Class Structure

Structure

Hierarchy

Structure
- StructureView

Implements

Structure

Implemented by

Index

Constructors

constructor

Properties

Accessors

type

Methods

Object literals

signals

Constructors

constructor

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

- Defined in src/structure/structure.ts:135
Parameters
- Default value name: string = ""
  
  structure name
- Default value path: string = ""
  
  source path
Returns Structure

Properties

_ap

_bp

_cp

_cp: ChainProxy

Optional _hasCoords

_hasCoords: undefined | false | true

_rp

_rp: ResidueProxy

atomCount

atomCount: number

atomMap

atomMap: AtomMap

Optional atomSet

atomSet: BitArray

atomSetCache

atomSetCache: {}

Type declaration

[k: string]: BitArray

atomSetDict

atomSetDict: {}

Type declaration

[k: string]: BitArray

atomStore

atomStore: AtomStore

backboneBondStore

backboneBondStore: BondStore

biomolDict

biomolDict: {}

Type declaration

[k: string]: Assembly

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

extraData: StructureExtraData

frames

frames: Float32Array[]

header

header: StructureHeader

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

- Defined in src/structure/structure.ts:194
Returns string

Methods

atomCenter

atomCenter(selection?: Selection): Vector3

- 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

- Defined in src/structure/structure.ts:1086
Calls dispose() method of property objects. Unsets properties to help garbage collection.

Returns void

eachAtom

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

- Defined in src/structure/structure.ts:512
Atom iterator

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

eachBond

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

- Defined in src/structure/structure.ts:481
Bond iterator

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

eachChain

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

- Defined in src/structure/structure.ts:613
Chain iterator

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

eachEntity

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

- 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) => void, selection?: Selection): void

- Defined in src/structure/structure.ts:634
Model iterator

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

eachPolymer

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

- 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) => void, selection?: Selection): void

- Defined in src/structure/structure.ts:533
Residue iterator

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

eachResidueN

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

- Defined in src/structure/structure.ts:567
Multi-residue iterator

Parameters
- n: number
  
  window size
- callback: (...entityArray: ResidueProxy[]) => void
  
  the callback
  - - (...entityArray: ResidueProxy[]): void
    - Parameters
      - Rest ...entityArray: ResidueProxy[]
      Returns void
Returns void

finalizeAtoms

finalizeAtoms(): void

- Defined in src/structure/structure.ts:196
Returns void

finalizeBonds

finalizeBonds(): void

- Defined in src/structure/structure.ts:204
Returns void

getAtomData

getAtomData(params: AtomDataParams): AtomData

- Defined in src/structure/structure.ts:663
Parameters
- params: AtomDataParams
Returns AtomData

getAtomIndices

getAtomIndices(selection?: Selection): undefined | Uint32Array

- Defined in src/structure/structure.ts:1033
Parameters
- Optional selection: Selection
Returns undefined | Uint32Array

getAtomProxy

getAtomProxy(index?: undefined | number): AtomProxy

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

getAtomSet

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

- Defined in src/structure/structure.ts:329
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

getAtomSetWithinGroup(selection: boolean | Selection): BitArray

- 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

- 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

- 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

- 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

- Defined in src/structure/structure.ts:890
Parameters
- params: AtomDataParams
Returns AtomData

getBackboneBondData

getBackboneBondData(params: BondDataParams): BondData

- Defined in src/structure/structure.ts:898
Parameters
- params: BondDataParams
Returns BondData

getBackboneBondSet

getBackboneBondSet(): BitArray

- Defined in src/structure/structure.ts:272
Returns BitArray

getBondData

getBondData(params: BondDataParams): BondData

- Defined in src/structure/structure.ts:719
Parameters
- params: BondDataParams
Returns BondData

getBondProxy

getBondProxy(index?: undefined | number): BondProxy

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

getBondSet

getBondSet(): BitArray

- Defined in src/structure/structure.ts:243
Returns BitArray

getBoundingBox

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

- 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

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

getChainnameCount

getChainnameCount(selection?: Selection): number

- 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

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

getPrincipalAxes

getPrincipalAxes(selection?: Selection): PrincipalAxes

- 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

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

getRungAtomData

getRungAtomData(params: AtomDataParams): AtomData

- Defined in src/structure/structure.ts:907
Parameters
- params: AtomDataParams
Returns AtomData

getRungBondData

getRungBondData(params: BondDataParams): BondData

- Defined in src/structure/structure.ts:915
Parameters
- params: BondDataParams
Returns BondData

getRungBondSet

getRungBondSet(): BitArray

- Defined in src/structure/structure.ts:296
Returns BitArray

getSelection

getSelection(): undefined | Selection

- Defined in src/structure/structure.ts:453
Returns undefined | Selection

getSequence

getSequence(selection?: Selection): string[]

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

getStructure

getStructure(): Structure | StructureView

- Defined in src/structure/structure.ts:457
Returns Structure | StructureView

getView

getView(selection: Selection): StructureView

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

hasCoords

hasCoords(): boolean

- Defined in src/structure/structure.ts:1004
Returns boolean

init

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

- Defined in src/structure/structure.ts:145
Parameters
- name: string
- path: string
Returns void

refreshPosition

refreshPosition(): void

- Defined in src/structure/structure.ts:1075
Returns void

updatePosition

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

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

Object literals

signals

signals: object

refreshed

refreshed: Signal<T> = new Signal()

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