Jmol JavaScript Object/JME
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 Jmol.getJMEApplet().
Syntax:
Jmol.getJMEApplet = function(id, Info, linkedJmolApplet)
linkedJmolApplet can be set to a Jmol JavaScript Object that will contain this JME drawing panel as a 2D input option in 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) --see syntax and examples below.
Syntax:
Jmol.jmeGetFile = function(jme, asJME) Jmol.jmeOptions = function(jme, options) Jmol.jmeReadMolecule = function(jme, jmeOrMolData) Jmol.jmeReset = function(jme) Jmol.jmeSmiles = function(jme, withStereoChemistry)
