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Class Structure

Structure

Hierarchy

Implements

Implemented by

Index

Constructors

constructor

  • new Structure(name?: string, path?: string): Structure

Properties

_ap

_bp

_cp

Optional _hasCoords

_hasCoords: undefined | false | true

_rp

atomCount

atomCount: number

atomMap

atomMap: AtomMap

Optional atomSet

atomSet: BitArray

atomSetCache

atomSetCache: {}

Type declaration

atomSetDict

atomSetDict: {}

Type declaration

atomStore

atomStore: AtomStore

backboneBondStore

backboneBondStore: BondStore

biomolDict

biomolDict: {}

Type declaration

bondCount

bondCount: number

Optional bondHash

bondHash: BondHash

Optional bondSet

bondSet: BitArray

bondStore

bondStore: BondStore

boundingBox

boundingBox: Box3

boxes

boxes: Float32Array[]

center

center: Vector3

chainStore

chainStore: ChainStore

data

data: Data

entityList

entityList: Entity[]

extraData

frames

frames: Float32Array[]

header

id

id: string

modelStore

modelStore: ModelStore

name

name: string

path

path: string

residueMap

residueMap: ResidueMap

residueStore

residueStore: ResidueStore

rungBondStore

rungBondStore: BondStore

Optional spatialHash

spatialHash: SpatialHash

title

title: string

Optional trajectory

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

Optional unitcell

unitcell: Unitcell

Optional validation

validation: Validation

Accessors

type

  • get type(): string

Methods

atomCenter

dispose

  • dispose(): void

eachAtom

eachBond

eachChain

eachEntity

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

eachModel

eachPolymer

eachResidue

eachResidueN

  • eachResidueN(n: number, callback: (...entityArray: ResidueProxy[]) => void): void

finalizeAtoms

  • finalizeAtoms(): void

finalizeBonds

  • finalizeBonds(): void

getAtomData

getAtomIndices

  • getAtomIndices(selection?: Selection): undefined | Uint32Array

getAtomProxy

  • getAtomProxy(index?: undefined | number): AtomProxy

getAtomSet

  • Get a set of atoms

    Parameters

    • Optional selection: boolean | Selection | BitArray

      object defining how to initialize the atom set. Boolean: init with value; Selection: init with selection; BitArray: return bit array

    Returns BitArray

    set of atoms

getAtomSetWithinGroup

getAtomSetWithinPoint

getAtomSetWithinSelection

getAtomSetWithinVolume

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

getBackboneBondData

getBackboneBondSet

getBondData

getBondProxy

  • getBondProxy(index?: undefined | number): BondProxy

getBondSet

getBoundingBox

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

getChainProxy

  • getChainProxy(index?: undefined | number): ChainProxy

getChainnameCount

  • getChainnameCount(selection?: Selection): number

getModelProxy

  • getModelProxy(index?: undefined | number): ModelProxy

getPrincipalAxes

getResidueProxy

getRungAtomData

getRungBondData

getRungBondSet

getSelection

getSequence

  • getSequence(selection?: Selection): string[]

getStructure

getView

hasCoords

  • hasCoords(): boolean

init

  • init(name: string, path: string): void

refreshPosition

  • refreshPosition(): void

updatePosition

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

Object literals

signals

signals: object

refreshed

refreshed: Signal<T> = new Signal()

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