User commands in OpenAstexViewer

OpenAstexViewer provides support for extending the scripting language with arbitrary commands. This document covers an example of this.

If the command part of a scripting command is not recognized a class file of that name is search for. If this is found an instance is created using reflection, and the static method handleCommand is called with a reference to the MoleculeViewer, the MoleculeRenderer and the argument list.

The command can do quite complicated things. The example below creates an instance of itself which is a subclass of GraphicalObject. This starts a thread which will animate the renderer. The object steps through the atoms that were passed as part of the command, and draws a green sphere in turn at the position of each atom.

The command would be used something like

animated -name calpha -atoms { atom CA };

Note the '{' and '}' characters that enclose the atom selection. These are important for the parser in commands that have arbitrary argument lists.

// Source code for the class animated
import astex.*;

public class animated extends GraphicalObject implements Runnable {
    /** The MoleculeRenderer we will animate. */
    public MoleculeRenderer moleculeRenderer = null;

    /** The atoms. */
    public DynamicArray atoms = null;

    /** The step we are on. */
    public int step = 0;

    /** The Thread that animates us. */
    public Thread thread = null;

    /** Handle a command. */
    public static void handleCommand(MoleculeViewer mv,
                                     MoleculeRenderer mr,
                                     Arguments args){

	    animated animationObject = new animated();

	    animationObject.atoms = (DynamicArray)args.get("-atoms");

	    String name = args.getString("-name", "animationObject");


	    animationObject.moleculeRenderer = mr;


	    animationObject.thread = new Thread(animationObject);

	    System.out.println("animated: no atoms specified");

    /** Extend the render method. */
    public void render(){
	Renderer renderer = getRenderer();

	// if we get deleted, our Renderer will get set to null
	// and we should stop the thread
	if(renderer == null){

	if(atoms != null){
	    Atom atom = (Atom)atoms.get(step);

	    renderer.drawSphere(atom.x, atom.y, atom.z, 2.0,, 128);

    /** Implement the Runnable interface. */
    public void run(){
	    if(atoms != null){
		if(step >= atoms.size()){
		    step = 0;



	    try {
	    }catch(InterruptedException e){

AstexViewer™ Copyright (C) 1999-2007 Astex Therapeutics Ltd.
OpenAstexViewer Copyright (C) 2007-2018 Mike Hartshorn