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, options)

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

Parameters:

Name	Type	Description
`prop`	String	property name
`sel`	AtomSelectionSpec
`options`	LabelSpec

Source: GLModel.ts

addResLabels(sel, 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
`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

calculateDashes()

Calculate dashed line segments along a bond, with proper centering and two-color support.

The dashes are centered along the bond using the pattern:
[halfGap]-[dash]-[gap]-[dash]-[gap]-...-[dash]-[halfGap]

For two-color bonds, the first half of dashes use colors[0], second half use colors[1].

Source: GLModel.ts

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>

getViewer()

Return viewer associated with this model.

Source: GLModel.ts

Returns:

GLViewer

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, options) → {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
`options`	Object	{fast: true} replays the frame's coordinates into the existing geometry via syncAtomPositions() instead of rebuilding it; falls back to a rebuild when the replay cannot apply. Off by default.

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();
        });

syncAtomPositions(optsopt)

Push the atoms' current coordinates into the existing geometry without rebuilding it.

Intended for animation: mutate model.selectedAtoms() / model.atoms x/y/z however you
like (linear interpolation between two conformations, torsion-space folding, MD frames)
and then call this instead of setFrame/setCoordinates. Those go through globj, which
regenerates every geometry in the model from scratch each frame. Here only position data
changes, so colors, radii, per-atom alphas and face indices are left alone and the
renderer respecifies just the affected buffers.

Covers sphere imposters, stick imposters (including their joint caps and color-split
half-bonds) and lines. NOT covered: cartoon, cross, surface, instanced and non-imposter
(tessellated) geometry -- a model showing those still needs a full regeneration. Requires
that the model has already been rendered once, since there is otherwise no geometry to
update.

Parameters:

Name	Type	Attributes	Description
`opts`	object	<optional>

Source: GLModel.ts

Returns:

true if positions were written. False means nothing was touched and the caller
should fall back to a full rebuild: either the model has not been rendered yet,
nothing trackable is styled, or the geometry contains something inexpressible as
a point on a bond axis (multi-bond side offsets), in which case a partial update
would leave visibly stale geometry behind.

syncSpherePositions() → {boolean}

Deprecated: Renamed to syncAtomPositions() once it grew beyond spheres.
Source: GLModel.ts

Returns:

Type:: boolean

syncSphereRadii(scale)

Rescale sphere-imposter radii in place, without rebuilding geometry.

scale is called once per sphere-styled atom and returns a multiplier on the radius that
atom was built with: 0 hides it, 1 is its natural size. Intended for entrance animations
(grow atoms in) and any effect that changes size without changing what is drawn.

This works because a sphere imposter has no radius uniform and no radius buffer of its
own -- the radius IS the billboard quad's extent, stored as the four corner offsets in the
normal array. Rewriting those corners resizes the sphere, and since only normals go dirty
the renderer respecifies one buffer instead of reallocating the group.

Parameters:

Name	Type	Description
`scale`	function

Source: GLModel.ts

Returns:

true if radii were written, false if there is nothing to update (no prior render,
or no sphere-imposter atoms in this model).

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, 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
`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();
          });