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Re: [Jmol-users] findNearestAtomIndex() and select atomno=
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From: Robert H. <ha...@st...> - 2009-02-26 16:20:02
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On Thu, Feb 26, 2009 at 10:09 AM, Chris Foley <
chr...@st...> wrote:
> Hi Robert,
>
> Thanks for the reply, but unfortunately it introduces another problem.
>
> My application offers several views of PDB files, one of which is Jmol
> (others include graphs and tables). Moving the mouse over any of the views
> highlights all the appropriate atoms in the other views (e.g. all the atoms
> in an amino acid residue or just a single single atom on a small molecule).
> Up until now I have done this by maintaining a list of all the PDB atom
> serial numbers for each residue in memory.
>
very nice. Could be a problem with multi-model PDB files, but....
>
>
> When I move the mouse over Jmol it currently uses findNearestAtomIndex()
> and looks up the corresponding residue (if any).
>
good.
>
> When I move the mouse over one of my other views, it correctly pulls out
> the residue and I "select atomno=" for all the associated PDB atom serials.
>
ok.
>
>
> In light of your last email, this is obviously flawed. Does Jmol provide a
> mechanism for converting between the serial numbers in the PDB file and its
> own atom indexes? Thanks again for the help.
>
Once you have the atom Object, you can do anything with it. Most of the
methods there are public. To get a pointer to the atom set -- KEEP THIS
LOCAL!! --
Atom[] atoms = viewer.getModelSet().atoms
And once you have that, you can, for instance, just check:
int atomNo = atoms[atomIndex].getAtomNumber();
>
>
> Chris.
>
>
>
>
>
>
> Robert Hanson wrote:
>
> Chris, we can't use the atomno property to uniquely identify an atom,
> because there may be multiple models loaded, and more than one may have,
> say, atomno=1. So instead we indicate an "atom index" which is a unique
> number relating to the entire set of models. These numbers start with 0. So
> all you need to do is
>
> select atomindex=
>
> instead of
>
> select atomno=
>
>
>
>
> On Thu, Feb 26, 2009 at 9:44 AM, Chris Foley <
> chr...@st...> wrote:
>
>> 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
>>
>>
>>
>>
>> }
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco,
>> CA
>> -OSBC tackles the biggest issue in open source: Open Sourcing the
>> Enterprise
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>>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco,
> CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the
> Enterprise
> -Strategies to boost innovation and cut costs with open source
> participation
> -Receive a $600 discount off the registration fee with the source code:
> SFAD
> http://p.sf.net/sfu/XcvMzF8H
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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