Difference between revisions of "Jmol JavaScript Object/JSV"
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AngelHerraez (talk | contribs) (Initialization and Info data) |
AngelHerraez (talk | contribs) (updating syntax for JSpecView (as html5 object)) |
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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 thanks to the [[Jmol JavaScript Object|JSO]] infrastructure. | + | Extensive work in 2012 integrated [http://jspecview.sourceforge.net JSpecView] into Jmol 13 thanks to the [[Jmol JavaScript Object|JSO]] infrastructure (the same used for '''JSmol'''). |
* The '''Jmol application''' now includes a new <code>tools</code> menu item that opens a frame for JSpecView. | * The '''Jmol application''' now includes a new <code>tools</code> menu item that opens a frame for JSpecView. | ||
| − | * The ''' | + | * 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. |
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. | ||
| Line 9: | Line 9: | ||
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 [{{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. | ||
| − | 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]. | + | :''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 == | ||
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</pre> | </pre> | ||
| − | + | And also define <tt>jsvInfo</tt> (''you can use whatever name for this variable'') which is an associative array (a set of key+value pairs) indicating all the desired characteristics of the JSpecView object. The keys that may be used and their default values are given below: | |
| − | + | * '''height''' <code>500</code> | |
| − | + | * '''width''' <code>300</code> | |
| − | + | * '''color''' <code>#FFFFFF</code> | |
| − | + | * '''jarPath''' <code>java</code> | |
| − | + | * '''jarFile''' <code>JSpecViewApplet.jar</code> | |
| − | <tt>jsvInfo</tt> is an associative array (a set of key+value pairs) indicating all the desired characteristics of the JSpecView object. The keys that may be used and their default values are given below: | + | * '''isSigned''' <code>false</code> |
| − | * '''height''' | ||
| − | * '''width''' | ||
| − | * ''' | ||
| − | * '''jarPath''' | ||
| − | * '''jarFile''' | ||
| − | * '''isSigned''' | ||
* '''initParams''' <empty> | * '''initParams''' <empty> | ||
* '''readyFunction''' <empty> | * '''readyFunction''' <empty> | ||
| Line 40: | Line 35: | ||
height: 300, | height: 300, | ||
width: 300, | width: 300, | ||
| − | |||
| − | |||
| − | |||
script: 'load "acetophenone.jdx"' | script: 'load "acetophenone.jdx"' | ||
}; | }; | ||
</pre> | </pre> | ||
| + | |||
| + | == Creating and inserting the JSpecView applet == | ||
| + | To create a JSpecView applet and insert it into the htm page, use for example: | ||
| + | Jmol.getJSVApplet("myJSV", jsvInfo) | ||
| + | |||
| + | This will create a <tt>myJSV</tt> global variable in JavaScript that holds the JSpecView object and is also the unique ID for that object in all functions and methods described below. | ||
| + | |||
| + | If you prefer to insert the JSpecView object later after page creation, you can use: | ||
| + | Jmol.getJSVAppletHtml("myJSV", jsvInfo) | ||
| + | |||
| + | For example like this: | ||
| + | $("#myPlace").html( Jmol.getJSVAppletHtml("myJSV", jsvInfo) ) | ||
| + | |||
| + | |||
== JSpecView-specific methods == | == JSpecView-specific methods == | ||
Revision as of 10:18, 11 June 2016
Contents
Integration of JSpecView into Jmol-JSO
Extensive work in 2012 integrated JSpecView into Jmol 13 thanks to the JSO infrastructure (the same used for JSmol).
- The Jmol application now includes a new
toolsmenu 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
synccommand. 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.
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.
- 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 JSpecView subdirectory at St.Olaf or the demo pages at the University of the West Indies.
Initialization
Add this in the head section of your page:
<script src="somePath/JSmol.min.js" type="text/javascript"></script> <script src="somePath/js/JSmolJSV.js" type="text/javascript"></script>
And also define jsvInfo (you can use whatever name for this variable) which is an associative array (a set of key+value pairs) indicating all the desired characteristics of the JSpecView object. The keys that may be used and their default values are given below:
- height
500 - width
300 - color
#FFFFFF - jarPath
java - jarFile
JSpecViewApplet.jar - isSigned
false - initParams <empty>
- readyFunction <empty>
- script <empty>
Example:
var jsvInfo = {
height: 300,
width: 300,
script: 'load "acetophenone.jdx"'
};
Creating and inserting the JSpecView applet
To create a JSpecView applet and insert it into the htm page, use for example:
Jmol.getJSVApplet("myJSV", jsvInfo)
This will create a myJSV global variable in JavaScript that holds the JSpecView object and is also the unique ID for that object in all functions and methods described below.
If you prefer to insert the JSpecView object later after page creation, you can use:
Jmol.getJSVAppletHtml("myJSV", jsvInfo)
For example like this:
$("#myPlace").html( Jmol.getJSVAppletHtml("myJSV", jsvInfo) )
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)
