Code

We are going to use Perl (Pedro) and Python (Raik). The Python code builds on the Biskit library. Our scripts are available through Google Code:

• http://code.google.com/p/phospho3d/

Access

1. Install a subversion (svn) client

2. Then check out the latest version of the code:

  svn checkout http://phospho3d.googlecode.com/svn/trunk/ phospho3d

• This will create a folder "phoshpho3d" in your current directory
• Project members can check out a write-access copy. See: http://code.google.com/p/phospho3d/source/checkout

3. Before running python scripts, you also need to install the Biskit library

• apart from the core library, the following helper applications will be useful:
  • surfaceracer
  • pymol

SVN usage

After the initial checkout, the basic principle is always:

1. Update your local copy from the code base on the server
2. Make your change
3. Update again
4. Submit (check in) your change to the server

Example:

 cd phospho3d
 svn update
   ...make your change...

 svn add myscript.py
   ...this schedules your new file for addition...

 svn status
   ...check what has changed locally...

 svn ci -m 'your checkin message'

By default, svn commands operate on the local folder and all sub-folders. You can limit them to certain files: svn ci myscript.py -m 'new script for annotating domains'