Difference between revisions of "Jmol JavaScript Object/JSV"
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AngelHerraez (talk | contribs) (Info variable for JSV) |
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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. | 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 [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- | + | 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 <sup>13</sup>C-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]. | 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]. | ||
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== 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) | + | All these functions must be applied to the unique '''<code>Jmol</code>''' object (this name is literal, cannot be changed): |
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Jmol.jsvAddHightlight(myJSV, x1, x2, r, g, b, a) | Jmol.jsvAddHightlight(myJSV, x1, x2, r, g, b, a) | ||
Jmol.jsvExport(myJSV, exportType, n) | Jmol.jsvExport(myJSV, exportType, n) | ||
Revision as of 19:25, 26 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 13C-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 for example:
var myJSV = Jmol.getJSVApplet("myJSV", Info)
Parameters making the Info variable (with default values shown between angular brackets):
- Info.height <
500> - Info.width <
300> - Info.debug <
false> - Info.jarPath <
.> - Info.jarFile <
JSpecViewApplet.jar> - Info.isSigned <
false> - Info.initParams <empty>
- Info.readyFunction <empty>
- Info.script <empty>
JSpecView-specific methods
All these functions must be applied to the unique Jmol object (this name is literal, cannot be changed):
Jmol.jsvAddHightlight(myJSV, x1, x2, r, g, b, a) Jmol.jsvExport(myJSV, exportType, n) Jmol.jsvGetCoordinate(myJSV) Jmol.jsvGetPropertyAsJavaObject(myJSV, key) Jmol.jsvGetPropertyAsJSON(myJSV, key) Jmol.jsvGetSolnColour(myJSV) Jmol.jsvIsPro(myJSV) Jmol.jsvIsSigned(myJSV) Jmol.jsvLoadInline(myJSV, data, params) Jmol.jsvRemoveAllHighlights(myJSV) Jmol.jsvRemoveHighlight(myJSV, x1, x2) Jmol.jsvReversePlot(myJSV) Jmol.jsvRunScript(myJSV, script) Jmol.jsvRunScriptNow(myJSV, script) Jmol.jsvSetFilePath(myJSV, tmpFilePath) Jmol.jsvSetSpectrumNumber(myJSV, n) Jmol.jsvSetVisible(myJSV, true/false) Jmol.jsvSyncScript(myJSV, peakScript) Jmol.jsvToggleCoordinate(myJSV) Jmol.jsvToggleGrid(myJSV) Jmol.jsvToggleIntegration(myJSV) Jmol.jsvWriteStatus(myJSV, message)
