import AtomProxy from 'ngl/src/proxy/atom-proxy.js'

public class | source

AtomProxy

Atom proxy

Constructor Summary

Public Constructor
public	constructor(structure: Structure, index: Integer)

Member Summary

Public Members
public set	altloc
public get	altloc: String Alternate location identifier
public	atomMap: AtomMap
public	atomStore: AtomStore
public get	atomType: AtomType
public get	atomname: String Atom name
public set	bfactor
public get	bfactor: Float B-factor value
public get	bondHash: BondHash
public get	chainIndex
public	chainStore: ChainStore
public get	chainid: String Chain id
public get	chainname: String Chain name
public get	covalent: Float Covalent radius
public get	element: String Element
public get	entity: Entity Molecular enity
public get	entityIndex
public set	formalCharge
public get	formalCharge: Integer \| null Formal charge
public get	hetero: Boolean Hetero flag
public	index: Integer The index of the atom, pointing to the data in the corresponding AtomStore
public get	inscode: String Insertion code
public get	modelIndex
public get	occupancy: Float Occupancy value
public set	occupancy
public set	partialCharge
public get	partialCharge: Float \| null Partial charge
public get	residue: ResidueProxy
public get	residueAtomOffset
public get	residueIndex
public set	residueIndex
public	residueMap: ResidueMap
public	residueStore: ResidueStore
public get	residueType: ResidueType
public get	resname: String Residue name
public get	resno: Integer Residue number/label
public get	serial: Integer Serial number
public set	serial
public get	sstruc: String Secondary structure code
public	structure: Structure The structure the atom belongs to.
public get	vdw: Float Van-der-Waals radius
public get	x: Float X coordinate
public set	x
public get	y: Float Y coordinate
public set	y
public get	z: Float Z coordinate
public set	z

Method Summary

Public Methods
public	clone(): AtomProxy Clone object
public	connectedTo(atom: AtomProxy): Boolean If connected to another atom
public	distanceTo(atom: AtomProxy): Number Distance to another atom
public	eachBond(callback: function(bond: BondProxy), bp: BondProxy): undefined Iterate over each bond
public	eachBondedAtom(callback: function(atom: AtomProxy), ap: AtomProxy): undefined Iterate over each bonded atom
public	getResidueBonds(firstOnly: Boolean): Integer[] \| Integer \| undefined Get intra group/residue bonds
public	hasBondTo(ap: AtomProxy): Boolean Check if this atom is bonded to the given atom, assumes both atoms are from the same structure
public	isBackbone(): Boolean If atom is part of a backbone
public	isBonded()
public	isCg(): Boolean If atom is part of a coarse-grain group
public	isDna(): Boolean If atom is part of a dna
public	isHelix(): Boolean If atom is part of a helix
public	isHetero(): Boolean If atom is part of a hetero group
public	isIon(): Boolean If atom is part of an ion
public	isNucleic(): Boolean If atom is part of a nucleic molecule
public	isPolymer(): Boolean If atom is part of a polymer
public	isProtein(): Boolean If atom is part of a protein molecule
public	isRing(): Boolean If atom is part of a ring
public	isRna(): Boolean If atom is part of a rna
public	isSaccharide(): Boolean If atom is part of a saccharide
public	isSheet(): Boolean If atom is part of a sheet
public	isSidechain(): Boolean If atom is part of a sidechin
public	isTurn(): Boolean If atom is part of a turn
public	isWater(): Boolean If atom is part of a water molecule
public	positionAdd(v: Vector3): AtomProxy Add vector to atom position
public	positionFromArray(array: Array \| TypedArray, offset: Integer): AtomProxy Set atom position from array
public	positionFromVector3(v: Vector3): AtomProxy Set atom position from vector
public	positionSub(v: Vector3): AtomProxy Subtract vector from atom position
public	positionToArray(array: Array \| TypedArray, offset: Integer): Array \| TypedArray Write atom position to array
public	positionToVector3(v: Vector3): Vector3 Write atom position to vector
public	qualifiedName()
public	toObject()

Public Constructors

public constructor(structure: Structure, index: Integer) source

Params:

Name	Type	Attribute	Description
structure	Structure		the structure
index	Integer		the index

Public Members

public set altloc source

public get altloc: String source

Alternate location identifier

public atomMap: AtomMap source

public atomStore: AtomStore source

public get atomType: AtomType source

public get atomname: String source

Atom name

public set bfactor source

public get bfactor: Float source

B-factor value

public get bondHash: BondHash source

public get chainIndex source

public chainStore: ChainStore source

public get chainid: String source

Chain id

public get chainname: String source

Chain name

public get covalent: Float source

Covalent radius

public get element: String source

Element

public get entity: Entity source

Molecular enity

public get entityIndex source

public set formalCharge source

public get formalCharge: Integer | null source

Formal charge

public get hetero: Boolean source

Hetero flag

public index: Integer source

The index of the atom, pointing to the data in the corresponding AtomStore

public get inscode: String source

Insertion code

public get modelIndex source

public get occupancy: Float source

Occupancy value

public set occupancy source

public set partialCharge source

public get partialCharge: Float | null source

Partial charge

public get residue: ResidueProxy source

public get residueAtomOffset source

public get residueIndex source

public set residueIndex source

public residueMap: ResidueMap source

public residueStore: ResidueStore source

public get residueType: ResidueType source

public get resname: String source

Residue name

public get resno: Integer source

Residue number/label

public get serial: Integer source

Serial number

public set serial source

public get sstruc: String source

Secondary structure code

public structure: Structure source

The structure the atom belongs to.

public get vdw: Float source

Van-der-Waals radius

public get x: Float source

X coordinate

public set x source

public get y: Float source

Y coordinate

public set y source

public get z: Float source

Z coordinate

public set z source

Public Methods

public clone(): AtomProxy source

Clone object

Return:

AtomProxy

cloned atom

public connectedTo(atom: AtomProxy): Boolean source

If connected to another atom

Params:

Name	Type	Attribute	Description
atom	AtomProxy		the other atom

Return:

Boolean

flag

public distanceTo(atom: AtomProxy): Number source

Distance to another atom

Params:

Name	Type	Attribute	Description
atom	AtomProxy		the other atom

Return:

Number

the distance

public eachBond(callback: function(bond: BondProxy), bp: BondProxy): undefined source

Iterate over each bond

Params:

Name	Type	Attribute	Description
callback	function(bond: BondProxy)		iterator callback function
bp	BondProxy	optional	optional target bond proxy for use in the callback

Return:

undefined

public eachBondedAtom(callback: function(atom: AtomProxy), ap: AtomProxy): undefined source

Iterate over each bonded atom

Params:

Name	Type	Attribute	Description
callback	function(atom: AtomProxy)		iterator callback function
ap	AtomProxy	optional	optional target atom proxy for use in the callback