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Class CouplingContainer

A CouplingContainer provides access to the coupling information of residue pairs.

Behind the scenes, it is backed by a sparse 2D array to avoid data duplication and provide O(1) access.

export

Hierarchy

  • CouplingContainer

Implements

Index

Constructors

constructor

Properties

Private colCounter

colCounter: number = 0

Used for iterator access.

Protected contacts

contacts: ICouplingScore[][] = new Array<ICouplingScore[]>()

Private derivedFromCouplingScoresFlag

derivedFromCouplingScoresFlag: boolean = true

Private rowCounter

rowCounter: number = 0

Used for iterator access.

scoreSource

Protected totalStoredContacts

totalStoredContacts: number = 0

How many distinct contacts are currently stored.

Accessors

allContacts

chainLength

  • get chainLength(): number

isDerivedFromCouplingScores

  • get isDerivedFromCouplingScores(): boolean
  • set isDerivedFromCouplingScores(value: boolean): void

rankedContacts

residueIndexRange

  • get residueIndexRange(): object

sequence

  • get sequence(): string

totalContacts

  • get totalContacts(): number

Methods

[Symbol.iterator]

addCouplingScore

  • Add a coupling score to this collection. If there is already an entry for this (i,j) contact, it will be overridden!

    Parameters

    Returns void

getAminoAcidOfContact

  • getAminoAcidOfContact(resno: number): AminoAcid | undefined

getCouplingScore

  • getCouplingScore(firstRes: number, secondRes: number): ICouplingScore | undefined
  • Primary interface for getting a coupling score, provides access to the same data object regardless of order of (firstRes, secondRes).

    Parameters

    • firstRes: number
    • secondRes: number

    Returns ICouplingScore | undefined

getObservedContacts

  • Determine which contacts in this coupling container are observed.

    Parameters

    • Default value distFilter: number = 10

    Returns ICouplingScore[]

    Contacts that should be considered observed in the current data set.

getPredictedContacts

  • getPredictedContacts(totalPredictionsToShow: number, measuredContactDistFilter?: number, filters?: ICouplingScoreFilter[]): object
  • Determine which contacts in this coupling container are both predicted and correct.

    Parameters

    • totalPredictionsToShow: number

      How many predictions, max, to return.

    • Default value measuredContactDistFilter: number = 5
    • Default value filters: ICouplingScoreFilter[] = []

    Returns object

    An object containing 2 array fields: correct and predicted.

includes

  • includes(firstRes: number, secondRes: number): boolean

next

updateContact

  • updateContact(i: number, j: number, couplingScore: Partial<Omit<ICouplingScore, "i" | "j">>): void

Static fromJSON

Static Protected getScore

Object literals

Protected indexRange

indexRange: object

max

max: number = 1

min

min: number = 1

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