RE: [PyMOL] Using PyMol as a library - no GUI

[Warren L. D. <wa...@de...>]

Truls,

	That looks to me like a crash where the PyMOL API was somehow
called before PyMOL was initialized...how and why this could happen is a
mystery to me though -- that's what pymol.finish_launching() is supposed
to prevent -- but there may be some flaw in the logic.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: Debian Chooser [mailto:ke...@he...] On Behalf Of Truls
A.
> Tangstad
> Sent: Friday, October 17, 2003 3:18 PM
> To: Warren L. DeLano
> Cc: pym...@li...
> Subject: Re: [PyMOL] Using PyMol as a library - no GUI
> 
> On Fri, Oct 17, 2003 at 09:41:24AM -0700, Warren L. DeLano wrote:
> > > Truls A. Tangstad wrote:
> > > I'm very interested in using alot of the functionality that PyMol
> > > offers programmatically from Python, i.e. without using a GUI at
> > > all. The chempy package seems to cover alot of my needs, loading
> > > different file formats etc. even though it doesn't seem to be
> > > documented.
> > >
> > > Is it also possible to use the rest of the functionality in PyMol
from
> > > other Python scripts? Right now, just importing the pymol package
> > > seems to force the GUI to open.
> 
> > If you've got PyMOL configured to open on
> >
> > import pymol
> > pymol.finish_launching()
> >
> > You can suppress the GUI feature and suppress startup output by
> > providing command line arguments as follows.  Before importing
PyMOL,
> > set a "pymol_argv" list in the __main__ namespace.  PyMOL will
interpret
> > this as a sys.argv styled list of command line arguments.
> >
> > import __main__
> > __main__.pymol_argv['pymol','-qc']
> >
> > import pymol
> > pymol.finish_launching()
> 
> Thanks, seems to work like a charm in scripts after adding the
> assignment operator:
> __main__.pymol_argv = ['pymol', '-qc'] # adding miss
> 
> Somehow it segfaults when trying the same thing in an interactive
> python interpreter though, right after importing pymol. This might be
> due to a shoddy install on my part, but I'm including a gdb backtrace:
> 
> #0  0x41d7b21a in SettingGetGlobal_f () from /usr/lib/python2.3/site-
> packages/pymol/_cmd.so
> #1  0x41d7c683 in SettingGet () from /usr/lib/python2.3/site-
> packages/pymol/_cmd.so
> #2  0x41d6296d in OrthoAddOutput () from /usr/lib/python2.3/site-
> packages/pymol/_cmd.so
> #3  0x41d679a5 in PCatchInit () from /usr/lib/python2.3/site-
> packages/pymol/_cmd.so
> #4  0x4006d74d in PyCFunction_Call () from
/usr/lib/libpython2.3.so.1.0
> #5  0x40045e37 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0
> #6  0x400a2a4a in PyEval_CallObjectWithKeywords () from
> /usr/lib/libpython2.3.so.1.0
> #7  0x40055550 in PyFile_WriteObject () from
/usr/lib/libpython2.3.so.1.0
> #8  0x400556e6 in PyFile_WriteString () from
/usr/lib/libpython2.3.so.1.0
> #9  0x400d56b6 in PySys_WriteStderr () from
/usr/lib/libpython2.3.so.1.0
> #10 0x400d4b2c in PySys_WriteStderr () from
/usr/lib/libpython2.3.so.1.0
> #11 0x400d2c74 in Py_AtExit () from /usr/lib/libpython2.3.so.1.0
> #12 0x40101043 in _PyUnicode_TypeRecords () from
> /usr/lib/libpython2.3.so.1.0
> 
> Any idea why it shouldn't work interactively?
> 
> I'm using PyMol 0.90 and Python 2.3.2 on Debian unstable.
> 
> --
> Truls - ker...@he...