Re: [PyMOL] stopping/restarting pymol from API

[Jason V. <jas...@sc...>]

Hi Patrick,

I hope this reply isn't too late to be useful.  This can be done, but
in an experimental "pymol2" kind of way.  See layer5/PyMOL.h for
ideas.  If you're building from source:

import sys, os

# make sure Python can find pymol2, I'm running this
# from the PyMOL home directory
sys.path.append( os.getcwd()+"/modules")

import pymol2

# create a new instance
p =pymol2.PyMOL()

# get its cmd
c = p.cmd

# start a 'session'
p.start()

# fetch and ray trace a file
c.fetch("1foo")
c.png("1foo.png", height=450, width=450, ray=1)
p.stop()

# try another instance & 'session'
p2 = pymol2.PyMOL()
c = p2.cmd
p2.start()
c.fetch("1rec")
c.png("1rec.png", height=450, width=450, ray=1)
p2.stop()

Cheers,

-- Jason


On Tue, Oct 12, 2010 at 1:50 PM, Patrick Winters
<pat...@gm...> wrote:
> Hi,
>  I'm generating PNG images for a webserver whose WSGI python process
> will stay alive.  For that reason I need to be able to startup and
> shutdown pymol using the API so it doesn't stay running (I assume
> that's how the API works).  I've tried every combination I could
> figure to start it up after calling cmd.quit() but none of this seems
> to work.  The second round hangs on cmd.quit and never saves a PNG.
> At this point the pymol process and thread are probably dead.  How can
> I properly quit and restart pymol from the API?
> --
> Patrick
>
> import __main__
> __main__.pymol_argv = [ 'pymol', '-qc'] # Quiet and no GUI
> import pymol
> from pymol import cmd
> pymol.finish_launching()
> cmd.load("http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1ZXE")
> cmd.png("/tmp/test1.png")
> cmd.sync()
> cmd.quit()
> print "Finished round 1"
> pymol.start_pymol()
> pymol.finish_launching()
> cmd.reinitialize()
> cmd.load("http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1ZXE")
> cmd.png("/tmp/test2.png")
> cmd.sync()
> cmd.quit()
> print "Finished round 2"
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120