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@rcsb/rcsb-saguaro-3d

Index

Type aliases

ChainType

ChainType: "polymer" | "water" | "branched" | "non-polymer" | "macrolide"

CustomViewStateInterface

CustomViewStateInterface: Omit<CustomViewInterface, "modelChangeCallback">

SaguaroPluginModelMapType

SaguaroPluginModelMapType: Map<string, { chains: Array<{ auth: string; entityId: string; label: string; title: string; type: "polymer" | "water" | "branched" | "non-polymer" | "macrolide" }>; entryId: string }>

StructureObject

StructureObject: StateObjectSelector<Structure, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>

Variables

Const RcsbRepresentationPreset

RcsbRepresentationPreset: TrajectoryHierarchyPresetProvider = TrajectoryHierarchyPresetProvider({id: "rcsb-saguaro-3d",display: {name: 'Feature View 3D'},params: () => ({}),async apply(trajectory, params, plugin) {const builder = plugin.builders.structure;const model = await builder.createModel(trajectory, {modelIndex: 0});const modelProperties = await builder.insertModelProperties(model);const structure: StructureObject = await builder.createStructure(modelProperties);const structureProperties: StructureObject = await builder.insertStructureProperties(structure);const unitcell: StateObjectSelector | undefined = await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: true });const representation: StructureRepresentationPresetProvider.Result | undefined = await plugin.builders.structure.representation.applyPreset(structureProperties, PresetStructureRepresentations.auto);components:for (const c of plugin.managers.structure.hierarchy.currentComponentGroups) {for (const comp of c) {if(comp.cell.obj?.label === "Water") {plugin.managers.structure.component.toggleVisibility(c);break components;}}}components:for (const c of plugin.managers.structure.hierarchy.currentComponentGroups) {for (const comp of c) {if(comp.cell.obj?.label === "Polymer") {plugin.managers.structure.component.updateRepresentationsTheme([comp], { color: 'chain-id' });break components;}}}return {model,modelProperties,unitcell,structure,structureProperties,representation};}})

Const rcsbFvWebAppPath

rcsbFvWebAppPath: string = path.resolve(path.join(__dirname, '..', 'dist'))

Functions

buildIntervals

  • Parameters

    • ids: Set<number>
    • source: "structure" | "sequence"

    Returns Array<RegionSelectionInterface>

createComponents

getChainValues

  • getChainValues(structure: Structure, modelEntityId: string): []
  • Parameters

    • structure: Structure
    • modelEntityId: string

    Returns []

getModelEntityOptions

  • getModelEntityOptions(structure: Structure): [][]
  • Parameters

    • structure: Structure

    Returns [][]

getStructure

  • getStructure(ref: string, state: State): Structure
  • Parameters

    • ref: string
    • state: State

    Returns Structure

getStructureOptions

  • getStructureOptions(plugin: PluginContext): [][]
  • Parameters

    • plugin: PluginContext

    Returns [][]

getStructureWithModelId

  • getStructureWithModelId(structures: StructureRef[], modelId: string): Structure | undefined
  • Parameters

    • structures: StructureRef[]
    • modelId: string

    Returns Structure | undefined

processGaps

  • processGaps(modelId: string, labelAsymId: string, e: RcsbFvTrackDataElementInterface): Array<{ begin: number; end: number; labelAsymId: string; modelId: string }>
  • Parameters

    • modelId: string
    • labelAsymId: string
    • e: RcsbFvTrackDataElementInterface

    Returns Array<{ begin: number; end: number; labelAsymId: string; modelId: string }>

processMultipleGaps

  • processMultipleGaps(modelId: string, labelAsymId: string, list: Array<RcsbFvTrackDataElementInterface>): Array<{ begin: number; end: number; labelAsymId: string; modelId: string }>
  • Parameters

    • modelId: string
    • labelAsymId: string
    • list: Array<RcsbFvTrackDataElementInterface>

    Returns Array<{ begin: number; end: number; labelAsymId: string; modelId: string }>

selectionFilter

  • selectionFilter(r: ChainSelectionInterface, selection: { labelAsymId?: undefined | string; modelId?: undefined | string }): boolean
  • Parameters

    • r: ChainSelectionInterface
    • selection: { labelAsymId?: undefined | string; modelId?: undefined | string }
      • Optional labelAsymId?: undefined | string
      • Optional modelId?: undefined | string

    Returns boolean

selectionFromResidueSelection

splitModelEntityId

  • splitModelEntityId(modelEntityId: string): (string | number)[]
  • Parameters

    • modelEntityId: string

    Returns (string | number)[]

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