Pymol-script-repo: Difference between revisions

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== Introduction ==
The [[Pymol-script-repo]] is the preferred place to host scripts which are published on the PyMOLWiki.
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 ==
== Benefits ==
The benefits from this project, is
# A convenient way, to let PyMOL users download all scripts at the PyMOLWiki, with a minimum of effort.
# 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.
# 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.


== 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:
== Naming convention ==
git://github.com/Pymol-Scripts/Pymol-script-repo.git
We recommend that the name for script filename and pagename at the PyMOLWiki are the same.
All letters should also be lower case.


== Same namespace ==
Example: '''colorbydisplacement'''
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
{| 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>
|}


=== Example of namespace ===
== Read more here ==
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.py
For the raw code
https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py
In the users local script librarr
/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 his/her local repo directory, and wonder what '''colorbydisplacement.py''' does.
* [[git install|Git install instructions]]
Then he/she can write:
* [[git authors|Information how to contribute scripts to the repository]].
http://www.pymolwiki.org/index.php/colorbydisplacement
* [[git script guidelines|Guidelines how to make a good PyMOL wiki script page]]
 
* [[git admin|Information how Repository admins handle the contributions]]
And then a easy description of the of script is presented, with example of use and images.
When he/she then wants to use the script, he/she simply write: '''import colorbydisplacement'''
 
Then find out the defined functions. He/she can then either look at the wiki page, OR write in PyMOL.
'''help(colorbydisplacement)''' which automatically returns the functions.
 
= Read more here =
 
# Install instructions
#: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
# Information how Repository admins handle the contributions
#:http://www.pymolwiki.org/index.php/Git_admin

Latest revision as of 07:36, 13 November 2018

The Pymol-script-repo is the preferred place to host scripts which are published on the PyMOLWiki.

Benefits

  1. A convenient way, to let PyMOL users download all scripts at the PyMOLWiki, 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

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