> Two more questions:
> Does the 'pymol -qc' takes command line variables (os.argv in python)?
> For example, the first line of my script would be:
> cmd.do('load %s' %os.argv[1])
That's not possible. In order to get this behavior (for now) you need
to treat PyMOL as a module (see below).
> Second question might be off a little bit.
> Is it possible to wrap PyMol as a module of Python?
Yes, but to do this (in most cases), you'll have to recompile and
install PyMOL as a standard "distutils" module. If you're not familiar
with compilation, then this isn't for you...
python setup.py build install
python setup2.py install
Then from python
import pymol
pymol.finish_launching()
can work
> I know can be
> installed as a Python module, but that doesn't seem to be able to let
me
> do things like:
>
> # Sample Python script
> import PyMol
> PyMol.cmd.do('......')
> distance = PyMol.cmd.do('distance ......')
Close.
from pymol import cmd
distance = cmd.distance('tmp',sele1,sele2)
> Does it make any difference whether or not I installed PyMol
independant
> of Python?
> I am a bit confused with cmd.do vs cmd.select.
cmd.do places string command to the PYMOL parser input queue and returns
nothing.
cmd.functionName calls the PyMOL API and returns the result (if any).
> So, if I am writing a script for running in PyMol(using
@some_script.py),
> I should use:
> import PyMol
> cmd.select('...')
>
> If I am writing a script for running PyMol in command line,
> I should use:
> from PyMol import cmd
> cmd.do('...')
The only time you'd use cmd.do is for convenience...
cmd.do("select cas, name ca")
will always be substantially slower than
cmd.select("cas","name ca")
because an extra parsing step in involved.
Cheers,
Warren
> Kind of confused...
>
> -shuhsien
>
> >Shu-hsien
> >
> >Sure, instead of cmd.select, use
> >
> >cmd.do("select ligand, resn XYZ")
> >cmd.do("select protein, ! ligand ")
> >
> >etc.
> >
> >./pymol -qc select_box.py
> >
> >Is the command line mode of PyMOL. "pymol -qc" can be used like
> >"python" in most cases.
> >
> >Cheers,
> >Warren
> >
> >
>
>
>
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