Class: GLViewer

Constructor

new GLViewer()

Source: GLViewer.ts

Classes

GLViewer

Members

userContextMenuHandler :function|null

User specified function for handling a context menu event.
Handler is passed the selected object, x and y in canvas coordinates,
and original event.

Type:

function | null

Source: GLViewer.ts

Methods

addArrow(spec) → {GLShape}

Create and add arrow shape

Parameters:

Name	Type	Description
`spec`	ArrowSpec	Style specification

Source: GLViewer.ts

Returns:

Type:: GLShape

Example

$3Dmol.download("pdb:4DM7",viewer,{},function(){

              viewer.setBackgroundColor(0xffffffff);
              viewer.addArrow({
                  start: {x:-10.0, y:0.0, z:0.0},
                  end: {x:0.0, y:-10.0, z:0.0},
                  radius: 1.0,
                  radiusRadio:1.0,
                  mid:1.0,
                  clickable:true,
                  callback:function(){
                      this.color.setHex(0xFF0000FF);
                      viewer.render( );
                  }
              });
              viewer.render();
            });

addAsOneMolecule(data, format) → {GLModel}

Create and add model to viewer. Given multimodel file and its format,
all atoms are added to one model

Parameters:

Name	Type	Description
`data`	string	Input data
`format`	string	Input format (see `FileFormats`)

Source: GLViewer.ts

Returns:

Type:: GLModel

Example

$3Dmol.get('../test_structs/multiple.sdf', function(data){
              viewer.addAsOneMolecule(data, "sdf");
              viewer.zoomTo();
              viewer.render();
          });

addBox(spec) → {GLShape}

Create and add box shape. This method provides a shorthand
way to create a box shape object

Parameters:

Name	Type	Description
`spec`	BoxSpec	Box shape style specification

Source: GLViewer.ts

Returns:

Type:: GLShape

Example

viewer.addLine({color:'red',start:{x:0,y:0,z:0},end:{x:5,y:0,z:0}});
     viewer.addLine({color:'blue',start:{x:0,y:0,z:0},end:{x:0,y:5,z:0}});
     viewer.addLine({color:'green',start:{x:0,y:0,z:0},end:{x:0,y:0,z:5}});

     viewer.addBox({center:{x:0,y:0,z:0},dimensions: {w:3,h:4,d:2},color:'magenta'});
     viewer.zoomTo();
     viewer.rotate(45, {x:1,y:1,z:1});
     viewer.render();

addCurve(spec) → {GLShape}

Create and add Curve shape

Parameters:

Name	Type	Description
`spec`	CurveSpec	Style specification

Source: GLViewer.ts

Returns:

Type:: GLShape

Example

viewer.addCurve({points: [{x:0.0,y:0.0,z:0.0}, {x:5.0,y:3.0,z:0.0}, {x:5.0,y:7.0,z:0.0}, {x:0.0,y:10.0,z:0.0}],
                              radius:0.5,
                              smooth: 10,
                              fromArrow:false,
                              toArrow: true,
                              color:'orange',
                              });
          viewer.addCurve({points: [{x:-1,y:0.0,z:0.0}, {x:-5.0,y:5.0,z:0.0}, {x:-2,y:10.0,z:0.0}],
                              radius:1,
                              fromArrow:true,
                              toArrow: false,
                              color:'purple',
                              });
          viewer.zoomTo();
          viewer.render();

addCustom(spec) → {GLShape}

Add custom shape component from user supplied function

Parameters:

Name	Type	Description
`spec`	CustomSpec	Style specification

Source: GLViewer.ts

Returns:

Type:: GLShape

Example

function triangle(viewer) {
        var vertices = [];
        var normals = [];
        var colors = [];
        var r = 20;
        //triangle
        vertices.push(new $3Dmol.Vector3(0,0,0));
        vertices.push(new $3Dmol.Vector3(r,0,0));
        vertices.push(new $3Dmol.Vector3(0,r,0));

        normals.push(new $3Dmol.Vector3(0,0,1));
        normals.push(new $3Dmol.Vector3(0,0,1));
        normals.push(new $3Dmol.Vector3(0,0,1));

        colors.push({r:1,g:0,b:0});
        colors.push({r:0,g:1,b:0});
        colors.push({r:0,g:0,b:1});

        var faces = [ 0,1,2 ];

        var spec = {vertexArr:vertices, normalArr: normals, faceArr:faces,color:colors};
        viewer.addCustom(spec);
    }
    triangle(viewer);
    viewer.render();

addCylinder(spec) → {GLShape}

Create and add cylinder shape

Parameters:

Name	Type	Description
`spec`	CylinderSpec	Style specification

Source: GLViewer.ts

Returns:

Type:: GLShape

Example

viewer.setBackgroundColor(0xffffffff);
          viewer.addCylinder({start:{x:0.0,y:0.0,z:0.0},
                              end:{x:10.0,y:0.0,z:0.0},
                              radius:1.0,
                              fromCap:1,
                              toCap:2,
                              color:'red',
                              hoverable:true,
                              clickable:true,
                              callback:function(){ this.color.setHex(0x00FFFF00);viewer.render( );},
                              hover_callback: function(){ viewer.render( );},
                              unhover_callback: function(){ this.color.setHex(0xFF000000);viewer.render( );}
                             });
          viewer.addCylinder({start:{x:0.0,y:2.0,z:0.0},
                              end:{x:0.0,y:10.0,z:0.0},
                              radius:0.5,
                              fromCap:false,
                              toCap:true,
                              color:'teal'});
          viewer.addCylinder({start:{x:15.0,y:0.0,z:0.0},
                              end:{x:20.0,y:0.0,z:0.0},
                              radius:1.0,
                              color:'black',
                              fromCap:false,
                              toCap:false});
          viewer.render();

addIsosurface(data, spec) → {GLShape}

Construct isosurface from volumetric data. This is more flexible
than addVolumetricData, but can not be used with py3Dmol.

Parameters:

Name	Type	Description
`data`	VolumeData	volumetric data
`spec`	IsoSurfaceSpec	Shape style specification

Source: GLViewer.ts

Returns:

Type:: GLShape

Example

$3Dmol.get('../test_structs/benzene-homo.cube', function(data){
              var voldata = new $3Dmol.VolumeData(data, "cube");
              viewer.addIsosurface(voldata, {isoval: 0.01,
                                             color: "blue"});
              viewer.addIsosurface(voldata, {isoval: -0.01,
                                             color: "red"});
              viewer.zoomTo();
              viewer.render();
            });

addLabel(text, options, sel, noshow) → {Label}

Add label to viewer

Parameters:

Name	Type	Description
`text`	string	Label text
`options`	LabelSpec	Label style specification
`sel`	AtomSelection	Set position of label to center of this selection
`noshow`	boolean	if true, do not immediately display label - when adding multiple labels this is more efficient

Source: GLViewer.ts

Returns:

Type:: Label

Example

$3Dmol.download("pdb:2EJ0",viewer,{},function(){

              viewer.addLabel("Aromatic", {position: {x:-6.89, y:0.75, z:0.35}, backgroundColor: 0x800080, backgroundOpacity: 0.8});
              viewer.addLabel("Label",{font:'sans-serif',fontSize:18,fontColor:'white',fontOpacity:1,borderThickness:1.0,
                                       borderColor:'red',borderOpacity:0.5,backgroundColor:'black',backgroundOpacity:0.5,
                                       position:{x:50.0,y:0.0,z:0.0},inFront:true,showBackground:true});
              viewer.setStyle({chain:'A'},{cross:{hidden:true}});
              viewer.setStyle({chain:'B'},{cross:{hidden:false,
                                                  linewidth:1.0,
                                                  colorscheme:'greenCarbon'}});
              viewer.setStyle({chain:'C'},{cross:{hidden:false,
                                                  linewidth:1.0,
                                                  radius:0.5}});
              viewer.setStyle({chain:'D'},{cross:{hidden:false,
                                                  linewidth:10.0}});
              viewer.setStyle({chain:'E'},{cross:{hidden:false,
                                                  linewidth:1.0,
                                                  color:'black'}});

              viewer.render();


            });

addLine(spec) → {GLShape}

Create and add line shape

Parameters:

Name	Type	Description
`spec`	LineSpec	Style specification, can specify dashed, dashLength, and gapLength

Source: GLViewer.ts

Returns:

Type:: GLShape

Example

$3Dmol.download("pdb:2ABJ",viewer,{},function(){

              viewer.setViewStyle({style:"outline"});
              viewer.setStyle({chain:'A'},{sphere:{hidden:true}});
              viewer.setStyle({chain:'D'},{sphere:{radius:3.0}});
              viewer.setStyle({chain:'G'},{sphere:{colorscheme:'greenCarbon'}});
              viewer.setStyle({chain:'J'},{sphere:{color:'blue'}});
              viewer.addLine({dashed:true,start:{x:0,y:0,z:0},end:{x:100,y:100,z:100}});
              viewer.render();
          });

addLineDashed(spec, s)

Add dashed line to shape

Parameters:

Name	Type	Description
`spec`	CylinderSpec
`s`	GLShape

Source: GLViewer.ts

addMesh(mesh, style) → {number}

Adds an explicit mesh as a surface object.

Parameters:

Name	Type	Description
`mesh`	Mesh
`style`	Object

Source: GLViewer.ts

Returns:

surfid

Type:: number

addModel(data, format, options) → {GLModel}

Create and add model to viewer, given molecular data and its format

Parameters:

Name	Type	Description
`data`	string	Input data
`format`	string	Input format ('pdb', 'sdf', 'xyz', 'pqr', or 'mol2')
`options`	ParserOptionsSpec	format dependent options. Attributes depend on the input file format.

Source: GLViewer.ts

Returns:

Type:: GLModel

Example

viewer.setViewStyle({style:"outline"});
          $3Dmol.get('data/1fas.pqr', function(data){
              viewer.addModel(data, "pqr");
              $3Dmol.get("data/1fas.cube",function(volumedata){
                  viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity:0.85,voldata: new $3Dmol.VolumeData(volumedata, "cube"), volscheme: new $3Dmol.Gradient.RWB(-10,10)},{});

              viewer.render();
              });
              viewer.zoomTo();
          });

addModels(data, format) → {Array.<GLModel>}

Given multimodel file and its format, add atom data to the viewer as separate models
and return list of these models

Parameters:

Name	Type	Description
`data`	string	Input data
`format`	string	Input format (see `FileFormats`)

Source: GLViewer.ts

Returns:

Type:: Array.<GLModel>

addModelsAsFrames(data, format) → {GLModel}

Create and add model to viewer. Given multimodel file and its format,
different atomlists are stored in model's frame
property and model's atoms are set to the 0th frame

Parameters:

Name	Type	Description
`data`	string	Input data
`format`	string	Input format (see `FileFormats`)

Source: GLViewer.ts

Returns:

Type:: GLModel

Example

$3Dmol.get('../test_structs/multiple2.xyz', function(data){
              viewer.addModelsAsFrames(data, "xyz");
              viewer.animate({loop: "forward",reps: 1});
              viewer.setStyle({stick:{colorscheme:'magentaCarbon'}});
              viewer.zoomTo();
              viewer.render();
          });

addPropertyLabels(prop, sel, style)

Add property labels. This will generate one label per a selected
atom at the atom's coordinates with the property value as the label text.

Parameters:

Name	Type	Description
`prop`	string	property name
`sel`	AtomSelectionSpec
`style`	AtomStyleSpec	@example $3Dmol.download("cid:5291",viewer,{},function(){ viewer.setStyle({stick: {radius:.2}}); viewer.addPropertyLabels("index",{not:{elem:'H'}}, {fontColor:'black',font: 'sans-serif', fontSize: 28, showBackground:false,alignment:'center'}); viewer.zoomTo(); viewer.render(); });

Source: GLViewer.ts

addResLabels(sel, style, byframe)

Add residue labels. This will generate one label per a
residue within the selected atoms. The label will be at the
centroid of the atoms and styled according to the passed style.
The label text will be [resn][resi]

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec
`style`	AtomStyleSpec
`byframe`	boolean	if true, create labels for every individual frame, not just current

Source: GLViewer.ts

Example

$3Dmol.download("mmtf:2ll5",viewer,{},function(){
              viewer.setStyle({stick:{radius:0.15},cartoon:{}});
              viewer.addResLabels({hetflag:false}, {font: 'Arial', fontColor:'black',showBackground:false, screenOffset: {x:0,y:0}});
              viewer.zoomTo();
              viewer.render();
            });

addShape(shapeSpec) → {GLShape}

Add shape object to viewer

Parameters:

Name	Type	Description
`shapeSpec`	ShapeSpec	style specification for label

Source: GLViewer.ts
See: {GLShape}

Returns:

Type:: GLShape

addSphere(spec) → {GLShape}

Create and add sphere shape. This method provides a shorthand
way to create a spherical shape object

Parameters:

Name	Type	Description
`spec`	SphereShapeSpec	Sphere shape style specification

Source: GLViewer.ts

Returns:

Type:: GLShape

Example

viewer.addSphere({center:{x:0,y:0,z:0},radius:10.0,color:'red'});

     viewer.render();

addStyle(sel, style)

Add style properties to all selected atoms

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec	Atom selection specification. Can be omitted to select all
`style`	AtomStyleSpec	style spec to add to specified atoms

Source: GLViewer.ts

Example

$3Dmol.download('pdb:5IRE',viewer,{doAssembly: false},function(m) {
    viewer.setStyle({cartoon:{}});
    //keep cartoon style, but show thick sticks for chain A
    viewer.addStyle({chain:'A'},{stick:{radius:.5,colorscheme:"magentaCarbon"}});
    viewer.zoomTo();
    viewer.render();
    });

addSurface(type, style, atomsel, allsel, focus, surfacecallback) → {Promise}

Add surface representation to atoms

Parameters:

Name	Type	Description
`type`	SurfaceType \| string	Surface type (VDW, MS, SAS, or SES)
`style`	SurfaceStyleSpec	optional style specification for surface material (e.g. for different coloring scheme, etc)
`atomsel`	AtomSelectionSpec	Show surface for atoms in this selection
`allsel`	AtomSelectionSpec	Use atoms in this selection to calculate surface; may be larger group than 'atomsel'
`focus`	AtomSelectionSpec	Optionally begin rendering surface specified atoms
`surfacecallback`	function	function to be called after setting the surface

Source: GLViewer.ts

Returns:

promise - Returns a promise that ultimately resovles to the surfid. Returns surfid immediately if surfacecallback is specified. Returned promise has a [surfid, GLViewer, style, atomsel, allsel, focus] fields for immediate access.

Type:: Promise

addUnitCell(model, spec)

Create and add unit cell visualization.

Parameters:

Name	Type	Description
`model`	GLModel \| number	Model with unit cell information (e.g., pdb derived). If omitted uses most recently added model.
`spec`	UnitCellStyleSpec	visualization style

Source: GLViewer.ts

Example

$3Dmol.get('data/1jpy.cif', function(data) {
              let m = viewer.addModel(data);
              viewer.addUnitCell(m, {box:{color:'purple'},alabel:'X',blabel:'Y',clabel:'Z',alabelstyle: {fontColor: 'black',backgroundColor:'white',inFront:true,fontSize:40},astyle:{color:'darkred', radius:5,midpos: -10}});
              viewer.zoomTo();
              viewer.render();
    });

addVolumetricData(data, format, spec) → {GLShape}

Construct isosurface from volumetric data in gaussian cube format

Parameters:

Name	Type	Description
`data`	String	Input file contents
`format`	String	Input file format
`spec`	VolumetricRendererSpec \| IsoSurfaceSpec	Shape style specification

Source: GLViewer.ts

Returns:

Type:: GLShape

Example

$3Dmol.get('data/bohr.cube', function(data) {

    viewer.addVolumetricData(data, "cube", {isoval: -0.01, color: "red", opacity: 0.95});
    viewer.setStyle({cartoon:{},stick:{}});
    viewer.zoomTo();
    viewer.render();
    });

addVolumetricRender(data, spec) → {GLShape}

Create volumetric renderer for volumetricData

Parameters:

Name	Type	Description
`data`	VolumeData	volumetric data
`spec`	VolumetricRenderSpec	specification of volumetric render

Source: GLViewer.ts

Returns:

Type:: GLShape

animate(options)

Animate all models in viewer from their respective frames

Parameters:

Name	Type	Description
`options`	Object	can specify interval (speed of animation), loop (direction of looping, 'backward', 'forward' or 'backAndForth'), step interval between frames ('step'), startFrame, and reps (numer of repetitions, 0 indicates infinite loop)

Source: GLViewer.ts

apngURI(nframes) → {Promise}

Return a promise that resolves to an animated PNG image URI of
viewer contents (base64 encoded) for nframes of viewer changes.

Parameters:

Name	Type	Description
`nframes`	number

Source: GLViewer.ts

Returns:

Type:: Promise

atomIsSelected(atom, sel) → {boolean}

Parameters:

Name	Type	Description
`atom`	AtomSpec
`sel`	AtomSelectionSpec

Source: GLViewer.ts

Returns:

Type:: boolean

carveUpExtent(extent, atomlist, atomstoshow) → {Array}

Parameters:

Name	Type	Description
`extent`	Array
`atomlist`	Array.<AtomSpec>
`atomstoshow`	Array.<AtomSpec>

Source: GLViewer.ts

Returns:

Type:: Array

center(selopt, animationDurationopt, fixedPathopt)

Re-center the viewer around the provided selection (unlike zoomTo, does not zoom).

Parameters:

Name	Type	Attributes	Description
`sel`	AtomSelectionSpec	<optional>	Selection specification specifying model and atom properties to select. Default: all atoms in viewer
`animationDuration`	number	<optional>	an optional parameter that denotes the duration of a zoom animation
`fixedPath`	Boolean	<optional>	if true animation is constrained to requested motion, overriding updates that happen during the animation *

Source: GLViewer.ts

Example

// if the user were to pass the animationDuration value to
          // the function like so viewer.zoomTo({resn:'STI'},1000);
        //   the program would center on resn 'STI' over the course
        //   of 1 second(1000 milleseconds).
 // Reposition to centroid of all atoms of all models in this
//viewer glviewer.center();
    $3Dmol.get('data/4csv.pdb', function(data) {
    viewer.addModel(data,'pdb');
    viewer.setStyle({cartoon:{},stick:{}});
    viewer.center();
    viewer.render(callback);
    });

clear()

Clear scene of all objects

Source: GLViewer.ts

closeEnoughForClick(event, options)

Determine if a positioned event is "close enough" to mouseStart to be considered a click.
With a mouse, the position should be exact, but allow a slight delta for a touch interface.

Parameters:

Name	Type	Description
`event`	Event
`options`	Object

Source: GLViewer.ts

createModelFrom(sel, extractopt) → {GLModel}

Create a new model from atoms specified by sel.
If extract, removes selected atoms from existing models

Parameters:

Name	Type	Attributes	Description
`sel`	AtomSelectionSpec		Atom selection specification
`extract`	boolean	<optional>	If true, remove selected atoms from existing models

Source: GLViewer.ts

Returns:

Type:: GLModel

enableContextMenu(sel, contextMenuEnabled)

enable context menu and callback of selected atoms

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec	atom selection to apply hoverable settings to
`contextMenuEnabled`	boolean	whether contextMenu-handling is enabled for the selection

Source: GLViewer.ts

enableFog(fog)

Enable/disable fog for content far from the camera

Parameters:

Name	Type	Description
`fog`	boolean	whether to enable or disable the fog

Source: GLViewer.ts

exportJSON(includeStyles, modelID) → {string}

Export one or all of the loaded models into ChemDoodle compatible JSON.

Parameters:

Name	Type	Description
`includeStyles`	boolean	Whether or not to include style information.
`modelID`	number	Optional parameter for which model to export. If left out, export all of them.

Source: GLViewer.ts

Returns:

Type:: string

exportVRML()

return a VRML string representation of the scene. Include VRML header information

Source: GLViewer.ts

Returns:

VRML

fitSlab(sel)

Adjust slab to fully enclose selection (default everything).

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec	Selection specification specifying model and atom properties to select. Default: all atoms in viewer

Source: GLViewer.ts

getAtomsFromSel(sel) → {Array.<AtomSpec>}

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec

Source: GLViewer.ts

Returns:

Type:: Array.<AtomSpec>

getCanvas() → {HTMLCanvasElement}

Return underlying canvas element.

Source: GLViewer.ts

Returns:

Type:: HTMLCanvasElement

getConfig()

Return configuration of viewer

Source: GLViewer.ts

getFrame()

Gets the current viewer frame.

Source: GLViewer.ts

getInternalState()

Return object representing internal state of
the viewer appropriate for passing to setInternalState

Source: GLViewer.ts

getModel(idopt) → {GLModel}

Return specified model

Parameters:

Name	Type	Attributes	Default	Description
`id`	number	<optional>	last model id	Retrieve model with specified id

Default Value: Returns last model added to viewer or null if there are no models
Source: GLViewer.ts

Returns:

Type:: GLModel

Example

// Retrieve reference to first GLModel added var m =
   $3Dmol.download("pdb:1UBQ",viewer,{},function(m1){
              $3Dmol.download("pdb:1UBI", viewer,{}, function(m2) {
                viewer.zoomTo();
                m1.setStyle({cartoon: {color:'green'}});
                //could use m2 here as well
                viewer.getModel().setStyle({cartoon: {color:'blue'}});
                viewer.render();
            })
          });

getNumFrames() → {number}

Returns the number of frames that the model with the most frames in the viewer has

Source: GLViewer.ts

Returns:

Type:: number

getPerceivedDistance() → {number}

Return the z distance between the model and the camera

Source: GLViewer.ts

Returns:

distance

Type:: number

getRenderer()

Return renderer element.

Source: GLViewer.ts

getSlab() → {Object}

Get slab of view (contents outside of slab are clipped).

Properties

Name	Type	Description
`near`	number	near clipping plane distance
`far`	number	far clipping plane distance

Source: GLViewer.ts

Returns:

Type:: Object

getSurface(surf)

Return surface object

Parameters:

Name	Type	Description
`surf`	number	surface id

Source: GLViewer.ts

getUniqueValues(attribute, sel) → {Array.<Object>}

Returns valid values for the specified attribute in the given selection

Parameters:

Name	Type	Description
`attribute`	string
`sel`	AtomSelectionSpec

Source: GLViewer.ts

Returns:

Type:: Array.<Object>

getView() → {Array.<number>}

Returns an array representing the current viewpoint.
Translation, zoom, and rotation quaternion.

Source: GLViewer.ts

Returns:

[ pos.x, pos.y, pos.z, rotationGroup.position.z, q.x, q.y, q.z, q.w ]

Type:: Array.<number>

hasVolumetricRender() → {boolean}

Return true if volumetric rendering is supported (WebGL 2.0 required)

Source: GLViewer.ts

Returns:

Type:: boolean

isAnimated() → {boolean}

Return true if viewer is currently being animated, false otherwise

Source: GLViewer.ts

Returns:

Type:: boolean

jmolMoveTo()

return Jmol moveto command to position this scene

Source: GLViewer.ts

linkViewer(otherview)

Synchronize this view matrix of this viewer to the passed viewer.
When the viewpoint of this viewer changes, the other viewer will
be set to this viewer's view.

Parameters:

Name	Type	Description
`otherview`	GLViewer

Source: GLViewer.ts

mapAtomProperties(props,, sel)

Add specified properties to all atoms matching input argument

Parameters:

Name	Type	Description
`props,`	Object	either array of atom selectors with associated props, or function that takes atom and sets its properties
`sel`	AtomSelectionSpec	subset of atoms to work on - model selection must be specified here

Source: GLViewer.ts

Example

$3Dmol.get('../test_structs/b.sdf', function(data){
                  viewer.addModel(data,'sdf');
                  let props = [];
                  //make the atom index a property x
                  for(let i = 0; i < 8; i++) {
                    props.push({index:i,props:{'x':i}});
                  }
                  viewer.mapAtomProperties(props);
                  viewer.setStyle({sphere:{colorscheme:{gradient:'roygb',prop:'x',min:0,max:8}}});
                  viewer.zoomTo();
                  viewer.render();
                });

modelToScreen() → {object|list}

Convert model coordinates to screen coordinates.

Parameters:

Type	Description
object \| list	an object or list of objects with x,y,z attributes (e.g. an atom)

Source: GLViewer.ts

Returns:

and object or list of {x: screenX, y: screenY}

Type:: object | list

pauseAnimate()

Pause animation of all models in viewer

Source: GLViewer.ts

pdbData(sel) → {string}

Return pdb output of selected atoms (if atoms from pdb input)

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec	Selection specification specifying model and atom properties to select. Default: all atoms in viewer

Source: GLViewer.ts

Returns:

PDB string of selected atoms

Type:: string

pngURI()

Return image URI of viewer contents (base64 encoded). *

Source: GLViewer.ts

removeAllLabels()

Remove all labels from viewer

Source: GLViewer.ts

Example

$3Dmol.download("pdb:1ubq",viewer,{},function(){

           viewer.addResLabels();
           viewer.setStyle({},{stick:{}});
           viewer.render( ); //show labels

           viewer.removeAllLabels();
           viewer.render(); //hide labels
    });

removeAllModels()

Delete all existing models

Source: GLViewer.ts

removeAllShapes()

Remove all shape objects from viewer

Source: GLViewer.ts

removeAllSurfaces()

Remove all surfaces.

Source: GLViewer.ts

removeLabel(label)

Remove label from viewer

Parameters:

Name	Type	Description
`label`	Label	$3Dmol label

Source: GLViewer.ts

Example

// Remove labels created in
     $3Dmol.download("pdb:2EJ0",viewer,{},function(){
              var toremove = viewer.addLabel("Aromatic", {position: {x:-6.89, y:0.75, z:0.35}, backgroundColor: 0x800080, backgroundOpacity: 0.8});
              viewer.addLabel("Label",{font:'sans-serif',fontSize:18,fontColor:'white',fontOpacity:1,borderThickness:1.0,
                                       borderColor:'red',borderOpacity:0.5,backgroundColor:'black',backgroundOpacity:0.5,
                                       position:{x:50.0,y:0.0,z:0.0},inFront:true,showBackground:true});
              viewer.removeLabel(toremove);
              viewer.render();


            });

removeModel(model)

Delete specified model from viewer

Parameters:

Name	Type	Description
`model`	GLModel \| number

Source: GLViewer.ts

removeShape(shape)

Remove shape object from viewer

Parameters:

Name	Type	Description
`shape`	GLShape	Reference to shape object to remove

Source: GLViewer.ts

removeSurface(surf)

Remove surface with given ID

Parameters:

Name	Type	Description
`surf`	number	surface id

Source: GLViewer.ts

removeUnitCell(model)

Remove unit cell visualization from model.

Parameters:

Name	Type	Description
`model`	GLModel \| number	Model with unit cell information (e.g., pdb derived). If omitted uses most recently added model.

Source: GLViewer.ts

Example

$3Dmol.get('data/icsd_200866.cif', function(data) {
             let m = viewer.addModel(data);
             viewer.setStyle({sphere:{}})
             viewer.addUnitCell();
             viewer.zoomTo();
             viewer.removeUnitCell();
             viewer.render();
       });

render(callbackopt, extsopt)

Render current state of viewer, after
adding/removing models, applying styles, etc.

Parameters:

Name	Type	Attributes	Description
`callback`		<optional>
`exts`		<optional>

Source: GLViewer.ts

replicateUnitCell(A, B, C, model, addBonds, prune)

Replicate atoms in model to form a super cell of the specified dimensions.
Original cell will be centered as much as possible.

Parameters:

Name	Type	Description
`A`	integer	number of times to replicate cell in X dimension.
`B`	integer	number of times to replicate cell in Y dimension. If absent, X value is used.
`C`	integer	number of times to replicate cell in Z dimension. If absent, Y value is used.
`model`	GLModel	Model with unit cell information (e.g., pdb derived). If omitted uses most recently added model.
`addBonds`	boolean	Create bonds between unit cells based on distances.
`prune`	boolean	Keep only atoms that are within the original unit cell (i.e., on edges). Alternatively, call replicateUnitCell(1).

Source: GLViewer.ts

Example

$3Dmol.get('data/icsd_200866.cif', function(data) {
             let m = viewer.addModel(data);
             viewer.setStyle({sphere:{scale:.25}})
             viewer.addUnitCell();
             viewer.zoomTo();
             viewer.replicateUnitCell(3,2,1,m);
             viewer.render();
       });

resize()

Resize viewer according to containing HTML element's dimensions

Source: GLViewer.ts

resumeAnimate()

Resume animation of all models in viewer

Source: GLViewer.ts

rotate(angleopt, axisopt, animationDurationopt, fixedPathopt)

Rotate scene by angle degrees around axis

Parameters:

Name	Type	Attributes	Description
`angle`	number	<optional>	Angle, in degrees, to rotate by.
`axis`	string	<optional>	Axis ("x", "y", "z", "vx", "vy", or "vz") to rotate around. Default "y". View relative (rather than model relative) axes are prefixed with v. Axis can also be specified as a vector.
`animationDuration`	number	<optional>	an optional parameter that denotes the duration of the rotation animation. Default 0 (no animation)
`fixedPath`	boolean	<optional>	if true animation is constrained to requested motion, overriding updates that happen during the animation *

Source: GLViewer.ts

Example

$3Dmol.download('cid:4000', viewer, {}, function() {
    viewer.setStyle({stick:{}});
    viewer.zoomTo();
    viewer.rotate(90,'y',1);
    viewer.render(callback);
    });

screenOffsetToModel()

For a given screen (x,y) displacement return model displacement

Source: GLViewer.ts

screenToModelDistance()

Distance from screen coordinate to model coordinate assuming screen point
is projected to the same depth as model coordinate

Source: GLViewer.ts

selectedAtoms(sel) → {Array.<AtomSpec>}

return list of atoms selected by sel

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec

Source: GLViewer.ts

Returns:

Type:: Array.<AtomSpec>

setAutoEyeSeparation(isright, x) → {number}

Used for setting an approx value of eyeSeparation. Created for calling by StereoViewer object

Parameters:

Name	Type	Description
`isright`	boolean
`x`	number

Source: GLViewer.ts

Returns:

camera x position

Type:: number

setBackgroundColor(hex, a)

Set the background color (default white)

Parameters:

Name	Type	Description
`hex`	number	Hexcode specified background color, or standard color spec
`a`	number	Alpha level (default 1.0)

Source: GLViewer.ts

Example

viewer.setBackgroundColor("green",0.5);

setCameraParameters()

Set camera parameters (distance to the origin and field of view)

Parameters:

Type	Description
parameters	new camera parameters, with possible fields being fov for the field of view, z for the distance to the origin, and orthographic (boolean) for kind of projection (default false).

Source: GLViewer.ts

Example

$3Dmol.get("data/set1_122_complex.mol2", function(data) {
            var m = viewer.addModel(data);
            viewer.setStyle({stick:{}});
            viewer.zoomTo();
            viewer.setCameraParameters({ fov: 10 , z: 300 });
            viewer.render();
        });

setClickable(sel, clickable, callback)

Set click-handling properties to all selected atoms. Important: render must be called for this to take effect.

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec	atom selection to apply clickable settings to
`clickable`	boolean	whether click-handling is enabled for the selection
`callback`	function	function called when an atom in the selection is clicked. The function is passed the selected (foremost) object, the viewer, the triggering event, the associated container, and a list of all intersecting objects with their distances from the viewer.

Source: GLViewer.ts

Example

$3Dmol.download("cid:307900",viewer,{},function(){

               viewer.setStyle({},{sphere:{}});
               viewer.setClickable({},true,function(atom,viewer,event,container) {
                   viewer.addLabel(atom.resn+":"+atom.atom,{position: atom, backgroundColor: 'darkgreen', backgroundOpacity: 0.8});
               });
               viewer.render();
    });

setColorByElement(sel, colors)

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec
`colors`	object

Source: GLViewer.ts

setColorByProperty(sel, prop, scheme, range)

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec
`prop`	string
`scheme`	Gradient \| string
`range`	object

Source: GLViewer.ts

setConfig(c)

Set the configuration object. Note that some settings may only
have an effect at viewer creation time.

Parameters:

Name	Type	Description
`c`	ViewerSpec

Source: GLViewer.ts

setContainer(element)

Change the viewer's container element
Also useful if the original container element was removed from the DOM.

Parameters:

Name	Type	Description
`element`	Object \| string	Either HTML element or string identifier. Defaults to the element used to initialize the viewer.

Source: GLViewer.ts

setDefaultCartoonQuality(val)

Set the default cartoon quality for newly created models. Default is 5.
Current models are not affected.

Parameters:

Name	Type	Description
`val`	number

Source: GLViewer.ts

setFrame(framenum) → {Promise}

Sets the atomlists of all models in the viewer to specified frame.
Shapes and labels can also be displayed by frame.
Sets to last frame if framenum out of range

Parameters:

Name	Type	Description
`framenum`	number	fame index to use, starts at zero

Source: GLViewer.ts

Returns:

Type:: Promise

setHeight(h)

Set viewer height independently of the HTML container. This is probably not what you want.

Parameters:

Name	Type	Description
`h`	number	Height in pixels

Source: GLViewer.ts

setHoverDuration(hoverDurationopt)

Set the duration of the hover delay

Parameters:

Name	Type	Attributes	Description
`hoverDuration`	number	<optional>	an optional parameter that denotes the duration of the hover delay (in milliseconds) before the hover action is called

Source: GLViewer.ts

setHoverable(sel, hoverable, hover_callback, unhover_callback)

Set hoverable and callback of selected atoms

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec	atom selection to apply hoverable settings to
`hoverable`	boolean	whether hover-handling is enabled for the selection
`hover_callback`	function	function called when an atom in the selection is hovered over. The function has the same signature as a click handler.
`unhover_callback`	function	function called when the mouse moves out of the hover area

Source: GLViewer.ts

Example

$3Dmol.download("pdb:1ubq",viewer,{},function(){

           viewer.setHoverable({},true,function(atom,viewer,event,container) {
               if(!atom.label) {
                atom.label = viewer.addLabel(atom.resn+":"+atom.atom,{position: atom, backgroundColor: 'mintcream', fontColor:'black'});
               }
           },
           function(atom) {
               if(atom.label) {
                viewer.removeLabel(atom.label);
                delete atom.label;
               }
            }
           );
           viewer.setStyle({},{stick:{}});
           viewer.render();
    });

setInternalState(state)

Overwrite internal state of the viewer with passed object
which should come from getInternalState.

Parameters:

Name	Type	Description
`state`

Source: GLViewer.ts

setLabelStyle(label, stylespec) → {Label}

Modify existing label's style

Parameters:

Name	Type	Description
`label`	Label	$3Dmol label
`stylespec`	LabelSpec	Label style specification

Source: GLViewer.ts

Returns:

Type:: Label

setLabelText(label, text) → {Label}

Modify existing label's text

Parameters:

Name	Type	Description
`label`	Label	$3Dmol label
`text`	String	Label text

Source: GLViewer.ts

Returns:

Type:: Label

setPerceivedDistance(dist)

Set the distance between the model and the camera
Essentially zooming. Useful while stereo rendering.

Parameters:

Name	Type	Description
`dist`	number

Source: GLViewer.ts

setProjection(proj)

Set view projection scheme. Either orthographic or perspective.
Default is perspective. Orthographic can also be enabled on viewer creation
by setting orthographic to true in the config object.

Parameters:

Name	Type	Description
`proj`

Source: GLViewer.ts

Example

viewer.setViewStyle({style:"outline"});
          $3Dmol.get('data/1fas.pqr', function(data){
              viewer.addModel(data, "pqr");
              $3Dmol.get("data/1fas.cube",function(volumedata){
                  viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity:0.85,voldata: new $3Dmol.VolumeData(volumedata, "cube"), volscheme: new $3Dmol.Gradient.RWB(-10,10)},{});
              });
              viewer.zoomTo();

              viewer.setProjection("orthographic");
              viewer.render(callback);
          });

setSlab(near, far)

Set slab of view (contents outside of slab are clipped).
Must call render to update.

Parameters:

Name	Type	Description
`near`	number	near clipping plane distance
`far`	number	far clipping plane distance

Source: GLViewer.ts

setStateChangeCallback(callback)

Set a callback to call when the view has potentially changed.

Parameters:

Name	Type	Description
`callback`

Source: GLViewer.ts

setStyle(sel, style)

Set style properties to all selected atoms

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec	Atom selection specification. Can be omitted to select all.
`style`	AtomStyleSpec	Style spec to apply to specified atoms

Source: GLViewer.ts

Example

viewer.setBackgroundColor(0xffffffff);
    $3Dmol.download('pdb:5IRE',viewer,{doAssembly: false},function(m) {
    m.setStyle({chain:'A'},{'cartoon':{color:'spectrum'}});
    m.setStyle({chain:'C'},{'cartoon':{style:'trace',color:'blue'}});
    m.setStyle({chain:'E'},{'cartoon':{tubes:true,arrows:true,color:'green',opacity:0.75}});
    m.setStyle({chain:'B'},{'cartoon':{color:'red',opacity:0.5}});
    m.setStyle({chain:'D'},{'cartoon':{style:'trace',color:'grey',opacity:0.75}});
    m.setStyle({chain:'F'},{'cartoon':{arrows:true,color:'white'}});
    // viewer.addStyle({chain:'B'},{line:{}});
    viewer.zoomTo();
    viewer.render();
    });

setSurfaceMaterialStyle(surf, style)

Set the surface material to something else, must render change

Parameters:

Name	Type	Description
`surf`	number	Surface ID to apply changes to
`style`	SurfaceStyleSpec	new material style specification

Source: GLViewer.ts

Example

$3Dmol.get("data/9002806.cif",function(data){
        viewer.addModel(data);
        viewer.setStyle({stick:{}});
        let surf = viewer.addSurface("SAS");
        surf.then(function() {
            viewer.setSurfaceMaterialStyle(surf.surfid, {color:'blue',opacity:0.5});
            viewer.render();
            });
       });

setView(arg)

Sets the view to the specified translation, zoom, and rotation.

Parameters:

Name	Type	Description
`arg`	Array.<number>	Array formatted identically to the return value of getView

Source: GLViewer.ts

setViewChangeCallback(callback)

Set a callback to call when the view has potentially changed.

Parameters:

Name	Type	Description
`callback`

Source: GLViewer.ts

setViewStyle(parameters)

Set global view styles.

Parameters:

Name	Type	Description
`parameters`	ViewStyle

Source: GLViewer.ts

Example

viewer.setViewStyle({style:"outline"});
          $3Dmol.get('data/1fas.pqr', function(data){
              viewer.addModel(data, "pqr");
              $3Dmol.get("data/1fas.cube",function(volumedata){
                  viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity:0.85,voldata: new $3Dmol.VolumeData(volumedata, "cube"), volscheme: new $3Dmol.Gradient.RWB(-10,10)},{});
              });
              viewer.zoomTo();
              viewer.render(callback);
          });

setWidth(w)

Set viewer width independently of the HTML container. This is probably not what you want.

Parameters:

Name	Type	Description
`w`	number	Width in pixels

Source: GLViewer.ts

setZoomLimits()

Set lower and upper limit stops for zoom.

Parameters:

Type	Description
lower	limit on zoom in (positive number). Default 0.
upper	limit on zoom out (positive number). Default infinite.

Source: GLViewer.ts

Example

$3Dmol.get("data/set1_122_complex.mol2", function(moldata) {
            var m = viewer.addModel(moldata);
            viewer.setStyle({stick:{colorscheme:"Jmol"}});
            viewer.setZoomLimits(100,200);
            viewer.zoomTo();
            viewer.zoom(10); //will not zoom all the way
            viewer.render();
        });

spin(axis, speed)

Continuously rotate a scene around the specified axis.

Call spin(false) to stop spinning.

Parameters:

Name	Type	Description
`axis`	string \| boolean \| Array	[axis] - Axis ("x", "y", "z", "vx", "vy", or "vz") to rotate around. Default "y". View relative (rather than model relative) axes are prefixed with v.
`speed`	number	[speed] - Speed multiplier for spinning the viewer. 1 is default and a negative value reverses the direction of the spin.

Source: GLViewer.ts

stopAnimate()

Stop animation of all models in viewer

Source: GLViewer.ts

targetedObjects(x, y)

Return a list of objects that intersect that at the specified viewer position.

Parameters:

Name	Type	Description
`x`		x position in screen coordinates
`y`		y position in screen coordinates
	Array.<Object>	list of objects or selection object specifying what object to check for targeting

Source: GLViewer.ts

translate(x, y, animationDurationopt, fixedPathopt)

Translate current view by x,y screen coordinates
This pans the camera rather than translating the model.

Parameters:

Name	Type	Attributes	Description
`x`	number		Relative change in view coordinates of camera
`y`	number		Relative change in view coordinates of camera
`animationDuration`	number	<optional>	an optional parameter that denotes the duration of a zoom animation
`fixedPath`	Boolean	<optional>	if true animation is constrained to requested motion, overriding updates that happen during the animation *

Source: GLViewer.ts

Example

$3Dmol.get('data/4csv.pdb', function(data) {
    viewer.addModel(data,'pdb');
    viewer.setStyle({cartoon:{},stick:{}});
    viewer.zoomTo();
    viewer.translate(200,50);
    viewer.rotate(90,'z');
    viewer.render(callback);
    });

translateScene(x, y, animationDurationopt, fixedPathopt)

Translate current models by x,y screen coordinates
This translates the models relative to the current view. It does
not change the center of rotation.

Parameters:

Name	Type	Attributes	Description
`x`	number		Relative change in x screen coordinate
`y`	number		Relative change in y screen coordinate
`animationDuration`	number	<optional>	an optional parameter that denotes the duration of a zoom animation
`fixedPath`	Boolean	<optional>	if true animation is constrained to requested motion, overriding updates that happen during the animation *

Source: GLViewer.ts

Example

$3Dmol.get('data/4csv.pdb', function(data) {
    viewer.addModel(data,'pdb');
    viewer.setStyle({cartoon:{},stick:{}});
    viewer.zoomTo();
    viewer.translateScene(200,50);
    viewer.rotate(90,'z'); // will no longer be around model center
    viewer.render(callback);
    });

vibrate(numFrames, amplitude, bothWays, arrowSpec)

If atoms have dx, dy, dz properties (in some xyz files), vibrate populates each model's frame property based on parameters.
Models can then be animated

Parameters:

Name	Type	Description
`numFrames`	number	number of frames to be created, default to 10
`amplitude`	number	amplitude of distortion, default to 1 (full)
`bothWays`	boolean	if true, extend both in positive and negative directions by numFrames
`arrowSpec`	ArrowSpec	specification for drawing animated arrows. If color isn't specified, atom color (sphere, stick, line preference) is used.

Source: GLViewer.ts

zoom(factoropt, animationDurationopt, fixedPathopt)

Zoom current view by a constant factor

Parameters:

Name	Type	Attributes	Description
`factor`	number	<optional>	Magnification factor. Values greater than 1 will zoom in, less than one will zoom out. Default 2.
`animationDuration`	number	<optional>	an optional parameter that denotes the duration of a zoom animation
`fixedPath`	Boolean	<optional>	if true animation is constrained to requested motion, overriding updates that happen during the animation

Source: GLViewer.ts

Example

$3Dmol.get('data/4csv.pdb', function(data) {
    viewer.addModel(data,'pdb');
    viewer.setStyle({cartoon:{},stick:{}});
    viewer.zoomTo()
    viewer.zoom(2,1000);
    viewer.render();
    });

zoomTo(selopt, animationDurationopt, fixedPathopt)

Zoom to center of atom selection. The slab will be set appropriately for
the selection, unless an empty selection is provided, in which case there will be no slab.

Parameters:

Name	Type	Attributes	Description
`sel`	Object	<optional>	Selection specification specifying model and atom properties to select. Default: all atoms in viewer
`animationDuration`	number	<optional>	an optional parameter that denotes the duration of a zoom animation
`fixedPath`	Boolean	<optional>	if true animation is constrained to requested motion, overriding updates that happen during the animation *

Source: GLViewer.ts

Example

$3Dmol.get('data/1fas.pqr', function(data){
              viewer.addModel(data, "pqr");
          viewer.zoomTo();
              $3Dmol.get("data/1fas.cube",function(volumedata){
                  viewer.addSurface($3Dmol.SurfaceType.VDW, {
                      opacity:0.85,
                      voldata: new $3Dmol.VolumeData(volumedata, "cube"),
                      volscheme: new $3Dmol.Gradient.Sinebow($3Dmol.getPropertyRange(viewer.selectedAtoms(),'charge'))
                  },{});

              viewer.render();
              });
            });

(static) generateMeshSyncHelper(type, expandedExtent, extendedAtoms, atomsToShow, atoms, vol) → {Object}

Parameters:

Name	Type	Description
`type`	SurfaceType
`expandedExtent`	Array
`extendedAtoms`	Array.<AtomSpec>
`atomsToShow`	Array.<AtomSpec>
`atoms`	Array.<AtomSpec>
`vol`	number

Source: GLViewer.ts

Returns:

Type:: Object

(static) generateSurfaceMesh(atoms, VandF, mat) → {Mesh}

Parameters:

Name	Type	Description
`atoms`	Array.<AtomSpec>
`VandF`	Object
`mat`	MeshLambertMaterial

Source: GLViewer.ts

Returns:

Type:: Mesh

(static) getAtomsWithin(atomlist, extent) → {Array}

Parameters:

Name	Type	Description
`atomlist`	Array.<AtomSpec>
`extent`	Array

Source: GLViewer.ts

Returns:

Type:: Array