Class: GLModel

Constructor

new GLModel()

Source: GLModel.ts

Classes

GLModel

Methods

addAtomSpecs(customAtomSpecs)

add atomSpecs to validAtomSelectionSpecs

Parameters:

Name Type Description

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. These messages are no longer generated as, in theory, typescript will catch problems at compile time. In practice, there may still be issues at run-time but we don't check for them... What we should do is use something like https://github.com/woutervh-/typescript-is to do runtime type checking, but it currently doesn't work with our types...

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.
These messages are no longer generated as, in theory, typescript will catch problems at compile time.
In practice, there may still be issues at run-time but we don't check for them...

What we should do is use something like https://github.com/woutervh-/typescript-is to do runtime
type checking, but it currently doesn't work with our types...

Deprecated: Yes
Source: GLModel.ts

addAtoms(newatoms)

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

Parameters:

Name	Type	Description
`newatoms`	Array.<AtomSpec>

Source: GLModel.ts

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();

addFrame(atoms)

Add atoms as frames of model

Parameters:

Name	Type	Description
`atoms`	Array.<AtomSpec>	atoms to be added

Source: GLModel.ts

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

Source: GLModel.ts

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`	GLViewer
`options`	LabelSpec

Source: GLModel.ts

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`	GLViewer
`options`	LabelSpec
`byframe`	boolean	if true, create labels for every individual frame, not just current; frames must be loaded already

Source: GLModel.ts

assignBonds()

Assign bonds based on atomic coordinates.
This currently uses a primitive distance-based algorithm that does not
consider valence constraints and will only create single bonds.

Source: GLModel.ts

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

Source: GLModel.ts

Returns:

Type:: boolean

createMolObj()

param {AtomSpec[]} atoms

Source: GLModel.ts

drawAtomClickSphere()

Source: GLModel.ts

drawAtomCross(atom, geos)

Parameters:

Name	Type	Description
`atom`	AtomSpec
`geos`	Record.<number, Geometry>

Source: GLModel.ts

drawAtomSphere(atom, geo)

Parameters:

Name	Type	Description
`atom`	AtomSpec
`geo`	Geometry

Source: GLModel.ts

drawBondLines(atom, atoms, geos)

Parameters:

Name	Type	Description
`atom`	AtomSpec
`atoms`	Array.<AtomSpec>
`geos`	Record.<number, Geometry>

Source: GLModel.ts

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

Source: GLModel.ts

expandAtomList()

returns a list of atoms in the expanded bounding box, but not in the current one

Bounding box:

[ [ xmin, ymin, zmin ],
[ xmax, ymax, zmax ],
[ xctr, yctr, zctr ] ]

Source: GLModel.ts

exportVRML()

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

Source: GLModel.ts

Returns:

VRML

getCrystData()

Returns crystallographic information if present.

Source: GLModel.ts

getID() → {number}

Returns model id number

Source: GLModel.ts

Returns:

Model ID

Type:: number

getInternalState()

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

Source: GLModel.ts

getNumFrames() → {number}

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

Source: GLModel.ts

Returns:

Type:: number

getRadiusFromStyle(atom, style) → {number}

Parameters:

Name	Type	Description
`atom`	AtomSpec
`style`	atomstyle

Source: GLModel.ts

Returns:

Type:: number

getSymmetries() → {Array.<Matrix4>}

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

Source: GLModel.ts

Returns:

Type:: Array.<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`	Object3D
`Object`		options

Source: GLModel.ts

hide()

Don't show this model in future renderings. Keep all styles and state
so it can be efficiencly shown again.

@see GLModel#show

Source: GLModel.ts

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`	Array.<AtomSpec>	list of atoms

Source: GLModel.ts

removegl(group)

Remove any renderable mol object from scene

Parameters:

Name	Type	Description
`group`	Object3D

Source: GLModel.ts

selectedAtoms(sel) → {Array.<Object>}

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

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec

Source: GLModel.ts

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

Source: GLModel.ts

setColorByElement(sel, colors)

given a mapping from element to color, set atom colors

Parameters:

Name	Type	Description
`sel`	AtomSelectionSpec
`colors`	object

Source: GLModel.ts

setColorByFunction(sel, func)

Parameters:

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

Deprecated: use setStyle and colorfunc attribute
Source: GLModel.ts

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();
          });

setColorByProperty(sel, prop, scheme)

Parameters:

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

Source: GLModel.ts

setCoordinates(str, format)

Set coordinates for the atoms from provided trajectory file.

Parameters:

Name	Type	Description
`str`	string \| ArrayBuffer	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.

Source: GLModel.ts

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)

Source: GLModel.ts

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)

Source: GLModel.ts

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`	Matrix3	unit cell matrix

Source: GLModel.ts

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

Source: GLModel.ts

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

Source: GLModel.ts

setInternalState(state)

Overwrite the internal model state with the passed state.

Parameters:

Name	Type	Description
`state`

Source: GLModel.ts

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

Source: GLModel.ts

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.<Matrix4>

Source: GLModel.ts

show()

Unhide a hidden model

Source: GLModel.ts
See: GLModel#hide

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.

Source: GLModel.ts

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.

Source: GLModel.ts

Example

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

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