Editing AAindex

{{Infobox script-repo
|type      = script
|filename  = scripts/aaindex.py
|author    = [[User:Speleo3|Thomas Holder]]
|license   = BSD
}}

{{Infobox psico
|module    =  psico.aaindex
}}

== Introduction ==
[[File:AAindexExample.png|200px|thumb|right|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('volume')
x = aaindex.get('KRIW790103')
print(x)
print(x.get('A'))

aaindex.init(index='2')
aaindex.grep('blosum')
x = aaindex.get('HENS920102')
print(x.get('A', 'K'))
</source>

== PyMOL Example ==

Solvent-accessible surface coloring by [https://www.genome.jp/dbget-bin/www_bget?aaindex:KYTJ820101 Hydropathy index (Kyte-Doolittle, 1982)]

<source lang="python">
run aaindex.py
aaindex2b KYTJ820101
spectrum b, white yellow forest
set surface_solvent
show surface
</source>

== See Also ==

* Protscale from [http://www.rubor.de/pymol_extensions_de.html rTools] does a similar job in coloring by amino acid properties

[[Category:Script_Library]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]
[[Category:Pymol-script-repo]]