Class StructureView

View on the structure, restricted to the selection

Hierarchy

Structure
- StructureView

Implements

Structure

Index

Constructors

constructor

Properties

Accessors

Methods

Constructors

constructor

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

Overrides Structure.constructor
- Defined in src/structure/structure-view.ts:49
Parameters
- structure: Structure
  
  the structure
- selection: Selection
  
  the selection
Returns StructureView

Properties

_ap

_bp

_cp

_cp: ChainProxy

_rp

_rp: ResidueProxy

atomCount

atomCount: number

Optional atomSet

atomSet: BitArray

atomSetCache

atomSetCache: {}

Type declaration

[k: string]: BitArray

bondCount

bondCount: number

Optional bondSet

bondSet: BitArray

boundingBox

boundingBox: Box3

center

center: Vector3

extraData

extraData: StructureExtraData

header

header: StructureHeader

selection

selection: Selection

signals

signals: StructureSignals

structure

structure: Structure

Optional trajectory

trajectory: undefined | { frame: number; name: string }

Accessors

_hasCoords

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

Overrides Structure._hasCoords
- Defined in src/structure/structure-view.ts:106
Returns undefined | false | true
Overrides Structure._hasCoords
- Defined in src/structure/structure-view.ts:107
Parameters
- value: undefined | false | true
Returns void

atomMap

get atomMap(): AtomMap

Overrides Structure.atomMap
- Defined in src/structure/structure-view.ts:101
Returns AtomMap

atomSetDict

get atomSetDict(): {}

Overrides Structure.atomSetDict
- Defined in src/structure/structure-view.ts:87
Returns {}
- [k: string]: BitArray

atomStore

get atomStore(): AtomStore

Overrides Structure.atomStore
- Defined in src/structure/structure-view.ts:97
Returns AtomStore

backboneBondStore

get backboneBondStore(): BondStore

Overrides Structure.backboneBondStore
- Defined in src/structure/structure-view.ts:95
Returns BondStore

biomolDict

get biomolDict(): {}

Overrides Structure.biomolDict
- Defined in src/structure/structure-view.ts:88
Returns {}
- [k: string]: Assembly

bondHash

get bondHash(): BondHash | undefined

Overrides Structure.bondHash
- Defined in src/structure/structure-view.ts:103
Returns BondHash | undefined

bondStore

get bondStore(): BondStore

Overrides Structure.bondStore
- Defined in src/structure/structure-view.ts:94
Returns BondStore

boxes

get boxes(): Float32Array[]

Overrides Structure.boxes
- Defined in src/structure/structure-view.ts:92
Returns Float32Array[]

chainStore

get chainStore(): ChainStore

Overrides Structure.chainStore
- Defined in src/structure/structure-view.ts:99
Returns ChainStore

data

get data(): Data

Overrides Structure.data
- Defined in src/structure/structure-view.ts:86
Returns Data

entityList

get entityList(): Entity[]

Overrides Structure.entityList
- Defined in src/structure/structure-view.ts:89
Returns Entity[]

frames

get frames(): Float32Array[]

Overrides Structure.frames
- Defined in src/structure/structure-view.ts:91
Returns Float32Array[]

id

get id(): string

Overrides Structure.id
- Defined in src/structure/structure-view.ts:85
Returns string

modelStore

get modelStore(): ModelStore

Overrides Structure.modelStore
- Defined in src/structure/structure-view.ts:100
Returns ModelStore

name

get name(): string

Overrides Structure.name
- Defined in src/structure/structure-view.ts:82
Returns string

path

get path(): string

Overrides Structure.path
- Defined in src/structure/structure-view.ts:83
Returns string

residueMap

get residueMap(): ResidueMap

Overrides Structure.residueMap
- Defined in src/structure/structure-view.ts:102
Returns ResidueMap

residueStore

get residueStore(): ResidueStore

Overrides Structure.residueStore
- Defined in src/structure/structure-view.ts:98
Returns ResidueStore

rungBondStore

get rungBondStore(): BondStore

Overrides Structure.rungBondStore
- Defined in src/structure/structure-view.ts:96
Returns BondStore

spatialHash

get spatialHash(): SpatialHash | undefined

Overrides Structure.spatialHash
- Defined in src/structure/structure-view.ts:104
Returns SpatialHash | undefined

title

get title(): string

Overrides Structure.title
- Defined in src/structure/structure-view.ts:84
Returns string

type

get type(): string

Overrides Structure.type
- Defined in src/structure/structure-view.ts:80
Returns string

unitcell

get unitcell(): Unitcell | undefined

Overrides Structure.unitcell
- Defined in src/structure/structure-view.ts:90
Returns Unitcell | undefined

validation

get validation(): Validation | undefined

Overrides Structure.validation
- Defined in src/structure/structure-view.ts:93
Returns Validation | undefined

Methods

atomCenter

atomCenter(selection?: Selection): Vector3

Inherited from StructureView.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:280
Returns void

eachAtom

eachAtom(callback: (entity: AtomProxy) => any, selection?: Selection): void

Overrides Structure.eachAtom
- Defined in src/structure/structure-view.ts:218
Parameters
- callback: (entity: AtomProxy) => any
  - - (entity: AtomProxy): any
    - Parameters
      - entity: AtomProxy
      Returns any
- Optional selection: Selection
Returns void

eachBond

eachBond(callback: (entity: BondProxy) => any, selection?: Selection): void

Overrides Structure.eachBond
- Defined in src/structure/structure-view.ts:214
Parameters
- callback: (entity: BondProxy) => any
  - - (entity: BondProxy): any
    - Parameters
      - entity: BondProxy
      Returns any
- Optional selection: Selection
Returns void

eachChain

eachChain(callback: (entity: ChainProxy) => any, selection?: Selection): void

Overrides Structure.eachChain
- Defined in src/structure/structure-view.ts:249
Parameters
- callback: (entity: ChainProxy) => any
  - - (entity: ChainProxy): any
    - Parameters
      - entity: ChainProxy
      Returns any
- Optional selection: Selection
Returns void

eachEntity

eachEntity(callback: (entity: Entity) => void, type: number): void

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

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

eachModel

eachModel(callback: (entity: ModelProxy) => any, selection?: Selection): void

Overrides Structure.eachModel
- Defined in src/structure/structure-view.ts:253
Parameters
- callback: (entity: ModelProxy) => any
  - - (entity: ModelProxy): any
    - Parameters
      - entity: ModelProxy
      Returns any
- Optional selection: Selection
Returns void

eachPolymer

eachPolymer(callback: (entity: Polymer) => void, selection?: Selection): void

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

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

eachResidue

eachResidue(callback: (entity: ResidueProxy) => any, selection?: Selection): void

Overrides Structure.eachResidue
- Defined in src/structure/structure-view.ts:236
Parameters
- callback: (entity: ResidueProxy) => any
  - - (entity: ResidueProxy): any
    - Parameters
      - entity: ResidueProxy
      Returns any
- Optional selection: Selection
Returns void

eachResidueN

eachResidueN(n: number, callback: (entity: ResidueProxy) => any): void

Overrides Structure.eachResidueN
- Defined in src/structure/structure-view.ts:245
Not implemented

alias

StructureView#eachResidueN

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

finalizeAtoms

finalizeAtoms(): void

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

finalizeBonds

finalizeBonds(): void

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

getAtomData

getAtomData(params: AtomDataParams): AtomData

Inherited from StructureView.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:270
Parameters
- Optional selection: Selection
Returns undefined | Uint32Array

getAtomProxy

getAtomProxy(index?: undefined | number): AtomProxy

Inherited from StructureView.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:259
Parameters
- Optional selection: boolean | Selection | BitArray
- Default value ignoreView: boolean = false
Returns BitArray

getAtomSetWithinGroup

getAtomSetWithinGroup(selection: boolean | Selection): BitArray

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

getBackboneBondData

getBackboneBondData(params: BondDataParams): BondData

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

getBackboneBondSet

getBackboneBondSet(): BitArray

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

getBondData

getBondData(params: BondDataParams): BondData

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

getBondProxy

getBondProxy(index?: undefined | number): BondProxy

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

getBondSet

getBondSet(): BitArray

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

getBoundingBox

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

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

getChainnameCount

getChainnameCount(selection?: Selection): number

Inherited from StructureView.getChainnameCount
- Defined in src/structure/structure.ts:1051
Get number of unique chainnames

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

count

getModelProxy

getModelProxy(index?: undefined | number): ModelProxy

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

getPrincipalAxes

getPrincipalAxes(selection?: Selection): PrincipalAxes

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

getRungAtomData

getRungAtomData(params: AtomDataParams): AtomData

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

getRungBondData

getRungBondData(params: BondDataParams): BondData

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

getRungBondSet

getRungBondSet(): BitArray

Inherited from StructureView.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:184
Parameters
- Optional selection: Selection
Returns Selection

getSequence

getSequence(selection?: Selection): string[]

Inherited from StructureView.getSequence
- Defined in src/structure/structure.ts:1019
Parameters
- Optional selection: Selection
Returns string[]

getStructure

getStructure(): Structure | StructureView

Overrides Structure.getStructure
- Defined in src/structure/structure-view.ts:208
Returns Structure | StructureView

getView

getView(selection: Selection): StructureView

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

hasCoords

hasCoords(): boolean

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

init

init(): void

Overrides Structure.init
- Defined in src/structure/structure-view.ts:78
Returns void

refresh

refresh(): void

- Defined in src/structure/structure-view.ts:114
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:274
Returns void

setSelection

setSelection(selection: Selection): void

- Defined in src/structure/structure-view.ts:178
Parameters
- selection: Selection
Returns void

updatePosition

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

Inherited from StructureView.updatePosition
- Defined in src/structure/structure.ts:1064
Parameters
- position: Float32Array | number[]
Returns void

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