Namespace: $3Dmol

Classes

GLModel

GLShape

GLShape

GLViewer

Label

VolumeData

Namespaces

GLDraw

Members

<static> builtinColorSchemes

Properties:

Name	Type	Description
built		in color schemes The user can pass all of these values directly as the colorscheme and they will use the respective colorscheme

<static, readonly> CAP :number

Enum for cylinder cap styles.

Type:

• number

Properties:

Name	Type	Default	Description
NONE	number	0
FLAT	number	1
ROUND	number	2

<static> elementColors

Preset element coloring - from individual element colors to entire mappings (e.g. '$3Dmol.elementColors.Jmol' colors atoms with Jmol stylings)

<static> Parsers

$3Dmol.Parsers stores functions for parsing molecular data. They all take a string of molecular data
and options. The default behavior is to only read the first model in the case of multimodel files, and
all parsers return a list of atom list(s)

$3Dmol.Parsers. corresponds to the parsers for files with extension ext

<static> ssColors

Preset secondary structure color scheme

<static> SurfaceType :number

$3Dmol surface types

Type:

• number

Properties:

Name	Type	Default	Description
VDW	number	1
MS	number	2
SAS	number	3
SES	number	4

<static> syncSurface :boolean

Render surface synchronously if true

Type:

• boolean

<static> viewers

Contains a dictionary of embedded viewers created from HTML elements
with a the viewer_3Dmoljs css class indexed by their id (or numerically
if they do not have an id).

Methods

<static> base64ToArray(base64)

Convert a base64 encoded string to a Uint8Array

Parameters:

Name	Type	Description
base64	string	encoded string

<static> createViewer(element, config) → {$3Dmol.GLViewer}

Create and initialize an appropriate viewer at supplied HTML element using specification in config

Parameters:

Name	Type	Description
element	Object | string	Either HTML element or string identifier
config	ViewerSpec	Viewer specification

Returns:

GLViewer, null if unable to instantiate WebGL

Type

$3Dmol.GLViewer

Example

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• raw
• —

var viewer = $3Dmol.createViewer(
     'gldiv', //id of div to create canvas in
     {
       defaultcolors: $3Dmol.elementColors.rasmol,
       backgroundColor: 'black'
     }
   );
                       

<static> createViewerGrid(element, grid, config)

Create and initialize an appropriate a grid of viewers that share a WebGL canvas

Parameters:

Name	Type	Description
element	Object | string	Either HTML element or string identifier
grid	GridSpec	configuration
config	ViewerGridSpec	Viewer specification to apply to all subviewers

Returns:

[[$3Dmol.GLViewer]] 2D array of GLViewers

Example

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• raw
• —

var viewers = $3Dmol.createViewerGrid(
     'gldiv', //id of div to create canvas in
     {
       rows: 2,
       cols: 2,
       control_all: true  //mouse controls all viewers
     },
     { backgroundColor: 'lightgrey' }
   );
   $.get('data/1jpy.cif', function(data) {
     var viewer = viewers[0][0];
     viewer.addModel(data,'cif');
     viewer.setStyle({sphere:{}});
     viewer.zoomTo();
     viewer.render( );

     viewer = viewers[0][1];
     viewer.addModel(data,'cif');
     viewer.setStyle({stick:{}});
     viewer.zoomTo();     
     viewer.render( );
     
     viewer = viewers[1][0];
     viewer.addModel(data,'cif');
     viewer.setStyle({cartoon:{color:'spectrum'}});
     viewer.zoomTo();     
     viewer.render( );
     
     viewer = viewers[1][1];
     viewer.addModel(data,'cif');
     viewer.setStyle({cartoon:{colorscheme:'chain'}});
     viewer.zoomTo();     
     viewer.render();
     
     
   });

<static> download(query, viewer, options, callback) → {$3Dmol.GLModel}

Load a PDB/PubChem structure into existing viewer. Automatically calls 'zoomTo' and 'render' on viewer after loading model

Parameters:

Name	Type	Description
query	string	String specifying pdb or pubchem id; must be prefaced with "pdb: " or "cid: ", respectively
viewer	$3Dmol.GLViewer	Add new model to existing viewer
options	Object	Specify additional options format: file format to download, if multiple are available, default format is pdb pdbUri: URI to retrieve PDB files, default URI is http://www.rcsb.org/pdb/files/
callback	function	Function to call with model as argument after data is loaded.

Returns:

GLModel, Promise if callback is not provided

Type

$3Dmol.GLModel

Example

• 
• raw
• —

viewer.setBackgroundColor(0xffffffff);
       $3Dmol.download('pdb:2nbd',viewer,{onemol: true,multimodel: true},function(m) {
        m.setStyle({'cartoon':{colorscheme:{prop:'ss',map:$3Dmol.ssColors.Jmol}}});
       viewer.zoomTo();
       viewer.render(callback);
    });

<static> getbin(uri, callback, request) → {Promise}

Download binary data (e.g. a gzipped file) into an array buffer and provide
arraybuffer to callback.

Parameters:

Name	Type	Description
uri	string	location of data
callback	function	Function to call with arraybuffer as argument.
request	string	type of request

Returns:

Type

Promise

<static> getColorFromStyle(atom, style) → {$3Dmol.Color}

Return proper color for atom given style

Parameters:

Name	Type	Description
atom	AtomSpec
style	AtomStyle

Returns:

Type

$3Dmol.Color

<static> getExtent(atomlist) → {Array}

computes the bounding box around the provided atoms

Parameters:

Name	Type	Description
atomlist	Array.<AtomSpec>

Returns:

Type

Array

<static> mergeGeos(geometry, mesh) → {undefined}

Parameters:

Name	Type	Description
geometry	$3Dmol.Geometry
mesh	$3Dmol.Mesh

Returns:

Type

undefined

<static> specStringToObject((String)) → {Object}

Parse a string that represents a style or atom selection and convert it
into an object. The goal is to make it easier to write out these specifications
without resorting to json. Objects cannot be defined recursively.
; - delineates fields of the object
: - if the field has a value other than an empty object, it comes after a colon
, - delineates key/value pairs of a value object
If the value object consists of ONLY keys (no = present) the keys are
converted to a list. Otherwise a object of key/value pairs is created with
any missing values set to null
= OR ~ - separates key/value pairs of a value object, if not provided value is null
twiddle is supported since = has special meaning in URLs

Parameters:

Name	Type	Description
(String)		str

Returns:

Type

Object