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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.
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 "\" and "/" 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 suggest a solution, so scripts can be used on both systems.


It could get solved, by implementing something like this
== Naming convention ==
<syntaxhighlight lang="python">
We recommend that the name for script filename and pagename at the PyMOLWiki are the same.
import sys,os,platform
All letters should also be lower case.
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():
Example: '''colorbydisplacement'''
    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()
{| class="wikitable"
</syntaxhighlight>
| 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>
|}


== External modules - numeric ==
== Read more here ==
Numeric is sometimes used in scripts. This module is easy to install in Linux, but not so easy to make part of a
PyMOL installation.


One could put in some "try" statements, to solve the problem.
* [[git install|Git install instructions]]
<syntaxhighlight lang="python">
* [[git authors|Information how to contribute scripts to the repository]].
import os,sys
* [[git script guidelines|Guidelines how to make a good PyMOL wiki script page]]
os.chdir("/home/tlinnet/Software/pymol/Pymol-script-repo")
* [[git admin|Information how Repository admins handle the contributions]]
sys.path.append(os.getcwd())
try:
    import mechanize
except ImportError:
    print("Could not import mechanize, trying again")
    try:
        import modules.mechanize
        print("I succeded importing mechanize")
    except:
        print("I am sorry, no mechanize for you today")
#help(modules.mechanize)
</syntaxhighlight>

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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