 AtomOnlyKeywords

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

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 Browser

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

Const BufferRegistry

BufferRegistry: Registry = new Registry('buffer')

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 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: { openEnded: false; radialSegments: number } & { 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 } = 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: { disableImpostor: false } & { openEnded: true; radialSegments: number } & { 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 } & { openEnded: false } = Object.assign({disableImpostor: false}, CylinderGeometryBufferDefaultParameters, CylinderImpostorBufferDefaultParameters)

Const CylinderGeometryBufferDefaultParameters

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

Const CylinderImpostorBufferDefaultParameters

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

Const CylinderImpostorBufferParameterTypes

CylinderImpostorBufferParameterTypes: { openEnded: object } & { matrix: {}; background: object; clipCenter: object; clipNear: object; clipRadius: object; depthWrite: object; diffuse: object; diffuseInterior: object; flatShaded: object; interiorColor: object; interiorDarkening: object; metalness: object; opacity: object; opaqueBack: object; roughness: object; side: object; useInteriorColor: object; wireframe: object } = Object.assign({openEnded: { updateShader: true }}, BufferParameterTypes)

Const DEG2RAD

DEG2RAD: number = Math.PI / 180

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', 'DI' ]

Const DnaType

DnaType: 5 = 5

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

Const EllipsoidBufferDefaultParameters

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

Let ExtensionFragDepth

ExtensionFragDepth: boolean = false

Flag indicating support for the EXT_frag_depth WebGL extension (Always present in WebGL2)

Const FLT_MIN

FLT_MIN: 1e-37 = 1e-37

Const FirstIdx

FirstIdx: 9 = 9

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: { disableImpostor: false } & { openEnded: true; radialSegments: number } & { 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 } & { shrink: number } = Object.assign({disableImpostor: false}, CylinderGeometryBufferDefaultParameters, HyperballStickImpostorBufferDefaultParameters)

Const HyperballStickImpostorBufferDefaultParameters

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

Const HyperballStickImpostorBufferParameterTypes

HyperballStickImpostorBufferParameterTypes: { shrink: object } & { matrix: {}; background: object; clipCenter: object; clipNear: object; clipRadius: object; depthWrite: object; diffuse: object; diffuseInterior: object; flatShaded: object; interiorColor: object; interiorDarkening: object; metalness: object; opacity: object; opaqueBack: object; roughness: object; side: object; useInteriorColor: object; wireframe: object } = Object.assign({shrink: { uniform: true }}, BufferParameterTypes)

Const ImageBufferDefaultParameters

ImageBufferDefaultParameters: { filter: "linear" | "nearest" | "cubic-bspline" | "cubic-catmulrom" | "cubic-mitchell"; forceTransparent: true } & { 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 } = Object.assign({filter: 'nearest' as ImageFilterTypes,forceTransparent: true}, BufferDefaultParameters)

Const ImageBufferParameterTypes

ImageBufferParameterTypes: { filter: object } & { matrix: {}; background: object; clipCenter: object; clipNear: object; clipRadius: object; depthWrite: object; diffuse: object; diffuseInterior: object; flatShaded: object; interiorColor: object; interiorDarkening: object; metalness: object; opacity: object; opaqueBack: object; roughness: object; side: object; useInteriorColor: object; wireframe: 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 ]]]

Private Const LeftMouseButton

LeftMouseButton: 1 = 1

file: Constants
author: Alexander Rose alexander.rose@weirdbyte.de

Let ListingDatasource

ListingDatasource: any

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 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 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', 'HOP2', 'HOP3',"O2'", "O3'", "O4'", "O5'", "C1'", "C2'", "C3'", "C4'", "C5'","H1'", "H2'", "H2''", "HO2'", "H3'", "H4'", "H5'", "H5''", "HO3'", "HO5'",'O2*', 'O3*', 'O4*', 'O5*', 'C1*', 'C2*', 'C3*', 'C4*', 'C5*']

Const NucleophilicResname

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

Private Const OBJLoader

OBJLoader: _OBJLoaderConstructor = (function OBJLoader (this: _OBJLoader) {this.regexp = {// v float float floatvertex_pattern: /^v\s+([\d.+\-eE]+)\s+([\d.+\-eE]+)\s+([\d.+\-eE]+)/,// vn float float floatnormal_pattern: /^vn\s+([\d.+\-eE]+)\s+([\d.+\-eE]+)\s+([\d.+\-eE]+)/,// vt float floatuv_pattern: /^vt\s+([\d.+\-eE]+)\s+([\d.+\-eE]+)/,// f vertex vertex vertexface_vertex: /^f\s+(-?\d+)\s+(-?\d+)\s+(-?\d+)(?:\s+(-?\d+))?/,// f vertex/uv vertex/uv vertex/uvface_vertex_uv: /^f\s+(-?\d+)\/(-?\d+)\s+(-?\d+)\/(-?\d+)\s+(-?\d+)\/(-?\d+)(?:\s+(-?\d+)\/(-?\d+))?/,// f vertex/uv/normal vertex/uv/normal vertex/uv/normalface_vertex_uv_normal: /^f\s+(-?\d+)\/(-?\d+)\/(-?\d+)\s+(-?\d+)\/(-?\d+)\/(-?\d+)\s+(-?\d+)\/(-?\d+)\/(-?\d+)(?:\s+(-?\d+)\/(-?\d+)\/(-?\d+))?/,// f vertex//normal vertex//normal vertex//normalface_vertex_normal: /^f\s+(-?\d+)\/\/(-?\d+)\s+(-?\d+)\/\/(-?\d+)\s+(-?\d+)\/\/(-?\d+)(?:\s+(-?\d+)\/\/(-?\d+))?/,// o object_name | g group_nameobject_pattern: /^[og]\s*(.+)?/,// s booleansmoothing_pattern: /^s\s+(\d+|on|off)/,// mtllib file_referencematerial_library_pattern: /^mtllib /,// usemtl material_namematerial_use_pattern: /^usemtl /}}) as _OBJLoaderConstructor

OBJLoader

author: mrdoob / http://mrdoob.com/

Const OptimalAcceptorAngle

OptimalAcceptorAngle: number = degToRad(120)

Const OptimalHalogenAngle

OptimalHalogenAngle: number = degToRad(180)

Const PLYLoader

PLYLoader: _PLYLoaderConstructor = (function PLYLoader (this: _PLYLoader) {this.propertyNameMapping = {}}) as _PLYLoaderConstructor

Const PickerRegistry

PickerRegistry: Registry = new Registry('picker')

Const PointBufferDefaultParameters

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

Const PointBufferParameterTypes

PointBufferParameterTypes: { forceTransparent: {}; sortParticles: {}; alphaTest: object; edgeBleach: object; pointSize: object; sizeAttenuation: object; useTexture: object } & { matrix: {}; background: object; clipCenter: object; clipNear: object; clipRadius: object; depthWrite: object; diffuse: object; diffuseInterior: object; flatShaded: object; interiorColor: object; interiorDarkening: object; metalness: object; opacity: object; opaqueBack: object; roughness: object; side: object; useInteriorColor: object; wireframe: object } = Object.assign({pointSize: { uniform: 'size' },sizeAttenuation: { updateShader: true },sortParticles: {},alphaTest: { updateShader: true },useTexture: { updateShader: true },forceTransparent: {},edgeBleach: { uniform: true }}, BufferParameterTypes)

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', 'OT1', 'OT2','H', 'H1', 'H2', 'H3', 'HA', 'HN','BB']

Const ProteinBackboneType

ProteinBackboneType: 1 = 1

Const ProteinType

ProteinType: 3 = 3

Const PurinBases

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

Const RAD2DEG

RAD2DEG: number = 180 / Math.PI

Const RepresentationElementDefaultParameters

RepresentationElementDefaultParameters: { visible: true } & { name: string; status: string } = Object.assign({visible: true}, ElementDefaultParameters)

Const RepresentationRegistry

RepresentationRegistry: Registry = new Registry('representatation')

Const ResidueTypeAtoms

ResidueTypeAtoms: {}

Type declaration

[k: number]: {}
- [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', 'I' ]

Const RnaType

RnaType: 4 = 4

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: { disableImpostor: false } & { sphereDetail: number } & { 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 } = Object.assign({disableImpostor: false}, SphereGeometryBufferDefaultParameters)

Const SphereGeometryBufferDefaultParameters

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

Const StructureComponentDefaultParameters

StructureComponentDefaultParameters: { defaultAssembly: string; sele: string } & { name: string; status: string; visible: boolean } = Object.assign({sele: '',defaultAssembly: ''}, ComponentDefaultParameters)

Const SubstitutionMatrices

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

Type declaration

blosum62: {}
- [k: string]: {}
  - [k: string]: number
blosum62x: {}
- [k: string]: {}
  - [k: string]: number

Let SupportsPassiveEventHandler

SupportsPassiveEventHandler: boolean = false

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

Let SupportsReadPixelsFloat

SupportsReadPixelsFloat: boolean = false

Const TextAtlasCache

TextAtlasCache: {}

Type declaration

[k: string]: TextAtlas

Const TextBufferDefaultParameters

TextBufferDefaultParameters: { attachment: "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right"; backgroundColor: string | number; backgroundMargin: number; backgroundOpacity: number; borderColor: string | number; borderWidth: number; fixedSize: false; fontFamily: "sans-serif" | "monospace" | "serif"; fontSize: number; fontStyle: "normal" | "italic"; fontWeight: "normal" | "bold"; forceTransparent: true; showBackground: false; showBorder: false; xOffset: number; yOffset: number; zOffset: number } & { 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 } = 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: { backgroundColor: object; backgroundOpacity: object; borderColor: object; borderWidth: object; fixedSize: object; fontFamily: object; fontSize: object; fontStyle: object; fontWeight: object; showBorder: object; xOffset: object; yOffset: object; zOffset: object } & { matrix: {}; background: object; clipCenter: object; clipNear: object; clipRadius: object; depthWrite: object; diffuse: object; diffuseInterior: object; flatShaded: object; interiorColor: object; interiorDarkening: object; metalness: object; opacity: object; opaqueBack: object; roughness: object; side: object; useInteriorColor: object; wireframe: 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: { radialSegments: number; radiusRatio: number; tubularSegments: number } & { 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 } = Object.assign({radiusRatio: 0.2,radialSegments: 16,tubularSegments: 32}, BufferDefaultParameters)

Let TrajectoryDatasource

TrajectoryDatasource: any

Const TrajectoryElementDefaultParameters

TrajectoryElementDefaultParameters: { defaultDirection: "forward" | "backward" | "bounce"; defaultInterpolateStep: number; defaultInterpolateType: "" | "linear" | "spline"; defaultMode: "loop" | "once"; defaultStep: number; defaultTimeout: number; initialFrame: number } & { name: string; status: string } = 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.

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: { aspectRatio: number; capped: false; radialSegments: number } & { 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 } = 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: { color: string; scale: number } & { 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 } = Object.assign({scale: 1,color: 'grey'}, BufferDefaultParameters)

Const Version

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

Version name

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

Const WideLineBufferParameterTypes

WideLineBufferParameterTypes: { linewidth: object } & { matrix: {}; background: object; clipCenter: object; clipNear: object; clipRadius: object; depthWrite: object; diffuse: object; diffuseInterior: object; flatShaded: object; interiorColor: object; interiorDarkening: object; metalness: object; opacity: object; opaqueBack: object; roughness: object; side: object; useInteriorColor: object; wireframe: 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

Const _m

_m: Matrix4 = new Matrix4()

Const _tmpBytes

_tmpBytes: Uint8Array = new Uint8Array(32)

Const _tmpIntBytes

_tmpIntBytes: Int32Array = new Int32Array(32)

Const _v

_v: Vector3 = new Vector3()

Const amberChargeUnitFactor

amberChargeUnitFactor: 18.2223 = 18.2223

Const aminoacids

aminoacids: "ARNDCQEGHILKMFPSTWYVBZ?" = "ARNDCQEGHILKMFPSTWYVBZ?"

Const aminoacidsX

aminoacidsX: "ACDEFGHIKLMNPQRSTVWY" = "ACDEFGHIKLMNPQRSTVWY"

Const baseUrl

baseUrl: "//pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" = "//pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"

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 = 'e'}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('')

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]

Const defaultByteLength

defaultByteLength: number = 1024 * 8

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)

Const halBondElements

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

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

Const pixelBufferFloat

pixelBufferFloat: Float32Array = new Float32Array(4 * 25)

Const pixelBufferUint

pixelBufferUint: Uint8Array = new Uint8Array(4 * 25)

Const pixelOrder

pixelOrder: number[] = [12,7,13,17,11,6,8,18,16,2,14,22,10,1,3,9,19,23,21,15,5,0,4,24,20]

Const pointArray

pointArray: Float32Array = new Float32Array(3)

Const pointLength

pointLength: 3 = 3

Const pointsInTriangle

pointsInTriangle: 3 = 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: {}

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

- Defined in src/math/matrix-utils.ts:305
Parameters
- A: NumberArray
- i0: number
- i1: number
- t: number
Returns 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

Const tmpRotateCameraMatrix

tmpRotateCameraMatrix: Matrix4 = new Matrix4()

Const tmpRotateMatrix

tmpRotateMatrix: Matrix4 = new Matrix4()

Const tmpRotateQuaternion

tmpRotateQuaternion: Quaternion = new Quaternion()

Const tmpRotateQuaternion2

tmpRotateQuaternion2: 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()

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()

Const vertex

vertex: Vector3 = new Vector3()

Functions

AVSurface

AVSurface(this: AVSurface, coordList: Float32Array, radiusList: Float32Array, indexList: Uint16Array | Uint32Array): void

- Defined in src/surface/av-surface.ts:177
Parameters
- this: AVSurface
- coordList: Float32Array
- radiusList: Float32Array
- indexList: Uint16Array | Uint32Array
Returns void

BooleanParam

BooleanParam(): { type: "boolean" }

- Defined in src/ui/parameters.ts:10
Returns { type: "boolean" }
- type: "boolean"

ColorParam

ColorParam(): { type: "color" }

- Defined in src/ui/parameters.ts:13
Returns { type: "color" }
- type: "color"

EDTSurface

EDTSurface(this: EDTSurface, coordList: Float32Array, radiusList: Float32Array, indexList: Uint16Array | Uint32Array): void

- Defined in src/surface/edt-surface.ts:24
Parameters
- this: EDTSurface
- coordList: Float32Array
- radiusList: Float32Array
- indexList: Uint16Array | Uint32Array
Returns void

IntegerParam

IntegerParam(max: number, min: number): { max: number; min: number; type: "integer" }

- Defined in src/ui/parameters.ts:16
Parameters
- max: number
- min: number
Returns { max: number; min: number; type: "integer" }
- max: number
- min: number
- type: "integer"

JacobiSVDImpl

JacobiSVDImpl(At: NumberArray, astep: number, _W: NumberArray, Vt: NumberArray, vstep: number, m: number, n: number, n1: number): void

- Defined in src/math/matrix-utils.ts:328
Parameters
- At: NumberArray
- astep: number
- _W: NumberArray
- Vt: NumberArray
- vstep: number
- m: number
- n: number
- n1: number
Returns void

MarchingCubes

MarchingCubes(this: MarchingCubes, field: number[], nx: number, ny: number, nz: number, atomindex: number[]): void

- Defined in src/surface/marching-cubes.ts:353
Parameters
- this: MarchingCubes
- field: number[]
- nx: number
- ny: number
- nz: number
- atomindex: number[]
Returns void

NumberParam

NumberParam(precision: number, max: number, min: number): { max: number; min: number; precision: number; type: "number" }

- Defined in src/ui/parameters.ts:21
Parameters
- precision: number
- max: number
- min: number
Returns { max: number; min: number; precision: number; type: "number" }
- max: number
- min: number
- precision: number
- type: "number"

RangeParam

RangeParam(step: number, max: number, min: number): { max: number; min: number; step: number; type: "range" }

- Defined in src/ui/parameters.ts:26
Parameters
- step: number
- max: number
- min: number
Returns { max: number; min: number; step: number; type: "range" }
- max: number
- min: number
- step: number
- type: "range"

RingFinderState

RingFinderState(bonds: BondGraph, capacity: number): RingFinderState

- Defined in src/store/residue-type.ts:732
Parameters
- bonds: BondGraph
- capacity: number
Returns RingFinderState

SelectParam

SelectParam(...options: string[]): { options: {}; type: "select" }

- Defined in src/ui/parameters.ts:31
Parameters
- Rest ...options: string[]
Returns { options: {}; type: "select" }
- options: {}
  - [k: string]: string
- type: "select"

ValenceModel

ValenceModel(data: Data, params: ValenceModelParams): { charge: Int8Array; idealGeometry: Int8Array; implicitH: Int8Array; totalH: Int8Array }

- Defined in src/chemistry/valence-model.ts:297
Parameters
- data: Data
- params: ValenceModelParams
Returns { charge: Int8Array; idealGeometry: Int8Array; implicitH: Int8Array; totalH: Int8Array }
- charge: Int8Array
- idealGeometry: Int8Array
- implicitH: Int8Array
- totalH: Int8Array

VolumeSurface

VolumeSurface(this: VolumeSurface, data: NumberArray, nx: number, ny: number, nz: number, atomindex: NumberArray): void

- Defined in src/surface/volume.ts:37
Parameters
- this: VolumeSurface
- data: NumberArray
- nx: number
- ny: number
- nz: number
- atomindex: NumberArray
Returns void

_ensureClassFromArg

_ensureClassFromArg(arg: any, constructor: { constructor: any }): any

- Defined in src/utils.ts:477
Parameters
- arg: any
- constructor: { constructor: any }
  - constructor: function
    - new __type(arg: any): any
    - Defined in src/utils.ts:477
      Parameters
      - arg: any
      Returns any
Returns any

_ensureClassFromArray

_ensureClassFromArray(array: any, constructor: { constructor: any }): any

- Defined in src/utils.ts:481
Parameters
- array: any
- constructor: { constructor: any }
  - constructor: function
    - new __type(): any
    - Defined in src/utils.ts:481
      Returns any
Returns any

_trimCanvas

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

- Defined in src/viewer/viewer-utils.ts:17
Parameters
- canvas: HTMLCanvasElement
- r: number
- g: number
- b: number
- a: number
Returns HTMLCanvasElement

addAromaticRings

addAromaticRings(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/charged.ts:137
Parameters
- structure: Structure
- features: Features
Returns void

addAtom

addAtom(state: FeatureState, atom: AtomProxy): void

- Defined in src/chemistry/interactions/features.ts:68
Parameters
- state: FeatureState
- atom: AtomProxy
Returns void

addChargedContacts

addChargedContacts(structure: Structure, contacts: Contacts, params?: ChargedContactsParams): void

- Defined in src/chemistry/interactions/charged.ts:183
Parameters
- structure: Structure
- contacts: Contacts
- Default value params: ChargedContactsParams = {}
Returns void

addCols

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

- Defined in src/math/matrix-utils.ts:293
Parameters
- A: Matrix
- col: number[]
Returns void

addElement

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

- Defined in src/geometry/primitive.ts:13
Parameters
- elm: any
- array: any[]
Returns void

addFeature

addFeature(features: Features, state: FeatureState): void

- Defined in src/chemistry/interactions/features.ts:75
Parameters
- features: Features
- state: FeatureState
Returns void

addHalogenAcceptors

addHalogenAcceptors(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/halogen-bonds.ts:39
Halogen bond acceptors (Y-{O|N|S}, with Y=C,P,N,S)

Parameters
- structure: Structure
- features: Features
Returns void

addHalogenBonds

addHalogenBonds(structure: Structure, contacts: Contacts, params?: HalogenBondsParams): void

- Defined in src/chemistry/interactions/halogen-bonds.ts:77
All pairs of halogen donor and acceptor atoms

Parameters
- structure: Structure
- contacts: Contacts
- Default value params: HalogenBondsParams = {}
Returns void

addHalogenDonors

addHalogenDonors(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/halogen-bonds.ts:23
Halogen bond donors (X-C, with X one of Cl, Br, I or At) not F!

Parameters
- structure: Structure
- features: Features
Returns void

addHydrogenAcceptors

addHydrogenAcceptors(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:100
Potential hydrogen acceptor

Parameters
- structure: Structure
- features: Features
Returns void

addHydrogenBonds

addHydrogenBonds(structure: Structure, contacts: Contacts, params?: HydrogenBondParams): void

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:203
All pairs of hydrogen donor and acceptor atoms

Parameters
- structure: Structure
- contacts: Contacts
- Default value params: HydrogenBondParams = {}
Returns void

addHydrogenDonors

addHydrogenDonors(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:30
Potential hydrogen donor

Parameters
- structure: Structure
- features: Features
Returns void

addHydrophobic

addHydrophobic(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/hydrophobic.ts:18
Hydrophobic carbon (only bonded to carbon or hydrogen); fluorine

Parameters
- structure: Structure
- features: Features
Returns void

addHydrophobicContacts

addHydrophobicContacts(structure: Structure, contacts: Contacts, params?: HydrophobicContactsParams): void

- Defined in src/chemistry/interactions/hydrophobic.ts:50
All hydrophobic contacts

Parameters
- structure: Structure
- contacts: Contacts
- Default value params: HydrophobicContactsParams = {}
Returns void

addMetalBinding

addMetalBinding(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/metal-binding.ts:27
Metal binding partners (dative bond or ionic-type interaction)

Parameters
- structure: Structure
- features: Features
Returns void

addMetalComplexation

addMetalComplexation(structure: Structure, contacts: Contacts, params?: MetalComplexationParams): void

- Defined in src/chemistry/interactions/metal-binding.ts:209
Metal complexes of metals and appropriate groups in protein and ligand, including water

Parameters
- structure: Structure
- contacts: Contacts
- Default value params: MetalComplexationParams = {}
Returns void

addMetals

addMetals(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/metal-binding.ts:174
Metal Pi complexation partner

Parameters
- structure: Structure
- features: Features
Returns void

addNegativeCharges

addNegativeCharges(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/charged.ts:73
Parameters
- structure: Structure
- features: Features
Returns void

addPositiveCharges

addPositiveCharges(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/charged.ts:26
Parameters
- structure: Structure
- features: Features
Returns void

addRing

addRing(state: RingFinderState, a: number, b: number): void

- Defined in src/store/residue-type.ts:613
Ring finding code below adapted from MolQL Copyright (c) 2017 MolQL contributors, licensed under MIT

author

David Sehnal david.sehnal@gmail.com

Parameters
- state: RingFinderState
- a: number
- b: number
Returns void

addRows

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

- Defined in src/math/matrix-utils.ts:281
Parameters
- A: Matrix
- row: number[]
Returns void

addWeakHydrogenDonors

addWeakHydrogenDonors(structure: Structure, features: Features): void

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:55
Weak hydrogen donor.

Parameters
- structure: Structure
- features: Features
Returns void

almostIdentity

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

- Defined in src/math/math-utils.ts:95
Parameters
- value: number
- start: number
- stop: number
Returns number

applyMatrix3toVector3array

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

- Defined in src/math/vector-utils.ts:133
Parameters
- m: Float32Array
- a: Float32Array
Returns void

applyMatrix4toVector3array

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

- Defined in src/math/vector-utils.ts:122
Parameters
- m: Float32Array
- a: Float32Array
Returns void

arrayMax

arrayMax(array: NumberArray): number

- Defined in src/math/array-utils.ts:478
Parameters
- array: NumberArray
Returns number

arrayMean

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

- Defined in src/math/array-utils.ts:503
Parameters
- array: NumberArray
- Default value stride: number = 1
- Default value offset: number = 0
Returns number

arrayMean3

arrayMean3(coords: NumberArray): number[]

- Defined in src/trajectory/trajectory.ts:103
Parameters
- coords: NumberArray
Returns number[]

arrayMin

arrayMin(array: NumberArray): number

- Defined in src/math/array-utils.ts:486
Parameters
- array: NumberArray
Returns number

arrayRms

arrayRms(array: NumberArray): number

- Defined in src/math/array-utils.ts:507
Parameters
- array: NumberArray
Returns number

arraySorted

arraySorted(array: NumberArray): boolean

- Defined in src/math/array-utils.ts:517
Parameters
- array: NumberArray
Returns boolean

arraySortedCmp

arraySortedCmp<T>(array: NumberArray | T[], cmp: (a: number | T, b: number | T) => number): boolean

- Defined in src/math/array-utils.ts:524
Type parameters
- T
Parameters
- array: NumberArray | T[]
- cmp: (a: number | T, b: number | T) => number
  - - (a: number | T, b: number | T): number
    - Parameters
      - a: number | T
      - b: number | T
      Returns number
Returns boolean

arraySum

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

- Defined in src/math/array-utils.ts:494
Parameters
- array: NumberArray
- Default value stride: number = 1
- Default value offset: number = 0
Returns number

assignGeometry

assignGeometry(totalCoordination: number): AtomGeometry

- Defined in src/chemistry/geometry.ts:27
Parameters
- totalCoordination: number
Returns AtomGeometry

assignResidueTypeBonds

assignResidueTypeBonds(structure: Structure): void

- Defined in src/structure/structure-utils.ts:926
Assigns ResidueType bonds.

Parameters
- structure: Structure
  
  the structure object
Returns void

assignSecondaryStructure

assignSecondaryStructure(structure: Structure, secStruct: SecStruct): void

- Defined in src/structure/structure-utils.ts:62
Parameters
- structure: Structure
- secStruct: SecStruct
Returns void

atomTestFn

atomTestFn(a: AtomProxy, s: SelectionRule): false | true | -1

- Defined in src/selection/selection-test.ts:40
Parameters
- a: AtomProxy
- s: SelectionRule
Returns false | true | -1

atomTriplePositions

atomTriplePositions(sview: StructureView, atomTriple: (string | number)[][]): Float32Array

- Defined in src/representation/angle-representation.ts:290
Parameters
- sview: StructureView
- atomTriple: (string | number)[][]
Returns Float32Array

autoLoad

autoLoad(file: LoaderInput, params?: Partial<LoaderParameters>): any

- Defined in src/loader/loader-utils.ts:109
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
- file: LoaderInput
  
  either a URL or an object containing the file data
- Default value params: Partial<LoaderParameters> = {}
  
  loading parameters
Returns any

Promise resolves to the loaded data

backboneNHPosition

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

- Defined in src/color/electrostatic-colormaker.ts:139
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

- Defined in src/utils.ts:341
Parameters
- array: number[]
- leftRange: number
Returns number

binarySearchForRightRange

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

- Defined in src/utils.ts:356
Parameters
- array: number[]
- rightRange: number
Returns number

binarySearchIndexOf

binarySearchIndexOf<T>(array: T[], element: T, compareFunction?: lexicographicCompare): number

- Defined in src/utils.ts:324
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

boolean

boolean(value: any): boolean

- Defined in src/utils.ts:22
Parameters
- value: any
Returns boolean

buildStoreLike

buildStoreLike(positions: Vector3[]): { count: number; x: Float32Array; y: Float32Array; z: Float32Array }

- Defined in src/color/electrostatic-colormaker.ts:180
Takes an array of Vector3 objects and converts to an object that looks like an AtomStore

Parameters
- positions: Vector3[]
  
  array of positions
Returns { count: number; x: Float32Array; y: Float32Array; z: Float32Array }

AtomStore-like object
- count: number
- x: Float32Array
- y: Float32Array
- z: Float32Array

buildUnitcellAssembly

buildUnitcellAssembly(structure: Structure): void

- Defined in src/structure/structure-utils.ts:788
Parameters
- structure: Structure
Returns void

calcAngles

calcAngles(ap1: AtomProxy, ap2: AtomProxy): number[]

- Defined in src/chemistry/geometry.ts:57
Calculate the angles x-1-2 for all x where x is a heavy atom bonded to ap1.

Parameters
- ap1: AtomProxy
  
  First atom (angle centre)
- ap2: AtomProxy
  
  Second atom
Returns number[]

Angles in radians

calcArcPoint

calcArcPoint(out: Float32Array, center: Float32Array, v1: Float32Array, v2: Float32Array, angle: number): void

- Defined in src/representation/measurement-representation.ts:382
Parameters
- out: Float32Array
- center: Float32Array
- v1: Float32Array
- v2: Float32Array
- angle: number
Returns void

calcPlaneAngle

calcPlaneAngle(ap1: AtomProxy, ap2: AtomProxy): number | undefined

- Defined in src/chemistry/geometry.ts:78
Find two neighbours of ap1 to define a plane (if possible) and measure angle out of plane to ap2

Parameters
- ap1: AtomProxy
  
  First atom (angle centre)
- ap2: AtomProxy
  
  Second atom (out-of-plane)
Returns number | undefined

Angle from plane to second atom

calculateAtomBondMap

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

- Defined in src/structure/structure-utils.ts:635
Parameters
- structure: Structure
Returns number[][]

calculateBonds

calculateBonds(structure: Structure): void

- Defined in src/structure/structure-utils.ts:504
Parameters
- structure: Structure
Returns void

calculateBondsBetween

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

- Defined in src/structure/structure-utils.ts:716
Parameters
- structure: Structure
- Default value onlyAddBackbone: boolean = false
- Default value useExistingBonds: boolean = false
Returns void

calculateBondsWithin

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

- Defined in src/structure/structure-utils.ts:652
Parameters
- structure: Structure
- Default value onlyAddRung: boolean = false
Returns void

calculateCenterArray

calculateCenterArray<T>(array1: NumberArray, array2: NumberArray, center?: T, offset?: number): T

- Defined in src/math/array-utils.ts:51
Type parameters
- T: NumberArray
Parameters
- array1: NumberArray
- array2: NumberArray
- Optional center: T
- Default value offset: number = 0
Returns T

calculateChainnames

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

- Defined in src/structure/structure-utils.ts:381
Parameters
- structure: Structure
- Default value useExistingBonds: boolean = false
Returns void

calculateContacts

calculateContacts(structure: Structure, params?: { 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 }): FrozenContacts

- Defined in src/chemistry/interactions/contact.ts:144
Parameters
- structure: Structure
- Default value params: { 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 } = 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

calculateDihedralHistogram

calculateDihedralHistogram(histogramData: HistogramData): undefined | { adjacentBondArrows: { endColors: Float32Array; endPoints: Float32Array; startColors: Float32Array; startPoints: Float32Array }; backHistogram: { triangleColors: Float32Array; triangles: Float32Array }; backHistogramBinBorders: { endColors: Float32Array; endPoints: Float32Array; startColors: Float32Array; startPoints: Float32Array }; distantBondArrows: { endColors: Float32Array; endPoints: Float32Array; startColors: Float32Array; startPoints: Float32Array }; frontHistogram: { triangleColors: Float32Array; triangles: Float32Array }; frontHistogramBinBorders: { endColors: Float32Array; endPoints: Float32Array; startColors: Float32Array; startPoints: Float32Array }; opaqueMiddleDisc: { triangleColors: Float32Array; triangles: Float32Array } }

- Defined in src/representation/dihedral-histogram-representation.ts:377
Calculates the data required to create {Buffer} objects for one histogram, given positions

Parameters
- histogramData: HistogramData
Returns undefined | { adjacentBondArrows: { endColors: Float32Array; endPoints: Float32Array; startColors: Float32Array; startPoints: Float32Array }; backHistogram: { triangleColors: Float32Array; triangles: Float32Array }; backHistogramBinBorders: { endColors: Float32Array; endPoints: Float32Array; startColors: Float32Array; startPoints: Float32Array }; distantBondArrows: { endColors: Float32Array; endPoints: Float32Array; startColors: Float32Array; startPoints: Float32Array }; frontHistogram: { triangleColors: Float32Array; triangles: Float32Array }; frontHistogramBinBorders: { endColors: Float32Array; endPoints: Float32Array; startColors: Float32Array; startPoints: Float32Array }; opaqueMiddleDisc: { triangleColors: Float32Array; triangles: Float32Array } }

Arrays for building buffers

calculateDirectionArray

calculateDirectionArray(array1: NumberArray, array2: NumberArray): Float32Array

- Defined in src/math/array-utils.ts:64
Parameters
- array1: NumberArray
- array2: NumberArray
Returns Float32Array

calculateFeatures

calculateFeatures(structure: Structure): Features

- Defined in src/chemistry/interactions/contact.ts:118
Parameters
- structure: Structure
Returns Features

calculateHydrogensCharge

calculateHydrogensCharge(a: AtomProxy, params: ValenceModelParams): number[]

- Defined in src/chemistry/valence-model.ts:104
Attempts to produce a consistent charge and implicit H-count for an atom.

If both params.assignCharge and params.assignH, this approximately followsthe rules described in https://docs.eyesopen.com/toolkits/python/oechemtk/valence.html#openeye-hydrogen-count-model

If only charge or hydrogens are to be assigned it takes a much simpler view and deduces one from the other

Parameters
- a: AtomProxy
  
  Atom to analyze
- params: ValenceModelParams
  
  What to assign
Returns number[]

calculateMeanArray

calculateMeanArray(array1: NumberArray, array2: NumberArray): Float32Array

- Defined in src/math/array-utils.ts:193
Parameters
- array1: NumberArray
- array2: NumberArray
Returns Float32Array

calculateMeanVector3

calculateMeanVector3(array: NumberArray): Vector3

- Defined in src/math/vector-utils.ts:64
Parameters
- array: NumberArray
Returns Vector3

calculateMinArray

calculateMinArray(array1: NumberArray, array2: NumberArray): Float32Array

- Defined in src/math/array-utils.ts:204
Parameters
- array1: NumberArray
- array2: NumberArray
Returns Float32Array

calculateResidueBonds

calculateResidueBonds(r: ResidueProxy): { atomIndices1: number[]; atomIndices2: number[]; bondOrders: number[] }

- Defined in src/structure/structure-utils.ts:576
Parameters
- r: ResidueProxy
Returns { atomIndices1: number[]; atomIndices2: number[]; bondOrders: number[] }
- atomIndices1: number[]
- atomIndices2: number[]
- bondOrders: number[]

centerArray3

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

- Defined in src/math/array-utils.ts:101
Parameters
- array: NumberArray
- Default value center: Vector3 = new Vector3()
Returns Vector3

centerPbc

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

- Defined in src/trajectory/trajectory.ts:21
Parameters
- coords: NumberArray
- mean: number[]
- box: ArrayLike<number>
Returns void

chainTestFn

chainTestFn(c: ChainProxy, s: SelectionRule): false | true | -1

- Defined in src/selection/selection-test.ts:154
Parameters
- c: ChainProxy
- s: SelectionRule
Returns false | true | -1

chargeForAtom

chargeForAtom(a: AtomProxy): number

- Defined in src/color/electrostatic-colormaker.ts:196
Parameters
- a: AtomProxy
Returns number

cifDefaults

cifDefaults(value: string, defaultValue: string): string

- Defined in src/parser/cif-parser.ts:51
Parameters
- value: string
- defaultValue: string
Returns string

circularMean

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

- Defined in src/math/array-utils.ts:12
Parameters
- array: NumberArray
- max: number
- Default value stride: number = 1
- Default value offset: number = 0
- Optional indices: NumberArray
Returns number

circularMean3

circularMean3(indices: NumberArray, coords: NumberArray, box: ArrayLike<number>): number[]

- Defined in src/trajectory/trajectory.ts:95
Parameters
- indices: NumberArray
- coords: NumberArray
- box: ArrayLike<number>
Returns number[]

clamp

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

- Defined in src/math/math-utils.ts:49
Parameters
- value: number
- min: number
- max: number
Returns number

closer

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

- Defined in src/controls/picking-proxy.ts:30
Parameters
- x: Vector3
- a: Vector3
- b: Vector3
Returns boolean

computeBoundingBox

computeBoundingBox(array: NumberArray): Float32Array[]

- Defined in src/math/vector-utils.ts:97
Parameters
- array: NumberArray
Returns Float32Array[]

computeVertexNormals

computeVertexNormals(position: Float32Array, index?: NumberArray, normal?: Float32Array): Float32Array

- Defined in src/surface/surface-utils.ts:227
Parameters
- position: Float32Array
- Optional index: NumberArray
- Optional normal: Float32Array
Returns Float32Array

concatStructures

concatStructures(name: string, ...structures: Structure[]): Structure

- Defined in src/structure/structure-utils.ts:988
Parameters
- name: string
- Rest ...structures: Structure[]
Returns Structure

contactColor

contactColor(type: ContactType): number[]

- Defined in src/chemistry/interactions/contact.ts:219
Parameters
- type: ContactType
Returns number[]

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"

- Defined in src/chemistry/interactions/contact.ts:169
Parameters
- type: ContactType
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: RibbonObject): { breakArray: boolean[]; colorArray: number[]; labelArray: string[]; masterArray: any[]; name: undefined | string; positionArray: number[] }

- Defined in src/parser/kin-parser.ts:204
Parameters
- ribbonObject: RibbonObject
Returns { breakArray: boolean[]; colorArray: number[]; labelArray: string[]; masterArray: any[]; name: undefined | string; positionArray: number[] }
- breakArray: boolean[]
- colorArray: number[]
- labelArray: string[]
- masterArray: any[]
- name: undefined | string
- positionArray: number[]

copyArray

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

- Defined in src/math/array-utils.ts:215
Type parameters
- T: any[] | NumberArray
Parameters
- src: T
- dst: T
- srcOffset: number
- dstOffset: number
- length: number
Returns void

copyWithin

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

- Defined in src/math/array-utils.ts:221
Parameters
- array: NumberArray | any[]
- srcOffset: number
- dstOffset: number
- length: number
Returns void

countSetBits

countSetBits(i: number): number

- Defined in src/math/math-utils.ts:39
Parameters
- i: number
Returns number

createAdjacencyList

createAdjacencyList(edges: Edges): AdjacencyList

- Defined in src/utils/adjacency-list.ts:23
Parameters
- edges: Edges
Returns AdjacencyList

createBoundingBox

createBoundingBox(positions: Positions): Box3

- Defined in src/geometry/spatial-hash.ts:16
Parameters
- positions: Positions
Returns Box3

createColorArray

createColorArray(color: ColorDefinition, arrayLength: number): Float32Array

- Defined in src/representation/dihedral-histogram-representation.ts:80
Parameters
- color: ColorDefinition
- arrayLength: number
Returns Float32Array

createContacts

createContacts(features: Features): Contacts

- Defined in src/chemistry/interactions/contact.ts:94
Parameters
- features: Features
Returns Contacts

createData

createData(structure: Structure): Data

- Defined in src/structure/data.ts:12
Parameters
- structure: Structure
Returns Data

createFeatureState

createFeatureState(type?: FeatureType, group?: FeatureGroup): FeatureState

- Defined in src/chemistry/interactions/features.ts:64
Parameters
- Default value type: FeatureType = FeatureType.Unknown
- Default value group: FeatureGroup = FeatureGroup.Unknown
Returns FeatureState

createFeatures

createFeatures(): Features

- Defined in src/chemistry/interactions/features.ts:46
Returns Features

createFrozenContacts

createFrozenContacts(contacts: Contacts): FrozenContacts

- Defined in src/chemistry/interactions/contact.ts:104
Parameters
- contacts: Contacts
Returns FrozenContacts

createParams

createParams<T>(params: {}, defaultParams: T): T

- Defined in src/utils.ts:38
Type parameters
- T
Parameters
- params: {}
- defaultParams: T
Returns T

Private createProgram

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

- Defined in src/viewer/gl-utils.ts:10
file

Viewer

author

Alexander Rose alexander.rose@weirdbyte.de

Parameters
- gl: WebGLRenderingContext
- shaders: WebGLShader[]
- Optional attribs: string[]
- Optional locations: number[]
Returns undefined | null | WebGLProgram

createRingBuffer

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

- Defined in src/utils.ts:519
Type parameters
- T
Parameters
- length: number
Returns RingBuffer<T>

createSimpleDict

createSimpleDict<K, V>(): SimpleDict<K, V>

- Defined in src/utils.ts:549
Type parameters
- K
- V
Returns SimpleDict<K, V>

createSimpleSet

createSimpleSet<T>(): SimpleSet<T>

- Defined in src/utils.ts:567
Type parameters
- T
Returns SimpleSet<T>

createUpdatedObject

createUpdatedObject(o: Object, updateSource: Object): {}

- Defined in src/representation/dihedral-histogram-representation.ts:66
Parameters
- o: Object
- updateSource: Object
Returns {}

dataURItoImage

dataURItoImage(dataURI: string): HTMLImageElement

- Defined in src/utils.ts:381
Parameters
- dataURI: string
Returns HTMLImageElement

decodeBits

decodeBits(buf: Int32Array, cbuf: Uint8Array, numOfBits: number, buf2: Uint32Array): number

- Defined in src/parser/xtc-parser.ts:63
Parameters
- buf: Int32Array
- cbuf: Uint8Array
- numOfBits: number
- buf2: Uint32Array
Returns number

decodeInts

decodeInts(buf: Int32Array, cbuf: Uint8Array, numOfInts: number, numOfBits: number, sizes: NumberArray, nums: Float32Array, buf2: Uint32Array): void

- Defined in src/parser/xtc-parser.ts:95
Parameters
- buf: Int32Array
- cbuf: Uint8Array
- numOfInts: number
- numOfBits: number
- sizes: NumberArray
- nums: Float32Array
- buf2: Uint32Array
Returns void

deepCopy

deepCopy(src: any): any

- Defined in src/utils.ts:110
Parameters
- src: any
Returns any

deepEqual

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

- Defined in src/utils.ts:124
Parameters
- a: any
- b: any
Returns boolean

defaults

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

- Defined in src/utils.ts:34
Parameters
- value: any
- defaultValue: any
Returns any

Private degToRad

degToRad(deg: number): number

- Defined in src/math/math-utils.ts:7
file

Math Utils

author

Alexander Rose alexander.rose@weirdbyte.de

Parameters
- deg: number
Returns number

distance

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

- Defined in src/buffer/point-buffer.ts:18
Parameters
- x0: number
- y0: number
- x1: number
- y1: number
Returns number

download

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

- Defined in src/utils.ts:176
Parameters
- data: Blob | string
- Default value downloadName: string = "download"
Returns void

edt

edt(data: NumberArray, width: number, height: number, f: NumberArray, d: NumberArray, v: NumberArray, z: NumberArray): void

- Defined in src/utils/edt.ts:10
Parameters
- data: NumberArray
- width: number
- height: number
- f: NumberArray
- d: NumberArray
- v: NumberArray
- z: NumberArray
Returns void

edt1d

edt1d(f: NumberArray, d: NumberArray, v: NumberArray, z: NumberArray, n: number): void

- Defined in src/utils/edt.ts:32
Parameters
- f: NumberArray
- d: NumberArray
- v: NumberArray
- z: NumberArray
- n: number
Returns void

ensureArray

ensureArray(value: any): any[]

- Defined in src/utils.ts:469
Parameters
- value: any
Returns any[]

ensureBuffer

ensureBuffer(a: any): any

- Defined in src/utils.ts:473
Parameters
- a: any
Returns any

ensureFloat32Array

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

- Defined in src/utils.ts:506
Parameters
- Optional a: number[] | Float32Array
Returns any

ensureMatrix4

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

- Defined in src/utils.ts:498
Parameters
- Optional m: number[] | Matrix4
Returns any

ensureQuaternion

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

- Defined in src/utils.ts:502
Parameters
- Optional q: number[] | Quaternion
Returns any

ensureVector2

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

- Defined in src/utils.ts:490
Parameters
- Optional v: number[] | Vector2
Returns any

ensureVector3

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

- Defined in src/utils.ts:494
Parameters
- Optional v: number[] | Vector3
Returns any

entityFromType

entityFromType(type: number): undefined | "polymer" | "non-polymer" | "macrolide" | "water"

- Defined in src/structure/entity.ts:29
Parameters
- type: number
Returns undefined | "polymer" | "non-polymer" | "macrolide" | "water"

entityTypeFromString

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

- Defined in src/structure/entity.ts:13
Parameters
- string: string
Returns 1 | 0 | 4 | 2 | 3

euclideanDist

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

- Defined in src/geometry/kdtree.ts:22
Parameters
- a: number[]
- b: number[]
Returns number

euclideanDistSq

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

- Defined in src/geometry/kdtree.ts:15
Parameters
- a: number[]
- b: number[]
Returns number

explicitValence

explicitValence(a: AtomProxy): number

- Defined in src/chemistry/valence-model.ts:84
Parameters
- a: AtomProxy
Returns number

filter

filter(selection: SelectionRule, fn: FilterFn): null | SelectionRule

- Defined in src/selection/selection-test.ts:265
Parameters
- selection: SelectionRule
- fn: FilterFn
Returns null | SelectionRule

findRings

findRings(state: RingFinderState, from: number): void

- Defined in src/store/residue-type.ts:678
Parameters
- state: RingFinderState
- from: number
Returns void

flatten

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

- Defined in src/utils.ts:63
Parameters
- array: any[]
- ret: any[]
Returns any[]

generateUUID

generateUUID(): string

- Defined in src/math/math-utils.ts:19
Returns string

getAbsolutePath

getAbsolutePath(relativePath: string): string

- Defined in src/utils.ts:102
Parameters
- relativePath: string
Returns string

getAllowedContours

getAllowedContours(): number[][]

- Defined in src/surface/marching-cubes.ts:325
Returns number[][]

getAngleData

getAngleData(position: Float32Array, params?: Partial<StructureRepresentationParameters>): { arcPosition1: Float32Array; arcPosition2: Float32Array; labelPosition: Float32Array; labelText: any[]; sectorPosition: Float32Array; vectorPosition1: Float32Array; vectorPosition2: Float32Array }

- Defined in src/representation/angle-representation.ts:297
Converts triple positions into data required to build various buffers.

Parameters
- position: Float32Array
- Default value params: Partial<StructureRepresentationParameters> = {}
Returns { arcPosition1: Float32Array; arcPosition2: Float32Array; labelPosition: Float32Array; labelText: any[]; sectorPosition: Float32Array; vectorPosition1: Float32Array; vectorPosition2: Float32Array }
- arcPosition1: Float32Array
- arcPosition2: Float32Array
- labelPosition: Float32Array
- labelText: any[]
- sectorPosition: Float32Array
- vectorPosition1: Float32Array
- vectorPosition2: Float32Array

getAtomSele

getAtomSele(ap: AtomProxy): string

- Defined in src/structure/validation.ts:56
Parameters
- ap: AtomProxy
Returns string

getBondOrder

getBondOrder(valueOrder: string): 1 | 0 | 4 | 2 | 3

- Defined in src/parser/cif-parser.ts:55
Parameters
- valueOrder: string
Returns 1 | 0 | 4 | 2 | 3

getBondOrderFromTable

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

- Defined in src/structure/structure-utils.ts:569
Parameters
- resname: string
- atomname1: string
- atomname2: string
Returns number

getBrowser

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

- Defined in src/utils.ts:80
Returns false | "Opera" | "Chrome" | "Firefox" | "Mobile Safari" | "Internet Explorer" | "Safari"

getChainname

getChainname(index: number): string

- Defined in src/structure/structure-utils.ts:358
Parameters
- index: number
Returns string

getCharCount

getCharCount(data: TextBufferData, params: Partial<TextBufferParameters>): number

- Defined in src/buffer/text-buffer.ts:326
Parameters
- data: TextBufferData
- params: Partial<TextBufferParameters>
Returns number

getContactData

getContactData(contacts: FrozenContacts, structure: Structure, params: ContactDataParams): ContactData

- Defined in src/chemistry/interactions/contact.ts:253
Parameters
- contacts: FrozenContacts
- structure: Structure
- params: ContactDataParams
Returns ContactData

getData

getData(data: BufferData, geo: BufferGeometry): { color: Float32Array; index: undefined | Uint16Array | Uint32Array; normal: Float32Array; picking: undefined | Picker; position: Float32Array; primitiveId: Float32Array }

- Defined in src/buffer/geometry-buffer.ts:20
Parameters
- data: BufferData
- geo: BufferGeometry
Returns { color: Float32Array; index: undefined | Uint16Array | Uint32Array; normal: Float32Array; picking: undefined | Picker; position: Float32Array; primitiveId: Float32Array }
- color: Float32Array
- index: undefined | Uint16Array | Uint32Array
- normal: Float32Array
- picking: undefined | Picker
- position: Float32Array
- primitiveId: Float32Array

getDataInfo

getDataInfo(src: LoaderInput): { base: string; compressed: string | false | true; dir: string; ext: string; name: string; path: string; protocol: string; query: string; src: string | Blob | File }

- Defined in src/loader/loader-utils.ts:72
Parameters
- src: LoaderInput
Returns { base: string; compressed: string | false | true; dir: string; ext: string; name: string; path: string; protocol: string; query: string; src: string | Blob | File }
- base: string
- compressed: string | false | true
- dir: string
- ext: string
- name: string
- path: string
- protocol: string
- query: string
- src: string | Blob | File

getDefines

getDefines(defines: ShaderDefines): string

- Defined in src/shader/shader-utils.ts:31
Parameters
- defines: ShaderDefines
Returns string

getDihedralData

getDihedralData(position: Float32Array, params?: Partial<DihedralRepresentationParameters>): { labelPosition: Float32Array; labelText: any[]; linePosition1: Float32Array; linePosition2: Float32Array; planePosition: Float32Array; sectorPosition: Float32Array }

- Defined in src/representation/dihedral-representation.ts:266
Build the data required to create {Buffer} objects, given positions

Parameters
- position: Float32Array
- Default value params: Partial<DihedralRepresentationParameters> = {}
Returns { labelPosition: Float32Array; labelText: any[]; linePosition1: Float32Array; linePosition2: Float32Array; planePosition: Float32Array; sectorPosition: Float32Array }

Arrays for building buffers
- labelPosition: Float32Array
- labelText: any[]
- linePosition1: Float32Array
- linePosition2: Float32Array
- planePosition: Float32Array
- sectorPosition: Float32Array

getEdgeTable

getEdgeTable(): Uint32Array

- Defined in src/surface/marching-cubes.ts:9
Returns 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"

- Defined in src/viewer/gl-utils.ts:56
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

- Defined in src/viewer/gl-utils.ts:69
Parameters
- gl: WebGLRenderingContext
- name: string
Returns any

getFileInfo

getFileInfo(file: LoaderInput): { base: string; compressed: string | false | true; dir: string; ext: string; name: string; path: string; protocol: string; query: string; src: string | Blob | File }

- Defined in src/loader/loader-utils.ts:27
Parameters
- file: LoaderInput
Returns { base: string; compressed: string | false | true; dir: string; ext: string; name: string; path: string; protocol: string; query: string; src: string | Blob | File }
- base: string
- compressed: string | false | true
- dir: string
- ext: string
- name: string
- path: string
- protocol: string
- query: string
- src: string | Blob | File

getFixedCountDashData

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

- Defined in src/geometry/dash.ts:16
Type parameters
- T: CylinderBufferData | WideLineBufferData
Parameters
- data: T
- Default value segmentCount: number = 9
Returns T

getFixedLengthDashData

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

- Defined in src/geometry/dash.ts:75
Type parameters
- T: CylinderBufferData | WideLineBufferData
Parameters
- data: T
- Default value segmentLength: number = 0.1
Returns T

getFixedLengthWrappedDashData

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

- Defined in src/geometry/dash.ts:155
Type parameters
- T: CylinderBufferData | WideLineBufferData
Parameters
- data: T
- Default value segmentLength: number = 0.1
Returns T

getGeo

getGeo(params?: Partial<CylinderGeometryBufferParameters>): CylinderBufferGeometry

- Defined in src/buffer/cylindergeometry-buffer.ts:45
Parameters
- Default value params: Partial<CylinderGeometryBufferParameters> = {}
Returns CylinderBufferGeometry

getHash

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

- Defined in src/store/residue-map.ts:11
Parameters
- resname: string
- atomTypeIdList: number[]
- hetero: boolean
- Default value chemCompType: string = ""
Returns string

getHydrogenBondType

getHydrogenBondType(ap1: AtomProxy, ap2: AtomProxy): HydrogenBond | WaterHydrogenBond | BackboneHydrogenBond

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:178
Parameters
- ap1: AtomProxy
- ap2: AtomProxy
Returns HydrogenBond | WaterHydrogenBond | BackboneHydrogenBond

getLabelData

getLabelData(contactData: ContactData, params: ContactLabelParams): TextBufferData

- Defined in src/chemistry/interactions/contact.ts:323
Parameters
- contactData: ContactData
- params: ContactLabelParams
Returns TextBufferData

getLoneAtomSet

getLoneAtomSet(structure: Structure | StructureView): BitArray

- Defined in src/representation/line-representation.ts:31
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: Structure | StructureView
  
  The Structure or StructureView object
Returns BitArray

AtomSet of lone atoms

getModresId

getModresId(resno: number, chainname?: undefined | string, inscode?: undefined | string): string

- Defined in src/parser/pdb-parser.ts:73
Parameters
- resno: number
- Optional chainname: undefined | string
- Optional inscode: undefined | string
Returns string

getMouseButtons

getMouseButtons(event: MouseEvent): number

- Defined in src/stage/mouse-observer.ts:34
Parameters
- event: MouseEvent
Returns number

getNamedItem

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

- Defined in src/structure/validation.ts:17
Parameters
- a: NamedNodeMap
- name: string
Returns string

getProblemCount

getProblemCount(clashDict: {}, g: Element, ga: NamedNodeMap): number

- Defined in src/structure/validation.ts:70
Parameters
- clashDict: {}
  - [k: string]: {}
    - [k: string]: string
- g: Element
- ga: NamedNodeMap
Returns number

getProtocol

getProtocol(): string

- Defined in src/utils.ts:75
Returns string

getQuery

getQuery(id: string): undefined | string

- Defined in src/utils.ts:9
Parameters
- id: string
Returns undefined | string

getRadiusDict

getRadiusDict(radiusList: number[]): {}

- Defined in src/surface/surface-utils.ts:305
Parameters
- radiusList: number[]
Returns {}
- [k: number]: boolean

getResSele

getResSele(a: NamedNodeMap): string

- Defined in src/structure/validation.ts:35
Parameters
- a: NamedNodeMap
Returns string

getSele

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

- Defined in src/structure/validation.ts:22
Parameters
- a: NamedNodeMap
- Optional atomname: undefined | string
- Default value useAltcode: boolean = false
Returns string

getShader

getShader(name: string, defines?: ShaderDefines): string

- Defined in src/shader/shader-utils.ts:50
Parameters
- name: string
- Default value defines: ShaderDefines = {}
Returns string

getSize

getSize(data: BufferData): number

- Defined in src/buffer/vector-buffer.ts:16
Parameters
- data: BufferData
Returns number

getSurfaceGrid

getSurfaceGrid(min: Float32Array, max: Float32Array, maxRadius: number, scaleFactor: number, extraMargin: number): { dim: Float32Array; matrix: Float32Array; scaleFactor: number; tran: Float32Array }

- Defined in src/surface/surface-utils.ts:313
Parameters
- min: Float32Array
- max: Float32Array
- maxRadius: number
- scaleFactor: number
- extraMargin: number
Returns { dim: Float32Array; matrix: Float32Array; scaleFactor: number; tran: Float32Array }
- dim: Float32Array
- matrix: Float32Array
- scaleFactor: number
- tran: Float32Array

getSymmetryOperations

getSymmetryOperations(spacegroup: string): {}

- Defined in src/symmetry/symmetry-utils.ts:14
Parameters
- spacegroup: string
Returns {}
- [k: string]: Matrix4

getTextAtlas

getTextAtlas(params: Partial<TextAtlasParams>): TextAtlas

- Defined in src/buffer/text-buffer.ts:22
Parameters
- params: Partial<TextAtlasParams>
Returns TextAtlas

getThreeSide

getThreeSide(side: BufferSide): Side

- Defined in src/buffer/buffer.ts:27
Parameters
- side: BufferSide
Returns Side

getTouchDistance

getTouchDistance(event: TouchEvent): number

- Defined in src/stage/mouse-observer.ts:28
example

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

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

- Defined in src/surface/marching-cubes.ts:46
Returns Int32Array

getTypedArray

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

- Defined in src/utils.ts:443
Parameters
- arrayType: TypedArrayString
- arraySize: number
Returns Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array

getUintArray

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

- Defined in src/utils.ts:464
Parameters
- sizeOrArray: any
- maxUint: number
Returns Uint16Array | Uint32Array

getWorkerDeps

getWorkerDeps(vars: FunctionWithDeps[]): ({ __deps?: Function[] } & Function)[]

- Defined in src/worker/worker-utils.ts:17
Parameters
- vars: FunctionWithDeps[]
Returns ({ __deps?: Function[] } & Function)[]

guessElement

guessElement(atomName: string): string

- Defined in src/structure/structure-utils.ts:901
Parameters
- atomName: string
Returns string

gzipDecompress

gzipDecompress(data: ArrayBuffer | Uint8Array): ArrayBuffer

- Defined in src/utils/gzip-decompressor.ts:11
Parameters
- data: ArrayBuffer | Uint8Array
Returns ArrayBuffer

hammingWeight

hammingWeight(v: number): number

- Defined in src/utils/bitarray.ts:13
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

- Defined in src/chemistry/functional-groups.ts:203
Parameters
- a: AtomProxy
Returns boolean

hasAttrValue

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

- Defined in src/structure/validation.ts:52
Parameters
- attr: Attr | null
- value: string
Returns boolean

hasPolarNeighbour

hasPolarNeighbour(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:195
Parameters
- a: AtomProxy
Returns boolean

hasValue

hasValue(d: string): boolean

- Defined in src/parser/cif-parser.ts:47
Parameters
- d: string
Returns boolean

hsvToRgb

hsvToRgb(h: number, s: number, v: number): number[]

- Defined in src/parser/kin-parser.ts:11
Parameters
- h: number
- s: number
- v: number
Returns number[]

hypot

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

- Defined in src/math/matrix-utils.ts:311
Parameters
- a: number
- b: number
Returns number

inAromaticRingWithElectronNegativeElement

inAromaticRingWithElectronNegativeElement(a: AtomProxy): boolean

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:75
Parameters
- a: AtomProxy
Returns boolean

interpolateLerp

interpolateLerp(c: NumberArray, cp: NumberArray, t: number): Float32Array

- Defined in src/trajectory/trajectory.ts:126
Parameters
- c: NumberArray
- cp: NumberArray
- t: number
Returns Float32Array

interpolateSpline

interpolateSpline(c: NumberArray, cp: NumberArray, cpp: NumberArray, cppp: NumberArray, t: number): Float32Array

- Defined in src/trajectory/trajectory.ts:111
Parameters
- c: NumberArray
- cp: NumberArray
- cpp: NumberArray
- cppp: NumberArray
- t: number
Returns Float32Array

invalidAtomContact

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

- Defined in src/chemistry/interactions/refine-contacts.ts:23
Parameters
- ap1: AtomProxy
- ap2: AtomProxy
- masterIdx: number
Returns false | true | ""

invert3x3

invert3x3(from: Matrix, to: Matrix): void

- Defined in src/math/matrix-utils.ts:134
Parameters
- from: Matrix
- to: Matrix
Returns void

isAcetamidine

isAcetamidine(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:169
Carbon in a acetamidine group

Parameters
- a: AtomProxy
Returns boolean

isAmide

isAmide(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:49
Nitrogen in an amide

Parameters
- a: AtomProxy
Returns boolean

isBackboneHydrogenBond

isBackboneHydrogenBond(ap1: AtomProxy, ap2: AtomProxy): boolean

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:156
Parameters
- ap1: AtomProxy
- ap2: AtomProxy
Returns boolean

isCarbonyl

isCarbonyl(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:116
Carbon in a carbonyl/acyl group

Parameters
- a: AtomProxy
Returns boolean

isCarboxylate

isCarboxylate(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:131
Carbon in a carboxylate group

Parameters
- a: AtomProxy
Returns boolean

isCationPi

isCationPi(ti: FeatureType, tj: FeatureType): boolean

- Defined in src/chemistry/interactions/charged.ts:166
Parameters
- ti: FeatureType
- tj: FeatureType
Returns boolean

isConjugated

isConjugated(a: AtomProxy): boolean

- Defined in src/chemistry/valence-model.ts:31
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
- a: AtomProxy
Returns boolean

isGuanidine

isGuanidine(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:150
Carbon in a guanidine group

Parameters
- a: AtomProxy
Returns boolean

isHalocarbon

isHalocarbon(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:105
Halogen with one bond to a carbon

Parameters
- a: AtomProxy
Returns boolean

isHalogenBond

isHalogenBond(ti: FeatureType, tj: FeatureType): boolean

- Defined in src/chemistry/interactions/halogen-bonds.ts:57
Parameters
- ti: FeatureType
- tj: FeatureType
Returns boolean

isHistidineNitrogen

isHistidineNitrogen(ap: AtomProxy): boolean

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:152
Atom that is only bound to carbon or hydrogen

Parameters
- ap: AtomProxy
Returns boolean

isHydrogenBond

isHydrogenBond(ti: FeatureType, tj: FeatureType): boolean

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:164
Parameters
- ti: FeatureType
- tj: FeatureType
Returns boolean

isHydrogenBondType

isHydrogenBondType(type: number): boolean

- Defined in src/chemistry/interactions/refine-contacts.ts:125
Parameters
- type: number
Returns boolean

isHydrophobicContact

isHydrophobicContact(ti: FeatureType, tj: FeatureType): boolean

- Defined in src/chemistry/interactions/hydrophobic.ts:38
Parameters
- ti: FeatureType
- tj: FeatureType
Returns boolean

isImide

isImide(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:34
Nitrogen in an imide

Parameters
- a: AtomProxy
Returns boolean

isIonicInteraction

isIonicInteraction(ti: FeatureType, tj: FeatureType): boolean

- Defined in src/chemistry/interactions/charged.ts:155
Parameters
- ti: FeatureType
- tj: FeatureType
Returns boolean

isMasterContact

isMasterContact(ap1: AtomProxy, ap2: AtomProxy, masterIdx: number): boolean

- Defined in src/chemistry/interactions/contact.ts:79
Parameters
- ap1: AtomProxy
- ap2: AtomProxy
- masterIdx: number
Returns boolean

isMetalComplex

isMetalComplex(ti: FeatureType, tj: FeatureType): undefined | false | true

- Defined in src/chemistry/interactions/metal-binding.ts:188
Parameters
- ti: FeatureType
- tj: FeatureType
Returns undefined | false | true

isPhosphate

isPhosphate(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:95
Phosphor in a phosphate group

Parameters
- a: AtomProxy
Returns boolean

isPiStacking

isPiStacking(ti: FeatureType, tj: FeatureType): boolean

- Defined in src/chemistry/interactions/charged.ts:162
Parameters
- ti: FeatureType
- tj: FeatureType
Returns boolean

isPointOnSegment

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

- Defined in src/math/vector-utils.ts:81
Parameters
- p: Vector3
- l1: Vector3
- l2: Vector3
Returns boolean

isPolar

isPolar(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:191
Parameters
- a: AtomProxy
Returns boolean

isQuaternaryAmine

isQuaternaryAmine(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:12
Nitrogen in a quaternary amine

Parameters
- a: AtomProxy
Returns boolean

isRingAromatic

isRingAromatic(ring: AtomProxy[]): boolean

- Defined in src/store/residue-type.ts:586
Parameters
- ring: AtomProxy[]
Returns boolean

isSulfate

isSulfate(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:85
Sulfur in a sulfate group

Parameters
- a: AtomProxy
Returns boolean

isSulfonicAcid

isSulfonicAcid(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:75
Sulfur in a sulfonic acid or sulfonate group

Parameters
- a: AtomProxy
Returns boolean

isSulfonium

isSulfonium(a: AtomProxy): boolean

- Defined in src/chemistry/functional-groups.ts:64
Sulfur in a sulfonium group

Parameters
- a: AtomProxy
Returns boolean

isTertiaryAmine

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

- Defined in src/chemistry/functional-groups.ts:23
Nitrogen in a tertiary amine

Parameters
- a: AtomProxy
- idealValence: number
Returns boolean

isWaterHydrogenBond

isWaterHydrogenBond(ap1: AtomProxy, ap2: AtomProxy): boolean

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:160
Parameters
- ap1: AtomProxy
- ap2: AtomProxy
Returns boolean

isWeakHydrogenBond

isWeakHydrogenBond(ti: FeatureType, tj: FeatureType): boolean

- Defined in src/chemistry/interactions/hydrogen-bonds.ts:171
Parameters
- ti: FeatureType
- tj: FeatureType
Returns boolean

laplacianSmooth

laplacianSmooth(verts: Float32Array, faces: Float32Array, numiter: number, inflate: boolean): void

- Defined in src/surface/surface-utils.ts:18
Parameters
- verts: Float32Array
- faces: Float32Array
- numiter: number
- inflate: boolean
Returns void

lerp

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

- Defined in src/math/math-utils.ts:61
Parameters
- start: number
- stop: number
- alpha: number
Returns number

lexicographicCompare

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

- Defined in src/utils.ts:305
Type parameters
- T
Parameters
- elm1: T
- elm2: T
Returns 1 | -1 | 0

lineLineIntersect

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

- Defined in src/math/vector-utils.ts:17
Calculate the two intersection points Converted to JavaScript from http://paulbourke.net/geometry/pointlineplane/lineline.c

Parameters
- p1: Vector3
- p2: Vector3
- p3: Vector3
- p4: Vector3
Returns null | Vector3[]

loadShader

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

- Defined in src/viewer/gl-utils.ts:34
Parameters
- gl: WebGLRenderingContext
- shaderSource: string
- shaderType: number
Returns undefined | null | WebGLShader

logReprUnknown

logReprUnknown(type: string): void

- Defined in src/representation/representation-utils.ts:20
Parameters
- type: string
Returns void

m3makeNormal

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

- Defined in src/math/matrix-utils.ts:714
Parameters
- out: Float32Array
- m4: Float32Array
Returns void

m3new

m3new(): Float32Array

- Defined in src/math/matrix-utils.ts:706
Returns Float32Array

m4identity

m4identity(out: Float32Array): void

- Defined in src/math/matrix-utils.ts:606
Parameters
- out: Float32Array
Returns void

m4makeRotationY

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

- Defined in src/math/matrix-utils.ts:692
Parameters
- out: Float32Array
- theta: number
Returns void

m4makeScale

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

- Defined in src/math/matrix-utils.ts:672
Parameters
- out: Float32Array
- x: number
- y: number
- z: number
Returns void

m4makeTranslation

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

- Defined in src/math/matrix-utils.ts:682
Parameters
- out: Float32Array
- x: number
- y: number
- z: number
Returns void

m4multiply

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

- Defined in src/math/matrix-utils.ts:616
Parameters
- out: Float32Array
- a: Float32Array
- b: Float32Array
Returns void

m4new

m4new(): Float32Array

- Defined in src/math/matrix-utils.ts:590
Returns 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

- Defined in src/math/matrix-utils.ts:599
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

makeAVHash

makeAVHash(atomsX: Float32Array, atomsY: Float32Array, atomsZ: Float32Array, atomsR: Float32Array, min: Float32Array, max: Float32Array, maxDistance: number): iAVHash

- Defined in src/surface/av-surface.ts:41
Parameters
- atomsX: Float32Array
- atomsY: Float32Array
- atomsZ: Float32Array
- atomsR: Float32Array
- min: Float32Array
- max: Float32Array
- maxDistance: number
Returns iAVHash

makeAtomTest

makeAtomTest(selection: SelectionRule, atomOnly?: boolean): false | ((e: ProxyEntity) => boolean | -1)

- Defined in src/selection/selection-test.ts:301
Parameters
- selection: SelectionRule
- Default value atomOnly: boolean = false
Returns false | ((e: ProxyEntity) => boolean | -1)

makeChainTest

makeChainTest(selection: SelectionRule, chainOnly?: boolean): false | ((e: ProxyEntity) => boolean | -1)

- Defined in src/selection/selection-test.ts:333
Parameters
- selection: SelectionRule
- Default value chainOnly: boolean = false
Returns false | ((e: ProxyEntity) => boolean | -1)

makeGrid

makeGrid(length: number, width: number, height: number, DataCtor: any, elemSize: number): iGrid

- Defined in src/geometry/grid.ts:18
Parameters
- length: number
- width: number
- height: number
- DataCtor: any
- elemSize: number
Returns iGrid

makeImage

makeImage(viewer: Viewer, params?: Partial<ImageParameters>): Promise<Blob>

- Defined in src/viewer/viewer-utils.ts:134
Make image from what is shown in a viewer canvas

Parameters
- viewer: Viewer
  
  the viewer
- Default value params: Partial<ImageParameters> = {}
  
  parameters object
Returns Promise<Blob>

A Promise object that resolves to an image {@link Blob}.

makeModelTest

makeModelTest(selection: SelectionRule, modelOnly?: boolean): false | ((e: ProxyEntity) => boolean | -1)

- Defined in src/selection/selection-test.ts:352
Parameters
- selection: SelectionRule
- Default value modelOnly: boolean = false
Returns false | ((e: ProxyEntity) => boolean | -1)

makePointTexture

makePointTexture(params: PointTextureParams): DataTexture

- Defined in src/buffer/point-buffer.ts:30
Parameters
- params: PointTextureParams
Returns DataTexture

makeRepresentation

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

- Defined in src/representation/representation-utils.ts:24
Parameters
- type: string
- object: any
- viewer: Viewer
- params: any
Returns any

makeResidueTest

makeResidueTest(selection: SelectionRule, residueOnly?: boolean): false | ((e: ProxyEntity) => boolean | -1)

- Defined in src/selection/selection-test.ts:317
Parameters
- selection: SelectionRule
- Default value residueOnly: boolean = false
Returns false | ((e: ProxyEntity) => boolean | -1)

makeTest

makeTest(selection: SelectionRule | null, fn: TestEntityFn): false | ((e: ProxyEntity) => boolean | -1)

- Defined in src/selection/selection-test.ts:189
Parameters
- selection: SelectionRule | null
- fn: TestEntityFn
Returns false | ((e: ProxyEntity) => boolean | -1)

makeTrajectory

makeTrajectory(trajSrc: string | Frames, structure: Structure, params: TrajectoryParameters): FramesTrajectory | StructureTrajectory | RemoteTrajectory | CallbackTrajectory

- Defined in src/trajectory/trajectory-utils.ts:15
Parameters
- trajSrc: string | Frames
- structure: Structure
- params: TrajectoryParameters
Returns FramesTrajectory | StructureTrajectory | RemoteTrajectory | CallbackTrajectory

makeWorkerBlob

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

- Defined in src/worker/worker-utils.ts:59
Parameters
- func: Function
- deps: Function[]
Returns Blob

makeWorkerString

makeWorkerString(vars: any): string

- Defined in src/worker/worker-utils.ts:27
Parameters
- vars: any
Returns string

mat3x3determinant

mat3x3determinant(M: Matrix): number

- Defined in src/math/matrix-utils.ts:165
Parameters
- M: Matrix
Returns number

matchName

matchName(name: string | RegExp, object: { name: string }): boolean

- Defined in src/stage/stage.ts:50
Parameters
- name: string | RegExp
- object: { name: string }
  - name: string
Returns boolean

meanCols

meanCols(A: Matrix): any[]

- Defined in src/math/matrix-utils.ts:234
Parameters
- A: Matrix
Returns any[]

meanRows

meanRows(A: Matrix): any[]

- Defined in src/math/matrix-utils.ts:211
Parameters
- A: Matrix
Returns any[]

modelTestFn

modelTestFn(m: ModelProxy, s: SelectionRule): false | true | -1

- Defined in src/selection/selection-test.ts:176
Parameters
- m: ModelProxy
- s: SelectionRule
Returns false | true | -1

multiply

multiply(C: Matrix, A: Matrix, B: Matrix): void

- Defined in src/math/matrix-utils.ts:44
Parameters
- C: Matrix
- A: Matrix
- B: Matrix
Returns void

multiply3x3

multiply3x3(C: Matrix, A: Matrix, B: Matrix): void

- Defined in src/math/matrix-utils.ts:176
Parameters
- C: Matrix
- A: Matrix
- B: Matrix
Returns void

multiplyABt

multiplyABt(C: Matrix, A: Matrix, B: Matrix): void

- Defined in src/math/matrix-utils.ts:75
Parameters
- C: Matrix
- A: Matrix
- B: Matrix
Returns void

multiplyAtB

multiplyAtB(C: Matrix, A: Matrix, B: Matrix): void

- Defined in src/math/matrix-utils.ts:104
Parameters
- C: Matrix
- A: Matrix
- B: Matrix
Returns void

normalize

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

- Defined in src/math/math-utils.ts:45
Parameters
- value: number
- min: number
- max: number
Returns number

normalizeVector3array

normalizeVector3array(a: Float32Array): void

- Defined in src/math/vector-utils.ts:144
Parameters
- a: Float32Array
Returns void

onBeforeRender

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

- Defined in src/viewer/viewer.ts:56
Parameters
- this: Object3D
- renderer: WebGLRenderer
- scene: Scene
- camera: PerspectiveCamera | OrthographicCamera
- geometry: Geometry
- material: ShaderMaterial
Returns void

onmessage

onmessage(e: WorkerEvent): void

- Defined in src/worker/worker-utils.ts:34
Parameters
- e: WorkerEvent
Returns void

open

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

- Defined in src/utils.ts:251
Parameters
- callback: Function
- Default value extensionList: string[] = ['*']
Returns void

openUrl

openUrl(url: string): void

- Defined in src/utils.ts:169
Parameters
- url: string
Returns void

parseChemComp

parseChemComp(cif: Cif, structure: Structure, structureBuilder: StructureBuilder): void

- Defined in src/parser/cif-parser.ts:70
Parameters
- cif: Cif
- structure: Structure
- structureBuilder: StructureBuilder
Returns void

parseCore

parseCore(cif: Cif, structure: Structure, structureBuilder: StructureBuilder): void

- Defined in src/parser/cif-parser.ts:166
Parameters
- cif: Cif
- structure: Structure
- structureBuilder: StructureBuilder
Returns void

parseFlag

parseFlag(line: string): undefined | string

- Defined in src/parser/kin-parser.ts:160
Parameters
- line: string
Returns undefined | string

parseGroup

parseGroup(line: string): { groupFlags: {}; groupMasters: string[]; groupName: string }

- Defined in src/parser/kin-parser.ts:165
Parameters
- line: string
Returns { groupFlags: {}; groupMasters: string[]; groupName: string }
- groupFlags: {}
  - [k: string]: string | boolean
- groupMasters: string[]
- groupName: string

parseIntSubstr

parseIntSubstr(line: string, start: number, length: number): number

- Defined in src/parser/prmtop-parser.ts:29
Parameters
- line: string
- start: number
- length: number
Returns number

parseListDef

parseListDef(line: string): { listColor: undefined | number[]; listMasters: string[]; listName: undefined | string; listWidth: undefined | number }

- Defined in src/parser/kin-parser.ts:69
Parameters
- line: string
Returns { listColor: undefined | number[]; listMasters: string[]; listName: undefined | string; listWidth: undefined | number }
- listColor: undefined | number[]
- listMasters: string[]
- listName: undefined | string
- listWidth: undefined | number

parseListElm

parseListElm(line: string): { color: undefined | number[]; isLineBreak: boolean; isTriangleBreak: boolean; label: string; position: number[]; radius: undefined | number; width: undefined | number }

- Defined in src/parser/kin-parser.ts:104
Parameters
- line: string
Returns { color: undefined | number[]; isLineBreak: boolean; isTriangleBreak: boolean; label: string; position: number[]; radius: undefined | number; width: undefined | number }
- color: undefined | number[]
- isLineBreak: boolean
- isTriangleBreak: boolean
- label: string
- position: number[]
- radius: undefined | number
- width: undefined | number

parseNestedAtoms

parseNestedAtoms(sview: StructureView, atoms: (string | number)[][]): Float32Array

- Defined in src/representation/measurement-representation.ts:334
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: StructureView
  
  The structure to which the atoms refer
- atoms: (string | number)[][]
  
  Nested array of atom pairs|triples|quads as Integer indices or selection expressions
Returns Float32Array

Flattened array of position coordinates

parseNumberLine

parseNumberLine(line: string): number[]

- Defined in src/parser/xplor-parser.ts:14
Parameters
- line: string
Returns number[]

parseSele

parseSele(string: string): SelectionRule

- Defined in src/selection/selection-parser.ts:15
Parameters
- string: string
Returns SelectionRule

parseStr

parseStr(line: string): string

- Defined in src/parser/kin-parser.ts:151
Parameters
- line: string
Returns string

parseXml

parseXml(xml: string): { declaration: undefined | XMLNode; root: undefined | XMLNode }

- Defined in src/utils/parse-xml.ts:27
Parameters
- xml: string
Returns { declaration: undefined | XMLNode; root: undefined | XMLNode }
- declaration: undefined | XMLNode
- root: undefined | XMLNode

pclamp

pclamp(value: number): number

- Defined in src/math/math-utils.ts:53
Parameters
- value: number
Returns number

pick

pick(object: {}): any

- Defined in src/utils.ts:55
Parameters
- object: {}
  - [index: string]: any
Returns any

prepareMatrix

prepareMatrix(cellNames: string, mat: number[][]): {}

- Defined in src/align/alignment.ts:63
Parameters
- cellNames: string
- mat: number[][]
Returns {}
- [k: string]: {}
  - [k: string]: number

processConnections

processConnections(cif: Cif, structure: Structure, asymIdDict: {}): void

- Defined in src/parser/cif-parser.ts:588
Parameters
- cif: Cif
- structure: Structure
- asymIdDict: {}
  - [k: string]: string
Returns void

processEntities

processEntities(cif: Cif, structure: Structure, chainIndexDict: {}): void

- Defined in src/parser/cif-parser.ts:707
Parameters
- cif: Cif
- structure: Structure
- chainIndexDict: {}
  - [k: string]: Set<number>
Returns void

processSecondaryStructure

processSecondaryStructure(cif: Cif, structure: Structure, asymIdDict: {}): false | { helices: [string, number, string, string, number, string, number][]; sheets: [string, number, string, string, number, string][] }

- Defined in src/parser/cif-parser.ts:279
Parameters
- cif: Cif
- structure: Structure
- asymIdDict: {}
  - [k: string]: string
Returns false | { helices: [string, number, string, string, number, string, number][]; sheets: [string, number, string, string, number, string][] }

processSymmetry

processSymmetry(cif: Cif, structure: Structure, asymIdDict: {}): void

- Defined in src/parser/cif-parser.ts:339
Parameters
- cif: Cif
- structure: Structure
- asymIdDict: {}
  - [k: string]: string
Returns void

projectPointOnVector

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

- Defined in src/math/vector-utils.ts:87
Parameters
- point: Vector3
- vector: Vector3
- Optional origin: Vector3
Returns Vector3

quickselectCmp

quickselectCmp<T>(arr: NumberArray | T[], n: number, cmp?: undefined | ((a: number | T, b: number | T) => number), left?: number, right?: undefined | number): number | T

- Defined in src/math/array-utils.ts:436
Type parameters
- T
Parameters
- arr: NumberArray | T[]
- n: number
- Optional cmp: undefined | ((a: number | T, b: number | T) => number)
- Default value left: number = 0
- Optional right: undefined | number
Returns number | T

quicksortCmp

quicksortCmp<T>(arr: NumberArray | T[], cmp?: undefined | ((a: number | T, b: number | T) => number), begin?: number, end?: undefined | number): Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[] | T[]

- Defined in src/math/array-utils.ts:349
Type parameters
- T
Parameters
- arr: NumberArray | T[]
- Optional cmp: undefined | ((a: number | T, b: number | T) => number)
- Default value begin: number = 0
- Optional end: undefined | number
Returns Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[] | T[]

quicksortIP

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

- Defined in src/math/array-utils.ts:251
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 Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[]

the input array

radToDeg

radToDeg(rad: number): number

- Defined in src/math/math-utils.ts:11
Parameters
- rad: number
Returns number

randomColor

randomColor(): number

- Defined in src/color/random-colormaker.ts:10
Returns number

randomColorArray

randomColorArray(n: number): Float32Array

- Defined in src/math/array-utils.ts:139
Parameters
- n: number
Returns Float32Array

rangeInSortedArray

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

- Defined in src/utils.ts:371
Parameters
- array: number[]
- min: number
- max: number
Returns number

refineHydrophobicContacts

refineHydrophobicContacts(structure: Structure, contacts: FrozenContacts): void

- Defined in src/chemistry/interactions/refine-contacts.ts:92
For atoms interacting with several atoms in the same residue only the one with the closest distance is kept.

Parameters
- structure: Structure
- contacts: FrozenContacts
Returns void

refineLineOfSight

refineLineOfSight(structure: Structure, contacts: FrozenContacts, params?: LineOfSightParams): void

- Defined in src/chemistry/interactions/refine-contacts.ts:30
Parameters
- structure: Structure
- contacts: FrozenContacts
- Default value params: LineOfSightParams = {}
Returns void

refineMetalCoordination

refineMetalCoordination(structure: Structure, contacts: FrozenContacts): void

- Defined in src/chemistry/interactions/refine-contacts.ts:249
Remove ionic interactions between groups that also form a metal coordination between each other

Parameters
- structure: Structure
- contacts: FrozenContacts
Returns void

refinePiStacking

refinePiStacking(structure: Structure, contacts: FrozenContacts): void

- Defined in src/chemistry/interactions/refine-contacts.ts:207
Remove hydrophobic and cation-pi interactions between groups that also form a pi-stacking interaction between each other

Parameters
- structure: Structure
- contacts: FrozenContacts
Returns void

refineSaltBridges

refineSaltBridges(structure: Structure, contacts: FrozenContacts): void

- Defined in src/chemistry/interactions/refine-contacts.ts:168
Remove hydrogen bonds between groups that also form a salt bridge between each other

Parameters
- structure: Structure
- contacts: FrozenContacts
Returns void

refineWeakHydrogenBonds

refineWeakHydrogenBonds(structure: Structure, contacts: FrozenContacts): void

- Defined in src/chemistry/interactions/refine-contacts.ts:137
Remove weak hydrogen bonds when the acceptor is involved in a normal/strong hydrogen bond

Parameters
- structure: Structure
- contacts: FrozenContacts
Returns void

removePbc

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

- Defined in src/trajectory/trajectory.ts:46
Parameters
- x: NumberArray
- box: ArrayLike<number>
Returns undefined | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[]

removePeriodicity

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

- Defined in src/trajectory/trajectory.ts:77
Parameters
- x: NumberArray
- box: ArrayLike<number>
- mean: number[]
Returns undefined | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[]

removePointBreaksTriangleArrays

removePointBreaksTriangleArrays(convertedRibbonObject: RibbonObject): { breakArray: boolean[]; colorArray: number[]; labelArray: string[]; masterArray: any[]; name: undefined | string; positionArray: number[] }

- Defined in src/parser/kin-parser.ts:249
Parameters
- convertedRibbonObject: RibbonObject
Returns { breakArray: boolean[]; colorArray: number[]; labelArray: string[]; masterArray: any[]; name: undefined | string; positionArray: number[] }
- breakArray: boolean[]
- colorArray: number[]
- labelArray: string[]
- masterArray: any[]
- name: undefined | string
- positionArray: number[]

reorderAtoms

reorderAtoms(structure: Structure): void

- Defined in src/structure/structure-utils.ts:22
Parameters
- structure: Structure
Returns void

replicateArray3Entries

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

- Defined in src/math/array-utils.ts:169
Parameters
- array: NumberArray
- m: number
Returns Float32Array

replicateArrayEntries

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

- Defined in src/math/array-utils.ts:153
Parameters
- array: NumberArray
- m: number
Returns Float32Array

residueTestFn

residueTestFn(r: ResidueProxy, s: SelectionRule): false | true | -1

- Defined in src/selection/selection-test.ts:104
Parameters
- r: ResidueProxy
- s: SelectionRule
Returns false | true | -1

saturate

saturate(value: number): number

- Defined in src/math/math-utils.ts:57
Parameters
- value: number
Returns number

selectionFromChains

selectionFromChains(chainList: string[]): Selection

- Defined in src/symmetry/assembly.ts:14
Parameters
- chainList: string[]
Returns Selection

serialArray

serialArray(n: number): Float32Array

- Defined in src/math/array-utils.ts:115
Parameters
- n: number
Returns Float32Array

serialBlockArray

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

- Defined in src/math/array-utils.ts:125
Parameters
- n: number
- b: number
- Default value offset: number = 0
- Optional optionalTarget: NumberArray
Returns Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[]

setBitDict

setBitDict(dict: {}, key: string, bit: number): void

- Defined in src/structure/validation.ts:44
Parameters
- dict: {}
  - [k: string]: number
- key: string
- bit: number
Returns void

setDebug

setDebug(value: boolean): void

- Defined in src/globals.ts:85
Parameters
- value: boolean
Returns void

setExtensionFragDepth

setExtensionFragDepth(value: boolean): void

- Defined in src/globals.ts:49
Parameters
- value: boolean
Returns void

setListingDatasource

setListingDatasource(value: boolean): void

- Defined in src/globals.ts:108
Parameters
- value: boolean
Returns void

setMeasurementDefaultParams

setMeasurementDefaultParams(params?: {}): void

- Defined in src/globals.ts:80
Parameters
- Default value params: {} = {}
Returns void

setObjectMatrix

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

- Defined in src/buffer/buffer.ts:43
Parameters
- object: Object3D
- matrix: Matrix4
Returns void

setSupportsReadPixelsFloat

setSupportsReadPixelsFloat(value: boolean): void

- Defined in src/globals.ts:40
Parameters
- value: boolean
Returns void

setTrajectoryDatasource

setTrajectoryDatasource(value: boolean): void

- Defined in src/globals.ts:113
Parameters
- value: boolean
Returns void

setVisibilityFalse

setVisibilityFalse(m: Object3D): void

- Defined in src/buffer/doublesided-buffer.ts:14
Parameters
- m: Object3D
Returns void

setVisibilityTrue

setVisibilityTrue(m: Object3D): void

- Defined in src/buffer/doublesided-buffer.ts:13
Parameters
- m: Object3D
Returns void

sizeOfInt

sizeOfInt(size: number): number

- Defined in src/parser/xtc-parser.ts:24
Parameters
- size: number
Returns number

sizeOfInts

sizeOfInts(numOfInts: number, sizes: Int32Array): number

- Defined in src/parser/xtc-parser.ts:36
Parameters
- numOfInts: number
- sizes: Int32Array
Returns number

smootherstep

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

- Defined in src/math/math-utils.ts:80
Parameters
- min: number
- max: number
- x: number
Returns number

smootheststep

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

- Defined in src/math/math-utils.ts:85
Parameters
- min: number
- max: number
- x: number
Returns number

smoothstep

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

- Defined in src/math/math-utils.ts:75
Parameters
- min: number
- max: number
- x: number
Returns number

sortProjectedPosition

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

- Defined in src/viewer/viewer-utils.ts:229
Parameters
- scene: Scene
- camera: Camera
Returns void

spatialLookup

spatialLookup(data: Data): SpatialHash

- Defined in src/structure/data.ts:20
Parameters
- data: Data
Returns SpatialHash

spline

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

- Defined in src/math/math-utils.ts:65
Parameters
- p0: number
- p1: number
- p2: number
- p3: number
- t: number
- tension: number
Returns number

strip

strip(val: string): string

- Defined in src/utils/parse-xml.ts:23
Parameters
- val: string
Returns string

subCols

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

- Defined in src/math/matrix-utils.ts:269
Parameters
- A: Matrix
- col: number[]
Returns void

subRows

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

- Defined in src/math/matrix-utils.ts:257
Parameters
- A: Matrix
- row: number[]
Returns void

submit

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

- Defined in src/utils.ts:230
Parameters
- url: string
- data: FormData
- callback: Function
- onerror: Function
Returns void

superpose

superpose(s1: Structure, s2: Structure, align?: boolean, sele1?: string, sele2?: string): undefined | number | Matrix4

- Defined in src/align/align-utils.ts:22
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 undefined | number | Matrix4

svd

svd(A: Matrix, W: Matrix, U: Matrix, V: Matrix): void

- Defined in src/math/matrix-utils.ts:538
Parameters
- A: Matrix
- W: Matrix
- U: Matrix
- V: Matrix
Returns void

testTextureSupport

testTextureSupport(type: number): boolean

- Defined in src/viewer/gl-utils.ts:95
Parameters
- type: number
Returns boolean

throttle

throttle(func: Function, wait: number, options: { leading?: undefined | false | true; trailing?: undefined | false | true }): throttle

- Defined in src/utils.ts:265
Parameters
- func: Function
- wait: number
- options: { leading?: undefined | false | true; trailing?: undefined | false | true }
  - Optional leading?: undefined | false | true
  - Optional trailing?: undefined | false | true
Returns throttle

toLowerCaseString

toLowerCaseString(value: string): any

- Defined in src/utils/registry.ts:9
Parameters
- value: string
Returns any

transpose

transpose(At: Matrix, A: Matrix): void

- Defined in src/math/matrix-utils.ts:26
Parameters
- At: Matrix
- A: Matrix
Returns void

triggerFromString

triggerFromString(str: string): ["" | "scroll" | "hoverPick" | "drag" | "click" | "doubleClick" | "hover" | "clickPick", number, number]

- Defined in src/controls/mouse-controls.ts:59
Get event type, key and button

Parameters
- str: string
  
  input trigger string
Returns ["" | "scroll" | "hoverPick" | "drag" | "click" | "doubleClick" | "hover" | "clickPick", number, number]

event type, key and button

trimQuotes

trimQuotes(str: string): string

- Defined in src/parser/cif-parser.ts:31
Parameters
- str: string
Returns string

uint8ToLines

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

- Defined in src/utils.ts:413
Parameters
- u8a: Uint8Array
- Default value chunkSize: number = 1024 * 1024 * 10
- Default value newline: string = ""
Returns string[]

uint8ToString

uint8ToString(u8a: Uint8Array): any

- Defined in src/utils.ts:395
Parameters
- u8a: Uint8Array
Returns any

uniformArray

uniformArray<T>(n: number, a: number, optionalTarget?: T): T

- Defined in src/math/array-utils.ts:77
Type parameters
- T: NumberArray
Parameters
- n: number
- a: number
- Optional optionalTarget: T
Returns T

uniformArray3

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

- Defined in src/math/array-utils.ts:87
Parameters
- n: number
- a: number
- b: number
- c: number
- Optional optionalTarget: NumberArray
Returns Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[]

uniqueArray

uniqueArray(array: any[]): any[]

- Defined in src/utils.ts:387
Parameters
- array: any[]
Returns any[]

updateCameraUniforms

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

- Defined in src/viewer/viewer-utils.ts:373
Parameters
- group: Object3D
- camera: Camera
Returns void

updateMaterialUniforms

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

- Defined in src/viewer/viewer-utils.ts:323
Parameters
- group: Object3D
- camera: Camera
- renderer: WebGLRenderer
- cDist: number
- bRadius: number
Returns void

updateParams

updateParams<T>(params: T, newParams: {}): T

- Defined in src/utils.ts:47
Type parameters
- T
Parameters
- params: T
- newParams: {}
Returns T

v3add

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

- Defined in src/math/vector-utils.ts:186
Parameters
- out: Float32Array
- a: Float32Array
- b: Float32Array
Returns void

v3addScalar

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

- Defined in src/math/vector-utils.ts:263
Parameters
- out: Float32Array
- a: Float32Array
- s: number
Returns void

v3angle

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

- Defined in src/math/vector-utils.ts:293
Parameters
- a: Float32Array
- b: Float32Array
Returns number

v3ceil

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

- Defined in src/math/vector-utils.ts:275
Parameters
- out: Float32Array
- a: Float32Array
Returns void

v3cross

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

- Defined in src/math/vector-utils.ts:164
Parameters
- out: Float32Array
- a: Float32Array
- b: Float32Array
Returns void

v3divide

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

- Defined in src/math/vector-utils.ts:222
Parameters
- out: Float32Array
- a: Float32Array
- b: Float32Array
Returns void

v3divideScalar

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

- Defined in src/math/vector-utils.ts:234
Parameters
- out: Float32Array
- a: Float32Array
- s: number
Returns void

v3dot

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

- Defined in src/math/vector-utils.ts:176
Parameters
- a: Float32Array
- b: Float32Array
Returns number

v3floor

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

- Defined in src/math/vector-utils.ts:269
Parameters
- out: Float32Array
- a: Float32Array
Returns void

v3forEach

v3forEach(array: Float32Array, fn: (i: Float32Array, j: Float32Array, k: Float32Array) => void, b: Float32Array): void

- Defined in src/math/vector-utils.ts:204
Parameters
- array: Float32Array
- fn: (i: Float32Array, j: Float32Array, k: Float32Array) => void
  - - (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

- Defined in src/math/vector-utils.ts:192
Parameters
- out: Float32Array
- array: Float32Array
- Default value offset: number = 0
Returns void

v3length

v3length(a: Float32Array): number

- Defined in src/math/vector-utils.ts:218
Parameters
- a: Float32Array
Returns number

v3length2

v3length2(a: Float32Array): number

- Defined in src/math/vector-utils.ts:214
Parameters
- a: Float32Array
Returns number

v3multiply

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

- Defined in src/math/vector-utils.ts:228
Parameters
- out: Float32Array
- a: Float32Array
- b: Float32Array
Returns void

v3multiplyScalar

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

- Defined in src/math/vector-utils.ts:239
Parameters
- out: Float32Array
- a: Float32Array
- s: number
Returns void

v3negate

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

- Defined in src/math/vector-utils.ts:287
Parameters
- out: Float32Array
- a: Float32Array
Returns void

v3new

v3new(array?: NumberArray): Float32Array

- Defined in src/math/vector-utils.ts:160
Parameters
- Optional array: NumberArray
Returns Float32Array

v3normalize

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

- Defined in src/math/vector-utils.ts:245
Parameters
- out: Float32Array
- a: Float32Array
Returns void

v3round

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

- Defined in src/math/vector-utils.ts:281
Parameters
- out: Float32Array
- a: Float32Array
Returns void

v3sub

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

- Defined in src/math/vector-utils.ts:180
Parameters
- out: Float32Array
- a: Float32Array
- b: Float32Array
Returns void

v3subScalar

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

- Defined in src/math/vector-utils.ts:257
Parameters
- out: Float32Array
- a: Float32Array
- s: number
Returns void

v3toArray

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

- Defined in src/math/vector-utils.ts:198
Parameters
- input: Float32Array
- array: Float32Array
- Default value offset: number = 0
Returns void

valenceModel

valenceModel(data: Data): ValenceModel

- Defined in src/structure/data.ts:27
Parameters
- data: Data
Returns ValenceModel

validatePositions

validatePositions(position: Float32Array): Float32Array

- Defined in src/representation/angle-representation.ts:266
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

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: {}

sky: number[] = hsvToRgb(210, 75, 95)

white

white: number[] = hsvToRgb(0, 0, 100)

yellow

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

yellowtint

yellowtint: number[] = 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 ContactLabelDefaultParams

ContactLabelDefaultParams: object

size

size: number = 2

unit

unit: string = ""

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: object

macrolide

macrolide: number = MacrolideEntity

non-polymer

non-polymer: number = NonPolymerEntity

polymer

polymer: number = PolymerEntity

water

water: number = WaterEntity

Const HelixTypes

HelixTypes: object

0

0: 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.

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: [string, (stage: Stage) => void][] = [[ '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: "bottom-center" = "bottom-center"

labelBorder

labelBorder: true = true

labelBorderColor

labelBorderColor: number = 13882323

labelBorderWidth

labelBorderWidth: number = 0.25

labelColor

labelColor: number = 8421504

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: [string, ((stage: Stage, delta: number) => void) | ((stage: Stage, dx: number, dy: number) => void) | ((stage: Stage, pickingProxy: PickingProxy) => void)][] = [[ '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: [string, ((stage: Stage, delta: number) => void) | ((stage: Stage, dx: number, dy: number) => void) | ((stage: Stage, pickingProxy: PickingProxy) => void)][] = [[ '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: [string, ((stage: Stage, delta: number) => void) | ((stage: Stage, dx: number, dy: number) => void) | ((stage: Stage, pickingProxy: PickingProxy) => void)][] = [[ '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: [string, ((stage: Stage, delta: number) => void) | ((stage: Stage, dx: number, dy: number) => void) | ((stage: Stage, pickingProxy: PickingProxy) => void)][] = [[ '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"

explicit

explicit: string = "explicit"

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: [number, number, number] = [ 0.17, 0.50, 0.33 ]

ARG

ARG: [number, number, number] = [ 0.81, 1.81, 1.00 ]

ASH

ASH: [number, number, number] = [ -0.07, 0.43, 0.50 ]

ASN

ASN: [number, number, number] = [ 0.42, 0.85, 0.43 ]

ASP

ASP: [number, number, number] = [ 1.23, 3.64, 2.41 ]

CYS

CYS: [number, number, number] = [ -0.24, -0.02, 0.22 ]

GLH

GLH: [number, number, number] = [ -0.01, 0.11, 0.12 ]

GLN

GLN: [number, number, number] = [ 0.58, 0.77, 0.19 ]

GLU

GLU: [number, number, number] = [ 2.02, 3.63, 1.61 ]

GLY

GLY: [number, number, number] = [ 0.01, 1.15, 1.14 ]

HIS

HIS: [number, number, number] = [ 0.17, 0.11, -0.06 ]

ILE

ILE: [number, number, number] = [ -0.31, -1.12, -0.81 ]

LEU

LEU: [number, number, number] = [ -0.56, -1.25, -0.69 ]

LYS

LYS: [number, number, number] = [ 0.99, 2.80, 1.81 ]

MET

MET: [number, number, number] = [ -0.23, -0.67, -0.44 ]

PHE

PHE: [number, number, number] = [ -1.13, -1.71, -0.58 ]

PRO

PRO: [number, number, number] = [ 0.45, 0.14, -0.31 ]

SER

SER: [number, number, number] = [ 0.13, 0.46, 0.33 ]

THR

THR: [number, number, number] = [ 0.14, 0.25, 0.11 ]

TRP

TRP: [number, number, number] = [ -1.85, -2.09, -0.24 ]

TYR

TYR: [number, number, number] = [ -0.94, -0.71, 0.23 ]

VAL

VAL: [number, number, number] = [ 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: "rgb" | "hsv" | "hsl" | "hsi" | "lab" | "hcl" = 'hcl' as ColorMode

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: {} = {} 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

clipMode

clipMode: string = "scene"

clipNear

clipNear: number = 0

clipScale

clipScale: string = "relative"

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: { type: "color" } = ColorParam()

Type declaration

type: "color"

ambientIntensity

ambientIntensity: { max: number; min: number; precision: number; type: "number" } = NumberParam(2, 10, 0)

Type declaration

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

backgroundColor

backgroundColor: { type: "color" } = ColorParam()

Type declaration

type: "color"

cameraEyeSep

cameraEyeSep: { max: number; min: number; precision: number; type: "number" } = NumberParam(3, 1.0, 0.01)

Type declaration

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

cameraFov

cameraFov: { max: number; min: number; step: number; type: "range" } = RangeParam(1, 120, 15)

Type declaration

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

cameraType

cameraType: { options: {}; type: "select" } = SelectParam('perspective', 'orthographic', 'stereo')

Type declaration

options: {}
- [k: string]: string
type: "select"

clipDist

clipDist: { max: number; min: number; type: "integer" } = IntegerParam(200, 0)

Type declaration

max: number
min: number
type: "integer"

clipFar

clipFar: { max: number; min: number; step: number; type: "range" } = RangeParam(1, 100, 0)

Type declaration

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

clipMode

clipMode: { options: {}; type: "select" } = SelectParam('scene', 'camera')

Type declaration

options: {}
- [k: string]: string
type: "select"

clipNear

clipNear: { max: number; min: number; step: number; type: "range" } = RangeParam(1, 100, 0)

Type declaration

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

clipScale

clipScale: { options: {}; type: "select" } = SelectParam('relative', 'absolute')

Type declaration

options: {}
- [k: string]: string
type: "select"

fogFar

fogFar: { max: number; min: number; step: number; type: "range" } = RangeParam(1, 100, 0)

Type declaration

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

fogNear

fogNear: { max: number; min: number; step: number; type: "range" } = RangeParam(1, 100, 0)

Type declaration

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

hoverTimeout

hoverTimeout: { max: number; min: number; type: "integer" } = IntegerParam(10000, -1)

Type declaration

max: number
min: number
type: "integer"

impostor

impostor: { type: "boolean" } = BooleanParam()

Type declaration

type: "boolean"

lightColor

lightColor: { type: "color" } = ColorParam()

Type declaration

type: "color"

lightIntensity

lightIntensity: { max: number; min: number; precision: number; type: "number" } = NumberParam(2, 10, 0)

Type declaration

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

mousePreset

mousePreset: { options: {}; type: "select" } = SelectParam(...Object.keys(MouseActionPresets))

Type declaration

options: {}
- [k: string]: string
type: "select"

panSpeed

panSpeed: { max: number; min: number; precision: number; type: "number" } = NumberParam(1, 10, 0)

Type declaration

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

quality

quality: { options: {}; type: "select" } = SelectParam('auto', 'low', 'medium', 'high')

Type declaration

options: {}
- [k: string]: string
type: "select"

rotateSpeed

rotateSpeed: { max: number; min: number; precision: number; type: "number" } = NumberParam(1, 10, 0)

Type declaration

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

sampleLevel

sampleLevel: { max: number; min: number; step: number; type: "range" } = RangeParam(1, 5, -1)

Type declaration

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

tooltip

tooltip: { type: "boolean" } = BooleanParam()

Type declaration

type: "boolean"

workerDefault

workerDefault: { type: "boolean" } = BooleanParam()

Type declaration

type: "boolean"

zoomSpeed

zoomSpeed: { max: number; min: number; precision: number; type: "number" } = 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

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

Index

Modules

Enumerations

Classes

Interfaces

Type aliases

Events

Variables

Functions

Object literals

Type aliases

ArrowBufferParameters

AtomPair

BooleanParam

Type declaration

type: "boolean"

BufferMaterials

BufferParameters

BufferSide

BufferTypes

CameraType

ChainidDict

Type declaration

[k: string]: number

ChainnameDict

Type declaration

[k: string]: number

ColorDefinition

ColorMode

ColorParam

Type declaration

type: "color"

ColormakerScale

Type declaration

Parameters

v: number

Returns number

ComponentParameters

ConeBufferParameters

ContactDataParams

ContactLabelParams

CylinderBufferParameters

CylinderGeometryBufferParameters

CylinderImpostorBufferParameters

DragCallback

Type declaration

Parameters

stage: Stage

dx: number

dy: number

Returns void

ElementParameters

EllipsoidBufferParameters

EntityTypeString

FilterFn

Type declaration

Parameters

s: SelectionRule

Returns boolean

FunctionWithDeps

HyperballStickBufferParameters

HyperballStickImpostorBufferParameters

ImageBufferParameters

ImageFilterTypes

ImageParameters

IntegerParam

Type declaration

max: number

min: number

type: "integer"

KeyActionCallback

Type declaration

Parameters

stage: Stage

Returns void

KeyActionPreset

KeyControlPreset

LabelType

LoaderInput

MappingType