From: Boris K. <khe...@gm...> - 2012-05-15 12:00:53
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Is there a way I can add a path to 'run' - so not to type the full path to the script when I run it: run /path/to/script.py |
From: Troels E. L. <tl...@gm...> - 2012-05-15 12:45:35
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write this in pymol command window: import sys print sys.path There you can see where pymol is looking. Or you can this to your .pymolrc in your home folder: import sys sys.path.append("/Path/to/your/Pymol-script/modules") Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2012/5/15 Boris Kheyfets <khe...@gm...> > Is there a way I can add a path to 'run' - so not to type the full > path to the script when I run it: > > run /path/to/script.py > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Boris K. <khe...@gm...> - 2012-05-15 12:52:27
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That's the point - I can import from these directories - but can't 'run' from there. I can only run a script by specifying the full path. Boris. On Tue, May 15, 2012 at 4:45 PM, Troels Emtekær Linnet <tl...@gm...> wrote: > write this in pymol command window: > > import sys > print sys.path > > There you can see where pymol is looking. > > Or you can this to your .pymolrc in your home folder: > > import sys > sys.path.append("/Path/to/your/Pymol-script/modules") > > Troels Emtekær Linnet > Ved kløvermarken 9, 1.th > 2300 København S > Mobil: +45 60210234 > > > > 2012/5/15 Boris Kheyfets <khe...@gm...> >> >> Is there a way I can add a path to 'run' - so not to type the full >> path to the script when I run it: >> >> run /path/to/script.py >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > |
From: Thomas H. <sp...@us...> - 2012-05-15 12:59:08
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Hi Boris, you can make your own run command which searches a path: python import os def run2(filename): for p in ['', '/path/to']: full = os.path.join(p, filename) if os.path.exists(full): cmd.do('run ' + full) return print ' Error: no such file' cmd.extend('run2', run2) python end Cheers, Thomas On 05/15/2012 02:51 PM, Boris Kheyfets wrote: > That's the point - I can import from these directories - but can't > 'run' from there. > > I can only run a script by specifying the full path. > > Boris. > > On Tue, May 15, 2012 at 4:45 PM, Troels Emtekær Linnet > <tl...@gm...> wrote: >> write this in pymol command window: >> >> import sys >> print sys.path >> >> There you can see where pymol is looking. >> >> Or you can this to your .pymolrc in your home folder: >> >> import sys >> sys.path.append("/Path/to/your/Pymol-script/modules") >> >> Troels Emtekær Linnet >> Ved kløvermarken 9, 1.th >> 2300 København S >> Mobil: +45 60210234 >> >> >> >> 2012/5/15 Boris Kheyfets<khe...@gm...> >>> >>> Is there a way I can add a path to 'run' - so not to type the full >>> path to the script when I run it: >>> >>> run /path/to/script.py -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Boris K. <khe...@gm...> - 2012-05-15 13:22:15
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It works: I have in ~/.pymol.rc: # let's add the custom srctip repo dir: sys.path.append(os.path.expanduser('~/.local/lib/python2.7/site-packages/pymol/scripts')) # custom scripts: import pmlrc And here's a pmlrc.py (which I put in ~/.local/lib/python2.7/site-packages/pymol/scripts): # code to be executed on start-up: from pymol import cmd # run from script dir: import os def Run(filename): for Path in ['', os.path.expanduser('~/.local/lib/python2.7/site-packages/pymol/scripts')]: full = os.path.join(Path, filename) if os.path.exists(full): cmd.do('run ' + full) return print ' Error: no such file: {0}'.format(filename) cmd.extend('Run', Run) Then Run script.py runs the script if it is either in a current dir, or in the ~/.local/lib/python2.7/site-packages/pymol/scripts Thanks to all responders, Boris. On Tue, May 15, 2012 at 4:58 PM, Thomas Holder <sp...@us...> wrote: > Hi Boris, > > you can make your own run command which searches a path: > > python > import os > def run2(filename): > for p in ['', '/path/to']: > full = os.path.join(p, filename) > if os.path.exists(full): > cmd.do('run ' + full) > return > print ' Error: no such file' > cmd.extend('run2', run2) > python end > > Cheers, > Thomas > > > On 05/15/2012 02:51 PM, Boris Kheyfets wrote: >> >> That's the point - I can import from these directories - but can't >> 'run' from there. >> >> I can only run a script by specifying the full path. >> >> Boris. >> >> On Tue, May 15, 2012 at 4:45 PM, Troels Emtekær Linnet >> <tl...@gm...> wrote: >>> >>> write this in pymol command window: >>> >>> import sys >>> print sys.path >>> >>> There you can see where pymol is looking. >>> >>> Or you can this to your .pymolrc in your home folder: >>> >>> import sys >>> sys.path.append("/Path/to/your/Pymol-script/modules") >>> >>> Troels Emtekær Linnet >>> Ved kløvermarken 9, 1.th >>> 2300 København S >>> Mobil: +45 60210234 >>> >>> >>> >>> 2012/5/15 Boris Kheyfets<khe...@gm...> >>>> >>>> >>>> Is there a way I can add a path to 'run' - so not to type the full >>>> path to the script when I run it: >>>> >>>> run /path/to/script.py > > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen |