pymol-users

[PyMOL] Convert pml script to Pymol Python script

[Matthias S. <mat...@gm...>]

Hi,

I have a few pml scripts for pymol that I would like to rewrite
properly in python, making use of Pymol's ability to interprete Python
scripts.

Do you know of an interpreter that converts pml scripts automatically
to python scripts for Pymol? Since the number of tasks that you can do
in pml is finite, this should be possible, or not?

Best,

Matthias

-- 
Structural Bioinformatics and Computational Biochemistry Unit
Dept. of Biochemistry
University of Oxford
South Parks Road
Oxford
OX1 3QU
U.K.

Telephone: 01865 613304
Fax: 01865 613238

Re: [PyMOL] Convert pml script to Pymol Python script

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

Hi Matthias,

There is no script that I'm aware of, but writing one should be rather
straightforward because of how the API is organized:

commandName arg1, arg2, arg3

becomes

cmd.commandName(arg1, arg2, arg3)

The hardest part would be determining when to quote strings versus not
quoting numbers and variables.  You might be able to reflect against
the API for a more robust script
(http://diveintopython.org/power_of_introspection/index.html).  Java's
great at that, not sure about Python.  Good luck.

Cheers,

-- Jason


On Fri, Apr 8, 2011 at 1:01 PM, Matthias Schmidt
<mat...@gm...> wrote:
> Hi,
>
> I have a few pml scripts for pymol that I would like to rewrite
> properly in python, making use of Pymol's ability to interprete Python
> scripts.
>
> Do you know of an interpreter that converts pml scripts automatically
> to python scripts for Pymol? Since the number of tasks that you can do
> in pml is finite, this should be possible, or not?
>
> Best,
>
> Matthias
>
> --
> Structural Bioinformatics and Computational Biochemistry Unit
> Dept. of Biochemistry
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QU
> U.K.
>
> Telephone: 01865 613304
> Fax: 01865 613238
>
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

Re: [PyMOL] Convert pml script to Pymol Python script

[Michael L. <mgl...@gm...>]

It's not elegant at all, but it's worth knowing that you can use
cmd.do("...") as a quick fix for lines that aren't immediately easy to
convert.

Even a mostly-working pml2py tool would be a useful addition to the wiki.

Cheers,

-Michael

On Fri, Apr 8, 2011 at 2:09 PM, Jason Vertrees <
jas...@sc...> wrote:

> Hi Matthias,
>
> There is no script that I'm aware of, but writing one should be rather
> straightforward because of how the API is organized:
>
> commandName arg1, arg2, arg3
>
> becomes
>
> cmd.commandName(arg1, arg2, arg3)
>
> The hardest part would be determining when to quote strings versus not
> quoting numbers and variables.  You might be able to reflect against
> the API for a more robust script
> (http://diveintopython.org/power_of_introspection/index.html).  Java's
> great at that, not sure about Python.  Good luck.
>
> Cheers,
>
> -- Jason
>
>
> On Fri, Apr 8, 2011 at 1:01 PM, Matthias Schmidt
> <mat...@gm...> wrote:
> > Hi,
> >
> > I have a few pml scripts for pymol that I would like to rewrite
> > properly in python, making use of Pymol's ability to interprete Python
> > scripts.
> >
> > Do you know of an interpreter that converts pml scripts automatically
> > to python scripts for Pymol? Since the number of tasks that you can do
> > in pml is finite, this should be possible, or not?
> >
> > Best,
> >
> > Matthias
> >
> > --
> > Structural Bioinformatics and Computational Biochemistry Unit
> > Dept. of Biochemistry
> > University of Oxford
> > South Parks Road
> > Oxford
> > OX1 3QU
> > U.K.
> >
> > Telephone: 01865 613304
> > Fax: 01865 613238
> >
> >
> ------------------------------------------------------------------------------
> > Xperia(TM) PLAY
> > It's a major breakthrough. An authentic gaming
> > smartphone on the nation's most reliable network.
> > And it wants your games.
> > http://p.sf.net/sfu/verizon-sfdev
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
>
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Re: [PyMOL] Convert pml script to Pymol Python script

[Thomas H. <sp...@us...>]

Jason Vertrees wrote, On 04/08/11 20:09:
> Hi Matthias,
> 
> There is no script that I'm aware of, but writing one should be rather
> straightforward because of how the API is organized:
> 
> commandName arg1, arg2, arg3
> 
> becomes
> 
> cmd.commandName(arg1, arg2, arg3)

I would use the cmd.keyword dictionary for the translation, I thinks not 
all commands have the exact same name in PyMOl API.

Also pml scripts can contain python code which must not be translated.

> The hardest part would be determining when to quote strings versus not
> quoting numbers and variables.

It should be save to just quote everything.

Cheers,
   Thomas

Re: [PyMOL] Convert pml script to Pymol Python script

[Thomas H. <sp...@us...>]

Michael Lerner wrote, On 04/08/11 20:16:
> It's not elegant at all, but it's worth knowing that you can use 
> cmd.do("...") as a quick fix for lines that aren't immediately easy to 
> convert.
> 
> Even a mostly-working pml2py tool would be a useful addition to the wiki.

mostly-working script attached, have fun!

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Re: [PyMOL] Convert pml script to Pymol Python script

[Thomas H. <sp...@us...>]

it's on the wiki now:
http://pymolwiki.org/index.php/Pml2py

Cheers,
   Thomas

Thomas Holder wrote, On 04/09/11 11:17:
> Michael Lerner wrote, On 04/08/11 20:16:
>> It's not elegant at all, but it's worth knowing that you can use 
>> cmd.do("...") as a quick fix for lines that aren't immediately easy to 
>> convert.
>>
>> Even a mostly-working pml2py tool would be a useful addition to the wiki.
> 
> mostly-working script attached, have fun!
> 
> Cheers,
>   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen