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bioblocks-viz - v0.0.158

Index

Modules

Enumerations

Classes

Interfaces

Type aliases

Variables

Functions

Object literals

Type aliases

AMINO_ACID_1LETTER_CODE

AMINO_ACID_1LETTER_CODE: keyof object

AMINO_ACID_3LETTER_CODE

AMINO_ACID_3LETTER_CODE: keyof object

AMINO_ACID_CODON

AMINO_ACID_CODON: keyof object

AMINO_ACID_FULL_NAME

AMINO_ACID_FULL_NAME: keyof object

BIOBLOCKS_CSS_STYLE

BIOBLOCKS_CSS_STYLE: Omit<CSSProperties, "height" | "width">

BIOBLOCKS_DATA_TYPE

BIOBLOCKS_DATA_TYPE: CONTACT_MAP_DATA_TYPE | NGL_DATA_TYPE | SPRING_DATA_TYPE | T_SNE_DATA_TYPE

BIOBLOCKS_PLOTLY_DATA

BIOBLOCKS_PLOTLY_DATA: REQUIRED_BIOBLOCKS_PLOTLY_DATA & Partial<IPlotlyData>

BioblocksHookCallback

BioblocksHookCallback<T>: function

Type parameters

  • T

Type declaration

    • (): T

    • Returns T

BioblocksRangeSliderCallback

BioblocksRangeSliderCallback: function

Function signature that is invoked on slider events.

Type declaration

    • (range: number[]): void

    • Parameters

      • range: number[]

        New value the slider is currently on top of.

      Returns void

BioblocksRangeSliderProps

BioblocksRangeSliderProps: object & Partial<Omit<RangeProps, "style">>

Properties that BioblocksSlider accepts.

export

BioblocksSliderCallback

BioblocksSliderCallback: function

Function signature that is invoked on slider events.

Type declaration

    • (value: number): void

    • Parameters

      • value: number

        New value the slider is currently on top of.

      Returns void

BioblocksSliderProps

BioblocksSliderProps: object & Partial<Omit<SliderProps, "style">>

Properties that BioblocksSlider accepts.

export

BioblocksWidgetConfig

BioblocksWidgetConfig: ButtonGroupWidgetConfig | ButtonWidgetConfig | CheckboxWidgetConfig | DropDownWidgetConfig | LabelWidgetConfig | RadioWidgetConfig | RangeSliderWidgetConfig | SliderWidgetConfig

ButtonGroupWidgetConfig

ButtonGroupWidgetConfig: IBaseBioblocksWidgetConfig & object

ButtonWidgetConfig

ButtonWidgetConfig: IBaseBioblocksWidgetConfig & object

CELL_TYPE

CELL_TYPE: number

Shared data between Spring/T-SNE. Refers to index in points collection.

CONFIG_ACCORDION_INDEX

CONFIG_ACCORDION_INDEX: string | number

CONTACT_MAP_CB_RESULT_TYPE

CONTACT_MAP_CB_RESULT_TYPE: ICouplingScore

CONTACT_MAP_DATA_TYPE

CONTACT_MAP_DATA_TYPE: IContactMapData

CheckboxWidgetConfig

CheckboxWidgetConfig: IBaseBioblocksWidgetConfig & object

ContactMapCallback

ContactMapCallback: function

Type declaration

ContactMapComponentState

ContactMapComponentState: Readonly<object>

ContactMapContainerState

ContactMapContainerState: object

Type declaration

  • linearDistFilter: number
  • minimumProbability: number
  • minimumScore: number
  • numPredictionsToShow: number
  • pointsToPlot: IContactMapChartData[]
  • rankFilter: number[]

DISTANCE_FN_TYPE

DISTANCE_FN_TYPE: function

Type declaration

    • (arg1: number[], arg2: number[]): number

    • Parameters

      • arg1: number[]
      • arg2: number[]

      Returns number

DropDownWidgetConfig

DropDownWidgetConfig: IBaseBioblocksWidgetConfig & object

FieldTypes

FieldTypes: "boolean" | "object" | "function" | "number" | "string" | "symbol" | "undefined"

IContainerReducerState

IContainerReducerState<T>: Set<T>

Type parameters

  • T

IDataReducerState

IDataReducerState<T>: T

Type parameters

  • T

IObjectReducerState

IObjectReducerState<T>: Map<string, T>

Type parameters

  • T

IUMAPTranscriptionalContainerProps

IUMAPTranscriptionalContainerProps: Required<Pick<IUMAPVisualizationProps, "dataMatrix" | "numIterationsBeforeReRender">> & Partial<IUMAPVisualizationProps> & object

IUMAPVisualizationState

IUMAPVisualizationState: object & object

IValueReducerState

IValueReducerState<T>: T

Type parameters

  • T

LabelWidgetConfig

LabelWidgetConfig: IBaseBioblocksWidgetConfig & object

LockedResiduePair

LockedResiduePair: Record<string, RESIDUE_TYPE[]>

NGLComponentState

NGLComponentState: Readonly<object>

NGL_DATA_TYPE

NGL_DATA_TYPE: Structure

NGL_HOVER_CB_RESULT_TYPE

NGL_HOVER_CB_RESULT_TYPE: number

Omit

Omit<T, K>: Pick<T, Exclude<keyof T, K>>

From T, get the set of properties that are not K.

link

https://github.com/Microsoft/TypeScript/wiki/What%27s-new-in-TypeScript#predefined-conditional-types

Type parameters

  • T

  • K

PLOTLY_DATA_RECORD

PLOTLY_DATA_RECORD: Record<string, Partial<IPlotlyData>>

PartialExcept

PartialExcept<T, K>: RecursivePartial<T> & Pick<T, K>

Type parameters

  • T

  • K: keyof T

REQUIRED_BIOBLOCKS_PLOTLY_DATA

REQUIRED_BIOBLOCKS_PLOTLY_DATA: Required<Pick<IPlotlyData, "connectgaps" | "hoverinfo" | "line" | "marker" | "mode" | "name" | "showlegend" | "type" | "x" | "y">>

RESIDUE_TYPE

RESIDUE_TYPE: number

RadioWidgetConfig

RadioWidgetConfig: IBaseBioblocksWidgetConfig & object

RangeSliderWidgetConfig

RangeSliderWidgetConfig: IBaseBioblocksWidgetConfig & IBioblocksWidgetRangeConfig & object

RecursivePartial

RecursivePartial<T>: object

Type parameters

  • T

Type declaration

RecursiveRequired

RecursiveRequired<T>: object

Type parameters

  • T

Type declaration

ReducerRegistryListener

ReducerRegistryListener: function

Type declaration

RepresentationDict

RepresentationDict: Map<string, RepresentationElement[]>

RootState

RootState: StateType<object>

SECONDARY_STRUCTURE

SECONDARY_STRUCTURE: Array<Bioblocks1DSection<SECONDARY_STRUCTURE_KEYS>>

SECONDARY_STRUCTURE_KEYS

SECONDARY_STRUCTURE_KEYS: keyof SECONDARY_STRUCTURE_CODES

SECONDARY_STRUCTURE_SECTION

SECONDARY_STRUCTURE_SECTION: Bioblocks1DSection<SECONDARY_STRUCTURE_KEYS>

SPECIES_TYPE

SPECIES_TYPE: "anolis_carolinensis" | "arabidopsis_thaliana" | "bos_taurus" | "brachypodium_distachyon" | "gallus_gallus" | "homo_sapiens" | "hordeum_vulgare" | "macaca_mulatta" | "monodelphis_domestica" | "mus_musculus" | "oryza_sativa" | "papio_anubis" | "rattus_norvegicus" | "solanum_lycopersicum" | "solanum_tuberosum" | "sorghum_bicolor" | "tetraodon_nigroviridis" | "triticum_aestivum" | "xenopus_tropicalis" | "zea_mays"

SPRING_DATA_TYPE

SPRING_DATA_TYPE: ISpringGraphData

SUPERPOSITION_STATUS_TYPE

SUPERPOSITION_STATUS_TYPE: "NONE" | "PREDICTED" | "EXPERIMENTAL" | "BOTH"

SliderWidgetConfig

SliderWidgetConfig: IBaseBioblocksWidgetConfig & IBioblocksWidgetValueConfig & object

T_SNE_DATA_TYPE

T_SNE_DATA_TYPE: number[][]

VIZ_EVENT_DATA_TYPE

VIZ_EVENT_DATA_TYPE<T>: T extends SPRING ? ISpringEventData : T extends VIZ_TYPE.UMAP_SEQUENCE ? IUMapEventData : Record<string, any>

Type parameters

  • T

VIZ_PROPS_DATA_TYPE

VIZ_PROPS_DATA_TYPE<T>: T extends SPRING ? ISpringContainerProps : T extends VIZ_TYPE.UMAP_SEQUENCE ? IUMAPSequenceContainerProps : T extends VIZ_TYPE.UMAP_TRANSCRIPTION ? IUMAPTranscriptionalContainerProps : T extends NGL ? INGLContainerProps : T extends CONTACT_MAP ? IContactMapContainerProps : T extends VIZ_TYPE.T_SNE ? ITensorContainerProps : T extends ANATOMOGRAM ? IAnatomogramContainerProps : Record<string, any>

Type parameters

  • T

requiredProps

requiredProps: Omit<ITensorComponentProps, keyof object> & Partial<ITensorComponentProps>

Variables

Const AnatomogramContainer

AnatomogramContainer: (Anonymous function) = connectWithBBStore(mapStateToProps, mapDispatchToProps, AnatomogramContainerClass)

Const BBStore

BBStore: Store<object & Object, AnyAction> & object = configureStore()

Const ContactMapContainer

ContactMapContainer: (Anonymous function) = connectWithBBStore(mapStateToProps, mapDispatchToProps, ContactMapContainerClass)

Const EVFOLD_EXPECTED_HEADERS

EVFOLD_EXPECTED_HEADERS: string[] = [UNI_PROT_RESNO_HEADER, UNI_PROT_RESNAME_HEADER, PDB_RESNO_HEADER, PDB_RESNAME_HEADER]

Const EVSERVER_EXPECTED_HEADERS

EVSERVER_EXPECTED_HEADERS: string[] = [EV_SERVER_COUPLING_HEADER,EV_SERVER_STRUCTURE_HEADER,EV_SERVER_STRUCTURE_CODE_HEADER,]

Const EV_SERVER_COUPLING_HEADER

EV_SERVER_COUPLING_HEADER: "id" = "id"

Const EV_SERVER_STRUCTURE_CODE_HEADER

EV_SERVER_STRUCTURE_CODE_HEADER: "one_letter_code" = "one_letter_code"

Const EV_SERVER_STRUCTURE_HEADER

EV_SERVER_STRUCTURE_HEADER: "coord_id" = "coord_id"

Const InfoPanelContainer

InfoPanelContainer: (Anonymous function) = connectWithBBStore(mapStateToProps, undefined, InfoPanelContainerClass)

Const NGLContainer

NGLContainer: (Anonymous function) = connectWithBBStore(mapStateToProps, mapDispatchToProps, NGLContainerClass)

Const PDB_RESNAME_HEADER

PDB_RESNAME_HEADER: "pdb_residue" = "pdb_residue"

Const PDB_RESNO_HEADER

PDB_RESNO_HEADER: "pdb_index" = "pdb_index"

Const RESIDUE_PAIR_DATASET_NAME

RESIDUE_PAIR_DATASET_NAME: "residuePair" = "residuePair"

Const ReducerRegistry

ReducerRegistry: ReducerRegistryClass = configureReducerRegistry()

Const SpringContainer

SpringContainer: (Anonymous function) = connectWithBBStore(mapStateToProps, mapDispatchToProps, SpringContainerClass)

Const TensorTContainer

TensorTContainer: (Anonymous function) = connectWithBBStore(mapStateToProps, mapDispatchToProps, TensorTContainerClass)

Const UMAPSequenceContainer

UMAPSequenceContainer: (Anonymous function) = connectWithBBStore(mapStateToProps,mapDispatchToProps,UMAPSequenceContainerClass,)

Const UMAPTranscriptionalContainer

UMAPTranscriptionalContainer: (Anonymous function) = connectWithBBStore(mapStateToProps,mapDispatchToProps,UMAPTranscriptionalContainerClass,)

Const UNI_PROT_RESNAME_HEADER

UNI_PROT_RESNAME_HEADER: "up_residue" = "up_residue"

Const UNI_PROT_RESNO_HEADER

UNI_PROT_RESNO_HEADER: "up_index" = "up_index"

Const ambiguousDnaComplement

ambiguousDnaComplement: object = {A: 'T',B: 'V',C: 'G',D: 'H',G: 'C',H: 'D',K: 'M',M: 'K',N: 'N',R: 'Y',S: 'S',T: 'A',V: 'B',W: 'W',X: 'X',Y: 'R',} as const

Type declaration

  • A: "T"
  • B: "V"
  • C: "G"
  • D: "H"
  • G: "C"
  • H: "D"
  • K: "M"
  • M: "K"
  • N: "N"
  • R: "Y"
  • S: "S"
  • T: "A"
  • V: "B"
  • W: "W"
  • X: "X"
  • Y: "R"

Const ambiguousDnaLetters

ambiguousDnaLetters: "GATCRYWSMKHBVDN" = "GATCRYWSMKHBVDN"

Const ambiguousDnaValues

ambiguousDnaValues: object = {A: 'A',B: 'CGT',C: 'C',D: 'AGT',G: 'G',H: 'ACT',K: 'GT',M: 'AC',N: 'GATC',R: 'AG',S: 'CG',T: 'T',V: 'ACG',W: 'AT',X: 'GATC',Y: 'CT',} as const

Type declaration

  • A: "A"
  • B: "CGT"
  • C: "C"
  • D: "AGT"
  • G: "G"
  • H: "ACT"
  • K: "GT"
  • M: "AC"
  • N: "GATC"
  • R: "AG"
  • S: "CG"
  • T: "T"
  • V: "ACG"
  • W: "AT"
  • X: "GATC"
  • Y: "CT"

Const ambiguousRnaComplement

ambiguousRnaComplement: object = {A: 'U',B: 'V',C: 'G',D: 'H',G: 'C',H: 'D',K: 'M',M: 'K',N: 'N',R: 'Y',S: 'S',U: 'A',V: 'B',W: 'W',X: 'X',Y: 'R',} as const

Type declaration

  • A: "U"
  • B: "V"
  • C: "G"
  • D: "H"
  • G: "C"
  • H: "D"
  • K: "M"
  • M: "K"
  • N: "N"
  • R: "Y"
  • S: "S"
  • U: "A"
  • V: "B"
  • W: "W"
  • X: "X"
  • Y: "R"

Const ambiguousRnaLetters

ambiguousRnaLetters: "GAUCRYWSMKHBVDN" = "GAUCRYWSMKHBVDN"

Const ambiguousRnaValues

ambiguousRnaValues: object = {A: 'A',B: 'CGU',C: 'C',D: 'AGU',G: 'G',H: 'ACU',K: 'GU',M: 'AC',N: 'GAUC',R: 'AG',S: 'CG',U: 'U',V: 'ACG',W: 'AU',X: 'GAUC',Y: 'CU',} as const

Type declaration

  • A: "A"
  • B: "CGU"
  • C: "C"
  • D: "AGU"
  • G: "G"
  • H: "ACU"
  • K: "GU"
  • M: "AC"
  • N: "GAUC"
  • R: "AG"
  • S: "CG"
  • U: "U"
  • V: "ACG"
  • W: "AU"
  • X: "GAUC"
  • Y: "CU"

Const bioblocksFrame

bioblocksFrame: null | HTMLElement = document.getElementById('bioblocks-frame')

Const extendedDnaLetters

extendedDnaLetters: "GATCBDSW" = "GATCBDSW"

Const extendedProteinLetters

extendedProteinLetters: "ACDEFGHIKLMNPQRSTVWYBXZJUO" = "ACDEFGHIKLMNPQRSTVWYBXZJUO"

Const getCategories

getCategories: function & object = createSelector([getGraphData], graphData => {const nodes = graphData && graphData.nodes ? graphData.nodes : [];const categories = Set<string>(nodes.length >= 1 ? Object.keys(nodes[0].labelForCategory) : []);const labelsByCategory = new Map<string, Set<string>>();categories.forEach(category => {if (category) {const labels = Set<string>(Array.from(nodes.map(node => node.labelForCategory[category])));labelsByCategory.set(category, labels);}});return categories;})

Const getLabels

getLabels: function & object = createSelector([getGraphData], graphData => {const nodes = graphData && graphData.nodes ? graphData.nodes : [];const categories = Set<string>(nodes.length >= 1 ? Object.keys(nodes[0].labelForCategory) : []);let labels = Set<string>();categories.forEach(category => {if (category) {labels = labels.merge(Set<string>(Array.from(nodes.map(node => node.labelForCategory[category]))));}});return labels;})

Const middleWares

middleWares: Middleware[] = [thunk.default]

Const monoisotopicUnambiguousDnaWeights

monoisotopicUnambiguousDnaWeights: object = {A: 331.06817,C: 307.056936,G: 347.063084,T: 322.056602,} as const

Type declaration

  • A: 331.06817
  • C: 307.056936
  • G: 347.063084
  • T: 322.056602

Const monoisotopicUnambiguousRnaWeights

monoisotopicUnambiguousRnaWeights: object = {A: 347.063084,C: 323.051851,G: 363.057999,U: 324.035867,} as const

Type declaration

  • A: 347.063084
  • C: 323.051851
  • G: 363.057999
  • U: 324.035867

Const proteinLetters

proteinLetters: "ACDEFGHIKLMNPQRSTVWY" = "ACDEFGHIKLMNPQRSTVWY"

Useful biological nomenclature. Derived from BioPython IUPACData.py: https://github.com/biopython/biopython/blob/master/Bio/Data/IUPACData.py which is under the BSD 3-Clause License with Copyright 2000 Andrew Dalke

Note: Currently unimplemented are a few functions and variables: function '_make_ranges()', which is needed to generate: - variable 'unambiguous_dna_weight_ranges' - variable 'unambiguous_rna_weight_ranges' - variable 'protein_weight_ranges' function '_make_ambiguous_ranges', which is needed to generate: - variable 'ambiguous_dna_weight_ranges' - variable 'ambiguous_rna_weight_ranges' - variable 'extended_protein_weight_ranges'

Const proteinLetters3to1

proteinLetters3to1: any = Object.assign({},...Object.entries(proteinLetters1to3).map(([a, b]) => ({ [b]: a })),)

Const proteinLetters3to1Extended

proteinLetters3to1Extended: any = Object.assign({},...Object.entries(proteinLetters1to3Extended).map(([a, b]) => ({ [b]: a })),)

Const reducer

reducer: function = combine(ReducerRegistry.getReducers())

Type declaration

    • (state: S | undefined, action: A): S

    • Parameters

      • state: S | undefined
      • action: A

      Returns S

Const standardDnaCodonTable

standardDnaCodonTable: CodonTable = new CodonTable(1,'standard','SGC0',{AAA: 'K',AAC: 'N',AAG: 'K',AAT: 'N',ACA: 'T',ACC: 'T',ACG: 'T',ACT: 'T',AGA: 'R',AGC: 'S',AGG: 'R',AGT: 'S',ATA: 'I',ATC: 'I',ATG: 'M',ATT: 'I',CAA: 'Q',CAC: 'H',CAG: 'Q',CAT: 'H',CCA: 'P',CCC: 'P',CCG: 'P',CCT: 'P',CGA: 'R',CGC: 'R',CGG: 'R',CGT: 'R',CTA: 'L',CTC: 'L',CTG: 'L',CTT: 'L',GAA: 'E',GAC: 'D',GAG: 'E',GAT: 'D',GCA: 'A',GCC: 'A',GCG: 'A',GCT: 'A',GGA: 'G',GGC: 'G',GGG: 'G',GGT: 'G',GTA: 'V',GTC: 'V',GTG: 'V',GTT: 'V',TAC: 'Y',TAT: 'Y',TCA: 'S',TCC: 'S',TCG: 'S',TCT: 'S',TGC: 'C',TGG: 'W',TGT: 'C',TTA: 'L',TTC: 'F',TTG: 'L',TTT: 'F',},['TAA', 'TAG', 'TGA'],['TTG', 'CTG', 'ATG'],)

Const standardRnaCodonTable

standardRnaCodonTable: CodonTable = CodonTable.rnaTableFromDNACodonTable(2, 'standard', 'SGC0', standardDnaCodonTable)

Const unambiguousDnaLetters

unambiguousDnaLetters: "GATC" = "GATC"

Const unambiguousDnaWeights

unambiguousDnaWeights: object = {A: 331.2218,C: 307.1971,G: 347.2212,T: 322.2085,} as const

Type declaration

  • A: 331.2218
  • C: 307.1971
  • G: 347.2212
  • T: 322.2085

Const unambiguousRnaLetters

unambiguousRnaLetters: "GAUC" = "GAUC"

Const unambiguousRnaWeights

unambiguousRnaWeights: object = {A: 347.2212,C: 323.1965,G: 363.2206,U: 324.1813,} as const

Type declaration

  • A: 347.2212
  • C: 323.1965
  • G: 363.2206
  • U: 324.1813

Functions

Const BioblocksMiddleware

  • BioblocksMiddleware(store: MiddlewareAPI<Dispatch, RootState>): (Anonymous function)

Const ContainerReducer

  • ContainerReducer<T>(dataset: string, namespace?: string): Reducer

Const DataReducer

  • DataReducer<T>(dataset: string, initialState: T, namespace?: string): Reducer

  • Type parameters

    • T

    Parameters

    • dataset: string
    • initialState: T
    • Default value namespace: string = "bioblocks"

    Returns Reducer

Const EMPTY_FUNCTION

  • EMPTY_FUNCTION(...args: any[]): void

  • A do-nothing function which has proved invaluable for concisely setting a default parameter for a callback.

    Parameters

    • Rest ...args: any[]

    Returns void

Const ObjectReducer

  • ObjectReducer<T>(dataset: string, namespace?: string): Reducer

Const ResiduePairReducer

  • ResiduePairReducer(namespace?: string): function

  • Parameters

    • Default value namespace: string = "bioblocks"

    Returns function

      • (state: S | undefined, action: A): S

      • Parameters

        • state: S | undefined
        • action: A

        Returns S

Const SpringReducer

  • SpringReducer(namespace?: string): function

  • Parameters

    • Default value namespace: string = "bioblocks"

    Returns function

      • (state: S | undefined, action: A): S

      • Parameters

        • state: S | undefined
        • action: A

        Returns S

Const TensorTComponent

Const ValueReducer

  • ValueReducer<T>(dataset: string, initialState: T, namespace?: string): Reducer

  • Type parameters

    • T

    Parameters

    • dataset: string
    • initialState: T
    • Default value namespace: string = "bioblocks"

    Returns Reducer

Const areTwoArraysEqual

  • areTwoArraysEqual<T>(a: T[], b: T[]): boolean

  • Helper function to check array equality by value, meaning the same amount of elements in the same order.

    Type parameters

    • T

    Parameters

    • a: T[]

      First array.

    • b: T[]

      Second array.

    Returns boolean

    true if they are equal, false if they are not.

Const augmentCouplingScoresWithResidueMapping

Const capitalizeEveryWord

  • capitalizeEveryWord(text: string, separator?: string): string

  • Sets the first letter of every word to uppercase and the rest to lowercase.

    Parameters

    • text: string

      Text to be transformed.

    • Default value separator: string = " "

    Returns string

Const capitalizeFirstLetter

  • capitalizeFirstLetter(text: string): string

  • Sets the first letter to uppercase and the rest to lowercase.

    Parameters

    • text: string

      Text to be transformed.

    Returns string

Const combine

Const configureReducerRegistry

Const configureStore

  • configureStore(): Store<object & Object, AnyAction> & object

Const connectWithBBStore

  • connectWithBBStore<TStateProps, TDispatchProps, TOwnProps, State>(mapStateToProps: MapStateToProps<TStateProps, TOwnProps, State>, mapDispatchToProps: MapDispatchToProps<TDispatchProps, TOwnProps>, WrappedComponent: React.ComponentType<any>): (Anonymous function)

  • Type parameters

    • TStateProps

    • TDispatchProps

    • TOwnProps

    • State

    Parameters

    • mapStateToProps: MapStateToProps<TStateProps, TOwnProps, State>
    • mapDispatchToProps: MapDispatchToProps<TDispatchProps, TOwnProps>
    • WrappedComponent: React.ComponentType<any>

    Returns (Anonymous function)

Const createBallStickRepresentation

Const createContainerActions

  • createContainerActions<T>(datasetName: string, namespace?: string): object

  • Type parameters

    • T

    Parameters

    • datasetName: string
    • Default value namespace: string = "bioblocks"

    Returns object

    • add:
    • addMultiple: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • clear: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • remove:
    • removeMultiple: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • set: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

Const createContainerReducer

  • createContainerReducer<T>(dataset: string, namespace?: string): void

Const createDataActions

  • createDataActions<T>(datasetName: string, namespace?: string): object

  • Type parameters

    • T

    Parameters

    • datasetName: string
    • Default value namespace: string = "bioblocks"

    Returns object

    • failure: FsaBuilder<T3, Box<P3>>
    • request: FsaBuilder<T1, Box<P1>>
    • success: FsaBuilder<T2, Box<P2>>

Const createDataReducer

  • createDataReducer<T>(dataset: string, initialState: T, namespace?: string): void

  • Type parameters

    • T

    Parameters

    • dataset: string
    • initialState: T
    • Default value namespace: string = "bioblocks"

    Returns void

Const createDistanceRepresentation

Const createObjectActions

  • createObjectActions<T>(datasetName: string, namespace?: string): object

  • Type parameters

    • T

    Parameters

    • datasetName: string
    • Default value namespace: string = "bioblocks"

    Returns object

    • add: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • clear: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • remove: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • removeMultiple: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • set: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • toggle: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

Const createObjectReducer

  • createObjectReducer<T>(dataset: string, namespace?: string): void

Const createResiduePairActions

  • createResiduePairActions(namespace?: string): object

  • Parameters

    • Default value namespace: string = "bioblocks"

    Returns object

    • candidates: object
      • add:
      • addMultiple: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

      • clear: function
          • (): EmptyAction<T>

          • Returns EmptyAction<T>

      • remove:
      • removeMultiple: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

      • set: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

    • hovered: object
      • add:
      • addMultiple: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

      • clear: function
          • (): EmptyAction<T>

          • Returns EmptyAction<T>

      • remove:
      • removeMultiple: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

      • set: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

    • locked: object
      • add: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

      • clear: function
          • (): EmptyAction<T>

          • Returns EmptyAction<T>

      • remove: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

      • removeMultiple: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

      • set: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

      • toggle: function
          • (payload: Unbox<P>): object & Unbox<R>

          • Parameters

            • payload: Unbox<P>

            Returns object & Unbox<R>

Const createResiduePairReducer

  • createResiduePairReducer(namespace?: string): void

Const createSecStructRepresentation

Const createSpringActions

  • createSpringActions(namespace?: string): object

  • Parameters

    • Default value namespace: string = "bioblocks"

    Returns object

    • category: object
    • graphData: object
    • species: object

Const createSpringReducer

  • createSpringReducer(namespace?: string): void

Const createValueActions

  • createValueActions<T>(datasetName: string, namespace?: string): object

  • Type parameters

    • T

    Parameters

    • datasetName: string
    • Default value namespace: string = "bioblocks"

    Returns object

    • clear: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • set:

Const createValueReducer

  • createValueReducer<T>(dataset: string, initialState: T, namespace?: string): void

  • Type parameters

    • T

    Parameters

    • dataset: string
    • initialState: T
    • Default value namespace: string = "bioblocks"

    Returns void

Const derivePlotlyColor

  • derivePlotlyColor(mirrorPoints: boolean, zValues: number[], entry: IContactMapChartData): (string | number | (undefined | null | string | number)[] | (undefined | null | string | number)[][])[]

Const derivePoints

  • derivePoints(mirrorPoints: boolean, points: number[], oppositePoints?: number[]): number[]

Const deriveScatterText

  • deriveScatterText(mirrorPoints: boolean, textValues: string[]): string[]

Const fetchAppropriateData

Const fetchAppropriateDataFromFile

  • fetchAppropriateDataFromFile(viz: VIZ_TYPE, file: File): Promise<Structure | object>

Const fetchCSVFile

  • fetchCSVFile(filename: string): Promise<string>

Const fetchCategoricalColorData

  • fetchCategoricalColorData(file: string): Promise<object>

Const fetchContactMapData

  • fetchContactMapData(dir: string, knownOrPredicted?: "known" | "predicted"): Promise<IContactMapData>

Const fetchDataset

  • fetchDataset<T>(datasetName: string, fetchFn: function, namespace?: string): (Anonymous function)

  • Type parameters

    • T

    Parameters

    • datasetName: string
    • fetchFn: function
        • (): Promise<T>

        • Returns Promise<T>

    • Default value namespace: string = "bioblocks"

    Returns (Anonymous function)

Const fetchFastaFile

  • fetchFastaFile(filename: string): Promise<SeqRecord[]>

Const fetchGraphData

Const fetchJSONFile

  • fetchJSONFile(filename: string): Promise<any>

Const fetchMatrixData

  • fetchMatrixData(filePath: string): Promise<number[][]>

Const fetchNGLDataFromDirectory

  • fetchNGLDataFromDirectory(dir: string): Promise<Structure>

Const fetchNGLDataFromFile

Const fetchSpringCoordinateData

  • fetchSpringCoordinateData(file: string): Promise<number[][]>

Const fetchSpringData

Const fetchSpringGraphData

  • fetchSpringGraphData(fetchFn: function, namespace?: string): (Anonymous function)

Const fetchTSneCoordinateData

  • fetchTSneCoordinateData(dataDir: string): Promise<number[][]>

Const fetchTensorTSneCoordinateData

  • fetchTensorTSneCoordinateData(dataDir: string): Promise<number[][]>

Const fetchTensorTSneCoordinateDataFromFile

  • fetchTensorTSneCoordinateDataFromFile(fileLocation: string): Promise<number[][]>

Const genErrorMsg

  • genErrorMsg(fileType: string, response: Response): string

Const generateChartDataEntry

Const generateCouplingScoreHoverText

  • Determines the appropriate hover text in plotly for this coupling score.

    Currently the following 3 fields will be appended if present:

    • Amino acid (A_i, A_j)
    • Score
    • Probability

    Parameters

    Returns string

Const generateDefaultHeaderIndices

  • generateDefaultHeaderIndices(items: string[]): object

  • Get the default header names/positions taken from the format of couplingScores.csv on EVServer.

    Parameters

    • items: string[]

      A single row of elements needed to determine column count.

    Returns object

    • [key: string]: number

Const generateFloat32ArrayFromContacts

  • generateFloat32ArrayFromContacts(array: Array<object>): Float32Array

Const generatePointCloudData

  • Generate data in the expected format for a Plotly PointCloud.

    Parameters

    • entry: IContactMapChartData

      A unit of Plotly data containing points, color, and any extras.

    • Default value mirrorPoints: boolean = false

      Should we mirror the points on the x/y axis?

    Returns Partial<IPlotlyData>

    Data suitable for consumption by Plotly.

Const generateResidueMapping

  • Determines the mapping of residues from a UniProt file to a PDB, given a indextableplus file.

    Parameters

    • text: string

      The contents of a indextableplus file.

    Returns IResidueMapping[]

    Array of all residue mappings.

Const generateScatterData

  • Generate data in the expected format for a Scatter plot.

    Parameters

    • entry: IContactMapChartData

      A unit of Plotly data containing points, color, name, and any extras.

    • Default value mirrorPoints: boolean = false

      Should we mirror the points on the x/y axis?

    Returns Partial<IPlotlyData>

    Data suitable for consumption by Plotly.

Const generateScatterGLData

  • Generate data in the expected format for a WebGL Scatter plot.

    Parameters

    • entry: IContactMapChartData

      A unit of Plotly data containing points, color, name, and any extras.

    • Default value mirrorPoints: boolean = false

      Should we mirror the points on the x/y axis?

    Returns Partial<IPlotlyData>

    Data suitable for consumption by Plotly.

Const getCandidates

  • getCandidates(state: RootState, namespace?: string): Set<number>

Const getCouplingHeaderIndices

  • getCouplingHeaderIndices(items: string[]): object

  • Get all of the headers in a nicely formatted object.

    Parameters

    • items: string[]

      List of headers.

    Returns object

    • [key: string]: number

Const getCouplingScoreFromCSVRow

  • getCouplingScoreFromCSVRow(row: string[], headerIndices: object): ICouplingScore

Const getCouplingScoresData

  • Parses a coupling_scores.csv file to generate the appropriate data structure.

    !Important! Currently 12 fields are assumed to be part of a single coupling score. As such, any rows with less will be ignored.

    Parameters

    • line: string

      The csv file as a single string.

    • Default value residueMapping: IResidueMapping[] = []

      Maps the coupling_score.csv residue number to the residue number for the PDB.

    Returns CouplingContainer

    Array of CouplingScores suitable for bioblocks-viz consumption.

Const getGraphData

Const getHovered

  • getHovered(state: RootState, namespace?: string): Set<number>

Const getLocked

  • getLocked(state: RootState, namespace?: string): Map<string, Set<number>>

Const getPDBAndCouplingMismatch

Const getParsedColor

Const getResidueMappingHeaders

  • getResidueMappingHeaders(headers: string[], isEvServer: boolean): object

Const getResiduePairs

Const getSecondaryStructureData

  • Parses a distance_map.csv file to generate the appropriate secondary structure mapping.

    !Important! The first line in the csv will be ignored as it is assumed to be a csv header.

    !Important! Currently 3 fields are assumed to be part of a single entry, with the second and third actually being relevant. As such, any other rows will be ignored.

    Parameters

    • line: string

      The csv file as a single string.

    Returns ISecondaryStructureData[]

    Array of SecondaryStructure mappings suitable for bioblocks-viz consumption.

Const getSequenceMismatch

Const getSpring

Const isCouplingHeaderPresent

  • isCouplingHeaderPresent(headerRow: string[]): boolean

Const isEvServerJob

  • isEvServerJob(headers: string[]): boolean

Const mapDispatchToProps

  • mapDispatchToProps(dispatch: Dispatch): object
  • mapDispatchToProps(dispatch: Dispatch): object
  • mapDispatchToProps(dispatch: Dispatch): object
  • mapDispatchToProps(dispatch: Dispatch): object
  • mapDispatchToProps(dispatch: Dispatch): object
  • mapDispatchToProps(dispatch: Dispatch): object
  • mapDispatchToProps(dispatch: Dispatch): object

  • Parameters

    • dispatch: Dispatch

    Returns object

    • onLabelAdd: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • onLabelRemove: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

  • Parameters

    • dispatch: Dispatch

    Returns object

    • addCandidateResidues: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • addHoveredResidues: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • addLockedResiduePair: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • removeAllLockedResiduePairs: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • removeAllSelectedSecondaryStructures: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • removeCandidateResidues: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • removeHoveredResidues: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • removeLockedResiduePair: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

  • Parameters

    • dispatch: Dispatch

    Returns object

    • addHoveredResidues: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • addHoveredSecondaryStructure: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • addSelectedSecondaryStructure: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • removeAllLockedResiduePairs: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • removeAllSelectedSecondaryStructures: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • removeHoveredResidues: function
        • (): EmptyAction<T>

        • Returns EmptyAction<T>

    • removeHoveredSecondaryStructure: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • removeSecondaryStructure: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • toggleLockedResiduePair: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

  • Parameters

    • dispatch: Dispatch

    Returns object

    • dispatchSpringFetch: fetchSpringGraphData
    • setCurrentCategory: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • setCurrentCells: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

  • Parameters

    • dispatch: Dispatch

    Returns object

    • setCurrentCells: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

  • Parameters

    • dispatch: Dispatch

    Returns object

    • setCurrentCells: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

  • Parameters

    • dispatch: Dispatch

    Returns object

    • onLabelAdd: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • onLabelRemove: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

    • setCurrentCells: function
        • (payload: Unbox<P>): object & Unbox<R>

        • Parameters

          • payload: Unbox<P>

          Returns object & Unbox<R>

Const mapStateToProps

  • mapStateToProps(state: RootState): object
  • mapStateToProps(state: object): object
  • mapStateToProps(state: RootState): object
  • mapStateToProps(state: object): object
  • mapStateToProps(state: object): object
  • mapStateToProps(state: object): object
  • mapStateToProps(state: object): object
  • mapStateToProps(state: object): object

Const readFileAsText

  • readFileAsText(inputFile: File): Promise<string>

Const selectCurrentItems

  • selectCurrentItems<T>(state: RootState, dataset: string, namespace?: string): Set<T>

Const selectCurrentValue

  • selectCurrentValue<T>(state: RootState, dataset: string, defaultValue?: T | null, namespace?: string): null | T

  • Type parameters

    • T

    Parameters

    • state: RootState
    • dataset: string
    • Default value defaultValue: T | null = null
    • Default value namespace: string = "bioblocks"

    Returns null | T

Const selectObject

  • selectObject<T>(state: RootState, dataset: string, namespace?: string): Map<string, T>

subsample

  • subsample<T, U>(arr: T[], n: number, returnIndices?: boolean): Array<T | number>

  • Randomly select and return "n" objects or indices (if returnIndices==true) and return in a new array.

    If "n" is larger than the array, return the array directly or all the indices in the array (if returnIndices==true).

    No duplicates are returned

    Type parameters

    • T

    • U: boolean

    Parameters

    • arr: T[]
    • n: number
    • Default value returnIndices: boolean = false

    Returns Array<T | number>

Const withBBStore

  • withBBStore<P>(WrappedComponent: React.ComponentType<P>): (Anonymous function)

Object literals

Const AnatomogramMapping

AnatomogramMapping: object

homo_sapiens

homo_sapiens: object

P11A

P11A: string[] = ['UBERON_0000178']

P11B

P11B: string[] = ['UBERON_0001155']

P12A

P12A: string[] = ['UBERON_0000955']

P9A

P9A: string[] = ['UBERON_0000977']

UBERON_0000178

UBERON_0000178: string[] = ['P11A']

UBERON_0000955

UBERON_0000955: string[] = ['P12A']

UBERON_0000977

UBERON_0000977: string[] = ['P9A']

UBERON_0001155

UBERON_0001155: string[] = ['P11B']

mus_musculus

mus_musculus: object

UBERON_0000948

UBERON_0000948: string[] = ['Heart', 'Heart_and_Aorta', 'Heart_and_Aorta-10X_P7_4']

UBERON_0001255

UBERON_0001255: string[] = ['Bladder', 'Bladder-10X_P4_3', 'Bladder-10X_P4_4', 'Bladder-10X_P7_7']

UBERON_0001723

UBERON_0001723: string[] = ['Tongue', 'Tongue-10X_P4_0', 'Tongue-10X_P4_1', 'Tongue-10X_P7_10']

UBERON_0001911

UBERON_0001911: string[] = ['Mammary', 'Mammary_Gland', 'Mammary_Gland-10X_P7_12', 'Mammary_Gland-10X_P7_13']

UBERON_0002048

UBERON_0002048: string[] = ['Lung', 'Lung-10X_P7_8', 'Lung-10X_P7_9', 'Lung-10X_P8_12', 'Lung-10X_P8_13']

UBERON_0002106

UBERON_0002106: string[] = ['Spleen', 'Spleen-10X_P4_7', 'Spleen-10X_P7_6']

UBERON_0002107

UBERON_0002107: string[] = ['Liver', 'Liver-10X_P4_2', 'Liver-10X_P7_0', 'Liver-10X_P7_1']

UBERON_0002113

UBERON_0002113: string[] = ['Kidney', 'Kidney-10X_P4_5', 'Kidney-10X_P4_6', 'Kidney-10X_P7_5']

UBERON_0002370

UBERON_0002370: string[] = ['Thymus', 'Thymus-10X_P7_11']

UBERON_0002371

UBERON_0002371: string[] = ['Marrow', 'Marrow-10X_P7_2', 'Marrow-10X_P7_3']

UBERON_0003126

UBERON_0003126: string[] = ['Trachea', 'Trachea-10X_P8_14', 'Trachea-10X_P8_15']

UBERON_0014892

UBERON_0014892: string[] = ['Muscle', 'Limb', 'Limb_Muscle', 'Limb_Muscle-10X_P7_14', 'Limb_Muscle-10X_P7_15']

Const DEFAULT_POPUP_PROPS

DEFAULT_POPUP_PROPS: object

closeOnPortalMouseLeave

closeOnPortalMouseLeave: false = false

closeOnTriggerClick

closeOnTriggerClick: true = true

closeOnTriggerMouseLeave

closeOnTriggerMouseLeave: false = false

hoverable

hoverable: false = false

openOnTriggerClick

openOnTriggerClick: true = true

openOnTriggerFocus

openOnTriggerFocus: false = false

openOnTriggerMouseEnter

openOnTriggerMouseEnter: false = false

position

position: "bottom left" = "bottom left"

style

style: object

marginTop

marginTop: number = 0

maxHeight

maxHeight: string = "350px"

overflow

overflow: string = "auto"

zIndex

zIndex: number = 3

Const SAMPLE_PROTEIN_IDS

SAMPLE_PROTEIN_IDS: object

3Domains

3Domains: string = "Q8TDF5"

5Domains

5Domains: string = "Q96L73"

DLL3_HUMAN

DLL3_HUMAN: string = "Q9NYJ7"

SMAD4_HUMAN

SMAD4_HUMAN: string = "Q13485"

Const atomWeights

atomWeights: object

Ac

Ac: number = 227.03

Ag

Ag: number = 107.8682

Al

Al: number = 26.981538

Am

Am: number = 243.06

Ar

Ar: number = 39.948

As

As: number = 74.9216

At

At: number = 209.99

Au

Au: number = 196.96655

B

B: number = 10.811

Ba

Ba: number = 137.327

Be

Be: number = 9.012182

Bh

Bh: number = 264.12

Bi

Bi: number = 208.98038

Bk

Bk: number = 247.07

Br

Br: number = 79.904

C

C: number = 12.0107

Ca

Ca: number = 40.078

Cd

Cd: number = 112.411

Ce

Ce: number = 140.116

Cf

Cf: number = 251.08

Cl

Cl: number = 35.453

Cm

Cm: number = 247.07

Co

Co: number = 58.9332

Cr

Cr: number = 51.9961

Cs

Cs: number = 132.90545

Cu

Cu: number = 63.546

D

D: number = 2.0141

Db

Db: number = 262.11

Dy

Dy: number = 162.5

Er

Er: number = 167.259

Es

Es: number = 252.08

Eu

Eu: number = 151.964

F

F: number = 18.9984032

Fe

Fe: number = 55.845

Fm

Fm: number = 257.1

Fr

Fr: number = 223.02

Ga

Ga: number = 69.723

Gd

Gd: number = 157.25

Ge

Ge: number = 72.64

H

H: number = 1.00794

He

He: number = 4.002602

Hf

Hf: number = 178.49

Hg

Hg: number = 200.59

Ho

Ho: number = 164.93032

Hs

Hs: number = 269.13

I

I: number = 126.90447

In

In: number = 114.818

Ir

Ir: number = 192.217

K

K: number = 39.0983

Kr

Kr: number = 83.8

La

La: number = 138.9055

Li

Li: number = 6.941

Lr

Lr: number = 262.11

Lu

Lu: number = 174.967

Md

Md: number = 258.1

Mg

Mg: number = 24.305

Mn

Mn: number = 54.938049

Mo

Mo: number = 95.94

Mt

Mt: number = 268.14

N

N: number = 14.0067

Na

Na: number = 22.98977

Nb

Nb: number = 92.90638

Nd

Nd: number = 144.24

Ne

Ne: number = 20.1797

Ni

Ni: number = 58.6934

No

No: number = 259.1

Np

Np: number = 237.05

O

O: number = 15.9994

Os

Os: number = 190.23

P

P: number = 30.973761

Pa

Pa: number = 231.03588

Pb

Pb: number = 207.2

Pd

Pd: number = 106.42

Pm

Pm: number = 145

Po

Po: number = 208.98

Pr

Pr: number = 140.90765

Pt

Pt: number = 195.078

Pu

Pu: number = 244.06

Ra

Ra: number = 226.03

Rb

Rb: number = 85.4678

Re

Re: number = 186.207

Rf

Rf: number = 261.11

Rh

Rh: number = 102.9055

Rn

Rn: number = 222.02

Ru

Ru: number = 101.07

S

S: number = 32.065

Sb

Sb: number = 121.76

Sc

Sc: number = 44.95591

Se

Se: number = 78.96

Sg

Sg: number = 266.12

Si

Si: number = 28.0855

Sm

Sm: number = 150.36

Sn

Sn: number = 118.71

Sr

Sr: number = 87.62

Ta

Ta: number = 180.9479

Tb

Tb: number = 158.92534

Tc

Tc: number = 98

Te

Te: number = 127.6

Th

Th: number = 232.0381

Ti

Ti: number = 47.867

Tl

Tl: number = 204.3833

Tm

Tm: number = 168.93421

U

U: number = 238.02891

V

V: number = 50.9415

W

W: number = 183.84

Xe

Xe: number = 131.293

Y

Y: number = 88.90585

Yb

Yb: number = 173.04

Zn

Zn: number = 65.39

Zr

Zr: number = 91.224

Const defaultDistanceParams

defaultDistanceParams: object

color

color: string = "red"

Const defaultDistanceTooltipParams

defaultDistanceTooltipParams: object

labelBackground

labelBackground: true = true

labelBackgroundColor

labelBackgroundColor: string = "lightgrey"

labelBackgroundMargin

labelBackgroundMargin: number = 0.75

labelBorder

labelBorder: true = true

labelBorderColor

labelBorderColor: string = "white"

labelBorderWidth

labelBorderWidth: number = 0.3

labelColor

labelColor: string = "black"

labelSize

labelSize: number = 5

labelUnit

labelUnit: "angstrom" = "angstrom"

labelZOffset

labelZOffset: number = 35

Const defaultPlotlyConfig

defaultPlotlyConfig: object

displayModeBar

displayModeBar: false = false

doubleClick

doubleClick: "reset" = "reset"

scrollZoom

scrollZoom: false = false

showAxisDragHandles

showAxisDragHandles: false = false

staticPlot

staticPlot: false = false

Const defaultPlotlyLayout

defaultPlotlyLayout: object

autosize

autosize: true = true

dragmode

dragmode: "zoom" = "zoom"

hovermode

hovermode: "closest" = "closest"

legend

legend: object

Type declaration

showlegend

showlegend: false = false

title

title: string = ""

margin

margin: object

b

b: number = 10

l

l: number = 40

r

r: number = 10

t

t: number = 10

Const extendedProteinValues

extendedProteinValues: object

A

A: string = "A"

B

B: string = "ND"

C

C: string = "C"

D

D: string = "D"

E

E: string = "E"

F

F: string = "F"

G

G: string = "G"

H

H: string = "H"

I

I: string = "I"

J

J: string = "IL"

K

K: string = "K"

L

L: string = "L"

M

M: string = "M"

N

N: string = "N"

O

O: string = "O"

P

P: string = "P"

Q

Q: string = "Q"

R

R: string = "R"

S

S: string = "S"

T

T: string = "T"

U

U: string = "U"

V

V: string = "V"

W

W: string = "W"

X

X: string = "ACDEFGHIKLMNPQRSTVWY"

Y

Y: string = "Y"

Z

Z: string = "QE"

Const initialContactMapContainerState

initialContactMapContainerState: object

linearDistFilter

linearDistFilter: number = 5

minimumProbability

minimumProbability: number = 0.9

minimumScore

minimumScore: number = 0

numPredictionsToShow

numPredictionsToShow: number = -1

pointsToPlot

pointsToPlot: IContactMapChartData[] = [] as IContactMapChartData[]

rankFilter

rankFilter: number[] = [1, 100]

Const initialContactMapState

initialContactMapState: object

pointsToPlot

pointsToPlot: IContactMapChartData[] = new Array<IContactMapChartData>()

Const initialNGLState

initialNGLState: object

isDistRepEnabled

isDistRepEnabled: boolean = true

isMovePickEnabled

isMovePickEnabled: boolean = false

stage

stage: undefined | Stage = undefined as Stage | undefined

superpositionStatus

superpositionStatus: "NONE" | "PREDICTED" | "EXPERIMENTAL" | "BOTH" = 'NONE' as SUPERPOSITION_STATUS_TYPE

activeRepresentations

activeRepresentations: object

experimental

experimental: object

reps

reps: RepresentationElement[] = new Array<RepresentationElement>()

structType

structType: "rocket" | "angle" | "axes" | "backbone" | "ball+stick" | "base" | "cartoon" | "contact" | "default" | "dihedral" | "distance" | "helixorient" | "hyperball" | "label" | "licorice" | "line" | "surface" | "ribbon" | "rope" | "spacefill" | "trace" | "tube" | "unitcell" = 'default' as StructureRepresentationType

predicted

predicted: object

reps

reps: RepresentationElement[] = new Array<RepresentationElement>()

structType

structType: "rocket" | "angle" | "axes" | "backbone" | "ball+stick" | "base" | "cartoon" | "contact" | "default" | "dihedral" | "distance" | "helixorient" | "hyperball" | "label" | "licorice" | "line" | "surface" | "ribbon" | "rope" | "spacefill" | "trace" | "tube" | "unitcell" = 'cartoon' as StructureRepresentationType

Const initialState

initialState: object

visualizations

visualizations: BioblocksVisualization<any, any, any>[] = new Array<BioblocksVisualization>()

Const monoisotopicProteinWeights

monoisotopicProteinWeights: object

A

A: number = 89.047678

C

C: number = 121.019749

D

D: number = 133.037508

E

E: number = 147.053158

F

F: number = 165.078979

G

G: number = 75.032028

H

H: number = 155.069477

I

I: number = 131.094629

K

K: number = 146.105528

L

L: number = 131.094629

M

M: number = 149.051049

N

N: number = 132.053492

O

O: number = 255.158292

P

P: number = 115.063329

Q

Q: number = 146.069142

R

R: number = 174.111676

S

S: number = 105.042593

T

T: number = 119.058243

U

U: number = 168.964203

V

V: number = 117.078979

W

W: number = 204.089878

Y

Y: number = 181.073893

Const proteinLetters1to3

proteinLetters1to3: object

A

A: string = "Ala"

C

C: string = "Cys"

D

D: string = "Asp"

E

E: string = "Glu"

F

F: string = "Phe"

G

G: string = "Gly"

H

H: string = "His"

I

I: string = "Ile"

K

K: string = "Lys"

L

L: string = "Leu"

M

M: string = "Met"

N

N: string = "Asn"

P

P: string = "Pro"

Q

Q: string = "Gln"

R

R: string = "Arg"

S

S: string = "Ser"

T

T: string = "Thr"

V

V: string = "Val"

W

W: string = "Trp"

Y

Y: string = "Tyr"

Const proteinLetters1to3Extended

proteinLetters1to3Extended: object

Const proteinWeights

proteinWeights: object

A

A: number = 89.0932

C

C: number = 121.1582

D

D: number = 133.1027

E

E: number = 147.1293

F

F: number = 165.1891

G

G: number = 75.0666

H

H: number = 155.1546

I

I: number = 131.1729

K

K: number = 146.1876

L

L: number = 131.1729

M

M: number = 149.2113

N

N: number = 132.1179

O

O: number = 255.3134

P

P: number = 115.1305

Q

Q: number = 146.1445

R

R: number = 174.201

S

S: number = 105.0926

T

T: number = 119.1192

U

U: number = 168.0532

V

V: number = 117.1463

W

W: number = 204.2252

Y

Y: number = 181.1885

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