Re: [PyMOL] Persistent PyMOL pipes? Preventing a call to 'cmd.quit()'.

When the "-p" option is used, PyMOL creates a dedicated thread for reading
commands on standard input.  This thread uses the normal blocking IO calls
to read each line of input and then hands it off to the main thread via
'cmd.do(..)'.   Unless the "-K" is also used, that thread will message the
main thread to terminate via 'cmd.quit()' when standard input is closed.

For the actual code, see 'stdin_reader' in modules/pymol/parser.py.

Cheers,

DeLano Scientific LLC
Email Support Services 

> -----Original Message-----
> From: edw...@gm... 
> [mailto:edw...@gm...] On Behalf Of Edward d'Auvergne
> Sent: Sunday, October 29, 2006 10:26 PM
> To: DeLano Scientific
> Cc: pym...@li...
> Subject: Re: [PyMOL] Persistent PyMOL pipes? Preventing a 
> call to 'cmd.quit()'.
> 
> Thank you.  That option kept the PyMOL pipe alive.  As the 
> option is stored in the structure 
> 'options.keep_thread_alive', would this '-K'
> option cause a different behaviour of the program or is the 
> program simply run as a parent thread and this option keeps 
> the parent alive?
> 
> Cheers,
> 
> Edward
> 
> 
> On 10/30/06, DeLano Scientific <de...@de...> wrote:
> > Edward,
> >
> > Add a "K" keepalive option along with the -p:
> >
> > pymol -pK
> >
> > Cheers,
> >
> > DeLano Scientific LLC
> > Email Support Services
> >
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On Behalf Of 
> > > Edward d'Auvergne
> > > Sent: Sunday, October 29, 2006 9:01 PM
> > > To: pym...@li...
> > > Subject: [PyMOL] Persistent PyMOL pipes? Preventing a call to 
> > > 'cmd.quit()'.
> > >
> > > Hi,
> > >
> > > I am the project administrator for the open source program relax 
> > > (http://nmr-relax.com or
> > > https://gna.org/projects/relax) and am interested in interfacing 
> > > relax with PyMOL.  relax is a program for studying the 
> dynamics of 
> > > proteins, RNA, or other organic molecules through the analysis of 
> > > NMR relaxation data and I would like to display the 
> dynamics results 
> > > superimposed onto molecular structures within PyMOL.  I have 
> > > attempted to open a PyMOL pipe using the '-p'
> > > flag however, when relax finishes and closes the pipe, PyMOL 
> > > terminates printing the message:
> > >
> > >   PyMOL: normal program termination.
> > >
> > > Is there a simple way to keep the PyMOL binary running after a 
> > > script terminates?  I've searched through the sources but 
> a solution 
> > > isn't immediately obvious.  I've tracked back from the file 
> > > 'layer5/main.c'
> > > where the 'printf()' statement is located back to the function 
> > > 'CmdQuit' in the file 'layer4/Cmd.c', but can't find what 
> is calling 
> > > the 'cmd.quit()' method.
> > >
> > > Thanks,
> > >
> > > Edward
> > >
> > > --------------------------------------------------------------
> > > -----------
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>