[chimera-dev] Wrapping Chimera in a Java program
goddard at cgl.ucsf.edu
Mon Mar 31 10:39:04 PDT 2008
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
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
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