import Structure from 'ngl/src/structure/structure.js'

public class | source

Structure

Direct Subclass:

StructureView

Structure

Constructor Summary

Public Constructor
public	constructor(name: String, path: String)

Member Summary

Public Members
public	atomCount
public	atomMap: AtomMap
public	atomSet
public	atomSetCache
public	atomSetDict
public	atomStore
public	backboneBondStore
public	biomolDict
public	bondCount
public	bondHash: BondHash
public	bondSet
public	bondStore
public	boundingBox: Box3
public	boxes
public	center: Vector3
public	chainStore
public	entityList: Entity[]
public	extraData: StructureExtraData
public	frames
public	header: StructureHeader
public	id
public	modelStore
public	name
public	path
public	residueMap: ResidueMap
public	residueStore
public	rungBondStore
public	signals: {refreshed: Signal}
public	spatialHash: SpatialHash
public	title
public get	type
public	unitcell: Unitcell
public	validation: Validation

Private Members
private	_ap
private	_bp
private	_cp
private	_rp

Method Summary

Public Methods
public	atomCenter(selection: Selection): Vector3 Gets the center of the (selected) structure atoms
public	dispose(): undefined Calls dispose() method of property objects.
public	eachAtom(callback: function(atom: AtomProxy), selection: Selection): undefined Atom iterator
public	eachBond(callback: function(bond: BondProxy), selection: Selection): undefined Bond iterator
public	eachChain(callback: function(chain: ChainProxy), selection: Selection): undefined Chain iterator
public	eachEntity(callback: function(entity: Entity), type: EntityType): undefined Entity iterator
public	eachModel(callback: function(model: ModelProxy), selection: Selection): undefined Model iterator
public	eachPolymer(callback: function(polymer: Polymer), selection: Selection): undefined Polymer iterator
public	eachResidue(callback: function(residue: ResidueProxy), selection: Selection): undefined Residue iterator
public	eachResidueN(n: Integer, callback: function(residueList: ResidueProxy[])): undefined Multi-residue iterator
public	finalizeAtoms()
public	finalizeBonds()
public	getAtomData()
public	getAtomIndices()
public	getAtomProxy()
public	getAtomSet(selection: Boolean \| Selection \| BitArray): BitArray Get a set of atoms
public	getAtomSetWithinGroup(selection: Selection): BitArray Get set of all atoms within the groups of a selection
public	getAtomSetWithinPoint(point: Vector3 \| AtomProxy, radius: Number): BitArray Get set of atoms around a point
public	getAtomSetWithinSelection(selection: Selection, radius: Number): BitArray Get set of atoms around a set of atoms from a selection
public	getAtomSetWithinVolume(volume: Volume, radius: Number, minValue: [type], maxValue: [type], outside: [type]): BitArray Get set of atoms within a volume
public	getBackboneAtomData()
public	getBackboneBondData()
public	getBackboneBondSet()
public	getBondData()
public	getBondProxy()
public	getBondSet()
public	getBoundingBox(selection: Selection, box: Box3): Vector3 Gets the bounding box of the (selected) structure atoms
public	getChainProxy()
public	getChainnameCount(selection: Selection): Integer Get number of unique chainnames
public	getModelProxy()
public	getPrincipalAxes(selection: Selection): PrincipalAxes Gets the principal axes of the (selected) structure atoms
public	getResidueProxy()
public	getRungAtomData()
public	getRungBondData()
public	getRungBondSet()
public	getSelection()
public	getSequence()
public	getStructure()
public	hasCoords()
public	init()
public	refreshPosition()
public	updatePosition()

Public Constructors

public constructor(name: String, path: String) source

Params:

Name	Type	Attribute	Description
name	String		structure name
path	String		source path

Public Members

public atomCount source

public atomMap: AtomMap source

public atomSet source

public atomSetCache source

public atomSetDict source

public atomStore source

public backboneBondStore source

public biomolDict source

public bondCount source

public bondHash: BondHash source

public bondSet source

public bondStore source

public boundingBox: Box3 source

public boxes source

public center: Vector3 source

public chainStore source

public entityList: Entity[] source

public extraData: StructureExtraData source

public frames source

public header: StructureHeader source

public id source

public modelStore source

public name source

public path source

public residueMap: ResidueMap source

public residueStore source

public rungBondStore source

public signals: {refreshed: Signal} source

public spatialHash: SpatialHash source

public title source

public get type source

public unitcell: Unitcell source

public validation: Validation source

Private Members

private _ap source

private _bp source

private _cp source

private _rp source

Public Methods

public atomCenter(selection: Selection): Vector3 source

Gets the center of the (selected) structure atoms

Params:

Name	Type	Attribute	Description
selection	Selection	optional	the selection

Return:

Vector3

the center

public dispose(): undefined source

Calls dispose() method of property objects. Unsets properties to help garbage collection.

Return:

undefined

public eachAtom(callback: function(atom: AtomProxy), selection: Selection): undefined source

Atom iterator

Params:

Name	Type	Attribute	Description
callback	function(atom: AtomProxy)		the callback
selection	Selection	optional	the selection

Return:

undefined

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

Bond iterator

Params:

Name	Type	Attribute	Description
callback	function(bond: BondProxy)		the callback
selection	Selection	optional	the selection

Return:

undefined

public eachChain(callback: function(chain: ChainProxy), selection: Selection): undefined source

Chain iterator

Params:

Name	Type	Attribute	Description
callback	function(chain: ChainProxy)		the callback
selection	Selection	optional	the selection

Return:

undefined

public eachEntity(callback: function(entity: Entity), type: EntityType): undefined source

Entity iterator

Params:

Name	Type	Attribute	Description
callback	function(entity: Entity)		the callback
type	EntityType		entity type

Return:

undefined

public eachModel(callback: function(model: ModelProxy), selection: Selection): undefined source

Model iterator

Params:

Name	Type	Attribute	Description
callback	function(model: ModelProxy)		the callback
selection	Selection	optional	the selection

Return:

undefined

public eachPolymer(callback: function(polymer: Polymer), selection: Selection): undefined source

Polymer iterator

Params:

Name	Type	Attribute	Description
callback	function(polymer: Polymer)		the callback
selection	Selection	optional	the selection

Return:

undefined

public eachResidue(callback: function(residue: ResidueProxy), selection: Selection): undefined source

Residue iterator

Params:

Name	Type	Attribute	Description
callback	function(residue: ResidueProxy)		the callback
selection	Selection	optional	the selection

Return:

undefined

public eachResidueN(n: Integer, callback: function(residueList: ResidueProxy[])): undefined source

Multi-residue iterator

Params:

Name	Type	Attribute	Description
n	Integer		window size
callback	function(residueList: ResidueProxy[])		the callback

Return:

undefined

public finalizeAtoms() source

public finalizeBonds() source

public getAtomData() source

public getAtomIndices() source

public getAtomProxy() source

public getAtomSet(selection: Boolean | Selection | BitArray): BitArray source

Get a set of atoms

Params:

Name	Type	Attribute	Description
selection	Boolean \| Selection \| BitArray		object defining how to initialize the atom set. Boolean: init with value; Selection: init with selection; BitArray: return bit array

Return:

BitArray

set of atoms

public getAtomSetWithinGroup(selection: Selection): BitArray source

Get set of all atoms within the groups of a selection

Params:

Name	Type	Attribute	Description
selection	Selection		the selection object

Return:

BitArray

set of atoms

public getAtomSetWithinPoint(point: Vector3 | AtomProxy, radius: Number): BitArray source

Get set of atoms around a point

Params:

Name	Type	Attribute	Description
point	Vector3 \| AtomProxy		the point
radius	Number		radius to select within

Return:

BitArray

set of atoms

public getAtomSetWithinSelection(selection: Selection, radius: Number): BitArray source

Get set of atoms around a set of atoms from a selection

Params:

Name	Type	Attribute	Description
selection	Selection		the selection object
radius	Number		radius to select within

Return:

BitArray

set of atoms

public getAtomSetWithinVolume(volume: Volume, radius: Number, minValue: [type], maxValue: [type], outside: [type]): BitArray source

Get set of atoms within a volume

Params:

Name	Type	Attribute	Description
volume	Volume		the volume
radius	Number		radius to select within
minValue	[type]		minimum value to be considered as within the volume
maxValue	[type]		maximum value to be considered as within the volume
outside	[type]		use only values falling outside of the min/max values

Return:

BitArray

set of atoms

public getBackboneAtomData() source

public getBackboneBondData() source

public getBackboneBondSet() source

public getBondData() source

public getBondProxy() source

public getBondSet() source

public getBoundingBox(selection: Selection, box: Box3): Vector3 source

Gets the bounding box of the (selected) structure atoms

Params:

Name	Type	Attribute	Description
selection	Selection	optional	the selection
box	Box3	optional	optional target

Return:

Vector3

the box

public getChainProxy() source

public getChainnameCount(selection: Selection): Integer source

Get number of unique chainnames

Params:

Name	Type	Attribute	Description
selection	Selection		limit count to selection

Return:

Integer

count

public getModelProxy() source

public getPrincipalAxes(selection: Selection): PrincipalAxes source

Gets the principal axes of the (selected) structure atoms

Params:

Name	Type	Attribute	Description
selection	Selection	optional	the selection