3Dmol.js

Class: GLModel

$3Dmol. 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:

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();
              });
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