From: lina <lin...@gm...> - 2011-09-19 05:10:08
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Hi, Just a quick Q: How can I better organize those *.py I mainly obtained from pymol wiki, not those can be installed by the plugins, pymol run in different directory each time. Thanks, -- Best Regards, lina |
From: Thomas H. <sp...@us...> - 2011-09-19 07:48:32
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Hi Lina, you can put a .pymolrc file in your home directory, it's a script that PyMOL will read on each startup. You can have it either in PyMOL syntax or as a python script, depending on the file extension. /home/lina/.pymolrc (in PyMOL syntax) /home/lina/.pymolrc.py (in python syntax) http://www.pymolwiki.org/index.php/Pymolrc Then create a directory -- lets say /home/lina/.pymol -- and put the PyMOLWiki scripts there. And in your .pymolrc you put lines like these (PyMOL syntax): run /home/lina/.pymol/Grepsel.py run /home/lina/.pymol/Polarpairs.py run /home/lina/.pymol/Propka.py ... and so on Cheers, Thomas lina wrote, On 09/19/11 07:10: > Hi, > > Just a quick Q: > > How can I better organize those *.py I mainly obtained from pymol wiki, > not those can be installed by the plugins, > > pymol run in different directory each time. > > Thanks, > > -- > Best Regards, > > lina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Arne D. <adi...@go...> - 2011-09-19 21:01:42
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That is a hot tip. However, can I also specify some path that would tell pymol the location of my scripts? I have a number of scripts that I need to call while already in Pymol and I do not want to type in the complete path every time. Also, copying these scripts to the current working directory is not a really good solution. Cheers, Arne On Sep 19, 2011, at 12:48 AM, Thomas Holder wrote: > Hi Lina, > > you can put a .pymolrc file in your home directory, it's a script that > PyMOL will read on each startup. You can have it either in PyMOL syntax > or as a python script, depending on the file extension. > > /home/lina/.pymolrc (in PyMOL syntax) > /home/lina/.pymolrc.py (in python syntax) > > http://www.pymolwiki.org/index.php/Pymolrc > > Then create a directory -- lets say /home/lina/.pymol -- and put the > PyMOLWiki scripts there. And in your .pymolrc you put lines like these > (PyMOL syntax): > > run /home/lina/.pymol/Grepsel.py > run /home/lina/.pymol/Polarpairs.py > run /home/lina/.pymol/Propka.py > ... and so on > > Cheers, > Thomas > > lina wrote, On 09/19/11 07:10: >> Hi, >> >> Just a quick Q: >> >> How can I better organize those *.py I mainly obtained from pymol wiki, >> not those can be installed by the plugins, >> >> pymol run in different directory each time. >> >> Thanks, >> >> -- >> Best Regards, >> >> lina > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > Learn about the latest advances in developing for the > BlackBerry® mobile platform with sessions, labs & more. > See new tools and technologies. Register for BlackBerry® DevCon today! > http://p.sf.net/sfu/rim-devcon-copy1 > _______________________________________________ > 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: Jason V. <jas...@sc...> - 2011-09-19 22:15:23
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Hi Arne, You could modify it like this: python # make a list of all your directories w/scripts known_directories = [ "/path/to/dir1", "/path/to/dir2", ... ] import glob for p in known_directories: for f in glob.glob(p+/*.py"): cmd.do("run " + f) python end Cheers, -- Jason On Mon, Sep 19, 2011 at 5:01 PM, Arne Dieckmann <adi...@go...> wrote: > That is a hot tip. However, can I also specify some path that would tell pymol the location of my scripts? I have a number of scripts that I need to call while already in Pymol and I do not want to type in the complete path every time. Also, copying these scripts to the current working directory is not a really good solution. > > > Cheers, > Arne > > > > On Sep 19, 2011, at 12:48 AM, Thomas Holder wrote: > >> Hi Lina, >> >> you can put a .pymolrc file in your home directory, it's a script that >> PyMOL will read on each startup. You can have it either in PyMOL syntax >> or as a python script, depending on the file extension. >> >> /home/lina/.pymolrc (in PyMOL syntax) >> /home/lina/.pymolrc.py (in python syntax) >> >> http://www.pymolwiki.org/index.php/Pymolrc >> >> Then create a directory -- lets say /home/lina/.pymol -- and put the >> PyMOLWiki scripts there. And in your .pymolrc you put lines like these >> (PyMOL syntax): >> >> run /home/lina/.pymol/Grepsel.py >> run /home/lina/.pymol/Polarpairs.py >> run /home/lina/.pymol/Propka.py >> ... and so on >> >> Cheers, >> Thomas >> >> lina wrote, On 09/19/11 07:10: >>> Hi, >>> >>> Just a quick Q: >>> >>> How can I better organize those *.py I mainly obtained from pymol wiki, >>> not those can be installed by the plugins, >>> >>> pymol run in different directory each time. >>> >>> Thanks, >>> >>> -- >>> Best Regards, >>> >>> lina >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> >> ------------------------------------------------------------------------------ >> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> Learn about the latest advances in developing for the >> BlackBerry® mobile platform with sessions, labs & more. >> See new tools and technologies. Register for BlackBerry® DevCon today! >> http://p.sf.net/sfu/rim-devcon-copy1 >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2dcopy1 > _______________________________________________ > 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 |
From: Pete M. <pa...@mc...> - 2011-09-19 22:43:23
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Another approach would be appending to sys.path, and loading the scripts with import instead of run. Arne Dieckmann wrote: > That is a hot tip. However, can I also specify some path that would tell pymol the location of my scripts? I have a number of scripts that I need to call while already in Pymol and I do not want to type in the complete path every time. Also, copying these scripts to the current working directory is not a really good solution. > > > Cheers, > Arne > > > > On Sep 19, 2011, at 12:48 AM, Thomas Holder wrote: > >> Hi Lina, >> >> you can put a .pymolrc file in your home directory, it's a script that >> PyMOL will read on each startup. You can have it either in PyMOL syntax >> or as a python script, depending on the file extension. >> >> /home/lina/.pymolrc (in PyMOL syntax) >> /home/lina/.pymolrc.py (in python syntax) >> >> http://www.pymolwiki.org/index.php/Pymolrc >> >> Then create a directory -- lets say /home/lina/.pymol -- and put the >> PyMOLWiki scripts there. And in your .pymolrc you put lines like these >> (PyMOL syntax): >> >> run /home/lina/.pymol/Grepsel.py >> run /home/lina/.pymol/Polarpairs.py >> run /home/lina/.pymol/Propka.py >> ... and so on >> >> Cheers, >> Thomas >> >> lina wrote, On 09/19/11 07:10: >>> Hi, >>> >>> Just a quick Q: >>> >>> How can I better organize those *.py I mainly obtained from pymol wiki, >>> not those can be installed by the plugins, >>> >>> pymol run in different directory each time. >>> >>> Thanks, >>> >>> -- >>> Best Regards, >>> >>> lina >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> >> ------------------------------------------------------------------------------ >> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> Learn about the latest advances in developing for the >> BlackBerry® mobile platform with sessions, labs & more. >> See new tools and technologies. Register for BlackBerry® DevCon today! >> http://p.sf.net/sfu/rim-devcon-copy1 >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2dcopy1 > _______________________________________________ > 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: Jason V. <jas...@sc...> - 2011-09-19 13:59:30
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Hi Lina, Here's my trick for doing this. I created a directory called pymol_scripts. Then, the scripts I download from the PyMOLWiki are put them into this directory. Then using the following code in my .pymolrc, PyMOL will automatically run these scripts for me on startup: python import glob for f in glob.glob("/home/vertrees/pymol_scripts/*.py"): cmd.do("run " + f) python end The obvious danger here is that you need to know what each script does. If you automatically run a malicious script, you could be in trouble. Of course, if anyone sees a malicious script on the PyMOLWiki, I hope it'd be noticed and removed very quickly--but regardless, one needs to be careful using resources created by another. Cheers, -- Jason On Mon, Sep 19, 2011 at 1:10 AM, lina <lin...@gm...> wrote: > Hi, > > Just a quick Q: > > How can I better organize those *.py I mainly obtained from pymol wiki, > not those can be installed by the plugins, > > pymol run in different directory each time. > > > > Thanks, > > > -- > Best Regards, > > lina > > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > Learn about the latest advances in developing for the > BlackBerry® mobile platform with sessions, labs & more. > See new tools and technologies. Register for BlackBerry® DevCon today! > http://p.sf.net/sfu/rim-devcon-copy1 > _______________________________________________ > 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 |