An example of integrating the Jmol viewer into a jython application, with optional console.

integration.py

#-*- coding:utf-8 -*-
#
#       Copyright 2012 Adrià Cereto Massagué <adrian.cereto@urv.cat>
#       This is the jython version of Jmol's Integration.java.
#       It is under public domain
"""
An example of integrating the Jmol viewer into a jython application, with optional console.
"""
from java.lang.System import exit

from java.awt import BorderLayout , Container, Dimension, Graphics
from java.awt.event import WindowAdapter

from javax.swing import JFrame, JPanel

from org.jmol.adapter.smarter import SmarterJmolAdapter
from org.jmol.api import JmolViewer
from org.jmol.util import Logger
from org.openscience.jmol.app.jmolpanel import AppConsole

#strXyzHOH = """3
#water
#O  0.0 0.0 0.0
#H  0.76923955 -0.59357141 0.0
#H -0.76923955 -0.59357141 0.0
#"""

strScript = "delay; move 360 0 0 0 0 0 0 0 4;"

def main():
    """
    Demonstrates a simple way to include an optional console along with the applet.
    """
    frame = JFrame("Hello", size = (410, 700))
    frame.addWindowListener(ApplicationCloser())
    contentPane = frame.getContentPane()
    jmolPanel = JmolPanel(preferredSize = Dimension(400, 400))
    # main panel -- Jmol panel on top
    panel = JPanel(layout = BorderLayout())
    panel.add(jmolPanel)
    # main panel -- console panel on bottom
    panel2 = JPanel(layout = BorderLayout(), preferredSize = Dimension(400, 300))
    console = AppConsole(jmolPanel.viewer, panel2,"History State Clear")
    # You can use a different JmolStatusListener or JmolCallbackListener interface
    # if you want to, but AppConsole itself should take care of any console-related callbacks
    jmolPanel.viewer.jmolCallbackListener = console
    panel.add("South", panel2)
    contentPane.add(panel)
    frame.visible = True
    # sample start-up script
    #viewer.openStringInline(strXyzHOH)
    strError = jmolPanel.viewer.openFile("http://chemapps.stolaf.edu/jmol/docs/examples-11/data/caffeine.xyz")
    if strError == None:
        jmolPanel.viewer.evalString(strScript)
    else:
        Logger.error(strError)

class ApplicationCloser(WindowAdapter):
    def windowClosing(self, e):
        exit(0)

class JmolPanel(JPanel):
    def __init__(self, preferredSize = None):
        self.preferredSize = preferredSize
        self.currentSize = Dimension()
        self.viewer = JmolViewer.allocateViewer(self, SmarterJmolAdapter(), None, None, None, None, None)

    def paint(self, g):
        self.getSize(self.currentSize)
        self.viewer.renderScreenImage(g, self.currentSize.width, self.currentSize.height)

if __name__ == "__main__":
    main()