Class Structure

Structure

Hierarchy

Structure
- StructureView

Implements

Structure

Implemented by

Index

Constructors

constructor

Properties

Accessors

Methods

Object literals

signals

Constructors

constructor

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

- Defined in backend/src/structure/structure.ts:137
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_Legacy

atomSetCache

atomSetCache: {}

Type declaration

[k: string]: BitArray_Legacy

atomSetDict

atomSetDict: {}

Type declaration

[k: string]: BitArray_Legacy

atomStore

atomStore: AtomStore

backboneBondStore

backboneBondStore: BondStore

biomolDict

biomolDict: {}

Type declaration

[k: string]: Assembly

bondCount

bondCount: number

Optional bondHash

bondHash: BondHash

Optional bondSet

bondSet: BitArray_Legacy

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

estimatedSizeInBytes

get estimatedSizeInBytes(): number

- Defined in backend/src/structure/structure.ts:1507
Returns number

type

get type(): string

- Defined in backend/src/structure/structure.ts:199
Returns string

Methods

atomCenter

atomCenter(filter?: Filter): Vector3

- 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

- 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

- Defined in backend/src/structure/structure.ts:1095
Calls dispose() method of property objects. Unsets properties to help garbage collection.

Returns void

eachAtom

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

- Defined in backend/src/structure/structure.ts:517
Atom iterator

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

eachBond

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

- Defined in backend/src/structure/structure.ts:486
Bond iterator

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

eachChain

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

- Defined in backend/src/structure/structure.ts:618
Chain iterator

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

eachEntity

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

- 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) => void, filter?: Filter): void

- Defined in backend/src/structure/structure.ts:639
Model iterator

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

eachPolymer

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

- 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) => void, filter?: Filter): void

- Defined in backend/src/structure/structure.ts:538
Residue iterator

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

eachResidueN

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

- Defined in backend/src/structure/structure.ts:572
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 backend/src/structure/structure.ts:201
Returns void

finalizeBonds

finalizeBonds(): void

- Defined in backend/src/structure/structure.ts:209
Returns void

Private forEachSet

forEachSet(callback: (s: BitArray_Legacy) => void): void

- Defined in backend/src/structure/structure.ts:1502
Parameters
- callback: (s: BitArray_Legacy) => void
  - - (s: BitArray_Legacy): void
    - Parameters
      - s: BitArray_Legacy
      Returns void
Returns void

Private forEachStore

forEachStore(callback: (s: Store) => void): void

- Defined in backend/src/structure/structure.ts:1492
Parameters
- callback: (s: Store) => void
  - - (s: Store): void
    - Parameters
      - s: Store
      Returns void
Returns void

getAtomData

getAtomData(params: AtomDataParams): AtomData

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

getAtomIndices

getAtomIndices(filter?: Filter): undefined | Uint32Array

- Defined in backend/src/structure/structure.ts:1042
Parameters
- Optional filter: Filter
Returns undefined | Uint32Array

getAtomProxy

getAtomProxy(index?: undefined | number): AtomProxy

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

getAtomSet

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

- Defined in backend/src/structure/structure.ts:334
Get a set of atoms

Parameters
- Optional filter: boolean | Filter | BitArray_Legacy
  
  object defining how to initialize the atom set. Boolean: init with value; Filter: init with filter; BitArray: return bit array
Returns BitArray_Legacy

set of atoms

getAtomSetWithinFilter

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

- 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

- 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

- 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

- 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

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

getBackboneBondData

getBackboneBondData(params: BondDataParams): BondData

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

getBackboneBondSet

getBackboneBondSet(): BitArray_Legacy

- Defined in backend/src/structure/structure.ts:277
Returns BitArray_Legacy

getBondData

getBondData(params: BondDataParams): BondData

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

getBondProxy

getBondProxy(index?: undefined | number): BondProxy

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

getBondSet

getBondSet(): BitArray_Legacy

- Defined in backend/src/structure/structure.ts:248
Returns BitArray_Legacy

getBoundingBox

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

- 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

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

getChainnameCount

getChainnameCount(filter?: Filter): number

- 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(): undefined | Filter

- Defined in backend/src/structure/structure.ts:458
Returns undefined | Filter

getModelProxy

getModelProxy(index?: undefined | number): ModelProxy

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

getPrincipalAxes

getPrincipalAxes(filter?: Filter): PrincipalAxes

- 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

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

getRungAtomData

getRungAtomData(params: AtomDataParams): AtomData

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

getRungBondData

getRungBondData(params: BondDataParams): BondData

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

getRungBondSet

getRungBondSet(): BitArray_Legacy

- Defined in backend/src/structure/structure.ts:301
Returns BitArray_Legacy

getSequence

getSequence(filter?: Filter): string[]

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

getSequenceFormatted

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

- 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

- Defined in backend/src/structure/structure.ts:462
Returns Structure | StructureView

getView

getView(filter: Filter): StructureView

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

hasCoords

hasCoords(): boolean

- Defined in backend/src/structure/structure.ts:1009
Returns boolean

init

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

- Defined in backend/src/structure/structure.ts:147
Parameters
- name: string
- path: string
Returns void

refreshPosition

refreshPosition(): void

- Defined in backend/src/structure/structure.ts:1084
Returns void

removeAtom

removeAtom(atom: AtomProxy): void

- 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

- 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

- 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

- 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

Private removeAtomsWherePredicate

removeAtomsWherePredicate(predicate: (a: AtomProxy) => boolean, startIdx?: number, atomsToCheckCount?: number, removeOnlyFirst: boolean): void

- Defined in backend/src/structure/structure.ts:1377
Parameters
- predicate: (a: AtomProxy) => boolean
  - - (a: AtomProxy): boolean
    - Parameters
      - a: AtomProxy
      Returns boolean
- Default value startIdx: number = -1
- Default value atomsToCheckCount: number = -1
- removeOnlyFirst: boolean
Returns void

removeChain

removeChain(chain: ChainProxy): void

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

Parameters
- chain: ChainProxy
  
  chain to be removed
Returns void

Private removeChainReferences

removeChainReferences(chainIdx: number): void

- Defined in backend/src/structure/structure.ts:1445
Parameters
- chainIdx: number
Returns void

removeElements

removeElements(element: string): void

- 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

- 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

Private removeResidueReferences

removeResidueReferences(residueIdx: number): void

- Defined in backend/src/structure/structure.ts:1395
Parameters
- residueIdx: number
Returns void

toString

toString(): string

- 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

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

Object literals

signals

signals: object

refreshed

refreshed: Signal<T> = new Signal()

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