Jmol JavaScript Object/JSV - Revision history

AngelHerraez: jsvExport

2025-08-27T11:45:54Z

jsvExport

AngelHerraez at 09:06, 25 August 2025

2025-08-25T09:06:10Z

AngelHerraez: /* Integration of JSpecView with JSmol */

2025-08-23T17:02:25Z

‎Integration of JSpecView with JSmol

AngelHerraez: /* Documentation */

2025-08-22T18:56:11Z

‎Documentation

AngelHerraez: /* Documentation */

2025-08-22T18:15:46Z

‎Documentation

AngelHerraez: specification doc

2025-08-22T18:14:09Z

specification doc

AngelHerraez: More details and up-to-date information

2025-08-20T16:42:38Z

More details and up-to-date information

AngelHerraez: /* Creating and inserting the JSpecView applet */

2019-04-28T18:51:11Z

‎Creating and inserting the JSpecView applet

AngelHerraez: update documentation on JSpecView

2019-04-28T01:13:11Z

update documentation on JSpecView

AngelHerraez: update documentation on JSpecView

2019-04-28T00:34:38Z

update documentation on JSpecView

@@ Line 77: / Line 77: @@
 * <code>Jmol.jsvSyncScript(myJSV, peakScript)</code>
 * <code>Jmol.jsvExport(myJSV, exportType, n)</code> Delivers the spectrum in one of these formats:
-** exportType: PDF, JDX, XY, SQZ, PAC, DIF, DIFDUP, FIX, AML, CML, PNG, JPG (apparently only PDF is functional)
+** exportType: PDF, JDX, XY, SQZ, PAC, DIF, DIFDUP, FIX, AML, CML, PNG, JPG  (between quotes)
 ** n: zero-based index of spectra available; -1 for the current one
 * <code>Jmol.jsvSetFilePath(myJSV, tmpFilePath)</code>

@@ Line 15: / Line 15: @@
 Associated with this integration, we have designed a specification<sup>[<big>[[#Documentation|1]]</big>]</sup> 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 <sup>13</sup>C-NMR spectrum automatically display and highlight the associated peak in JSpecView.
 For a demonstration of the Jmol <-> JSpecView connection, see [https://jmol.sourceforge.net/demo/JSV/demos/ here]
 (a copy of [{{JSV_UWI}} this collection]).

@@ Line 15: / Line 15: @@
 Associated with this integration, we have designed a specification<sup>[<big>[[#Documentation|1]]</big>]</sup> 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 <sup>13</sup>C-NMR spectrum automatically display and highlight the associated peak in JSpecView.
-For a demonstration of the Jmol <-> JSpecView connection, see
+For a demonstration of the Jmol <-> JSpecView connection, see [https://jmol.sourceforge.net/demo/JSV/demos/ here]
-* [{{JSV_UWI}}test1jsv_mol.html Infrared spectra and vibrational modes of hexane and cyclohexane derivatives]
+(a copy of [{{JSV_UWI}} this collection]).
 <!-- obsolete

@@ Line 109: / Line 109: @@
 # JCAMP-MOL: A JCAMP-DX extension to allow interactive model/spectrum exploration using Jmol and JSpecView. Robert M. Hanson & Robert J. Lancashire. Specification Draft 4/1/2012. Available (pdf) from:
-#* Jmol Project website
+#* [https://jmol.sourceforge.net/demo/JSV/Jmol-JSpecView-specs.pdf Jmol Project website]
 #* [{{StOlaf}}docs/misc/Jmol-JSpecView-specs.pdf St. Olaf College website]
 #* [https://docs.google.com/document/d/16Ht5baVsDogiJlZr7IvugM0sE5r22rLmFw5fVHSNLeE/ Google Docs]

@@ Line 109: / Line 109: @@
 # JCAMP-MOL: A JCAMP-DX extension to allow interactive model/spectrum exploration using Jmol and JSpecView. Robert M. Hanson & Robert J. Lancashire. Specification Draft 4/1/2012. Available (pdf) from:
 #* [{{StOlaf}}docs/misc/Jmol-JSpecView-specs.pdf St. Olaf College website]
 #* [https://docs.google.com/document/d/16Ht5baVsDogiJlZr7IvugM0sE5r22rLmFw5fVHSNLeE/ Google Docs]

@@ Line 13: / Line 13: @@
 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 [{{StOlaf}}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 <sup>13</sup>C-NMR spectrum automatically display and highlight the associated peak in JSpecView.
+Associated with this integration, we have designed a specification<sup>[<big>[[#Documentation|1]]</big>]</sup> 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 <sup>13</sup>C-NMR spectrum automatically display and highlight the associated peak in JSpecView.
 For a demonstration of the Jmol <-> JSpecView connection, see
@@ Line 105: / Line 105: @@
   Jmol.jsvToggleIntegration(myJSV) // Toggles display of he integration plot
   Jmol.jsvWriteStatus(myJSV, message) // Writes a message to the status label.

@@ Line 1: / Line 1: @@
-= JSpecView =
+== JSpecView ==
 [http://jspecview.sourceforge.net/ JSpecView] is a graphical viewer for spectral data in the [http://www.jcamp-dx.org/ JCAMP-DX format].
 It was initially developed as a Java application and Java applet, at the Department of Chemistry of the University of the West Indies, Mona, Jamaica.
@@ Line 5: / Line 5: @@
 It was later integrated into Jmol distribution and converted, to avoid Java, as a JavaScript-HTML5 version. This page documents this latter version.
-= Integration of JSpecView into Jmol-JSO =
+== Integration of JSpecView with JSmol ==
-Extensive work in 2012 integrated JSpecView into Jmol 13 thanks to the [[Jmol JavaScript Object|JSO]] infrastructure (the same used for '''JSmol''').
+Extensive work in 2012 integrated JSpecView into Jmol 13 thanks to the [[Jmol JavaScript Object|JSO]] infrastructure used for '''JSmol'''.
 * The '''Jmol application''' now includes a new <code>tools</code> menu item that opens a frame for JSpecView.
 * The '''JSmol object''' can communicate to and from a JSpecView object in the same page, using the Jmol <code>sync</code> command. The JSmol object syntax (Jmol-JSO) brokers this transaction and allows coordinated  start-up of both kind of objects so that one does not send a command to the other before both are ready.
@@ Line 15: / Line 15: @@
 Associated with this integration, we have designed a [{{StOlaf}}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 <sup>13</sup>C-NMR spectrum automatically display and highlight the associated peak in JSpecView.
 :''Note: this needs updating, StOlaf pages are broken at UWI pages use old Java versions, not JSmol.''
 :For a demonstration of the Jmol <-> JSpecView connection, see the [{{StOlaf}}jspecview JSpecView subdirectory] at St.Olaf or the demo pages at [http://wwwchem.uwimona.edu.jm/spectra/JSpecView/ the University of the West Indies].
-== Initialization ==
+=== Initialization ===
 Add this in the <code>head</code> section of your page:
 <pre>
@@ Line 31: / Line 40: @@
 * '''color''' <code>#A0A0A0</code>  (background around the spectrum box)
 * '''j2sPath''' <code>j2s</code>
 * '''initParams''' <empty>
 * '''readyFunction''' <empty>
@@ Line 48: / Line 54: @@
 </pre>
-== Creating and inserting the JSpecView applet ==
+=== Creating and inserting the JSpecView object ===
-To create a JSpecView applet and insert it into the htm page, use for example:
+To create a JSpecView object and insert it into the htm page, use for example:
   Jmol.getJSVApplet("myJSV", jsvInfo)
@@ Line 60: / Line 66: @@
   $("#myPlace").html( Jmol.getJSVAppletHtml("myJSV", jsvInfo) )
 You can visit an [http://jsmol.000webhostapp.com/test_JSV.htm example page] that load spectra from files or from inline data.
-== JSpecView-specific methods ==
+=== JSpecView-specific methods ===
 All these functions must be applied to the unique '''<code>Jmol</code>''' object (this name is literal, cannot be changed):

← Older revision		Revision as of 18:51, 28 April 2019
Line 60:		Line 60:
	$("#myPlace").html( Jmol.getJSVAppletHtml("myJSV", jsvInfo) )		$("#myPlace").html( Jmol.getJSVAppletHtml("myJSV", jsvInfo) )

		+	You can visit an [http://jsmol.000webhostapp.com/test_JSV.htm example page] that load spectra from files or from inline data.

	== JSpecView-specific methods ==		== JSpecView-specific methods ==

@@ Line 66: / Line 66: @@
 Handling files and scripting:
- Jmol.jsvLoadInline(myJSV, data, params)
+* <code>Jmol.jsvLoadInline(myJSV, data, params)</code> Loads JCAMP-DX data from a string variable.
- Jmol.jsvRunScript(myJSV, script)
+* <code>Jmol.jsvRunScript(myJSV, script)</code> Uses a queue, possibly waiting until the viewer object has been loaded.
- Jmol.jsvRunScriptNow(myJSV, script)
+* <code>Jmol.jsvRunScriptNow(myJSV, script)</code> Runs a script without queuing it, and returns only after completion.
- Jmol.jsvSyncScript(myJSV, peakScript)
+* <code>Jmol.jsvSyncScript(myJSV, peakScript)</code>
- Jmol.jsvExport(myJSV, exportType, n)
+* <code>Jmol.jsvExport(myJSV, exportType, n)</code> Delivers the spectrum in one of these formats:
- Jmol.jsvSetFilePath(myJSV, tmpFilePath)
+** exportType: XY, SQZ, PAC, DIF, DIFDUP, FIX, AML, CML
 Configuration:
@@ Line 78: / Line 80: @@
 Interface:
-  Jmol.jsvAddHighlight(myJSV, x1, x2, r, g, b, a)
+  Jmol.jsvAddHighlight(myJSV, x1, x2, r, g, b, a) // Adds a highlight to a portion of the plot area.
   Jmol.jsvRemoveHighlight(myJSV, x1, x2)
   Jmol.jsvRemoveAllHighlights(myJSV)
-  Jmol.jsvToggleCoordinate(myJSV)
+  Jmol.jsvToggleCoordinate(myJSV) // Toggles display of coordinate.
   Jmol.jsvToggleGrid(myJSV)
 Other features:
-  Jmol.jsvGetCoordinate(myJSV)
+  Jmol.jsvGetCoordinate(myJSV) // returns the coordinate of clicked point in the plot area
   Jmol.jsvGetPropertyAsJavaObject(myJSV, key)
   Jmol.jsvGetPropertyAsJSON(myJSV, key)
-  Jmol.jsvGetSolnColour(myJSV)
+  Jmol.jsvGetSolnColour(myJSV) // Returns the calculated colour of a visible spectrum.
   Jmol.jsvReversePlot(myJSV) // Inverts the direction of the X axis (chemical shift, ppm)
   Jmol.jsvSetSpectrumNumber(myJSV, n)
   Jmol.jsvSetVisible(myJSV, true/false)
-  Jmol.jsvToggleIntegration(myJSV)
+  Jmol.jsvToggleIntegration(myJSV) // Toggles display of he integration plot
-  Jmol.jsvWriteStatus(myJSV, message)
+  Jmol.jsvWriteStatus(myJSV, message) // Writes a message to the status label.