Introduction
Hydrophobicity coloring with KYTJ820101
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='.')
aaindex.grep ..→
