Hi all,
I'm having a bit of trouble with atom indexes. I'm using mouse over
events to get the atom under the mouse cursor and then trying to select
the same atom in Jmol. In essence it's this:
int atom = findNearestAtomIndex(e.getPoint()); // e is of type MouseEvent
evalString("select atomno=" + atom + ";");
However, the selected atom is not the same as under the mouse. Here's a
demo app so you can see what I mean (please excuse the messy use of
reflection). You will need Jmol and the 2 PDB files in the same
directory as the compiled class file to run it.
Thanks in advance for any help.
Cheers,
Chris Foley.
package JmolAtomDemo;
import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionAdapter;
import java.lang.reflect.Method;
import javax.swing.JFrame;
import javax.swing.JPanel;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.viewer.Viewer;
public class JmolAtomDemo extends JPanel {
private static final long serialVersionUID = 1L;
// Oh so messy!
private static Method findNearestAtomIndex;
static {
Class<?> c = Viewer.class;
Class<?>[] findNearestAtomIndexParams = {int.class, int.class};
try {findNearestAtomIndex =
c.getDeclaredMethod("findNearestAtomIndex", findNearestAtomIndexParams);
} catch (Exception e) {e.printStackTrace();}
findNearestAtomIndex.setAccessible(true);
}
private Viewer viewer;
public JmolAtomDemo(String pdb) {
viewer = new Viewer(this, new SmarterJmolAdapter() );
viewer.setAppletContext("",null,null,"");
viewer.openFile(pdb);
viewer.evalString("selectionHalos ON;");
addMouseMotionListener(new MouseMotionAdapter() {
@Override
public void mouseMoved(MouseEvent e) {
int atomIndex = findNearestAtomIndex(e.getPoint());
String script = "select atomno=" + atomIndex + ";";
System.out.println(script);
viewer.evalString(script);
}
});
} // constructor
private final Dimension currentSize = new Dimension();
private final Rectangle rectClip = new Rectangle();
@Override
public void paint(Graphics g) {
getSize(currentSize);
g.getClipBounds(rectClip);
viewer.renderScreenImage(g, currentSize, rectClip);
} // paint
public int findNearestAtomIndex(Point mousePosition) {
Integer rv = -1;
try {
rv = (Integer)findNearestAtomIndex.invoke(
viewer, mousePosition.x, mousePosition.y);
} catch (Exception e) {
e.printStackTrace();
} // try
return rv;
} // findNearestAtomIndex
public static void main(String[] args) {
JFrame frame1 = new JFrame("1NCP");
frame1.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame1.getContentPane().add(new JmolAtomDemo("1NCP.pdb"));
frame1.setSize(300, 300);
frame1.setVisible(true);
JFrame frame2 = new JFrame("1CDH");
frame2.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame2.getContentPane().add(new JmolAtomDemo("1cdh.pdb"));
frame2.setLocation(300, 0);
frame2.setSize(300, 300);
frame2.setVisible(true);
} // main
}
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