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Class AtomProxy

Atom proxy

Hierarchy

  • AtomProxy

Index

Constructors

Properties

Accessors

Methods

Constructors

constructor

Properties

atomMap

atomMap: AtomMap

atomStore

atomStore: AtomStore

chainStore

chainStore: ChainStore

index

index: number

residueMap

residueMap: ResidueMap

residueStore

residueStore: ResidueStore

structure

structure: Structure

the structure

Accessors

altloc

  • get altloc(): string
  • set altloc(value: string): void

aromatic

  • get aromatic(): number
  • set aromatic(value: number): void

atomType

atomname

  • get atomname(): string

bfactor

  • get bfactor(): number
  • set bfactor(value: number): void

bondCount

  • get bondCount(): number

bondHash

chainIndex

  • get chainIndex(): number

chainid

  • get chainid(): string

chainname

  • get chainname(): string

covalent

  • get covalent(): number

element

  • get element(): string

entity

entityIndex

  • get entityIndex(): number

formalCharge

  • get formalCharge(): null | number
  • set formalCharge(value: null | number): void

hetero

  • get hetero(): number

inscode

  • get inscode(): string

modelIndex

  • get modelIndex(): number

number

  • get number(): number

occupancy

  • get occupancy(): number
  • set occupancy(value: number): void

partialCharge

  • get partialCharge(): null | number
  • set partialCharge(value: null | number): void

residue

residueAtomOffset

  • get residueAtomOffset(): number

residueIndex

  • get residueIndex(): number
  • set residueIndex(value: number): void

residueType

resname

  • get resname(): string

resno

  • get resno(): number

serial

  • get serial(): number
  • set serial(value: number): void

sstruc

  • get sstruc(): string

vdw

  • get vdw(): number

x

  • get x(): number
  • set x(value: number): void

y

  • get y(): number
  • set y(value: number): void

z

  • get z(): number
  • set z(value: number): void

Methods

bondToElementCount

  • bondToElementCount(element: Elements): number

clone

connectedTo

distanceTo

eachBond

  • eachBond(callback: function, bp?: BondProxy): void

eachBondedAtom

  • eachBondedAtom(callback: function, _ap?: AtomProxy): void

getDefaultValence

  • getDefaultValence(): number

getOuterShellElectronCount

  • getOuterShellElectronCount(): number

getResidueBonds

  • getResidueBonds(firstOnly?: boolean): undefined | number | number[]

  • Get intra group/residue bonds

    Parameters

    • Default value firstOnly: boolean = false

      immediately return the first connected atomIndex

    Returns undefined | number | number[]

    connected atomIndices

getValenceList

  • getValenceList(): number[]

hasBondTo

  • Check if this atom is bonded to the given atom, assumes both atoms are from the same structure

    Parameters

    Returns boolean

    whether a bond exists or not

hasBondToElement

  • hasBondToElement(element: Elements): boolean

isActinide

  • isActinide(): boolean

isAlkaliMetal

  • isAlkaliMetal(): boolean

isAlkalineEarthMetal

  • isAlkalineEarthMetal(): boolean

isAromatic

  • isAromatic(): boolean

isBackbone

  • isBackbone(): boolean

isBonded

  • isBonded(): boolean

isCg

  • isCg(): boolean

isDiatomicNonmetal

  • isDiatomicNonmetal(): boolean

isDna

  • isDna(): boolean

isHalogen

  • isHalogen(): boolean

isHelix

  • isHelix(): boolean

isHetero

  • isHetero(): boolean

isIon

  • isIon(): boolean

isLanthanide

  • isLanthanide(): boolean

isMetal

  • isMetal(): boolean

isMetalloid

  • isMetalloid(): boolean

isNobleGas

  • isNobleGas(): boolean

isNonmetal

  • isNonmetal(): boolean

isNucleic

  • isNucleic(): boolean

isPolyatomicNonmetal

  • isPolyatomicNonmetal(): boolean

isPolymer

  • isPolymer(): boolean

isPostTransitionMetal

  • isPostTransitionMetal(): boolean

isProtein

  • isProtein(): boolean

isRing

  • isRing(): boolean

isRna

  • isRna(): boolean

isSaccharide

  • isSaccharide(): boolean

isSheet

  • isSheet(): boolean

isSidechain

  • isSidechain(): boolean

isTrace

  • isTrace(): boolean

isTransitionMetal

  • isTransitionMetal(): boolean

isTurn

  • isTurn(): boolean

isWater

  • isWater(): boolean

positionAdd

positionFromArray

  • positionFromArray(array: NumberArray, offset?: number): this

positionFromVector3

  • positionFromVector3(v: Vector3): this

positionSub

positionToArray

  • positionToArray(array?: NumberArray, offset?: number): number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

  • Write atom position to array

    Parameters

    • Default value array: NumberArray = []
    • Default value offset: number = 0

    Returns number[] | Uint8Array | Int8Array | Int16Array | Int32Array | Uint16Array | Uint32Array | Float32Array | Uint8ClampedArray | Float64Array

    target array

positionToVector3

  • positionToVector3(v: Vector3): Vector3

qualifiedName

  • qualifiedName(noResname?: boolean): string

toObject

  • toObject(): object

  • Returns object

    • altloc: string
    • atomname: string
    • bfactor: number
    • chainname: string
    • covalent: number
    • element: string
    • hetero: number
    • index: number
    • modelIndex: number
    • residueIndex: number
    • resname: string
    • resno: number
    • serial: number
    • vdw: number
    • x: number
    • y: number
    • z: number

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