Difference between revisions of "Pymol-script-repo"

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(clean up some misleading statements)
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# The possibility to let script authors push changes to their script out to PyMOL users.
 
# The possibility to let script authors push changes to their script out to PyMOL users.
 
# Easier requiring assistance from the PyMOL [http://sourceforge.net/mail/?group_id=4546 mailing list].
 
# Easier requiring assistance from the PyMOL [http://sourceforge.net/mail/?group_id=4546 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
 
  
 
== Official repository ==
 
== Official repository ==
−
The official repository is located at:
+
The repository is located at:
−
https://github.com/Pymol-Scripts/Pymol-script-repo
+
: https://github.com/Pymol-Scripts/Pymol-script-repo
−
 
 
−
And the Git Read-Only access is:
 
−
git://github.com/Pymol-Scripts/Pymol-script-repo.git
 
−
 
 
−
== Same namespace ==
 
−
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. <br>
 
−
This will ease the use of the script
 
−
 
 
−
Example: colorbydisplacement
 
−
 
 
−
=== Example of namespace ===
 
−
For a description of use
 
−
http://www.pymolwiki.org/index.php/colorbydisplacement
 
−
For a color coded view
 
−
https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py
 
−
See the raw code or download manually, by right clicking the following link here -> Save as: colorbydisplacement.py
 
−
https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py
 
−
In the users local script library
 
−
/home/tlinnet/Software/pymol/Pymol-script-repo/colorbydisplacement.py
 
−
To import in PyMOL
 
−
import colorbydisplacement
 
−
To print the available functions in PyMOL
 
−
help(colorbydisplacement)
 
−
 
 
−
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.
 
−
#:http://www.pymolwiki.org/index.php/git_install
 
−
# Information how to contribute scripts to the repository. It's easy!
 
−
#:http://www.pymolwiki.org/index.php/git_authors
 
−
# Guidelines how to make a good PyMOL wiki script page.
 
−
#:http://www.pymolwiki.org/index.php/git_script_guidelines
 
−
# Information how Repository admins handle the contributions
 
−
#:http://www.pymolwiki.org/index.php/git_admin
 
−
 
 
−
= Know problems =
 
−
 
 
−
== The slash \ / problem ==
 
−
Windows uses backslash '''\''', and Linux uses forwardslash '''/''' in folder and path definitions. <br>
 
−
This give sometimes problems, when joining paths in script and plugins, if the author has not foreseen this. <br>
 
−
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
 
−
<syntaxhighlight lang="python">
 
−
import sys,os,platform
 
−
print sys.path
 
−
for path in sys.path:
 
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    if platform.system() == 'Windows':
 
−
        path_desc = "\\"
 
−
    if platform.system() == 'Linux':
 
−
        path_desc = "/"
 
−
    else:
 
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        pass
 
−
sys.path.append(os.getcwd()+path_desc+"Pymol-script-repo")
 
−
print sys.path
 
  
−
def add_to_path():
+
== Naming convention ==
−
    for path in sys.path:
+
We recommend that the name for script filename and pagename at the PyMOLWiki are the same.
−
        if 'Pymol-script-repo' in path:
+
All letters should also be lower case.
−
            if platform.system() == 'Windows':
 
−
                modules_path = path + "\\modules"
 
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                path_desc = "\\"
 
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            if platform.system() == 'Linux':
 
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                modules_path = path + "/modules"
 
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                path_desc = "/"
 
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            break
 
−
        else:
 
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            pass
 
−
    return(modules_path,path_desc)
 
  
−
print "\n", add_to_path()
+
Example: '''colorbydisplacement'''
−
</syntaxhighlight>
 
  
 +
{| class="wikitable"
 +
| For a description of use
 +
| http://pymolwiki.org/index.php/colorbydisplacement
 +
|-
 +
| For a color coded view
 +
| https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py
 +
|-
 +
| Raw download
 +
| https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py
 +
|-
 +
| In the users local script library
 +
| /home/tlinnet/Software/pymol/Pymol-script-repo/colorbydisplacement.py
 +
|-
 +
| To import in PyMOL
 +
| <code>import colorbydisplacement</code>
 +
|-
 +
| To print the available functions in PyMOL
 +
| <code>help(colorbydisplacement)</code>
 +
|}
  
 +
== Read more here ==
  
−
== External modules - numeric ==
+
* [[git install|Git install instructions]]
−
Numeric is sometimes used in scripts. This module is
+
* [[git authors|Information how to contribute scripts to the repository]].
 +
* [[git script guidelines|Guidelines how to make a good PyMOL wiki script page]]
 +
* [[git admin|Information how Repository admins handle the contributions]]

Revision as of 07:20, 13 January 2012

Introduction

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.

Benefits

The benefits from this project, is

  1. A convenient way, to let PyMOL users download all scripts at the PyMOL wiki, with a minimum of effort.
  2. The possibility to let script authors push changes to their script out to PyMOL users.
  3. Easier requiring assistance from the PyMOL mailing list.

Official repository

The repository is located at:

https://github.com/Pymol-Scripts/Pymol-script-repo

Naming convention

We recommend that the name for script filename and pagename at the PyMOLWiki are the same. All letters should also be lower case.

Example: colorbydisplacement

For a description of use http://pymolwiki.org/index.php/colorbydisplacement
For a color coded view https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py
Raw download https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py
In the users local script library /home/tlinnet/Software/pymol/Pymol-script-repo/colorbydisplacement.py
To import in PyMOL import colorbydisplacement
To print the available functions in PyMOL help(colorbydisplacement)

Read more here

Retrieved from "http://pymolwiki.org/index.php?title=Pymol-script-repo&oldid=10314"