Class: AtomImage

Constructor

new AtomImage(model, index, ijk)

Parameters:

Name	Type	Description
`model`	Model	The model from which the image is from
`index`	int	Index of the atom in the model
`ijk`	Array	Indices of the cell in which the image is located

Source: model.js, line 32

Members

(readonly) aura :AuraMesh

Aura used to highlight this atom image

Type:

AuraMesh

Source: model.js, line 364

baseRadius :float

Starting radius of the atom

Type:

float

Source: model.js, line 418

(readonly) bondedAtoms :Array.<AtomImage>

All atoms bonded to this atom

Type:

Array.<AtomImage>

Source: model.js, line 282

(readonly) bonds :Array.<BondImage>

All bonds connected to this atom

Type:

Array.<BondImage>

Source: model.js, line 273

(readonly) bondsFrom :Array.<BondImage>

Bonds from this atom

Type:

Array.<BondImage>

Source: model.js, line 255

(readonly) bondsTo :Array.<BondImage>

Bonds to this atom

Type:

Array.<BondImage>

Source: model.js, line 264

color :int

Color of the atom

Type:

Source: model.js, line 467

(readonly) cpkColor :int

Hex integer code of the conventional CPK color used for this element (altered in case of non-standard isotopes)

Type:

Source: model.js, line 237

(readonly) crystLabel :String

Crystal site label of this atom

Type:

String

Source: model.js, line 162

(readonly) element :String

Symbol of this atom's element

Type:

String

Source: model.js, line 153

(readonly) elementData :Object

Periodic table information for this atom's element

Type:

Object

Source: model.js, line 171

(readonly) fxyz :Array.<float>

Fractional coordinates of this atom image

Type:

Array.<float>

Source: model.js, line 332

(readonly) fxyz0 :Array.<float>

Fractional coordinates of this atom's original

Type:

Array.<float>

Source: model.js, line 323

highlighted :bool

Whether the atom is highlighted

Type:

bool

Source: model.js, line 524

(readonly) id :String

String ID of the image

Type:

String

Source: model.js, line 126

(readonly) ijk :Array.<int>

Cell indices of this atom image

Type:

Array.<int>

Source: model.js, line 296

(readonly) imgIndex :int

Index of this image

Type:

Source: model.js, line 135

(readonly) index :int

Index of the atom

Type:

Source: model.js, line 117

isotope :int

Atomic mass of this atom's isotope

Type:

Source: model.js, line 191

(readonly) isotopeData :Object

Information for this atom's isotope

Type:

Object

Source: model.js, line 180

isotopeGlobal :int

Atomic mass of the global isotope set as default for this atom's species

Type:

Source: model.js, line 209

(readonly) mesh :AtomMesh

Mesh corresponding to this atom image

Type:

AtomMesh

Source: model.js, line 350

(readonly) model :Model

Model this atom belongs to

Type:

Model

Source: model.js, line 93

(readonly) moleculeIndex :int

Index of the molecule this atom belongs to

Type:

Source: model.js, line 341

(readonly) number :int

Atomic number of element

Type:

Source: model.js, line 226

opacity :float

Opacity of the atom

Type:

float

Source: model.js, line 499

radius :float

Final radius of the atom (starting radius * scale)

Type:

float

Source: model.js, line 452

(readonly) renderer :Renderer

Renderer used by this atom

Type:

Renderer

Source: model.js, line 102

scale :float

Scale of the atom

Type:

float

Source: model.js, line 435

(readonly) speciesIndex :int

Index of the species of this atom

Type:

Source: model.js, line 144

(readonly) vdwRadius :float

Van dew Waals radius for this element

Type:

float

Source: model.js, line 246

visible :bool

Whether the atom is visible

Type:

bool

Source: model.js, line 383

(readonly) xyz :Array.<float>

Position of this atom image

Type:

Array.<float>

Source: model.js, line 314

(readonly) xyz0 :Array.<float>

Position of this atom's original

Type:

Array.<float>

Source: model.js, line 305

Methods

addEllipsoid(data, name, parameters)

Add an ellipsoid to the atom.

Parameters:

Name	Type	Description
`data`	TensorData \| Object \| Array	The data to base the ellipsoid on. Can be: - a TensorData object; - an Object with 'eigenvalues' and 'eigenvectors' members - an Array of the form [eigenvalues, eigenvectors]
`name`	String	Name of the ellipsoid
`parameters`	Object	Additional options to pass (see EllipsoidMesh)

Source: model.js, line 612

addLabel(text, name, parameters)

Add a text label to the atom.

Parameters:

Name	Type	Description
`text`	String	Content of the label
`name`	String	Name to use to refer to the label (necessary to overwrite/erase later)
`parameters`	Object	Dictionary of other options (e.g. font family, text color, etc. See TextSprite)

Source: model.js, line 548

ellipsoidProperty(name, property, value)

Retrieve or set an ellipsoid's properties

Parameters:

Name	Type	Default	Description
`name`	String		Name of the ellipsoid
`property`	String		Property to set
`value`	?	null	Value to set. If omitted, returns the current value instead.

Source: model.js, line 662

getArrayValue(name) → {*}

Get the value for one array for this image

Parameters:

Name	Type	Description
`name`	String	Name of the array

Source: model.js, line 676

Returns:

Value of the array for this atom

Type:: *

labelProperty(name, property, value)

Retrieve or set a label's properties

Parameters:

Name	Type	Default	Description
`name`	String		Name of the label
`property`	String		Property to set
`value`	?	null	Value to set. If omitted, returns the current value instead.

Source: model.js, line 590

removeEllipsoid(name)

Remove the ellipsoid with a given name

Parameters:

Name	Type	Description
`name`	String	Name of the ellipsoid

Source: model.js, line 647

removeLabel(name)

Remove the label of a given name

Parameters:

Name	Type	Description
`name`	String	Name of the label

Source: model.js, line 574