StructureTrajectory

Structure trajectory class. Gets data from a structure object.

Hierarchy

Trajectory
- StructureTrajectory

Index

Constructors

constructor

Accessors

Object literals

signals

Constructors

constructor

new StructureTrajectory(trajPath: string, structure: Structure, params: TrajectoryParameters): StructureTrajectory

Overrides Trajectory.constructor
- Defined in src/trajectory/structure-trajectory.ts:14
Parameters
- trajPath: string
- structure: Structure
- params: TrajectoryParameters
Returns StructureTrajectory

Properties

atomCount

atomCount: number

Optional atomIndices

atomIndices: ArrayLike<number>

backboneIndices

backboneIndices: NumberArray

boxCache

boxCache: object

Type declaration

[k: number]: ArrayLike<number>

centerPbc

centerPbc: boolean

coords1

coords1: Float32Array

coords2

coords2: Float32Array

deltaTime

deltaTime: number

frame

frame: number

frameCache

frameCache: object

Type declaration

[k: number]: Float32Array

frameCacheSize

frameCacheSize: number = 0

inProgress

inProgress: boolean

initialCoords

initialCoords: Float32Array

loadQueue

loadQueue: object

Type declaration

[k: number]: boolean

name

name: string

pathCache

pathCache: object

Type declaration

player

player: TrajectoryPlayer

removePbc

removePbc: boolean

removePeriodicity

removePeriodicity: boolean

sele

sele: string

selection

selection: Selection

selectionIndices

selectionIndices: NumberArray

structure

structure: Structure

structureCoords

structureCoords: Float32Array

superpose

superpose: boolean

timeOffset

timeOffset: number

trajPath

trajPath: string

Accessors

currentFrame

get currentFrame(): number

Inherited from Trajectory.currentFrame
- Defined in src/trajectory/trajectory.ts:266
Currently set frame of the trajectory

Returns number

frameCount

get frameCount(): number

Inherited from Trajectory.frameCount
- Defined in src/trajectory/trajectory.ts:259
Number of frames in the trajectory

Returns number

type

get type(): string

- Defined in src/trajectory/structure-trajectory.ts:21
Returns string

Methods

_doSuperpose

_doSuperpose(x: Float32Array): void

Inherited from Trajectory._doSuperpose
- Defined in src/trajectory/trajectory.ts:541
Parameters
- x: Float32Array
Returns void

_getIndices

_getIndices(selection: Selection): number[]

Inherited from Trajectory._getIndices
- Defined in src/trajectory/trajectory.ts:316
Parameters
- selection: Selection
Returns number[]

_init

_init(structure: Structure): void

Inherited from Trajectory._init
- Defined in src/trajectory/trajectory.ts:270
Parameters
- structure: Structure
Returns void

_interpolate

_interpolate(i: number, ip: number, ipp: number, ippp: number, t: number, type: TrajectoryPlayerInterpolateType): void

Inherited from Trajectory._interpolate
- Defined in src/trajectory/trajectory.ts:432
Parameters
- i: number
- ip: number
- ipp: number
- ippp: number
- t: number
- type: TrajectoryPlayerInterpolateType
Returns void

_loadFrame

_loadFrame(i: number, callback?: Function): void

Overrides Trajectory._loadFrame
- Defined in src/trajectory/structure-trajectory.ts:31
Parameters
- i: number
- Optional callback: Function
Returns void

_loadFrameCount

_loadFrameCount(): void

Overrides Trajectory._loadFrameCount
- Defined in src/trajectory/structure-trajectory.ts:64
Returns void

_makeAtomIndices

_makeAtomIndices(): void

Overrides Trajectory._makeAtomIndices
- Defined in src/trajectory/structure-trajectory.ts:23
Returns void

_makeSuperposeCoords

_makeSuperposeCoords(): void

Inherited from Trajectory._makeSuperposeCoords
- Defined in src/trajectory/trajectory.ts:331
Returns void

_process

_process(i: number, box: ArrayLike<number>, coords: Float32Array, frameCount: number): void

Inherited from Trajectory._process
- Defined in src/trajectory/trajectory.ts:560
Parameters
- i: number
- box: ArrayLike<number>
- coords: Float32Array
- frameCount: number
Returns void

_resetCache

_resetCache(): void

Inherited from Trajectory._resetCache
- Defined in src/trajectory/trajectory.ts:353
Returns void

_saveInitialCoords

_saveInitialCoords(): void

Inherited from Trajectory._saveInitialCoords
- Defined in src/trajectory/trajectory.ts:294
Returns void

_saveStructureCoords

_saveStructureCoords(): void

Inherited from Trajectory._saveStructureCoords
- Defined in src/trajectory/trajectory.ts:306
Returns void

_setFrameCount

_setFrameCount(n: number): void

Inherited from Trajectory._setFrameCount
- Defined in src/trajectory/trajectory.ts:589
Parameters
- n: number
Returns void

_updateStructure

_updateStructure(i: number): void

Inherited from Trajectory._updateStructure
- Defined in src/trajectory/trajectory.ts:517
Parameters
- i: number
Returns void

dispose

dispose(): void

Inherited from Trajectory.dispose
- Defined in src/trajectory/trajectory.ts:600
Dispose of the trajectory object

Returns void

getFrameTime

getFrameTime(i: number): number

Inherited from Trajectory.getFrameTime
- Defined in src/trajectory/trajectory.ts:620
Get time for frame

Parameters
- i: number
  
  frame index
Returns number

time in picoseconds

hasFrame

hasFrame(i: number | number[]): boolean

Inherited from Trajectory.hasFrame
- Defined in src/trajectory/trajectory.ts:399
Check if a frame is available

Parameters
- i: number | number[]
  
  the frame index
Returns boolean

frame availability

loadFrame

loadFrame(i: number | number[], callback?: Function): void

Inherited from Trajectory.loadFrame
- Defined in src/trajectory/trajectory.ts:486
Load frame index

Parameters
- i: number | number[]
  
  the frame index
- Optional callback: Function
  
  fired when the frame has been loaded
Returns void

setFrame

setFrame(i: number, callback?: Function): this

Inherited from Trajectory.setFrame
- Defined in src/trajectory/trajectory.ts:412
Set trajectory to a frame index

Parameters
- i: number
  
  the frame index
- Optional callback: Function
Returns this

setFrameInterpolated

setFrameInterpolated(i: number, ip: number, ipp: number, ippp: number, t: number, type: TrajectoryPlayerInterpolateType, callback?: Function): this

Inherited from Trajectory.setFrameInterpolated
- Defined in src/trajectory/trajectory.ts:457
Interpolated and set trajectory to frame indices

Parameters
- i: number
  
  the frame index
- ip: number
  
  one before frame index
- ipp: number
  
  two before frame index
- ippp: number
  
  three before frame index
- t: number
  
  interpolation step [0,1]
- type: TrajectoryPlayerInterpolateType
  
  interpolation type, '', 'spline' or 'linear'
- Optional callback: Function
  
  fired when the frame has been set
Returns this

setParameters

setParameters(params?: Partial<TrajectoryParameters>): void

Inherited from Trajectory.setParameters
- Defined in src/trajectory/trajectory.ts:362
Parameters
- Default value params: Partial<TrajectoryParameters> = {}
Returns void

setPlayer

setPlayer(player: TrajectoryPlayer): void

Inherited from Trajectory.setPlayer
- Defined in src/trajectory/trajectory.ts:610
Set player for this trajectory

Parameters
- player: TrajectoryPlayer
  
  the player
Returns void

setSelection

setSelection(string: string): this

Inherited from Trajectory.setSelection
- Defined in src/trajectory/trajectory.ts:311
Parameters
- string: string
Returns this

setStructure

setStructure(structure: Structure): void

Inherited from Trajectory.setStructure
- Defined in src/trajectory/trajectory.ts:278
Parameters
- structure: Structure
Returns void

Object literals

signals

signals: object

countChanged

countChanged: Signal<T> = new Signal()

frameChanged

frameChanged: Signal<T> = new Signal()

playerChanged

playerChanged: Signal<T> = new Signal()

Hierarchy

Index

Constructors

Properties

Accessors

Methods

Object literals

Constructors

constructor

Parameters

trajPath: string

structure: Structure

params: TrajectoryParameters

Returns StructureTrajectory

Properties

atomCount

Optional atomIndices

backboneIndices

boxCache

Type declaration

[k: number]: ArrayLike<number>

centerPbc

coords1

coords2

deltaTime

frame

frameCache

Type declaration

[k: number]: Float32Array

frameCacheSize

inProgress

initialCoords

loadQueue

Type declaration

[k: number]: boolean

name

pathCache

Type declaration

player

removePbc

removePeriodicity

sele

selection

selectionIndices

structure

structureCoords

superpose

timeOffset

trajPath

Accessors

currentFrame

Returns number

frameCount

Returns number

type

Returns string

Methods

_doSuperpose

Parameters

x: Float32Array

Returns void

_getIndices

Parameters

selection: Selection

Returns number[]

_init

Parameters

structure: Structure

Returns void

_interpolate

Parameters

i: number

ip: number

ipp: number

ippp: number

t: number

type: TrajectoryPlayerInterpolateType

Returns void

_loadFrame

Parameters