Jmol JavaScript Object/JSV

Integration of JSpecView into Jmol-JSO

Extensive work in 2012 integrated JSpecView into Jmol 13.

• The Jmol application now includes a new tools menu item that opens a frame for JSpecView.
• The Jmol applet can communicate to and from a JSpecView applet in the same page, using the Jmol sync command. Jmol-JSO brokers this transaction and allows coordinated applet start-up so that one applet does not send a command to the other before both are ready.

This makes it possible to tie 3D models to IR, NMR, UV/VIS, GC, and GC/MS spectra, using the JCAMP-DX Version 6 standard.

Associated with this integration, we have designed a specification for an extension of the JCAMP-DX format that allows one JDX file to contain both Jmol-readable 3D models and peak information, allowing the user to click on, for example, a carbon atom in Jmol and have the C-13 NMR spectrum automatically display and highlight the associated peak in JSpecView.

For a demonstration of the Jmol <-> JSpecView connection, see the JSpecView subdirectory at chemapps.stolaf.edu or the demo pages at the University of the West Indies.

Creating and inserting the JSpecView applet

To create a JSpecView applet, use Jmol.getJSVApplet().

Syntax:

Jmol.getJSVApplet = function(id, Info)

JSpecView-specific methods

All these functions must be applied to the unique Jmol object (this name is literal, cannot be changed) --see syntax and examples below.

Syntax:

Jmol.jsvAddHightlight = function(jsvApplet, x1, x2, r, g, b, a) 
Jmol.jsvExport = function(jsvApplet, exportType, n) 
Jmol.jsvGetCoordinate = function(jsvApplet) 
Jmol.jsvGetPropertyAsJavaObject = function(jsvApplet, key) 
Jmol.jsvGetPropertyAsJSON = function(jsvApplet, key) 
Jmol.jsvGetSolnColour = function(jsvApplet) 
Jmol.jsvIsPro = function(jsvApplet) 
Jmol.jsvIsSigned = function(jsvApplet) 
Jmol.jsvLoadInline = function(jsvApplet, data, params)
Jmol.jsvRemoveAllHighlights = function(jsvApplet) 
Jmol.jsvRemoveHighlight = function(jsvApplet, x1, x2)
Jmol.jsvReversePlot = function(jsvApplet) 
Jmol.jsvRunScript = function(jsvApplet, script)
Jmol.jsvRunScriptNow = function(jsvApplet, script) 
Jmol.jsvSetFilePath = function(jsvApplet, tmpFilePath) 
Jmol.jsvSetSpectrumNumber = function(jsvApplet, n) 
Jmol.jsvSetVisible = function(jsvApplet, TF)
Jmol.jsvSyncScript = function(jsvApplet, peakScript)
Jmol.jsvToggleCoordinate = function(jsvApplet)
Jmol.jsvToggleGrid = function(jsvApplet) 
Jmol.jsvToggleIntegration = function(jsvApplet)
Jmol.jsvWriteStatus = function(jsvApplet, msg)

Contributors

AngelHerraez