# Namespace: $3Dmol

## $3Dmol

All of the functionality of $3Dmol.js is contained within the
$3Dmol global namespace

### Classes

GLModel
GLShape
GLShape
GLViewer
GLVolumetricRender
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, shared_viewer_resources) → {$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 configuration
  `shared_viewer_resources` | Object | shared resources between viewers' renderers

  ##### Returns:

  GLViewer, null if unable to instantiate WebGL

  Type
    $3Dmol.GLViewer

  ##### Example

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

#### <static> createViewerGrid(element, config, viewer_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
  `config` | GridSpec | grid configuration
  `viewer_config` | ViewerGridSpec | Viewer specification to apply to all subviewers

  ##### Returns:

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

  ##### Example

      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

      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