In November 2011, a group of PyMOL users initiated together with Jason Vertrees, a project to let PyMOL scripts be under version control system (VCS) called Git.
We hope that script authors and PyMOL users would be interested in this option.
The benefits from this project, is
- A convenient way, to let PyMOL users download all scripts at the PyMOL wiki, with a minimum of effort.
- The possibility to let script authors push changes to their script out to PyMOL users.
- Easier requiring assistance from the PyMOL mailing list.
- Script will be tested for malicious code before added to the official repository.
Read here to install: http://www.pymolwiki.org/index.php/git_install
The official repository is located at:
And the Git Read-Only access is:
As a part of this project, we recommend that the name for script filename and pagename at the PyMOL wiki are the same.
All letters should also be small for both.
This will ease the use of the script
Example of namespace
For a description of use
For a color coded view
See the raw code or download manually, by right clicking the following link here -> Save as: colorbydisplacement.py
In the users local script library
To import in PyMOL
To print the available functions in PyMOL
This means, that if a PyMOL user look in their local repo directory, and wonder what colorbydisplacement.py does. Then user can write: http://www.pymolwiki.org/index.php/colorbydisplacement
Here a description of the of script is presented, with example of use and images. When the user then wants to use the script, one can simply write: import colorbydisplacement
To find out the defined functions, one can then either look at the wiki page, OR write in PyMOL. help(colorbydisplacement) which automatically returns the functions.
Read more here
- Simple install instructions for all PyMOL users.
- Information how to contribute scripts to the repository. It's easy!
- Guidelines how to make a good PyMOL wiki script page.
- Information how Repository admins handle the contributions
The slash "\" and "/" problem
Windows uses backslash \, and Linux uses forwardslash / in folder and path definitions.
This give sometimes problems, when joining paths in script and plugins, if the author has not foreseen this.
We hope windows users can help report this of find a solution, so scripts can be used on both systems.
It could get solved, by implementing something like this
import sys,os,platform print sys.path for path in sys.path: if platform.system() == 'Windows': path_desc = "\\" if platform.system() == 'Linux': path_desc = "/" else: pass sys.path.append(os.getcwd()+path_desc+"Pymol-script-repo") print sys.path def add_to_path(): for path in sys.path: if 'Pymol-script-repo' in path: if platform.system() == 'Windows': modules_path = path + "\\modules" path_desc = "\\" if platform.system() == 'Linux': modules_path = path + "/modules" path_desc = "/" break else: pass return(modules_path,path_desc) print "\n", add_to_path()
External modules - numeric
Numeric is sometimes used in scripts. This module is