AxesRepresentation

Axes representation. Show principal axes and/or a box aligned with them that fits the structure or selection.

Name: axes

example: stage.loadFile( "rcsb://3pqr", { assembly: "BU1" } ).then( function( o ){ o.addRepresentation( "cartoon" ); o.addRepresentation( "axes", { sele: "RET", showAxes: false, showBox: true, radius: 0.2 } ); o.addRepresentation( "ball+stick", { sele: "RET" } ); o.addRepresentation( "axes", { sele: ":B and backbone", showAxes: false, showBox: true, radius: 0.2 } ); stage.autoView(); var pa = o.structure.getPrincipalAxes(); stage.animationControls.rotate( pa.getRotationQuaternion(), 1500 ); } );

Hierarchy

StructureRepresentation
- AxesRepresentation

Indexable

[key: string]: any

Axes representation. Show principal axes and/or a box aligned with them that fits the structure or selection.

Name: axes

example: stage.loadFile( "rcsb://3pqr", { assembly: "BU1" } ).then( function( o ){ o.addRepresentation( "cartoon" ); o.addRepresentation( "axes", { sele: "RET", showAxes: false, showBox: true, radius: 0.2 } ); o.addRepresentation( "ball+stick", { sele: "RET" } ); o.addRepresentation( "axes", { sele: ":B and backbone", showAxes: false, showBox: true, radius: 0.2 } ); stage.autoView(); var pa = o.structure.getPrincipalAxes(); stage.animationControls.rotate( pa.getRotationQuaternion(), 1500 ); } );

Index

Constructors

constructor

Properties

Accessors

defaultScale

Constructors

constructor

new AxesRepresentation(structure: Structure, viewer: Viewer, params: Partial<AxesRepresentationParameters>): AxesRepresentation

Overrides StructureRepresentation.constructor
- Defined in src/representation/axes-representation.ts:57
Parameters
- structure: Structure
  
  the structure object
- viewer: Viewer
  
  the viewer object
- params: Partial<AxesRepresentationParameters>
  
  parameters object
Returns AxesRepresentation

Properties

Protected assembly

assembly: string

bufferList

bufferList: Buffer[]

Protected clipCenter

clipCenter: Vector3

Protected clipNear

clipNear: number

Protected clipRadius

clipRadius: number

Protected colorDomain

colorDomain: number[]

Protected colorMode

colorMode: ColorMode

Protected colorReverse

colorReverse: boolean

Protected colorScale

colorScale: string | string[]

Protected colorScheme

colorScheme: string

Protected colorValue

colorValue: number

Protected cylinderBuffer

cylinderBuffer: CylinderBuffer

Protected dataList

dataList: StructureRepresentationData[]

Protected defaultAssembly

defaultAssembly: string

Protected depthWrite

depthWrite: boolean

Protected diffuse

diffuse: number

Protected Optional diffuseInterior

diffuseInterior: undefined | false | true

Protected disableImpostor

disableImpostor: boolean

Protected disablePicking

disablePicking: boolean

Protected disposed

disposed: boolean

Protected flatShaded

flatShaded: boolean

Protected interiorColor

interiorColor: number

Protected interiorDarkening

interiorDarkening: number

lazy

lazy: boolean

lazyProps

lazyProps: { bufferParams: BufferParameters | {}; build: boolean; what: {} }

Type declaration

bufferParams: BufferParameters | {}
build: boolean
what: {}

Protected manualAttach

manualAttach: () => any

Type declaration

- (): any
- Returns any

Protected matrix

matrix: Matrix4

Protected metalness

metalness: number

Protected name

name: string

Protected needsBuild

needsBuild: boolean

Protected opacity

opacity: number

Protected openEnded

openEnded: boolean

parameters

parameters: any

Protected radialSegments

radialSegments: number

Protected radiusData

radiusData: {}

Type declaration

[k: number]: number

Protected radiusScale

radiusScale: number

Protected radiusSize

radiusSize: number

Protected radiusType

radiusType: RadiusType

Protected roughness

roughness: number

Protected selection

selection: Selection

Protected showAxes

showAxes: boolean

Protected showBox

showBox: boolean

Protected side

side: BufferSide

Protected sphereBuffer

sphereBuffer: SphereBuffer

Protected sphereDetail

sphereDetail: number

structure

structure: Structure

structureView

structureView: StructureView

tasks

tasks: Counter

Protected toBePrepared

toBePrepared: boolean

type

type: string

Protected Optional useInteriorColor

useInteriorColor: undefined | false | true

viewer

viewer: Viewer

visible

visible: boolean

Protected wireframe

wireframe: boolean

Accessors

defaultScale

get defaultScale(): { bfactor: number; covalent: number; sstruc: number; vdw: number }

Inherited from LabelRepresentation.defaultScale
- Defined in src/representation/structure-representation.ts:137
Returns { bfactor: number; covalent: number; sstruc: number; vdw: number }
- bfactor: number
- covalent: number
- sstruc: number
- vdw: number

Methods

attach

attach(callback: () => void): void

Inherited from LabelRepresentation.attach

Overrides Representation.attach
- Defined in src/representation/structure-representation.ts:376
Parameters
- callback: () => void
  - - (): void
    - Returns void
Returns void

build

build(updateWhat?: undefined | {}): void

Inherited from Representation.build
- Defined in src/representation/representation.ts:447
Parameters
- Optional updateWhat: undefined | {}
Returns void

clear

clear(): void

Inherited from LabelRepresentation.clear

Overrides Representation.clear
- Defined in src/representation/structure-representation.ts:391
Returns void

create

create(): void

Overrides LabelRepresentation.create
- Defined in src/representation/axes-representation.ts:221
Returns void

createData

createData(sview: StructureView): undefined

Overrides MeasurementRepresentation.createData
- Defined in src/representation/axes-representation.ts:249
Parameters
- sview: StructureView
Returns undefined

dispose

dispose(): void

Inherited from LabelRepresentation.dispose

Overrides Representation.dispose
- Defined in src/representation/structure-representation.ts:397
Returns void

getAssembly

getAssembly(): Assembly

Inherited from LabelRepresentation.getAssembly
- Defined in src/representation/structure-representation.ts:185
Returns Assembly

getAtomParams

getAtomParams(what?: AtomDataFields, params?: AtomDataParams): { colorParams: { structure: Structure }; radiusParams: { data: {}; scale: number; size: number; type: "" | "data" | "sstruc" | "bfactor" | "size" | "explicit" | "vdw" | "covalent" }; what: undefined | AtomDataFields } & AtomDataParams

Inherited from LabelRepresentation.getAtomParams
- Defined in src/representation/structure-representation.ts:288
Parameters
- Optional what: AtomDataFields
- Optional params: AtomDataParams
Returns { colorParams: { structure: Structure }; radiusParams: { data: {}; scale: number; size: number; type: "" | "data" | "sstruc" | "bfactor" | "size" | "explicit" | "vdw" | "covalent" }; what: undefined | AtomDataFields } & AtomDataParams

getAtomRadius

getAtomRadius(atom: AtomProxy): number

Inherited from AxesRepresentation.getAtomRadius
- Defined in src/representation/structure-representation.ts:304
Parameters
- atom: AtomProxy
Returns number

getAxesData

getAxesData(sview: StructureView): { edge: object; vertex: object }

- Defined in src/representation/axes-representation.ts:113
Parameters
- sview: StructureView
Returns { edge: object; vertex: object }
- edge: object
  - color: Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[]
  - color2: Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[]
  - picking: AxesPicker
  - position1: Float32Array
  - position2: Float32Array
  - radius: Float32Array
- vertex: object
  - color: Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array | number[]
  - picking: AxesPicker
  - position: Float32Array
  - radius: Float32Array

getBondParams

getBondParams(what?: BondDataFields, params?: BondDataParams): { colorParams: { structure: Structure }; radiusParams: { data: {}; scale: number; size: number; type: "" | "data" | "sstruc" | "bfactor" | "size" | "explicit" | "vdw" | "covalent" }; what: undefined | BondDataFields } & BondDataParams

Inherited from LabelRepresentation.getBondParams
- Defined in src/representation/structure-representation.ts:296
Parameters
- Optional what: BondDataFields
- Optional params: BondDataParams
Returns { colorParams: { structure: Structure }; radiusParams: { data: {}; scale: number; size: number; type: "" | "data" | "sstruc" | "bfactor" | "size" | "explicit" | "vdw" | "covalent" }; what: undefined | BondDataFields } & BondDataParams

getBufferParams

getBufferParams(p?: {}): { clipCenter: Vector3; clipNear: number; clipRadius: number; depthWrite: boolean; diffuse: number; diffuseInterior: undefined | false | true; disablePicking: boolean; flatShaded: boolean; interiorColor: number; interiorDarkening: number; matrix: Matrix4; metalness: number; opacity: number; roughness: number; side: "double" | "front" | "back"; useInteriorColor: undefined | false | true; wireframe: boolean } & {}

Inherited from Representation.getBufferParams
- Defined in src/representation/representation.ts:382
Parameters
- Default value p: {} = {}
  - [k: string]: any
Returns { clipCenter: Vector3; clipNear: number; clipRadius: number; depthWrite: boolean; diffuse: number; diffuseInterior: undefined | false | true; disablePicking: boolean; flatShaded: boolean; interiorColor: number; interiorDarkening: number; matrix: Matrix4; metalness: number; opacity: number; roughness: number; side: "double" | "front" | "back"; useInteriorColor: undefined | false | true; wireframe: boolean } & {}

getColorParams

getColorParams(): { structure: Structure }

Inherited from LabelRepresentation.getColorParams

Overrides Representation.getColorParams
- Defined in src/representation/structure-representation.ts:272
Returns { structure: Structure }
- structure: Structure

getParameters

getParameters(): {} & { defaultAssembly: string; sele: undefined | string }

Inherited from LabelRepresentation.getParameters

Overrides Representation.getParameters
- Defined in src/representation/structure-representation.ts:364
Returns {} & { defaultAssembly: string; sele: undefined | string }

getPrincipalAxes

getPrincipalAxes(): PrincipalAxes

- Defined in src/representation/axes-representation.ts:102
Returns PrincipalAxes

getQuality

getQuality(): "high" | "medium" | "low"

Inherited from LabelRepresentation.getQuality
- Defined in src/representation/structure-representation.ts:190
Returns "high" | "medium" | "low"

getRadiusParams

getRadiusParams(param?: any): { data: {}; scale: number; size: number; type: "" | "data" | "sstruc" | "bfactor" | "size" | "explicit" | "vdw" | "covalent" }

Inherited from LabelRepresentation.getRadiusParams
- Defined in src/representation/structure-representation.ts:279
Parameters
- Optional param: any
Returns { data: {}; scale: number; size: number; type: "" | "data" | "sstruc" | "bfactor" | "size" | "explicit" | "vdw" | "covalent" }
- data: {}
  - [k: number]: number
- scale: number
- size: number
- type: "" | "data" | "sstruc" | "bfactor" | "size" | "explicit" | "vdw" | "covalent"

init

init(params: Partial<AxesRepresentationParameters>): void

Overrides StructureRepresentation.init
- Defined in src/representation/axes-representation.ts:90
Parameters
- params: Partial<AxesRepresentationParameters>
Returns void

make

make(updateWhat?: undefined | false | true, callback?: undefined | (() => void)): void

Inherited from Representation.make
- Defined in src/representation/representation.ts:470
Parameters
- Optional updateWhat: undefined | false | true
- Optional callback: undefined | (() => void)
Returns void

prepare

prepare(cb: () => void): void

Inherited from Representation.prepare
- Defined in src/representation/representation.ts:435
Parameters
- cb: () => void
  - - (): void
    - Returns void
Returns void

setColor

setColor(value: number | string | Color | undefined, p?: Partial<RepresentationParameters>): this

Inherited from Representation.setColor
- Defined in src/representation/representation.ts:410
Parameters
- value: number | string | Color | undefined
- Optional p: Partial<RepresentationParameters>
Returns this

setParameters

setParameters(params: Partial<StructureRepresentationParameters>, what?: AtomDataFields, rebuild?: boolean): this

Inherited from LabelRepresentation.setParameters

Overrides Representation.setParameters
- Defined in src/representation/structure-representation.ts:339
Set representation parameters

alias

StructureRepresentation#setParameters

Parameters
- params: Partial<StructureRepresentationParameters>
  
  structure parameter object
- Default value what: AtomDataFields = {}
- Default value rebuild: boolean = false
Returns this

this object

setRadius

setRadius(value: string | number | undefined, p: Partial<StructureRepresentationParameters>): this

Inherited from LabelRepresentation.setRadius
- Defined in src/representation/structure-representation.ts:172
Parameters
- value: string | number | undefined
- p: Partial<StructureRepresentationParameters>
Returns this

setSelection

setSelection(string: string, silent?: undefined | false | true): this

Inherited from LabelRepresentation.setSelection
- Defined in src/representation/structure-representation.ts:319
Set representation parameters

alias

StructureRepresentation#setSelection

Parameters
- string: string
  
  selection string, see {@tutorial selection-language}
- Optional silent: undefined | false | true
Returns this

this object

setVisibility

setVisibility(value: boolean, noRenderRequest?: undefined | false | true): Representation

Inherited from Representation.setVisibility
- Defined in src/representation/representation.ts:514
Set the visibility of the representation

Parameters
- value: boolean
  
  visibility flag
- Optional noRenderRequest: undefined | false | true
Returns Representation

this object

update

update(what: AtomDataFields | BondDataFields): void

Inherited from LabelRepresentation.update

Overrides Representation.update
- Defined in src/representation/structure-representation.ts:250
Parameters
- what: AtomDataFields | BondDataFields
Returns void

updateData

updateData(what: AtomDataFields, data: StructureRepresentationData): void

Overrides ContactRepresentation.updateData
- Defined in src/representation/axes-representation.ts:253
Parameters
- what: AtomDataFields
- data: StructureRepresentationData
Returns void

updateParameters

updateParameters(bufferParams?: BufferParameters | {}, what?: any): void

Inherited from Representation.updateParameters
- Defined in src/representation/representation.ts:629
Parameters
- Default value bufferParams: BufferParameters | {} = {}
- Optional what: any
Returns void

Hierarchy

Indexable

Index

Constructors

Properties

Accessors

Methods

Constructors

constructor

Parameters

structure: Structure

viewer: Viewer

params: Partial<AxesRepresentationParameters>

Returns AxesRepresentation

Properties

Protected assembly

bufferList

Protected clipCenter

Protected clipNear

Protected clipRadius

Protected colorDomain

Protected colorMode

Protected colorReverse

Protected colorScale

Protected colorScheme

Protected colorValue

Protected cylinderBuffer

Protected dataList

Protected defaultAssembly

Protected depthWrite

Protected diffuse

Protected Optional diffuseInterior

Protected disableImpostor

Protected disablePicking

Protected disposed

Protected flatShaded

Protected interiorColor

Protected interiorDarkening

lazy

lazyProps

Type declaration

bufferParams: BufferParameters | {}

build: boolean

what: {}

Protected manualAttach

Type declaration

Returns any

Protected matrix

Protected metalness

Protected name

Protected needsBuild

Protected opacity

Protected openEnded

parameters

Protected radialSegments

Protected radiusData

Type declaration

[k: number]: number

Protected radiusScale

Protected radiusSize

Protected radiusType

Protected roughness

Protected selection

Protected showAxes

Protected showBox

Protected side

Protected sphereBuffer

Protected sphereDetail

structure

structureView

tasks

Protected toBePrepared

type

Protected Optional useInteriorColor

viewer

visible

Protected wireframe

Accessors

defaultScale

Returns { bfactor: number; covalent: number; sstruc: number; vdw: number }