Class StructureView

View on the structure, restricted to the selection

Hierarchy

Structure
- StructureView

Implements

Structure

Index

Constructors

constructor

Properties

Accessors

Methods

Object literals

signals

Constructors

constructor

new StructureView(structure: Structure, selection: Selection): StructureView

Overrides Structure.constructor
- Defined in src/structure/structure-view.ts:35
Parameters
- structure: Structure
  
  the structure
- selection: Selection
  
  the selection
Returns StructureView

Properties

selection

selection: Selection

structure

structure: Structure

Static _ap

Static _bp

Static _cp

_cp: ChainProxy

Static Optional _hasCoords

_hasCoords: undefined | true | false

Static _rp

_rp: ResidueProxy

Static atomCount

atomCount: number

Static atomMap

atomMap: AtomMap

Static Optional atomSet

atomSet: BitArray

Static atomSetCache

atomSetCache: object

Type declaration

[k: string]: BitArray

Static atomSetDict

atomSetDict: object

Type declaration

[k: string]: BitArray

Static atomStore

atomStore: AtomStore

Static backboneBondStore

backboneBondStore: BondStore

Static biomolDict

biomolDict: object

Type declaration

[k: string]: Assembly

Static bondCount

bondCount: number

Static Optional bondHash

bondHash: BondHash

Static Optional bondSet

bondSet: BitArray

Static bondStore

bondStore: BondStore

Static boundingBox

boundingBox: Box3

Static boxes

boxes: Float32Array[]

Static center

center: Vector3

Static chainStore

chainStore: ChainStore

Static data

data: Data

Static entityList

entityList: Entity[]

Static extraData

extraData: StructureExtraData

Static frames

frames: Float32Array[]

Static header

header: StructureHeader

Static id

id: string

Static modelStore

modelStore: ModelStore

Static name

name: string

Static path

path: string

Static residueMap

residueMap: ResidueMap

Static residueStore

residueStore: ResidueStore

Static rungBondStore

rungBondStore: BondStore

Static signals

signals: StructureSignals

Static Optional spatialHash

spatialHash: SpatialHash

Static title

title: string

Static Optional trajectory

trajectory: undefined | object

Static Optional unitcell

unitcell: Unitcell

Static Optional validation

validation: Validation

Accessors

_hasCoords

get _hasCoords(): undefined | true | false
set _hasCoords(value: undefined | true | false): void

- Defined in src/structure/structure-view.ts:92
Returns undefined | true | false
- Defined in src/structure/structure-view.ts:93
Parameters
- value: undefined | true | false
Returns void

atomMap

get atomMap(): AtomMap

- Defined in src/structure/structure-view.ts:87
Returns AtomMap

atomSetDict

get atomSetDict(): object

- Defined in src/structure/structure-view.ts:73
Returns object
- [k: string]: BitArray

atomStore

get atomStore(): AtomStore

- Defined in src/structure/structure-view.ts:83
Returns AtomStore

backboneBondStore

get backboneBondStore(): BondStore

- Defined in src/structure/structure-view.ts:81
Returns BondStore

biomolDict

get biomolDict(): object

- Defined in src/structure/structure-view.ts:74
Returns object
- [k: string]: Assembly

bondHash

get bondHash(): undefined | BondHash

- Defined in src/structure/structure-view.ts:89
Returns undefined | BondHash

bondStore

get bondStore(): BondStore

- Defined in src/structure/structure-view.ts:80
Returns BondStore

boxes

get boxes(): Float32Array[]

- Defined in src/structure/structure-view.ts:78
Returns Float32Array[]

chainStore

get chainStore(): ChainStore

- Defined in src/structure/structure-view.ts:85
Returns ChainStore

data

get data(): Data

- Defined in src/structure/structure-view.ts:72
Returns Data

entityList

get entityList(): Entity[]

- Defined in src/structure/structure-view.ts:75
Returns Entity[]

frames

get frames(): Float32Array[]

- Defined in src/structure/structure-view.ts:77
Returns Float32Array[]

id

get id(): string

- Defined in src/structure/structure-view.ts:71
Returns string

modelStore

get modelStore(): ModelStore

- Defined in src/structure/structure-view.ts:86
Returns ModelStore

name

get name(): string

- Defined in src/structure/structure-view.ts:68
Returns string

path

get path(): string

- Defined in src/structure/structure-view.ts:69
Returns string

residueMap

get residueMap(): ResidueMap

- Defined in src/structure/structure-view.ts:88
Returns ResidueMap

residueStore

get residueStore(): ResidueStore

- Defined in src/structure/structure-view.ts:84
Returns ResidueStore

rungBondStore

get rungBondStore(): BondStore

- Defined in src/structure/structure-view.ts:82
Returns BondStore

spatialHash

get spatialHash(): undefined | SpatialHash

- Defined in src/structure/structure-view.ts:90
Returns undefined | SpatialHash

title

get title(): string

- Defined in src/structure/structure-view.ts:70
Returns string

type

get type(): string

Overrides Structure.type
- Defined in src/structure/structure-view.ts:66
Returns string

unitcell

get unitcell(): undefined | Unitcell

- Defined in src/structure/structure-view.ts:76
Returns undefined | Unitcell

validation

get validation(): undefined | Validation

- Defined in src/structure/structure-view.ts:79
Returns undefined | Validation

Methods

atomCenter

atomCenter(selection?: Selection): Vector3

Inherited from Structure.atomCenter
- Defined in src/structure/structure.ts:996
Gets the center of the (selected) structure atoms

Parameters
- Optional selection: Selection
Returns Vector3

the center

dispose

dispose(): void

Overrides Structure.dispose
- Defined in src/structure/structure-view.ts:266
Returns void

eachAtom

eachAtom(callback: function, selection?: Selection): void

Overrides Structure.eachAtom
- Defined in src/structure/structure-view.ts:204
Parameters
- callback: function
  - - (entity: AtomProxy): any
    - Parameters
      - entity: AtomProxy
      Returns any
- Optional selection: Selection
Returns void

eachBond

eachBond(callback: function, selection?: Selection): void

Overrides Structure.eachBond
- Defined in src/structure/structure-view.ts:200
Parameters
- callback: function
  - - (entity: BondProxy): any
    - Parameters
      - entity: BondProxy
      Returns any
- Optional selection: Selection
Returns void

eachChain

eachChain(callback: function, selection?: Selection): void

Overrides Structure.eachChain
- Defined in src/structure/structure-view.ts:235
Parameters
- callback: function
  - - (entity: ChainProxy): any
    - Parameters
      - entity: ChainProxy
      Returns any
- Optional selection: Selection
Returns void

eachEntity

eachEntity(callback: function, type: number): void

Inherited from Structure.eachEntity
- Defined in src/structure/structure.ts:467
Entity iterator

Parameters
- callback: function
  
  the callback
  - - (entity: Entity): void
    - Parameters
      - entity: Entity
      Returns void
- type: number
  
  entity type
Returns void

eachModel

eachModel(callback: function, selection?: Selection): void

Overrides Structure.eachModel
- Defined in src/structure/structure-view.ts:239
Parameters
- callback: function
  - - (entity: ModelProxy): any
    - Parameters
      - entity: ModelProxy
      Returns any
- Optional selection: Selection
Returns void

eachPolymer

eachPolymer(callback: function, selection?: Selection): void

Inherited from Structure.eachPolymer
- Defined in src/structure/structure.ts:591
Polymer iterator

Parameters
- callback: function
  
  the callback
  - - (entity: Polymer): void
    - Parameters
      - entity: Polymer
      Returns void
- Optional selection: Selection
Returns void

eachResidue

eachResidue(callback: function, selection?: Selection): void

Overrides Structure.eachResidue
- Defined in src/structure/structure-view.ts:222
Parameters
- callback: function
  - - (entity: ResidueProxy): any
    - Parameters
      - entity: ResidueProxy
      Returns any
- Optional selection: Selection
Returns void

eachResidueN

eachResidueN(n: number, callback: function): void

Overrides Structure.eachResidueN
- Defined in src/structure/structure-view.ts:231
Not implemented

alias

StructureView#eachResidueN

Parameters
- n: number
- callback: function
  - - (entity: ResidueProxy): any
    - Parameters
      - entity: ResidueProxy
      Returns any
Returns void

finalizeAtoms

finalizeAtoms(): void

Inherited from Structure.finalizeAtoms
- Defined in src/structure/structure.ts:196
Returns void

finalizeBonds

finalizeBonds(): void

Inherited from Structure.finalizeBonds
- Defined in src/structure/structure.ts:204
Returns void

getAtomData

getAtomData(params: AtomDataParams): AtomData

Inherited from Structure.getAtomData
- Defined in src/structure/structure.ts:663
Parameters
- params: AtomDataParams
Returns AtomData

getAtomIndices

getAtomIndices(selection?: Selection): undefined | Uint32Array

Overrides Structure.getAtomIndices
- Defined in src/structure/structure-view.ts:256
Parameters
- Optional selection: Selection
Returns undefined | Uint32Array

getAtomProxy

getAtomProxy(index?: undefined | number): AtomProxy

Inherited from Structure.getAtomProxy
- Defined in src/structure/structure.ts:225
Parameters
- Optional index: undefined | number
Returns AtomProxy

getAtomSet

getAtomSet(selection?: boolean | Selection | BitArray, ignoreView?: boolean): BitArray

Overrides Structure.getAtomSet
- Defined in src/structure/structure-view.ts:245
Parameters
- Optional selection: boolean | Selection | BitArray
- Default value ignoreView: boolean = false
Returns BitArray

getAtomSetWithinGroup

getAtomSetWithinGroup(selection: boolean | Selection): BitArray

Inherited from Structure.getAtomSetWithinGroup
- Defined in src/structure/structure.ts:436
Get set of all atoms within the groups of a selection

Parameters
- selection: boolean | Selection
  
  the selection object
Returns BitArray

set of atoms

getAtomSetWithinPoint

getAtomSetWithinPoint(point: Vector3 | AtomProxy, radius: number): BitArray

Inherited from Structure.getAtomSetWithinPoint
- Defined in src/structure/structure.ts:390
Get set of atoms around a point

Parameters
- point: Vector3 | AtomProxy
  
  the point
- radius: number
  
  radius to select within
Returns BitArray

set of atoms

getAtomSetWithinSelection

getAtomSetWithinSelection(selection: boolean | Selection | BitArray, radius: number): BitArray

Inherited from Structure.getAtomSetWithinSelection
- Defined in src/structure/structure.ts:367
Get set of atoms around a set of atoms from a selection

Parameters
- selection: boolean | Selection | BitArray
  
  the selection object
- radius: number
  
  radius to select within
Returns BitArray

set of atoms

getAtomSetWithinVolume

getAtomSetWithinVolume(volume: Volume, radius: number, minValue: number, maxValue: number, outside: boolean): BitArray

Inherited from Structure.getAtomSetWithinVolume
- Defined in src/structure/structure.ts:412
Get set of atoms within a volume

Parameters
- volume: Volume
  
  the volume
- radius: number
  
  radius to select within
- minValue: number
  
  minimum value to be considered as within the volume
- maxValue: number
  
  maximum value to be considered as within the volume
- outside: boolean
  
  use only values falling outside of the min/max values
Returns BitArray

set of atoms

getBackboneAtomData

getBackboneAtomData(params: AtomDataParams): AtomData

Inherited from Structure.getBackboneAtomData
- Defined in src/structure/structure.ts:890
Parameters
- params: AtomDataParams
Returns AtomData

getBackboneBondData

getBackboneBondData(params: BondDataParams): BondData

Inherited from Structure.getBackboneBondData
- Defined in src/structure/structure.ts:898
Parameters
- params: BondDataParams
Returns BondData

getBackboneBondSet

getBackboneBondSet(): BitArray

Inherited from Structure.getBackboneBondSet
- Defined in src/structure/structure.ts:272
Returns BitArray

getBondData

getBondData(params: BondDataParams): BondData

Inherited from Structure.getBondData
- Defined in src/structure/structure.ts:719
Parameters
- params: BondDataParams
Returns BondData

getBondProxy

getBondProxy(index?: undefined | number): BondProxy

Inherited from Structure.getBondProxy
- Defined in src/structure/structure.ts:221
Parameters
- Optional index: undefined | number
Returns BondProxy

getBondSet

getBondSet(): BitArray

Inherited from Structure.getBondSet
- Defined in src/structure/structure.ts:243
Returns BitArray

getBoundingBox

getBoundingBox(selection?: Selection, box?: Box3): Box3

Inherited from Structure.getBoundingBox
- Defined in src/structure/structure.ts:932
Gets the bounding box of the (selected) structure atoms

Parameters
- Optional selection: Selection
- Optional box: Box3
Returns Box3

the box

getChainProxy

getChainProxy(index?: undefined | number): ChainProxy

Inherited from Structure.getChainProxy
- Defined in src/structure/structure.ts:233
Parameters
- Optional index: undefined | number
Returns ChainProxy

getChainnameCount

getChainnameCount(selection?: Selection): number

Inherited from Structure.getChainnameCount
- Defined in src/structure/structure.ts:1048
Get number of unique chainnames

Parameters
- Optional selection: Selection
  
  limit count to selection
Returns number

count

getModelProxy

getModelProxy(index?: undefined | number): ModelProxy

Inherited from Structure.getModelProxy
- Defined in src/structure/structure.ts:237
Parameters
- Optional index: undefined | number
Returns ModelProxy

getPrincipalAxes

getPrincipalAxes(selection?: Selection): PrincipalAxes

Inherited from Structure.getPrincipalAxes
- Defined in src/structure/structure.ts:972
Gets the principal axes of the (selected) structure atoms

Parameters
- Optional selection: Selection
Returns PrincipalAxes

the principal axes

getResidueProxy

getResidueProxy(index?: undefined | number): ResidueProxy

Inherited from Structure.getResidueProxy
- Defined in src/structure/structure.ts:229
Parameters
- Optional index: undefined | number
Returns ResidueProxy

getRungAtomData

getRungAtomData(params: AtomDataParams): AtomData

Inherited from Structure.getRungAtomData
- Defined in src/structure/structure.ts:907
Parameters
- params: AtomDataParams
Returns AtomData

getRungBondData

getRungBondData(params: BondDataParams): BondData

Inherited from Structure.getRungBondData
- Defined in src/structure/structure.ts:915
Parameters
- params: BondDataParams
Returns BondData

getRungBondSet

getRungBondSet(): BitArray

Inherited from Structure.getRungBondSet
- Defined in src/structure/structure.ts:296
Returns BitArray

getSelection

getSelection(selection?: Selection): Selection

Overrides Structure.getSelection
- Defined in src/structure/structure-view.ts:170
Parameters
- Optional selection: Selection
Returns Selection

getSequence

getSequence(selection?: Selection): string[]

Inherited from Structure.getSequence
- Defined in src/structure/structure.ts:1016
Parameters
- Optional selection: Selection
Returns string[]

getStructure

getStructure(): Structure | StructureView

Overrides Structure.getStructure
- Defined in src/structure/structure-view.ts:194
Returns Structure | StructureView

hasCoords

hasCoords(): boolean

Inherited from Structure.hasCoords
- Defined in src/structure/structure.ts:1004
Returns boolean

init

init(): void

Overrides Structure.init
- Defined in src/structure/structure-view.ts:64
Returns void

refresh

refresh(): void

- Defined in src/structure/structure-view.ts:100
Updates atomSet, bondSet, atomSetCache, atomCount, bondCount, boundingBox, center.

emits

{Structure.signals.refreshed} when refreshed

Returns void

refreshPosition

refreshPosition(): void

Overrides Structure.refreshPosition
- Defined in src/structure/structure-view.ts:260
Returns void

setSelection

setSelection(selection: Selection): void

- Defined in src/structure/structure-view.ts:164
Parameters
- selection: Selection
Returns void

updatePosition

updatePosition(position: Float32Array | number[]): void

Inherited from Structure.updatePosition
- Defined in src/structure/structure.ts:1061
Parameters
- position: Float32Array | number[]
Returns void

Static getView

getView(selection: Selection): StructureView

Inherited from Structure.getView
- Defined in src/structure/structure.ts:101
Parameters
- selection: Selection
Returns StructureView

Object literals

signals

signals: object

refreshed

refreshed: Signal<T> = new Signal()

Generated using TypeDoc