Re: [PyMOL] using pymol from python script

[John R. <lam...@gm...>]

Thank you,
this indeed solves the problem! Now everything seems to work smoothely.
I also set an alias to  mypymol="pyplot -r script.py -- " so now 
everything is
very simple.

Thanks to all for the help.

   John


On 02/17/2011 07:30 PM, David Hall wrote:
> No idea if this will fix your problem, but what I've found is portable
> across binaries from Delano Scientific/Schroedinger and
> OS/self-compiled versions of pymol is to instead run:
>
> pymol -r examply.py -- mymolecule.xyz
>
> (or if I'm making pngs, usually pymol -qrck examply.py -- mymolecule.xyz )
>
> The -- makes it so mymolecule.xyz is passed as an argument to the
> python script instead of as an argument to pymol
>
> Then examply.py is just
>
> from pymol import cmd
> import argv
> import mymodule
>
> cmd.load(sys.argv[1])
> cmd.hide()
> cmd.show("spheres")
> mymodule.dosomething()
>
>
> Note, that pymol has to be able to find mymodule, which if you're
> using a Delano Scientific/Schrodinger binary can be annoying, but it
> looks like that is already working for you.
>
> Also, http://pymolwiki.org/index.php/Python_Integration makes it look like
> pymol -l examply.py -- mymolecule.xyz
>
> may work, but I've never done it, so no idea how the behavior differs.
>
> -David
>
>
> On Thu, Feb 17, 2011 at 3:05 AM, John Russo<lam...@gm...>  wrote:
>> Thanks, that is what I was looking for! I just made a simple
>> script out of it which looks like this
>>
>> #!/usr/bin/env python
>>
>> import pymol
>> from pymol import cmd
>> import mymodule
>>
>> pymol.finish_launching()
>>
>> cmd.load("mymolecule.xyz")
>> cmd.hide()
>> cmd.show("spheres")
>> mymodule.dosomething()
>>
>>
>> I've noticed something strange though. The dosomething() function just
>> colors atoms according to some order parameter. If I execute in the script
>> above it is quite slow, I can see individual atoms being colored. Instead if
>> I execute dosomething() from within the pymol interpreter it is much faster.
>> Any reason for this?
>>
>>
>>
>>
>>
>>
>> On 02/17/2011 04:33 PM, Tsjerk Wassenaar wrote:
>>> Hi John,
>>>
>>> Is this what you're looking for?:
>>>
>>> http://www.pymolwiki.org/index.php/Launching_From_a_Script
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Thu, Feb 17, 2011 at 8:19 AM, John Russo<lam...@gm...>    wrote:
>>>> Hi,
>>>> I'm sorry for making such beginner's questions but searching the manual,
>>>> google
>>>> or the wiki didn't help me.
>>>>
>>>> I know how to extend pymol by writing python functions (through the
>>>> extend command).
>>>> But is it possible to do the opposite? I want to write a script that
>>>> loads a molecule, does something
>>>> to it and then displays the pymol window or outputs a png file. I want
>>>> to this without having to
>>>> enter commands in the pymol command line, since I need to put these
>>>> operations in a script,
>>>> without interactive control on pymol.
>>>>
>>>> Example. I want to write a script examply.py with which I can do
>>>>
>>>> ./examply.py mymolecule.xyz
>>>>
>>>> And for output I want to get mymolecule.png or the pymol window with all
>>>> the operations
>>>> already done.
>>>>
>>>> Any hints? Thank you.
>>>>
>>>>
>>>>     John
>>>>
>>>>
>>>>
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>>
>> ------------------------------------------------------------------------------
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>> Pinpoint memory and threading errors before they happen.
>> Find and fix more than 250 security defects in the development cycle.
>> Locate bottlenecks in serial and parallel code that limit performance.
>> http://p.sf.net/sfu/intel-dev2devfeb
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