[Chimera-users] [chimera-dev] Wrapping Chimera in a Java program

Tom Goddard goddard at cgl.ucsf.edu
Mon Mar 31 10:39:04 PDT 2008

Hi Fabrice,

  I do not think Chimera could run using Jython because Chimera uses 
dozens of compiled C/Python modules.

  You can communicate with Chimera via a pipe.  One approach is to start 
Chimera with a popen() system call and send commands to Chimera's stdin 
using the ReadStdin capability:


  It is also possible to talk to an already running instance of Chimera 
using the "chimera --send <file>" shell command.  This is used to have a 
web browser helper application directly send files to Chimera.


The implementation uses a socket that Chimera is listening on but it is 
somewhat tricky to find the right port number.  It is saved on the local 
machine in a file as a security measure to prevent network connections.  
The details of that implementation are in your Chimera distribution


Scooter Morris in our lab has written code to communicate with Chimera 
from a Java application called Cytoscape.  He might be able to provide 
more advice.


Fabrice Jossinet wrote:
> Dear developers,
> I would like to launch Chimera from my Java program. I would like to  
> send messages to Chimera to highlight in its own display selections I  
> do in my Java program's display. I already did that with PyMOL using a  
> pipe communication.
> So, several questions:
> - is it possible to start Chimera from a classical python distribution  
> (not the embedded python of Chimera)? One of my ideas is to start  
> Chimera from Jython, a Java implementation of Python
> - is it possible to communicate with Chimera using a pipe ?
> - and the most general question: is it possible to communicate with  
> Chimera from the outside?
> Thank you for your answers
> Fabrice

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