3Dmol.js Class: GLModel

new GLModel(mid, defaultcolors)

GLModel represents a group of related atoms

Parameters:

Name	Type	Argument	Description
`mid`	number	<optional>
`defaultcolors`	Object	<optional>	Object defining default atom colors as atom => color property value pairs

See:

$3Dmol.download

Methods

<static> setColorByProperty(sel, prop, gradient)

Parameters:

Name	Type	Description
`sel`	type
`prop`	type
`gradient`	type

addAtoms(newatoms)

Add list of new atoms to model. Adjusts bonds appropriately.

Parameters:

Name	Type	Description
`newatoms`	type

Example

var atoms = [{elem: 'C', x: 0, y: 0, z: 0, bonds: [1,2], bondOrder: [1,2]}, {elem: 'O', x: -1.5, y: 0, z: 0, bonds: [0]},{elem: 'O', x: 1.5, y: 0, z: 0, bonds: [0], bondOrder: [2]}];
           
            viewer.setBackgroundColor(0xffffffff);
            var m = viewer.addModel();
            m.addAtoms(atoms);
            m.setStyle({},{stick:{}});
            viewer.zoomTo();
            viewer.render();

addAtomSpecs(customAtomSpecs)

add atomSpecs to validAtomSelectionSpecs

Parameters:

Name	Type	Description
`customAtomSpecs`	Array	array of strings that can be used as atomSelectionSpecs this is to prevent the 'Unknown Selector x' message on the console for the strings passed

addFrame(atom)

Add atoms as frames of model

Parameters:

Name	Type	Description
`atom`	AtomSpec	atoms to be added

addMolData(data, format, options)

add atoms to this model from molecular data string

Parameters:

Name	Type	Description
`data`	string \| ArrayBuffer	atom structure file input data string, for gzipped input use ArrayBuffer
`format`	string	input file string format (e.g 'pdb', 'sdf', 'sdf.gz', etc.)
`options`	ParserOptionsSpec	format dependent options. Attributes depend on the input format

addPropertyLabels(prop, sel, viewer, options)

Create labels for atoms that show the value of the passed property.

Parameters:

Name	Type	Description
`prop`	String	property name
`sel`	AtomSelectionSpec
`viewer`	$3Dmol.GLViewer
`options`	LabelSpec

addResLabels(sel, viewer, options, byframe)

Create labels for residues of selected atoms.
Will create a single label at the center of mass of all atoms
with the same chain,resn, and resi.

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec
`viewer`	$3Dmol.GLViewer
`options`	LabelSpec
`byframe`	boolean	if true, create labels for every individual frame, not just current; frames must be loaded already

atomIsSelected(atom, sel) → {boolean}

given a selection specification, return true if atom is selected.
Does not support context-aware selectors like expand/within/byres.

Parameters:

Name	Type	Description
`atom`	AtomSpec
`sel`	AtomSelectionSpec

Returns:

Type: boolean

enableContextMenu(sel, contextMenuEnabled)

enable context menu 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

exportVRML()

return a VRML string representation of the model. Does not include VRML header information

Returns:

VRML

getCrystData()

Returns crystallographic information if present.

getID() → {number}

Returns model id number

Returns:

Model ID

Type: number

getInternalState()

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

getNumFrames() → {number}

Returns model's frames property, a list of atom lists

Returns:

Type: number

getSymmetries() → {Array.<$3Dmol.Matrix4>}

Returns list of rotational/translational matrices if there is BIOMT data
Otherwise returns a list of just the ID matrix

Returns:

Type: Array.<$3Dmol.Matrix4>

globj(group, Object)

manage the globj for this model in the possed modelGroup - if it has to be regenerated, remove and add

Parameters:

Name	Type	Description
`group`	$3Dmol.Object3D
`Object`		options

hide()

Example

$3Dmol.download("pdb:3ucr",viewer,{},function(){  
            viewer.setStyle({},{stick:{}});
            viewer.getModel().hide();  
            viewer.render();
            });

removeAtoms(badatoms)

Remove specified atoms from model

Parameters:

Name	Type	Description
`badatoms`	type	list of atoms

removegl(group)

Remove any renderable mol object from scene

Parameters:

Name	Type	Description
`group`	$3Dmol.Object3D

selectedAtoms(sel) → {Array.<Object>}

return list of atoms selected by sel, this is specific to glmodel

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec

Returns:

Type: Array.<Object>

Example

$3Dmol.download("pdb:4wwy",viewer,{},function(){
                  var atoms = viewer.selectedAtoms({chain:'A'});
                  for(var i = 0, n = atoms.length; i < n; i++) {
                     atoms[i].b = 0.0;
                  }
                  viewer.setStyle({cartoon:{colorscheme:{prop:'b',gradient: 'roygb',min:0,max:30}}});
                  viewer.render();
              });

setClickable(sel, clickable, callback)

Set clickable and callback of selected atoms

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

setColorByElement(sel, colors)

given a mapping from element to color, set atom colors

Parameters:

Name	Type	Description
`sel`	type
`colors`	type

setColorByFunction(sel, func)

Parameters:

Name	Type	Description
`sel`	type	selection object
`func`	type	function to be used to set the color

Deprecated:

use setStyle and colorfunc attribute

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();
              });

setCoordinates(str, format)

Set coordinates for the atoms from provided trajectory file.

Parameters:

Name	Type	Description
`str`	string	contains the data of the file
`format`	string	contains the format of the file (mdcrd, inpcrd, pdb, netcdf, or array). Arrays should be TxNx3 where T is the number of timesteps and N the number of atoms.

Example

let m = viewer.addModel()  //create an empty model
         m.addAtoms([{x:0,y:0,z:0,elem:'C'},{x:2,y:0,z:0,elem:'C'}]) //provide a list of dictionaries representing the atoms
         viewer.setStyle({'sphere':{}})
         m.setCoordinates([[[0.0, 0.0, 0.0], [2.0, 0.0, 0.0]], [[0.0, 0.0, 0.0], [2.8888888359069824, 0.0, 0.0]], [[0.0, 0.0, 0.0], [3.777777671813965, 0.0, 0.0]], [[0.0, 0.0, 0.0], [4.666666507720947, 0.0, 0.0]], [[0.0, 0.0, 0.0], [5.55555534362793, 0.0, 0.0]], [[0.0, 0.0, 0.0], [6.44444465637207, 0.0, 0.0]], [[0.0, 0.0, 0.0], [7.333333492279053, 0.0, 0.0]], [[0.0, 0.0, 0.0], [8.222222328186035, 0.0, 0.0]], [[0.0, 0.0, 0.0], [9.11111068725586, 0.0, 0.0]], [[0.0, 0.0, 0.0], [10.0, 0.0, 0.0]]],'array');
         viewer.animate({loop: "forward",reps: 1});
         viewer.zoomTo();
         viewer.zoom(0.5);
         viewer.render();

setCoordinatesFromURL(url, path) → {Promise}

Set coordinates from remote trajectory file.

Parameters:

Name	Type	Description
`url`	string	contains the url where mdsrv has been hosted
`path`	string	contains the path of the file (/filename)

Returns:

Type: Promise

setCrystData(a, b, c, alpha, beta, gamma)

Set crystallographic information using three angles and three lengths

Parameters:

Name	Type	Description
`a`	number	length of unit cell side
`b`	number	length of unit cell side
`c`	number	length of unit cell side
`alpha`	number	unit cell angle in degrees (default 90)
`beta`	number	unit cell angle in degrees (default 90)
`gamma`	number	unit cell angle in degrees (default 90)

setCrystMatrix(matrix)

Set the crystallographic matrix to the given matrix.

This function removes a, b, c, alpha, beta, gamma from
the crystal data.

Parameters:

Name	Type	Description
`matrix`	$3Dmol.Matrix3	unit cell matrix

setFrame(framenum) → {Promise}

Sets model's atomlist to specified frame
Sets to last frame if framenum out of range

Parameters:

Name	Type	Description
`framenum`	number	model's atoms are set to this index in frames list

Returns:

Type: Promise

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
`unhover_callback`	function	function called when the mouse moves out of the hover area

setInternalState()

Overwrite the internal model state with the passed state.

setStyle(sel, style, add)

Set atom style of selected atoms

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec
`style`	AtomStyleSpec
`add`	boolean	if true, add to current style, don't replace

Example

$3Dmol.download("pdb:4UB9",viewer,{},function(){
                  viewer.setBackgroundColor(0xffffffff);

                  viewer.setStyle({chain:'A'},{line:{hidden:true,colorscheme:{prop:'b',gradient: new $3Dmol.Gradient.Sinebow($3Dmol.getPropertyRange(viewer.selectedAtoms(),'b'))}}});
                  viewer.setStyle({chain:'B'},{line:{colorscheme:{prop:'b',gradient: new $3Dmol.Gradient.Sinebow($3Dmol.getPropertyRange(viewer.selectedAtoms(),'b'))}}});
                  viewer.setStyle({chain:'C'},{cross:{hidden:true,colorscheme:{prop:'b',gradient: new $3Dmol.Gradient.Sinebow($3Dmol.getPropertyRange(viewer.selectedAtoms(),'b'))}}});
                  viewer.setStyle({chain:'D'},{cross:{colorscheme:{prop:'b',gradient: new $3Dmol.Gradient.RWB($3Dmol.getPropertyRange(viewer.selectedAtoms(),'b'))}}});
                  viewer.setStyle({chain:'E'},{cross:{radius:2.0,colorscheme:{prop:'b',gradient: new $3Dmol.Gradient.RWB($3Dmol.getPropertyRange(viewer.selectedAtoms(),'b'))}}});
                  viewer.setStyle({chain:'F'},{stick:{hidden:true,colorscheme:{prop:'b',gradient: new $3Dmol.Gradient.RWB($3Dmol.getPropertyRange(viewer.selectedAtoms(),'b'))}}});
                  viewer.setStyle({chain:'G'},{stick:{radius:0.8,colorscheme:{prop:'b',gradient: new $3Dmol.Gradient.ROYGB($3Dmol.getPropertyRange(viewer.selectedAtoms(),'b'))}}});
                  viewer.setStyle({chain:'H'},{stick:{singleBonds:true,colorscheme:{prop:'b',gradient: new $3Dmol.Gradient.ROYGB($3Dmol.getPropertyRange(viewer.selectedAtoms(),'b'))}}});
                  viewer.render();
              });

setSymmetries(list)

Sets symmetries based on specified matrices in list

Parameters:

Name	Type	Description
`list`	Array.<$3Dmol.Matrix4>

show()

Example

$3Dmol.download("pdb:3ucr",viewer,{},function(){  
            viewer.setStyle({},{stick:{}});
            viewer.getModel().hide();  
            viewer.render(  )
            viewer.getModel().show()
            viewer.render();
            });

toCDObject(whether) → {Object}

Convert the model into an object in the format of a ChemDoodle JSON model.

Parameters:

Name	Type	Description
`whether`	boolean	or not to include style information. Defaults to false.

Returns:

Type: Object

vibrate(numFrames, amplitude, bothWays, viewer, arrowSpec)

If model atoms have dx, dy, dz properties (in some xyz files), vibrate populates the model's frame property based on parameters.
Model 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
`viewer`	GLViewer	required if arrowSpec is provided
`arrowSpec`	ArrowSpec	specification for drawing animated arrows. If color isn't specified, atom color (sphere, stick, line preference) is used.

Example

$3Dmol.download("pdb:4UAA",viewer,{},function(){  
            viewer.setStyle({},{stick:{}});
            viewer.vibrate(10, 1);
            viewer.animate({loop: "forward",reps: 1});

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