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@rcsb/rcsb-saguaro-3d

Index

Type aliases

ChainInfo

ChainInfo: { auth: string; entityId: string; label: string; operators: OperatorInfo[]; title: string; type: ChainType }

Type declaration

ChainType

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

CustomViewStateInterface

CustomViewStateInterface: Omit<CustomViewInterface, "modelChangeCallback">

OperatorInfo

OperatorInfo: { ids: string[]; name: string }

Type declaration

  • ids: string[]
  • name: string

RcsbFv3DAssemblyAdditionalConfig

RcsbFv3DAssemblyAdditionalConfig: RcsbFvAdditionalConfig & { operatorChangeCallback?: undefined | ((operatorInfo: OperatorInfo) => void) }

SaguaroPluginModelMapType

SaguaroPluginModelMapType: Map<string, { assemblyId: string; chains: Array<ChainInfo>; 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 [][]

getOperator

  • getOperator(entryInfo: { assemblyId: string; chains: Array<ChainInfo>; entryId: string }, defaultAuthId?: undefined | string, defaultOperatorName?: undefined | string): OperatorInfo | undefined
  • Parameters

    • entryInfo: { assemblyId: string; chains: Array<ChainInfo>; entryId: string }
      • assemblyId: string
      • chains: Array<ChainInfo>
      • entryId: string
    • Optional defaultAuthId: undefined | string
    • Optional defaultOperatorName: undefined | string

    Returns OperatorInfo | undefined

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

opKey

  • Parameters

    • l: Location

    Returns OperatorInfo

processGaps

  • processGaps(modelId: string, labelAsymId: string, e: RcsbFvTrackDataElementInterface, operatorName?: undefined | string): Array<SaguaroRange>
  • Parameters

    • modelId: string
    • labelAsymId: string
    • e: RcsbFvTrackDataElementInterface
    • Optional operatorName: undefined | string

    Returns Array<SaguaroRange>

processMultipleGaps

  • processMultipleGaps(modelId: string, labelAsymId: string, list: Array<RcsbFvTrackDataElementInterface>, operatorName?: undefined | string): Array<SaguaroRange>
  • Parameters

    • modelId: string
    • labelAsymId: string
    • list: Array<RcsbFvTrackDataElementInterface>
    • Optional operatorName: undefined | string

    Returns Array<SaguaroRange>

selectionFilter

selectionFromResidueSelection

  • selectionFromResidueSelection(res: Array<SaguaroSet>, mode: "select" | "hover", source: "structure" | "sequence"): Array<SaguaroRegionList>
  • Parameters

    • res: Array<SaguaroSet>
    • mode: "select" | "hover"
    • source: "structure" | "sequence"

    Returns Array<SaguaroRegionList>

splitModelEntityId

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

    • modelEntityId: string

    Returns (string | number)[]

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