Class StructureView

View on the structure, restricted to the filter

Hierarchy

Structure
- StructureView

Implements

Structure

Index

Constructors

constructor

Properties

Accessors

Methods

Constructors

constructor

new StructureView(structure: Structure, filter: Filter): StructureView

Overrides Structure.constructor
- Defined in backend/src/structure/structure-view.ts:49
Parameters
- structure: Structure
  
  the structure
- filter: Filter
  
  the filter
Returns StructureView

Properties

_ap

_bp

_cp

_cp: ChainProxy

_rp

_rp: ResidueProxy

atomCount

atomCount: number

Optional atomSet

atomSet: BitArray_Legacy

atomSetCache

atomSetCache: {}

Type declaration

[k: string]: BitArray_Legacy

bondCount

bondCount: number

Optional bondSet

bondSet: BitArray_Legacy

boundingBox

boundingBox: Box3

center

center: Vector3

extraData

extraData: StructureExtraData

filter

filter: Filter

header

header: StructureHeader

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

atomMap

get atomMap(): AtomMap

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

atomSetDict

get atomSetDict(): {}

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

atomStore

get atomStore(): AtomStore

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

backboneBondStore

get backboneBondStore(): BondStore

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

biomolDict

get biomolDict(): {}

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

bondHash

get bondHash(): BondHash | undefined

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

bondStore

get bondStore(): BondStore

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

boxes

get boxes(): Float32Array[]

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

chainStore

get chainStore(): ChainStore

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

data

get data(): Data

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

entityList

get entityList(): Entity[]

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

estimatedSizeInBytes

get estimatedSizeInBytes(): number

Inherited from StructureView.estimatedSizeInBytes
- Defined in backend/src/structure/structure.ts:1507
Returns number

frames

get frames(): Float32Array[]

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

id

get id(): string

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

modelStore

get modelStore(): ModelStore

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

name

get name(): string

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

path

get path(): string

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

residueMap

get residueMap(): ResidueMap

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

residueStore

get residueStore(): ResidueStore

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

rungBondStore

get rungBondStore(): BondStore

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

spatialHash

get spatialHash(): SpatialHash | undefined

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

title

get title(): string

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

type

get type(): string

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

unitcell

get unitcell(): Unitcell | undefined

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

validation

get validation(): Validation | undefined

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

Methods

atomCenter

atomCenter(filter?: Filter): Vector3

Inherited from StructureView.atomCenter
- Defined in backend/src/structure/structure.ts:1001
Gets the center of the (filtered) structure atoms

Parameters
- Optional filter: Filter
Returns Vector3

the center

clone

clone(): Structure

Inherited from StructureView.clone
- Defined in backend/src/structure/structure.ts:1129
Creates a copy of this structure.

Returns Structure

new structure being a copy of this one

dispose

dispose(): void

Overrides Structure.dispose
- Defined in backend/src/structure/structure-view.ts:280
Returns void

eachAtom

eachAtom(callback: (entity: AtomProxy) => any, filter?: Filter): void

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

eachBond

eachBond(callback: (entity: BondProxy) => any, filter?: Filter): void

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

eachChain

eachChain(callback: (entity: ChainProxy) => any, filter?: Filter): void

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

eachEntity

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

Inherited from StructureView.eachEntity
- Defined in backend/src/structure/structure.ts:472
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, filter?: Filter): void

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

eachPolymer

eachPolymer(callback: (entity: Polymer) => void, filter?: Filter): void

Inherited from StructureView.eachPolymer
- Defined in backend/src/structure/structure.ts:596
Polymer iterator

Parameters
- callback: (entity: Polymer) => void
  
  the callback
  - - (entity: Polymer): void
    - Parameters
      - entity: Polymer
      Returns void
- Optional filter: Filter
Returns void

eachResidue

eachResidue(callback: (entity: ResidueProxy) => any, filter?: Filter): void

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

eachResidueN

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

Overrides Structure.eachResidueN
- Defined in backend/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 backend/src/structure/structure.ts:201
Returns void

finalizeBonds

finalizeBonds(): void

Inherited from StructureView.finalizeBonds
- Defined in backend/src/structure/structure.ts:209
Returns void

getAtomData

getAtomData(params: AtomDataParams): AtomData

Inherited from StructureView.getAtomData
- Defined in backend/src/structure/structure.ts:668
Parameters
- params: AtomDataParams
Returns AtomData

getAtomIndices

getAtomIndices(filter?: Filter): undefined | Uint32Array

Overrides Structure.getAtomIndices
- Defined in backend/src/structure/structure-view.ts:270
Parameters
- Optional filter: Filter
Returns undefined | Uint32Array

getAtomProxy

getAtomProxy(index?: undefined | number): AtomProxy

Inherited from StructureView.getAtomProxy
- Defined in backend/src/structure/structure.ts:230
Parameters
- Optional index: undefined | number
Returns AtomProxy

getAtomSet

getAtomSet(filter?: boolean | Filter | BitArray_Legacy, ignoreView?: boolean): BitArray_Legacy

Overrides Structure.getAtomSet
- Defined in backend/src/structure/structure-view.ts:259
Parameters
- Optional filter: boolean | Filter | BitArray_Legacy
- Default value ignoreView: boolean = false
Returns BitArray_Legacy

getAtomSetWithinFilter

getAtomSetWithinFilter(filter: boolean | Filter | BitArray_Legacy, radius: number): BitArray_Legacy

Inherited from StructureView.getAtomSetWithinFilter
- Defined in backend/src/structure/structure.ts:372
Get set of atoms around a set of atoms from a filter

Parameters
- filter: boolean | Filter | BitArray_Legacy
  
  the filter object
- radius: number
  
  radius to filter within
Returns BitArray_Legacy

set of atoms

getAtomSetWithinGroup

getAtomSetWithinGroup(filter: boolean | Filter): BitArray_Legacy

Inherited from StructureView.getAtomSetWithinGroup
- Defined in backend/src/structure/structure.ts:441
Get set of all atoms within the groups of a filter

Parameters
- filter: boolean | Filter
  
  the filter object
Returns BitArray_Legacy

set of atoms

getAtomSetWithinPoint

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

Inherited from StructureView.getAtomSetWithinPoint
- Defined in backend/src/structure/structure.ts:395
Get set of atoms around a point

Parameters
- point: Vector3 | AtomProxy
  
  the point
- radius: number
  
  radius to filter within
Returns BitArray_Legacy

set of atoms

getAtomSetWithinVolume

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

Inherited from StructureView.getAtomSetWithinVolume
- Defined in backend/src/structure/structure.ts:417
Get set of atoms within a volume

Parameters
- volume: Volume
  
  the volume
- radius: number
  
  radius to filter 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_Legacy

set of atoms

getBackboneAtomData

getBackboneAtomData(params: AtomDataParams): AtomData

Inherited from StructureView.getBackboneAtomData
- Defined in backend/src/structure/structure.ts:895
Parameters
- params: AtomDataParams
Returns AtomData

getBackboneBondData

getBackboneBondData(params: BondDataParams): BondData

Inherited from StructureView.getBackboneBondData
- Defined in backend/src/structure/structure.ts:903
Parameters
- params: BondDataParams
Returns BondData

getBackboneBondSet

getBackboneBondSet(): BitArray_Legacy

Inherited from StructureView.getBackboneBondSet
- Defined in backend/src/structure/structure.ts:277
Returns BitArray_Legacy

getBondData

getBondData(params: BondDataParams): BondData

Inherited from StructureView.getBondData
- Defined in backend/src/structure/structure.ts:724
Parameters
- params: BondDataParams
Returns BondData

getBondProxy

getBondProxy(index?: undefined | number): BondProxy

Inherited from StructureView.getBondProxy
- Defined in backend/src/structure/structure.ts:226
Parameters
- Optional index: undefined | number
Returns BondProxy

getBondSet

getBondSet(): BitArray_Legacy

Inherited from StructureView.getBondSet
- Defined in backend/src/structure/structure.ts:248
Returns BitArray_Legacy

getBoundingBox

getBoundingBox(filter?: Filter, box?: Box3): Box3

Inherited from StructureView.getBoundingBox
- Defined in backend/src/structure/structure.ts:937
Gets the bounding box of the (filtered) structure atoms

Parameters
- Optional filter: Filter
- Optional box: Box3
Returns Box3

the box

getChainProxy

getChainProxy(index?: undefined | number): ChainProxy

Inherited from StructureView.getChainProxy
- Defined in backend/src/structure/structure.ts:238
Parameters
- Optional index: undefined | number
Returns ChainProxy

getChainnameCount

getChainnameCount(filter?: Filter): number

Inherited from StructureView.getChainnameCount
- Defined in backend/src/structure/structure.ts:1060
Get number of unique chainnames

Parameters
- Optional filter: Filter
  
  limit count to filter
Returns number

count

getFilter

getFilter(filter?: Filter): Filter

Overrides Structure.getFilter
- Defined in backend/src/structure/structure-view.ts:184
Parameters
- Optional filter: Filter
Returns Filter

getModelProxy

getModelProxy(index?: undefined | number): ModelProxy

Inherited from StructureView.getModelProxy
- Defined in backend/src/structure/structure.ts:242
Parameters
- Optional index: undefined | number
Returns ModelProxy

getPrincipalAxes

getPrincipalAxes(filter?: Filter): PrincipalAxes

Inherited from StructureView.getPrincipalAxes
- Defined in backend/src/structure/structure.ts:977
Gets the principal axes of the (filtered) structure atoms

Parameters
- Optional filter: Filter
Returns PrincipalAxes

the principal axes

getResidueProxy

getResidueProxy(index?: undefined | number): ResidueProxy

Inherited from StructureView.getResidueProxy
- Defined in backend/src/structure/structure.ts:234
Parameters
- Optional index: undefined | number
Returns ResidueProxy

getRungAtomData

getRungAtomData(params: AtomDataParams): AtomData

Inherited from StructureView.getRungAtomData
- Defined in backend/src/structure/structure.ts:912
Parameters
- params: AtomDataParams
Returns AtomData

getRungBondData

getRungBondData(params: BondDataParams): BondData

Inherited from StructureView.getRungBondData
- Defined in backend/src/structure/structure.ts:920
Parameters
- params: BondDataParams
Returns BondData

getRungBondSet

getRungBondSet(): BitArray_Legacy

Inherited from StructureView.getRungBondSet
- Defined in backend/src/structure/structure.ts:301
Returns BitArray_Legacy

getSequence

getSequence(filter?: Filter): string[]

Inherited from StructureView.getSequence
- Defined in backend/src/structure/structure.ts:1024
Parameters
- Optional filter: Filter
Returns string[]

getSequenceFormatted

getSequenceFormatted(convFunc: (rp: ResidueProxy) => string, filter?: Filter): string[]

Inherited from StructureView.getSequenceFormatted
- Defined in backend/src/structure/structure.ts:1028
Parameters
- convFunc: (rp: ResidueProxy) => string
  - - (rp: ResidueProxy): string
    - Parameters
      - rp: ResidueProxy
      Returns string
- Optional filter: Filter
Returns string[]

getStructure

getStructure(): Structure | StructureView

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

getView

getView(filter: Filter): StructureView

Inherited from StructureView.getView
- Defined in backend/src/structure/structure.ts:103
Parameters
- filter: Filter
Returns StructureView

hasCoords

hasCoords(): boolean

Inherited from StructureView.hasCoords
- Defined in backend/src/structure/structure.ts:1009
Returns boolean

init

init(): void

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

refresh

refresh(): void

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

removeAtom

removeAtom(atom: AtomProxy): void

Inherited from StructureView.removeAtom
- Defined in backend/src/structure/structure.ts:1299
Removes provided atom

Parameters
- atom: AtomProxy
  
  atom to remove
Returns void

removeAtomWhere

removeAtomWhere(predicate: (a: AtomProxy) => boolean, startIdx?: number, count?: number): void

Inherited from StructureView.removeAtomWhere
- Defined in backend/src/structure/structure.ts:1312
Removes first atom meeting the given condition. The additional parameters determine the subset of atoms to check. If startIdx and count are less than zero, all atoms are checked for predicate.

Parameters
- predicate: (a: AtomProxy) => boolean
  
  predicate that evaluates to true for the atom to be removed
  - - (a: AtomProxy): boolean
    - Parameters
      - a: AtomProxy
      Returns boolean
- Default value startIdx: number = -1
  
  start index of the interval to search through
- Default value count: number = -1
  
  length of the interval
Returns void

removeAtomsStartingAtIndex

removeAtomsStartingAtIndex(atomIdx: number, count?: number): void

Inherited from StructureView.removeAtomsStartingAtIndex
- Defined in backend/src/structure/structure.ts:1161
Removes given number of atoms starting at provided index

Parameters
- atomIdx: number
  
  index to start at (refers to the location in atom store)
- Default value count: number = 1
  
  number of atoms to remove
Returns void

removeAtomsWhere

removeAtomsWhere(predicate: (a: AtomProxy) => boolean, startIdx?: number, count?: number): void

Inherited from StructureView.removeAtomsWhere
- Defined in backend/src/structure/structure.ts:1325
Removes all atoms meeting the given condition. The additional parameters determine the subset of atoms to check. If startIdx and count are less than zero, all atoms are checked for predicate.

Parameters
- predicate: (a: AtomProxy) => boolean
  
  predicate that evaluates to true for atoms to be removed
  - - (a: AtomProxy): boolean
    - Parameters
      - a: AtomProxy
      Returns boolean
- Default value startIdx: number = -1
  
  start index of the interval to search through
- Default value count: number = -1
  
  length of the interval
Returns void

removeChain

removeChain(chain: ChainProxy): void

Inherited from StructureView.removeChain
- Defined in backend/src/structure/structure.ts:1369
Removes given chain from the structure.

Parameters
- chain: ChainProxy
  
  chain to be removed
Returns void

removeElements

removeElements(element: string): void

Inherited from StructureView.removeElements
- Defined in backend/src/structure/structure.ts:1337
Removes atoms corresponding to the provided chemical element.

example

structure.removeElements("H") // removes all hydrogen atoms

Parameters
- element: string
  
  element name to remove
Returns void

removeResidue

removeResidue(residue: ResidueProxy): void

Inherited from StructureView.removeResidue
- Defined in backend/src/structure/structure.ts:1354
Removes given residue from the structure. The chain is not affected by the removal, i.e., the function does not handle any potential "discontinuity" that might be caused by this operation.

Parameters
- residue: ResidueProxy
  
  residue to be removed
Returns void

setFilter

setFilter(filter: Filter): void

- Defined in backend/src/structure/structure-view.ts:178
Parameters
- filter: Filter
Returns void

toString

toString(): string

Inherited from StructureView.toString
- Defined in backend/src/structure/structure.ts:1138
Returns a string containing some information about the structure

Returns string

string with information about the structure

updatePosition

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

Inherited from StructureView.updatePosition
- Defined in backend/src/structure/structure.ts:1073
Parameters
- position: Float32Array | number[]
Returns void

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