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	Included in psico; This command or function is available from psico, which is a PyMOL extension.
Module	psico.aaindex

Type	Python Script
Download	scripts/aaindex.py
Author(s)	Thomas Holder
License	BSD
	This code has been put under version control in the project Pymol-script-repo

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AAindex

Introduction

AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. See http://www.genome.jp/aaindex/

This script is a python parser for the AAindex flat files which will be downloaded from ftp://ftp.genome.jp/pub/db/community/aaindex/

The script provides two PyMOL commands (but can also be used without PyMOL).

aaindex2b: Loads numerical indices from aaindex1 as b-factors into your structure
pmf: Potential of Mean Force (aaindex3)

Python Example

Consider the script is called aaindex.py, it is placed somewhere in your PYTHONPATH and the aaindex flatfiles are found in the current directory.

<source lang="python"> import aaindex aaindex.init(path='.')

aai ..→