[MMTK] PyMol

greg landrum drgergl@mindspring.com
Tue, 22 Oct 2002 12:51:55 -0700


At 11:45 AM 10/22/2002, Konrad Hinsen wrote:
>greg landrum <drgergl@mindspring.com> writes:
>
> > Back at the beginning of the year, I wrote a little xml-rpc server
> > thing for PyMol which allows molecules to be loaded from other
> > processes.  It should be reasonably easy to adapt Konrad's MMTK
> > display stuff to use this.
>
>That's an interesting approach as well... Is your server documented in
>any way? What kind of molecule representation does it expect?

I just did a big more investigating.  Warren is indeed distributing the 
xml-rpc thing.  There's little in the way of documentation (it's in the 
code, which is in PyMol/modules/pymol/rpc.py), but the whole thing is 
pretty simple.

Basically, you get PyMol to run the xml-rpc server by starting it with the 
-X option.  It'll tell you what port to use when it starts.

You connect to the server using xmlrpclib:

# connect to the server:
import xmlrpclib
serv = xmlrpclib.Server('http://localhost:9123')

You can then send PyMol API calls to the server using the do command:

# load one of the test files that comes with pymol
#   (path is, of course, installation specific)
serv.do('load c:/Progra~1/DeLano~1/PyMOL/test/dat/small01.mol')

So you can load pretty much any kind of molecule that PyMol normally 
supports.   The limitation is, of course, that you have to create a file 
first.  It'd be reasonably trivial to work around this problem.

You've got the whole PyMol API to play with so you can change display style 
and the like:

# switch to using sticks for the display
serv.do('show sticks')

To demonstrate some of the other things that one could do with the 
interface, there are also sphere and cylinder commands available:

# now, show off some extra features to draw in a 3-point pharmacophore
serv.sphere((-3.62,-0.54, -0.68),1.0,(.9,0.5,.9),"pharm")
serv.sphere((-0.05,1.96, 1.55),1.0,(.9,0.5,.9),"pharm")
serv.sphere((0.07,-0.16, 2.52),1.0,(.9,0.5,.9),"pharm")
serv.cylinder((-3.62,-0.54, -0.68),(0.07,-0.16, 2.52),0.3,(.9,0.5,.9),"pharm")
serv.cylinder((-3.62,-0.54, -0.68),(-0.05,1.96, 1.55),0.3,(.9,0.5,.9),"pharm")
serv.cylinder((0.07,-0.16, 2.52),(-0.05,1.96, 1.55),0.3,(.9,0.5,.9),"pharm")

If there's significant interest in this, I can probably be convinced to do 
a bit more work on it.  I think the idea is potentially very useful, but I 
haven't needed it recently.

-greg

----
greg Landrum (greglandrum@earthlink.net)
Software Carpenter/Computational Chemist