Jmol JavaScript Object/JME

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Integration of JME into Jmol-JSO

The JME applet (Java Molecular Editor by Peter Ertl) allows the user to draw a molecular structure in 2D. Jmol-JSO includes the capability to pass information back and forth between JME and Jmol in a seamless manner. The "information panel" that Jmol-JSO implements can be set up to hold the JME applet, allowing tight integration. Alternatively, the JME applet and the Jmol applet can be set side-by-side on a web page, and applet-applet communication can be handled by the page developer.

Creating and inserting the JME applet

To create a JME applet, use for example:

var myJME = Jmol.getJMEApplet("myJME", Info, myJmol)

The 3rd argument, if provided, is a pointer to a Jmol JavaScript Object that will contain this JME drawing panel as a 2D input option inside its Info panel.

Parameters making the Info variable (with default values shown between angular brackets):

  • height <300>
  • width <300>
  • jarPath <.>
  • jarFile <JME.jar>
  • options <autoez>
    • rbutton, norbutton - show / hide R button
    • hydrogens, nohydrogens - display / hide hydrogens
    • query, noquery - enable / disable query features
    • autoez, noautoez - automatic generation of SMILES with E,Z stereochemistry
    • nocanonize - SMILES canonicalization and detection of aromaticity supressed
    • nostereo - stereochemistry not considered when creating SMILES
    • reaction, noreaction - enable / disable reaction input
    • multipart - possibility to enter multipart structures
    • number - possibility to number (mark) atoms
    • depict - the applet will appear without editing butons,this is used for structure display only
    • Documented at [1]

JME-specific methods

All these functions must be applied to the unique Jmol object (this name is literal, cannot be changed):

Jmol.jmeGetFile(myJME, asJME) 
Jmol.jmeOptions(myJME, options)
Jmol.jmeReadMolecule(myJME, jmeOrMolData)
Jmol.jmeSmiles(myJME, withStereoChemistry)
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