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Class BioblocksPDB

A BioblocksPDB instance provides an API to interact with a loaded PDB file while hiding the implementation details of how it is loaded.

export

Hierarchy

  • BioblocksPDB

Index

Constructors

Properties

Accessors

Methods

Constructors

Private constructor

Properties

Protected Optional contactInfo

contactInfo: CouplingContainer

Protected fileName

fileName: string = ""

Protected id

id: string = ""

Protected nglData

nglData: Structure = new NGLInstanceManager.instance.Structure()

Static NGL_C_ALPHA_INDEX

NGL_C_ALPHA_INDEX: "CA|C" = "CA|C"

Accessors

contactInformation

name

  • get name(): string

nglStructure

path

  • get path(): string

rank

  • get rank(): string

secondaryStructure

secondaryStructureSections

sequence

  • get sequence(): string

source

  • get source(): string

uuid

  • get uuid(): string
  • set uuid(uuid: string): void

Methods

amendPDBWithCouplingScores

  • Given some existing coupling scores, a new CouplingContainer will be created with data augmented with info derived from this PDB.

    Parameters

    Returns CouplingContainer

    A CouplingContainer with contact information from both the original array and this PDB file.

eachResidue

  • eachResidue(callback: function): void

getCAlphaAtomIndexFromResidue

  • getCAlphaAtomIndexFromResidue(residueIndex: number, alphaId: number): number

  • Find the index of the c-alpha atom for a given residue.

    Parameters

    • residueIndex: number

      Index of the residue to find the c-alpha atom for.

    • alphaId: number

      Index that determines if an atom is a c-alpha.

    Returns number

    Index of the c-alpha atom with respect to the array of all of the atoms.

Protected getMinDistBetweenResidueIndices

  • getMinDistBetweenResidueIndices(indexI: number, indexJ: number): object

  • Helper function to find the smallest possible distance between two residues via their atoms.

    Parameters

    • indexI: number

      Index of the first residue with respect to the array of all residues.

    • indexJ: number

      Index of the second residue with respect to the array of all residues.

    Returns object

    Shortest distance between the two residues in ångströms.

    • atomIndexI: number
    • atomIndexJ: number
    • dist: number

getMinDistBetweenResidues

  • getMinDistBetweenResidues(resnoI: number, resnoJ: number): object

  • Helper function to find the smallest possible distance between two residues via their atoms.

    Parameters

    • resnoI: number

      The first residue.

    • resnoJ: number

      The second residue.

    Returns object

    Shortest distance between the two residues in ångströms.

    • atomIndexI: number
    • atomIndexJ: number
    • dist: number

getResidueNumberingMismatches

Protected getSecStructFromNGLResidue

getTrimmedName

  • getTrimmedName(separator?: string, wordsToTrim?: number, direction?: "front" | "back"): string

  • Parameters

    • Default value separator: string = "_"
    • Default value wordsToTrim: number = 3
    • Default value direction: "front" | "back" = "back"

    Returns string

Static arePDBArraysEqual

  • Helper function to determine if two BioblocksPDB arrays are equal. By default, PDB equality is determined by PDB name - this can be overridden by supplying a custom comparison function.

    Parameters

    • firstArray: BioblocksPDB[]
    • secondArray: BioblocksPDB[]
    • Default value compFn: (Anonymous function) = (a: BioblocksPDB, b: BioblocksPDB) => a.uuid === b.uuid

    Returns boolean

Static createEmptyPDB

Static createPDB

  • Creates an instance of BioblocksPDB with PDB data.

    !IMPORTANT! Since fetching the data is an asynchronous action, this must be used to create a new instance!

    Parameters

    • Default value file: File | string = ""
    • Default value fileLoaderParams: Partial<ILoaderParameters> = {}

    Returns Promise<BioblocksPDB>

Static createPDBFromNGLData

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