pymol-users

[PyMOL] How do I get current selection name from python?

[Boris K. <khe...@gm...>]

I want to save current selection as a uniquetly-named pdb file. So I need
tempfile of python.

So I write def, and I want it have current selection as default one (not
the '(all)'). How do I do that?

I think it will be somewhere under
 cmd.get_session()

I read the sources, but couldn't find a single instance where current
selection would be a default one.

Re: [PyMOL] How do I get current selection name from python?

[Thomas H. <tho...@sc...>]

Hi Boris,

this will give you the list of active selections, which has by default only one entry (or zero, if no selection is enabled).

active_selections = cmd.get_names('selections', 1)

Hope that helps.

Cheers,
  Thomas

On Jan 22, 2013, at 2:08 PM, Boris Kheyfets <khe...@gm...> wrote:
> I want to save current selection as a uniquetly-named pdb file. So I need tempfile of python.
> 
> So I write def, and I want it have current selection as default one (not the '(all)'). How do I do that?
> 
> I think it will be somewhere under
>  cmd.get_session()
> 
> I read the sources, but couldn't find a single instance where current selection would be a default one.

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Re: [PyMOL] How do I get current selection name from python?

[Boris K. <khe...@gm...>]

It prints the selection all right. Why then save wouldn't save it:

def bk_saves_unique_pdb(Selection = None):
    """Takes current selection (or "all" -- if nothing selected) and
saves it as a uniquetly named pdb file
(Frame_Selection_RandomString.pdb) in the current working
directory."""
    if not Selection:
        Selection = cmd.get_names('selections', 1)
        if Selection:
            Selection = Selection[0] # it was a list
        else:
            Selection = 'all'
    tempFile = tempfile.NamedTemporaryFile(dir=os.curdir,
prefix="{frame:03d}_{sel}_".format(frame=cmd.get_frame(),
sel=Selection) , suffix=".pdb")
    print tempFile.name, Selection # prints righteous file name and
selection name (though not in quotes)
    cmd.save(tempFile.name, Selection) # but still saves nothing
cmd.extend("bk_saves_unique_pdb", bk_saves_unique_pdb)



On Tue, Jan 22, 2013 at 10:49 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Boris,
>
> this will give you the list of active selections, which has by default
> only one entry (or zero, if no selection is enabled).
>
> active_selections = cmd.get_names('selections', 1)
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> On Jan 22, 2013, at 2:08 PM, Boris Kheyfets <khe...@gm...> wrote:
> > I want to save current selection as a uniquetly-named pdb file. So I
> need tempfile of python.
> >
> > So I write def, and I want it have current selection as default one (not
> the '(all)'). How do I do that?
> >
> > I think it will be somewhere under
> >  cmd.get_session()
> >
> > I read the sources, but couldn't find a single instance where current
> selection would be a default one.
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>

Re: [PyMOL] How do I get current selection name from python?

[Thomas H. <tho...@sc...>]

http://docs.python.org/2/library/tempfile.html#tempfile.NamedTemporaryFile

Quote: "If delete is true (the default), the file is deleted as soon as
it is closed."

Cheers,
  Thomas

Boris Kheyfets wrote, On 01/23/13 14:47:
> It prints the selection all right. Why then save wouldn't save it:
> 
> 
> def bk_saves_unique_pdb(Selection = None):
>     """Takes current selection (or "all" -- if nothing selected) and saves it as a uniquetly named pdb file (Frame_Selection_RandomString.pdb) in the current working directory."""
>     if not Selection:
>         Selection = cmd.get_names('selections', 1)
>         if Selection:
>             Selection = Selection[0] # it was a list
>         else:
>             Selection = 'all'
>     tempFile = tempfile.NamedTemporaryFile(dir=os.curdir, prefix="{frame:03d}_{sel}_".format(frame=cmd.get_frame(), sel=Selection) , suffix=".pdb")
>     print tempFile.name, Selection # prints righteous file name and selection name (though not in quotes)
>     cmd.save(tempFile.name, Selection) # but still saves nothing
> cmd.extend("bk_saves_unique_pdb", bk_saves_unique_pdb)

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor