Personal tools
You are here: Home FAQs & Help How-tos Setting up AutoDockTools utility scripts
Document Actions

Setting up AutoDockTools utility scripts

This How-to applies to: Any version.
This How-to is intended for: User

Describes how to configure Python interpreter so that it can find packages from MGLTools. This How-to is intended for users who use pre-compiled Python interpreter that comes with MGLTools.

If you installed MGLTools using one of our latest standalone installers, then you are all set. If you are using older version of MGLTools or installed it using binary tarballs, then you need to do some additional steps before you can run these scripts. Here is how.

ADT utility scripts are located in MGLToolsPckgs/AutoDockTools/Utilities24 folder and start with something like:

#!/usr/bin/env python

This tells your shell to use python when running ADT scripts. Unless you installed MGLTools from source, python from your system does not know where to find MGLTools packages, and chances are that you'll get ImportError. The following FAQ shows how to fix this problem: http://mgltools.scripps.edu/documentation/faq/ImportError

An alternative solution is to replace python from the first line with $MGL_ROOT/bin/pythonsh. For instance:

#!/usr/bin/env /Library/MGLTools/1.5.0/bin/pythonsh

Linux version of MGLTools includes two new scripts, mglenv.csh and mglenv.sh located in MGLTools-$Version/bin folder. If you source these files, then you don't need to modify ADT scripts or call them with pythonsh in front.

       c-shell:
> source mglenv.csh
bash-shell:
> source mglenv.sh

Note that, you need to source for environment variables to remain in effect.

Mac OS X users and others can create mglenv as described here.

Ubuntu/Debian users who installed ADT using apt-get install autodocktools can find these scripts in /usr/share/pyshared/AutoDockTools/Utilities24. Please use python2.5 interpreter instead of python2.6 which is system default python onĀ  Ubuntu 9.04.

see also:

Where can I find the Python scripts for preparing and analysing AutoDock dockings?
I've read about the Python prepare scripts like "prepare_dpf4.py" in places like the virtual screening tutorial. This FAQ answers the questions, "Which Python scripts are available?", "Where do I download the Python scripts from?" and "Where are these Python scripts installed?".
by Sargis Dallakyan last modified 2009-09-08 10:24

Powered by Plone CMS, the Open Source Content Management System

This site conforms to the following standards: