JMol

Wrapper for the chemical structure viewer based on JMol.

Simple demo application available here.

Summary

JMol	Wrapper for the chemical structure viewer based on JMol.
Functions
jmol	Convert DIV panel into JMol / JSmol viewer.
Types
Options
Functions
setCSID
setSMILES
reload	Reloads jmol/jsmol based on currently set options
setMOL	Show molecule with this mol.
setMoleculeDisplayType	sets the display type of molecule in JMol
setZoomScaling	Sets the zoom scale
setSpinRates	Set the X, Y coordinate spins based on specified frames/second value
setOptions	Set new options to update the widget’s view
toggleSpin	If JSMol spin is on then it sets it to off, and vice-versa

Functions

jmol

Convert DIV panel into JMol / JSmol viewer.

Parameters

options

Initialization Options

$('#jmolView').jmol ({
        width: 300,
        height: 300,
        csid: 236,
        modality: 'JAVA',
        spin: true,
        spinRateX: 10,
        spinRateY: 14,
        spinFPS: 20,
        zoomScaling: 1.5,
        vibration: false,
        useSignedApplet: true
});

Types

Options

Properties

width	Width of the widget in pixels. Default value - 300
height	Height of the widget in pixels. Default value - 300
csid	ChemSpider ID to be displayed
smiles	SMILES string of the molecule that should be displayed
mol	string containing contents of mol connection file of the molecule to be displayed (with each new line delimited by \n) e.g. mol:”” +”\n” +”\n” +”\n 2 1 0 0000 0 0 0 0 0999 V2000” +”\n 2.4000 -0.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0” +”\n 3.7167 -0.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0” +”\n 2 1 2 0” +”\nM END” +”\n” +”\n$$$$\n”
modality	determines the various options to be tried (applet and surrogates) and the order in which to try them. Note that Jmol-JSO cannot detect if the user has intentionally disabled Java in some browsers.
spin	set to true to make molecule spin when displayed, or false if not
spinRateX	set spin Rate of molecule in JSmol in x direction (if spin is set to true)
spinRateY	set spin Rate of molecule in JSmol in y direction (if spin is set to true)
spinFPS	set spin frames per second of molecule in JSmol (if spin is set to true)
moleculeStyle	display style used for molecular representation. One of: ‘WIREFRAME\|SPACEFILL\|BALLSTICK
zoomScaling	set zoom scaling factor of JSmol
vibration	whether structure animation should vibrate
useSignedApplet	When set to true, you can put applet files, model files and page files wherever you want to and run them from local disk. It also allows to load local files into Jmol faster than from elsewhere.

Functions

setCSID

setCSID: function ( csid )

Show molecule with this ChemSpider ID

retrieves mol from ChemSpider webservice.

Parameters

csid	ChemSpider ID

jmol.setCSID(10368587);

setSMILES

setSMILES: function ( smiles )

Show molecule that has this smiles

converts smiles to mol using ChemSpider webservice.

Parameters

smiles

SMILES string

jmol.setSMILES('CC(=O)Oc1ccccc1C(=O)O');

reload

reload: function ()

Reloads jmol/jsmol based on currently set options

jmol.reload();

setMOL

setMOL: function ( mol )

Show molecule with this mol.

Parameters

mol	contents of mol connection file defining structure

jmol.setMOL(""
                +"\n"
                +"\n"
                +"\n  2  1  0  0000  0  0  0  0  0999 V2000"
                +"\n    2.4000   -0.4625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0"
                +"\n    3.7167   -0.4667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0"
                +"\n  2  1  2  0"
                +"\nM  END"
                +"\n"
                +"\n$$$$\n");

setMoleculeDisplayType

setMoleculeDisplayType: function ( displayType )

sets the display type of molecule in JMol

Parameters

displayTpe

WIREFRAME|SPACEFILL|BALLSTICK

jmol.setMoleculeDisplayType('WIREFRAME');

setZoomScaling

setZoomScaling: function ( zoomScaling )

Sets the zoom scale

Parameters

zoomScaling

the zoom scaling factor for molecule

jmol.setZoomScaling(1.5);

setSpinRates

setSpinRates: function ( spinRateX,
spinRateY,
spinFPS )

Set the X, Y coordinate spins based on specified frames/second value

Parameters

spinRateX	spin Rate of molecule in x direction
spinRateY	spin Rate of molecule in y direction
spinFPS	spin frames per second of molecule

jmol.setSpinRates(10, 10, 25);

setOptions

setOptions: function ( options )

Set new options to update the widget’s view

jmol.setOptions({
    bondWidth: 2,
    spinRateX: 0.1,
    spinRateY: 0.1
});

toggleSpin

toggleSpin: function ()

If JSMol spin is on then it sets it to off, and vice-versa

jmol.toggleSpin();