Are you talking about integrating Jmol into a java application as opposed to
a web application?
If so the way I accomplish that is to create a class for housing jmol that
is an extension of JPanel
In that class declare
JmolViewer viewer;
JmolAdapter adapter;
Dimension currentSize;
Rectangle clipRect;
In the constructor create instances of currentSize and clipRect using the
standard constructor.
Create adapter using new SmarterJmolAdapter();
Create viewer using
JmolViewer.allocateViewer(this,adapter,null,null,null,null,null);
Instead of the nulls you can have the desired URLs and handler if needed
(see documentation for allocate viewer)
Create a getViewer method that just returns viewer
Override paint with
Public void paint (Graphics g){
getSize(currentSize);
g.getClipBounds(clipRect);
viewer.renderScreenImage(g,currentSize,clipRect);
You can then add the jmol class you created as a JPanel to what ever you
need to in your application. Get viewer and you have an instance of jmol
viewer.
Joe
> -----Original Message-----
> From: Vincent Le Guilloux [mailto:[email protected]]
> Sent: Sunday, October 04, 2009 10:29 AM
> To: [email protected]
> Subject: [Jmol-users] Jmol integration
>
>
> Hi,
>
> I'm planing to integrate JMol to my application to view PDB files and
> ligand pockets. Basically, my pockets will be represented by several
> spheres placed in the structure (input as PQR format), and atoms next
> to those speres, and I want the user to be able to select and extract
> pocket interactively.
>
> Anyway, I'm currently using a small code snippet taken from the
> biojava documentation. It makes use of the JmolSimpleViewer class.
>
> So currently, I'm able to display a pdb file in the viewer and execute
> some rasmol-like queries.
>
> My question would be: is there any way to get the Jmol popup menu that
> one get when right clicking on the desktop version of Jmol ?
>
> And more generally, what is the best and most recent place to learn
> how to integrate Jmol into an application? I'm currently using
> Biojava's examples, and I've checked the Jmol wiki here:
> http://wiki.jmol.org/index.php?title=Applications_Embedding_Jmol
>
> but currently I haven't found the way to do what I want to do.
>
> Thanks in advance!
> Vincent
>
>
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