All of the functionality of $3Dmol.js is contained within the $3Dmol global namespace
Classes
Namespaces
Members
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<static> builtinColorSchemes
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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
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<static> elementColors
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Preset element coloring - from individual element colors to entire mappings (e.g. '$3Dmol.elementColors.Jmol' colors atoms with Jmol stylings)
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<static> Parsers
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$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
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Preset secondary structure color scheme
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<static> SurfaceType :number
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$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
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Render surface synchronously if true
Type:
- boolean
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<static> viewers
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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
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<static> createViewer(element, config) → {$3Dmol.GLViewer}
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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
$3Dmol.download("pdb:4UAA",viewer,{},function(){ viewer.setBackgroundColor(0xffffffff); var colorAsSnake = function(atom) { return atom.resi % 2 ? 'white': 'green' }; viewer.setStyle( {}, { cartoon: {colorfunc: colorAsSnake }}); viewer.render(); });
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<static> download(query, viewer, options, callback) → {$3Dmol.GLModel}
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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
- 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); });
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<static> getbin(uri, callback)
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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.
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<static> getColorFromStyle(atom, style) → {$3Dmol.Color}
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Return proper color for atom given style
Parameters:
Name Type Description atom
AtomSpec style
AtomStyle Returns:
- Type
- $3Dmol.Color
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<static> getExtent(atomlist) → {Array}
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computes the bounding box around the provided atoms
Parameters:
Name Type Description atomlist
Array.<AtomSpec> Returns:
- Type
- Array
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<static> mergeGeos(geometry, mesh) → {undefined}
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Parameters:
Name Type Description geometry
$3Dmol.Geometry mesh
$3Dmol.Mesh Returns:
- Type
- undefined
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<static> specStringToObject((String)) → {Object}
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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