Difference between revisions of "Jmol JavaScript Object/JSV"
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AngelHerraez (talk | contribs) (getting specialized subsections out of the main Jmol-JSO page) |
AngelHerraez (talk | contribs) (getting specialized subsections out of the main Jmol-JSO page) |
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= Integration of JSpecView into Jmol-JSO = | = Integration of JSpecView into Jmol-JSO = | ||
| − | Extensive work in 2012 integrated [http://jspecview.sourceforge.net JSpecView] into Jmol 13. The | + | Extensive work in 2012 integrated [http://jspecview.sourceforge.net JSpecView] into Jmol 13. |
| + | * The '''Jmol application''' now includes a new <code>tools</code> 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 <code>sync</code> 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. | |
| − | For a demonstration of the Jmol | + | Associated with this integration, we have designed a [http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf 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 [http://chemapps.stolaf.edu/jmol/jspecview JSpecView subdirectory] at chemapps.stolaf.edu or the demo pages at [http://wwwchem.uwimona.edu.jm/spectra/JSpecView/ the University of the West Indies]. | ||
== Creating and inserting the JSpecView applet == | == Creating and inserting the JSpecView applet == | ||
Revision as of 21:05, 25 February 2013
Integration of JSpecView into Jmol-JSO
Extensive work in 2012 integrated JSpecView into Jmol 13.
- The Jmol application now includes a new
toolsmenu 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
synccommand. 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)
